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February 24, 2026 10:15
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IWC Workflow Test Results - Run 22339836776
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| # Test Results (powered by Planemo) | |
| ## Test Summary | |
| <div class="progress"> | |
| <div class="progress-bar progress-bar-success" style="width: 92.7927927927928%" aria-valuenow="103" aria-valuemin="0" aria-valuemax="111" data-toggle="tooltip" title="103 Passed"> | |
| </div> | |
| <div class="progress-bar progress-bar-warning" style="width: 0.0%" aria-valuenow="0" aria-valuemin="0" aria-valuemax="111" data-toggle="tooltip" title="0 Skipped"> | |
| </div> | |
| <div class="progress-bar progress-bar-danger" style="width: 7.207207207207207%" aria-valuenow="8" aria-valuemin="0" aria-valuemax="111" title="8 Failed or Errored"> | |
| </div> | |
| </div> | |
| | Test State | Count | | |
| | ---------- | ----- | | |
| | Total | 111 | | |
| | Passed | 103 | | |
| | Error | 3 | | |
| | Failure | 5 | | |
| | Skipped | 0 | | |
| <details open><summary>Errored Tests</summary> | |
| * <details class="rcorners light-red"><summary class="light-red">❌ Assembly-decontamination-VGP9.ga_1</summary><div class="padded"> | |
| #### Workflow invocation details | |
| * Invocation Messages | |
| * <details><summary>Steps</summary> | |
| - **Step 1: Scaffolded assembly (fasta)**: | |
| * step_state: scheduled | |
| - **Step 2: Database for NCBI FCS GX**: | |
| * step_state: scheduled | |
| - **Step 3: Taxonomic Identifier**: | |
| * step_state: scheduled | |
| - **Step 4: Species Binomial Name**: | |
| * step_state: scheduled | |
| - **Step 5: Assembly Name**: | |
| * step_state: scheduled | |
| - **Step 6: Haplotype**: | |
| * step_state: scheduled | |
| - **Step 7: Maximum length of sequence to consider for mitochondrial scaffolds**: | |
| * step_state: scheduled | |
| - **Step 8: Unlabelled step (toolshed.g2.bx.psu.edu/repos/richard-burhans/ncbi\_fcs\_adaptor/ncbi\_fcs\_adaptor/0.5.0+galaxy0)**: | |
| * step_state: scheduled | |
| * <details><summary>Jobs</summary> | |
| - **Job 1:** | |
| * Job state is ok | |
| **Container:** | |
| * ```console | |
| ncbi/fcs-adaptor:0.5.0 | |
| ``` | |
| **Command Line:** | |
| * ```console | |
| /app/fcs/bin/av_screen_x -o "$(pwd)" '--euk' '/tmp/tmpp0nq3lk8/files/9/8/1/dataset_98123420-5e06-4aba-bff8-43b9cb37e164.dat' | |
| ``` | |
| **Exit Code:** | |
| * ```console | |
| 0 | |
| ``` | |
| **Standard Error:** | |
| * ```console | |
| Resolved '/app/fcs/progs/ForeignContaminationScreening.cwl' to 'file:///app/fcs/progs/ForeignContaminationScreening.cwl' | |
| [workflow ] start | |
| [workflow ] starting step ValidateInputSequences | |
| [step ValidateInputSequences] start | |
| [job ValidateInputSequences] /tmp/tmpp0nq3lk8/job_working_directory/000/26/tmp/2dt9ehif$ validate_fasta \ | |
| --jsonl \ | |
| validate_fasta.log \ | |
| --fasta-output \ | |
| validated.fna \ | |
| /tmp/tmpp0nq3lk8/job_working_directory/000/26/tmp/r9h1i2rf/stgd750c6d0-e82e-410d-b2dc-a3261f6de73b/dataset_98123420-5e06-4aba-bff8-43b9cb37e164.dat > /tmp/tmpp0nq3lk8/job_working_directory/000/26/tmp/2dt9ehif/validate_fasta.txt | |
| [job ValidateInputSequences] Max memory used: 37MiB | |
| [job ValidateInputSequences] completed success | |
| [step ValidateInputSequences] completed success | |
| [workflow ] starting step parallel_section | |
| [step parallel_section] start | |
| [workflow parallel_section] start | |
| [workflow parallel_section] starting step SplitInputSequences | |
| [step SplitInputSequences] start | |
| [workflow SplitInputSequences] start | |
| [workflow SplitInputSequences] starting step fasta_split | |
| [step fasta_split] start | |
| [job fasta_split] /tmp/tmpp0nq3lk8/job_working_directory/000/26/tmp/dju63sez$ fasta_split \ | |
| -in_file \ | |
| /tmp/tmpp0nq3lk8/job_working_directory/000/26/tmp/nxelcmsg/stgf9904e56-15fa-4a22-8f9f-4cef55abe32f/validated.fna_0.fna \ | |
| -out_file \ | |
| split_fasta.fna \ | |
| -logfile \ | |
| fast_split.log \ | |
| -mapping_json \ | |
| seq_mapping.jsonl | |
| protobuf arena allocated space: 10000000, used: 14792 | |
| [job fasta_split] completed success | |
| [step fasta_split] completed success | |
| [workflow SplitInputSequences] starting step log | |
| [step log] start | |
| [job log] /tmp/tmpp0nq3lk8/job_working_directory/000/26/tmp/4g___pow$ cxxlog2pb \ | |
| --stage \ | |
| SplitInputSequences < /tmp/tmpp0nq3lk8/job_working_directory/000/26/tmp/3pq3akvt/stgb6800dfd-96d8-43df-ab38-92025f717c15/fast_split.log > /tmp/tmpp0nq3lk8/job_working_directory/000/26/tmp/4g___pow/45ec615881c92e938694dd3ccaea7a9c03748313 | |
| [job log] Max memory used: 39MiB | |
| [job log] completed success | |
| [step log] completed success | |
| [workflow SplitInputSequences] completed success | |
| [step SplitInputSequences] completed success | |
| [workflow parallel_section] starting step AdaptorScreeningAndFilterResults | |
| [step AdaptorScreeningAndFilterResults] start | |
| [workflow AdaptorScreeningAndFilterResults] start | |
| [workflow AdaptorScreeningAndFilterResults] starting step blast | |
| [step blast] start | |
| [job blast] /tmp/tmpp0nq3lk8/job_working_directory/000/26/tmp/cpn91l_k$ vecscreen \ | |
| -db \ | |
| adaptors_for_euks \ | |
| -logfile \ | |
| vecscreen.log \ | |
| -out \ | |
| vs_unfiltered.hit \ | |
| -query \ | |
| /tmp/tmpp0nq3lk8/job_working_directory/000/26/tmp/hj3pdii7/stgdba10270-eb21-4f21-880e-426ef88f6eda/split_fasta.fna \ | |
| -term-flex \ | |
| 25 | |
| [job blast] completed success | |
| [step blast] completed success | |
| [workflow AdaptorScreeningAndFilterResults] starting step log_2 | |
| [step log_2] start | |
| [job log_2] /tmp/tmpp0nq3lk8/job_working_directory/000/26/tmp/x0zyh166$ cxxlog2pb \ | |
| --stage \ | |
| AdaptorScreening < /tmp/tmpp0nq3lk8/job_working_directory/000/26/tmp/ixeilpls/stg9a2341c5-855a-486e-8202-d7b14f25da28/vecscreen.log > /tmp/tmpp0nq3lk8/job_working_directory/000/26/tmp/x0zyh166/45ec615881c92e938694dd3ccaea7a9c03748313 | |
| [job log_2] Max memory used: 39MiB | |
| [job log_2] completed success | |
| [step log_2] completed success | |
| [workflow AdaptorScreeningAndFilterResults] starting step filter | |
| [step filter] start | |
| [job filter] /tmp/tmpp0nq3lk8/job_working_directory/000/26/tmp/cpsdkotg$ vecscreen_filter \ | |
| --filtered \ | |
| vs_filtered.jsonl \ | |
| --unfiltered \ | |
| /tmp/tmpp0nq3lk8/job_working_directory/000/26/tmp/zb_8_mqy/stgea6c344e-5990-48c0-a15d-dd06bccdb841/vs_unfiltered.hit | |
| [job filter] Max memory used: 17MiB | |
| [job filter] completed success | |
| [step filter] completed success | |
| [workflow AdaptorScreeningAndFilterResults] completed success | |
| [step AdaptorScreeningAndFilterResults] completed success | |
| [workflow parallel_section] starting step ApplyHeuristicsToMakeExcludeAndTrimCalls | |
| [step ApplyHeuristicsToMakeExcludeAndTrimCalls] start | |
| [workflow ApplyHeuristicsToMakeExcludeAndTrimCalls] start | |
| [workflow ApplyHeuristicsToMakeExcludeAndTrimCalls] starting step make_calls | |
| [step make_calls] start | |
| [job make_calls] /tmp/tmpp0nq3lk8/job_working_directory/000/26/tmp/kgjbksva$ make_calls \ | |
| -a \ | |
| /tmp/tmpp0nq3lk8/job_working_directory/000/26/tmp/2cfjq0xs/stg58f56ee7-dba6-4133-a0f3-39b3eb23dc57/vs_filtered.jsonl \ | |
| -logfile \ | |
| make_calls.log \ | |
| -seq-len \ | |
| /tmp/tmpp0nq3lk8/job_working_directory/000/26/tmp/2cfjq0xs/stg57f0c649-8f75-4f32-9dbc-5d434cdc6b20/seq_mapping.jsonl > /tmp/tmpp0nq3lk8/job_working_directory/000/26/tmp/kgjbksva/combined.calls.jsonl | |
| [job make_calls] completed success | |
| [step make_calls] completed success | |
| [workflow ApplyHeuristicsToMakeExcludeAndTrimCalls] starting step log_3 | |
| [step log_3] start | |
| [job log_3] /tmp/tmpp0nq3lk8/job_working_directory/000/26/tmp/p8_ye3ri$ cxxlog2pb \ | |
| --stage \ | |
| ApplyHeuristicsToMakeExcludeAndTrimCalls < /tmp/tmpp0nq3lk8/job_working_directory/000/26/tmp/aev5a1en/stg45a387a7-b960-45d9-9b27-323c45ff48c9/make_calls.log > /tmp/tmpp0nq3lk8/job_working_directory/000/26/tmp/p8_ye3ri/45ec615881c92e938694dd3ccaea7a9c03748313 | |
| [job log_3] Max memory used: 40MiB | |
| [job log_3] completed success | |
| [step log_3] completed success | |
| [workflow ApplyHeuristicsToMakeExcludeAndTrimCalls] completed success | |
| [step ApplyHeuristicsToMakeExcludeAndTrimCalls] completed success | |
| [workflow parallel_section] starting step log_merging | |
| [step log_merging] start | |
| [job log_merging] /tmp/tmpp0nq3lk8/job_working_directory/000/26/tmp/c1xuctey$ cat \ | |
| /tmp/tmpp0nq3lk8/job_working_directory/000/26/tmp/gm88lf62/stg39489618-b7fc-4bab-8537-4af172cfcd9f/45ec615881c92e938694dd3ccaea7a9c03748313 \ | |
| /tmp/tmpp0nq3lk8/job_working_directory/000/26/tmp/gm88lf62/stg9ebc3b21-577a-4529-9014-e3729e2b786e/45ec615881c92e938694dd3ccaea7a9c03748313 \ | |
| /tmp/tmpp0nq3lk8/job_working_directory/000/26/tmp/gm88lf62/stgf7428869-c32b-4c27-96f0-1beb7c70d073/45ec615881c92e938694dd3ccaea7a9c03748313 > /tmp/tmpp0nq3lk8/job_working_directory/000/26/tmp/c1xuctey/par_sec.log | |
| [job log_merging] completed success | |
| [step log_merging] completed success | |
| [workflow parallel_section] completed success | |
| [step parallel_section] completed success | |
| [workflow ] starting step gather_logs | |
| [step gather_logs] start | |
| [job gather_logs] /tmp/tmpp0nq3lk8/job_working_directory/000/26/tmp/nh78xkii$ cat \ | |
| /tmp/tmpp0nq3lk8/job_working_directory/000/26/tmp/khzxr85t/stg1c8709c7-dc17-4286-a52a-6bc06feab4e9/par_sec.log > /tmp/tmpp0nq3lk8/job_working_directory/000/26/tmp/nh78xkii/par_sec_logs.log | |
| [job gather_logs] completed success | |
| [step gather_logs] completed success | |
| [workflow ] starting step adaptor_calls | |
| [step adaptor_calls] start | |
| [job adaptor_calls] /tmp/tmpp0nq3lk8/job_working_directory/000/26/tmp/tr2_iog4$ cat \ | |
| /tmp/tmpp0nq3lk8/job_working_directory/000/26/tmp/_5o80e3g/stg8b791d67-63e8-4c9c-ac0b-7b37bc96f05e/combined.calls.jsonl > /tmp/tmpp0nq3lk8/job_working_directory/000/26/tmp/tr2_iog4/adaptor_calls.jsonl | |
| [job adaptor_calls] completed success | |
| [step adaptor_calls] completed success | |
| [workflow ] starting step seq_mapping | |
| [step seq_mapping] start | |
| [job seq_mapping] /tmp/tmpp0nq3lk8/job_working_directory/000/26/tmp/j0_k5zt3$ cat \ | |
| /tmp/tmpp0nq3lk8/job_working_directory/000/26/tmp/na19uo2r/stg2fd1b616-68cd-41ae-8ac5-6f0616d89fd4/seq_mapping.jsonl > /tmp/tmpp0nq3lk8/job_working_directory/000/26/tmp/j0_k5zt3/seq_mapping.jsonl | |
| [job seq_mapping] completed success | |
| [step seq_mapping] completed success | |
| [workflow ] starting step post_processor | |
| [step post_processor] start | |
| [workflow post_processor] start | |
| [workflow post_processor] starting step postproc_calls | |
| [step postproc_calls] start | |
| [job postproc_calls] /tmp/tmpp0nq3lk8/job_working_directory/000/26/tmp/z1ku0mbz$ postproc_calls \ | |
| -in_calls \ | |
| /tmp/tmpp0nq3lk8/job_working_directory/000/26/tmp/j5401w_x/stgbf165e87-014a-4b1e-9401-7f3096fdc4a5/adaptor_calls.jsonl \ | |
| -logfile \ | |
| postproc_calls.log \ | |
| -input_mapping \ | |
| /tmp/tmpp0nq3lk8/job_working_directory/000/26/tmp/j5401w_x/stg8704ef0a-527f-4c88-9165-c6f4f4200098/seq_mapping.jsonl \ | |
| -out_file \ | |
| combined.calls.jsonl | |
| [job postproc_calls] completed success | |
| [step postproc_calls] completed success | |
| [workflow post_processor] starting step log_4 | |
| [step log_4] start | |
| [job log_4] /tmp/tmpp0nq3lk8/job_working_directory/000/26/tmp/ft6a_bn4$ cxxlog2pb \ | |
| --stage \ | |
| PostProcessCalls < /tmp/tmpp0nq3lk8/job_working_directory/000/26/tmp/y8cjk9gi/stg680915e2-2600-4577-8756-82e8f48c0089/postproc_calls.log > /tmp/tmpp0nq3lk8/job_working_directory/000/26/tmp/ft6a_bn4/3bc8758dc9026d571fb8c6b8383da3db38612251 | |
| [job log_4] Max memory used: 39MiB | |
| [job log_4] completed success | |
| [step log_4] completed success | |
| [workflow post_processor] completed success | |
| [step post_processor] completed success | |
| [workflow ] starting step collect_logs | |
| [step collect_logs] start | |
| [job collect_logs] /tmp/tmpp0nq3lk8/job_working_directory/000/26/tmp/sn4aucs0$ cat \ | |
| /tmp/tmpp0nq3lk8/job_working_directory/000/26/tmp/yr2q5vql/stgaa4282a9-8dfd-47f2-9745-eea51a55dcba/validate_fasta.log \ | |
| /tmp/tmpp0nq3lk8/job_working_directory/000/26/tmp/yr2q5vql/stg3b51371c-8d39-450f-9731-315d7dccc4fb/par_sec_logs.log \ | |
| /tmp/tmpp0nq3lk8/job_working_directory/000/26/tmp/yr2q5vql/stg551a8c0f-2a65-468c-80e7-d9c528bac73b/3bc8758dc9026d571fb8c6b8383da3db38612251 > /tmp/tmpp0nq3lk8/job_working_directory/000/26/tmp/sn4aucs0/logs.jsonl | |
| [job collect_logs] completed success | |
| [step collect_logs] completed success | |
| [workflow ] starting step GenerateCleanedFasta | |
| [step GenerateCleanedFasta] start | |
| [workflow GenerateCleanedFasta] start | |
| [workflow GenerateCleanedFasta] starting step prepare_xml_step | |
| [step prepare_xml_step] start | |
| [job prepare_xml_step] /tmp/tmpp0nq3lk8/job_working_directory/000/26/tmp/n59zy053$ pbcalls2seqtransform \ | |
| --skipped \ | |
| skipped_trims.jsonl < /tmp/tmpp0nq3lk8/job_working_directory/000/26/tmp/_mu0tg4v/stg21ee5ac5-cab2-4ecb-a5e7-9ba454686031/combined.calls.jsonl > /tmp/tmpp0nq3lk8/job_working_directory/000/26/tmp/n59zy053/fcs_calls.xml | |
| [job prepare_xml_step] Max memory used: 39MiB | |
| [job prepare_xml_step] completed success | |
| [step prepare_xml_step] completed success | |
| [workflow GenerateCleanedFasta] starting step seqtransform_step | |
| [step seqtransform_step] start | |
| [job seqtransform_step] /tmp/tmpp0nq3lk8/job_working_directory/000/26/tmp/coejgige$ seqtransform \ | |
| -out \ | |
| validated.fna_0.cleaned_fa \ | |
| -in \ | |
| /tmp/tmpp0nq3lk8/job_working_directory/000/26/tmp/zxr8nmru/stge213bf6b-3f93-40d2-9f0d-d284cc1e54e9/validated.fna_0.fna \ | |
| -seqaction-xml-file \ | |
| /tmp/tmpp0nq3lk8/job_working_directory/000/26/tmp/zxr8nmru/stg934c59b9-fa3b-4630-b437-fa31140ecf60/fcs_calls.xml \ | |
| -report \ | |
| seqtransform.log | |
| [job seqtransform_step] completed success | |
| [step seqtransform_step] completed success | |
| [workflow GenerateCleanedFasta] completed success | |
| [step GenerateCleanedFasta] completed success | |
| [workflow ] starting step all_cleaned_fasta | |
| [step all_cleaned_fasta] start | |
| [step all_cleaned_fasta] completed success | |
| [workflow ] starting step GenerateReport | |
| [step GenerateReport] start | |
| [workflow GenerateReport] start | |
| [workflow GenerateReport] starting step calls_step | |
| [step calls_step] start | |
| [job calls_step] /tmp/tmpp0nq3lk8/job_working_directory/000/26/tmp/bh8yzyb1$ pbcalls2tsv < /tmp/tmpp0nq3lk8/job_working_directory/000/26/tmp/musftbzf/stgc62079af-abb4-4e95-93cc-2db57f2c99b9/combined.calls.jsonl > /tmp/tmpp0nq3lk8/job_working_directory/000/26/tmp/bh8yzyb1/fcs_adaptor_report.txt | |
| [job calls_step] Max memory used: 17MiB | |
| [job calls_step] completed success | |
| [step calls_step] completed success | |
| [workflow GenerateReport] starting step log_step | |
| [step log_step] start | |
| [job log_step] /tmp/tmpp0nq3lk8/job_working_directory/000/26/tmp/eqqxpo13$ log_jl2tsv \ | |
| --infile \ | |
| /tmp/tmpp0nq3lk8/job_working_directory/000/26/tmp/2tdhmymi/stg1ce706d8-9d0b-407a-a0db-e501f2b55a4a/logs.jsonl \ | |
| --outfile \ | |
| fcs.log | |
| [job log_step] Max memory used: 17MiB | |
| [job log_step] completed success | |
| [step log_step] completed success | |
| [workflow GenerateReport] completed success | |
| [step GenerateReport] completed success | |
| [workflow ] starting step all_skipped_trims | |
| [step all_skipped_trims] start | |
| [job all_skipped_trims] /tmp/tmpp0nq3lk8/job_working_directory/000/26/tmp/ioczbyec$ cat \ | |
| /tmp/tmpp0nq3lk8/job_working_directory/000/26/tmp/tljxmrct/stgcafff39a-2490-464c-aa28-dff1adb6af5c/skipped_trims.jsonl > /tmp/tmpp0nq3lk8/job_working_directory/000/26/tmp/ioczbyec/skipped_trims.jsonl | |
| [job all_skipped_trims] completed success | |
| [step all_skipped_trims] completed success | |
| [workflow ] completed success | |
| ``` | |
| **Standard Output:** | |
| * ```console | |
| Output will be placed in: /tmp/tmpp0nq3lk8/job_working_directory/000/26/working | |
| Executing the workflow | |
| ``` | |
| **Traceback:** | |
| * ```console | |
| ``` | |
| **Job Parameters:** | |
| * | Job parameter | Parameter value | | |
| | ------------- | --------------- | | |
| | \_\_input\_ext | ` "input" ` | | |
| | \_\_workflow\_invocation\_uuid\_\_ | ` "59801ec8114f11f189517ced8d626a0c" ` | | |
| | advanced | ` {"optional_log": null} ` | | |
| | chromInfo | ` "/tmp/tmpp0nq3lk8/galaxy-dev/tool-data/shared/ucsc/chrom/?.len" ` | | |
| | dbkey | ` "?" ` | | |
| | tax | ` "--euk" ` | | |
| </details> | |
| - **Step 9: Unlabelled step (toolshed.g2.bx.psu.edu/repos/iuc/compose\_text\_param/compose\_text\_param/0.1.1)**: | |
| * step_state: scheduled | |
| * <details><summary>Jobs</summary> | |
| - **Job 1:** | |
| * Job state is ok | |
| **Command Line:** | |
| * ```console | |
| cd ../; python _evaluate_expression_.py | |
| ``` | |
| **Exit Code:** | |
| * ```console | |
| 0 | |
| ``` | |
| **Traceback:** | |
| * ```console | |
| ``` | |
| **Job Parameters:** | |
| * | Job parameter | Parameter value | | |
| | ------------- | --------------- | | |
| | \_\_input\_ext | ` "input" ` | | |
| | \_\_workflow\_invocation\_uuid\_\_ | ` "59801ec8114f11f189517ced8d626a0c" ` | | |
| | chromInfo | ` "/tmp/tmpp0nq3lk8/galaxy-dev/tool-data/shared/ucsc/chrom/?.len" ` | | |
| | components | ` [{"__index__": 0, "param_type": {"__current_case__": 0, "component_value": "Species : ", "select_param_type": "text"}}, {"__index__": 1, "param_type": {"__current_case__": 0, "component_value": "Homo Sapiens", "select_param_type": "text"}}, {"__index__": 2, "param_type": {"__current_case__": 0, "component_value": ". Assembly: ", "select_param_type": "text"}}, {"__index__": 3, "param_type": {"__current_case__": 0, "component_value": "Hg19", "select_param_type": "text"}}, {"__index__": 4, "param_type": {"__current_case__": 0, "component_value": " ", "select_param_type": "text"}}, {"__index__": 5, "param_type": {"__current_case__": 0, "component_value": "Haplotype 1", "select_param_type": "text"}}] ` | | |
| | dbkey | ` "?" ` | | |
| </details> | |
| - **Step 10: Unlabelled step**: | |
| * step_state: scheduled | |
| * <details><summary>Subworkflow Steps</summary> | |
| - **Step 1: Adaptor Action report**: | |
| * step_state: scheduled | |
| - **Step 2: Unlabelled step (wc\_gnu)**: | |
| * step_state: scheduled | |
| * <details><summary>Jobs</summary> | |
| - **Job 1:** | |
| * Job state is ok | |
| **Command Line:** | |
| * ```console | |
| echo "#lines" > /tmp/tmpp0nq3lk8/job_working_directory/000/28/outputs/dataset_24234a3c-b65c-4584-8db6-0cd753c3131a.dat && cat '/tmp/tmpp0nq3lk8/files/c/d/e/dataset_cde5072a-a2cd-442d-8bde-c68c33c8476a.dat' | wc -l | awk '{ print $1 }' >> /tmp/tmpp0nq3lk8/job_working_directory/000/28/outputs/dataset_24234a3c-b65c-4584-8db6-0cd753c3131a.dat | |
| ``` | |
| **Exit Code:** | |
| * ```console | |
| 0 | |
| ``` | |
| **Traceback:** | |
| * ```console | |
| ``` | |
| **Job Parameters:** | |
| * | Job parameter | Parameter value | | |
| | ------------- | --------------- | | |
| | \_\_input\_ext | ` "tabular" ` | | |
| | \_\_workflow\_invocation\_uuid\_\_ | ` "59801ec9114f11f189517ced8d626a0c" ` | | |
| | chromInfo | ` "/tmp/tmpp0nq3lk8/galaxy-dev/tool-data/shared/ucsc/chrom/?.len" ` | | |
| | dbkey | ` "?" ` | | |
| | include\_header | ` true ` | | |
| | options | ` ["lines"] ` | | |
| </details> | |
| - **Step 3: Unlabelled step (Show tail1)**: | |
| * step_state: scheduled | |
| * <details><summary>Jobs</summary> | |
| - **Job 1:** | |
| * Job state is ok | |
| **Container:** | |
| * ```console | |
| quay.io/biocontainers/coreutils:8.31--h14c3975_0 | |
| ``` | |
| **Command Line:** | |
| * ```console | |
| set -eo pipefail; ( cat '/tmp/tmpp0nq3lk8/files/2/4/2/dataset_24234a3c-b65c-4584-8db6-0cd753c3131a.dat' | tail -n 1 ) > '/tmp/tmpp0nq3lk8/job_working_directory/000/29/outputs/dataset_8a497b9f-ff1b-4558-8bbf-a78d1f6a14f7.dat' | |
| ``` | |
| **Exit Code:** | |
| * ```console | |
| 0 | |
| ``` | |
| **Traceback:** | |
| * ```console | |
| ``` | |
| **Job Parameters:** | |
| * | Job parameter | Parameter value | | |
| | ------------- | --------------- | | |
| | \_\_input\_ext | ` "input" ` | | |
| | \_\_workflow\_invocation\_uuid\_\_ | ` "59801ec9114f11f189517ced8d626a0c" ` | | |
| | chromInfo | ` "/tmp/tmpp0nq3lk8/galaxy-dev/tool-data/shared/ucsc/chrom/?.len" ` | | |
| | dbkey | ` "?" ` | | |
| | header | ` false ` | | |
| | lineNum | ` "1" ` | | |
| </details> | |
| - **Step 4: Unlabelled step (param\_value\_from\_file)**: | |
| * step_state: scheduled | |
| * <details><summary>Jobs</summary> | |
| - **Job 1:** | |
| * Job state is ok | |
| **Command Line:** | |
| * ```console | |
| cd ../; python _evaluate_expression_.py | |
| ``` | |
| **Exit Code:** | |
| * ```console | |
| 0 | |
| ``` | |
| **Traceback:** | |
| * ```console | |
| ``` | |
| **Job Parameters:** | |
| * | Job parameter | Parameter value | | |
| | ------------- | --------------- | | |
| | \_\_input\_ext | ` "input" ` | | |
| | \_\_workflow\_invocation\_uuid\_\_ | ` "59801ec9114f11f189517ced8d626a0c" ` | | |
| | chromInfo | ` "/tmp/tmpp0nq3lk8/galaxy-dev/tool-data/shared/ucsc/chrom/?.len" ` | | |
| | dbkey | ` "?" ` | | |
| | param\_type | ` "integer" ` | | |
| | remove\_newlines | ` true ` | | |
| </details> | |
| - **Step 5: Unlabelled step (toolshed.g2.bx.psu.edu/repos/iuc/map\_param\_value/map\_param\_value/0.2.0)**: | |
| * step_state: scheduled | |
| * <details><summary>Jobs</summary> | |
| - **Job 1:** | |
| * Job state is ok | |
| **Command Line:** | |
| * ```console | |
| cd ../; python _evaluate_expression_.py | |
| ``` | |
| **Exit Code:** | |
| * ```console | |
| 0 | |
| ``` | |
| **Traceback:** | |
| * ```console | |
| ``` | |
| **Job Parameters:** | |
| * | Job parameter | Parameter value | | |
| | ------------- | --------------- | | |
| | \_\_input\_ext | ` "input" ` | | |
| | \_\_workflow\_invocation\_uuid\_\_ | ` "59801ec9114f11f189517ced8d626a0c" ` | | |
| | chromInfo | ` "/tmp/tmpp0nq3lk8/galaxy-dev/tool-data/shared/ucsc/chrom/?.len" ` | | |
| | dbkey | ` "?" ` | | |
| | input\_param\_type | ` {"__current_case__": 1, "input_param": "3", "mappings": [{"__index__": 0, "from": "1", "to": "False"}], "type": "integer"} ` | | |
| | output\_param\_type | ` "boolean" ` | | |
| | unmapped | ` {"__current_case__": 2, "default_value": "True", "on_unmapped": "default"} ` | | |
| </details> | |
| - **Step 6: Select middle adaptors (Filter1)**: | |
| * step_state: scheduled | |
| * <details><summary>Jobs</summary> | |
| - **Job 1:** | |
| * Job state is ok | |
| **Container:** | |
| * ```console | |
| quay.io/biocontainers/python:3.13 | |
| ``` | |
| **Command Line:** | |
| * ```console | |
| python '/tmp/tmpp0nq3lk8/galaxy-dev/tools/stats/filtering.py' '/tmp/tmpp0nq3lk8/files/c/d/e/dataset_cde5072a-a2cd-442d-8bde-c68c33c8476a.dat' '/tmp/tmpp0nq3lk8/job_working_directory/000/32/outputs/dataset_c86d4379-2c13-4c99-8bb0-bab69f79114a.dat' '/tmp/tmpp0nq3lk8/job_working_directory/000/32/configs/tmp_anzp_7y' 5 "str,int,str,str,str" 1 | |
| ``` | |
| **Exit Code:** | |
| * ```console | |
| 0 | |
| ``` | |
| **Standard Output:** | |
| * ```console | |
| Filtering with int(c4.split('..')[0])>100 and int(c4.split('..')[1])<int(c2)-100, | |
| kept 33.33% of 3 valid lines (3 total lines). | |
| Skipped 1 invalid line(s) starting at line #3: "seq_00018 522 ACTION_EXCLUDE CONTAMINATION_SOURCE_TYPE_ADAPTOR:NGB00360.1:Illumina PCR Primer" | |
| ``` | |
| **Traceback:** | |
| * ```console | |
| ``` | |
| **Job Parameters:** | |
| * | Job parameter | Parameter value | | |
| | ------------- | --------------- | | |
| | \_\_input\_ext | ` "input" ` | | |
| | \_\_workflow\_invocation\_uuid\_\_ | ` "59801ec9114f11f189517ced8d626a0c" ` | | |
| | chromInfo | ` "/tmp/tmpp0nq3lk8/galaxy-dev/tool-data/shared/ucsc/chrom/?.len" ` | | |
| | cond | ` "int(c4.split('..')[0])>100 and int(c4.split('..')[1])<int(c2)-100" ` | | |
| | dbkey | ` "?" ` | | |
| | header\_lines | ` "1" ` | | |
| </details> | |
| - **Step 7: Select end adaptors (Filter1)**: | |
| * step_state: scheduled | |
| * <details><summary>Jobs</summary> | |
| - **Job 1:** | |
| * Job state is ok | |
| **Container:** | |
| * ```console | |
| quay.io/biocontainers/python:3.13 | |
| ``` | |
| **Command Line:** | |
| * ```console | |
| python '/tmp/tmpp0nq3lk8/galaxy-dev/tools/stats/filtering.py' '/tmp/tmpp0nq3lk8/files/c/d/e/dataset_cde5072a-a2cd-442d-8bde-c68c33c8476a.dat' '/tmp/tmpp0nq3lk8/job_working_directory/000/33/outputs/dataset_6dece441-68a4-41cd-9c8f-098eae737271.dat' '/tmp/tmpp0nq3lk8/job_working_directory/000/33/configs/tmpjna15dev' 5 "str,int,str,str,str" 0 | |
| ``` | |
| **Exit Code:** | |
| * ```console | |
| 0 | |
| ``` | |
| **Standard Output:** | |
| * ```console | |
| Filtering with int(c4.split('..')[0])<=100 or int(c4.split('..')[1])>=int(c2)-100, | |
| kept 50.00% of 2 valid lines (3 total lines). | |
| Skipped 1 invalid line(s) starting at line #3: "seq_00018 522 ACTION_EXCLUDE CONTAMINATION_SOURCE_TYPE_ADAPTOR:NGB00360.1:Illumina PCR Primer" | |
| Skipped 1 comment (starting with #) or blank line(s) | |
| ``` | |
| **Traceback:** | |
| * ```console | |
| ``` | |
| **Job Parameters:** | |
| * | Job parameter | Parameter value | | |
| | ------------- | --------------- | | |
| | \_\_input\_ext | ` "input" ` | | |
| | \_\_workflow\_invocation\_uuid\_\_ | ` "59801ec9114f11f189517ced8d626a0c" ` | | |
| | chromInfo | ` "/tmp/tmpp0nq3lk8/galaxy-dev/tool-data/shared/ucsc/chrom/?.len" ` | | |
| | cond | ` "int(c4.split('..')[0])<=100 or int(c4.split('..')[1])>=int(c2)-100" ` | | |
| | dbkey | ` "?" ` | | |
| | header\_lines | ` "0" ` | | |
| </details> | |
| - **Step 8: Select sequences to exclude (Filter1)**: | |
| * step_state: scheduled | |
| * <details><summary>Jobs</summary> | |
| - **Job 1:** | |
| * Job state is ok | |
| **Container:** | |
| * ```console | |
| quay.io/biocontainers/python:3.13 | |
| ``` | |
| **Command Line:** | |
| * ```console | |
| python '/tmp/tmpp0nq3lk8/galaxy-dev/tools/stats/filtering.py' '/tmp/tmpp0nq3lk8/files/c/d/e/dataset_cde5072a-a2cd-442d-8bde-c68c33c8476a.dat' '/tmp/tmpp0nq3lk8/job_working_directory/000/34/outputs/dataset_155be2c6-bf5e-4ef7-91d3-fbd1b6250e08.dat' '/tmp/tmpp0nq3lk8/job_working_directory/000/34/configs/tmpwt6983cg' 5 "str,int,str,str,str" 0 | |
| ``` | |
| **Exit Code:** | |
| * ```console | |
| 0 | |
| ``` | |
| **Standard Output:** | |
| * ```console | |
| Filtering with c4=="", | |
| kept 50.00% of 2 valid lines (3 total lines). | |
| Skipped 1 comment (starting with #) or blank line(s) | |
| ``` | |
| **Traceback:** | |
| * ```console | |
| ``` | |
| **Job Parameters:** | |
| * | Job parameter | Parameter value | | |
| | ------------- | --------------- | | |
| | \_\_input\_ext | ` "input" ` | | |
| | \_\_workflow\_invocation\_uuid\_\_ | ` "59801ec9114f11f189517ced8d626a0c" ` | | |
| | chromInfo | ` "/tmp/tmpp0nq3lk8/galaxy-dev/tool-data/shared/ucsc/chrom/?.len" ` | | |
| | cond | ` "c4==\"\"" ` | | |
| | dbkey | ` "?" ` | | |
| | header\_lines | ` "0" ` | | |
| </details> | |
| - **Step 9: Unlabelled step (toolshed.g2.bx.psu.edu/repos/iuc/pick\_value/pick\_value/0.2.0)**: | |
| * step_state: scheduled | |
| * <details><summary>Jobs</summary> | |
| - **Job 1:** | |
| * Job state is ok | |
| **Command Line:** | |
| * ```console | |
| cd ../; python _evaluate_expression_.py | |
| ``` | |
| **Exit Code:** | |
| * ```console | |
| 0 | |
| ``` | |
| **Traceback:** | |
| * ```console | |
| ``` | |
| **Job Parameters:** | |
| * | Job parameter | Parameter value | | |
| | ------------- | --------------- | | |
| | \_\_input\_ext | ` "input" ` | | |
| | \_\_workflow\_invocation\_uuid\_\_ | ` "59801ec9114f11f189517ced8d626a0c" ` | | |
| | chromInfo | ` "/tmp/tmpp0nq3lk8/galaxy-dev/tool-data/shared/ucsc/chrom/?.len" ` | | |
| | dbkey | ` "?" ` | | |
| | style\_cond | ` {"__current_case__": 0, "pick_style": "first", "type_cond": {"__current_case__": 4, "param_type": "data", "pick_from": [{"__index__": 0, "value": {"values": [{"id": 38, "src": "hda"}]}}]}} ` | | |
| </details> | |
| - **Step 10: Replace trimming by masking (toolshed.g2.bx.psu.edu/repos/bgruening/text\_processing/tp\_replace\_in\_line/9.5+galaxy3)**: | |
| * step_state: scheduled | |
| * <details><summary>Jobs</summary> | |
| - **Job 1:** | |
| * Job state is ok | |
| **Container:** | |
| * ```console | |
| quay.io/biocontainers/sed:4.9 | |
| ``` | |
| **Command Line:** | |
| * ```console | |
| sed -r --sandbox -e '' -e 's/ACTION_TRIM/FIX/g' '/tmp/tmpp0nq3lk8/files/c/8/6/dataset_c86d4379-2c13-4c99-8bb0-bab69f79114a.dat' > '/tmp/tmpp0nq3lk8/job_working_directory/000/36/outputs/dataset_e7c7e5ca-28fa-44c8-bc4f-fdea4eba9e7a.dat' | |
| ``` | |
| **Exit Code:** | |
| * ```console | |
| 0 | |
| ``` | |
| **Traceback:** | |
| * ```console | |
| ``` | |
| **Job Parameters:** | |
| * | Job parameter | Parameter value | | |
| | ------------- | --------------- | | |
| | \_\_input\_ext | ` "input" ` | | |
| | \_\_workflow\_invocation\_uuid\_\_ | ` "59801ec9114f11f189517ced8d626a0c" ` | | |
| | chromInfo | ` "/tmp/tmpp0nq3lk8/galaxy-dev/tool-data/shared/ucsc/chrom/?.len" ` | | |
| | dbkey | ` "?" ` | | |
| | replacements | ` [{"__index__": 0, "find_pattern": "ACTION_TRIM", "replace_pattern": "FIX", "sed_options": ""}] ` | | |
| </details> | |
| - **Step 11: Unlabelled step (toolshed.g2.bx.psu.edu/repos/bgruening/text\_processing/tp\_cat/9.5+galaxy3)**: | |
| * step_state: scheduled | |
| * <details><summary>Jobs</summary> | |
| - **Job 1:** | |
| * Job state is ok | |
| **Container:** | |
| * ```console | |
| quay.io/biocontainers/coreutils:9.5 | |
| ``` | |
| **Command Line:** | |
| * ```console | |
| cat '/tmp/tmpp0nq3lk8/files/e/7/c/dataset_e7c7e5ca-28fa-44c8-bc4f-fdea4eba9e7a.dat' >> '/tmp/tmpp0nq3lk8/job_working_directory/000/37/outputs/dataset_0034d27e-dde3-43a7-adb7-009f70c24186.dat' && cat '/tmp/tmpp0nq3lk8/files/6/d/e/dataset_6dece441-68a4-41cd-9c8f-098eae737271.dat' >> '/tmp/tmpp0nq3lk8/job_working_directory/000/37/outputs/dataset_0034d27e-dde3-43a7-adb7-009f70c24186.dat' && cat '/tmp/tmpp0nq3lk8/files/1/5/5/dataset_155be2c6-bf5e-4ef7-91d3-fbd1b6250e08.dat' >> '/tmp/tmpp0nq3lk8/job_working_directory/000/37/outputs/dataset_0034d27e-dde3-43a7-adb7-009f70c24186.dat' && exit 0 | |
| ``` | |
| **Exit Code:** | |
| * ```console | |
| 0 | |
| ``` | |
| **Traceback:** | |
| * ```console | |
| ``` | |
| **Job Parameters:** | |
| * | Job parameter | Parameter value | | |
| | ------------- | --------------- | | |
| | \_\_input\_ext | ` "input" ` | | |
| | \_\_workflow\_invocation\_uuid\_\_ | ` "59801ec9114f11f189517ced8d626a0c" ` | | |
| | chromInfo | ` "/tmp/tmpp0nq3lk8/galaxy-dev/tool-data/shared/ucsc/chrom/?.len" ` | | |
| | dbkey | ` "?" ` | | |
| | queries | ` [{"__index__": 0, "inputs2": {"values": [{"id": 39, "src": "hda"}]}}, {"__index__": 1, "inputs2": {"values": [{"id": 40, "src": "hda"}]}}] ` | | |
| </details> | |
| - **Step 12: Unlabelled step (toolshed.g2.bx.psu.edu/repos/iuc/pick\_value/pick\_value/0.2.0)**: | |
| * step_state: scheduled | |
| * <details><summary>Jobs</summary> | |
| - **Job 1:** | |
| * Job state is ok | |
| **Command Line:** | |
| * ```console | |
| cd ../; python _evaluate_expression_.py | |
| ``` | |
| **Exit Code:** | |
| * ```console | |
| 0 | |
| ``` | |
| **Traceback:** | |
| * ```console | |
| ``` | |
| **Job Parameters:** | |
| * | Job parameter | Parameter value | | |
| | ------------- | --------------- | | |
| | \_\_input\_ext | ` "input" ` | | |
| | \_\_workflow\_invocation\_uuid\_\_ | ` "59801ec9114f11f189517ced8d626a0c" ` | | |
| | chromInfo | ` "/tmp/tmpp0nq3lk8/galaxy-dev/tool-data/shared/ucsc/chrom/?.len" ` | | |
| | dbkey | ` "?" ` | | |
| | style\_cond | ` {"__current_case__": 0, "pick_style": "first", "type_cond": {"__current_case__": 4, "param_type": "data", "pick_from": [{"__index__": 0, "value": {"values": [{"id": 43, "src": "hda"}]}}, {"__index__": 1, "value": {"values": [{"id": 31, "src": "hda"}]}}]}} ` | | |
| </details> | |
| </details> | |
| - **Step 11: Unlabelled step (toolshed.g2.bx.psu.edu/repos/iuc/ncbi\_fcs\_gx/ncbi\_fcs\_gx/0.5.5+galaxy2)**: | |
| * step_state: scheduled | |
| * <details><summary>Jobs</summary> | |
| - **Job 1:** | |
| * Job state is ok | |
| **Container:** | |
| * ```console | |
| quay.io/biocontainers/ncbi-fcs-gx:0.5.5--h9948957_0 | |
| ``` | |
| **Command Line:** | |
| * ```console | |
| GX_NUM_CORES=${GALAXY_SLOTS:-2} gx clean-genome --input '/tmp/tmpp0nq3lk8/files/9/8/1/dataset_98123420-5e06-4aba-bff8-43b9cb37e164.dat' --action-report '/tmp/tmpp0nq3lk8/files/0/0/3/dataset_0034d27e-dde3-43a7-adb7-009f70c24186.dat' --contam-fasta-out 'contam.fa' --min-seq-len '200' --output 'clean.fa' | |
| ``` | |
| **Exit Code:** | |
| * ```console | |
| 0 | |
| ``` | |
| **Standard Error:** | |
| * ```console | |
| Applied 2 actions; 2 seqs dropped; 580 bps dropped; 0 bps lowercased; 0 bps hardmasked. | |
| ``` | |
| **Traceback:** | |
| * ```console | |
| ``` | |
| **Job Parameters:** | |
| * | Job parameter | Parameter value | | |
| | ------------- | --------------- | | |
| | \_\_input\_ext | ` "input" ` | | |
| | \_\_workflow\_invocation\_uuid\_\_ | ` "59801ec8114f11f189517ced8d626a0c" ` | | |
| | chromInfo | ` "/tmp/tmpp0nq3lk8/galaxy-dev/tool-data/shared/ucsc/chrom/?.len" ` | | |
| | dbkey | ` "?" ` | | |
| | mode | ` {"__current_case__": 1, "action_report": {"values": [{"id": 44, "src": "hda"}]}, "input": {"values": [{"id": 30, "src": "hda"}]}, "min_seq_len": "200", "mode_selector": "clean"} ` | | |
| </details> | |
| - **Step 12: soft-masking (toolshed.g2.bx.psu.edu/repos/devteam/ncbi\_blast\_plus/ncbi\_dustmasker\_wrapper/2.16.0+galaxy0)**: | |
| * step_state: scheduled | |
| * <details><summary>Jobs</summary> | |
| - **Job 1:** | |
| * Job state is ok | |
| **Container:** | |
| * ```console | |
| quay.io/biocontainers/blast:2.16.0--h66d330f_5 | |
| ``` | |
| **Command Line:** | |
| * ```console | |
| dustmasker -in '/tmp/tmpp0nq3lk8/files/1/c/f/dataset_1cf01f0d-6496-4163-97d2-8d7d54db9729.dat' -infmt fasta -out '/tmp/tmpp0nq3lk8/job_working_directory/000/40/outputs/dataset_5dabd551-2506-4c14-b688-d6980f63d6f9.dat' -window 64 -level 40 -linker 1 -outfmt fasta | |
| ``` | |
| **Exit Code:** | |
| * ```console | |
| 0 | |
| ``` | |
| **Traceback:** | |
| * ```console | |
| ``` | |
| **Job Parameters:** | |
| * | Job parameter | Parameter value | | |
| | ------------- | --------------- | | |
| | \_\_input\_ext | ` "input" ` | | |
| | \_\_workflow\_invocation\_uuid\_\_ | ` "59801ec8114f11f189517ced8d626a0c" ` | | |
| | chromInfo | ` "/tmp/tmpp0nq3lk8/galaxy-dev/tool-data/shared/ucsc/chrom/?.len" ` | | |
| | db\_opts | ` {"__current_case__": 2, "database": "", "db_opts_selector": "file", "histdb": "", "subject": {"values": [{"id": 46, "src": "hda"}]}} ` | | |
| | dbkey | ` "?" ` | | |
| | level | ` "40" ` | | |
| | linker | ` "1" ` | | |
| | outformat | ` "fasta" ` | | |
| | window | ` "64" ` | | |
| </details> | |
| - **Step 13: Unlabelled step (toolshed.g2.bx.psu.edu/repos/devteam/fasta\_filter\_by\_length/fasta\_filter\_by\_length/1.2)**: | |
| * step_state: scheduled | |
| * <details><summary>Jobs</summary> | |
| - **Job 1:** | |
| * Job state is ok | |
| **Container:** | |
| * ```console | |
| quay.io/biocontainers/python:3.7--1 | |
| ``` | |
| **Command Line:** | |
| * ```console | |
| python '/tmp/shed_dir/toolshed.g2.bx.psu.edu/repos/devteam/fasta_filter_by_length/8cacfcf96a52/fasta_filter_by_length/fasta_filter_by_length.py' '/tmp/tmpp0nq3lk8/files/5/d/a/dataset_5dabd551-2506-4c14-b688-d6980f63d6f9.dat' 0 0 '/tmp/tmpp0nq3lk8/job_working_directory/000/41/outputs/dataset_bd7359bb-64c0-4698-ad17-c7282035ae46.dat' | |
| ``` | |
| **Exit Code:** | |
| * ```console | |
| 0 | |
| ``` | |
| **Traceback:** | |
| * ```console | |
| ``` | |
| **Job Parameters:** | |
| * | Job parameter | Parameter value | | |
| | ------------- | --------------- | | |
| | \_\_input\_ext | ` "input" ` | | |
| | \_\_workflow\_invocation\_uuid\_\_ | ` "59801ec8114f11f189517ced8d626a0c" ` | | |
| | chromInfo | ` "/tmp/tmpp0nq3lk8/galaxy-dev/tool-data/shared/ucsc/chrom/?.len" ` | | |
| | dbkey | ` "?" ` | | |
| | max\_length | ` "0" ` | | |
| | min\_length | ` "0" ` | | |
| </details> | |
| - **Step 14: Unlabelled step (toolshed.g2.bx.psu.edu/repos/iuc/ncbi\_fcs\_gx/ncbi\_fcs\_gx/0.5.5+galaxy2)**: | |
| * step_state: scheduled | |
| * <details open><summary>Jobs</summary> | |
| - **Job 1:** | |
| * Job state is error | |
| **Container:** | |
| * ```console | |
| quay.io/biocontainers/ncbi-fcs-gx:0.5.5--h9948957_0 | |
| ``` | |
| **Command Line:** | |
| * ```console | |
| GX_DB_DIR="${TMPDIR}/test-only" && if [ ! -e "${GX_DB_DIR}/sync-files-completed.txt" ]; then mkdir -p "${GX_DB_DIR}" && sync_files.py get --mft 'https://ftp.ncbi.nlm.nih.gov/genomes/TOOLS/FCS/database/test-only/test-only.manifest' --dir "${GX_DB_DIR}" > sync_files.log 2>&1 || { cat sync_files.log >&2 ; false ; } && touch "${GX_DB_DIR}/sync-files-completed.txt"; fi && GX_NUM_CORES=${GALAXY_SLOTS:-2} run_gx.py --fasta '/tmp/tmpp0nq3lk8/files/5/d/a/dataset_5dabd551-2506-4c14-b688-d6980f63d6f9.dat' --tax-id '9606' --species 'Homo Sapiens' --split-fasta 'true' --gx-db "${GX_DB_DIR}" --out-basename output --action-report true --generate-logfile false | |
| ``` | |
| **Exit Code:** | |
| * ```console | |
| 1 | |
| ``` | |
| **Standard Error:** | |
| * ```console | |
| =============================================================================== | |
| Source: https://ftp.ncbi.nlm.nih.gov/genomes/TOOLS/FCS/database/test-only | |
| Destination: /tmp/tmpp0nq3lk8/job_working_directory/000/42/tmp/test-only | |
| Space check: Available:81.92GiB; Existing:0B; Incoming:4.29GiB; Delta:4.29GiB | |
| Requires transfer: 56B test-only.meta.jsonl | |
| [#4de5ac 0B/0B CN:1 DL:0B] | |
| Download Results: | |
| gid |stat|avg speed |path/URI | |
| ======+====+===========+======================================================= | |
| 4de5ac|OK | 18KiB/s|/tmp/tmpp0nq3lk8/job_working_directory/000/42/tmp/test-only.in_progress/test-only.meta.jsonl.part | |
| Status Legend: | |
| (OK):download completed. | |
| Computing md5 hash of /tmp/tmpp0nq3lk8/job_working_directory/000/42/tmp/test-only.in_progress/test-only.meta.jsonl.part... e1db5eeb49f25ca0f0c1f2febf8ae177 | |
| Requires transfer: 5.92KiB test-only.taxa.tsv | |
| Download Results: | |
| gid |stat|avg speed |path/URI | |
| ======+====+===========+======================================================= | |
| c10547|OK | 5.7MiB/s|/tmp/tmpp0nq3lk8/job_working_directory/000/42/tmp/test-only.in_progress/test-only.taxa.tsv.part | |
| Status Legend: | |
| (OK):download completed. | |
| Computing md5 hash of /tmp/tmpp0nq3lk8/job_working_directory/000/42/tmp/test-only.in_progress/test-only.taxa.tsv.part... 6425dc690849872ea22f5072ed34688a | |
| Requires transfer: 21.33KiB test-only.seq_info.tsv.gz | |
| Download Results: | |
| gid |stat|avg speed |path/URI | |
| ======+====+===========+======================================================= | |
| 0aab3f|OK | 426KiB/s|/tmp/tmpp0nq3lk8/job_working_directory/000/42/tmp/test-only.in_progress/test-only.seq_info.tsv.gz.part | |
| Status Legend: | |
| (OK):download completed. | |
| Computing md5 hash of /tmp/tmpp0nq3lk8/job_working_directory/000/42/tmp/test-only.in_progress/test-only.seq_info.tsv.gz.part... c4dae6d238aae59fada93da721b6a254 | |
| Requires transfer: 7.85MiB test-only.blast_div.tsv.gz | |
| 02/24 07:09:13 [[1;31mERROR[0m] CUID#7 - Download aborted. URI=https://ftp.ncbi.nlm.nih.gov/genomes/TOOLS/FCS/database/test-only/test-only.blast_div.tsv.gz | |
| Exception: [AbstractCommand.cc:351] errorCode=22 URI=https://ftp.ncbi.nlm.nih.gov/genomes/TOOLS/FCS/database/test-only/test-only.blast_div.tsv.gz | |
| -> [HttpSkipResponseCommand.cc:239] errorCode=22 The response status is not successful. status=403 | |
| Download Results: | |
| gid |stat|avg speed |path/URI | |
| ======+====+===========+======================================================= | |
| 4a0286|ERR | 0B/s|/tmp/tmpp0nq3lk8/job_working_directory/000/42/tmp/test-only.in_progress/test-only.blast_div.tsv.gz.part | |
| Status Legend: | |
| (ERR):error occurred. | |
| aria2 will resume download if the transfer is restarted. | |
| If there are any errors, then see the log file. See '-l' option in help/man page for details. | |
| Traceback (most recent call last): | |
| File "/usr/local/bin/sync_files.py", line 749, in <module> | |
| main() | |
| ~~~~^^ | |
| File "/usr/local/bin/sync_files.py", line 725, in main | |
| transfer_file(mi, src_mft_dir, work_dir) | |
| ~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^ | |
| File "/usr/local/bin/sync_files.py", line 585, in transfer_file | |
| download_file_with_aria(url, tmp_file_path) | |
| ~~~~~~~~~~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^ | |
| File "/usr/local/bin/sync_files.py", line 401, in download_file_with_aria | |
| subprocess.run( | |
| ~~~~~~~~~~~~~~^ | |
| ["aria2c", f"--conf-path={aria_config}", f"--dir={file_path.parent}", f"--out={file_path.name}", url], | |
| ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ | |
| check=True, | |
| ^^^^^^^^^^^ | |
| ) | |
| ^ | |
| File "/usr/local/lib/python3.13/subprocess.py", line 579, in run | |
| raise CalledProcessError(retcode, process.args, | |
| output=stdout, stderr=stderr) | |
| subprocess.CalledProcessError: Command '['aria2c', '--conf-path=/tmp/tmpp0nq3lk8/job_working_directory/000/42/tmp/test-only.in_progress/test-only.blast_div.tsv.gz.aria2_config', '--dir=/tmp/tmpp0nq3lk8/job_working_directory/000/42/tmp/test-only.in_progress', '--out=test-only.blast_div.tsv.gz.part', 'https://ftp.ncbi.nlm.nih.gov/genomes/TOOLS/FCS/database/test-only/test-only.blast_div.tsv.gz']' returned non-zero exit status 22. | |
| Removing /tmp/tmpp0nq3lk8/job_working_directory/000/42/tmp/test-only.lockfile. | |
| ``` | |
| **Traceback:** | |
| * ```console | |
| ``` | |
| **Job Parameters:** | |
| * | Job parameter | Parameter value | | |
| | ------------- | --------------- | | |
| | \_\_input\_ext | ` "input" ` | | |
| | \_\_workflow\_invocation\_uuid\_\_ | ` "59801ec8114f11f189517ced8d626a0c" ` | | |
| | chromInfo | ` "/tmp/tmpp0nq3lk8/galaxy-dev/tool-data/shared/ucsc/chrom/?.len" ` | | |
| | dbkey | ` "?" ` | | |
| | mode | ` {"__current_case__": 0, "config_tag": "test-only", "fasta": {"values": [{"id": 47, "src": "hda"}]}, "id": {"__current_case__": 1, "id_selector": "ncbi_tax", "tax_id": "9606"}, "mode_selector": "screen", "screen_adv": {"div": "", "gx_align_exclude_taxa": "", "gx_extra_contam_divs": null, "ignore_same_kingdom": false, "split_fasta": true}, "species": "Homo Sapiens"} ` | | |
| </details> | |
| - **Step 15: hard-masking (toolshed.g2.bx.psu.edu/repos/bgruening/text\_processing/tp\_sed\_tool/9.5+galaxy3)**: | |
| * step_state: scheduled | |
| * <details><summary>Jobs</summary> | |
| - **Job 1:** | |
| * Job state is ok | |
| **Container:** | |
| * ```console | |
| quay.io/biocontainers/sed:4.9 | |
| ``` | |
| **Command Line:** | |
| * ```console | |
| sed --sandbox -r -f '/tmp/tmpp0nq3lk8/job_working_directory/000/43/configs/tmp7hvx8tc0' '/tmp/tmpp0nq3lk8/files/b/d/7/dataset_bd7359bb-64c0-4698-ad17-c7282035ae46.dat' > '/tmp/tmpp0nq3lk8/job_working_directory/000/43/outputs/dataset_e0568c69-c75f-45bb-8609-41bb315515d1.dat' | |
| ``` | |
| **Exit Code:** | |
| * ```console | |
| 0 | |
| ``` | |
| **Traceback:** | |
| * ```console | |
| ``` | |
| **Job Parameters:** | |
| * | Job parameter | Parameter value | | |
| | ------------- | --------------- | | |
| | \_\_input\_ext | ` "input" ` | | |
| | \_\_workflow\_invocation\_uuid\_\_ | ` "59801ec8114f11f189517ced8d626a0c" ` | | |
| | adv\_opts | ` {"__current_case__": 0, "adv_opts_selector": "basic"} ` | | |
| | chromInfo | ` "/tmp/tmpp0nq3lk8/galaxy-dev/tool-data/shared/ucsc/chrom/?.len" ` | | |
| | code | ` "/^>/!y/atcgn/NNNNN/" ` | | |
| | dbkey | ` "?" ` | | |
| </details> | |
| - **Step 16: Unlabelled step (toolshed.g2.bx.psu.edu/repos/iuc/ncbi\_fcs\_gx/ncbi\_fcs\_gx/0.5.5+galaxy2)**: | |
| * step_state: scheduled | |
| * <details><summary>Jobs</summary> | |
| - **Job 1:** | |
| * Job state is paused | |
| **Traceback:** | |
| * ```console | |
| ``` | |
| **Job Parameters:** | |
| * | Job parameter | Parameter value | | |
| | ------------- | --------------- | | |
| | \_\_input\_ext | ` "input" ` | | |
| | \_\_workflow\_invocation\_uuid\_\_ | ` "59801ec8114f11f189517ced8d626a0c" ` | | |
| | chromInfo | ` "/tmp/tmpp0nq3lk8/galaxy-dev/tool-data/shared/ucsc/chrom/?.len" ` | | |
| | dbkey | ` "?" ` | | |
| | mode | ` {"__current_case__": 1, "action_report": {"values": [{"id": 50, "src": "hda"}]}, "input": {"values": [{"id": 47, "src": "hda"}]}, "min_seq_len": "200", "mode_selector": "clean"} ` | | |
| </details> | |
| - **Step 17: blast mitochondria DB (toolshed.g2.bx.psu.edu/repos/devteam/ncbi\_blast\_plus/ncbi\_blastn\_wrapper/2.16.0+galaxy0)**: | |
| * step_state: scheduled | |
| * <details><summary>Jobs</summary> | |
| - **Job 1:** | |
| * Job state is ok | |
| **Container:** | |
| * ```console | |
| quay.io/biocontainers/blast:2.16.0--h66d330f_5 | |
| ``` | |
| **Command Line:** | |
| * ```console | |
| blastn -query '/tmp/tmpp0nq3lk8/files/e/0/5/dataset_e0568c69-c75f-45bb-8609-41bb315515d1.dat' -db '"/cvmfs/data.galaxyproject.org/byhand/refseq/mitochondrion/genomic/2022-03-10/mitochondrion"' -task 'blastn' -evalue '0.001' -out '/tmp/tmpp0nq3lk8/job_working_directory/000/45/outputs/dataset_052f65e7-d01e-460c-9c3f-a554bdbc0c5f.dat' -outfmt '6 qseqid sseqid length qstart qend evalue qlen qcovs qcovhsp' -num_threads "${GALAXY_SLOTS:-8}" | |
| ``` | |
| **Exit Code:** | |
| * ```console | |
| 0 | |
| ``` | |
| **Traceback:** | |
| * ```console | |
| ``` | |
| **Job Parameters:** | |
| * | Job parameter | Parameter value | | |
| | ------------- | --------------- | | |
| | \_\_input\_ext | ` "input" ` | | |
| | \_\_workflow\_invocation\_uuid\_\_ | ` "59801ec8114f11f189517ced8d626a0c" ` | | |
| | adv\_opts | ` {"__current_case__": 0, "adv_opts_selector": "basic"} ` | | |
| | blast\_type | ` "blastn" ` | | |
| | chromInfo | ` "/tmp/tmpp0nq3lk8/galaxy-dev/tool-data/shared/ucsc/chrom/?.len" ` | | |
| | db\_opts | ` {"__current_case__": 0, "database": ["refseq_mitochondrion"], "db_opts_selector": "db", "histdb": "", "subject": ""} ` | | |
| | dbkey | ` "?" ` | | |
| | evalue\_cutoff | ` "0.001" ` | | |
| | output | ` {"__current_case__": 2, "ext_cols": ["qlen"], "ids_cols": null, "misc_cols": ["qcovs", "qcovhsp"], "out_format": "cols", "std_cols": ["qseqid", "sseqid", "length", "qstart", "qend", "evalue"], "tax_cols": null} ` | | |
| </details> | |
| - **Step 18: parsing blast output (toolshed.g2.bx.psu.edu/repos/iuc/parse\_mito\_blast/parse\_mito\_blast/1.0.2+galaxy0)**: | |
| * step_state: scheduled | |
| * <details><summary>Jobs</summary> | |
| - **Job 1:** | |
| * Job state is ok | |
| **Container:** | |
| * ```console | |
| quay.io/biocontainers/parse_mito_blast:1.0.2--hdfd78af_0 | |
| ``` | |
| **Command Line:** | |
| * ```console | |
| parse_mito_blast.py --blastout '/tmp/tmpp0nq3lk8/files/0/5/2/dataset_052f65e7-d01e-460c-9c3f-a554bdbc0c5f.dat' | |
| ``` | |
| **Exit Code:** | |
| * ```console | |
| 0 | |
| ``` | |
| **Traceback:** | |
| * ```console | |
| ``` | |
| **Job Parameters:** | |
| * | Job parameter | Parameter value | | |
| | ------------- | --------------- | | |
| | \_\_input\_ext | ` "input" ` | | |
| | \_\_workflow\_invocation\_uuid\_\_ | ` "59801ec8114f11f189517ced8d626a0c" ` | | |
| | chromInfo | ` "/tmp/tmpp0nq3lk8/galaxy-dev/tool-data/shared/ucsc/chrom/?.len" ` | | |
| | dbkey | ` "?" ` | | |
| </details> | |
| - **Step 19: removing scaffolds (toolshed.g2.bx.psu.edu/repos/bgruening/gfastats/gfastats/1.3.11+galaxy1)**: | |
| * step_state: scheduled | |
| * <details><summary>Jobs</summary> | |
| - **Job 1:** | |
| * Job state is paused | |
| **Traceback:** | |
| * ```console | |
| ``` | |
| **Job Parameters:** | |
| * | Job parameter | Parameter value | | |
| | ------------- | --------------- | | |
| | \_\_input\_ext | ` "input" ` | | |
| | \_\_workflow\_invocation\_uuid\_\_ | ` "59801ec8114f11f189517ced8d626a0c" ` | | |
| | chromInfo | ` "/tmp/tmpp0nq3lk8/galaxy-dev/tool-data/shared/ucsc/chrom/?.len" ` | | |
| | dbkey | ` "?" ` | | |
| | mode\_condition | ` {"__current_case__": 0, "homopolymer_compress": null, "output_condition": {"__current_case__": 1, "line_length": null, "out_format": "fasta.gz"}, "remove_terminal_gaps": true, "selector": "manipulation", "sort": "", "swiss_army_knife": null} ` | | |
| | target\_condition | ` {"__current_case__": 1, "exclude_bed": {"values": [{"id": 56, "src": "hda"}]}, "include_bed": null, "target_option": "true", "target_sequence": ""} ` | | |
| </details> | |
| </details> | |
| * <details><summary>Other invocation details</summary> | |
| - **history_id** | |
| * 03c48f567261f25d | |
| - **history_state** | |
| * error | |
| - **invocation_id** | |
| * 9241cb19c51da669 | |
| - **invocation_state** | |
| * scheduled | |
| - **workflow_id** | |
| * d0f859496eca71d9 | |
| </details> | |
| </div></details> | |
| * <details class="rcorners light-red"><summary class="light-red">❌ RepeatMasking-Workflow.ga_0</summary><div class="padded"> | |
| #### Workflow invocation details | |
| * Invocation Messages | |
| * <details><summary>Steps</summary> | |
| - **Step 1: input**: | |
| * step_state: scheduled | |
| - **Step 2: Unlabelled step (toolshed.g2.bx.psu.edu/repos/csbl/repeatmodeler/repeatmodeler/2.0.4+galaxy1)**: | |
| * step_state: scheduled | |
| * <details><summary>Jobs</summary> | |
| - **Job 1:** | |
| * Job state is ok | |
| **Container:** | |
| * ```console | |
| quay.io/biocontainers/repeatmodeler:2.0.4--pl5321hdfd78af_0 | |
| ``` | |
| **Command Line:** | |
| * ```console | |
| BuildDatabase -name 'rmdb' '/tmp/tmp07g19wax/files/f/7/3/dataset_f73d671c-db27-4835-8a0c-f67860c48191.dat' && RepeatModeler -database 'rmdb' -threads ${GALAXY_SLOTS:-1} | |
| ``` | |
| **Exit Code:** | |
| * ```console | |
| 0 | |
| ``` | |
| **Standard Output:** | |
| * ```console | |
| Building database rmdb: | |
| Reading /tmp/tmp07g19wax/files/f/7/3/dataset_f73d671c-db27-4835-8a0c-f67860c48191.dat... | |
| Number of sequences (bp) added to database: 1 ( 5942969 bp ) | |
| WARNING: RepeatModeler is a computationally intensive program. | |
| It is recommended that for anything other than debugging | |
| purposes the program should run with greater than eight | |
| threads (-threads #). | |
| RepeatModeler Version 2.0.4 | |
| =========================== | |
| Using output directory = /tmp/tmp07g19wax/job_working_directory/000/2/working/RM_10.TueFeb240657362026 | |
| Search Engine = rmblast 2.13.0+ | |
| Threads = 1 | |
| Dependencies: TRF 4.09, RECON , RepeatScout 1.0.6, RepeatMasker 4.1.5 | |
| LTR Structural Analysis: Disabled [use -LTRStruct to enable] | |
| Random Number Seed: 1771916256 | |
| Database = /tmp/tmp07g19wax/job_working_directory/000/2/working/rmdb | |
| - Sequences = 1 | |
| - Bases = 5942969 | |
| Storage Throughput = good ( 910.93 MB/s ) | |
| Ready to start the sampling process. | |
| INFO: The runtime of RepeatModeler heavily depends on the quality of the assembly | |
| and the repetitive content of the sequences. It is not imperative | |
| that RepeatModeler completes all rounds in order to obtain useful | |
| results. At the completion of each round, the files ( consensi.fa, and | |
| families.stk ) found in: | |
| /tmp/tmp07g19wax/job_working_directory/000/2/working/RM_10.TueFeb240657362026/ | |
| will contain all results produced thus far. These files may be | |
| manually copied and run through RepeatClassifier should the program | |
| be terminated early. | |
| RepeatModeler Round # 1 | |
| ======================== | |
| Searching for Repeats | |
| -- Sampling from the database... | |
| - Gathering up to 40000000 bp | |
| - Final Sample Size = 5942880 bp ( 5942880 non ambiguous ) | |
| - Num Contigs Represented = 1 | |
| - Sequence extraction : 00:00:01 (hh:mm:ss) Elapsed Time | |
| -- Running RepeatScout on the sequences... | |
| - RepeatScout: Running build_lmer_table ( l = 13 ).. | |
| - RepeatScout: Running RepeatScout.. : 160 raw families identified | |
| - RepeatScout: Running filtering stage.. 159 families remaining | |
| - RepeatScout: 00:00:52 (hh:mm:ss) Elapsed Time | |
| - Large Satellite Filtering.. : 0 found in 00:00:01 (hh:mm:ss) Elapsed Time | |
| - Collecting repeat instances...: 00:00:29 (hh:mm:ss) Elapsed Time | |
| Refinement: 00:00:12 (hh:mm:ss) Elapsed Time | |
| Family Refinement: 00:00:12 (hh:mm:ss) Elapsed Time | |
| Round Time: 00:01:35 (hh:mm:ss) Elapsed Time : 6 families discovered. | |
| RepeatModeler Round # 2 | |
| ======================== | |
| Searching for Repeats | |
| -- Sampling from the database... | |
| - Gathering up to 10000000 bp | |
| - Sequence extraction : 00:00:01 (hh:mm:ss) Elapsed Time | |
| -- Running TRFMask on the sequence... | |
| 14 Tandem Repeats Masked | |
| - TRFMask time 00:00:03 (hh:mm:ss) Elapsed Time | |
| -- Masking repeats from the previous rounds... | |
| -- Collecting 322 ranges... | |
| 311 repeats masked totaling 106797 bp(s). | |
| - TE Masking time 00:00:02 (hh:mm:ss) Elapsed Time | |
| -- Sample Stats: | |
| Sample Size 5942880 bp | |
| Num Contigs Represented = 1 | |
| Non ambiguous bp: | |
| Initial: 5942880 bp | |
| After Masking: 5834097 bp | |
| Masked: 1.83 % | |
| -- Input Database Coverage: 5942880 bp out of 5942969 bp ( 100.00 % ) | |
| Sampling Time: 00:00:07 (hh:mm:ss) Elapsed Time | |
| Running all-by-other comparisons... | |
| - Total Comparisons = 11026 | |
| 1% completed, 00:9:48 (hh:mm:ss) est. time remaining. | |
| 2% completed, 00:9:42 (hh:mm:ss) est. time remaining. | |
| 3% completed, 00:9:36 (hh:mm:ss) est. time remaining. | |
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| Comparison Time: 00:10:15 (hh:mm:ss) Elapsed Time, 4993 HSPs Collected | |
| - RECON: Running imagespread.. | |
| RECON Elapsed: 00:00:00 (hh:mm:ss) Elapsed Time | |
| - RECON: Running initial definition of elements ( eledef ).. | |
| RECON Elapsed: 00:00:01 (hh:mm:ss) Elapsed Time | |
| - RECON: Running re-definition of elements ( eleredef ).. | |
| RECON Elapsed: 00:00:00 (hh:mm:ss) Elapsed Time | |
| - RECON: Running re-definition of edges ( edgeredef ).. | |
| RECON Elapsed: 00:00:01 (hh:mm:ss) Elapsed Time | |
| - RECON: Running family definition ( famdef ).. | |
| RECON Elapsed: 00:00:00 (hh:mm:ss) Elapsed Time | |
| - Obtaining element sequences | |
| Number of families returned by RECON: 838 | |
| Processing families with greater than 15 elements | |
| Instance Gathering: 00:00:00 (hh:mm:ss) Elapsed Time | |
| About to run 2 refinement jobs | |
| Refinement: 00:01:47 (hh:mm:ss) Elapsed Time | |
| Family Refinement: 00:01:47 (hh:mm:ss) Elapsed Time | |
| Round Time: 00:12:11 (hh:mm:ss) Elapsed Time : 2 families discovered. | |
| RepeatScout/RECON discovery complete: 8 families found | |
| RepeatClassifier Version 2.0.4 | |
| ====================================== | |
| - Looking for Simple and Low Complexity sequences.. | |
| - Looking for similarity to known repeat proteins.. | |
| - Looking for similarity to known repeat consensi.. | |
| Classification Time: 00:01:16 (hh:mm:ss) Elapsed Time | |
| Program Time: 00:15:02 (hh:mm:ss) Elapsed Time | |
| Working directory: /tmp/tmp07g19wax/job_working_directory/000/2/working/RM_10.TueFeb240657362026 | |
| may be deleted unless there were problems with the run. | |
| The results have been saved to: | |
| /tmp/tmp07g19wax/job_working_directory/000/2/working/rmdb-families.fa - Consensus sequences for each family identified. | |
| /tmp/tmp07g19wax/job_working_directory/000/2/working/rmdb-families.stk - Seed alignments for each family identified. | |
| /tmp/tmp07g19wax/job_working_directory/000/2/working/rmdb-rmod.log - Execution log. Useful for reproducing results. | |
| The RepeatModeler stockholm file is formatted so that it can | |
| easily be submitted to the Dfam database. Please consider contributing | |
| curated families to this open database and be a part of this growing | |
| community resource. For more information contact help@dfam.org. | |
| ``` | |
| **Traceback:** | |
| * ```console | |
| ``` | |
| **Job Parameters:** | |
| * | Job parameter | Parameter value | | |
| | ------------- | --------------- | | |
| | \_\_input\_ext | ` "input" ` | | |
| | \_\_workflow\_invocation\_uuid\_\_ | ` "e3cd8c02114d11f189517ced8d7b3cca" ` | | |
| | chromInfo | ` "/tmp/tmp07g19wax/galaxy-dev/tool-data/shared/ucsc/chrom/?.len" ` | | |
| | dbkey | ` "?" ` | | |
| </details> | |
| - **Step 3: Unlabelled step (toolshed.g2.bx.psu.edu/repos/bgruening/repeat\_masker/repeatmasker\_wrapper/4.1.5+galaxy0)**: | |
| * step_state: scheduled | |
| * <details open><summary>Jobs</summary> | |
| - **Job 1:** | |
| * Job state is error | |
| **Container:** | |
| * ```console | |
| quay.io/biocontainers/repeatmasker:4.1.5--pl5321hdfd78af_1 | |
| ``` | |
| **Command Line:** | |
| * ```console | |
| RM_PATH=$(which RepeatMasker) && if [ -z "$RM_PATH" ] ; then echo "Failed to find RepeatMasker in PATH ($PATH)" >&2 ; exit 1 ; fi && if [ -z "$RM_LIB_PATH" ] ; then RM_LIB_PATH=$(dirname $RM_PATH)/../share/RepeatMasker/Libraries ; fi && ln -s '/tmp/tmp07g19wax/files/5/b/6/dataset_5b6deafc-dcd9-4eac-a46d-18dd8c5571ce.dat' rm_input.fasta && RepeatMasker -dir $(pwd) -libdir $RM_LIB_PATH -species '' -parallel ${GALAXY_SLOTS:-1} -gff -excln -frag 40000 -xsmall rm_input.fasta && mv rm_input.fasta.masked '/tmp/tmp07g19wax/job_working_directory/000/3/outputs/dataset_6b59ec54-af6f-4eb7-917e-afc1213f1478.dat' && sed -E 's/^ *// ; s/ *$//; s/\+ //; s/ +/\t/g ; 1,2c SW score\t% div.\t% del.\t% ins.\tquery sequence\tpos in query: begin\tend\t(left)\trepeat\tclass/family\tpos in repeat: begin\tend\t(left)\tID' rm_input.fasta.out >'/tmp/tmp07g19wax/job_working_directory/000/3/outputs/dataset_d5f16622-70df-4d97-a880-e8961f0868dc.dat' && mv rm_input.fasta.tbl '/tmp/tmp07g19wax/job_working_directory/000/3/outputs/dataset_fca89bf4-45c6-43e0-b508-b489ead6f5fc.dat' && mv rm_input.fasta.out.gff '/tmp/tmp07g19wax/job_working_directory/000/3/outputs/dataset_8dd7bb09-ee01-43ed-8a24-f702b2c3fbf6.dat' && if [ -f 'rm_input.fasta.cat.gz' ]; then zcat 'rm_input.fasta.cat.gz' > '/tmp/tmp07g19wax/job_working_directory/000/3/outputs/dataset_93e65255-a52e-4474-83a9-b08228c0d0a6.dat'; else mv rm_input.fasta.cat '/tmp/tmp07g19wax/job_working_directory/000/3/outputs/dataset_93e65255-a52e-4474-83a9-b08228c0d0a6.dat'; fi | |
| ``` | |
| **Exit Code:** | |
| * ```console | |
| 255 | |
| ``` | |
| **Standard Error:** | |
| * ```console | |
| Species "homo sapiens" is not known to RepeatMasker. There may | |
| not be any TE families defined in the libraries for this | |
| species/clade or there may be an error in the spelling. | |
| Please check your entry against the NCBI Taxonomy database | |
| and/or try using a broader clade or related species instead. | |
| The full list of species/clades defined in the library may be | |
| obtained using the famdb.py script. | |
| ``` | |
| **Standard Output:** | |
| * ```console | |
| RepeatMasker version 4.1.5 | |
| Search Engine: NCBI/RMBLAST [ 2.14.1+ ] | |
| Using Master RepeatMasker Database: /usr/local/bin/../share/RepeatMasker/Libraries/RepeatMaskerLib.h5 | |
| Title : | |
| Version : | |
| Date : | |
| Families : | |
| ``` | |
| **Traceback:** | |
| * ```console | |
| ``` | |
| **Job Parameters:** | |
| * | Job parameter | Parameter value | | |
| | ------------- | --------------- | | |
| | \_\_input\_ext | ` "input" ` | | |
| | \_\_workflow\_invocation\_uuid\_\_ | ` "e3cd8c02114d11f189517ced8d7b3cca" ` | | |
| | advanced | ` {"alu": false, "div": false, "frag": "40000", "gc": null, "gccalc": false, "invert_alignments": false, "is_clip": false, "is_only": false, "keep_alignments": false, "no_is": false, "nocut": false, "noint": false, "nolow": false, "norna": false, "poly": false, "primspec": false, "rodspec": false, "search_speed": "", "xout": false} ` | | |
| | chromInfo | ` "/tmp/tmp07g19wax/galaxy-dev/tool-data/shared/ucsc/chrom/?.len" ` | | |
| | dbkey | ` "?" ` | | |
| | excln | ` true ` | | |
| | gff | ` true ` | | |
| | repeat\_source | ` {"__current_case__": 0, "source_type": "dfam", "species_source": {"__current_case__": 1, "species_from_list": "no", "species_name": ""}} ` | | |
| | xsmall | ` true ` | | |
| </details> | |
| </details> | |
| * <details><summary>Other invocation details</summary> | |
| - **history_id** | |
| * 9d92d153e1c44df1 | |
| - **history_state** | |
| * error | |
| - **invocation_id** | |
| * 9d92d153e1c44df1 | |
| - **invocation_state** | |
| * scheduled | |
| - **workflow_id** | |
| * 9d92d153e1c44df1 | |
| </details> | |
| </div></details> | |
| * <details class="rcorners light-red"><summary class="light-red">❌ fragment-based-docking-scoring.ga_0</summary><div class="padded"> | |
| #### Workflow invocation details | |
| * Invocation Messages | |
| * <details><summary>Steps</summary> | |
| - **Step 1: Receptor (PDB)**: | |
| * step_state: scheduled | |
| - **Step 2: All fragments (SDF)**: | |
| * step_state: scheduled | |
| - **Step 3: Candidate compounds (SMILES)**: | |
| * step_state: scheduled | |
| - **Step 4: Collection size for docking**: | |
| * step_state: scheduled | |
| - **Step 5: Number of poses**: | |
| * step_state: scheduled | |
| - **Step 6: SuCOS threshold**: | |
| * step_state: scheduled | |
| - **Step 7: Fragment for SuCOS scoring (SDF/MOL)**: | |
| * step_state: scheduled | |
| - **Step 8: Unlabelled step (toolshed.g2.bx.psu.edu/repos/bgruening/openbabel\_compound\_convert/openbabel\_compound\_convert/3.1.1+galaxy0)**: | |
| * step_state: scheduled | |
| * <details><summary>Jobs</summary> | |
| - **Job 1:** | |
| * Job state is ok | |
| **Container:** | |
| * ```console | |
| quay.io/biocontainers/mulled-v2-45c58cad0c5dcd0f8d3c19e5016a20177e140973:1eae5deab2c501ac02c1fd2cf9eadb43c1fb0c61-2 | |
| ``` | |
| **Command Line:** | |
| * ```console | |
| obabel -i 'pdb' '/tmp/tmp3awx_m9b/files/f/5/e/dataset_f5eec253-b687-4a00-a1b4-228c2f4332af.dat' -o 'mol2' -O '/tmp/tmp3awx_m9b/job_working_directory/000/19/outputs/dataset_8dbd5c9b-5d4f-4720-8491-20725c960d3d.dat' -e -p 7.4 | |
| ``` | |
| **Exit Code:** | |
| * ```console | |
| 0 | |
| ``` | |
| **Standard Error:** | |
| * ```console | |
| ============================== | |
| *** Open Babel Warning in PerceiveBondOrders | |
| Failed to kekulize aromatic bonds in OBMol::PerceiveBondOrders (title is /tmp/tmp3awx_m9b/files/f/5/e/dataset_f5eec253-b687-4a00-a1b4-228c2f4332af.dat) | |
| 1 molecule converted | |
| ``` | |
| **Traceback:** | |
| * ```console | |
| ``` | |
| **Job Parameters:** | |
| * | Job parameter | Parameter value | | |
| | ------------- | --------------- | | |
| | \_\_input\_ext | ` "pdb" ` | | |
| | \_\_workflow\_invocation\_uuid\_\_ | ` "ee1d9032115511f18951000d3a9202a3" ` | | |
| | appendtotitle | ` "" ` | | |
| | chromInfo | ` "/tmp/tmp3awx_m9b/galaxy-dev/tool-data/shared/ucsc/chrom/?.len" ` | | |
| | dative\_bonds | ` false ` | | |
| | dbkey | ` "?" ` | | |
| | oformat | ` {"__current_case__": 41, "gen2d": false, "gen3d": false, "mol2_ignore_res": false, "oformat_opts_selector": "mol2"} ` | | |
| | ph | ` "7.4" ` | | |
| | remove\_h | ` false ` | | |
| | split | ` false ` | | |
| | unique | ` {"__current_case__": 0, "unique_opts_selector": ""} ` | | |
| </details> | |
| - **Step 9: Unlabelled step (toolshed.g2.bx.psu.edu/repos/bgruening/ctb\_frankenstein\_ligand/ctb\_frankenstein\_ligand/2013.1-0+galaxy0)**: | |
| * step_state: scheduled | |
| * <details><summary>Jobs</summary> | |
| - **Job 1:** | |
| * Job state is ok | |
| **Container:** | |
| * ```console | |
| quay.io/biocontainers/python:3.7--1 | |
| ``` | |
| **Command Line:** | |
| * ```console | |
| python '/tmp/shed_dir/toolshed.g2.bx.psu.edu/repos/bgruening/ctb_frankenstein_ligand/7255688c77f3/ctb_frankenstein_ligand/select_points_SDF.py' -i '/tmp/tmp3awx_m9b/files/c/5/d/dataset_c5d61587-50fb-44a7-aa37-d799124a83ba.dat' -o '/tmp/tmp3awx_m9b/job_working_directory/000/20/outputs/dataset_1aea4940-2f26-42d1-aa07-336c82b07941.dat' | |
| ``` | |
| **Exit Code:** | |
| * ```console | |
| 0 | |
| ``` | |
| **Traceback:** | |
| * ```console | |
| ``` | |
| **Job Parameters:** | |
| * | Job parameter | Parameter value | | |
| | ------------- | --------------- | | |
| | \_\_input\_ext | ` "sdf" ` | | |
| | \_\_workflow\_invocation\_uuid\_\_ | ` "ee1d9032115511f18951000d3a9202a3" ` | | |
| | chromInfo | ` "/tmp/tmp3awx_m9b/galaxy-dev/tool-data/shared/ucsc/chrom/?.len" ` | | |
| | dbkey | ` "?" ` | | |
| </details> | |
| - **Step 10: Unlabelled step (toolshed.g2.bx.psu.edu/repos/bgruening/enumerate\_charges/enumerate\_charges/2020.03.4+galaxy0)**: | |
| * step_state: scheduled | |
| * <details><summary>Jobs</summary> | |
| - **Job 1:** | |
| * Job state is ok | |
| **Container:** | |
| * ```console | |
| quay.io/biocontainers/rdkit:2020.03.4--2 | |
| ``` | |
| **Command Line:** | |
| * ```console | |
| python '/tmp/shed_dir/toolshed.g2.bx.psu.edu/repos/bgruening/enumerate_charges/67ee76f0e497/enumerate_charges/dimorphite_dl.py' --smiles_file '/tmp/tmp3awx_m9b/files/d/c/d/dataset_dcd3185e-a443-49c1-9d59-8b1d608efa38.dat' --output_file '/tmp/tmp3awx_m9b/job_working_directory/000/21/outputs/dataset_21691924-9ff8-43eb-871a-cb8c401296d1.dat' --min_ph 4.4 --max_ph 10.4 | |
| ``` | |
| **Exit Code:** | |
| * ```console | |
| 0 | |
| ``` | |
| **Standard Error:** | |
| * ```console | |
| /tmp/shed_dir/toolshed.g2.bx.psu.edu/repos/bgruening/enumerate_charges/67ee76f0e497/enumerate_charges/dimorphite_dl.py:654: SyntaxWarning: "is not" with a literal. Did you mean "!="? | |
| if line is not "": | |
| WARNING: Skipping poorly formed SMILES string: NC(CC(=O)NC1=CC=C(S(N)(=O)=O)C=C1)=NHO | |
| ``` | |
| **Standard Output:** | |
| * ```console | |
| For help, use: python dimorphite_dl.py --help | |
| If you use Dimorphite-DL in your research, please cite: | |
| Ropp PJ, Kaminsky JC, Yablonski S, Durrant JD (2019) Dimorphite-DL: An | |
| open-source program for enumerating the ionization states of drug-like small | |
| molecules. J Cheminform 11:14. doi:10.1186/s13321-019-0336-9. | |
| PARAMETERS: | |
| label_states: False | |
| max_ph: 10.4 | |
| min_ph: 4.4 | |
| output_file: /tmp/tmp3awx_m9b/job_working_directory/000/21/outputs/dataset_21691924-9ff8-43eb-871a-cb8c401296d1.dat | |
| pka_precision: 1.0 | |
| smiles: None | |
| smiles_file: /tmp/tmp3awx_m9b/files/d/c/d/dataset_dcd3185e-a443-49c1-9d59-8b1d608efa38.dat | |
| test: False | |
| ``` | |
| **Traceback:** | |
| * ```console | |
| ``` | |
| **Job Parameters:** | |
| * | Job parameter | Parameter value | | |
| | ------------- | --------------- | | |
| | \_\_input\_ext | ` "smi" ` | | |
| | \_\_workflow\_invocation\_uuid\_\_ | ` "ee1d9032115511f18951000d3a9202a3" ` | | |
| | chromInfo | ` "/tmp/tmp3awx_m9b/galaxy-dev/tool-data/shared/ucsc/chrom/?.len" ` | | |
| | dbkey | ` "?" ` | | |
| | max\_ph | ` "10.4" ` | | |
| | min\_ph | ` "4.4" ` | | |
| </details> | |
| - **Step 11: Unlabelled step (toolshed.g2.bx.psu.edu/repos/iuc/compose\_text\_param/compose\_text\_param/0.1.1)**: | |
| * step_state: scheduled | |
| * <details><summary>Jobs</summary> | |
| - **Job 1:** | |
| * Job state is ok | |
| **Command Line:** | |
| * ```console | |
| cd ../; python _evaluate_expression_.py | |
| ``` | |
| **Exit Code:** | |
| * ```console | |
| 0 | |
| ``` | |
| **Traceback:** | |
| * ```console | |
| ``` | |
| **Job Parameters:** | |
| * | Job parameter | Parameter value | | |
| | ------------- | --------------- | | |
| | \_\_input\_ext | ` "input" ` | | |
| | \_\_workflow\_invocation\_uuid\_\_ | ` "ee1d9032115511f18951000d3a9202a3" ` | | |
| | chromInfo | ` "/tmp/tmp3awx_m9b/galaxy-dev/tool-data/shared/ucsc/chrom/?.len" ` | | |
| | components | ` [{"__index__": 0, "param_type": {"__current_case__": 0, "component_value": "$SuCOS_Score >= ", "select_param_type": "text"}}, {"__index__": 1, "param_type": {"__current_case__": 2, "component_value": "0", "select_param_type": "float"}}] ` | | |
| | dbkey | ` "?" ` | | |
| </details> | |
| - **Step 12: Unlabelled step (toolshed.g2.bx.psu.edu/repos/bgruening/rxdock\_rbcavity/rxdock\_rbcavity/2013.1.1\_148c5bd1+galaxy0)**: | |
| * step_state: scheduled | |
| * <details open><summary>Jobs</summary> | |
| - **Job 1:** | |
| * Job state is error | |
| **Container:** | |
| * ```console | |
| quay.io/biocontainers/rxdock:2013.1.1_148c5bd1--pl5321he88f293_3 | |
| ``` | |
| **Command Line:** | |
| * ```console | |
| ln -s '/tmp/tmp3awx_m9b/job_working_directory/000/23/configs/tmph3o6y3wb' receptor.prm && ln -s '/tmp/tmp3awx_m9b/files/8/d/b/dataset_8dbd5c9b-5d4f-4720-8491-20725c960d3d.dat' receptor.mol2 && ln -s '/tmp/tmp3awx_m9b/files/1/a/e/dataset_1aea4940-2f26-42d1-aa07-336c82b07941.dat' ligand.sdf && rbcavity -W -d -r receptor.prm && ls -l | |
| ``` | |
| **Exit Code:** | |
| * ```console | |
| 127 | |
| ``` | |
| **Standard Error:** | |
| * ```console | |
| /tmp/tmp3awx_m9b/job_working_directory/000/23/tool_script.sh: line 22: rbcavity: command not found | |
| ``` | |
| **Traceback:** | |
| * ```console | |
| ``` | |
| **Job Parameters:** | |
| * | Job parameter | Parameter value | | |
| | ------------- | --------------- | | |
| | \_\_input\_ext | ` "mol2" ` | | |
| | \_\_workflow\_invocation\_uuid\_\_ | ` "ee1d9032115511f18951000d3a9202a3" ` | | |
| | chromInfo | ` "/tmp/tmp3awx_m9b/galaxy-dev/tool-data/shared/ucsc/chrom/?.len" ` | | |
| | dbkey | ` "?" ` | | |
| | gridstep | ` "0.5" ` | | |
| | min\_volume | ` "100" ` | | |
| | radius | ` "3.0" ` | | |
| | sphere | ` "1.0" ` | | |
| | vol\_incr | ` "0.0" ` | | |
| | weight | ` "1.0" ` | | |
| </details> | |
| - **Step 13: Unlabelled step (toolshed.g2.bx.psu.edu/repos/bgruening/openbabel\_compound\_convert/openbabel\_compound\_convert/3.1.1+galaxy0)**: | |
| * step_state: scheduled | |
| * <details><summary>Jobs</summary> | |
| - **Job 1:** | |
| * Job state is ok | |
| **Container:** | |
| * ```console | |
| quay.io/biocontainers/mulled-v2-45c58cad0c5dcd0f8d3c19e5016a20177e140973:1eae5deab2c501ac02c1fd2cf9eadb43c1fb0c61-2 | |
| ``` | |
| **Command Line:** | |
| * ```console | |
| obabel -i 'smi' '/tmp/tmp3awx_m9b/files/2/1/6/dataset_21691924-9ff8-43eb-871a-cb8c401296d1.dat' -o 'sdf' -O '/tmp/tmp3awx_m9b/job_working_directory/000/24/outputs/dataset_d25623a1-646b-4482-8719-17825b735b65.dat' -e --gen3d -p 7.4 | |
| ``` | |
| **Exit Code:** | |
| * ```console | |
| 0 | |
| ``` | |
| **Standard Error:** | |
| * ```console | |
| 4 molecules converted | |
| ``` | |
| **Traceback:** | |
| * ```console | |
| ``` | |
| **Job Parameters:** | |
| * | Job parameter | Parameter value | | |
| | ------------- | --------------- | | |
| | \_\_input\_ext | ` "smi" ` | | |
| | \_\_workflow\_invocation\_uuid\_\_ | ` "ee1d9032115511f18951000d3a9202a3" ` | | |
| | appendtotitle | ` "" ` | | |
| | chromInfo | ` "/tmp/tmp3awx_m9b/galaxy-dev/tool-data/shared/ucsc/chrom/?.len" ` | | |
| | dative\_bonds | ` false ` | | |
| | dbkey | ` "?" ` | | |
| | oformat | ` {"__current_case__": 58, "gen2d": false, "gen3d": true, "oformat_opts_selector": "sdf", "sdf_alias_out": false, "sdf_exp_h": false, "sdf_no_prop": false, "sdf_wedge_bonds": false} ` | | |
| | ph | ` "7.4" ` | | |
| | remove\_h | ` false ` | | |
| | split | ` false ` | | |
| | unique | ` {"__current_case__": 0, "unique_opts_selector": ""} ` | | |
| </details> | |
| - **Step 14: Unlabelled step (toolshed.g2.bx.psu.edu/repos/bgruening/split\_file\_to\_collection/split\_file\_to\_collection/0.5.0)**: | |
| * step_state: scheduled | |
| * <details><summary>Jobs</summary> | |
| - **Job 1:** | |
| * Job state is ok | |
| **Container:** | |
| * ```console | |
| quay.io/biocontainers/python:3.5--2 | |
| ``` | |
| **Command Line:** | |
| * ```console | |
| mkdir ./out && python '/tmp/shed_dir/toolshed.g2.bx.psu.edu/repos/bgruening/split_file_to_collection/6cbe2f30c2d7/split_file_to_collection/split_file_to_collection.py' --out ./out --in '/tmp/tmp3awx_m9b/files/d/2/5/dataset_d25623a1-646b-4482-8719-17825b735b65.dat' --ftype 'sdf' --numnew '2' --file_names 'split_file' --file_ext 'sdf' | |
| ``` | |
| **Exit Code:** | |
| * ```console | |
| 0 | |
| ``` | |
| **Traceback:** | |
| * ```console | |
| ``` | |
| **Job Parameters:** | |
| * | Job parameter | Parameter value | | |
| | ------------- | --------------- | | |
| | \_\_input\_ext | ` "sdf" ` | | |
| | \_\_workflow\_invocation\_uuid\_\_ | ` "ee1d9032115511f18951000d3a9202a3" ` | | |
| | chromInfo | ` "/tmp/tmp3awx_m9b/galaxy-dev/tool-data/shared/ucsc/chrom/?.len" ` | | |
| | dbkey | ` "?" ` | | |
| | split\_parms | ` {"__current_case__": 4, "input": {"values": [{"id": 51, "src": "hda"}]}, "newfilenames": "split_file", "select_allocate": {"__current_case__": 2, "allocate": "byrow"}, "select_ftype": "sdf", "select_mode": {"__current_case__": 1, "mode": "numnew", "numnew": "2"}} ` | | |
| </details> | |
| - **Step 15: Unlabelled step (toolshed.g2.bx.psu.edu/repos/bgruening/rxdock\_rbdock/rxdock\_rbdock/2013.1.1\_148c5bd1+galaxy0)**: | |
| * step_state: scheduled | |
| * <details><summary>Jobs</summary> | |
| - **Job 1:** | |
| * Job state is paused | |
| **Traceback:** | |
| * ```console | |
| ``` | |
| **Job Parameters:** | |
| * | Job parameter | Parameter value | | |
| | ------------- | --------------- | | |
| | \_\_input\_ext | ` "mol2" ` | | |
| | \_\_workflow\_invocation\_uuid\_\_ | ` "ee1d9032115511f18951000d3a9202a3" ` | | |
| | chromInfo | ` "/tmp/tmp3awx_m9b/galaxy-dev/tool-data/shared/ucsc/chrom/?.len" ` | | |
| | custom\_rec | ` {"__current_case__": 1, "custom_rec_select": "false", "flex": "3.0"} ` | | |
| | dbkey | ` "?" ` | | |
| | filter | ` {"__current_case__": 1, "filter_select": "no_filter"} ` | | |
| | name | ` false ` | | |
| | num | ` "1" ` | | |
| | seed | ` "1" ` | | |
| - **Job 2:** | |
| * Job state is paused | |
| **Traceback:** | |
| * ```console | |
| ``` | |
| **Job Parameters:** | |
| * | Job parameter | Parameter value | | |
| | ------------- | --------------- | | |
| | \_\_input\_ext | ` "mol2" ` | | |
| | \_\_workflow\_invocation\_uuid\_\_ | ` "ee1d9032115511f18951000d3a9202a3" ` | | |
| | chromInfo | ` "/tmp/tmp3awx_m9b/galaxy-dev/tool-data/shared/ucsc/chrom/?.len" ` | | |
| | custom\_rec | ` {"__current_case__": 1, "custom_rec_select": "false", "flex": "3.0"} ` | | |
| | dbkey | ` "?" ` | | |
| | filter | ` {"__current_case__": 1, "filter_select": "no_filter"} ` | | |
| | name | ` false ` | | |
| | num | ` "1" ` | | |
| | seed | ` "1" ` | | |
| </details> | |
| - **Step 16: Unlabelled step (toolshed.g2.bx.psu.edu/repos/nml/collapse\_collections/collapse\_dataset/4.2)**: | |
| * step_state: scheduled | |
| * <details><summary>Jobs</summary> | |
| - **Job 1:** | |
| * Job state is paused | |
| **Traceback:** | |
| * ```console | |
| ``` | |
| **Job Parameters:** | |
| * | Job parameter | Parameter value | | |
| | ------------- | --------------- | | |
| | \_\_input\_ext | ` "sdf" ` | | |
| | \_\_workflow\_invocation\_uuid\_\_ | ` "ee1d9032115511f18951000d3a9202a3" ` | | |
| | chromInfo | ` "/tmp/tmp3awx_m9b/galaxy-dev/tool-data/shared/ucsc/chrom/?.len" ` | | |
| | dbkey | ` "?" ` | | |
| | filename | ` {"__current_case__": 1, "add_name": false} ` | | |
| | one\_header | ` false ` | | |
| </details> | |
| - **Step 17: Unlabelled step (toolshed.g2.bx.psu.edu/repos/bgruening/sucos\_docking\_scoring/sucos\_docking\_scoring/2020.03.4+galaxy1)**: | |
| * step_state: scheduled | |
| * <details><summary>Jobs</summary> | |
| - **Job 1:** | |
| * Job state is paused | |
| **Traceback:** | |
| * ```console | |
| ``` | |
| **Job Parameters:** | |
| * | Job parameter | Parameter value | | |
| | ------------- | --------------- | | |
| | \_\_input\_ext | ` "sdf" ` | | |
| | \_\_workflow\_invocation\_uuid\_\_ | ` "ee1d9032115511f18951000d3a9202a3" ` | | |
| | chromInfo | ` "/tmp/tmp3awx_m9b/galaxy-dev/tool-data/shared/ucsc/chrom/?.len" ` | | |
| | dbkey | ` "?" ` | | |
| | tanimoto | ` false ` | | |
| </details> | |
| - **Step 18: Unlabelled step (toolshed.g2.bx.psu.edu/repos/bgruening/rdock\_sort\_filter/rdock\_sort\_filter/2013.1-0+galaxy0)**: | |
| * step_state: scheduled | |
| * <details><summary>Jobs</summary> | |
| - **Job 1:** | |
| * Job state is paused | |
| **Traceback:** | |
| * ```console | |
| ``` | |
| **Job Parameters:** | |
| * | Job parameter | Parameter value | | |
| | ------------- | --------------- | | |
| | \_\_input\_ext | ` "sdf" ` | | |
| | \_\_workflow\_invocation\_uuid\_\_ | ` "ee1d9032115511f18951000d3a9202a3" ` | | |
| | chromInfo | ` "/tmp/tmp3awx_m9b/galaxy-dev/tool-data/shared/ucsc/chrom/?.len" ` | | |
| | dbkey | ` "?" ` | | |
| | descending | ` true ` | | |
| | filter | ` "$SuCOS_Score >= 0" ` | | |
| | global\_sort | ` true ` | | |
| | name\_field | ` "" ` | | |
| | sort\_field | ` "SuCOS_Score" ` | | |
| | top | ` None ` | | |
| </details> | |
| </details> | |
| * <details><summary>Other invocation details</summary> | |
| - **history_id** | |
| * ac40d82565c3695c | |
| - **history_state** | |
| * error | |
| - **invocation_id** | |
| * ac40d82565c3695c | |
| - **invocation_state** | |
| * scheduled | |
| - **workflow_id** | |
| * ac40d82565c3695c | |
| </details> | |
| </div></details> | |
| </details> | |
| <details open><summary>Failed Tests</summary> | |
| * <details class="rcorners light-red"><summary class="light-red">❌ Generic-variation-analysis-on-WGS-PE-data.ga_0</summary><div class="padded"> | |
| **Problems**: | |
| * ``` | |
| Output with path /tmp/tmpkbcjv9uz/SnpEff eff on dataset 12__0f82a125-51d9-4fc1-a1d1-4026047fcaae.vcf different than expected, difference (using diff): | |
| ( /home/runner/work/iwc/iwc/workflows/variant-calling/generic-variant-calling-wgs-pe/test-data/SnpEff variants.vcf v. /tmp/tmp9r4jmamoSnpEff variants.vcf ) | |
| --- local_file | |
| +++ history_data | |
| @@ -1,6 +1,7 @@ | |
| ##fileformat=VCFv4.0 | |
| -##fileDate=20220601 | |
| -##source=lofreq call --verbose --ref reference.fa --call-indels --min-cov 5 --max-depth 1000000 --min-bq 30 --min-alt-bq 30 --min-mq 0 --max-mq 255 --min-jq 0 --min-alt-jq 0 --def-alt-jq 0 --sig 0.0005 --bonf dynamic --no-default-filter --no-default-filter -r KP849471:1-49312 -o /tmp/lofreq2_call_parallelvorvr7qw/0.vcf.gz reads.bam | |
| +##FILTER=<ID=PASS,Description="All filters passed"> | |
| +##fileDate=20260224 | |
| +##source=lofreq call --verbose --ref reference.fa --call-indels --min-cov 5 --max-depth 1000000 --min-bq 30 --min-alt-bq 30 --min-mq 0 --max-mq 255 --min-jq 0 --min-alt-jq 0 --def-alt-jq 0 --sig 0.0005 --bonf dynamic --no-default-filter --no-default-filter -r KP849471:1-49312 -o /tmp/tmpabqaptbl/job_working_directory/000/55/tmp/lofreq2_call_parallelx8rrn5pb/0.vcf.gz reads.bam | |
| ##reference=reference.fa | |
| ##INFO=<ID=DP,Number=1,Type=Integer,Description="Raw Depth"> | |
| ##INFO=<ID=AF,Number=1,Type=Float,Description="Allele Frequency"> | |
| @@ -11,104 +12,112 @@ | |
| ##INFO=<ID=HRUN,Number=1,Type=Integer,Description="Homopolymer length to the right of report indel position"> | |
| ##FILTER=<ID=min_snvqual_51,Description="Minimum SNV Quality (Phred) 51"> | |
| ##FILTER=<ID=min_indelqual_42,Description="Minimum Indel Quality (Phred) 42"> | |
| +##contig=<ID=KP849471> | |
| +##FILTER=<ID=min_snvqual_46,Description="Minimum SNV Quality (Phred) 46"> | |
| +##FILTER=<ID=min_indelqual_39,Description="Minimum Indel Quality (Phred) 39"> | |
| +##FILTER=<ID=min_snvqual_50,Description="Minimum SNV Quality (Phred) 50"> | |
| +##FILTER=<ID=min_snvqual_55,Description="Minimum SNV Quality (Phred) 55"> | |
| +##FILTER=<ID=min_indelqual_44,Description="Minimum Indel Quality (Phred) 44"> | |
| +##bcftools_concatVersion=1.21+htslib-1.21 | |
| +##bcftools_concatCommand=concat -a -O z -o /tmp/tmpabqaptbl/job_working_directory/000/55/tmp/lofreq2_call_parallelx8rrn5pb/concat.vcf.gz /tmp/tmpabqaptbl/job_working_directory/000/55/tmp/lofreq2_call_parallelx8rrn5pb/0.vcf.gz /tmp/tmpabqaptbl/job_working_directory/000/55/tmp/lofreq2_call_parallelx8rrn5pb/1.vcf.gz /tmp/tmpabqaptbl/job_working_directory/000/55/tmp/lofreq2_call_parallelx8rrn5pb/2.vcf.gz /tmp/tmpabqaptbl/job_working_directory/000/55/tmp/lofreq2_call_parallelx8rrn5pb/3.vcf.gz; Date=Tue Feb 24 07:10:25 2026 | |
| ##FILTER=<ID=min_snvqual_58,Description="Minimum SNV Quality (Phred) 58"> | |
| ******** | |
| *SNIP * | |
| ******** | |
| KP849471 189835 . T A 62.0 PASS DP=7;AF=0.285714;SB=0;DP4=2,3,1,1 | |
| -KP849471 189951 . TAC T 238.0 PASS DP=8;AF=0.750000;SB=0;DP4=1,1,2,4;INDEL;HRUN=1 | |
| -KP849471 189971 . GAT G 179.0 PASS DP=5;AF=1.000000;SB=0;DP4=0,1,2,3;INDEL;HRUN=1 | |
| -KP849471 190055 . A G 177.0 PASS DP=5;AF=1.000000;SB=0;DP4=0,0,2,3 | |
| -KP849471 190237 . C T 229.0 PASS DP=6;AF=1.000000;SB=0;DP4=0,0,3,3 | |
| -KP849471 190294 . T TA 248.0 PASS DP=7;AF=1.000000;SB=0;DP4=0,0,4,3;INDEL;HRUN=6 | |
| -KP849471 190302 . T G 205.0 PASS DP=8;AF=1.000000;SB=0;DP4=0,0,5,3 | |
| -KP849471 190494 . G T 258.0 PASS DP=7;AF=1.000000;SB=0;DP4=0,0,4,3;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Gcg/Tcg|A13S|126|N3R|protein_coding|CODING|AKG51535.1|1|T) | |
| -KP849471 190546 . T A 262.0 PASS DP=7;AF=1.000000;SB=0;DP4=0,0,3,4;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|gTa/gAa|V30E|126|N3R|protein_coding|CODING|AKG51535.1|1|A) | |
| -KP849471 190851 . GA G 88.0 PASS DP=5;AF=0.800000;SB=0;DP4=0,1,1,3;INDEL;HRUN=8 | |
| -KP849471 190951 . G A 182.0 sb_fdr DP=7;AF=1.000000;SB=2147483647;DP4=0,0,0,7 | |
| -KP849471 190964 . C T 190.0 PASS DP=8;AF=1.000000;SB=0;DP4=0,0,1,7;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|gCa/gTa|A4V|437|N4R|protein_coding|CODING|AKG51536.1|1|T) | |
| -KP849471 191034 . C T 111.0 PASS DP=5;AF=1.000000;SB=0;DP4=0,0,1,4;EFF=SYNONYMOUS_CODING(LOW|SILENT|gaC/gaT|D27|437|N4R|protein_coding|CODING|AKG51536.1|1|T) | |
| +KP849471 189951 . TAC T 238.0 PASS DP=8;AF=0.75;SB=0;DP4=1,1,2,4;INDEL;HRUN=1 | |
| +KP849471 189971 . GAT G 179.0 PASS DP=5;AF=1;SB=0;DP4=0,1,2,3;INDEL;HRUN=1 | |
| +KP849471 190055 . A G 177.0 PASS DP=5;AF=1;SB=0;DP4=0,0,2,3 | |
| +KP849471 190237 . C T 229.0 PASS DP=6;AF=1;SB=0;DP4=0,0,3,3 | |
| +KP849471 190294 . T TA 248.0 PASS DP=7;AF=1;SB=0;DP4=0,0,4,3;INDEL;HRUN=6 | |
| +KP849471 190302 . T G 205.0 PASS DP=8;AF=1;SB=0;DP4=0,0,5,3 | |
| +KP849471 190494 . G T 258.0 PASS DP=7;AF=1;SB=0;DP4=0,0,4,3;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Gcg/Tcg|A13S|126|N3R|protein_coding|CODING|AKG51535.1|1|T) | |
| +KP849471 190546 . T A 262.0 PASS DP=7;AF=1;SB=0;DP4=0,0,3,4;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|gTa/gAa|V30E|126|N3R|protein_coding|CODING|AKG51535.1|1|A) | |
| +KP849471 190851 . GA G 88.0 PASS DP=5;AF=0.8;SB=0;DP4=0,1,1,3;INDEL;HRUN=8 | |
| +KP849471 190951 . G A 182.0 sb_fdr DP=7;AF=1;SB=2147483647;DP4=0,0,0,7 | |
| +KP849471 190964 . C T 190.0 PASS DP=8;AF=1;SB=0;DP4=0,0,1,7;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|gCa/gTa|A4V|437|N4R|protein_coding|CODING|AKG51536.1|1|T) | |
| +KP849471 191034 . C T 111.0 PASS DP=5;AF=1;SB=0;DP4=0,0,1,4;EFF=SYNONYMOUS_CODING(LOW|SILENT|gaC/gaT|D27|437|N4R|protein_coding|CODING|AKG51536.1|1|T) | |
| ``` | |
| * ``` | |
| Output with path /tmp/tmpcqe200v2/Call variants on dataset 13__d599a823-fd09-4417-92d9-893b94e24cb7.vcf different than expected, difference (using diff): | |
| ( /home/runner/work/iwc/iwc/workflows/variant-calling/generic-variant-calling-wgs-pe/test-data/called_variants.vcf v. /tmp/tmprkx1le0ucalled_variants.vcf ) | |
| --- local_file | |
| +++ history_data | |
| @@ -1,6 +1,7 @@ | |
| ##fileformat=VCFv4.0 | |
| -##fileDate=20220601 | |
| -##source=lofreq call --verbose --ref reference.fa --call-indels --min-cov 5 --max-depth 1000000 --min-bq 30 --min-alt-bq 30 --min-mq 0 --max-mq 255 --min-jq 0 --min-alt-jq 0 --def-alt-jq 0 --sig 0.0005 --bonf dynamic --no-default-filter --no-default-filter -r KP849471:1-49312 -o /tmp/lofreq2_call_parallelvorvr7qw/0.vcf.gz reads.bam | |
| +##FILTER=<ID=PASS,Description="All filters passed"> | |
| +##fileDate=20260224 | |
| +##source=lofreq call --verbose --ref reference.fa --call-indels --min-cov 5 --max-depth 1000000 --min-bq 30 --min-alt-bq 30 --min-mq 0 --max-mq 255 --min-jq 0 --min-alt-jq 0 --def-alt-jq 0 --sig 0.0005 --bonf dynamic --no-default-filter --no-default-filter -r KP849471:1-49312 -o /tmp/tmpabqaptbl/job_working_directory/000/55/tmp/lofreq2_call_parallelx8rrn5pb/0.vcf.gz reads.bam | |
| ##reference=reference.fa | |
| ##INFO=<ID=DP,Number=1,Type=Integer,Description="Raw Depth"> | |
| ##INFO=<ID=AF,Number=1,Type=Float,Description="Allele Frequency"> | |
| @@ -11,98 +12,106 @@ | |
| ##INFO=<ID=HRUN,Number=1,Type=Integer,Description="Homopolymer length to the right of report indel position"> | |
| ##FILTER=<ID=min_snvqual_51,Description="Minimum SNV Quality (Phred) 51"> | |
| ##FILTER=<ID=min_indelqual_42,Description="Minimum Indel Quality (Phred) 42"> | |
| +##contig=<ID=KP849471> | |
| +##FILTER=<ID=min_snvqual_46,Description="Minimum SNV Quality (Phred) 46"> | |
| +##FILTER=<ID=min_indelqual_39,Description="Minimum Indel Quality (Phred) 39"> | |
| +##FILTER=<ID=min_snvqual_50,Description="Minimum SNV Quality (Phred) 50"> | |
| +##FILTER=<ID=min_snvqual_55,Description="Minimum SNV Quality (Phred) 55"> | |
| +##FILTER=<ID=min_indelqual_44,Description="Minimum Indel Quality (Phred) 44"> | |
| +##bcftools_concatVersion=1.21+htslib-1.21 | |
| +##bcftools_concatCommand=concat -a -O z -o /tmp/tmpabqaptbl/job_working_directory/000/55/tmp/lofreq2_call_parallelx8rrn5pb/concat.vcf.gz /tmp/tmpabqaptbl/job_working_directory/000/55/tmp/lofreq2_call_parallelx8rrn5pb/0.vcf.gz /tmp/tmpabqaptbl/job_working_directory/000/55/tmp/lofreq2_call_parallelx8rrn5pb/1.vcf.gz /tmp/tmpabqaptbl/job_working_directory/000/55/tmp/lofreq2_call_parallelx8rrn5pb/2.vcf.gz /tmp/tmpabqaptbl/job_working_directory/000/55/tmp/lofreq2_call_parallelx8rrn5pb/3.vcf.gz; Date=Tue Feb 24 07:10:25 2026 | |
| ##FILTER=<ID=min_snvqual_58,Description="Minimum SNV Quality (Phred) 58"> | |
| ******** | |
| *SNIP * | |
| ******** | |
| KP849471 189835 . T A 62 PASS DP=7;AF=0.285714;SB=0;DP4=2,3,1,1 | |
| -KP849471 189951 . TAC T 238 PASS DP=8;AF=0.750000;SB=0;DP4=1,1,2,4;INDEL;HRUN=1 | |
| -KP849471 189971 . GAT G 179 PASS DP=5;AF=1.000000;SB=0;DP4=0,1,2,3;INDEL;HRUN=1 | |
| -KP849471 190055 . A G 177 PASS DP=5;AF=1.000000;SB=0;DP4=0,0,2,3 | |
| -KP849471 190237 . C T 229 PASS DP=6;AF=1.000000;SB=0;DP4=0,0,3,3 | |
| -KP849471 190294 . T TA 248 PASS DP=7;AF=1.000000;SB=0;DP4=0,0,4,3;INDEL;HRUN=6 | |
| -KP849471 190302 . T G 205 PASS DP=8;AF=1.000000;SB=0;DP4=0,0,5,3 | |
| -KP849471 190494 . G T 258 PASS DP=7;AF=1.000000;SB=0;DP4=0,0,4,3 | |
| -KP849471 190546 . T A 262 PASS DP=7;AF=1.000000;SB=0;DP4=0,0,3,4 | |
| -KP849471 190851 . GA G 88 PASS DP=5;AF=0.800000;SB=0;DP4=0,1,1,3;INDEL;HRUN=8 | |
| -KP849471 190951 . G A 182 PASS DP=7;AF=1.000000;SB=2147483647;DP4=0,0,0,7 | |
| -KP849471 190964 . C T 190 PASS DP=8;AF=1.000000;SB=0;DP4=0,0,1,7 | |
| -KP849471 191034 . C T 111 PASS DP=5;AF=1.000000;SB=0;DP4=0,0,1,4 | |
| +KP849471 189951 . TAC T 238 PASS DP=8;AF=0.75;SB=0;DP4=1,1,2,4;INDEL;HRUN=1 | |
| +KP849471 189971 . GAT G 179 PASS DP=5;AF=1;SB=0;DP4=0,1,2,3;INDEL;HRUN=1 | |
| +KP849471 190055 . A G 177 PASS DP=5;AF=1;SB=0;DP4=0,0,2,3 | |
| +KP849471 190237 . C T 229 PASS DP=6;AF=1;SB=0;DP4=0,0,3,3 | |
| +KP849471 190294 . T TA 248 PASS DP=7;AF=1;SB=0;DP4=0,0,4,3;INDEL;HRUN=6 | |
| +KP849471 190302 . T G 205 PASS DP=8;AF=1;SB=0;DP4=0,0,5,3 | |
| +KP849471 190494 . G T 258 PASS DP=7;AF=1;SB=0;DP4=0,0,4,3 | |
| +KP849471 190546 . T A 262 PASS DP=7;AF=1;SB=0;DP4=0,0,3,4 | |
| +KP849471 190851 . GA G 88 PASS DP=5;AF=0.8;SB=0;DP4=0,1,1,3;INDEL;HRUN=8 | |
| +KP849471 190951 . G A 182 PASS DP=7;AF=1;SB=2147483647;DP4=0,0,0,7 | |
| +KP849471 190964 . C T 190 PASS DP=8;AF=1;SB=0;DP4=0,0,1,7 | |
| +KP849471 191034 . C T 111 PASS DP=5;AF=1;SB=0;DP4=0,0,1,4 | |
| ``` | |
| * ``` | |
| Output with path /tmp/tmpcgl8r0ue/Lofreq filter__f85f9551-f258-4714-910c-f48a7739d01f.vcf different than expected, difference (using diff): | |
| ( /home/runner/work/iwc/iwc/workflows/variant-calling/generic-variant-calling-wgs-pe/test-data/soft_filtered_variants.vcf v. /tmp/tmpz3lp9yw7soft_filtered_variants.vcf ) | |
| --- local_file | |
| +++ history_data | |
| @@ -1,6 +1,7 @@ | |
| ##fileformat=VCFv4.0 | |
| -##fileDate=20220601 | |
| -##source=lofreq call --verbose --ref reference.fa --call-indels --min-cov 5 --max-depth 1000000 --min-bq 30 --min-alt-bq 30 --min-mq 0 --max-mq 255 --min-jq 0 --min-alt-jq 0 --def-alt-jq 0 --sig 0.0005 --bonf dynamic --no-default-filter --no-default-filter -r KP849471:1-49312 -o /tmp/lofreq2_call_parallelvorvr7qw/0.vcf.gz reads.bam | |
| +##FILTER=<ID=PASS,Description="All filters passed"> | |
| +##fileDate=20260224 | |
| +##source=lofreq call --verbose --ref reference.fa --call-indels --min-cov 5 --max-depth 1000000 --min-bq 30 --min-alt-bq 30 --min-mq 0 --max-mq 255 --min-jq 0 --min-alt-jq 0 --def-alt-jq 0 --sig 0.0005 --bonf dynamic --no-default-filter --no-default-filter -r KP849471:1-49312 -o /tmp/tmpabqaptbl/job_working_directory/000/55/tmp/lofreq2_call_parallelx8rrn5pb/0.vcf.gz reads.bam | |
| ##reference=reference.fa | |
| ##INFO=<ID=DP,Number=1,Type=Integer,Description="Raw Depth"> | |
| ##INFO=<ID=AF,Number=1,Type=Float,Description="Allele Frequency"> | |
| @@ -11,99 +12,107 @@ | |
| ##INFO=<ID=HRUN,Number=1,Type=Integer,Description="Homopolymer length to the right of report indel position"> | |
| ##FILTER=<ID=min_snvqual_51,Description="Minimum SNV Quality (Phred) 51"> | |
| ##FILTER=<ID=min_indelqual_42,Description="Minimum Indel Quality (Phred) 42"> | |
| +##contig=<ID=KP849471> | |
| +##FILTER=<ID=min_snvqual_46,Description="Minimum SNV Quality (Phred) 46"> | |
| +##FILTER=<ID=min_indelqual_39,Description="Minimum Indel Quality (Phred) 39"> | |
| +##FILTER=<ID=min_snvqual_50,Description="Minimum SNV Quality (Phred) 50"> | |
| +##FILTER=<ID=min_snvqual_55,Description="Minimum SNV Quality (Phred) 55"> | |
| +##FILTER=<ID=min_indelqual_44,Description="Minimum Indel Quality (Phred) 44"> | |
| +##bcftools_concatVersion=1.21+htslib-1.21 | |
| +##bcftools_concatCommand=concat -a -O z -o /tmp/tmpabqaptbl/job_working_directory/000/55/tmp/lofreq2_call_parallelx8rrn5pb/concat.vcf.gz /tmp/tmpabqaptbl/job_working_directory/000/55/tmp/lofreq2_call_parallelx8rrn5pb/0.vcf.gz /tmp/tmpabqaptbl/job_working_directory/000/55/tmp/lofreq2_call_parallelx8rrn5pb/1.vcf.gz /tmp/tmpabqaptbl/job_working_directory/000/55/tmp/lofreq2_call_parallelx8rrn5pb/2.vcf.gz /tmp/tmpabqaptbl/job_working_directory/000/55/tmp/lofreq2_call_parallelx8rrn5pb/3.vcf.gz; Date=Tue Feb 24 07:10:25 2026 | |
| ##FILTER=<ID=min_snvqual_58,Description="Minimum SNV Quality (Phred) 58"> | |
| ******** | |
| *SNIP * | |
| ******** | |
| KP849471 189835 . T A 62 PASS DP=7;AF=0.285714;SB=0;DP4=2,3,1,1 | |
| -KP849471 189951 . TAC T 238 PASS DP=8;AF=0.750000;SB=0;DP4=1,1,2,4;INDEL;HRUN=1 | |
| -KP849471 189971 . GAT G 179 PASS DP=5;AF=1.000000;SB=0;DP4=0,1,2,3;INDEL;HRUN=1 | |
| -KP849471 190055 . A G 177 PASS DP=5;AF=1.000000;SB=0;DP4=0,0,2,3 | |
| -KP849471 190237 . C T 229 PASS DP=6;AF=1.000000;SB=0;DP4=0,0,3,3 | |
| -KP849471 190294 . T TA 248 PASS DP=7;AF=1.000000;SB=0;DP4=0,0,4,3;INDEL;HRUN=6 | |
| -KP849471 190302 . T G 205 PASS DP=8;AF=1.000000;SB=0;DP4=0,0,5,3 | |
| -KP849471 190494 . G T 258 PASS DP=7;AF=1.000000;SB=0;DP4=0,0,4,3 | |
| -KP849471 190546 . T A 262 PASS DP=7;AF=1.000000;SB=0;DP4=0,0,3,4 | |
| -KP849471 190851 . GA G 88 PASS DP=5;AF=0.800000;SB=0;DP4=0,1,1,3;INDEL;HRUN=8 | |
| -KP849471 190951 . G A 182 sb_fdr DP=7;AF=1.000000;SB=2147483647;DP4=0,0,0,7 | |
| -KP849471 190964 . C T 190 PASS DP=8;AF=1.000000;SB=0;DP4=0,0,1,7 | |
| -KP849471 191034 . C T 111 PASS DP=5;AF=1.000000;SB=0;DP4=0,0,1,4 | |
| +KP849471 189951 . TAC T 238 PASS DP=8;AF=0.75;SB=0;DP4=1,1,2,4;INDEL;HRUN=1 | |
| +KP849471 189971 . GAT G 179 PASS DP=5;AF=1;SB=0;DP4=0,1,2,3;INDEL;HRUN=1 | |
| +KP849471 190055 . A G 177 PASS DP=5;AF=1;SB=0;DP4=0,0,2,3 | |
| +KP849471 190237 . C T 229 PASS DP=6;AF=1;SB=0;DP4=0,0,3,3 | |
| +KP849471 190294 . T TA 248 PASS DP=7;AF=1;SB=0;DP4=0,0,4,3;INDEL;HRUN=6 | |
| +KP849471 190302 . T G 205 PASS DP=8;AF=1;SB=0;DP4=0,0,5,3 | |
| +KP849471 190494 . G T 258 PASS DP=7;AF=1;SB=0;DP4=0,0,4,3 | |
| +KP849471 190546 . T A 262 PASS DP=7;AF=1;SB=0;DP4=0,0,3,4 | |
| +KP849471 190851 . GA G 88 PASS DP=5;AF=0.8;SB=0;DP4=0,1,1,3;INDEL;HRUN=8 | |
| +KP849471 190951 . G A 182 sb_fdr DP=7;AF=1;SB=2147483647;DP4=0,0,0,7 | |
| +KP849471 190964 . C T 190 PASS DP=8;AF=1;SB=0;DP4=0,0,1,7 | |
| +KP849471 191034 . C T 111 PASS DP=5;AF=1;SB=0;DP4=0,0,1,4 | |
| ``` | |
| #### Workflow invocation details | |
| * Invocation Messages | |
| * <details><summary>Steps</summary> | |
| - **Step 1: Paired Collection**: | |
| * step_state: scheduled | |
| - **Step 2: GenBank genome**: | |
| * step_state: scheduled | |
| - **Step 3: Name for genome database**: | |
| * step_state: scheduled | |
| - **Step 4: Unlabelled step (toolshed.g2.bx.psu.edu/repos/iuc/fastp/fastp/0.23.2+galaxy0)**: | |
| * step_state: scheduled | |
| * <details><summary>Jobs</summary> | |
| - **Job 1:** | |
| * Job state is ok | |
| **Container:** | |
| * ```console | |
| quay.io/biocontainers/fastp:0.23.2--hadf994f_5 | |
| ``` | |
| **Command Line:** | |
| * ```console | |
| ln -s '/tmp/tmpabqaptbl/files/d/7/5/dataset_d75b9bcc-5c5f-4c47-8998-29008cccb43f.dat' 'ERR3485802.fastq.gz' && ln -s '/tmp/tmpabqaptbl/files/2/6/a/dataset_26a5c5aa-ce3a-419d-a31c-db7b8ef056c9.dat' 'ERR3485802_R2.fastq.gz' && fastp --thread ${GALAXY_SLOTS:-1} --report_title 'fastp report for ERR3485802.fastq.gz' -i 'ERR3485802.fastq.gz' -o first.fastq.gz -I 'ERR3485802_R2.fastq.gz' -O second.fastq.gz --detect_adapter_for_pe && mv first.fastq.gz '/tmp/tmpabqaptbl/job_working_directory/000/46/outputs/dataset_1bc93155-b90e-4053-9798-0b5bfa9b7cad.dat' && mv second.fastq.gz '/tmp/tmpabqaptbl/job_working_directory/000/46/outputs/dataset_7761a43a-88aa-47fd-81db-d554537eb2ae.dat' | |
| ``` | |
| **Exit Code:** | |
| * ```console | |
| 0 | |
| ``` | |
| **Standard Error:** | |
| * ```console | |
| Detecting adapter sequence for read1... | |
| No adapter detected for read1 | |
| Detecting adapter sequence for read2... | |
| No adapter detected for read2 | |
| Read1 before filtering: | |
| total reads: 2500 | |
| total bases: 376657 | |
| Q20 bases: 371549(98.6439%) | |
| Q30 bases: 370136(98.2687%) | |
| Read2 before filtering: | |
| total reads: 2500 | |
| total bases: 376700 | |
| Q20 bases: 355761(94.4415%) | |
| Q30 bases: 351290(93.2546%) | |
| Read1 after filtering: | |
| total reads: 2492 | |
| total bases: 375257 | |
| Q20 bases: 370593(98.7571%) | |
| Q30 bases: 369355(98.4272%) | |
| Read2 after filtering: | |
| total reads: 2492 | |
| total bases: 375297 | |
| Q20 bases: 355082(94.6136%) | |
| Q30 bases: 350732(93.4545%) | |
| Filtering result: | |
| reads passed filter: 4984 | |
| reads failed due to low quality: 16 | |
| reads failed due to too many N: 0 | |
| reads failed due to too short: 0 | |
| reads with adapter trimmed: 30 | |
| bases trimmed due to adapters: 393 | |
| Duplication rate: 17.96% | |
| Insert size peak (evaluated by paired-end reads): 263 | |
| JSON report: fastp.json | |
| HTML report: fastp.html | |
| fastp --thread 1 --report_title fastp report for ERR3485802.fastq.gz -i ERR3485802.fastq.gz -o first.fastq.gz -I ERR3485802_R2.fastq.gz -O second.fastq.gz --detect_adapter_for_pe | |
| fastp v0.23.2, time used: 0 seconds | |
| ``` | |
| **Traceback:** | |
| * ```console | |
| ``` | |
| **Job Parameters:** | |
| * | Job parameter | Parameter value | | |
| | ------------- | --------------- | | |
| | \_\_input\_ext | ` "fastqsanger.gz" ` | | |
| | \_\_workflow\_invocation\_uuid\_\_ | ` "97b31678114f11f1895170a8a5197e48" ` | | |
| | chromInfo | ` "/tmp/tmpabqaptbl/galaxy-dev/tool-data/shared/ucsc/chrom/?.len" ` | | |
| | dbkey | ` "?" ` | | |
| | filter\_options | ` {"length_filtering_options": {"disable_length_filtering": false, "length_limit": null, "length_required": null}, "low_complexity_filter": {"complexity_threshold": null, "enable_low_complexity_filter": false}, "quality_filtering_options": {"disable_quality_filtering": false, "n_base_limit": null, "qualified_quality_phred": null, "unqualified_percent_limit": null}} ` | | |
| | output\_options | ` {"report_html": true, "report_json": true} ` | | |
| | overrepresented\_sequence\_analysis | ` {"overrepresentation_analysis": false, "overrepresentation_sampling": null} ` | | |
| | read\_mod\_options | ` {"base_correction_options": {"correction": false}, "cutting_by_quality_options": {"cut_by_quality3": false, "cut_by_quality5": false, "cut_mean_quality": null, "cut_window_size": null}, "polyg_tail_trimming": {"__current_case__": 1, "poly_g_min_len": null, "trimming_select": ""}, "polyx_tail_trimming": {"__current_case__": 1, "polyx_trimming_select": ""}, "umi_processing": {"umi": false, "umi_len": null, "umi_loc": "", "umi_prefix": ""}} ` | | |
| | single\_paired | ` {"__current_case__": 2, "adapter_trimming_options": {"adapter_sequence1": "", "adapter_sequence2": "", "disable_adapter_trimming": false}, "global_trimming_options": {"trim_front1": null, "trim_front2": null, "trim_tail1": null, "trim_tail2": null}, "paired_input": {"values": [{"id": 45, "src": "dce"}]}, "single_paired_selector": "paired_collection"} ` | | |
| </details> | |
| - **Step 5: Unlabelled step (toolshed.g2.bx.psu.edu/repos/iuc/snpeff/snpEff\_build\_gb/4.3+T.galaxy4)**: | |
| * step_state: scheduled | |
| * <details><summary>Jobs</summary> | |
| - **Job 1:** | |
| * Job state is ok | |
| **Container:** | |
| * ```console | |
| quay.io/biocontainers/mulled-v2-a0befa8208a1194e8046a119d802824811d98efe:5eeecf5d1ece2d5ed914cb65967a744b8bf0a27c-2 | |
| ``` | |
| **Command Line:** | |
| * ```console | |
| python3 '/tmp/shed_dir/toolshed.g2.bx.psu.edu/repos/iuc/snpeff/cfcf33df7fc0/snpeff/gbk2fa.py' '/tmp/tmpabqaptbl/files/3/7/4/dataset_37406485-d13f-4c6c-ad71-5a3211a31298.dat' '/tmp/tmpabqaptbl/job_working_directory/000/47/outputs/dataset_11fc3eb2-e36b-431a-b14b-0d1387fb1e42.dat' '--remove_version' && mkdir -p '/tmp/tmpabqaptbl/job_working_directory/000/47/outputs/dataset_78688b18-d967-4ce3-8d23-2be910df88cf_files'/'mpxv' && ln -s '/tmp/tmpabqaptbl/files/3/7/4/dataset_37406485-d13f-4c6c-ad71-5a3211a31298.dat' '/tmp/tmpabqaptbl/job_working_directory/000/47/outputs/dataset_78688b18-d967-4ce3-8d23-2be910df88cf_files'/'mpxv'/genes.gbk && snpEff -Xmx${GALAXY_MEMORY_MB:-8192}m build -v -configOption 'mpxv'.genome='mpxv' -configOption 'mpxv'.codonTable='Standard' -genbank -dataDir '/tmp/tmpabqaptbl/job_working_directory/000/47/outputs/dataset_78688b18-d967-4ce3-8d23-2be910df88cf_files' 'mpxv' && echo "mpxv.genome : mpxv" >> '/tmp/tmpabqaptbl/job_working_directory/000/47/outputs/dataset_78688b18-d967-4ce3-8d23-2be910df88cf_files'/snpEff.config && echo "mpxv.codonTable : Standard" >> '/tmp/tmpabqaptbl/job_working_directory/000/47/outputs/dataset_78688b18-d967-4ce3-8d23-2be910df88cf_files'/snpEff.config | |
| ``` | |
| **Exit Code:** | |
| * ```console | |
| 0 | |
| ``` | |
| **Standard Error:** | |
| * ```console | |
| 00:00:00 SnpEff version SnpEff 4.3t (build 2017-11-24 10:18), by Pablo Cingolani | |
| 00:00:00 Command: 'build' | |
| 00:00:00 Building database for 'mpxv' | |
| 00:00:00 Reading configuration file 'snpEff.config'. Genome: 'mpxv' | |
| 00:00:00 Reading config file: /tmp/tmpabqaptbl/job_working_directory/000/47/working/snpEff.config | |
| 00:00:00 Reading config file: /usr/local/share/snpeff-4.3.1t-3/snpEff.config | |
| 00:00:01 done | |
| Chromosome: 'KP849471' length: 197248 | |
| 00:00:01 Caracterizing exons by splicing (stage 1) : | |
| 00:00:01 Caracterizing exons by splicing (stage 2) : | |
| 00:00:01 done. | |
| 00:00:01 [Optional] Rare amino acid annotations | |
| 00:00:01 Warning: Cannot read optional protein sequence file '/tmp/tmpabqaptbl/job_working_directory/000/47/outputs/dataset_78688b18-d967-4ce3-8d23-2be910df88cf_files/mpxv/protein.fa', nothing done. | |
| 00:00:01 Protein check file: '/tmp/tmpabqaptbl/job_working_directory/000/47/outputs/dataset_78688b18-d967-4ce3-8d23-2be910df88cf_files/mpxv/genes.gbk' | |
| 00:00:01 Checking database using protein sequences | |
| 00:00:01 Comparing Proteins... | |
| Labels: | |
| '+' : OK | |
| '.' : Missing | |
| '*' : Error | |
| 00:00:01 Saving database | |
| 00:00:02 [Optional] Reading regulation elements: GFF | |
| 00:00:02 Warning: Cannot read optional regulation file '/tmp/tmpabqaptbl/job_working_directory/000/47/outputs/dataset_78688b18-d967-4ce3-8d23-2be910df88cf_files/mpxv/regulation.gff', nothing done. | |
| 00:00:02 [Optional] Reading regulation elements: BED | |
| 00:00:02 Cannot find optional regulation dir '/tmp/tmpabqaptbl/job_working_directory/000/47/outputs/dataset_78688b18-d967-4ce3-8d23-2be910df88cf_files/mpxv/regulation.bed/', nothing done. | |
| 00:00:02 [Optional] Reading motifs: GFF | |
| 00:00:02 Warning: Cannot open PWMs file /tmp/tmpabqaptbl/job_working_directory/000/47/outputs/dataset_78688b18-d967-4ce3-8d23-2be910df88cf_files/mpxv/pwms.bin. Nothing done | |
| 00:00:02 Done | |
| 00:00:02 Logging | |
| 00:00:03 Checking for updates... | |
| 00:00:04 Done. | |
| ``` | |
| **Standard Output:** | |
| * ```console | |
| Writing FASTA record: KP849471 | |
| Create exons from CDS (if needed): ............................................................................................................................................................................................ | |
| Exons created for 188 transcripts. | |
| Deleting redundant exons (if needed): | |
| Total transcripts with deleted exons: 0 | |
| Collapsing zero length introns (if needed): | |
| Total collapsed transcripts: 0 | |
| Adding genomic sequences to exons: Done (188 sequences added, 0 ignored). | |
| Adjusting transcripts: | |
| Adjusting genes: | |
| Adjusting chromosomes lengths: | |
| Ranking exons: | |
| Create UTRs from CDS (if needed): | |
| Remove empty chromosomes: | |
| Marking as 'coding' from CDS information: | |
| Done: 0 transcripts marked | |
| +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ | |
| +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ | |
| Protein check: mpxv OK: 188 Not found: 0 Errors: 0 Error percentage: 0.0% | |
| ``` | |
| **Traceback:** | |
| * ```console | |
| ``` | |
| **Job Parameters:** | |
| * | Job parameter | Parameter value | | |
| | ------------- | --------------- | | |
| | \_\_input\_ext | ` "genbank" ` | | |
| | \_\_workflow\_invocation\_uuid\_\_ | ` "97b31678114f11f1895170a8a5197e48" ` | | |
| | chromInfo | ` "/tmp/tmpabqaptbl/galaxy-dev/tool-data/shared/ucsc/chrom/?.len" ` | | |
| | codon\_table | ` "Standard" ` | | |
| | dbkey | ` "?" ` | | |
| | genome\_version | ` "mpxv" ` | | |
| | input\_type | ` {"__current_case__": 0, "fasta": "yes", "input_gbk": {"values": [{"id": 64, "src": "hda"}]}, "input_type_selector": "gb", "remove_version": true} ` | | |
| </details> | |
| - **Step 6: Unlabelled step (toolshed.g2.bx.psu.edu/repos/devteam/bwa/bwa\_mem/0.7.17.2)**: | |
| * step_state: scheduled | |
| * <details><summary>Jobs</summary> | |
| - **Job 1:** | |
| * Job state is ok | |
| **Container:** | |
| * ```console | |
| quay.io/biocontainers/mulled-v2-fe8faa35dbf6dc65a0f7f5d4ea12e31a79f73e40:1476e745a911a5a2ac22207311b275c51e745ba9-2 | |
| ``` | |
| **Command Line:** | |
| * ```console | |
| set -o | grep -q pipefail && set -o pipefail; ln -s '/tmp/tmpabqaptbl/files/1/1/f/dataset_11fc3eb2-e36b-431a-b14b-0d1387fb1e42.dat' 'localref.fa' && bwa index 'localref.fa' && bwa mem -t "${GALAXY_SLOTS:-1}" -v 1 -T '30' -h '5' -Y -q 'localref.fa' '/tmp/tmpabqaptbl/files/1/b/c/dataset_1bc93155-b90e-4053-9798-0b5bfa9b7cad.dat' '/tmp/tmpabqaptbl/files/7/7/6/dataset_7761a43a-88aa-47fd-81db-d554537eb2ae.dat' | samtools sort -@${GALAXY_SLOTS:-2} -T "${TMPDIR:-.}" -O bam -o '/tmp/tmpabqaptbl/job_working_directory/000/48/outputs/dataset_f83638cf-5d0c-4375-8d7d-7a37d346985d.dat' | |
| ``` | |
| **Exit Code:** | |
| * ```console | |
| 0 | |
| ``` | |
| **Standard Error:** | |
| * ```console | |
| [bwa_index] Pack FASTA... 0.00 sec | |
| [bwa_index] Construct BWT for the packed sequence... | |
| [bwa_index] 0.03 seconds elapse. | |
| [bwa_index] Update BWT... 0.00 sec | |
| [bwa_index] Pack forward-only FASTA... 0.00 sec | |
| [bwa_index] Construct SA from BWT and Occ... 0.01 sec | |
| [main] Version: 0.7.17-r1188 | |
| [main] CMD: bwa index localref.fa | |
| [main] Real time: 0.048 sec; CPU: 0.045 sec | |
| [M::mem_pestat] skip orientation FF as there are not enough pairs | |
| [M::mem_pestat] analyzing insert size distribution for orientation FR... | |
| [M::mem_pestat] (25, 50, 75) percentile: (277, 334, 393) | |
| [M::mem_pestat] low and high boundaries for computing mean and std.dev: (45, 625) | |
| [M::mem_pestat] mean and std.dev: (338.50, 89.49) | |
| [M::mem_pestat] low and high boundaries for proper pairs: (1, 741) | |
| [M::mem_pestat] skip orientation RF as there are not enough pairs | |
| [M::mem_pestat] skip orientation RR as there are not enough pairs | |
| [main] Version: 0.7.17-r1188 | |
| [main] CMD: bwa mem -t 1 -v 1 -T 30 -h 5 -Y -q localref.fa /tmp/tmpabqaptbl/files/1/b/c/dataset_1bc93155-b90e-4053-9798-0b5bfa9b7cad.dat /tmp/tmpabqaptbl/files/7/7/6/dataset_7761a43a-88aa-47fd-81db-d554537eb2ae.dat | |
| [main] Real time: 0.242 sec; CPU: 0.237 sec | |
| ``` | |
| **Traceback:** | |
| * ```console | |
| ``` | |
| **Job Parameters:** | |
| * | Job parameter | Parameter value | | |
| | ------------- | --------------- | | |
| | \_\_input\_ext | ` "fasta" ` | | |
| | \_\_workflow\_invocation\_uuid\_\_ | ` "97b31678114f11f1895170a8a5197e48" ` | | |
| | analysis\_type | ` {"__current_case__": 4, "algorithmic_options": {"__current_case__": 1, "algorithmic_options_selector": "do_not_set"}, "analysis_type_selector": "full", "io_options": {"C": false, "M": false, "T": "30", "V": false, "Y": true, "__current_case__": 0, "a": false, "five": false, "h": "5", "io_options_selector": "set", "q": true}, "scoring_options": {"__current_case__": 1, "scoring_options_selector": "do_not_set"}} ` | | |
| | chromInfo | ` "/tmp/tmpabqaptbl/galaxy-dev/tool-data/shared/ucsc/chrom/?.len" ` | | |
| | dbkey | ` "?" ` | | |
| | fastq\_input | ` {"__current_case__": 2, "fastq_input1": {"values": [{"id": 48, "src": "dce"}]}, "fastq_input_selector": "paired_collection", "iset_stats": ""} ` | | |
| | output\_sort | ` "coordinate" ` | | |
| | reference\_source | ` {"__current_case__": 1, "index_a": "auto", "ref_file": {"values": [{"id": 72, "src": "hda"}]}, "reference_source_selector": "history"} ` | | |
| | rg | ` {"__current_case__": 3, "rg_selector": "do_not_set"} ` | | |
| </details> | |
| - **Step 7: Unlabelled step (toolshed.g2.bx.psu.edu/repos/iuc/samtools\_view/samtools\_view/1.13+galaxy1)**: | |
| * step_state: scheduled | |
| * <details><summary>Jobs</summary> | |
| - **Job 1:** | |
| * Job state is ok | |
| **Container:** | |
| * ```console | |
| quay.io/biocontainers/mulled-v2-8dd8177cf5b9476288c149088f4340b576b866e3:9f68127d7d238031667ddd68ffaf2d33a89c565c-0 | |
| ``` | |
| **Command Line:** | |
| * ```console | |
| addthreads=${GALAXY_SLOTS:-1} && (( addthreads-- )) && addmemory=${GALAXY_MEMORY_MB_PER_SLOT:-768} && ((addmemory=addmemory*75/100)) && ln -s '/tmp/tmpabqaptbl/files/f/8/3/dataset_f83638cf-5d0c-4375-8d7d-7a37d346985d.dat' infile && ln -s '/tmp/tmpabqaptbl/files/_metadata_files/e/1/e/metadata_e1efc12c-03f3-453f-9d0e-439a2c18aad7.dat' infile.bai && samtools view -@ $addthreads -b -f 3 -F 0 -G 0 -o outfile infile | |
| ``` | |
| **Exit Code:** | |
| * ```console | |
| 0 | |
| ``` | |
| **Traceback:** | |
| * ```console | |
| ``` | |
| **Job Parameters:** | |
| * | Job parameter | Parameter value | | |
| | ------------- | --------------- | | |
| | \_\_input\_ext | ` "input" ` | | |
| | \_\_workflow\_invocation\_uuid\_\_ | ` "97b31678114f11f1895170a8a5197e48" ` | | |
| | addref\_cond | ` {"__current_case__": 0, "addref_select": "no"} ` | | |
| | chromInfo | ` "/tmp/tmpabqaptbl/galaxy-dev/tool-data/shared/ucsc/chrom/?.len" ` | | |
| | dbkey | ` "?" ` | | |
| | mode | ` {"__current_case__": 1, "filter_config": {"cigarcons": null, "cond_region": {"__current_case__": 0, "select_region": "no"}, "cond_rg": {"__current_case__": 0, "select_rg": "no"}, "exclusive_filter": null, "exclusive_filter_all": null, "inclusive_filter": ["1", "2"], "library": "", "qname_file": null, "quality": "0", "tag": ""}, "output_options": {"__current_case__": 0, "adv_output": {"collapsecigar": false, "readtags": []}, "complementary_output": false, "output_format": {"__current_case__": 2, "oformat": "bam"}, "reads_report_type": "retained"}, "outtype": "selected_reads", "subsample_config": {"subsampling_mode": {"__current_case__": 0, "factor": "1.0", "seed": null, "select_subsample": "fraction"}}} ` | | |
| </details> | |
| - **Step 8: Unlabelled step (toolshed.g2.bx.psu.edu/repos/devteam/picard/picard\_MarkDuplicates/2.18.2.2)**: | |
| * step_state: scheduled | |
| * <details><summary>Jobs</summary> | |
| - **Job 1:** | |
| * Job state is ok | |
| **Container:** | |
| * ```console | |
| quay.io/biocontainers/picard:2.18.2--py36_0 | |
| ``` | |
| **Command Line:** | |
| * ```console | |
| _JAVA_OPTIONS=${_JAVA_OPTIONS:-'-Xmx2048m -Xms256m'} && export _JAVA_OPTIONS && ln -f -s '/tmp/tmpabqaptbl/files/5/f/1/dataset_5f13e1a5-7b1f-48e7-905a-2bec005fdeac.dat' 'ERR3485802' && picard MarkDuplicates INPUT='ERR3485802' OUTPUT='/tmp/tmpabqaptbl/job_working_directory/000/50/outputs/dataset_8df32a51-b918-4843-a4d9-86e95b3a6ab2.dat' METRICS_FILE='/tmp/tmpabqaptbl/job_working_directory/000/50/outputs/dataset_cf4ed0a1-2cf3-434c-b350-6f1fd5585b8d.dat' REMOVE_DUPLICATES='true' ASSUME_SORTED='true' DUPLICATE_SCORING_STRATEGY='SUM_OF_BASE_QUALITIES' OPTICAL_DUPLICATE_PIXEL_DISTANCE='100' VALIDATION_STRINGENCY='LENIENT' QUIET=true VERBOSITY=ERROR `if [ -n "$TMPDIR" ] ; then echo 'TMP_DIR=$TMPDIR' ; else if [ -n "$TEMP" ] ; then echo 'TMP_DIR=$TEMP' ; fi ; fi` | |
| ``` | |
| **Exit Code:** | |
| * ```console | |
| 0 | |
| ``` | |
| **Standard Error:** | |
| * ```console | |
| /usr/local/bin/picard: line 5: warning: setlocale: LC_ALL: cannot change locale (en_US.UTF-8): No such file or directory | |
| Picked up _JAVA_OPTIONS: -Xmx2048m -Xms256m | |
| 07:09:45.979 INFO NativeLibraryLoader - Loading libgkl_compression.so from jar:file:/usr/local/share/picard-2.18.2-0/picard.jar!/com/intel/gkl/native/libgkl_compression.so | |
| ``` | |
| **Traceback:** | |
| * ```console | |
| ``` | |
| **Job Parameters:** | |
| * | Job parameter | Parameter value | | |
| | ------------- | --------------- | | |
| | \_\_input\_ext | ` "bam" ` | | |
| | \_\_workflow\_invocation\_uuid\_\_ | ` "97b31678114f11f1895170a8a5197e48" ` | | |
| | assume\_sorted | ` true ` | | |
| | barcode\_tag | ` "" ` | | |
| | chromInfo | ` "/tmp/tmpabqaptbl/galaxy-dev/tool-data/shared/ucsc/chrom/?.len" ` | | |
| | comments | ` [] ` | | |
| | dbkey | ` "?" ` | | |
| | duplicate\_scoring\_strategy | ` "SUM_OF_BASE_QUALITIES" ` | | |
| | optical\_duplicate\_pixel\_distance | ` "100" ` | | |
| | read\_name\_regex | ` "" ` | | |
| | remove\_duplicates | ` true ` | | |
| | validation\_stringency | ` "LENIENT" ` | | |
| </details> | |
| - **Step 9: Unlabelled step (toolshed.g2.bx.psu.edu/repos/devteam/samtools\_stats/samtools\_stats/2.0.2+galaxy2)**: | |
| * step_state: scheduled | |
| * <details><summary>Jobs</summary> | |
| - **Job 1:** | |
| * Job state is ok | |
| **Container:** | |
| * ```console | |
| quay.io/biocontainers/samtools:1.9--h10a08f8_12 | |
| ``` | |
| **Command Line:** | |
| * ```console | |
| addthreads=${GALAXY_SLOTS:-1} && (( addthreads-- )) && ln -s '/tmp/tmpabqaptbl/files/5/f/1/dataset_5f13e1a5-7b1f-48e7-905a-2bec005fdeac.dat' infile && ln -s '/tmp/tmpabqaptbl/files/_metadata_files/a/6/a/metadata_a6a36343-7d7e-4df4-905f-b81ac8032018.dat' infile.bai && samtools stats -@ $addthreads infile > '/tmp/tmpabqaptbl/job_working_directory/000/51/outputs/dataset_12efb2de-6161-4c9c-ae30-72efc6f15b85.dat' | |
| ``` | |
| **Exit Code:** | |
| * ```console | |
| 0 | |
| ``` | |
| **Traceback:** | |
| * ```console | |
| ``` | |
| **Job Parameters:** | |
| * | Job parameter | Parameter value | | |
| | ------------- | --------------- | | |
| | \_\_input\_ext | ` "bam" ` | | |
| | \_\_workflow\_invocation\_uuid\_\_ | ` "97b31678114f11f1895170a8a5197e48" ` | | |
| | addref\_cond | ` {"__current_case__": 0, "addref_select": "no"} ` | | |
| | chromInfo | ` "/tmp/tmpabqaptbl/galaxy-dev/tool-data/shared/ucsc/chrom/?.len" ` | | |
| | cond\_region | ` {"__current_case__": 0, "select_region": "no"} ` | | |
| | cov\_threshold | ` None ` | | |
| | coverage\_cond | ` {"__current_case__": 0, "coverage_select": "no"} ` | | |
| | dbkey | ` "?" ` | | |
| | filter\_by\_flags | ` {"__current_case__": 1, "filter_flags": "nofilter"} ` | | |
| | gc\_depth | ` None ` | | |
| | insert\_size | ` None ` | | |
| | most\_inserts | ` None ` | | |
| | read\_length | ` None ` | | |
| | remove\_dups | ` false ` | | |
| | remove\_overlaps | ` false ` | | |
| | sparse | ` false ` | | |
| | split\_output\_cond | ` {"__current_case__": 0, "split_output_selector": "no"} ` | | |
| | trim\_quality | ` None ` | | |
| </details> | |
| - **Step 10: Unlabelled step (toolshed.g2.bx.psu.edu/repos/iuc/lofreq\_viterbi/lofreq\_viterbi/2.1.5+galaxy0)**: | |
| * step_state: scheduled | |
| * <details><summary>Jobs</summary> | |
| - **Job 1:** | |
| * Job state is ok | |
| **Container:** | |
| * ```console | |
| quay.io/biocontainers/lofreq:2.1.5--py312ha5e83ca_15 | |
| ``` | |
| **Command Line:** | |
| * ```console | |
| ln -s '/tmp/tmpabqaptbl/files/1/1/f/dataset_11fc3eb2-e36b-431a-b14b-0d1387fb1e42.dat' reference.fa && lofreq faidx reference.fa 2>&1 || echo "Error running samtools faidx for indexing fasta reference for lofreq" >&2 && lofreq viterbi --ref 'reference.fa' --defqual 2 --out tmp.bam '/tmp/tmpabqaptbl/files/8/d/f/dataset_8df32a51-b918-4843-a4d9-86e95b3a6ab2.dat' && samtools sort --no-PG -T "${TMPDIR:-.}" -@ ${GALAXY_SLOTS:-1} -O BAM -o '/tmp/tmpabqaptbl/job_working_directory/000/52/outputs/dataset_0f878cd4-ff8e-402a-b0bf-dd195a88411b.dat' tmp.bam | |
| ``` | |
| **Exit Code:** | |
| * ```console | |
| 0 | |
| ``` | |
| **Traceback:** | |
| * ```console | |
| ``` | |
| **Job Parameters:** | |
| * | Job parameter | Parameter value | | |
| | ------------- | --------------- | | |
| | \_\_input\_ext | ` "input" ` | | |
| | \_\_workflow\_invocation\_uuid\_\_ | ` "97b31678114f11f1895170a8a5197e48" ` | | |
| | adv\_options | ` {"bq2_handling": {"__current_case__": 0, "defqual": "2", "replace_bq2": "keep"}, "keepflags": false} ` | | |
| | chromInfo | ` "/tmp/tmpabqaptbl/galaxy-dev/tool-data/shared/ucsc/chrom/?.len" ` | | |
| | dbkey | ` "?" ` | | |
| | reference\_source | ` {"__current_case__": 1, "ref": {"values": [{"id": 72, "src": "hda"}]}, "ref_selector": "history"} ` | | |
| </details> | |
| - **Step 11: Unlabelled step (toolshed.g2.bx.psu.edu/repos/iuc/multiqc/multiqc/1.11+galaxy0)**: | |
| * step_state: scheduled | |
| * <details><summary>Jobs</summary> | |
| - **Job 1:** | |
| * Job state is ok | |
| **Container:** | |
| * ```console | |
| quay.io/biocontainers/multiqc:1.11--pyhdfd78af_0 | |
| ``` | |
| **Command Line:** | |
| * ```console | |
| die() { echo "$@" 1>&2 ; exit 1; } && mkdir multiqc_WDir && mkdir multiqc_WDir/fastp_0 && ln -s '/tmp/tmpabqaptbl/files/2/2/8/dataset_228b0905-3022-4860-8ebe-8cb10c81ec07.dat' 'multiqc_WDir/fastp_0/ERR3485802fastp.json' && grep -q "report_title" 'multiqc_WDir/fastp_0/ERR3485802fastp.json' || die "'report_title' or 'report_title' not found in the file" && mkdir multiqc_WDir/samtools_1 && mkdir 'multiqc_WDir/samtools_1/stats_0' && grep -q 'This file was produced by samtools stats' /tmp/tmpabqaptbl/files/1/2/e/dataset_12efb2de-6161-4c9c-ae30-72efc6f15b85.dat || die "Module 'samtools: 'This file was produced by samtools stats' not found in the file 'ERR3485802'" && ln -s '/tmp/tmpabqaptbl/files/1/2/e/dataset_12efb2de-6161-4c9c-ae30-72efc6f15b85.dat' 'multiqc_WDir/samtools_1/stats_0/ERR3485802' && mkdir multiqc_WDir/picard_2 && mkdir 'multiqc_WDir/picard_2/markdups_0' && grep -q 'MarkDuplicates' /tmp/tmpabqaptbl/files/c/f/4/dataset_cf4ed0a1-2cf3-434c-b350-6f1fd5585b8d.dat || die "Module 'picard: 'MarkDuplicates' not found in the file 'ERR3485802'" && ln -s '/tmp/tmpabqaptbl/files/c/f/4/dataset_cf4ed0a1-2cf3-434c-b350-6f1fd5585b8d.dat' 'multiqc_WDir/picard_2/markdups_0/ERR3485802' && multiqc multiqc_WDir --filename 'report' | |
| ``` | |
| **Exit Code:** | |
| * ```console | |
| 0 | |
| ``` | |
| **Standard Error:** | |
| * ```console | |
| /// MultiQC 🔍 | v1.11 | |
| | multiqc | MultiQC Version v1.33 now available! | |
| | multiqc | Search path : /tmp/tmpabqaptbl/job_working_directory/000/53/working/multiqc_WDir | |
| | picard | Found 1 MarkDuplicates reports | |
| | samtools | Found 1 stats reports | |
| | fastp | Found 1 reports | |
| | multiqc | Compressing plot data | |
| | multiqc | Report : report.html | |
| | multiqc | Data : report_data | |
| | multiqc | MultiQC complete | |
| ``` | |
| **Standard Output:** | |
| * ```console | |
| | searching | ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 100% 3/3 | |
| ``` | |
| **Traceback:** | |
| * ```console | |
| ``` | |
| **Job Parameters:** | |
| * | Job parameter | Parameter value | | |
| | ------------- | --------------- | | |
| | \_\_input\_ext | ` "input" ` | | |
| | \_\_workflow\_invocation\_uuid\_\_ | ` "97b31678114f11f1895170a8a5197e48" ` | | |
| | chromInfo | ` "/tmp/tmpabqaptbl/galaxy-dev/tool-data/shared/ucsc/chrom/?.len" ` | | |
| | comment | ` "" ` | | |
| | dbkey | ` "?" ` | | |
| | export | ` false ` | | |
| | flat | ` false ` | | |
| | results | ` [{"__index__": 0, "software_cond": {"__current_case__": 7, "input": {"values": [{"id": 46, "src": "hdca"}]}, "software": "fastp"}}, {"__index__": 1, "software_cond": {"__current_case__": 24, "output": [{"__index__": 0, "type": {"__current_case__": 0, "input": {"values": [{"id": 51, "src": "hdca"}]}, "type": "stats"}}], "software": "samtools"}}, {"__index__": 2, "software_cond": {"__current_case__": 17, "output": [{"__index__": 0, "input": {"values": [{"id": 49, "src": "hdca"}]}, "type": "markdups"}], "software": "picard"}}] ` | | |
| | saveLog | ` false ` | | |
| | title | ` "" ` | | |
| </details> | |
| - **Step 12: Unlabelled step (toolshed.g2.bx.psu.edu/repos/iuc/lofreq\_indelqual/lofreq\_indelqual/2.1.5+galaxy0)**: | |
| * step_state: scheduled | |
| * <details><summary>Jobs</summary> | |
| - **Job 1:** | |
| * Job state is ok | |
| **Container:** | |
| * ```console | |
| quay.io/biocontainers/lofreq:2.1.5--py312ha5e83ca_15 | |
| ``` | |
| **Command Line:** | |
| * ```console | |
| ln -s '/tmp/tmpabqaptbl/files/1/1/f/dataset_11fc3eb2-e36b-431a-b14b-0d1387fb1e42.dat' reference.fa && lofreq faidx reference.fa 2>&1 || echo "Error running samtools faidx for indexing fasta reference for lofreq" >&2 && lofreq indelqual --dindel --ref reference.fa -o output.bam /tmp/tmpabqaptbl/files/0/f/8/dataset_0f878cd4-ff8e-402a-b0bf-dd195a88411b.dat | |
| ``` | |
| **Exit Code:** | |
| * ```console | |
| 0 | |
| ``` | |
| **Traceback:** | |
| * ```console | |
| ``` | |
| **Job Parameters:** | |
| * | Job parameter | Parameter value | | |
| | ------------- | --------------- | | |
| | \_\_input\_ext | ` "input" ` | | |
| | \_\_workflow\_invocation\_uuid\_\_ | ` "97b31678114f11f1895170a8a5197e48" ` | | |
| | chromInfo | ` "/tmp/tmpabqaptbl/galaxy-dev/tool-data/shared/ucsc/chrom/?.len" ` | | |
| | dbkey | ` "?" ` | | |
| | strategy | ` {"__current_case__": 1, "reference_source": {"__current_case__": 1, "ref": {"values": [{"id": 72, "src": "hda"}]}, "ref_selector": "history"}, "selector": "dindel"} ` | | |
| </details> | |
| - **Step 13: Unlabelled step (toolshed.g2.bx.psu.edu/repos/iuc/lofreq\_call/lofreq\_call/2.1.5+galaxy1)**: | |
| * step_state: scheduled | |
| * <details><summary>Jobs</summary> | |
| - **Job 1:** | |
| * Job state is ok | |
| **Container:** | |
| * ```console | |
| quay.io/biocontainers/lofreq:2.1.5--py312ha5e83ca_15 | |
| ``` | |
| **Command Line:** | |
| * ```console | |
| ln -s '/tmp/tmpabqaptbl/files/1/1/f/dataset_11fc3eb2-e36b-431a-b14b-0d1387fb1e42.dat' reference.fa && lofreq faidx reference.fa 2>&1 || echo "Error running samtools faidx for indexing fasta reference for lofreq" >&2 && ln -s '/tmp/tmpabqaptbl/files/0/d/3/dataset_0d3419cf-dd66-400f-bc97-5116584ffce2.dat' reads.bam && ln -s -f '/tmp/tmpabqaptbl/files/_metadata_files/0/6/2/metadata_062e7851-c1ae-4cf1-8268-31740f3aab78.dat' reads.bam.bai && lofreq call-parallel --pp-threads ${GALAXY_SLOTS:-1} --verbose --ref 'reference.fa' --out variants.vcf --call-indels --min-cov 5 --max-depth 1000000 --min-bq 30 --min-alt-bq 30 --min-mq 0 --max-mq 255 --min-jq 0 --min-alt-jq 0 --def-alt-jq 0 --sig 0.0005 --bonf dynamic --no-default-filter reads.bam 2>&1 || (tool_exit_code=$? && cat "$TMPDIR/lofreq2_call_parallel*/*.log" 1>&2 && exit $tool_exit_code) | |
| ``` | |
| **Exit Code:** | |
| * ```console | |
| 0 | |
| ``` | |
| **Standard Output:** | |
| * ```console | |
| INFO [2026-02-24 07:10:23,372]: Using 1 threads with following basic args: lofreq call --verbose --ref reference.fa --call-indels --min-cov 5 --max-depth 1000000 --min-bq 30 --min-alt-bq 30 --min-mq 0 --max-mq 255 --min-jq 0 --min-alt-jq 0 --def-alt-jq 0 --sig 0.0005 --bonf dynamic --no-default-filter reads.bam | |
| INFO [2026-02-24 07:10:23,381]: Adding 4 commands to mp-pool | |
| Checking the headers and starting positions of 4 files | |
| Number of substitution tests performed: 324 | |
| Number of indel tests performed: 27 | |
| INFO [2026-02-24 07:10:25,057]: Executing lofreq filter -i /tmp/tmpabqaptbl/job_working_directory/000/55/tmp/lofreq2_call_parallelx8rrn5pb/concat.vcf.gz -o variants.vcf --no-defaults --snvqual-thresh 58 --indelqual-thresh 47 | |
| ``` | |
| **Traceback:** | |
| * ```console | |
| ``` | |
| **Job Parameters:** | |
| * | Job parameter | Parameter value | | |
| | ------------- | --------------- | | |
| | \_\_input\_ext | ` "input" ` | | |
| | \_\_workflow\_invocation\_uuid\_\_ | ` "97b31678114f11f1895170a8a5197e48" ` | | |
| | call\_control | ` {"__current_case__": 1, "align_quals": {"alnqual": {"__current_case__": 0, "alnqual_choice": {"__current_case__": 1, "alnquals_to_use": "", "extended_baq": true}, "use_alnqual": ""}}, "bc_quals": {"alt_bq": {"__current_case__": 0, "modify": ""}, "min_alt_bq": "30", "min_bq": "30"}, "coverage": {"max_depth": "1000000", "min_cov": "5"}, "joint_qual": {"def_alt_jq": "0", "min_alt_jq": "0", "min_jq": "0"}, "map_quals": {"min_mq": "0", "use_mq": {"__current_case__": 0, "max_mq": "255", "no_mq": ""}}, "pe": {"use_orphan": false}, "set_call_options": "yes", "source_qual": {"use_src_qual": {"__current_case__": 0, "src_qual": ""}}} ` | | |
| | chromInfo | ` "/tmp/tmpabqaptbl/galaxy-dev/tool-data/shared/ucsc/chrom/?.len" ` | | |
| | dbkey | ` "?" ` | | |
| | filter\_control | ` {"__current_case__": 3, "bonf": "0", "filter_type": "set_custom", "others": false, "sig": "0.0005"} ` | | |
| | reference\_source | ` {"__current_case__": 1, "ref": {"values": [{"id": 72, "src": "hda"}]}, "ref_selector": "history"} ` | | |
| | regions | ` {"__current_case__": 0, "restrict_to_region": "genome"} ` | | |
| | variant\_types | ` "--call-indels" ` | | |
| </details> | |
| - **Step 14: Unlabelled step (toolshed.g2.bx.psu.edu/repos/iuc/lofreq\_filter/lofreq\_filter/2.1.5+galaxy0)**: | |
| * step_state: scheduled | |
| * <details><summary>Jobs</summary> | |
| - **Job 1:** | |
| * Job state is ok | |
| **Container:** | |
| * ```console | |
| quay.io/biocontainers/lofreq:2.1.5--py312ha5e83ca_15 | |
| ``` | |
| **Command Line:** | |
| * ```console | |
| lofreq filter -i /tmp/tmpabqaptbl/files/d/5/9/dataset_d599a823-fd09-4417-92d9-893b94e24cb7.dat --no-defaults --verbose --print-all -v 0 -V 0 -a 0.0 -A 0.0 -b fdr -c 0.001 -o filtered.vcf | |
| ``` | |
| **Exit Code:** | |
| * ```console | |
| 0 | |
| ``` | |
| **Standard Error:** | |
| * ```console | |
| Skipping default settings | |
| At least one type of multiple testing correction requested. Doing first pass of vcf | |
| MTC application completed | |
| Successful exit. | |
| ``` | |
| **Traceback:** | |
| * ```console | |
| ``` | |
| **Job Parameters:** | |
| * | Job parameter | Parameter value | | |
| | ------------- | --------------- | | |
| | \_\_input\_ext | ` "input" ` | | |
| | \_\_workflow\_invocation\_uuid\_\_ | ` "97b31678114f11f1895170a8a5197e48" ` | | |
| | af | ` {"af_max": "0.0", "af_min": "0.0"} ` | | |
| | chromInfo | ` "/tmp/tmpabqaptbl/galaxy-dev/tool-data/shared/ucsc/chrom/?.len" ` | | |
| | coverage | ` {"cov_max": "0", "cov_min": "0"} ` | | |
| | dbkey | ` "?" ` | | |
| | filter\_by\_type | ` {"__current_case__": 0, "keep_only": "", "qual": {"indelqual_filter": {"__current_case__": 0, "indelqual": "no"}, "snvqual_filter": {"__current_case__": 0, "snvqual": "no"}}} ` | | |
| | flag\_or\_drop | ` "--print-all" ` | | |
| | sb | ` {"sb_filter": {"__current_case__": 2, "sb_alpha": "0.001", "sb_compound": true, "sb_indels": false, "sb_mtc": "fdr", "strand_bias": "mtc"}} ` | | |
| </details> | |
| - **Step 15: Unlabelled step (toolshed.g2.bx.psu.edu/repos/iuc/snpeff/snpEff/4.3+T.galaxy1)**: | |
| * step_state: scheduled | |
| * <details><summary>Jobs</summary> | |
| - **Job 1:** | |
| * Job state is ok | |
| **Container:** | |
| * ```console | |
| quay.io/biocontainers/snpeff:4.3.1t--hdfd78af_5 | |
| ``` | |
| **Command Line:** | |
| * ```console | |
| snpEff -Xmx${GALAXY_MEMORY_MB:-8192}m eff -i vcf -o vcf -upDownStreamLen 0 -formatEff -classic -no-downstream -no-intergenic -no-intron -no-upstream -no-utr -stats '/tmp/tmpabqaptbl/job_working_directory/000/57/outputs/dataset_337a3e0a-ac50-4d1f-9a48-808d9c6eb06b.dat' -noLog -dataDir '/tmp/tmpabqaptbl/files/7/8/6/dataset_78688b18-d967-4ce3-8d23-2be910df88cf_files' -configOption 'mpxv'.genome='mpxv' -configOption 'mpxv'.codonTable='Standard' 'mpxv' '/tmp/tmpabqaptbl/files/f/8/5/dataset_f85f9551-f258-4714-910c-f48a7739d01f.dat' > '/tmp/tmpabqaptbl/job_working_directory/000/57/outputs/dataset_0f82a125-51d9-4fc1-a1d1-4026047fcaae.dat' && mkdir '/tmp/tmpabqaptbl/job_working_directory/000/57/outputs/dataset_337a3e0a-ac50-4d1f-9a48-808d9c6eb06b_files' && mv '/tmp/tmpabqaptbl/job_working_directory/000/57/outputs/dataset_337a3e0a-ac50-4d1f-9a48-808d9c6eb06b.dat.genes.txt' '/tmp/tmpabqaptbl/job_working_directory/000/57/outputs/dataset_337a3e0a-ac50-4d1f-9a48-808d9c6eb06b_files/dataset_337a3e0a-ac50-4d1f-9a48-808d9c6eb06b.dat.genes.txt' | |
| ``` | |
| **Exit Code:** | |
| * ```console | |
| 0 | |
| ``` | |
| **Traceback:** | |
| * ```console | |
| ``` | |
| **Job Parameters:** | |
| * | Job parameter | Parameter value | | |
| | ------------- | --------------- | | |
| | \_\_input\_ext | ` "vcf" ` | | |
| | \_\_workflow\_invocation\_uuid\_\_ | ` "97b31678114f11f1895170a8a5197e48" ` | | |
| | annotations | ` ["-formatEff", "-classic"] ` | | |
| | chr | ` "" ` | | |
| | chromInfo | ` "/tmp/tmpabqaptbl/galaxy-dev/tool-data/shared/ucsc/chrom/?.len" ` | | |
| | csvStats | ` false ` | | |
| | dbkey | ` "?" ` | | |
| | filter | ` {"__current_case__": 0, "specificEffects": "no"} ` | | |
| | filterOut | ` ["-no-downstream", "-no-intergenic", "-no-intron", "-no-upstream", "-no-utr"] ` | | |
| | generate\_stats | ` true ` | | |
| | inputFormat | ` "vcf" ` | | |
| | intervals | ` None ` | | |
| | noLog | ` true ` | | |
| | offset | ` "default" ` | | |
| | outputConditional | ` {"__current_case__": 0, "outputFormat": "vcf"} ` | | |
| | snpDb | ` {"__current_case__": 3, "codon_table": "Standard", "genomeSrc": "custom", "snpeff_db": {"values": [{"id": 71, "src": "hda"}]}} ` | | |
| | spliceRegion | ` {"__current_case__": 0, "setSpliceRegions": "no"} ` | | |
| | spliceSiteSize | ` None ` | | |
| | transcripts | ` None ` | | |
| | udLength | ` "0" ` | | |
| </details> | |
| </details> | |
| * <details><summary>Other invocation details</summary> | |
| - **history_id** | |
| * 19071dfbd1f6ddd6 | |
| - **history_state** | |
| * ok | |
| - **invocation_id** | |
| * 79fa989660592e35 | |
| - **invocation_state** | |
| * scheduled | |
| - **workflow_id** | |
| * 79fa989660592e35 | |
| </details> | |
| </div></details> | |
| * <details class="rcorners light-red"><summary class="light-red">❌ Mass_spectrometry__LC-MS_preprocessing_with_XCMS.ga_0</summary><div class="padded"> | |
| **Problems**: | |
| * ``` | |
| Output with path /tmp/tmpuw2l6abc/xset.merged.groupChromPeaks.adjustRtime.groupChromPeaks.fillpeaks.dataMatrix.tsv__61a2ac70-5ac7-484c-b739-06a2a81d4686.tabular different than expected, difference (using diff): | |
| ( /home/runner/work/iwc/iwc/workflows/metabolomics/lcms-preprocessing/test-data/xset.merged.groupChromPeaks.adjustRtime.groupChromPeaks.fillpeaks.dataMatrix.tsv v. /tmp/tmp9zwhpycgxset.merged.groupChromPeaks.adjustRtime.groupChromPeaks.fillpeaks.dataMatrix.tsv ) | |
| --- local_file | |
| +++ history_data | |
| @@ -139,9 +139,9 @@ | |
| M89T27 24068745.0215765 4869930.59711174 2080713.92967363 10138880.1434232 4739535.99910773 6070385.43512832 3744317.84722194 2577850.86209479 3330677.53763546 10578951.9845016 6202958.6095835 2846600.2524822 | |
| M89T93 5447877.22699263 4407979.09737723 2083027.51172599 6890726.00736439 5034583.4401032 3728154.98309092 2993589.46897539 2323587.0436625 2198352.82022574 6833764.50812055 4184597.81437483 1576177.49095221 | |
| M89T215 8099288.74216109 8675262.53914529 2353380.00309361 8238337.67408834 6807265.9436068 3479154.06631962 5625252.85011187 4274617.05383978 1900368.9135465 7561168.02814822 4726765.34912698 1422265.72454762 | |
| -M89T169 24067553.4520313 4911643.04132449 3373129.48326298 9387734.2253519 5885936.38411498 3916214.13381158 5504761.17010357 4128508.6305386 1636607.60862243 9382700.40951732 5877760.76688202 2271366.85544203 | |
| +M89T169 24067553.4520313 4911643.04132449 3373129.48326298 9387734.22535187 5885936.38411498 3916214.13381157 5504761.17010357 4128508.6305386 1636607.60862242 9382700.4095173 5877760.76688201 2271366.85544202 | |
| M89T193 7700918.27308799 6530592.18224246 2677615.71676107 8146595.61450529 4820985.02682287 5486008.24656713 4289864.55050989 3688813.49985 1868708.93366394 8026284.26126046 5198788.44517844 1691276.99404415 | |
| -M89T129 6878178.92995715 9091764.54598374 2301057.12032563 16919.332116328 5142953.77118891 3000725.96465447 2480479.59304246 6774058.28593948 2350962.51924541 11475300.9806089 6361148.11197238 2084674.60684629 | |
| +M89T129 6878178.92995715 9091764.54598374 2301057.12032563 16919.332116328 5142953.77118891 3000725.96465448 2480479.59304246 6774058.28593948 2350962.51924541 11475300.9806089 6361148.11197239 2084674.6068463 | |
| M89T1125 1021306.3826609 497995.760654315 163962.761867945 635318.5861652 584412.694978076 222802.865600683 381966.204712657 407286.204846464 194792.087224546 496766.840761311 379821.401964231 147207.67027229 | |
| M89T1032 418678.081155903 421176.507875375 122754.470345962 2099831.6685236 771796.683709966 313225.462503283 591237.981546018 1367931.38718545 294734.298934858 710838.276726863 392032.489507633 245123.93477762 | |
| M89T1061 630490.067103076 769793.113172472 641535.315246448 689822.054016539 1060215.04717269 592374.031342852 741654.017138674 673632.434799984 366850.926057127 975492.824857026 555283.665388441 225111.042281641 | |
| @@ -151,7 +151,7 @@ | |
| M89T600 1999924.35121853 377964.677109374 215896.137243969 515724.27330087 330128.770500736 299627.502323065 189805.937512992 242524.020967079 141117.178102405 658810.825369625 326306.633683399 136230.0760229 | |
| M89T421 1543200.05963014 704786.896942327 382400.029184567 337676.000757771 275980.874025801 286040.738022326 245572.193290785 279558.204331281 123429.43524029 446750.853665078 286289.982078563 234353.826040006 | |
| M89T485 1065437.24860258 986735.443206955 584740.895146097 541044.047231613 455870.082577794 448689.241397218 348856.704273818 279497.611463853 130651.982593251 529563.525675067 359605.579128174 164662.712707706 | |
| -M89T244 867652.16060598 552214.181935128 185339.878880469 518910.887679968 542827.927473598 281957.743471512 243776.089590172 208606.050030527 136154.617055205 692064.787443913 312433.491931966 112807.557324816 | |
| +M89T244 867652.16060598 552214.181935128 185339.878880469 518910.88767997 542827.9274736 281957.743471513 243776.089590173 208606.050030527 136154.617055206 692064.787443915 312433.491931967 112807.557324816 | |
| M89T526 905720.482337008 1011145.87718318 304948.511806566 461808.160695692 466121.455826814 476262.288496049 368036.666579689 310608.757926965 138958.812646494 670255.808904786 422299.335775248 119726.095741603 | |
| M89T83 912542.652763693 478907.262791887 247820.722934212 3173847.65968285 1675029.23624861 755068.673850099 985732.96682867 1617992.34572493 615000.946209679 7125179.57624038 2697067.17265295 1171692.57423852 | |
| M89T350 1292035.53395497 850149.615368739 420462.874694166 270494.283439926 259297.989869583 226733.872165836 76806.9420371513 226007.62876777 68699.0245359099 374095.394208104 267979.414409065 85119.5244173844 | |
| @@ -160,11 +160,11 @@ | |
| M89T504 1787630.3973014 1185246.04905738 220403.541283595 1225466.61117453 952191.668248462 835402.921813138 688723.022091531 502154.273009119 327993.186301089 1447419.49308423 837818.656490624 303632.369212227 | |
| ******** | |
| *SNIP * | |
| ******** | |
| M340T434 0 0 0 0 0 45680.6175405273 0 32179.6729546879 0 69210.5633300216 53634.0579799761 30023.8829860341 | |
| M341T353 0 0 0 84873.7565432816 0 253180.908064061 131989.234441587 49893.4213620791 110639.883619119 72876.5474560551 113271.034136867 84772.335665411 | |
| -M341T417 0 0 0 0 29758.6847612168 36910.5206386215 173112.699339255 67119.1540947011 34006.0105681223 122995.258725679 131578.247946171 86503.6873206731 | |
| +M341T417 0 0 0 0 29758.6847612164 36910.5206386215 173112.699339255 67119.1540947011 34006.0105681223 122995.258725679 131578.247946171 86503.6873206731 | |
| M341T393 0 0 0 35230.0257766288 610276.584714961 0 0 126433.233227824 0 102918.764902943 107519.239395081 64927.2321144074 | |
| M341T57 0 0 0 0 238465.876053092 31286.4691715907 129918.668919609 403918.048489307 8271.86445555041 118513.25639183 103044.249750236 55670.8613894643 | |
| M341T467 0 0 0 466250.400910839 34612.9474620873 158084.21202577 224773.361581672 170316.869243385 569422.012066653 1895083.01083756 1313948.00752297 783441.042665306 | |
| @@ -1887,7 +1887,7 @@ | |
| M363T388 0 0 0 291916.663047114 232019.202044545 299659.681237647 248743.230300661 37631.0781666192 55984.6266588813 708096.06665596 536990.886277635 404936.125435197 | |
| M363T484 0 0 0 204829.587813222 110456.906107384 56809.9678398554 133846.334976437 0 45953.2970957338 172678.085119299 132405.37385742 88566.5201976588 | |
| M363T438 0 0 0 106596.483680625 90800.0194598532 96269.7763224929 39277.2927230085 2858.31038908697 48540.7357995904 84771.6036200887 73019.6951343748 41206.9783504853 | |
| -M364T244 0 0 0 4568.04792569397 182784.591799477 178449.174845779 174132.934742346 123187.799438679 112976.776229021 233456.605840689 236789.076172003 127691.369905557 | |
| +M364T244 0 0 0 4568.04792569395 182784.591799477 178449.174845779 174132.934742346 123187.799438679 112976.776229021 233456.605840689 236789.076172003 127691.369905557 | |
| M364T322 0 0 0 834551.658226095 0 120218.748171677 97617.2433952227 342017.464792643 58635.2218714808 341955.733292058 254200.621328118 82815.7382941366 | |
| M365T420 0 0 0 107223.804615933 10815.385433194 128168.827067976 65279.628974216 36542.0467156647 31393.5804781644 47537.2434035544 73640.0704722057 51972.1816875005 | |
| M365T289 0 0 0 236239.521337969 128554.264253001 110614.441740705 263482.852579101 104870.839520441 79447.3605071659 226039.615040251 152422.313558834 91761.5341751984 | |
| @@ -2193,7 +2193,7 @@ | |
| M507T436 0 0 0 0 14016.515112945 855365.132637795 122884.858515405 19403.6365266587 0 206444.022307941 154916.735475293 114171.56193676 | |
| M507T476 0 0 0 0 74442.3379147136 0 23705.1354847966 28115.9772717774 26392.7932267188 34562.4094502029 28061.5219241972 14317.933074258 | |
| M507T582 0 0 0 0 191686.526681673 15930.6618940625 18217.6203093726 0 3776.30770874038 77705.9849149548 95150.2733286633 50392.1108551035 | |
| -M508T245 0 0 0 0 33449.3955578757 0 3431.0745495838 0 0 350609.008165308 296906.094445225 192564.323799241 | |
| +M508T245 0 0 0 0 33449.3955578757 0 3431.07454958381 0 0 350609.008165308 296906.094445225 192564.323799241 | |
| M509T438 0 0 0 164490.552794887 139884.102986628 89679.5827304115 129536.888361528 3816.03976291475 53767.1700458853 147403.860447997 89923.5855446471 78701.3677793104 | |
| M509T524 0 0 0 53570.029514355 820695.772044424 307461.284570504 223024.337142206 0 242322.051738295 451649.017756745 370299.791569856 206317.800590179 | |
| M509T487 0 0 0 65895.3941959665 206460.942567596 182015.496150952 79925.5679101518 3155.05576989027 56652.9210228581 150214.021447608 117080.717613361 70535.1085884851 | |
| ``` | |
| * ``` | |
| Output with path /tmp/tmpl1m4s66q/xset.merged.groupChromPeaks.adjustRtime.groupChromPeaks.fillChromPeaks.annotate.variableMetadata.tsv__9adb80ec-f45e-4126-868e-6aa8bd69c880.tabular different than expected, difference (using diff): | |
| ( /home/runner/work/iwc/iwc/workflows/metabolomics/lcms-preprocessing/test-data/xset.merged.groupChromPeaks.adjustRtime.groupChromPeaks.fillChromPeaks.annotate.variableMetadata.tsv v. /tmp/tmplzespse7xset.merged.groupChromPeaks.adjustRtime.groupChromPeaks.fillChromPeaks.annotate.variableMetadata.tsv ) | |
| --- local_file | |
| +++ history_data | |
| @@ -630,7 +630,7 @@ | |
| M179T1133 M178.9772T18.89 178.977202525253 178.977162022288 178.977263455921 18.8895988396958 18.7421155063628 18.9881982807016 21 3 3 6 1 167 | |
| M179T8 M178.9772T0.13 178.977239867878 178.977190065427 178.977278267681 0.132155256585676 0.0587816666663333 0.254131174277155 16 3 1 6 1 204 | |
| M179T37 M178.9772T0.62 178.977240361404 178.977178255518 178.977304527088 0.616747604357913 0.495395548537502 0.673145414409948 15 3 3 6 1 170 | |
| -M179T23 M178.9772T0.39 178.977214412914 178.977149053062 178.977287116263 0.385527313396682 0.288538333333333 0.480956940551991 15 3 1 6 1 31 | |
| +M179T23 M178.9772T0.39 178.977214412914 178.977149053062 178.977287116263 0.385527313396682 0.288538333333333 0.480956940551992 15 3 1 6 1 31 | |
| M179T1005 M178.9771T16.75 178.977127823385 178.977059108829 178.97722043066 16.7493907191989 16.7325044185554 16.8017817032546 12 3 3 6 1 66 | |
| M179T68 M178.9772T1.13 178.977241304954 178.977193385955 178.977249845111 1.13297937766181 0.969720400747266 1.29282749127762 6 0 3 0 1 79 | |
| M179T340 M179.0345T5.66 179.034462509045 179.034437190968 179.034569545606 5.66039239424463 5.6546628448033 5.92191410529413 10 3 0 6 1 78 | |
| @@ -754,7 +754,7 @@ | |
| M191T1045 M190.9278T17.42 190.92782378804 190.927744818148 190.927912514051 17.4156864903608 17.1480081184766 17.6812051486709 44 3 3 6 1 208 | |
| M191T1072 M190.9278T17.86 190.927831981826 190.92778695185 190.927912711629 17.8641794601795 17.7422202549135 17.9706882230588 21 3 3 6 1 238 | |
| M191T41 M190.9279T0.69 190.927855488178 190.927744736378 190.927893129519 0.688761666667 0.651822632605868 0.69313721262346 11 2 3 6 1 241 | |
| -M191T16 M190.9278T0.27 190.92783523722 190.927728809444 190.927926053921 0.270531272587163 0.0409002898331895 0.497888607218991 22 2 0 6 1 284 | |
| +M191T16 M190.9278T0.27 190.92783523722 190.927728809444 190.927926053921 0.270531272587163 0.0409002898331896 0.497888607218992 22 2 0 6 1 284 | |
| M191T118 M190.9651T1.97 190.965077879734 190.965033336021 190.965120133481 1.97091750385889 1.85892845155207 2.01157335660259 6 3 0 2 1 265 | |
| M191T295_1 M190.9814T4.91_1 190.981388691589 190.981243467587 190.981513912505 4.90860464679387 4.88720471332665 4.93562893838205 9 3 0 6 1 [53][M+2]+ 19 | |
| M191T295_2 M190.9897T4.91_2 190.989653841077 190.989432696278 190.989801424326 4.90860464679387 4.89309438802856 4.93562893838205 9 3 0 6 1 19 | |
| @@ -897,7 +897,7 @@ | |
| M207T1136 M206.972T18.94 206.972029529118 206.971983582283 206.972093720235 18.9373332807016 18.824261733433 18.9924351841146 21 3 3 6 1 167 | |
| M207T1057 M206.972T17.61 206.972031481861 206.971972386389 206.972122512079 17.6095938288322 17.4568910258587 17.7252602549135 25 3 3 6 1 177 | |
| M207T1078 M206.972T17.96 206.972035593775 206.971959073477 206.972115021375 17.9587544791491 17.7549591126835 18.1748200294433 36 3 3 6 1 192 | |
| -M207T8 M206.9721T0.13 206.972072603445 206.97202243015 206.972127336469 0.12766690595236 0.0409002898331895 0.277258333333333 15 3 2 5 1 204 | |
| +M207T8 M206.9721T0.13 206.972072603445 206.97202243015 206.972127336469 0.12766690595236 0.0409002898331896 0.277258333333333 15 3 2 5 1 204 | |
| M207T38 M206.9721T0.63 206.972082494119 206.972015362307 206.972160987475 0.631538608919414 0.521916593599214 0.673145414409948 12 3 3 5 1 170 | |
| M207T505 M206.9721T8.42 206.972080086242 206.971994093549 206.972118196968 8.42142256012633 8.26991889824415 8.53789037968998 13 1 3 2 1 112 | |
| M207T433 M206.9721T7.22 206.972050000113 206.972025125229 206.972101712925 7.21742533968748 7.0284634464034 7.36469416485683 14 1 3 1 1 33 | |
| ``` | |
| #### Workflow invocation details | |
| * Invocation Messages | |
| * <details><summary>Steps</summary> | |
| - **Step 1: SampleMetadata**: | |
| * step_state: scheduled | |
| - **Step 2: Mass-spectrometry Dataset Collection**: | |
| * step_state: scheduled | |
| - **Step 3: Unlabelled step (toolshed.g2.bx.psu.edu/repos/lecorguille/msnbase\_readmsdata/msnbase\_readmsdata/2.16.1+galaxy3)**: | |
| * step_state: scheduled | |
| * <details><summary>Jobs</summary> | |
| - **Job 1:** | |
| * Job state is ok | |
| **Container:** | |
| * ```console | |
| quay.io/biocontainers/mulled-v2-60009da30ffd85f87811b22d88de712b63dd80ae:cc2137eb85da1abc40c3a2155cb79d881f9c05c8-2 | |
| ``` | |
| **Command Line:** | |
| * ```console | |
| LC_ALL=C Rscript /tmp/shed_dir/toolshed.g2.bx.psu.edu/repos/lecorguille/msnbase_readmsdata/35b6fe4d481c/msnbase_readmsdata/msnbase_readmsdata.r singlefile_galaxyPath '/tmp/tmpni2hmxgh/files/d/c/4/dataset_dc402255-58af-45ad-a111-e32b3ebb32f3.dat' singlefile_sampleName 'HU_neg_192.mzML' ; return=$?; cat 'log.txt'; sh -c "exit $return" | |
| ``` | |
| **Exit Code:** | |
| * ```console | |
| 0 | |
| ``` | |
| **Standard Output:** | |
| * ```console | |
| SESSION INFO | |
| R version 4.0.5 (2021-03-31) | |
| Main packages: | |
| batch 1.1.5 MSnbase 2.16.1 ProtGenerics 1.22.0 S4Vectors 0.28.1 mzR 2.24.1 Rcpp 1.0.6 Biobase 2.50.0 BiocGenerics 0.36.0 | |
| Other loaded packages: | |
| pillar 1.6.0 compiler 4.0.5 BiocManager 1.30.15 plyr 1.8.6 iterators 1.0.13 zlibbioc 1.36.0 digest 0.6.27 ncdf4 1.17 MALDIquant 1.19.3 lifecycle 1.0.0 tibble 3.1.1 preprocessCore 1.52.1 gtable 0.3.0 lattice 0.20.44 pkgconfig 2.0.3 rlang 0.4.11 foreach 1.5.1 IRanges 2.24.1 vctrs 0.3.8 grid 4.0.5 glue 1.4.2 impute 1.64.0 R6 2.5.0 fansi 0.4.2 XML 3.99.0.6 BiocParallel 1.24.1 limma 3.46.0 ggplot2 3.3.3 magrittr 2.0.1 scales 1.1.1 pcaMethods 1.82.0 codetools 0.2.18 ellipsis 0.3.2 MASS 7.3.54 mzID 1.28.0 colorspace 2.0.1 utf8 1.2.1 affy 1.68.0 doParallel 1.0.16 munsell 0.5.0 vsn 3.58.0 crayon 1.4.1 affyio 1.60.0 | |
| ARGUMENTS INFO | |
| singlefile_galaxyPath /tmp/tmpni2hmxgh/files/d/c/4/dataset_dc402255-58af-45ad-a111-e32b3ebb32f3.dat | |
| singlefile_sampleName HU_neg_192.mzML | |
| ARGUMENTS PROCESSING INFO | |
| INFILE PROCESSING INFO | |
| Compute md5 checksum... | |
| MAIN PROCESSING INFO | |
| COMPUTE | |
| Create a phenodata data.frame | |
| sample_name sample_group | |
| HU_neg_192.mzML HU_neg_192 . | |
| Load Raw Data | |
| Creating the sampleMetadata file... | |
| Error in R_nc4_open: NetCDF: Unknown file format | |
| MSnExp OBJECT INFO | |
| MSn experiment data ("OnDiskMSnExp") | |
| Object size in memory: 0.63 Mb | |
| - - - Spectra data - - - | |
| MS level(s): 1 | |
| Number of spectra: 1647 | |
| MSn retention times: 0:1 - 18:60 minutes | |
| - - - Processing information - - - | |
| Data loaded [Tue Feb 24 07:03:01 2026] | |
| MSnbase version: 2.16.1 | |
| - - - Meta data - - - | |
| phenoData | |
| rowNames: HU_neg_192.mzML | |
| varLabels: sample_name sample_group | |
| varMetadata: labelDescription | |
| Loaded from: | |
| HU_neg_192.mzML | |
| protocolData: none | |
| featureData | |
| featureNames: F1.S0001 F1.S0002 ... F1.S1647 (1647 total) | |
| fvarLabels: fileIdx spIdx ... spectrum (35 total) | |
| fvarMetadata: labelDescription | |
| experimentData: use 'experimentData(object)' | |
| phenoData | |
| sample_name sample_group | |
| HU_neg_192.mzML HU_neg_192 . | |
| DONE | |
| ``` | |
| **Traceback:** | |
| * ```console | |
| ``` | |
| **Job Parameters:** | |
| * | Job parameter | Parameter value | | |
| | ------------- | --------------- | | |
| | \_\_input\_ext | ` "mzml" ` | | |
| | \_\_workflow\_invocation\_uuid\_\_ | ` "b39b8d62114e11f189517ced8d633c14" ` | | |
| | chromInfo | ` "/tmp/tmpni2hmxgh/galaxy-dev/tool-data/shared/ucsc/chrom/?.len" ` | | |
| | dbkey | ` "?" ` | | |
| - **Job 2:** | |
| * Job state is ok | |
| **Container:** | |
| * ```console | |
| quay.io/biocontainers/mulled-v2-60009da30ffd85f87811b22d88de712b63dd80ae:cc2137eb85da1abc40c3a2155cb79d881f9c05c8-2 | |
| ``` | |
| **Command Line:** | |
| * ```console | |
| LC_ALL=C Rscript /tmp/shed_dir/toolshed.g2.bx.psu.edu/repos/lecorguille/msnbase_readmsdata/35b6fe4d481c/msnbase_readmsdata/msnbase_readmsdata.r singlefile_galaxyPath '/tmp/tmpni2hmxgh/files/9/5/6/dataset_95626824-aff4-4070-b1ac-44db6fac0eae.dat' singlefile_sampleName 'Blanc10.mzML' ; return=$?; cat 'log.txt'; sh -c "exit $return" | |
| ``` | |
| **Exit Code:** | |
| * ```console | |
| 0 | |
| ``` | |
| **Standard Output:** | |
| * ```console | |
| SESSION INFO | |
| R version 4.0.5 (2021-03-31) | |
| Main packages: | |
| batch 1.1.5 MSnbase 2.16.1 ProtGenerics 1.22.0 S4Vectors 0.28.1 mzR 2.24.1 Rcpp 1.0.6 Biobase 2.50.0 BiocGenerics 0.36.0 | |
| Other loaded packages: | |
| pillar 1.6.0 compiler 4.0.5 BiocManager 1.30.15 plyr 1.8.6 iterators 1.0.13 zlibbioc 1.36.0 digest 0.6.27 ncdf4 1.17 MALDIquant 1.19.3 lifecycle 1.0.0 tibble 3.1.1 preprocessCore 1.52.1 gtable 0.3.0 lattice 0.20.44 pkgconfig 2.0.3 rlang 0.4.11 foreach 1.5.1 IRanges 2.24.1 vctrs 0.3.8 grid 4.0.5 glue 1.4.2 impute 1.64.0 R6 2.5.0 fansi 0.4.2 XML 3.99.0.6 BiocParallel 1.24.1 limma 3.46.0 ggplot2 3.3.3 magrittr 2.0.1 scales 1.1.1 pcaMethods 1.82.0 codetools 0.2.18 ellipsis 0.3.2 MASS 7.3.54 mzID 1.28.0 colorspace 2.0.1 utf8 1.2.1 affy 1.68.0 doParallel 1.0.16 munsell 0.5.0 vsn 3.58.0 crayon 1.4.1 affyio 1.60.0 | |
| ARGUMENTS INFO | |
| singlefile_galaxyPath /tmp/tmpni2hmxgh/files/9/5/6/dataset_95626824-aff4-4070-b1ac-44db6fac0eae.dat | |
| singlefile_sampleName Blanc10.mzML | |
| ARGUMENTS PROCESSING INFO | |
| INFILE PROCESSING INFO | |
| Compute md5 checksum... | |
| MAIN PROCESSING INFO | |
| COMPUTE | |
| Create a phenodata data.frame | |
| sample_name sample_group | |
| Blanc10.mzML Blanc10 . | |
| Load Raw Data | |
| Creating the sampleMetadata file... | |
| Error in R_nc4_open: NetCDF: Unknown file format | |
| MSnExp OBJECT INFO | |
| MSn experiment data ("OnDiskMSnExp") | |
| Object size in memory: 0.72 Mb | |
| - - - Spectra data - - - | |
| MS level(s): 1 | |
| Number of spectra: 1882 | |
| MSn retention times: 0:1 - 18:59 minutes | |
| - - - Processing information - - - | |
| Data loaded [Tue Feb 24 07:03:01 2026] | |
| MSnbase version: 2.16.1 | |
| - - - Meta data - - - | |
| phenoData | |
| rowNames: Blanc10.mzML | |
| varLabels: sample_name sample_group | |
| varMetadata: labelDescription | |
| Loaded from: | |
| Blanc10.mzML | |
| protocolData: none | |
| featureData | |
| featureNames: F1.S0001 F1.S0002 ... F1.S1882 (1882 total) | |
| fvarLabels: fileIdx spIdx ... spectrum (35 total) | |
| fvarMetadata: labelDescription | |
| experimentData: use 'experimentData(object)' | |
| phenoData | |
| sample_name sample_group | |
| Blanc10.mzML Blanc10 . | |
| DONE | |
| ``` | |
| **Traceback:** | |
| * ```console | |
| ``` | |
| **Job Parameters:** | |
| * | Job parameter | Parameter value | | |
| | ------------- | --------------- | | |
| | \_\_input\_ext | ` "mzml" ` | | |
| | \_\_workflow\_invocation\_uuid\_\_ | ` "b39b8d62114e11f189517ced8d633c14" ` | | |
| | chromInfo | ` "/tmp/tmpni2hmxgh/galaxy-dev/tool-data/shared/ucsc/chrom/?.len" ` | | |
| | dbkey | ` "?" ` | | |
| - **Job 3:** | |
| * Job state is ok | |
| **Container:** | |
| * ```console | |
| quay.io/biocontainers/mulled-v2-60009da30ffd85f87811b22d88de712b63dd80ae:cc2137eb85da1abc40c3a2155cb79d881f9c05c8-2 | |
| ``` | |
| **Command Line:** | |
| * ```console | |
| LC_ALL=C Rscript /tmp/shed_dir/toolshed.g2.bx.psu.edu/repos/lecorguille/msnbase_readmsdata/35b6fe4d481c/msnbase_readmsdata/msnbase_readmsdata.r singlefile_galaxyPath '/tmp/tmpni2hmxgh/files/3/e/1/dataset_3e17868c-f97f-4000-b5db-62e02603c8ad.dat' singlefile_sampleName 'HU_neg_173.mzML' ; return=$?; cat 'log.txt'; sh -c "exit $return" | |
| ``` | |
| **Exit Code:** | |
| * ```console | |
| 0 | |
| ``` | |
| **Standard Output:** | |
| * ```console | |
| SESSION INFO | |
| R version 4.0.5 (2021-03-31) | |
| Main packages: | |
| batch 1.1.5 MSnbase 2.16.1 ProtGenerics 1.22.0 S4Vectors 0.28.1 mzR 2.24.1 Rcpp 1.0.6 Biobase 2.50.0 BiocGenerics 0.36.0 | |
| Other loaded packages: | |
| pillar 1.6.0 compiler 4.0.5 BiocManager 1.30.15 plyr 1.8.6 iterators 1.0.13 zlibbioc 1.36.0 digest 0.6.27 ncdf4 1.17 MALDIquant 1.19.3 lifecycle 1.0.0 tibble 3.1.1 preprocessCore 1.52.1 gtable 0.3.0 lattice 0.20.44 pkgconfig 2.0.3 rlang 0.4.11 foreach 1.5.1 IRanges 2.24.1 vctrs 0.3.8 grid 4.0.5 glue 1.4.2 impute 1.64.0 R6 2.5.0 fansi 0.4.2 XML 3.99.0.6 BiocParallel 1.24.1 limma 3.46.0 ggplot2 3.3.3 magrittr 2.0.1 scales 1.1.1 pcaMethods 1.82.0 codetools 0.2.18 ellipsis 0.3.2 MASS 7.3.54 mzID 1.28.0 colorspace 2.0.1 utf8 1.2.1 affy 1.68.0 doParallel 1.0.16 munsell 0.5.0 vsn 3.58.0 crayon 1.4.1 affyio 1.60.0 | |
| ARGUMENTS INFO | |
| singlefile_galaxyPath /tmp/tmpni2hmxgh/files/3/e/1/dataset_3e17868c-f97f-4000-b5db-62e02603c8ad.dat | |
| singlefile_sampleName HU_neg_173.mzML | |
| ARGUMENTS PROCESSING INFO | |
| INFILE PROCESSING INFO | |
| Compute md5 checksum... | |
| MAIN PROCESSING INFO | |
| COMPUTE | |
| Create a phenodata data.frame | |
| sample_name sample_group | |
| HU_neg_173.mzML HU_neg_173 . | |
| Load Raw Data | |
| Creating the sampleMetadata file... | |
| Error in R_nc4_open: NetCDF: Unknown file format | |
| MSnExp OBJECT INFO | |
| MSn experiment data ("OnDiskMSnExp") | |
| Object size in memory: 0.66 Mb | |
| - - - Spectra data - - - | |
| MS level(s): 1 | |
| Number of spectra: 1710 | |
| MSn retention times: 0:1 - 18:60 minutes | |
| - - - Processing information - - - | |
| Data loaded [Tue Feb 24 07:03:02 2026] | |
| MSnbase version: 2.16.1 | |
| - - - Meta data - - - | |
| phenoData | |
| rowNames: HU_neg_173.mzML | |
| varLabels: sample_name sample_group | |
| varMetadata: labelDescription | |
| Loaded from: | |
| HU_neg_173.mzML | |
| protocolData: none | |
| featureData | |
| featureNames: F1.S0001 F1.S0002 ... F1.S1710 (1710 total) | |
| fvarLabels: fileIdx spIdx ... spectrum (35 total) | |
| fvarMetadata: labelDescription | |
| experimentData: use 'experimentData(object)' | |
| phenoData | |
| sample_name sample_group | |
| HU_neg_173.mzML HU_neg_173 . | |
| DONE | |
| ``` | |
| **Traceback:** | |
| * ```console | |
| ``` | |
| **Job Parameters:** | |
| * | Job parameter | Parameter value | | |
| | ------------- | --------------- | | |
| | \_\_input\_ext | ` "mzml" ` | | |
| | \_\_workflow\_invocation\_uuid\_\_ | ` "b39b8d62114e11f189517ced8d633c14" ` | | |
| | chromInfo | ` "/tmp/tmpni2hmxgh/galaxy-dev/tool-data/shared/ucsc/chrom/?.len" ` | | |
| | dbkey | ` "?" ` | | |
| - **Job 4:** | |
| * Job state is ok | |
| **Container:** | |
| * ```console | |
| quay.io/biocontainers/mulled-v2-60009da30ffd85f87811b22d88de712b63dd80ae:cc2137eb85da1abc40c3a2155cb79d881f9c05c8-2 | |
| ``` | |
| **Command Line:** | |
| * ```console | |
| LC_ALL=C Rscript /tmp/shed_dir/toolshed.g2.bx.psu.edu/repos/lecorguille/msnbase_readmsdata/35b6fe4d481c/msnbase_readmsdata/msnbase_readmsdata.r singlefile_galaxyPath '/tmp/tmpni2hmxgh/files/9/c/7/dataset_9c765975-dff0-4c7e-b204-52228629d2d6.dat' singlefile_sampleName 'QC1_002.mzML' ; return=$?; cat 'log.txt'; sh -c "exit $return" | |
| ``` | |
| **Exit Code:** | |
| * ```console | |
| 0 | |
| ``` | |
| **Standard Output:** | |
| * ```console | |
| SESSION INFO | |
| R version 4.0.5 (2021-03-31) | |
| Main packages: | |
| batch 1.1.5 MSnbase 2.16.1 ProtGenerics 1.22.0 S4Vectors 0.28.1 mzR 2.24.1 Rcpp 1.0.6 Biobase 2.50.0 BiocGenerics 0.36.0 | |
| Other loaded packages: | |
| pillar 1.6.0 compiler 4.0.5 BiocManager 1.30.15 plyr 1.8.6 iterators 1.0.13 zlibbioc 1.36.0 digest 0.6.27 ncdf4 1.17 MALDIquant 1.19.3 lifecycle 1.0.0 tibble 3.1.1 preprocessCore 1.52.1 gtable 0.3.0 lattice 0.20.44 pkgconfig 2.0.3 rlang 0.4.11 foreach 1.5.1 IRanges 2.24.1 vctrs 0.3.8 grid 4.0.5 glue 1.4.2 impute 1.64.0 R6 2.5.0 fansi 0.4.2 XML 3.99.0.6 BiocParallel 1.24.1 limma 3.46.0 ggplot2 3.3.3 magrittr 2.0.1 scales 1.1.1 pcaMethods 1.82.0 codetools 0.2.18 ellipsis 0.3.2 MASS 7.3.54 mzID 1.28.0 colorspace 2.0.1 utf8 1.2.1 affy 1.68.0 doParallel 1.0.16 munsell 0.5.0 vsn 3.58.0 crayon 1.4.1 affyio 1.60.0 | |
| ARGUMENTS INFO | |
| singlefile_galaxyPath /tmp/tmpni2hmxgh/files/9/c/7/dataset_9c765975-dff0-4c7e-b204-52228629d2d6.dat | |
| singlefile_sampleName QC1_002.mzML | |
| ARGUMENTS PROCESSING INFO | |
| INFILE PROCESSING INFO | |
| Compute md5 checksum... | |
| MAIN PROCESSING INFO | |
| COMPUTE | |
| Create a phenodata data.frame | |
| sample_name sample_group | |
| QC1_002.mzML QC1_002 . | |
| Load Raw Data | |
| Creating the sampleMetadata file... | |
| Error in R_nc4_open: NetCDF: Unknown file format | |
| MSnExp OBJECT INFO | |
| MSn experiment data ("OnDiskMSnExp") | |
| Object size in memory: 0.78 Mb | |
| - - - Spectra data - - - | |
| MS level(s): 1 | |
| Number of spectra: 2039 | |
| MSn retention times: 0:1 - 18:60 minutes | |
| - - - Processing information - - - | |
| Data loaded [Tue Feb 24 07:03:17 2026] | |
| MSnbase version: 2.16.1 | |
| - - - Meta data - - - | |
| phenoData | |
| rowNames: QC1_002.mzML | |
| varLabels: sample_name sample_group | |
| varMetadata: labelDescription | |
| Loaded from: | |
| QC1_002.mzML | |
| protocolData: none | |
| featureData | |
| featureNames: F1.S0001 F1.S0002 ... F1.S2039 (2039 total) | |
| fvarLabels: fileIdx spIdx ... spectrum (35 total) | |
| fvarMetadata: labelDescription | |
| experimentData: use 'experimentData(object)' | |
| phenoData | |
| sample_name sample_group | |
| QC1_002.mzML QC1_002 . | |
| DONE | |
| ``` | |
| **Traceback:** | |
| * ```console | |
| ``` | |
| **Job Parameters:** | |
| * | Job parameter | Parameter value | | |
| | ------------- | --------------- | | |
| | \_\_input\_ext | ` "mzml" ` | | |
| | \_\_workflow\_invocation\_uuid\_\_ | ` "b39b8d62114e11f189517ced8d633c14" ` | | |
| | chromInfo | ` "/tmp/tmpni2hmxgh/galaxy-dev/tool-data/shared/ucsc/chrom/?.len" ` | | |
| | dbkey | ` "?" ` | | |
| - **Job 5:** | |
| * Job state is ok | |
| **Container:** | |
| * ```console | |
| quay.io/biocontainers/mulled-v2-60009da30ffd85f87811b22d88de712b63dd80ae:cc2137eb85da1abc40c3a2155cb79d881f9c05c8-2 | |
| ``` | |
| **Command Line:** | |
| * ```console | |
| LC_ALL=C Rscript /tmp/shed_dir/toolshed.g2.bx.psu.edu/repos/lecorguille/msnbase_readmsdata/35b6fe4d481c/msnbase_readmsdata/msnbase_readmsdata.r singlefile_galaxyPath '/tmp/tmpni2hmxgh/files/f/1/5/dataset_f15f2a15-390b-4a04-9ac5-0225af4cc01e.dat' singlefile_sampleName 'QC1_008.mzML' ; return=$?; cat 'log.txt'; sh -c "exit $return" | |
| ``` | |
| **Exit Code:** | |
| * ```console | |
| 0 | |
| ``` | |
| **Standard Output:** | |
| * ```console | |
| SESSION INFO | |
| R version 4.0.5 (2021-03-31) | |
| Main packages: | |
| batch 1.1.5 MSnbase 2.16.1 ProtGenerics 1.22.0 S4Vectors 0.28.1 mzR 2.24.1 Rcpp 1.0.6 Biobase 2.50.0 BiocGenerics 0.36.0 | |
| Other loaded packages: | |
| pillar 1.6.0 compiler 4.0.5 BiocManager 1.30.15 plyr 1.8.6 iterators 1.0.13 zlibbioc 1.36.0 digest 0.6.27 ncdf4 1.17 MALDIquant 1.19.3 lifecycle 1.0.0 tibble 3.1.1 preprocessCore 1.52.1 gtable 0.3.0 lattice 0.20.44 pkgconfig 2.0.3 rlang 0.4.11 foreach 1.5.1 IRanges 2.24.1 vctrs 0.3.8 grid 4.0.5 glue 1.4.2 impute 1.64.0 R6 2.5.0 fansi 0.4.2 XML 3.99.0.6 BiocParallel 1.24.1 limma 3.46.0 ggplot2 3.3.3 magrittr 2.0.1 scales 1.1.1 pcaMethods 1.82.0 codetools 0.2.18 ellipsis 0.3.2 MASS 7.3.54 mzID 1.28.0 colorspace 2.0.1 utf8 1.2.1 affy 1.68.0 doParallel 1.0.16 munsell 0.5.0 vsn 3.58.0 crayon 1.4.1 affyio 1.60.0 | |
| ARGUMENTS INFO | |
| singlefile_galaxyPath /tmp/tmpni2hmxgh/files/f/1/5/dataset_f15f2a15-390b-4a04-9ac5-0225af4cc01e.dat | |
| singlefile_sampleName QC1_008.mzML | |
| ARGUMENTS PROCESSING INFO | |
| INFILE PROCESSING INFO | |
| Compute md5 checksum... | |
| MAIN PROCESSING INFO | |
| COMPUTE | |
| Create a phenodata data.frame | |
| sample_name sample_group | |
| QC1_008.mzML QC1_008 . | |
| Load Raw Data | |
| Creating the sampleMetadata file... | |
| Error in R_nc4_open: NetCDF: Unknown file format | |
| MSnExp OBJECT INFO | |
| MSn experiment data ("OnDiskMSnExp") | |
| Object size in memory: 0.72 Mb | |
| - - - Spectra data - - - | |
| MS level(s): 1 | |
| Number of spectra: 1879 | |
| MSn retention times: 0:1 - 18:60 minutes | |
| - - - Processing information - - - | |
| Data loaded [Tue Feb 24 07:03:18 2026] | |
| MSnbase version: 2.16.1 | |
| - - - Meta data - - - | |
| phenoData | |
| rowNames: QC1_008.mzML | |
| varLabels: sample_name sample_group | |
| varMetadata: labelDescription | |
| Loaded from: | |
| QC1_008.mzML | |
| protocolData: none | |
| featureData | |
| featureNames: F1.S0001 F1.S0002 ... F1.S1879 (1879 total) | |
| fvarLabels: fileIdx spIdx ... spectrum (35 total) | |
| fvarMetadata: labelDescription | |
| experimentData: use 'experimentData(object)' | |
| phenoData | |
| sample_name sample_group | |
| QC1_008.mzML QC1_008 . | |
| DONE | |
| ``` | |
| **Traceback:** | |
| * ```console | |
| ``` | |
| **Job Parameters:** | |
| * | Job parameter | Parameter value | | |
| | ------------- | --------------- | | |
| | \_\_input\_ext | ` "mzml" ` | | |
| | \_\_workflow\_invocation\_uuid\_\_ | ` "b39b8d62114e11f189517ced8d633c14" ` | | |
| | chromInfo | ` "/tmp/tmpni2hmxgh/galaxy-dev/tool-data/shared/ucsc/chrom/?.len" ` | | |
| | dbkey | ` "?" ` | | |
| - **Job 6:** | |
| * Job state is ok | |
| **Container:** | |
| * ```console | |
| quay.io/biocontainers/mulled-v2-60009da30ffd85f87811b22d88de712b63dd80ae:cc2137eb85da1abc40c3a2155cb79d881f9c05c8-2 | |
| ``` | |
| **Command Line:** | |
| * ```console | |
| LC_ALL=C Rscript /tmp/shed_dir/toolshed.g2.bx.psu.edu/repos/lecorguille/msnbase_readmsdata/35b6fe4d481c/msnbase_readmsdata/msnbase_readmsdata.r singlefile_galaxyPath '/tmp/tmpni2hmxgh/files/8/d/6/dataset_8d6ef331-b385-4a59-be28-2c910a3cd42b.dat' singlefile_sampleName 'QC1_014.mzML' ; return=$?; cat 'log.txt'; sh -c "exit $return" | |
| ``` | |
| **Exit Code:** | |
| * ```console | |
| 0 | |
| ``` | |
| **Standard Output:** | |
| * ```console | |
| SESSION INFO | |
| R version 4.0.5 (2021-03-31) | |
| Main packages: | |
| batch 1.1.5 MSnbase 2.16.1 ProtGenerics 1.22.0 S4Vectors 0.28.1 mzR 2.24.1 Rcpp 1.0.6 Biobase 2.50.0 BiocGenerics 0.36.0 | |
| Other loaded packages: | |
| pillar 1.6.0 compiler 4.0.5 BiocManager 1.30.15 plyr 1.8.6 iterators 1.0.13 zlibbioc 1.36.0 digest 0.6.27 ncdf4 1.17 MALDIquant 1.19.3 lifecycle 1.0.0 tibble 3.1.1 preprocessCore 1.52.1 gtable 0.3.0 lattice 0.20.44 pkgconfig 2.0.3 rlang 0.4.11 foreach 1.5.1 IRanges 2.24.1 vctrs 0.3.8 grid 4.0.5 glue 1.4.2 impute 1.64.0 R6 2.5.0 fansi 0.4.2 XML 3.99.0.6 BiocParallel 1.24.1 limma 3.46.0 ggplot2 3.3.3 magrittr 2.0.1 scales 1.1.1 pcaMethods 1.82.0 codetools 0.2.18 ellipsis 0.3.2 MASS 7.3.54 mzID 1.28.0 colorspace 2.0.1 utf8 1.2.1 affy 1.68.0 doParallel 1.0.16 munsell 0.5.0 vsn 3.58.0 crayon 1.4.1 affyio 1.60.0 | |
| ARGUMENTS INFO | |
| singlefile_galaxyPath /tmp/tmpni2hmxgh/files/8/d/6/dataset_8d6ef331-b385-4a59-be28-2c910a3cd42b.dat | |
| singlefile_sampleName QC1_014.mzML | |
| ARGUMENTS PROCESSING INFO | |
| INFILE PROCESSING INFO | |
| Compute md5 checksum... | |
| MAIN PROCESSING INFO | |
| COMPUTE | |
| Create a phenodata data.frame | |
| sample_name sample_group | |
| QC1_014.mzML QC1_014 . | |
| Load Raw Data | |
| Creating the sampleMetadata file... | |
| Error in R_nc4_open: NetCDF: Unknown file format | |
| MSnExp OBJECT INFO | |
| MSn experiment data ("OnDiskMSnExp") | |
| Object size in memory: 0.59 Mb | |
| - - - Spectra data - - - | |
| MS level(s): 1 | |
| Number of spectra: 1533 | |
| MSn retention times: 0:1 - 18:60 minutes | |
| - - - Processing information - - - | |
| Data loaded [Tue Feb 24 07:03:18 2026] | |
| MSnbase version: 2.16.1 | |
| - - - Meta data - - - | |
| phenoData | |
| rowNames: QC1_014.mzML | |
| varLabels: sample_name sample_group | |
| varMetadata: labelDescription | |
| Loaded from: | |
| QC1_014.mzML | |
| protocolData: none | |
| featureData | |
| featureNames: F1.S0001 F1.S0002 ... F1.S1533 (1533 total) | |
| fvarLabels: fileIdx spIdx ... spectrum (35 total) | |
| fvarMetadata: labelDescription | |
| experimentData: use 'experimentData(object)' | |
| phenoData | |
| sample_name sample_group | |
| QC1_014.mzML QC1_014 . | |
| DONE | |
| ``` | |
| **Traceback:** | |
| * ```console | |
| ``` | |
| **Job Parameters:** | |
| * | Job parameter | Parameter value | | |
| | ------------- | --------------- | | |
| | \_\_input\_ext | ` "mzml" ` | | |
| | \_\_workflow\_invocation\_uuid\_\_ | ` "b39b8d62114e11f189517ced8d633c14" ` | | |
| | chromInfo | ` "/tmp/tmpni2hmxgh/galaxy-dev/tool-data/shared/ucsc/chrom/?.len" ` | | |
| | dbkey | ` "?" ` | | |
| - **Job 7:** | |
| * Job state is ok | |
| **Container:** | |
| * ```console | |
| quay.io/biocontainers/mulled-v2-60009da30ffd85f87811b22d88de712b63dd80ae:cc2137eb85da1abc40c3a2155cb79d881f9c05c8-2 | |
| ``` | |
| **Command Line:** | |
| * ```console | |
| LC_ALL=C Rscript /tmp/shed_dir/toolshed.g2.bx.psu.edu/repos/lecorguille/msnbase_readmsdata/35b6fe4d481c/msnbase_readmsdata/msnbase_readmsdata.r singlefile_galaxyPath '/tmp/tmpni2hmxgh/files/6/2/5/dataset_625c3dc6-856a-479a-b081-c2f1eee49693.dat' singlefile_sampleName 'HU_neg_048.mzML' ; return=$?; cat 'log.txt'; sh -c "exit $return" | |
| ``` | |
| **Exit Code:** | |
| * ```console | |
| 0 | |
| ``` | |
| **Standard Output:** | |
| * ```console | |
| SESSION INFO | |
| R version 4.0.5 (2021-03-31) | |
| Main packages: | |
| batch 1.1.5 MSnbase 2.16.1 ProtGenerics 1.22.0 S4Vectors 0.28.1 mzR 2.24.1 Rcpp 1.0.6 Biobase 2.50.0 BiocGenerics 0.36.0 | |
| Other loaded packages: | |
| pillar 1.6.0 compiler 4.0.5 BiocManager 1.30.15 plyr 1.8.6 iterators 1.0.13 zlibbioc 1.36.0 digest 0.6.27 ncdf4 1.17 MALDIquant 1.19.3 lifecycle 1.0.0 tibble 3.1.1 preprocessCore 1.52.1 gtable 0.3.0 lattice 0.20.44 pkgconfig 2.0.3 rlang 0.4.11 foreach 1.5.1 IRanges 2.24.1 vctrs 0.3.8 grid 4.0.5 glue 1.4.2 impute 1.64.0 R6 2.5.0 fansi 0.4.2 XML 3.99.0.6 BiocParallel 1.24.1 limma 3.46.0 ggplot2 3.3.3 magrittr 2.0.1 scales 1.1.1 pcaMethods 1.82.0 codetools 0.2.18 ellipsis 0.3.2 MASS 7.3.54 mzID 1.28.0 colorspace 2.0.1 utf8 1.2.1 affy 1.68.0 doParallel 1.0.16 munsell 0.5.0 vsn 3.58.0 crayon 1.4.1 affyio 1.60.0 | |
| ARGUMENTS INFO | |
| singlefile_galaxyPath /tmp/tmpni2hmxgh/files/6/2/5/dataset_625c3dc6-856a-479a-b081-c2f1eee49693.dat | |
| singlefile_sampleName HU_neg_048.mzML | |
| ARGUMENTS PROCESSING INFO | |
| INFILE PROCESSING INFO | |
| Compute md5 checksum... | |
| MAIN PROCESSING INFO | |
| COMPUTE | |
| Create a phenodata data.frame | |
| sample_name sample_group | |
| HU_neg_048.mzML HU_neg_048 . | |
| Load Raw Data | |
| Creating the sampleMetadata file... | |
| Error in R_nc4_open: NetCDF: Unknown file format | |
| MSnExp OBJECT INFO | |
| MSn experiment data ("OnDiskMSnExp") | |
| Object size in memory: 0.77 Mb | |
| - - - Spectra data - - - | |
| MS level(s): 1 | |
| Number of spectra: 2031 | |
| MSn retention times: 0:1 - 18:60 minutes | |
| - - - Processing information - - - | |
| Data loaded [Tue Feb 24 07:03:34 2026] | |
| MSnbase version: 2.16.1 | |
| - - - Meta data - - - | |
| phenoData | |
| rowNames: HU_neg_048.mzML | |
| varLabels: sample_name sample_group | |
| varMetadata: labelDescription | |
| Loaded from: | |
| HU_neg_048.mzML | |
| protocolData: none | |
| featureData | |
| featureNames: F1.S0001 F1.S0002 ... F1.S2031 (2031 total) | |
| fvarLabels: fileIdx spIdx ... spectrum (35 total) | |
| fvarMetadata: labelDescription | |
| experimentData: use 'experimentData(object)' | |
| phenoData | |
| sample_name sample_group | |
| HU_neg_048.mzML HU_neg_048 . | |
| DONE | |
| ``` | |
| **Traceback:** | |
| * ```console | |
| ``` | |
| **Job Parameters:** | |
| * | Job parameter | Parameter value | | |
| | ------------- | --------------- | | |
| | \_\_input\_ext | ` "mzml" ` | | |
| | \_\_workflow\_invocation\_uuid\_\_ | ` "b39b8d62114e11f189517ced8d633c14" ` | | |
| | chromInfo | ` "/tmp/tmpni2hmxgh/galaxy-dev/tool-data/shared/ucsc/chrom/?.len" ` | | |
| | dbkey | ` "?" ` | | |
| - **Job 8:** | |
| * Job state is ok | |
| **Container:** | |
| * ```console | |
| quay.io/biocontainers/mulled-v2-60009da30ffd85f87811b22d88de712b63dd80ae:cc2137eb85da1abc40c3a2155cb79d881f9c05c8-2 | |
| ``` | |
| **Command Line:** | |
| * ```console | |
| LC_ALL=C Rscript /tmp/shed_dir/toolshed.g2.bx.psu.edu/repos/lecorguille/msnbase_readmsdata/35b6fe4d481c/msnbase_readmsdata/msnbase_readmsdata.r singlefile_galaxyPath '/tmp/tmpni2hmxgh/files/e/8/8/dataset_e88e0111-1c8f-4466-b3d5-28b33f5b704a.dat' singlefile_sampleName 'Blanc05.mzML' ; return=$?; cat 'log.txt'; sh -c "exit $return" | |
| ``` | |
| **Exit Code:** | |
| * ```console | |
| 0 | |
| ``` | |
| **Standard Output:** | |
| * ```console | |
| SESSION INFO | |
| R version 4.0.5 (2021-03-31) | |
| Main packages: | |
| batch 1.1.5 MSnbase 2.16.1 ProtGenerics 1.22.0 S4Vectors 0.28.1 mzR 2.24.1 Rcpp 1.0.6 Biobase 2.50.0 BiocGenerics 0.36.0 | |
| Other loaded packages: | |
| pillar 1.6.0 compiler 4.0.5 BiocManager 1.30.15 plyr 1.8.6 iterators 1.0.13 zlibbioc 1.36.0 digest 0.6.27 ncdf4 1.17 MALDIquant 1.19.3 lifecycle 1.0.0 tibble 3.1.1 preprocessCore 1.52.1 gtable 0.3.0 lattice 0.20.44 pkgconfig 2.0.3 rlang 0.4.11 foreach 1.5.1 IRanges 2.24.1 vctrs 0.3.8 grid 4.0.5 glue 1.4.2 impute 1.64.0 R6 2.5.0 fansi 0.4.2 XML 3.99.0.6 BiocParallel 1.24.1 limma 3.46.0 ggplot2 3.3.3 magrittr 2.0.1 scales 1.1.1 pcaMethods 1.82.0 codetools 0.2.18 ellipsis 0.3.2 MASS 7.3.54 mzID 1.28.0 colorspace 2.0.1 utf8 1.2.1 affy 1.68.0 doParallel 1.0.16 munsell 0.5.0 vsn 3.58.0 crayon 1.4.1 affyio 1.60.0 | |
| ARGUMENTS INFO | |
| singlefile_galaxyPath /tmp/tmpni2hmxgh/files/e/8/8/dataset_e88e0111-1c8f-4466-b3d5-28b33f5b704a.dat | |
| singlefile_sampleName Blanc05.mzML | |
| ARGUMENTS PROCESSING INFO | |
| INFILE PROCESSING INFO | |
| Compute md5 checksum... | |
| MAIN PROCESSING INFO | |
| COMPUTE | |
| Create a phenodata data.frame | |
| sample_name sample_group | |
| Blanc05.mzML Blanc05 . | |
| Load Raw Data | |
| Creating the sampleMetadata file... | |
| Error in R_nc4_open: NetCDF: Unknown file format | |
| MSnExp OBJECT INFO | |
| MSn experiment data ("OnDiskMSnExp") | |
| Object size in memory: 0.77 Mb | |
| - - - Spectra data - - - | |
| MS level(s): 1 | |
| Number of spectra: 2022 | |
| MSn retention times: 0:1 - 18:60 minutes | |
| - - - Processing information - - - | |
| Data loaded [Tue Feb 24 07:03:01 2026] | |
| MSnbase version: 2.16.1 | |
| - - - Meta data - - - | |
| phenoData | |
| rowNames: Blanc05.mzML | |
| varLabels: sample_name sample_group | |
| varMetadata: labelDescription | |
| Loaded from: | |
| Blanc05.mzML | |
| protocolData: none | |
| featureData | |
| featureNames: F1.S0001 F1.S0002 ... F1.S2022 (2022 total) | |
| fvarLabels: fileIdx spIdx ... spectrum (35 total) | |
| fvarMetadata: labelDescription | |
| experimentData: use 'experimentData(object)' | |
| phenoData | |
| sample_name sample_group | |
| Blanc05.mzML Blanc05 . | |
| DONE | |
| ``` | |
| **Traceback:** | |
| * ```console | |
| ``` | |
| **Job Parameters:** | |
| * | Job parameter | Parameter value | | |
| | ------------- | --------------- | | |
| | \_\_input\_ext | ` "mzml" ` | | |
| | \_\_workflow\_invocation\_uuid\_\_ | ` "b39b8d62114e11f189517ced8d633c14" ` | | |
| | chromInfo | ` "/tmp/tmpni2hmxgh/galaxy-dev/tool-data/shared/ucsc/chrom/?.len" ` | | |
| | dbkey | ` "?" ` | | |
| - **Job 9:** | |
| * Job state is ok | |
| **Container:** | |
| * ```console | |
| quay.io/biocontainers/mulled-v2-60009da30ffd85f87811b22d88de712b63dd80ae:cc2137eb85da1abc40c3a2155cb79d881f9c05c8-2 | |
| ``` | |
| **Command Line:** | |
| * ```console | |
| LC_ALL=C Rscript /tmp/shed_dir/toolshed.g2.bx.psu.edu/repos/lecorguille/msnbase_readmsdata/35b6fe4d481c/msnbase_readmsdata/msnbase_readmsdata.r singlefile_galaxyPath '/tmp/tmpni2hmxgh/files/b/0/1/dataset_b017e65d-feaf-4c04-9cc3-210e12340136.dat' singlefile_sampleName 'HU_neg_090.mzML' ; return=$?; cat 'log.txt'; sh -c "exit $return" | |
| ``` | |
| **Exit Code:** | |
| * ```console | |
| 0 | |
| ``` | |
| **Standard Output:** | |
| * ```console | |
| SESSION INFO | |
| R version 4.0.5 (2021-03-31) | |
| Main packages: | |
| batch 1.1.5 MSnbase 2.16.1 ProtGenerics 1.22.0 S4Vectors 0.28.1 mzR 2.24.1 Rcpp 1.0.6 Biobase 2.50.0 BiocGenerics 0.36.0 | |
| Other loaded packages: | |
| pillar 1.6.0 compiler 4.0.5 BiocManager 1.30.15 plyr 1.8.6 iterators 1.0.13 zlibbioc 1.36.0 digest 0.6.27 ncdf4 1.17 MALDIquant 1.19.3 lifecycle 1.0.0 tibble 3.1.1 preprocessCore 1.52.1 gtable 0.3.0 lattice 0.20.44 pkgconfig 2.0.3 rlang 0.4.11 foreach 1.5.1 IRanges 2.24.1 vctrs 0.3.8 grid 4.0.5 glue 1.4.2 impute 1.64.0 R6 2.5.0 fansi 0.4.2 XML 3.99.0.6 BiocParallel 1.24.1 limma 3.46.0 ggplot2 3.3.3 magrittr 2.0.1 scales 1.1.1 pcaMethods 1.82.0 codetools 0.2.18 ellipsis 0.3.2 MASS 7.3.54 mzID 1.28.0 colorspace 2.0.1 utf8 1.2.1 affy 1.68.0 doParallel 1.0.16 munsell 0.5.0 vsn 3.58.0 crayon 1.4.1 affyio 1.60.0 | |
| ARGUMENTS INFO | |
| singlefile_galaxyPath /tmp/tmpni2hmxgh/files/b/0/1/dataset_b017e65d-feaf-4c04-9cc3-210e12340136.dat | |
| singlefile_sampleName HU_neg_090.mzML | |
| ARGUMENTS PROCESSING INFO | |
| INFILE PROCESSING INFO | |
| Compute md5 checksum... | |
| MAIN PROCESSING INFO | |
| COMPUTE | |
| Create a phenodata data.frame | |
| sample_name sample_group | |
| HU_neg_090.mzML HU_neg_090 . | |
| Load Raw Data | |
| Creating the sampleMetadata file... | |
| Error in R_nc4_open: NetCDF: Unknown file format | |
| MSnExp OBJECT INFO | |
| MSn experiment data ("OnDiskMSnExp") | |
| Object size in memory: 0.76 Mb | |
| - - - Spectra data - - - | |
| MS level(s): 1 | |
| Number of spectra: 1991 | |
| MSn retention times: 0:1 - 18:60 minutes | |
| - - - Processing information - - - | |
| Data loaded [Tue Feb 24 07:03:34 2026] | |
| MSnbase version: 2.16.1 | |
| - - - Meta data - - - | |
| phenoData | |
| rowNames: HU_neg_090.mzML | |
| varLabels: sample_name sample_group | |
| varMetadata: labelDescription | |
| Loaded from: | |
| HU_neg_090.mzML | |
| protocolData: none | |
| featureData | |
| featureNames: F1.S0001 F1.S0002 ... F1.S1991 (1991 total) | |
| fvarLabels: fileIdx spIdx ... spectrum (35 total) | |
| fvarMetadata: labelDescription | |
| experimentData: use 'experimentData(object)' | |
| phenoData | |
| sample_name sample_group | |
| HU_neg_090.mzML HU_neg_090 . | |
| DONE | |
| ``` | |
| **Traceback:** | |
| * ```console | |
| ``` | |
| **Job Parameters:** | |
| * | Job parameter | Parameter value | | |
| | ------------- | --------------- | | |
| | \_\_input\_ext | ` "mzml" ` | | |
| | \_\_workflow\_invocation\_uuid\_\_ | ` "b39b8d62114e11f189517ced8d633c14" ` | | |
| | chromInfo | ` "/tmp/tmpni2hmxgh/galaxy-dev/tool-data/shared/ucsc/chrom/?.len" ` | | |
| | dbkey | ` "?" ` | | |
| - **Job 10:** | |
| * Job state is ok | |
| **Container:** | |
| * ```console | |
| quay.io/biocontainers/mulled-v2-60009da30ffd85f87811b22d88de712b63dd80ae:cc2137eb85da1abc40c3a2155cb79d881f9c05c8-2 | |
| ``` | |
| **Command Line:** | |
| * ```console | |
| LC_ALL=C Rscript /tmp/shed_dir/toolshed.g2.bx.psu.edu/repos/lecorguille/msnbase_readmsdata/35b6fe4d481c/msnbase_readmsdata/msnbase_readmsdata.r singlefile_galaxyPath '/tmp/tmpni2hmxgh/files/d/6/3/dataset_d63ad184-7e45-42f8-a3f2-7de8fb2ea4b0.dat' singlefile_sampleName 'HU_neg_123.mzML' ; return=$?; cat 'log.txt'; sh -c "exit $return" | |
| ``` | |
| **Exit Code:** | |
| * ```console | |
| 0 | |
| ``` | |
| **Standard Output:** | |
| * ```console | |
| SESSION INFO | |
| R version 4.0.5 (2021-03-31) | |
| Main packages: | |
| batch 1.1.5 MSnbase 2.16.1 ProtGenerics 1.22.0 S4Vectors 0.28.1 mzR 2.24.1 Rcpp 1.0.6 Biobase 2.50.0 BiocGenerics 0.36.0 | |
| Other loaded packages: | |
| pillar 1.6.0 compiler 4.0.5 BiocManager 1.30.15 plyr 1.8.6 iterators 1.0.13 zlibbioc 1.36.0 digest 0.6.27 ncdf4 1.17 MALDIquant 1.19.3 lifecycle 1.0.0 tibble 3.1.1 preprocessCore 1.52.1 gtable 0.3.0 lattice 0.20.44 pkgconfig 2.0.3 rlang 0.4.11 foreach 1.5.1 IRanges 2.24.1 vctrs 0.3.8 grid 4.0.5 glue 1.4.2 impute 1.64.0 R6 2.5.0 fansi 0.4.2 XML 3.99.0.6 BiocParallel 1.24.1 limma 3.46.0 ggplot2 3.3.3 magrittr 2.0.1 scales 1.1.1 pcaMethods 1.82.0 codetools 0.2.18 ellipsis 0.3.2 MASS 7.3.54 mzID 1.28.0 colorspace 2.0.1 utf8 1.2.1 affy 1.68.0 doParallel 1.0.16 munsell 0.5.0 vsn 3.58.0 crayon 1.4.1 affyio 1.60.0 | |
| ARGUMENTS INFO | |
| singlefile_galaxyPath /tmp/tmpni2hmxgh/files/d/6/3/dataset_d63ad184-7e45-42f8-a3f2-7de8fb2ea4b0.dat | |
| singlefile_sampleName HU_neg_123.mzML | |
| ARGUMENTS PROCESSING INFO | |
| INFILE PROCESSING INFO | |
| Compute md5 checksum... | |
| MAIN PROCESSING INFO | |
| COMPUTE | |
| Create a phenodata data.frame | |
| sample_name sample_group | |
| HU_neg_123.mzML HU_neg_123 . | |
| Load Raw Data | |
| Creating the sampleMetadata file... | |
| Error in R_nc4_open: NetCDF: Unknown file format | |
| MSnExp OBJECT INFO | |
| MSn experiment data ("OnDiskMSnExp") | |
| Object size in memory: 0.72 Mb | |
| - - - Spectra data - - - | |
| MS level(s): 1 | |
| Number of spectra: 1892 | |
| MSn retention times: 0:1 - 18:60 minutes | |
| - - - Processing information - - - | |
| Data loaded [Tue Feb 24 07:03:35 2026] | |
| MSnbase version: 2.16.1 | |
| - - - Meta data - - - | |
| phenoData | |
| rowNames: HU_neg_123.mzML | |
| varLabels: sample_name sample_group | |
| varMetadata: labelDescription | |
| Loaded from: | |
| HU_neg_123.mzML | |
| protocolData: none | |
| featureData | |
| featureNames: F1.S0001 F1.S0002 ... F1.S1892 (1892 total) | |
| fvarLabels: fileIdx spIdx ... spectrum (35 total) | |
| fvarMetadata: labelDescription | |
| experimentData: use 'experimentData(object)' | |
| phenoData | |
| sample_name sample_group | |
| HU_neg_123.mzML HU_neg_123 . | |
| DONE | |
| ``` | |
| **Traceback:** | |
| * ```console | |
| ``` | |
| **Job Parameters:** | |
| * | Job parameter | Parameter value | | |
| | ------------- | --------------- | | |
| | \_\_input\_ext | ` "mzml" ` | | |
| | \_\_workflow\_invocation\_uuid\_\_ | ` "b39b8d62114e11f189517ced8d633c14" ` | | |
| | chromInfo | ` "/tmp/tmpni2hmxgh/galaxy-dev/tool-data/shared/ucsc/chrom/?.len" ` | | |
| | dbkey | ` "?" ` | | |
| - **Job 11:** | |
| * Job state is ok | |
| **Container:** | |
| * ```console | |
| quay.io/biocontainers/mulled-v2-60009da30ffd85f87811b22d88de712b63dd80ae:cc2137eb85da1abc40c3a2155cb79d881f9c05c8-2 | |
| ``` | |
| **Command Line:** | |
| * ```console | |
| LC_ALL=C Rscript /tmp/shed_dir/toolshed.g2.bx.psu.edu/repos/lecorguille/msnbase_readmsdata/35b6fe4d481c/msnbase_readmsdata/msnbase_readmsdata.r singlefile_galaxyPath '/tmp/tmpni2hmxgh/files/4/3/6/dataset_43621608-bee3-4895-81aa-c045d2cc5d12.dat' singlefile_sampleName 'HU_neg_157.mzML' ; return=$?; cat 'log.txt'; sh -c "exit $return" | |
| ``` | |
| **Exit Code:** | |
| * ```console | |
| 0 | |
| ``` | |
| **Standard Output:** | |
| * ```console | |
| SESSION INFO | |
| R version 4.0.5 (2021-03-31) | |
| Main packages: | |
| batch 1.1.5 MSnbase 2.16.1 ProtGenerics 1.22.0 S4Vectors 0.28.1 mzR 2.24.1 Rcpp 1.0.6 Biobase 2.50.0 BiocGenerics 0.36.0 | |
| Other loaded packages: | |
| pillar 1.6.0 compiler 4.0.5 BiocManager 1.30.15 plyr 1.8.6 iterators 1.0.13 zlibbioc 1.36.0 digest 0.6.27 ncdf4 1.17 MALDIquant 1.19.3 lifecycle 1.0.0 tibble 3.1.1 preprocessCore 1.52.1 gtable 0.3.0 lattice 0.20.44 pkgconfig 2.0.3 rlang 0.4.11 foreach 1.5.1 IRanges 2.24.1 vctrs 0.3.8 grid 4.0.5 glue 1.4.2 impute 1.64.0 R6 2.5.0 fansi 0.4.2 XML 3.99.0.6 BiocParallel 1.24.1 limma 3.46.0 ggplot2 3.3.3 magrittr 2.0.1 scales 1.1.1 pcaMethods 1.82.0 codetools 0.2.18 ellipsis 0.3.2 MASS 7.3.54 mzID 1.28.0 colorspace 2.0.1 utf8 1.2.1 affy 1.68.0 doParallel 1.0.16 munsell 0.5.0 vsn 3.58.0 crayon 1.4.1 affyio 1.60.0 | |
| ARGUMENTS INFO | |
| singlefile_galaxyPath /tmp/tmpni2hmxgh/files/4/3/6/dataset_43621608-bee3-4895-81aa-c045d2cc5d12.dat | |
| singlefile_sampleName HU_neg_157.mzML | |
| ARGUMENTS PROCESSING INFO | |
| INFILE PROCESSING INFO | |
| Compute md5 checksum... | |
| MAIN PROCESSING INFO | |
| COMPUTE | |
| Create a phenodata data.frame | |
| sample_name sample_group | |
| HU_neg_157.mzML HU_neg_157 . | |
| Load Raw Data | |
| Creating the sampleMetadata file... | |
| Error in R_nc4_open: NetCDF: Unknown file format | |
| MSnExp OBJECT INFO | |
| MSn experiment data ("OnDiskMSnExp") | |
| Object size in memory: 0.68 Mb | |
| - - - Spectra data - - - | |
| MS level(s): 1 | |
| Number of spectra: 1767 | |
| MSn retention times: 0:1 - 18:60 minutes | |
| - - - Processing information - - - | |
| Data loaded [Tue Feb 24 07:03:36 2026] | |
| MSnbase version: 2.16.1 | |
| - - - Meta data - - - | |
| phenoData | |
| rowNames: HU_neg_157.mzML | |
| varLabels: sample_name sample_group | |
| varMetadata: labelDescription | |
| Loaded from: | |
| HU_neg_157.mzML | |
| protocolData: none | |
| featureData | |
| featureNames: F1.S0001 F1.S0002 ... F1.S1767 (1767 total) | |
| fvarLabels: fileIdx spIdx ... spectrum (35 total) | |
| fvarMetadata: labelDescription | |
| experimentData: use 'experimentData(object)' | |
| phenoData | |
| sample_name sample_group | |
| HU_neg_157.mzML HU_neg_157 . | |
| DONE | |
| ``` | |
| **Traceback:** | |
| * ```console | |
| ``` | |
| **Job Parameters:** | |
| * | Job parameter | Parameter value | | |
| | ------------- | --------------- | | |
| | \_\_input\_ext | ` "mzml" ` | | |
| | \_\_workflow\_invocation\_uuid\_\_ | ` "b39b8d62114e11f189517ced8d633c14" ` | | |
| | chromInfo | ` "/tmp/tmpni2hmxgh/galaxy-dev/tool-data/shared/ucsc/chrom/?.len" ` | | |
| | dbkey | ` "?" ` | | |
| - **Job 12:** | |
| * Job state is ok | |
| **Container:** | |
| * ```console | |
| quay.io/biocontainers/mulled-v2-60009da30ffd85f87811b22d88de712b63dd80ae:cc2137eb85da1abc40c3a2155cb79d881f9c05c8-2 | |
| ``` | |
| **Command Line:** | |
| * ```console | |
| LC_ALL=C Rscript /tmp/shed_dir/toolshed.g2.bx.psu.edu/repos/lecorguille/msnbase_readmsdata/35b6fe4d481c/msnbase_readmsdata/msnbase_readmsdata.r singlefile_galaxyPath '/tmp/tmpni2hmxgh/files/0/3/5/dataset_0357f0fc-4a32-45a3-bd12-a09eb5be67c6.dat' singlefile_sampleName 'Blanc16.mzML' ; return=$?; cat 'log.txt'; sh -c "exit $return" | |
| ``` | |
| **Exit Code:** | |
| * ```console | |
| 0 | |
| ``` | |
| **Standard Output:** | |
| * ```console | |
| SESSION INFO | |
| R version 4.0.5 (2021-03-31) | |
| Main packages: | |
| batch 1.1.5 MSnbase 2.16.1 ProtGenerics 1.22.0 S4Vectors 0.28.1 mzR 2.24.1 Rcpp 1.0.6 Biobase 2.50.0 BiocGenerics 0.36.0 | |
| Other loaded packages: | |
| pillar 1.6.0 compiler 4.0.5 BiocManager 1.30.15 plyr 1.8.6 iterators 1.0.13 zlibbioc 1.36.0 digest 0.6.27 ncdf4 1.17 MALDIquant 1.19.3 lifecycle 1.0.0 tibble 3.1.1 preprocessCore 1.52.1 gtable 0.3.0 lattice 0.20.44 pkgconfig 2.0.3 rlang 0.4.11 foreach 1.5.1 IRanges 2.24.1 vctrs 0.3.8 grid 4.0.5 glue 1.4.2 impute 1.64.0 R6 2.5.0 fansi 0.4.2 XML 3.99.0.6 BiocParallel 1.24.1 limma 3.46.0 ggplot2 3.3.3 magrittr 2.0.1 scales 1.1.1 pcaMethods 1.82.0 codetools 0.2.18 ellipsis 0.3.2 MASS 7.3.54 mzID 1.28.0 colorspace 2.0.1 utf8 1.2.1 affy 1.68.0 doParallel 1.0.16 munsell 0.5.0 vsn 3.58.0 crayon 1.4.1 affyio 1.60.0 | |
| ARGUMENTS INFO | |
| singlefile_galaxyPath /tmp/tmpni2hmxgh/files/0/3/5/dataset_0357f0fc-4a32-45a3-bd12-a09eb5be67c6.dat | |
| singlefile_sampleName Blanc16.mzML | |
| ARGUMENTS PROCESSING INFO | |
| INFILE PROCESSING INFO | |
| Compute md5 checksum... | |
| MAIN PROCESSING INFO | |
| COMPUTE | |
| Create a phenodata data.frame | |
| sample_name sample_group | |
| Blanc16.mzML Blanc16 . | |
| Load Raw Data | |
| Creating the sampleMetadata file... | |
| Error in R_nc4_open: NetCDF: Unknown file format | |
| MSnExp OBJECT INFO | |
| MSn experiment data ("OnDiskMSnExp") | |
| Object size in memory: 0.57 Mb | |
| - - - Spectra data - - - | |
| MS level(s): 1 | |
| Number of spectra: 1485 | |
| MSn retention times: 0:1 - 18:59 minutes | |
| - - - Processing information - - - | |
| Data loaded [Tue Feb 24 07:03:18 2026] | |
| MSnbase version: 2.16.1 | |
| - - - Meta data - - - | |
| phenoData | |
| rowNames: Blanc16.mzML | |
| varLabels: sample_name sample_group | |
| varMetadata: labelDescription | |
| Loaded from: | |
| Blanc16.mzML | |
| protocolData: none | |
| featureData | |
| featureNames: F1.S0001 F1.S0002 ... F1.S1485 (1485 total) | |
| fvarLabels: fileIdx spIdx ... spectrum (35 total) | |
| fvarMetadata: labelDescription | |
| experimentData: use 'experimentData(object)' | |
| phenoData | |
| sample_name sample_group | |
| Blanc16.mzML Blanc16 . | |
| DONE | |
| ``` | |
| **Traceback:** | |
| * ```console | |
| ``` | |
| **Job Parameters:** | |
| * | Job parameter | Parameter value | | |
| | ------------- | --------------- | | |
| | \_\_input\_ext | ` "mzml" ` | | |
| | \_\_workflow\_invocation\_uuid\_\_ | ` "b39b8d62114e11f189517ced8d633c14" ` | | |
| | chromInfo | ` "/tmp/tmpni2hmxgh/galaxy-dev/tool-data/shared/ucsc/chrom/?.len" ` | | |
| | dbkey | ` "?" ` | | |
| </details> | |
| - **Step 4: Unlabelled step (toolshed.g2.bx.psu.edu/repos/lecorguille/xcms\_plot\_chromatogram/xcms\_plot\_chromatogram/3.12.0+galaxy3)**: | |
| * step_state: scheduled | |
| * <details><summary>Jobs</summary> | |
| - **Job 1:** | |
| * Job state is ok | |
| **Container:** | |
| * ```console | |
| quay.io/biocontainers/mulled-v2-007db2e42e47018763bae6b2bd1e69345120fe7f:ffab248635d36a246a435f3341c896269df9943c-2 | |
| ``` | |
| **Command Line:** | |
| * ```console | |
| LC_ALL=C Rscript /tmp/shed_dir/toolshed.g2.bx.psu.edu/repos/lecorguille/xcms_plot_chromatogram/9291271ec4d9/xcms_plot_chromatogram/xcms_plot_chromatogram.r images 'c("/tmp/tmpni2hmxgh/files/6/f/c/dataset_6fc81557-2824-4fb8-9d96-0ed012e17179.dat","/tmp/tmpni2hmxgh/files/d/9/c/dataset_d9c5a090-65ec-4499-8150-43f22dc151d3.dat","/tmp/tmpni2hmxgh/files/e/8/5/dataset_e859e7ca-e523-41d8-b7fe-2823fc656111.dat","/tmp/tmpni2hmxgh/files/c/b/6/dataset_cb63844d-f873-4bdb-8068-efd5f971c4c9.dat","/tmp/tmpni2hmxgh/files/f/4/0/dataset_f4089d4b-1664-4047-a835-230c5156506a.dat","/tmp/tmpni2hmxgh/files/c/5/7/dataset_c576fbfb-5cc5-478d-8512-776dc069f519.dat","/tmp/tmpni2hmxgh/files/b/d/d/dataset_bddb3ff5-69cb-42db-a401-91c0443b16f9.dat","/tmp/tmpni2hmxgh/files/0/8/9/dataset_0894a220-d002-40d1-a0fa-0f8f10a25ea3.dat","/tmp/tmpni2hmxgh/files/3/0/2/dataset_30226968-a841-44ff-91f2-2ec68d035d57.dat","/tmp/tmpni2hmxgh/files/1/9/0/dataset_19048e68-7357-4058-baf8-816307779515.dat","/tmp/tmpni2hmxgh/files/2/5/9/dataset_2598e943-3223-4009-beb6-78b89dd9375d.dat","/tmp/tmpni2hmxgh/files/b/3/f/dataset_b3f6d71d-e5d0-4943-9aa1-22f92575fcd1.dat")' sampleMetadata '/tmp/tmpni2hmxgh/files/9/a/6/dataset_9a642ccc-4da5-4a7e-8b38-ba2e1b5a4979.dat' | |
| ``` | |
| **Exit Code:** | |
| * ```console | |
| 0 | |
| ``` | |
| **Standard Error:** | |
| * ```console | |
| There were 12 warnings (use warnings() to see them) | |
| There were 12 warnings (use warnings() to see them) | |
| ``` | |
| **Standard Output:** | |
| * ```console | |
| SESSION INFO | |
| R version 4.0.5 (2021-03-31) | |
| Main packages: | |
| RColorBrewer 1.1.2 batch 1.1.5 xcms 3.12.0 MSnbase 2.16.1 ProtGenerics 1.22.0 S4Vectors 0.28.1 mzR 2.24.1 Rcpp 1.0.6 BiocParallel 1.24.1 Biobase 2.50.0 BiocGenerics 0.36.0 | |
| Other loaded packages: | |
| SummarizedExperiment 1.20.0 lattice 0.20.44 colorspace 2.0.1 vctrs 0.3.8 vsn 3.58.0 utf8 1.2.1 XML 3.99.0.6 rlang 0.4.11 pillar 1.6.0 glue 1.4.2 affy 1.68.0 affyio 1.60.0 matrixStats 0.58.0 GenomeInfoDbData 1.2.4 foreach 1.5.1 lifecycle 1.0.0 plyr 1.8.6 mzID 1.28.0 robustbase 0.93.7 zlibbioc 1.36.0 MatrixGenerics 1.2.1 munsell 0.5.0 pcaMethods 1.82.0 gtable 0.3.0 codetools 0.2.18 IRanges 2.24.1 doParallel 1.0.16 GenomeInfoDb 1.26.4 MassSpecWavelet 1.56.0 fansi 0.4.2 preprocessCore 1.52.1 DEoptimR 1.0.8 scales 1.1.1 BiocManager 1.30.15 DelayedArray 0.16.3 limma 3.46.0 XVector 0.30.0 MsCoreUtils 1.2.0 RANN 2.6.1 impute 1.64.0 ggplot2 3.3.3 digest 0.6.27 ncdf4 1.17 GenomicRanges 1.42.0 grid 4.0.5 tools 4.0.5 bitops 1.0.7 magrittr 2.0.1 RCurl 1.98.1.3 tibble 3.1.1 crayon 1.4.1 pkgconfig 2.0.3 Matrix 1.3.2 MASS 7.3.54 ellipsis 0.3.2 iterators 1.0.13 R6 2.5.0 MALDIquant 1.19.3 compiler 4.0.5 | |
| ARGUMENTS INFO | |
| images c("/tmp/tmpni2hmxgh/files/6/f/c/dataset_6fc81557-2824-4fb8-9d96-0ed012e17179.dat", "/tmp/tmpni2hmxgh/files/d/9/c/dataset_d9c5a090-65ec-4499-8150-43f22dc151d3.dat", "/tmp/tmpni2hmxgh/files/e/8/5/dataset_e859e7ca-e523-41d8-b7fe-2823fc656111.dat", "/tmp/tmpni2hmxgh/files/c/b/6/dataset_cb63844d-f873-4bdb-8068-efd5f971c4c9.dat", "/tmp/tmpni2hmxgh/files/f/4/0/dataset_f4089d4b-1664-4047-a835-230c5156506a.dat", "/tmp/tmpni2hmxgh/files/c/5/7/dataset_c576fbfb-5cc5-478d-8512-776dc069f519.dat", "/tmp/tmpni2hmxgh/files/b/d/d/dataset_bddb3ff5-69cb-42db-a401-91c0443b16f9.dat", | |
| "/tmp/tmpni2hmxgh/files/0/8/9/dataset_0894a220-d002-40d1-a0fa-0f8f10a25ea3.dat", "/tmp/tmpni2hmxgh/files/3/0/2/dataset_30226968-a841-44ff-91f2-2ec68d035d57.dat", "/tmp/tmpni2hmxgh/files/1/9/0/dataset_19048e68-7357-4058-baf8-816307779515.dat", "/tmp/tmpni2hmxgh/files/2/5/9/dataset_2598e943-3223-4009-beb6-78b89dd9375d.dat", "/tmp/tmpni2hmxgh/files/b/3/f/dataset_b3f6d71d-e5d0-4943-9aa1-22f92575fcd1.dat") | |
| sampleMetadata /tmp/tmpni2hmxgh/files/9/a/6/dataset_9a642ccc-4da5-4a7e-8b38-ba2e1b5a4979.dat | |
| ARGUMENTS PROCESSING INFO | |
| INFILE PROCESSING INFO | |
| Blanc05 | |
| Blanc10 | |
| Blanc16 | |
| HU_neg_048 | |
| HU_neg_090 | |
| HU_neg_123 | |
| HU_neg_157 | |
| HU_neg_173 | |
| HU_neg_192 | |
| QC1_002 | |
| QC1_008 | |
| QC1_014 | |
| XSET PHENODATA SETTING... | |
| MAIN PROCESSING INFO | |
| DRAW GRAPHICS | |
| Compute TIC | |
| Compute BPI | |
| null device | |
| 1 | |
| null device | |
| 1 | |
| XCMSnExp OBJECT INFO | |
| MSn experiment data ("OnDiskMSnExp") | |
| Object size in memory: 6.23 Mb | |
| - - - Spectra data - - - | |
| MS level(s): 1 | |
| Number of spectra: 21878 | |
| MSn retention times: 0:1 - 18:60 minutes | |
| - - - Processing information - - - | |
| Concatenated [Tue Feb 24 07:05:39 2026] | |
| MSnbase version: 2.16.1 | |
| - - - Meta data - - - | |
| phenoData | |
| rowNames: Blanc05.mzML Blanc10.mzML ... QC1_014.mzML (12 total) | |
| varLabels: sample_name sample_group | |
| varMetadata: labelDescription | |
| Loaded from: | |
| [1] Blanc05.mzML... [12] QC1_014.mzML | |
| Use 'fileNames(.)' to see all files. | |
| protocolData: none | |
| featureData | |
| featureNames: F1.S0001 F1.S0002 ... F12.S1533 (21878 total) | |
| fvarLabels: fileIdx spIdx ... spectrum (35 total) | |
| fvarMetadata: labelDescription | |
| experimentData: use 'experimentData(object)' | |
| DONE | |
| ``` | |
| **Traceback:** | |
| * ```console | |
| ``` | |
| **Job Parameters:** | |
| * | Job parameter | Parameter value | | |
| | ------------- | --------------- | | |
| | \_\_input\_ext | ` "input" ` | | |
| | \_\_workflow\_invocation\_uuid\_\_ | ` "b39b8d62114e11f189517ced8d633c14" ` | | |
| | chromInfo | ` "/tmp/tmpni2hmxgh/galaxy-dev/tool-data/shared/ucsc/chrom/?.len" ` | | |
| | dbkey | ` "?" ` | | |
| | file\_load\_section | ` {"file_load_conditional": {"__current_case__": 0, "file_load_select": "no"}} ` | | |
| </details> | |
| - **Step 5: Unlabelled step (toolshed.g2.bx.psu.edu/repos/lecorguille/xcms\_xcmsset/abims\_xcms\_xcmsSet/3.12.0+galaxy3)**: | |
| * step_state: scheduled | |
| * <details><summary>Jobs</summary> | |
| - **Job 1:** | |
| * Job state is ok | |
| **Container:** | |
| * ```console | |
| quay.io/biocontainers/mulled-v2-007db2e42e47018763bae6b2bd1e69345120fe7f:ffab248635d36a246a435f3341c896269df9943c-2 | |
| ``` | |
| **Command Line:** | |
| * ```console | |
| LC_ALL=C Rscript /tmp/shed_dir/toolshed.g2.bx.psu.edu/repos/lecorguille/xcms_xcmsset/3990a65b45a4/xcms_xcmsset/xcms_xcmsSet.r image '/tmp/tmpni2hmxgh/files/0/8/9/dataset_0894a220-d002-40d1-a0fa-0f8f10a25ea3.dat' BPPARAM ${GALAXY_SLOTS:-1} method CentWave ppm 3.0 peakwidth "c(5,20)" snthresh 10 prefilter "c(3,5000)" mzCenterFun wMean integrate 1 mzdiff -0.001 fitgauss FALSE noise 1000 verboseColumns FALSE peaklist FALSE ; return=$?; cat 'log.txt'; sh -c "exit $return" | |
| ``` | |
| **Exit Code:** | |
| * ```console | |
| 0 | |
| ``` | |
| **Standard Error:** | |
| * ```console | |
| Detecting mass traces at 3 ppm ... OK | |
| Detecting chromatographic peaks in 5440 regions of interest ... OK: 3051 found. | |
| Note: you might want to set/adjust the 'sampclass' of the returned xcmSet object before proceeding with the analysis. | |
| ``` | |
| **Standard Output:** | |
| * ```console | |
| SESSION INFO | |
| R version 4.0.5 (2021-03-31) | |
| Main packages: | |
| batch 1.1.5 xcms 3.12.0 MSnbase 2.16.1 ProtGenerics 1.22.0 S4Vectors 0.28.1 mzR 2.24.1 Rcpp 1.0.6 BiocParallel 1.24.1 Biobase 2.50.0 BiocGenerics 0.36.0 | |
| Other loaded packages: | |
| SummarizedExperiment 1.20.0 lattice 0.20.44 colorspace 2.0.1 vctrs 0.3.8 vsn 3.58.0 utf8 1.2.1 XML 3.99.0.6 rlang 0.4.11 pillar 1.6.0 glue 1.4.2 affy 1.68.0 RColorBrewer 1.1.2 affyio 1.60.0 matrixStats 0.58.0 GenomeInfoDbData 1.2.4 foreach 1.5.1 lifecycle 1.0.0 plyr 1.8.6 mzID 1.28.0 robustbase 0.93.7 zlibbioc 1.36.0 MatrixGenerics 1.2.1 munsell 0.5.0 pcaMethods 1.82.0 gtable 0.3.0 codetools 0.2.18 IRanges 2.24.1 doParallel 1.0.16 GenomeInfoDb 1.26.4 MassSpecWavelet 1.56.0 fansi 0.4.2 preprocessCore 1.52.1 DEoptimR 1.0.8 scales 1.1.1 BiocManager 1.30.15 DelayedArray 0.16.3 limma 3.46.0 XVector 0.30.0 MsCoreUtils 1.2.0 RANN 2.6.1 impute 1.64.0 ggplot2 3.3.3 digest 0.6.27 ncdf4 1.17 GenomicRanges 1.42.0 grid 4.0.5 tools 4.0.5 bitops 1.0.7 magrittr 2.0.1 RCurl 1.98.1.3 tibble 3.1.1 crayon 1.4.1 pkgconfig 2.0.3 Matrix 1.3.2 MASS 7.3.54 ellipsis 0.3.2 iterators 1.0.13 R6 2.5.0 MALDIquant 1.19.3 compiler 4.0.5 | |
| ARGUMENTS INFO | |
| image /tmp/tmpni2hmxgh/files/0/8/9/dataset_0894a220-d002-40d1-a0fa-0f8f10a25ea3.dat | |
| BPPARAM 1 | |
| method CentWave | |
| ppm 3 | |
| peakwidth c(5, 20) | |
| snthresh 10 | |
| prefilter c(3, 5000) | |
| mzCenterFun wMean | |
| integrate 1 | |
| mzdiff -0.001 | |
| fitgauss FALSE | |
| noise 1000 | |
| verboseColumns FALSE | |
| peaklist FALSE | |
| ARGUMENTS PROCESSING INFO | |
| INFILE PROCESSING INFO | |
| MAIN PROCESSING INFO | |
| COMPUTE | |
| Apply filter[s] (if asked) | |
| Chromatographic peak detection | |
| Object of class: CentWaveParam | |
| Parameters: | |
| ppm: 3 | |
| peakwidth: 5, 20 | |
| snthresh: 10 | |
| prefilter: 3, 5000 | |
| mzCenterFun: wMean | |
| integrate: 1 | |
| mzdiff: -0.001 | |
| fitgauss: FALSE | |
| noise: 1000 | |
| verboseColumns: FALSE | |
| roiList length: 0 | |
| firstBaselineCheck TRUE | |
| roiScales length: 0 | |
| Creating the sampleMetadata file... | |
| Error in R_nc4_open: NetCDF: Unknown file format | |
| XCMSnExp OBJECT INFO | |
| MSn experiment data ("XCMSnExp") | |
| Object size in memory: 0.67 Mb | |
| - - - Spectra data - - - | |
| MS level(s): 1 | |
| Number of spectra: 1710 | |
| MSn retention times: 0:1 - 18:60 minutes | |
| - - - Processing information - - - | |
| Data loaded [Tue Feb 24 07:03:02 2026] | |
| MSnbase version: 2.16.1 | |
| - - - Meta data - - - | |
| phenoData | |
| rowNames: HU_neg_173.mzML | |
| varLabels: sample_name sample_group | |
| varMetadata: labelDescription | |
| Loaded from: | |
| HU_neg_173.mzML | |
| protocolData: none | |
| featureData | |
| featureNames: F1.S0001 F1.S0002 ... F1.S1710 (1710 total) | |
| fvarLabels: fileIdx spIdx ... spectrum (35 total) | |
| fvarMetadata: labelDescription | |
| experimentData: use 'experimentData(object)' | |
| - - - xcms preprocessing - - - | |
| Chromatographic peak detection: | |
| method: centWave | |
| 3051 peaks identified in 1 samples. | |
| On average 3051 chromatographic peaks per sample. | |
| xcmsSet OBJECT INFO | |
| An "xcmsSet" object with 1 samples | |
| Time range: 4.4-1139.2 seconds (0.1-19 minutes) | |
| Mass range: 50.0321-774.0387 m/z | |
| Peaks: 3051 (about 3051 per sample) | |
| Peak Groups: 0 | |
| Sample classes: . | |
| Feature detection: | |
| o Peak picking performed on MS1. | |
| o Scan range limited to 1 - 1710 | |
| Profile settings: method = bin | |
| step = 0.1 | |
| Memory usage: 0.718 MB | |
| DONE | |
| ``` | |
| **Traceback:** | |
| * ```console | |
| ``` | |
| **Job Parameters:** | |
| * | Job parameter | Parameter value | | |
| | ------------- | --------------- | | |
| | \_\_input\_ext | ` "input" ` | | |
| | \_\_workflow\_invocation\_uuid\_\_ | ` "b39b8d62114e11f189517ced8d633c14" ` | | |
| | chromInfo | ` "/tmp/tmpni2hmxgh/galaxy-dev/tool-data/shared/ucsc/chrom/?.len" ` | | |
| | dbkey | ` "?" ` | | |
| | file\_load\_section | ` {"file_load_conditional": {"__current_case__": 0, "file_load_select": "no"}} ` | | |
| | filterSection | ` {"filterAcquisitionNum": "", "filterMz": "", "filterRt": ""} ` | | |
| | methods | ` {"CentWaveAdv": {"CentWaveAdvROI": {"firstBaselineCheck": true, "roiList": null, "roiScales": ""}, "fitgauss": false, "integrate": "1", "mzCenterFun": "wMean", "mzdiff": "-0.001", "noise": "1000", "peaklist": false, "prefilter": "3,5000", "snthresh": "10", "verboseColumns": false}, "__current_case__": 0, "method": "CentWave", "peakwidth": "5,20", "ppm": "3.0"} ` | | |
| - **Job 2:** | |
| * Job state is ok | |
| **Container:** | |
| * ```console | |
| quay.io/biocontainers/mulled-v2-007db2e42e47018763bae6b2bd1e69345120fe7f:ffab248635d36a246a435f3341c896269df9943c-2 | |
| ``` | |
| **Command Line:** | |
| * ```console | |
| LC_ALL=C Rscript /tmp/shed_dir/toolshed.g2.bx.psu.edu/repos/lecorguille/xcms_xcmsset/3990a65b45a4/xcms_xcmsset/xcms_xcmsSet.r image '/tmp/tmpni2hmxgh/files/2/5/9/dataset_2598e943-3223-4009-beb6-78b89dd9375d.dat' BPPARAM ${GALAXY_SLOTS:-1} method CentWave ppm 3.0 peakwidth "c(5,20)" snthresh 10 prefilter "c(3,5000)" mzCenterFun wMean integrate 1 mzdiff -0.001 fitgauss FALSE noise 1000 verboseColumns FALSE peaklist FALSE ; return=$?; cat 'log.txt'; sh -c "exit $return" | |
| ``` | |
| **Exit Code:** | |
| * ```console | |
| 0 | |
| ``` | |
| **Standard Error:** | |
| * ```console | |
| Detecting mass traces at 3 ppm ... OK | |
| Detecting chromatographic peaks in 7872 regions of interest ... OK: 3881 found. | |
| Note: you might want to set/adjust the 'sampclass' of the returned xcmSet object before proceeding with the analysis. | |
| ``` | |
| **Standard Output:** | |
| * ```console | |
| SESSION INFO | |
| R version 4.0.5 (2021-03-31) | |
| Main packages: | |
| batch 1.1.5 xcms 3.12.0 MSnbase 2.16.1 ProtGenerics 1.22.0 S4Vectors 0.28.1 mzR 2.24.1 Rcpp 1.0.6 BiocParallel 1.24.1 Biobase 2.50.0 BiocGenerics 0.36.0 | |
| Other loaded packages: | |
| SummarizedExperiment 1.20.0 lattice 0.20.44 colorspace 2.0.1 vctrs 0.3.8 vsn 3.58.0 utf8 1.2.1 XML 3.99.0.6 rlang 0.4.11 pillar 1.6.0 glue 1.4.2 affy 1.68.0 RColorBrewer 1.1.2 affyio 1.60.0 matrixStats 0.58.0 GenomeInfoDbData 1.2.4 foreach 1.5.1 lifecycle 1.0.0 plyr 1.8.6 mzID 1.28.0 robustbase 0.93.7 zlibbioc 1.36.0 MatrixGenerics 1.2.1 munsell 0.5.0 pcaMethods 1.82.0 gtable 0.3.0 codetools 0.2.18 IRanges 2.24.1 doParallel 1.0.16 GenomeInfoDb 1.26.4 MassSpecWavelet 1.56.0 fansi 0.4.2 preprocessCore 1.52.1 DEoptimR 1.0.8 scales 1.1.1 BiocManager 1.30.15 DelayedArray 0.16.3 limma 3.46.0 XVector 0.30.0 MsCoreUtils 1.2.0 RANN 2.6.1 impute 1.64.0 ggplot2 3.3.3 digest 0.6.27 ncdf4 1.17 GenomicRanges 1.42.0 grid 4.0.5 tools 4.0.5 bitops 1.0.7 magrittr 2.0.1 RCurl 1.98.1.3 tibble 3.1.1 crayon 1.4.1 pkgconfig 2.0.3 Matrix 1.3.2 MASS 7.3.54 ellipsis 0.3.2 iterators 1.0.13 R6 2.5.0 MALDIquant 1.19.3 compiler 4.0.5 | |
| ARGUMENTS INFO | |
| image /tmp/tmpni2hmxgh/files/2/5/9/dataset_2598e943-3223-4009-beb6-78b89dd9375d.dat | |
| BPPARAM 1 | |
| method CentWave | |
| ppm 3 | |
| peakwidth c(5, 20) | |
| snthresh 10 | |
| prefilter c(3, 5000) | |
| mzCenterFun wMean | |
| integrate 1 | |
| mzdiff -0.001 | |
| fitgauss FALSE | |
| noise 1000 | |
| verboseColumns FALSE | |
| peaklist FALSE | |
| ARGUMENTS PROCESSING INFO | |
| INFILE PROCESSING INFO | |
| MAIN PROCESSING INFO | |
| COMPUTE | |
| Apply filter[s] (if asked) | |
| Chromatographic peak detection | |
| Object of class: CentWaveParam | |
| Parameters: | |
| ppm: 3 | |
| peakwidth: 5, 20 | |
| snthresh: 10 | |
| prefilter: 3, 5000 | |
| mzCenterFun: wMean | |
| integrate: 1 | |
| mzdiff: -0.001 | |
| fitgauss: FALSE | |
| noise: 1000 | |
| verboseColumns: FALSE | |
| roiList length: 0 | |
| firstBaselineCheck TRUE | |
| roiScales length: 0 | |
| Creating the sampleMetadata file... | |
| Error in R_nc4_open: NetCDF: Unknown file format | |
| XCMSnExp OBJECT INFO | |
| MSn experiment data ("XCMSnExp") | |
| Object size in memory: 0.73 Mb | |
| - - - Spectra data - - - | |
| MS level(s): 1 | |
| Number of spectra: 1879 | |
| MSn retention times: 0:1 - 18:60 minutes | |
| - - - Processing information - - - | |
| Data loaded [Tue Feb 24 07:03:18 2026] | |
| MSnbase version: 2.16.1 | |
| - - - Meta data - - - | |
| phenoData | |
| rowNames: QC1_008.mzML | |
| varLabels: sample_name sample_group | |
| varMetadata: labelDescription | |
| Loaded from: | |
| QC1_008.mzML | |
| protocolData: none | |
| featureData | |
| featureNames: F1.S0001 F1.S0002 ... F1.S1879 (1879 total) | |
| fvarLabels: fileIdx spIdx ... spectrum (35 total) | |
| fvarMetadata: labelDescription | |
| experimentData: use 'experimentData(object)' | |
| - - - xcms preprocessing - - - | |
| Chromatographic peak detection: | |
| method: centWave | |
| 3881 peaks identified in 1 samples. | |
| On average 3881 chromatographic peaks per sample. | |
| xcmsSet OBJECT INFO | |
| An "xcmsSet" object with 1 samples | |
| Time range: 2-1139.3 seconds (0-19 minutes) | |
| Mass range: 50.0321-987.0559 m/z | |
| Peaks: 3881 (about 3881 per sample) | |
| Peak Groups: 0 | |
| Sample classes: . | |
| Feature detection: | |
| o Peak picking performed on MS1. | |
| o Scan range limited to 1 - 1879 | |
| Profile settings: method = bin | |
| step = 0.1 | |
| Memory usage: 0.864 MB | |
| DONE | |
| ``` | |
| **Traceback:** | |
| * ```console | |
| ``` | |
| **Job Parameters:** | |
| * | Job parameter | Parameter value | | |
| | ------------- | --------------- | | |
| | \_\_input\_ext | ` "input" ` | | |
| | \_\_workflow\_invocation\_uuid\_\_ | ` "b39b8d62114e11f189517ced8d633c14" ` | | |
| | chromInfo | ` "/tmp/tmpni2hmxgh/galaxy-dev/tool-data/shared/ucsc/chrom/?.len" ` | | |
| | dbkey | ` "?" ` | | |
| | file\_load\_section | ` {"file_load_conditional": {"__current_case__": 0, "file_load_select": "no"}} ` | | |
| | filterSection | ` {"filterAcquisitionNum": "", "filterMz": "", "filterRt": ""} ` | | |
| | methods | ` {"CentWaveAdv": {"CentWaveAdvROI": {"firstBaselineCheck": true, "roiList": null, "roiScales": ""}, "fitgauss": false, "integrate": "1", "mzCenterFun": "wMean", "mzdiff": "-0.001", "noise": "1000", "peaklist": false, "prefilter": "3,5000", "snthresh": "10", "verboseColumns": false}, "__current_case__": 0, "method": "CentWave", "peakwidth": "5,20", "ppm": "3.0"} ` | | |
| - **Job 3:** | |
| * Job state is ok | |
| **Container:** | |
| * ```console | |
| quay.io/biocontainers/mulled-v2-007db2e42e47018763bae6b2bd1e69345120fe7f:ffab248635d36a246a435f3341c896269df9943c-2 | |
| ``` | |
| **Command Line:** | |
| * ```console | |
| LC_ALL=C Rscript /tmp/shed_dir/toolshed.g2.bx.psu.edu/repos/lecorguille/xcms_xcmsset/3990a65b45a4/xcms_xcmsset/xcms_xcmsSet.r image '/tmp/tmpni2hmxgh/files/b/3/f/dataset_b3f6d71d-e5d0-4943-9aa1-22f92575fcd1.dat' BPPARAM ${GALAXY_SLOTS:-1} method CentWave ppm 3.0 peakwidth "c(5,20)" snthresh 10 prefilter "c(3,5000)" mzCenterFun wMean integrate 1 mzdiff -0.001 fitgauss FALSE noise 1000 verboseColumns FALSE peaklist FALSE ; return=$?; cat 'log.txt'; sh -c "exit $return" | |
| ``` | |
| **Exit Code:** | |
| * ```console | |
| 0 | |
| ``` | |
| **Standard Error:** | |
| * ```console | |
| Detecting mass traces at 3 ppm ... OK | |
| Detecting chromatographic peaks in 5007 regions of interest ... OK: 3599 found. | |
| Note: you might want to set/adjust the 'sampclass' of the returned xcmSet object before proceeding with the analysis. | |
| ``` | |
| **Standard Output:** | |
| * ```console | |
| SESSION INFO | |
| R version 4.0.5 (2021-03-31) | |
| Main packages: | |
| batch 1.1.5 xcms 3.12.0 MSnbase 2.16.1 ProtGenerics 1.22.0 S4Vectors 0.28.1 mzR 2.24.1 Rcpp 1.0.6 BiocParallel 1.24.1 Biobase 2.50.0 BiocGenerics 0.36.0 | |
| Other loaded packages: | |
| SummarizedExperiment 1.20.0 lattice 0.20.44 colorspace 2.0.1 vctrs 0.3.8 vsn 3.58.0 utf8 1.2.1 XML 3.99.0.6 rlang 0.4.11 pillar 1.6.0 glue 1.4.2 affy 1.68.0 RColorBrewer 1.1.2 affyio 1.60.0 matrixStats 0.58.0 GenomeInfoDbData 1.2.4 foreach 1.5.1 lifecycle 1.0.0 plyr 1.8.6 mzID 1.28.0 robustbase 0.93.7 zlibbioc 1.36.0 MatrixGenerics 1.2.1 munsell 0.5.0 pcaMethods 1.82.0 gtable 0.3.0 codetools 0.2.18 IRanges 2.24.1 doParallel 1.0.16 GenomeInfoDb 1.26.4 MassSpecWavelet 1.56.0 fansi 0.4.2 preprocessCore 1.52.1 DEoptimR 1.0.8 scales 1.1.1 BiocManager 1.30.15 DelayedArray 0.16.3 limma 3.46.0 XVector 0.30.0 MsCoreUtils 1.2.0 RANN 2.6.1 impute 1.64.0 ggplot2 3.3.3 digest 0.6.27 ncdf4 1.17 GenomicRanges 1.42.0 grid 4.0.5 tools 4.0.5 bitops 1.0.7 magrittr 2.0.1 RCurl 1.98.1.3 tibble 3.1.1 crayon 1.4.1 pkgconfig 2.0.3 Matrix 1.3.2 MASS 7.3.54 ellipsis 0.3.2 iterators 1.0.13 R6 2.5.0 MALDIquant 1.19.3 compiler 4.0.5 | |
| ARGUMENTS INFO | |
| image /tmp/tmpni2hmxgh/files/b/3/f/dataset_b3f6d71d-e5d0-4943-9aa1-22f92575fcd1.dat | |
| BPPARAM 1 | |
| method CentWave | |
| ppm 3 | |
| peakwidth c(5, 20) | |
| snthresh 10 | |
| prefilter c(3, 5000) | |
| mzCenterFun wMean | |
| integrate 1 | |
| mzdiff -0.001 | |
| fitgauss FALSE | |
| noise 1000 | |
| verboseColumns FALSE | |
| peaklist FALSE | |
| ARGUMENTS PROCESSING INFO | |
| INFILE PROCESSING INFO | |
| MAIN PROCESSING INFO | |
| COMPUTE | |
| Apply filter[s] (if asked) | |
| Chromatographic peak detection | |
| Object of class: CentWaveParam | |
| Parameters: | |
| ppm: 3 | |
| peakwidth: 5, 20 | |
| snthresh: 10 | |
| prefilter: 3, 5000 | |
| mzCenterFun: wMean | |
| integrate: 1 | |
| mzdiff: -0.001 | |
| fitgauss: FALSE | |
| noise: 1000 | |
| verboseColumns: FALSE | |
| roiList length: 0 | |
| firstBaselineCheck TRUE | |
| roiScales length: 0 | |
| Creating the sampleMetadata file... | |
| Error in R_nc4_open: NetCDF: Unknown file format | |
| XCMSnExp OBJECT INFO | |
| MSn experiment data ("XCMSnExp") | |
| Object size in memory: 0.6 Mb | |
| - - - Spectra data - - - | |
| MS level(s): 1 | |
| Number of spectra: 1533 | |
| MSn retention times: 0:1 - 18:60 minutes | |
| - - - Processing information - - - | |
| Data loaded [Tue Feb 24 07:03:18 2026] | |
| MSnbase version: 2.16.1 | |
| - - - Meta data - - - | |
| phenoData | |
| rowNames: QC1_014.mzML | |
| varLabels: sample_name sample_group | |
| varMetadata: labelDescription | |
| Loaded from: | |
| QC1_014.mzML | |
| protocolData: none | |
| featureData | |
| featureNames: F1.S0001 F1.S0002 ... F1.S1533 (1533 total) | |
| fvarLabels: fileIdx spIdx ... spectrum (35 total) | |
| fvarMetadata: labelDescription | |
| experimentData: use 'experimentData(object)' | |
| - - - xcms preprocessing - - - | |
| Chromatographic peak detection: | |
| method: centWave | |
| 3599 peaks identified in 1 samples. | |
| On average 3599 chromatographic peaks per sample. | |
| xcmsSet OBJECT INFO | |
| An "xcmsSet" object with 1 samples | |
| Time range: 2.1-1138.8 seconds (0-19 minutes) | |
| Mass range: 50.0321-963.0639 m/z | |
| Peaks: 3599 (about 3599 per sample) | |
| Peak Groups: 0 | |
| Sample classes: . | |
| Feature detection: | |
| o Peak picking performed on MS1. | |
| o Scan range limited to 1 - 1533 | |
| Profile settings: method = bin | |
| step = 0.1 | |
| Memory usage: 0.77 MB | |
| DONE | |
| ``` | |
| **Traceback:** | |
| * ```console | |
| ``` | |
| **Job Parameters:** | |
| * | Job parameter | Parameter value | | |
| | ------------- | --------------- | | |
| | \_\_input\_ext | ` "input" ` | | |
| | \_\_workflow\_invocation\_uuid\_\_ | ` "b39b8d62114e11f189517ced8d633c14" ` | | |
| | chromInfo | ` "/tmp/tmpni2hmxgh/galaxy-dev/tool-data/shared/ucsc/chrom/?.len" ` | | |
| | dbkey | ` "?" ` | | |
| | file\_load\_section | ` {"file_load_conditional": {"__current_case__": 0, "file_load_select": "no"}} ` | | |
| | filterSection | ` {"filterAcquisitionNum": "", "filterMz": "", "filterRt": ""} ` | | |
| | methods | ` {"CentWaveAdv": {"CentWaveAdvROI": {"firstBaselineCheck": true, "roiList": null, "roiScales": ""}, "fitgauss": false, "integrate": "1", "mzCenterFun": "wMean", "mzdiff": "-0.001", "noise": "1000", "peaklist": false, "prefilter": "3,5000", "snthresh": "10", "verboseColumns": false}, "__current_case__": 0, "method": "CentWave", "peakwidth": "5,20", "ppm": "3.0"} ` | | |
| - **Job 4:** | |
| * Job state is ok | |
| **Container:** | |
| * ```console | |
| quay.io/biocontainers/mulled-v2-007db2e42e47018763bae6b2bd1e69345120fe7f:ffab248635d36a246a435f3341c896269df9943c-2 | |
| ``` | |
| **Command Line:** | |
| * ```console | |
| LC_ALL=C Rscript /tmp/shed_dir/toolshed.g2.bx.psu.edu/repos/lecorguille/xcms_xcmsset/3990a65b45a4/xcms_xcmsset/xcms_xcmsSet.r image '/tmp/tmpni2hmxgh/files/c/b/6/dataset_cb63844d-f873-4bdb-8068-efd5f971c4c9.dat' BPPARAM ${GALAXY_SLOTS:-1} method CentWave ppm 3.0 peakwidth "c(5,20)" snthresh 10 prefilter "c(3,5000)" mzCenterFun wMean integrate 1 mzdiff -0.001 fitgauss FALSE noise 1000 verboseColumns FALSE peaklist FALSE ; return=$?; cat 'log.txt'; sh -c "exit $return" | |
| ``` | |
| **Exit Code:** | |
| * ```console | |
| 0 | |
| ``` | |
| **Standard Error:** | |
| * ```console | |
| Detecting mass traces at 3 ppm ... OK | |
| Detecting chromatographic peaks in 8869 regions of interest ... OK: 3343 found. | |
| Note: you might want to set/adjust the 'sampclass' of the returned xcmSet object before proceeding with the analysis. | |
| ``` | |
| **Standard Output:** | |
| * ```console | |
| SESSION INFO | |
| R version 4.0.5 (2021-03-31) | |
| Main packages: | |
| batch 1.1.5 xcms 3.12.0 MSnbase 2.16.1 ProtGenerics 1.22.0 S4Vectors 0.28.1 mzR 2.24.1 Rcpp 1.0.6 BiocParallel 1.24.1 Biobase 2.50.0 BiocGenerics 0.36.0 | |
| Other loaded packages: | |
| SummarizedExperiment 1.20.0 lattice 0.20.44 colorspace 2.0.1 vctrs 0.3.8 vsn 3.58.0 utf8 1.2.1 XML 3.99.0.6 rlang 0.4.11 pillar 1.6.0 glue 1.4.2 affy 1.68.0 RColorBrewer 1.1.2 affyio 1.60.0 matrixStats 0.58.0 GenomeInfoDbData 1.2.4 foreach 1.5.1 lifecycle 1.0.0 plyr 1.8.6 mzID 1.28.0 robustbase 0.93.7 zlibbioc 1.36.0 MatrixGenerics 1.2.1 munsell 0.5.0 pcaMethods 1.82.0 gtable 0.3.0 codetools 0.2.18 IRanges 2.24.1 doParallel 1.0.16 GenomeInfoDb 1.26.4 MassSpecWavelet 1.56.0 fansi 0.4.2 preprocessCore 1.52.1 DEoptimR 1.0.8 scales 1.1.1 BiocManager 1.30.15 DelayedArray 0.16.3 limma 3.46.0 XVector 0.30.0 MsCoreUtils 1.2.0 RANN 2.6.1 impute 1.64.0 ggplot2 3.3.3 digest 0.6.27 ncdf4 1.17 GenomicRanges 1.42.0 grid 4.0.5 tools 4.0.5 bitops 1.0.7 magrittr 2.0.1 RCurl 1.98.1.3 tibble 3.1.1 crayon 1.4.1 pkgconfig 2.0.3 Matrix 1.3.2 MASS 7.3.54 ellipsis 0.3.2 iterators 1.0.13 R6 2.5.0 MALDIquant 1.19.3 compiler 4.0.5 | |
| ARGUMENTS INFO | |
| image /tmp/tmpni2hmxgh/files/c/b/6/dataset_cb63844d-f873-4bdb-8068-efd5f971c4c9.dat | |
| BPPARAM 1 | |
| method CentWave | |
| ppm 3 | |
| peakwidth c(5, 20) | |
| snthresh 10 | |
| prefilter c(3, 5000) | |
| mzCenterFun wMean | |
| integrate 1 | |
| mzdiff -0.001 | |
| fitgauss FALSE | |
| noise 1000 | |
| verboseColumns FALSE | |
| peaklist FALSE | |
| ARGUMENTS PROCESSING INFO | |
| INFILE PROCESSING INFO | |
| MAIN PROCESSING INFO | |
| COMPUTE | |
| Apply filter[s] (if asked) | |
| Chromatographic peak detection | |
| Object of class: CentWaveParam | |
| Parameters: | |
| ppm: 3 | |
| peakwidth: 5, 20 | |
| snthresh: 10 | |
| prefilter: 3, 5000 | |
| mzCenterFun: wMean | |
| integrate: 1 | |
| mzdiff: -0.001 | |
| fitgauss: FALSE | |
| noise: 1000 | |
| verboseColumns: FALSE | |
| roiList length: 0 | |
| firstBaselineCheck TRUE | |
| roiScales length: 0 | |
| Creating the sampleMetadata file... | |
| Error in R_nc4_open: NetCDF: Unknown file format | |
| XCMSnExp OBJECT INFO | |
| MSn experiment data ("XCMSnExp") | |
| Object size in memory: 0.78 Mb | |
| - - - Spectra data - - - | |
| MS level(s): 1 | |
| Number of spectra: 2031 | |
| MSn retention times: 0:1 - 18:60 minutes | |
| - - - Processing information - - - | |
| Data loaded [Tue Feb 24 07:03:34 2026] | |
| MSnbase version: 2.16.1 | |
| - - - Meta data - - - | |
| phenoData | |
| rowNames: HU_neg_048.mzML | |
| varLabels: sample_name sample_group | |
| varMetadata: labelDescription | |
| Loaded from: | |
| HU_neg_048.mzML | |
| protocolData: none | |
| featureData | |
| featureNames: F1.S0001 F1.S0002 ... F1.S2031 (2031 total) | |
| fvarLabels: fileIdx spIdx ... spectrum (35 total) | |
| fvarMetadata: labelDescription | |
| experimentData: use 'experimentData(object)' | |
| - - - xcms preprocessing - - - | |
| Chromatographic peak detection: | |
| method: centWave | |
| 3343 peaks identified in 1 samples. | |
| On average 3343 chromatographic peaks per sample. | |
| xcmsSet OBJECT INFO | |
| An "xcmsSet" object with 1 samples | |
| Time range: 10.2-1139.3 seconds (0.2-19 minutes) | |
| Mass range: 50.0321-988.5896 m/z | |
| Peaks: 3343 (about 3343 per sample) | |
| Peak Groups: 0 | |
| Sample classes: . | |
| Feature detection: | |
| o Peak picking performed on MS1. | |
| o Scan range limited to 1 - 2031 | |
| Profile settings: method = bin | |
| step = 0.1 | |
| Memory usage: 0.809 MB | |
| DONE | |
| ``` | |
| **Traceback:** | |
| * ```console | |
| ``` | |
| **Job Parameters:** | |
| * | Job parameter | Parameter value | | |
| | ------------- | --------------- | | |
| | \_\_input\_ext | ` "input" ` | | |
| | \_\_workflow\_invocation\_uuid\_\_ | ` "b39b8d62114e11f189517ced8d633c14" ` | | |
| | chromInfo | ` "/tmp/tmpni2hmxgh/galaxy-dev/tool-data/shared/ucsc/chrom/?.len" ` | | |
| | dbkey | ` "?" ` | | |
| | file\_load\_section | ` {"file_load_conditional": {"__current_case__": 0, "file_load_select": "no"}} ` | | |
| | filterSection | ` {"filterAcquisitionNum": "", "filterMz": "", "filterRt": ""} ` | | |
| | methods | ` {"CentWaveAdv": {"CentWaveAdvROI": {"firstBaselineCheck": true, "roiList": null, "roiScales": ""}, "fitgauss": false, "integrate": "1", "mzCenterFun": "wMean", "mzdiff": "-0.001", "noise": "1000", "peaklist": false, "prefilter": "3,5000", "snthresh": "10", "verboseColumns": false}, "__current_case__": 0, "method": "CentWave", "peakwidth": "5,20", "ppm": "3.0"} ` | | |
| - **Job 5:** | |
| * Job state is ok | |
| **Container:** | |
| * ```console | |
| quay.io/biocontainers/mulled-v2-007db2e42e47018763bae6b2bd1e69345120fe7f:ffab248635d36a246a435f3341c896269df9943c-2 | |
| ``` | |
| **Command Line:** | |
| * ```console | |
| LC_ALL=C Rscript /tmp/shed_dir/toolshed.g2.bx.psu.edu/repos/lecorguille/xcms_xcmsset/3990a65b45a4/xcms_xcmsset/xcms_xcmsSet.r image '/tmp/tmpni2hmxgh/files/c/5/7/dataset_c576fbfb-5cc5-478d-8512-776dc069f519.dat' BPPARAM ${GALAXY_SLOTS:-1} method CentWave ppm 3.0 peakwidth "c(5,20)" snthresh 10 prefilter "c(3,5000)" mzCenterFun wMean integrate 1 mzdiff -0.001 fitgauss FALSE noise 1000 verboseColumns FALSE peaklist FALSE ; return=$?; cat 'log.txt'; sh -c "exit $return" | |
| ``` | |
| **Exit Code:** | |
| * ```console | |
| 0 | |
| ``` | |
| **Standard Error:** | |
| * ```console | |
| Detecting mass traces at 3 ppm ... OK | |
| Detecting chromatographic peaks in 7597 regions of interest ... OK: 3408 found. | |
| Note: you might want to set/adjust the 'sampclass' of the returned xcmSet object before proceeding with the analysis. | |
| ``` | |
| **Standard Output:** | |
| * ```console | |
| SESSION INFO | |
| R version 4.0.5 (2021-03-31) | |
| Main packages: | |
| batch 1.1.5 xcms 3.12.0 MSnbase 2.16.1 ProtGenerics 1.22.0 S4Vectors 0.28.1 mzR 2.24.1 Rcpp 1.0.6 BiocParallel 1.24.1 Biobase 2.50.0 BiocGenerics 0.36.0 | |
| Other loaded packages: | |
| SummarizedExperiment 1.20.0 lattice 0.20.44 colorspace 2.0.1 vctrs 0.3.8 vsn 3.58.0 utf8 1.2.1 XML 3.99.0.6 rlang 0.4.11 pillar 1.6.0 glue 1.4.2 affy 1.68.0 RColorBrewer 1.1.2 affyio 1.60.0 matrixStats 0.58.0 GenomeInfoDbData 1.2.4 foreach 1.5.1 lifecycle 1.0.0 plyr 1.8.6 mzID 1.28.0 robustbase 0.93.7 zlibbioc 1.36.0 MatrixGenerics 1.2.1 munsell 0.5.0 pcaMethods 1.82.0 gtable 0.3.0 codetools 0.2.18 IRanges 2.24.1 doParallel 1.0.16 GenomeInfoDb 1.26.4 MassSpecWavelet 1.56.0 fansi 0.4.2 preprocessCore 1.52.1 DEoptimR 1.0.8 scales 1.1.1 BiocManager 1.30.15 DelayedArray 0.16.3 limma 3.46.0 XVector 0.30.0 MsCoreUtils 1.2.0 RANN 2.6.1 impute 1.64.0 ggplot2 3.3.3 digest 0.6.27 ncdf4 1.17 GenomicRanges 1.42.0 grid 4.0.5 tools 4.0.5 bitops 1.0.7 magrittr 2.0.1 RCurl 1.98.1.3 tibble 3.1.1 crayon 1.4.1 pkgconfig 2.0.3 Matrix 1.3.2 MASS 7.3.54 ellipsis 0.3.2 iterators 1.0.13 R6 2.5.0 MALDIquant 1.19.3 compiler 4.0.5 | |
| ARGUMENTS INFO | |
| image /tmp/tmpni2hmxgh/files/c/5/7/dataset_c576fbfb-5cc5-478d-8512-776dc069f519.dat | |
| BPPARAM 1 | |
| method CentWave | |
| ppm 3 | |
| peakwidth c(5, 20) | |
| snthresh 10 | |
| prefilter c(3, 5000) | |
| mzCenterFun wMean | |
| integrate 1 | |
| mzdiff -0.001 | |
| fitgauss FALSE | |
| noise 1000 | |
| verboseColumns FALSE | |
| peaklist FALSE | |
| ARGUMENTS PROCESSING INFO | |
| INFILE PROCESSING INFO | |
| MAIN PROCESSING INFO | |
| COMPUTE | |
| Apply filter[s] (if asked) | |
| Chromatographic peak detection | |
| Object of class: CentWaveParam | |
| Parameters: | |
| ppm: 3 | |
| peakwidth: 5, 20 | |
| snthresh: 10 | |
| prefilter: 3, 5000 | |
| mzCenterFun: wMean | |
| integrate: 1 | |
| mzdiff: -0.001 | |
| fitgauss: FALSE | |
| noise: 1000 | |
| verboseColumns: FALSE | |
| roiList length: 0 | |
| firstBaselineCheck TRUE | |
| roiScales length: 0 | |
| Creating the sampleMetadata file... | |
| Error in R_nc4_open: NetCDF: Unknown file format | |
| XCMSnExp OBJECT INFO | |
| MSn experiment data ("XCMSnExp") | |
| Object size in memory: 0.73 Mb | |
| - - - Spectra data - - - | |
| MS level(s): 1 | |
| Number of spectra: 1892 | |
| MSn retention times: 0:1 - 18:60 minutes | |
| - - - Processing information - - - | |
| Data loaded [Tue Feb 24 07:03:35 2026] | |
| MSnbase version: 2.16.1 | |
| - - - Meta data - - - | |
| phenoData | |
| rowNames: HU_neg_123.mzML | |
| varLabels: sample_name sample_group | |
| varMetadata: labelDescription | |
| Loaded from: | |
| HU_neg_123.mzML | |
| protocolData: none | |
| featureData | |
| featureNames: F1.S0001 F1.S0002 ... F1.S1892 (1892 total) | |
| fvarLabels: fileIdx spIdx ... spectrum (35 total) | |
| fvarMetadata: labelDescription | |
| experimentData: use 'experimentData(object)' | |
| - - - xcms preprocessing - - - | |
| Chromatographic peak detection: | |
| method: centWave | |
| 3408 peaks identified in 1 samples. | |
| On average 3408 chromatographic peaks per sample. | |
| xcmsSet OBJECT INFO | |
| An "xcmsSet" object with 1 samples | |
| Time range: 6-1136 seconds (0.1-18.9 minutes) | |
| Mass range: 50.0321-963.0516 m/z | |
| Peaks: 3408 (about 3408 per sample) | |
| Peak Groups: 0 | |
| Sample classes: . | |
| Feature detection: | |
| o Peak picking performed on MS1. | |
| o Scan range limited to 1 - 1892 | |
| Profile settings: method = bin | |
| step = 0.1 | |
| Memory usage: 0.797 MB | |
| DONE | |
| ``` | |
| **Traceback:** | |
| * ```console | |
| ``` | |
| **Job Parameters:** | |
| * | Job parameter | Parameter value | | |
| | ------------- | --------------- | | |
| | \_\_input\_ext | ` "input" ` | | |
| | \_\_workflow\_invocation\_uuid\_\_ | ` "b39b8d62114e11f189517ced8d633c14" ` | | |
| | chromInfo | ` "/tmp/tmpni2hmxgh/galaxy-dev/tool-data/shared/ucsc/chrom/?.len" ` | | |
| | dbkey | ` "?" ` | | |
| | file\_load\_section | ` {"file_load_conditional": {"__current_case__": 0, "file_load_select": "no"}} ` | | |
| | filterSection | ` {"filterAcquisitionNum": "", "filterMz": "", "filterRt": ""} ` | | |
| | methods | ` {"CentWaveAdv": {"CentWaveAdvROI": {"firstBaselineCheck": true, "roiList": null, "roiScales": ""}, "fitgauss": false, "integrate": "1", "mzCenterFun": "wMean", "mzdiff": "-0.001", "noise": "1000", "peaklist": false, "prefilter": "3,5000", "snthresh": "10", "verboseColumns": false}, "__current_case__": 0, "method": "CentWave", "peakwidth": "5,20", "ppm": "3.0"} ` | | |
| - **Job 6:** | |
| * Job state is ok | |
| **Container:** | |
| * ```console | |
| quay.io/biocontainers/mulled-v2-007db2e42e47018763bae6b2bd1e69345120fe7f:ffab248635d36a246a435f3341c896269df9943c-2 | |
| ``` | |
| **Command Line:** | |
| * ```console | |
| LC_ALL=C Rscript /tmp/shed_dir/toolshed.g2.bx.psu.edu/repos/lecorguille/xcms_xcmsset/3990a65b45a4/xcms_xcmsset/xcms_xcmsSet.r image '/tmp/tmpni2hmxgh/files/3/0/2/dataset_30226968-a841-44ff-91f2-2ec68d035d57.dat' BPPARAM ${GALAXY_SLOTS:-1} method CentWave ppm 3.0 peakwidth "c(5,20)" snthresh 10 prefilter "c(3,5000)" mzCenterFun wMean integrate 1 mzdiff -0.001 fitgauss FALSE noise 1000 verboseColumns FALSE peaklist FALSE ; return=$?; cat 'log.txt'; sh -c "exit $return" | |
| ``` | |
| **Exit Code:** | |
| * ```console | |
| 0 | |
| ``` | |
| **Standard Error:** | |
| * ```console | |
| Detecting mass traces at 3 ppm ... OK | |
| Detecting chromatographic peaks in 6293 regions of interest ... OK: 4264 found. | |
| Note: you might want to set/adjust the 'sampclass' of the returned xcmSet object before proceeding with the analysis. | |
| ``` | |
| **Standard Output:** | |
| * ```console | |
| SESSION INFO | |
| R version 4.0.5 (2021-03-31) | |
| Main packages: | |
| batch 1.1.5 xcms 3.12.0 MSnbase 2.16.1 ProtGenerics 1.22.0 S4Vectors 0.28.1 mzR 2.24.1 Rcpp 1.0.6 BiocParallel 1.24.1 Biobase 2.50.0 BiocGenerics 0.36.0 | |
| Other loaded packages: | |
| SummarizedExperiment 1.20.0 lattice 0.20.44 colorspace 2.0.1 vctrs 0.3.8 vsn 3.58.0 utf8 1.2.1 XML 3.99.0.6 rlang 0.4.11 pillar 1.6.0 glue 1.4.2 affy 1.68.0 RColorBrewer 1.1.2 affyio 1.60.0 matrixStats 0.58.0 GenomeInfoDbData 1.2.4 foreach 1.5.1 lifecycle 1.0.0 plyr 1.8.6 mzID 1.28.0 robustbase 0.93.7 zlibbioc 1.36.0 MatrixGenerics 1.2.1 munsell 0.5.0 pcaMethods 1.82.0 gtable 0.3.0 codetools 0.2.18 IRanges 2.24.1 doParallel 1.0.16 GenomeInfoDb 1.26.4 MassSpecWavelet 1.56.0 fansi 0.4.2 preprocessCore 1.52.1 DEoptimR 1.0.8 scales 1.1.1 BiocManager 1.30.15 DelayedArray 0.16.3 limma 3.46.0 XVector 0.30.0 MsCoreUtils 1.2.0 RANN 2.6.1 impute 1.64.0 ggplot2 3.3.3 digest 0.6.27 ncdf4 1.17 GenomicRanges 1.42.0 grid 4.0.5 tools 4.0.5 bitops 1.0.7 magrittr 2.0.1 RCurl 1.98.1.3 tibble 3.1.1 crayon 1.4.1 pkgconfig 2.0.3 Matrix 1.3.2 MASS 7.3.54 ellipsis 0.3.2 iterators 1.0.13 R6 2.5.0 MALDIquant 1.19.3 compiler 4.0.5 | |
| ARGUMENTS INFO | |
| image /tmp/tmpni2hmxgh/files/3/0/2/dataset_30226968-a841-44ff-91f2-2ec68d035d57.dat | |
| BPPARAM 1 | |
| method CentWave | |
| ppm 3 | |
| peakwidth c(5, 20) | |
| snthresh 10 | |
| prefilter c(3, 5000) | |
| mzCenterFun wMean | |
| integrate 1 | |
| mzdiff -0.001 | |
| fitgauss FALSE | |
| noise 1000 | |
| verboseColumns FALSE | |
| peaklist FALSE | |
| ARGUMENTS PROCESSING INFO | |
| INFILE PROCESSING INFO | |
| MAIN PROCESSING INFO | |
| COMPUTE | |
| Apply filter[s] (if asked) | |
| Chromatographic peak detection | |
| Object of class: CentWaveParam | |
| Parameters: | |
| ppm: 3 | |
| peakwidth: 5, 20 | |
| snthresh: 10 | |
| prefilter: 3, 5000 | |
| mzCenterFun: wMean | |
| integrate: 1 | |
| mzdiff: -0.001 | |
| fitgauss: FALSE | |
| noise: 1000 | |
| verboseColumns: FALSE | |
| roiList length: 0 | |
| firstBaselineCheck TRUE | |
| roiScales length: 0 | |
| Creating the sampleMetadata file... | |
| Error in R_nc4_open: NetCDF: Unknown file format | |
| XCMSnExp OBJECT INFO | |
| MSn experiment data ("XCMSnExp") | |
| Object size in memory: 0.64 Mb | |
| - - - Spectra data - - - | |
| MS level(s): 1 | |
| Number of spectra: 1647 | |
| MSn retention times: 0:1 - 18:60 minutes | |
| - - - Processing information - - - | |
| Data loaded [Tue Feb 24 07:03:01 2026] | |
| MSnbase version: 2.16.1 | |
| - - - Meta data - - - | |
| phenoData | |
| rowNames: HU_neg_192.mzML | |
| varLabels: sample_name sample_group | |
| varMetadata: labelDescription | |
| Loaded from: | |
| HU_neg_192.mzML | |
| protocolData: none | |
| featureData | |
| featureNames: F1.S0001 F1.S0002 ... F1.S1647 (1647 total) | |
| fvarLabels: fileIdx spIdx ... spectrum (35 total) | |
| fvarMetadata: labelDescription | |
| experimentData: use 'experimentData(object)' | |
| - - - xcms preprocessing - - - | |
| Chromatographic peak detection: | |
| method: centWave | |
| 4264 peaks identified in 1 samples. | |
| On average 4264 chromatographic peaks per sample. | |
| xcmsSet OBJECT INFO | |
| An "xcmsSet" object with 1 samples | |
| Time range: 6.2-1139.1 seconds (0.1-19 minutes) | |
| Mass range: 50.025-963.0566 m/z | |
| Peaks: 4264 (about 4264 per sample) | |
| Peak Groups: 0 | |
| Sample classes: . | |
| Feature detection: | |
| o Peak picking performed on MS1. | |
| o Scan range limited to 1 - 1647 | |
| Profile settings: method = bin | |
| step = 0.1 | |
| Memory usage: 0.884 MB | |
| DONE | |
| ``` | |
| **Traceback:** | |
| * ```console | |
| ``` | |
| **Job Parameters:** | |
| * | Job parameter | Parameter value | | |
| | ------------- | --------------- | | |
| | \_\_input\_ext | ` "input" ` | | |
| | \_\_workflow\_invocation\_uuid\_\_ | ` "b39b8d62114e11f189517ced8d633c14" ` | | |
| | chromInfo | ` "/tmp/tmpni2hmxgh/galaxy-dev/tool-data/shared/ucsc/chrom/?.len" ` | | |
| | dbkey | ` "?" ` | | |
| | file\_load\_section | ` {"file_load_conditional": {"__current_case__": 0, "file_load_select": "no"}} ` | | |
| | filterSection | ` {"filterAcquisitionNum": "", "filterMz": "", "filterRt": ""} ` | | |
| | methods | ` {"CentWaveAdv": {"CentWaveAdvROI": {"firstBaselineCheck": true, "roiList": null, "roiScales": ""}, "fitgauss": false, "integrate": "1", "mzCenterFun": "wMean", "mzdiff": "-0.001", "noise": "1000", "peaklist": false, "prefilter": "3,5000", "snthresh": "10", "verboseColumns": false}, "__current_case__": 0, "method": "CentWave", "peakwidth": "5,20", "ppm": "3.0"} ` | | |
| - **Job 7:** | |
| * Job state is ok | |
| **Container:** | |
| * ```console | |
| quay.io/biocontainers/mulled-v2-007db2e42e47018763bae6b2bd1e69345120fe7f:ffab248635d36a246a435f3341c896269df9943c-2 | |
| ``` | |
| **Command Line:** | |
| * ```console | |
| LC_ALL=C Rscript /tmp/shed_dir/toolshed.g2.bx.psu.edu/repos/lecorguille/xcms_xcmsset/3990a65b45a4/xcms_xcmsset/xcms_xcmsSet.r image '/tmp/tmpni2hmxgh/files/f/4/0/dataset_f4089d4b-1664-4047-a835-230c5156506a.dat' BPPARAM ${GALAXY_SLOTS:-1} method CentWave ppm 3.0 peakwidth "c(5,20)" snthresh 10 prefilter "c(3,5000)" mzCenterFun wMean integrate 1 mzdiff -0.001 fitgauss FALSE noise 1000 verboseColumns FALSE peaklist FALSE ; return=$?; cat 'log.txt'; sh -c "exit $return" | |
| ``` | |
| **Exit Code:** | |
| * ```console | |
| 0 | |
| ``` | |
| **Standard Error:** | |
| * ```console | |
| Detecting mass traces at 3 ppm ... OK | |
| Detecting chromatographic peaks in 9690 regions of interest ... OK: 3868 found. | |
| Note: you might want to set/adjust the 'sampclass' of the returned xcmSet object before proceeding with the analysis. | |
| ``` | |
| **Standard Output:** | |
| * ```console | |
| SESSION INFO | |
| R version 4.0.5 (2021-03-31) | |
| Main packages: | |
| batch 1.1.5 xcms 3.12.0 MSnbase 2.16.1 ProtGenerics 1.22.0 S4Vectors 0.28.1 mzR 2.24.1 Rcpp 1.0.6 BiocParallel 1.24.1 Biobase 2.50.0 BiocGenerics 0.36.0 | |
| Other loaded packages: | |
| SummarizedExperiment 1.20.0 lattice 0.20.44 colorspace 2.0.1 vctrs 0.3.8 vsn 3.58.0 utf8 1.2.1 XML 3.99.0.6 rlang 0.4.11 pillar 1.6.0 glue 1.4.2 affy 1.68.0 RColorBrewer 1.1.2 affyio 1.60.0 matrixStats 0.58.0 GenomeInfoDbData 1.2.4 foreach 1.5.1 lifecycle 1.0.0 plyr 1.8.6 mzID 1.28.0 robustbase 0.93.7 zlibbioc 1.36.0 MatrixGenerics 1.2.1 munsell 0.5.0 pcaMethods 1.82.0 gtable 0.3.0 codetools 0.2.18 IRanges 2.24.1 doParallel 1.0.16 GenomeInfoDb 1.26.4 MassSpecWavelet 1.56.0 fansi 0.4.2 preprocessCore 1.52.1 DEoptimR 1.0.8 scales 1.1.1 BiocManager 1.30.15 DelayedArray 0.16.3 limma 3.46.0 XVector 0.30.0 MsCoreUtils 1.2.0 RANN 2.6.1 impute 1.64.0 ggplot2 3.3.3 digest 0.6.27 ncdf4 1.17 GenomicRanges 1.42.0 grid 4.0.5 tools 4.0.5 bitops 1.0.7 magrittr 2.0.1 RCurl 1.98.1.3 tibble 3.1.1 crayon 1.4.1 pkgconfig 2.0.3 Matrix 1.3.2 MASS 7.3.54 ellipsis 0.3.2 iterators 1.0.13 R6 2.5.0 MALDIquant 1.19.3 compiler 4.0.5 | |
| ARGUMENTS INFO | |
| image /tmp/tmpni2hmxgh/files/f/4/0/dataset_f4089d4b-1664-4047-a835-230c5156506a.dat | |
| BPPARAM 1 | |
| method CentWave | |
| ppm 3 | |
| peakwidth c(5, 20) | |
| snthresh 10 | |
| prefilter c(3, 5000) | |
| mzCenterFun wMean | |
| integrate 1 | |
| mzdiff -0.001 | |
| fitgauss FALSE | |
| noise 1000 | |
| verboseColumns FALSE | |
| peaklist FALSE | |
| ARGUMENTS PROCESSING INFO | |
| INFILE PROCESSING INFO | |
| MAIN PROCESSING INFO | |
| COMPUTE | |
| Apply filter[s] (if asked) | |
| Chromatographic peak detection | |
| Object of class: CentWaveParam | |
| Parameters: | |
| ppm: 3 | |
| peakwidth: 5, 20 | |
| snthresh: 10 | |
| prefilter: 3, 5000 | |
| mzCenterFun: wMean | |
| integrate: 1 | |
| mzdiff: -0.001 | |
| fitgauss: FALSE | |
| noise: 1000 | |
| verboseColumns: FALSE | |
| roiList length: 0 | |
| firstBaselineCheck TRUE | |
| roiScales length: 0 | |
| Creating the sampleMetadata file... | |
| Error in R_nc4_open: NetCDF: Unknown file format | |
| XCMSnExp OBJECT INFO | |
| MSn experiment data ("XCMSnExp") | |
| Object size in memory: 0.77 Mb | |
| - - - Spectra data - - - | |
| MS level(s): 1 | |
| Number of spectra: 1991 | |
| MSn retention times: 0:1 - 18:60 minutes | |
| - - - Processing information - - - | |
| Data loaded [Tue Feb 24 07:03:34 2026] | |
| MSnbase version: 2.16.1 | |
| - - - Meta data - - - | |
| phenoData | |
| rowNames: HU_neg_090.mzML | |
| varLabels: sample_name sample_group | |
| varMetadata: labelDescription | |
| Loaded from: | |
| HU_neg_090.mzML | |
| protocolData: none | |
| featureData | |
| featureNames: F1.S0001 F1.S0002 ... F1.S1991 (1991 total) | |
| fvarLabels: fileIdx spIdx ... spectrum (35 total) | |
| fvarMetadata: labelDescription | |
| experimentData: use 'experimentData(object)' | |
| - - - xcms preprocessing - - - | |
| Chromatographic peak detection: | |
| method: centWave | |
| 3868 peaks identified in 1 samples. | |
| On average 3868 chromatographic peaks per sample. | |
| xcmsSet OBJECT INFO | |
| An "xcmsSet" object with 1 samples | |
| Time range: 5.1-1139.5 seconds (0.1-19 minutes) | |
| Mass range: 50.0321-987.5531 m/z | |
| Peaks: 3868 (about 3868 per sample) | |
| Peak Groups: 0 | |
| Sample classes: . | |
| Feature detection: | |
| o Peak picking performed on MS1. | |
| o Scan range limited to 1 - 1991 | |
| Profile settings: method = bin | |
| step = 0.1 | |
| Memory usage: 0.879 MB | |
| DONE | |
| ``` | |
| **Traceback:** | |
| * ```console | |
| ``` | |
| **Job Parameters:** | |
| * | Job parameter | Parameter value | | |
| | ------------- | --------------- | | |
| | \_\_input\_ext | ` "input" ` | | |
| | \_\_workflow\_invocation\_uuid\_\_ | ` "b39b8d62114e11f189517ced8d633c14" ` | | |
| | chromInfo | ` "/tmp/tmpni2hmxgh/galaxy-dev/tool-data/shared/ucsc/chrom/?.len" ` | | |
| | dbkey | ` "?" ` | | |
| | file\_load\_section | ` {"file_load_conditional": {"__current_case__": 0, "file_load_select": "no"}} ` | | |
| | filterSection | ` {"filterAcquisitionNum": "", "filterMz": "", "filterRt": ""} ` | | |
| | methods | ` {"CentWaveAdv": {"CentWaveAdvROI": {"firstBaselineCheck": true, "roiList": null, "roiScales": ""}, "fitgauss": false, "integrate": "1", "mzCenterFun": "wMean", "mzdiff": "-0.001", "noise": "1000", "peaklist": false, "prefilter": "3,5000", "snthresh": "10", "verboseColumns": false}, "__current_case__": 0, "method": "CentWave", "peakwidth": "5,20", "ppm": "3.0"} ` | | |
| - **Job 8:** | |
| * Job state is ok | |
| **Container:** | |
| * ```console | |
| quay.io/biocontainers/mulled-v2-007db2e42e47018763bae6b2bd1e69345120fe7f:ffab248635d36a246a435f3341c896269df9943c-2 | |
| ``` | |
| **Command Line:** | |
| * ```console | |
| LC_ALL=C Rscript /tmp/shed_dir/toolshed.g2.bx.psu.edu/repos/lecorguille/xcms_xcmsset/3990a65b45a4/xcms_xcmsset/xcms_xcmsSet.r image '/tmp/tmpni2hmxgh/files/b/d/d/dataset_bddb3ff5-69cb-42db-a401-91c0443b16f9.dat' BPPARAM ${GALAXY_SLOTS:-1} method CentWave ppm 3.0 peakwidth "c(5,20)" snthresh 10 prefilter "c(3,5000)" mzCenterFun wMean integrate 1 mzdiff -0.001 fitgauss FALSE noise 1000 verboseColumns FALSE peaklist FALSE ; return=$?; cat 'log.txt'; sh -c "exit $return" | |
| ``` | |
| **Exit Code:** | |
| * ```console | |
| 0 | |
| ``` | |
| **Standard Error:** | |
| * ```console | |
| Detecting mass traces at 3 ppm ... OK | |
| Detecting chromatographic peaks in 6220 regions of interest ... OK: 3590 found. | |
| Note: you might want to set/adjust the 'sampclass' of the returned xcmSet object before proceeding with the analysis. | |
| ``` | |
| **Standard Output:** | |
| * ```console | |
| SESSION INFO | |
| R version 4.0.5 (2021-03-31) | |
| Main packages: | |
| batch 1.1.5 xcms 3.12.0 MSnbase 2.16.1 ProtGenerics 1.22.0 S4Vectors 0.28.1 mzR 2.24.1 Rcpp 1.0.6 BiocParallel 1.24.1 Biobase 2.50.0 BiocGenerics 0.36.0 | |
| Other loaded packages: | |
| SummarizedExperiment 1.20.0 lattice 0.20.44 colorspace 2.0.1 vctrs 0.3.8 vsn 3.58.0 utf8 1.2.1 XML 3.99.0.6 rlang 0.4.11 pillar 1.6.0 glue 1.4.2 affy 1.68.0 RColorBrewer 1.1.2 affyio 1.60.0 matrixStats 0.58.0 GenomeInfoDbData 1.2.4 foreach 1.5.1 lifecycle 1.0.0 plyr 1.8.6 mzID 1.28.0 robustbase 0.93.7 zlibbioc 1.36.0 MatrixGenerics 1.2.1 munsell 0.5.0 pcaMethods 1.82.0 gtable 0.3.0 codetools 0.2.18 IRanges 2.24.1 doParallel 1.0.16 GenomeInfoDb 1.26.4 MassSpecWavelet 1.56.0 fansi 0.4.2 preprocessCore 1.52.1 DEoptimR 1.0.8 scales 1.1.1 BiocManager 1.30.15 DelayedArray 0.16.3 limma 3.46.0 XVector 0.30.0 MsCoreUtils 1.2.0 RANN 2.6.1 impute 1.64.0 ggplot2 3.3.3 digest 0.6.27 ncdf4 1.17 GenomicRanges 1.42.0 grid 4.0.5 tools 4.0.5 bitops 1.0.7 magrittr 2.0.1 RCurl 1.98.1.3 tibble 3.1.1 crayon 1.4.1 pkgconfig 2.0.3 Matrix 1.3.2 MASS 7.3.54 ellipsis 0.3.2 iterators 1.0.13 R6 2.5.0 MALDIquant 1.19.3 compiler 4.0.5 | |
| ARGUMENTS INFO | |
| image /tmp/tmpni2hmxgh/files/b/d/d/dataset_bddb3ff5-69cb-42db-a401-91c0443b16f9.dat | |
| BPPARAM 1 | |
| method CentWave | |
| ppm 3 | |
| peakwidth c(5, 20) | |
| snthresh 10 | |
| prefilter c(3, 5000) | |
| mzCenterFun wMean | |
| integrate 1 | |
| mzdiff -0.001 | |
| fitgauss FALSE | |
| noise 1000 | |
| verboseColumns FALSE | |
| peaklist FALSE | |
| ARGUMENTS PROCESSING INFO | |
| INFILE PROCESSING INFO | |
| MAIN PROCESSING INFO | |
| COMPUTE | |
| Apply filter[s] (if asked) | |
| Chromatographic peak detection | |
| Object of class: CentWaveParam | |
| Parameters: | |
| ppm: 3 | |
| peakwidth: 5, 20 | |
| snthresh: 10 | |
| prefilter: 3, 5000 | |
| mzCenterFun: wMean | |
| integrate: 1 | |
| mzdiff: -0.001 | |
| fitgauss: FALSE | |
| noise: 1000 | |
| verboseColumns: FALSE | |
| roiList length: 0 | |
| firstBaselineCheck TRUE | |
| roiScales length: 0 | |
| Creating the sampleMetadata file... | |
| Error in R_nc4_open: NetCDF: Unknown file format | |
| XCMSnExp OBJECT INFO | |
| MSn experiment data ("XCMSnExp") | |
| Object size in memory: 0.69 Mb | |
| - - - Spectra data - - - | |
| MS level(s): 1 | |
| Number of spectra: 1767 | |
| MSn retention times: 0:1 - 18:60 minutes | |
| - - - Processing information - - - | |
| Data loaded [Tue Feb 24 07:03:36 2026] | |
| MSnbase version: 2.16.1 | |
| - - - Meta data - - - | |
| phenoData | |
| rowNames: HU_neg_157.mzML | |
| varLabels: sample_name sample_group | |
| varMetadata: labelDescription | |
| Loaded from: | |
| HU_neg_157.mzML | |
| protocolData: none | |
| featureData | |
| featureNames: F1.S0001 F1.S0002 ... F1.S1767 (1767 total) | |
| fvarLabels: fileIdx spIdx ... spectrum (35 total) | |
| fvarMetadata: labelDescription | |
| experimentData: use 'experimentData(object)' | |
| - - - xcms preprocessing - - - | |
| Chromatographic peak detection: | |
| method: centWave | |
| 3590 peaks identified in 1 samples. | |
| On average 3590 chromatographic peaks per sample. | |
| xcmsSet OBJECT INFO | |
| An "xcmsSet" object with 1 samples | |
| Time range: 2.5-1138.9 seconds (0-19 minutes) | |
| Mass range: 50.0321-963.0747 m/z | |
| Peaks: 3590 (about 3590 per sample) | |
| Peak Groups: 0 | |
| Sample classes: . | |
| Feature detection: | |
| o Peak picking performed on MS1. | |
| o Scan range limited to 1 - 1767 | |
| Profile settings: method = bin | |
| step = 0.1 | |
| Memory usage: 0.805 MB | |
| DONE | |
| ``` | |
| **Traceback:** | |
| * ```console | |
| ``` | |
| **Job Parameters:** | |
| * | Job parameter | Parameter value | | |
| | ------------- | --------------- | | |
| | \_\_input\_ext | ` "input" ` | | |
| | \_\_workflow\_invocation\_uuid\_\_ | ` "b39b8d62114e11f189517ced8d633c14" ` | | |
| | chromInfo | ` "/tmp/tmpni2hmxgh/galaxy-dev/tool-data/shared/ucsc/chrom/?.len" ` | | |
| | dbkey | ` "?" ` | | |
| | file\_load\_section | ` {"file_load_conditional": {"__current_case__": 0, "file_load_select": "no"}} ` | | |
| | filterSection | ` {"filterAcquisitionNum": "", "filterMz": "", "filterRt": ""} ` | | |
| | methods | ` {"CentWaveAdv": {"CentWaveAdvROI": {"firstBaselineCheck": true, "roiList": null, "roiScales": ""}, "fitgauss": false, "integrate": "1", "mzCenterFun": "wMean", "mzdiff": "-0.001", "noise": "1000", "peaklist": false, "prefilter": "3,5000", "snthresh": "10", "verboseColumns": false}, "__current_case__": 0, "method": "CentWave", "peakwidth": "5,20", "ppm": "3.0"} ` | | |
| - **Job 9:** | |
| * Job state is ok | |
| **Container:** | |
| * ```console | |
| quay.io/biocontainers/mulled-v2-007db2e42e47018763bae6b2bd1e69345120fe7f:ffab248635d36a246a435f3341c896269df9943c-2 | |
| ``` | |
| **Command Line:** | |
| * ```console | |
| LC_ALL=C Rscript /tmp/shed_dir/toolshed.g2.bx.psu.edu/repos/lecorguille/xcms_xcmsset/3990a65b45a4/xcms_xcmsset/xcms_xcmsSet.r image '/tmp/tmpni2hmxgh/files/6/f/c/dataset_6fc81557-2824-4fb8-9d96-0ed012e17179.dat' BPPARAM ${GALAXY_SLOTS:-1} method CentWave ppm 3.0 peakwidth "c(5,20)" snthresh 10 prefilter "c(3,5000)" mzCenterFun wMean integrate 1 mzdiff -0.001 fitgauss FALSE noise 1000 verboseColumns FALSE peaklist FALSE ; return=$?; cat 'log.txt'; sh -c "exit $return" | |
| ``` | |
| **Exit Code:** | |
| * ```console | |
| 0 | |
| ``` | |
| **Standard Error:** | |
| * ```console | |
| Detecting mass traces at 3 ppm ... OK | |
| Detecting chromatographic peaks in 5041 regions of interest ... OK: 767 found. | |
| Note: you might want to set/adjust the 'sampclass' of the returned xcmSet object before proceeding with the analysis. | |
| ``` | |
| **Standard Output:** | |
| * ```console | |
| SESSION INFO | |
| R version 4.0.5 (2021-03-31) | |
| Main packages: | |
| batch 1.1.5 xcms 3.12.0 MSnbase 2.16.1 ProtGenerics 1.22.0 S4Vectors 0.28.1 mzR 2.24.1 Rcpp 1.0.6 BiocParallel 1.24.1 Biobase 2.50.0 BiocGenerics 0.36.0 | |
| Other loaded packages: | |
| SummarizedExperiment 1.20.0 lattice 0.20.44 colorspace 2.0.1 vctrs 0.3.8 vsn 3.58.0 utf8 1.2.1 XML 3.99.0.6 rlang 0.4.11 pillar 1.6.0 glue 1.4.2 affy 1.68.0 RColorBrewer 1.1.2 affyio 1.60.0 matrixStats 0.58.0 GenomeInfoDbData 1.2.4 foreach 1.5.1 lifecycle 1.0.0 plyr 1.8.6 mzID 1.28.0 robustbase 0.93.7 zlibbioc 1.36.0 MatrixGenerics 1.2.1 munsell 0.5.0 pcaMethods 1.82.0 gtable 0.3.0 codetools 0.2.18 IRanges 2.24.1 doParallel 1.0.16 GenomeInfoDb 1.26.4 MassSpecWavelet 1.56.0 fansi 0.4.2 preprocessCore 1.52.1 DEoptimR 1.0.8 scales 1.1.1 BiocManager 1.30.15 DelayedArray 0.16.3 limma 3.46.0 XVector 0.30.0 MsCoreUtils 1.2.0 RANN 2.6.1 impute 1.64.0 ggplot2 3.3.3 digest 0.6.27 ncdf4 1.17 GenomicRanges 1.42.0 grid 4.0.5 tools 4.0.5 bitops 1.0.7 magrittr 2.0.1 RCurl 1.98.1.3 tibble 3.1.1 crayon 1.4.1 pkgconfig 2.0.3 Matrix 1.3.2 MASS 7.3.54 ellipsis 0.3.2 iterators 1.0.13 R6 2.5.0 MALDIquant 1.19.3 compiler 4.0.5 | |
| ARGUMENTS INFO | |
| image /tmp/tmpni2hmxgh/files/6/f/c/dataset_6fc81557-2824-4fb8-9d96-0ed012e17179.dat | |
| BPPARAM 1 | |
| method CentWave | |
| ppm 3 | |
| peakwidth c(5, 20) | |
| snthresh 10 | |
| prefilter c(3, 5000) | |
| mzCenterFun wMean | |
| integrate 1 | |
| mzdiff -0.001 | |
| fitgauss FALSE | |
| noise 1000 | |
| verboseColumns FALSE | |
| peaklist FALSE | |
| ARGUMENTS PROCESSING INFO | |
| INFILE PROCESSING INFO | |
| MAIN PROCESSING INFO | |
| COMPUTE | |
| Apply filter[s] (if asked) | |
| Chromatographic peak detection | |
| Object of class: CentWaveParam | |
| Parameters: | |
| ppm: 3 | |
| peakwidth: 5, 20 | |
| snthresh: 10 | |
| prefilter: 3, 5000 | |
| mzCenterFun: wMean | |
| integrate: 1 | |
| mzdiff: -0.001 | |
| fitgauss: FALSE | |
| noise: 1000 | |
| verboseColumns: FALSE | |
| roiList length: 0 | |
| firstBaselineCheck TRUE | |
| roiScales length: 0 | |
| Creating the sampleMetadata file... | |
| Error in R_nc4_open: NetCDF: Unknown file format | |
| XCMSnExp OBJECT INFO | |
| MSn experiment data ("XCMSnExp") | |
| Object size in memory: 0.78 Mb | |
| - - - Spectra data - - - | |
| MS level(s): 1 | |
| Number of spectra: 2022 | |
| MSn retention times: 0:1 - 18:60 minutes | |
| - - - Processing information - - - | |
| Data loaded [Tue Feb 24 07:03:01 2026] | |
| MSnbase version: 2.16.1 | |
| - - - Meta data - - - | |
| phenoData | |
| rowNames: Blanc05.mzML | |
| varLabels: sample_name sample_group | |
| varMetadata: labelDescription | |
| Loaded from: | |
| Blanc05.mzML | |
| protocolData: none | |
| featureData | |
| featureNames: F1.S0001 F1.S0002 ... F1.S2022 (2022 total) | |
| fvarLabels: fileIdx spIdx ... spectrum (35 total) | |
| fvarMetadata: labelDescription | |
| experimentData: use 'experimentData(object)' | |
| - - - xcms preprocessing - - - | |
| Chromatographic peak detection: | |
| method: centWave | |
| 767 peaks identified in 1 samples. | |
| On average 767 chromatographic peaks per sample. | |
| xcmsSet OBJECT INFO | |
| An "xcmsSet" object with 1 samples | |
| Time range: 4.6-1139.1 seconds (0.1-19 minutes) | |
| Mass range: 63.6207-989.2024 m/z | |
| Peaks: 767 (about 767 per sample) | |
| Peak Groups: 0 | |
| Sample classes: . | |
| Feature detection: | |
| o Peak picking performed on MS1. | |
| o Scan range limited to 1 - 2022 | |
| Profile settings: method = bin | |
| step = 0.1 | |
| Memory usage: 0.434 MB | |
| DONE | |
| ``` | |
| **Traceback:** | |
| * ```console | |
| ``` | |
| **Job Parameters:** | |
| * | Job parameter | Parameter value | | |
| | ------------- | --------------- | | |
| | \_\_input\_ext | ` "input" ` | | |
| | \_\_workflow\_invocation\_uuid\_\_ | ` "b39b8d62114e11f189517ced8d633c14" ` | | |
| | chromInfo | ` "/tmp/tmpni2hmxgh/galaxy-dev/tool-data/shared/ucsc/chrom/?.len" ` | | |
| | dbkey | ` "?" ` | | |
| | file\_load\_section | ` {"file_load_conditional": {"__current_case__": 0, "file_load_select": "no"}} ` | | |
| | filterSection | ` {"filterAcquisitionNum": "", "filterMz": "", "filterRt": ""} ` | | |
| | methods | ` {"CentWaveAdv": {"CentWaveAdvROI": {"firstBaselineCheck": true, "roiList": null, "roiScales": ""}, "fitgauss": false, "integrate": "1", "mzCenterFun": "wMean", "mzdiff": "-0.001", "noise": "1000", "peaklist": false, "prefilter": "3,5000", "snthresh": "10", "verboseColumns": false}, "__current_case__": 0, "method": "CentWave", "peakwidth": "5,20", "ppm": "3.0"} ` | | |
| - **Job 10:** | |
| * Job state is ok | |
| **Container:** | |
| * ```console | |
| quay.io/biocontainers/mulled-v2-007db2e42e47018763bae6b2bd1e69345120fe7f:ffab248635d36a246a435f3341c896269df9943c-2 | |
| ``` | |
| **Command Line:** | |
| * ```console | |
| LC_ALL=C Rscript /tmp/shed_dir/toolshed.g2.bx.psu.edu/repos/lecorguille/xcms_xcmsset/3990a65b45a4/xcms_xcmsset/xcms_xcmsSet.r image '/tmp/tmpni2hmxgh/files/d/9/c/dataset_d9c5a090-65ec-4499-8150-43f22dc151d3.dat' BPPARAM ${GALAXY_SLOTS:-1} method CentWave ppm 3.0 peakwidth "c(5,20)" snthresh 10 prefilter "c(3,5000)" mzCenterFun wMean integrate 1 mzdiff -0.001 fitgauss FALSE noise 1000 verboseColumns FALSE peaklist FALSE ; return=$?; cat 'log.txt'; sh -c "exit $return" | |
| ``` | |
| **Exit Code:** | |
| * ```console | |
| 0 | |
| ``` | |
| **Standard Error:** | |
| * ```console | |
| Detecting mass traces at 3 ppm ... OK | |
| Detecting chromatographic peaks in 4136 regions of interest ... OK: 770 found. | |
| Note: you might want to set/adjust the 'sampclass' of the returned xcmSet object before proceeding with the analysis. | |
| ``` | |
| **Standard Output:** | |
| * ```console | |
| SESSION INFO | |
| R version 4.0.5 (2021-03-31) | |
| Main packages: | |
| batch 1.1.5 xcms 3.12.0 MSnbase 2.16.1 ProtGenerics 1.22.0 S4Vectors 0.28.1 mzR 2.24.1 Rcpp 1.0.6 BiocParallel 1.24.1 Biobase 2.50.0 BiocGenerics 0.36.0 | |
| Other loaded packages: | |
| SummarizedExperiment 1.20.0 lattice 0.20.44 colorspace 2.0.1 vctrs 0.3.8 vsn 3.58.0 utf8 1.2.1 XML 3.99.0.6 rlang 0.4.11 pillar 1.6.0 glue 1.4.2 affy 1.68.0 RColorBrewer 1.1.2 affyio 1.60.0 matrixStats 0.58.0 GenomeInfoDbData 1.2.4 foreach 1.5.1 lifecycle 1.0.0 plyr 1.8.6 mzID 1.28.0 robustbase 0.93.7 zlibbioc 1.36.0 MatrixGenerics 1.2.1 munsell 0.5.0 pcaMethods 1.82.0 gtable 0.3.0 codetools 0.2.18 IRanges 2.24.1 doParallel 1.0.16 GenomeInfoDb 1.26.4 MassSpecWavelet 1.56.0 fansi 0.4.2 preprocessCore 1.52.1 DEoptimR 1.0.8 scales 1.1.1 BiocManager 1.30.15 DelayedArray 0.16.3 limma 3.46.0 XVector 0.30.0 MsCoreUtils 1.2.0 RANN 2.6.1 impute 1.64.0 ggplot2 3.3.3 digest 0.6.27 ncdf4 1.17 GenomicRanges 1.42.0 grid 4.0.5 tools 4.0.5 bitops 1.0.7 magrittr 2.0.1 RCurl 1.98.1.3 tibble 3.1.1 crayon 1.4.1 pkgconfig 2.0.3 Matrix 1.3.2 MASS 7.3.54 ellipsis 0.3.2 iterators 1.0.13 R6 2.5.0 MALDIquant 1.19.3 compiler 4.0.5 | |
| ARGUMENTS INFO | |
| image /tmp/tmpni2hmxgh/files/d/9/c/dataset_d9c5a090-65ec-4499-8150-43f22dc151d3.dat | |
| BPPARAM 1 | |
| method CentWave | |
| ppm 3 | |
| peakwidth c(5, 20) | |
| snthresh 10 | |
| prefilter c(3, 5000) | |
| mzCenterFun wMean | |
| integrate 1 | |
| mzdiff -0.001 | |
| fitgauss FALSE | |
| noise 1000 | |
| verboseColumns FALSE | |
| peaklist FALSE | |
| ARGUMENTS PROCESSING INFO | |
| INFILE PROCESSING INFO | |
| MAIN PROCESSING INFO | |
| COMPUTE | |
| Apply filter[s] (if asked) | |
| Chromatographic peak detection | |
| Object of class: CentWaveParam | |
| Parameters: | |
| ppm: 3 | |
| peakwidth: 5, 20 | |
| snthresh: 10 | |
| prefilter: 3, 5000 | |
| mzCenterFun: wMean | |
| integrate: 1 | |
| mzdiff: -0.001 | |
| fitgauss: FALSE | |
| noise: 1000 | |
| verboseColumns: FALSE | |
| roiList length: 0 | |
| firstBaselineCheck TRUE | |
| roiScales length: 0 | |
| Creating the sampleMetadata file... | |
| Error in R_nc4_open: NetCDF: Unknown file format | |
| XCMSnExp OBJECT INFO | |
| MSn experiment data ("XCMSnExp") | |
| Object size in memory: 0.73 Mb | |
| - - - Spectra data - - - | |
| MS level(s): 1 | |
| Number of spectra: 1882 | |
| MSn retention times: 0:1 - 18:59 minutes | |
| - - - Processing information - - - | |
| Data loaded [Tue Feb 24 07:03:01 2026] | |
| MSnbase version: 2.16.1 | |
| - - - Meta data - - - | |
| phenoData | |
| rowNames: Blanc10.mzML | |
| varLabels: sample_name sample_group | |
| varMetadata: labelDescription | |
| Loaded from: | |
| Blanc10.mzML | |
| protocolData: none | |
| featureData | |
| featureNames: F1.S0001 F1.S0002 ... F1.S1882 (1882 total) | |
| fvarLabels: fileIdx spIdx ... spectrum (35 total) | |
| fvarMetadata: labelDescription | |
| experimentData: use 'experimentData(object)' | |
| - - - xcms preprocessing - - - | |
| Chromatographic peak detection: | |
| method: centWave | |
| 770 peaks identified in 1 samples. | |
| On average 770 chromatographic peaks per sample. | |
| xcmsSet OBJECT INFO | |
| An "xcmsSet" object with 1 samples | |
| Time range: 2.7-1139 seconds (0-19 minutes) | |
| Mass range: 65.2842-963.063 m/z | |
| Peaks: 770 (about 770 per sample) | |
| Peak Groups: 0 | |
| Sample classes: . | |
| Feature detection: | |
| o Peak picking performed on MS1. | |
| o Scan range limited to 1 - 1882 | |
| Profile settings: method = bin | |
| step = 0.1 | |
| Memory usage: 0.413 MB | |
| DONE | |
| ``` | |
| **Traceback:** | |
| * ```console | |
| ``` | |
| **Job Parameters:** | |
| * | Job parameter | Parameter value | | |
| | ------------- | --------------- | | |
| | \_\_input\_ext | ` "input" ` | | |
| | \_\_workflow\_invocation\_uuid\_\_ | ` "b39b8d62114e11f189517ced8d633c14" ` | | |
| | chromInfo | ` "/tmp/tmpni2hmxgh/galaxy-dev/tool-data/shared/ucsc/chrom/?.len" ` | | |
| | dbkey | ` "?" ` | | |
| | file\_load\_section | ` {"file_load_conditional": {"__current_case__": 0, "file_load_select": "no"}} ` | | |
| | filterSection | ` {"filterAcquisitionNum": "", "filterMz": "", "filterRt": ""} ` | | |
| | methods | ` {"CentWaveAdv": {"CentWaveAdvROI": {"firstBaselineCheck": true, "roiList": null, "roiScales": ""}, "fitgauss": false, "integrate": "1", "mzCenterFun": "wMean", "mzdiff": "-0.001", "noise": "1000", "peaklist": false, "prefilter": "3,5000", "snthresh": "10", "verboseColumns": false}, "__current_case__": 0, "method": "CentWave", "peakwidth": "5,20", "ppm": "3.0"} ` | | |
| - **Job 11:** | |
| * Job state is ok | |
| **Container:** | |
| * ```console | |
| quay.io/biocontainers/mulled-v2-007db2e42e47018763bae6b2bd1e69345120fe7f:ffab248635d36a246a435f3341c896269df9943c-2 | |
| ``` | |
| **Command Line:** | |
| * ```console | |
| LC_ALL=C Rscript /tmp/shed_dir/toolshed.g2.bx.psu.edu/repos/lecorguille/xcms_xcmsset/3990a65b45a4/xcms_xcmsset/xcms_xcmsSet.r image '/tmp/tmpni2hmxgh/files/e/8/5/dataset_e859e7ca-e523-41d8-b7fe-2823fc656111.dat' BPPARAM ${GALAXY_SLOTS:-1} method CentWave ppm 3.0 peakwidth "c(5,20)" snthresh 10 prefilter "c(3,5000)" mzCenterFun wMean integrate 1 mzdiff -0.001 fitgauss FALSE noise 1000 verboseColumns FALSE peaklist FALSE ; return=$?; cat 'log.txt'; sh -c "exit $return" | |
| ``` | |
| **Exit Code:** | |
| * ```console | |
| 0 | |
| ``` | |
| **Standard Error:** | |
| * ```console | |
| Detecting mass traces at 3 ppm ... OK | |
| Detecting chromatographic peaks in 977 regions of interest ... OK: 848 found. | |
| Note: you might want to set/adjust the 'sampclass' of the returned xcmSet object before proceeding with the analysis. | |
| ``` | |
| **Standard Output:** | |
| * ```console | |
| SESSION INFO | |
| R version 4.0.5 (2021-03-31) | |
| Main packages: | |
| batch 1.1.5 xcms 3.12.0 MSnbase 2.16.1 ProtGenerics 1.22.0 S4Vectors 0.28.1 mzR 2.24.1 Rcpp 1.0.6 BiocParallel 1.24.1 Biobase 2.50.0 BiocGenerics 0.36.0 | |
| Other loaded packages: | |
| SummarizedExperiment 1.20.0 lattice 0.20.44 colorspace 2.0.1 vctrs 0.3.8 vsn 3.58.0 utf8 1.2.1 XML 3.99.0.6 rlang 0.4.11 pillar 1.6.0 glue 1.4.2 affy 1.68.0 RColorBrewer 1.1.2 affyio 1.60.0 matrixStats 0.58.0 GenomeInfoDbData 1.2.4 foreach 1.5.1 lifecycle 1.0.0 plyr 1.8.6 mzID 1.28.0 robustbase 0.93.7 zlibbioc 1.36.0 MatrixGenerics 1.2.1 munsell 0.5.0 pcaMethods 1.82.0 gtable 0.3.0 codetools 0.2.18 IRanges 2.24.1 doParallel 1.0.16 GenomeInfoDb 1.26.4 MassSpecWavelet 1.56.0 fansi 0.4.2 preprocessCore 1.52.1 DEoptimR 1.0.8 scales 1.1.1 BiocManager 1.30.15 DelayedArray 0.16.3 limma 3.46.0 XVector 0.30.0 MsCoreUtils 1.2.0 RANN 2.6.1 impute 1.64.0 ggplot2 3.3.3 digest 0.6.27 ncdf4 1.17 GenomicRanges 1.42.0 grid 4.0.5 tools 4.0.5 bitops 1.0.7 magrittr 2.0.1 RCurl 1.98.1.3 tibble 3.1.1 crayon 1.4.1 pkgconfig 2.0.3 Matrix 1.3.2 MASS 7.3.54 ellipsis 0.3.2 iterators 1.0.13 R6 2.5.0 MALDIquant 1.19.3 compiler 4.0.5 | |
| ARGUMENTS INFO | |
| image /tmp/tmpni2hmxgh/files/e/8/5/dataset_e859e7ca-e523-41d8-b7fe-2823fc656111.dat | |
| BPPARAM 1 | |
| method CentWave | |
| ppm 3 | |
| peakwidth c(5, 20) | |
| snthresh 10 | |
| prefilter c(3, 5000) | |
| mzCenterFun wMean | |
| integrate 1 | |
| mzdiff -0.001 | |
| fitgauss FALSE | |
| noise 1000 | |
| verboseColumns FALSE | |
| peaklist FALSE | |
| ARGUMENTS PROCESSING INFO | |
| INFILE PROCESSING INFO | |
| MAIN PROCESSING INFO | |
| COMPUTE | |
| Apply filter[s] (if asked) | |
| Chromatographic peak detection | |
| Object of class: CentWaveParam | |
| Parameters: | |
| ppm: 3 | |
| peakwidth: 5, 20 | |
| snthresh: 10 | |
| prefilter: 3, 5000 | |
| mzCenterFun: wMean | |
| integrate: 1 | |
| mzdiff: -0.001 | |
| fitgauss: FALSE | |
| noise: 1000 | |
| verboseColumns: FALSE | |
| roiList length: 0 | |
| firstBaselineCheck TRUE | |
| roiScales length: 0 | |
| Creating the sampleMetadata file... | |
| Error in R_nc4_open: NetCDF: Unknown file format | |
| XCMSnExp OBJECT INFO | |
| MSn experiment data ("XCMSnExp") | |
| Object size in memory: 0.58 Mb | |
| - - - Spectra data - - - | |
| MS level(s): 1 | |
| Number of spectra: 1485 | |
| MSn retention times: 0:1 - 18:59 minutes | |
| - - - Processing information - - - | |
| Data loaded [Tue Feb 24 07:03:18 2026] | |
| MSnbase version: 2.16.1 | |
| - - - Meta data - - - | |
| phenoData | |
| rowNames: Blanc16.mzML | |
| varLabels: sample_name sample_group | |
| varMetadata: labelDescription | |
| Loaded from: | |
| Blanc16.mzML | |
| protocolData: none | |
| featureData | |
| featureNames: F1.S0001 F1.S0002 ... F1.S1485 (1485 total) | |
| fvarLabels: fileIdx spIdx ... spectrum (35 total) | |
| fvarMetadata: labelDescription | |
| experimentData: use 'experimentData(object)' | |
| - - - xcms preprocessing - - - | |
| Chromatographic peak detection: | |
| method: centWave | |
| 848 peaks identified in 1 samples. | |
| On average 848 chromatographic peaks per sample. | |
| xcmsSet OBJECT INFO | |
| An "xcmsSet" object with 1 samples | |
| Time range: 6.1-1138.6 seconds (0.1-19 minutes) | |
| Mass range: 65.2841-963.0739 m/z | |
| Peaks: 848 (about 848 per sample) | |
| Peak Groups: 0 | |
| Sample classes: . | |
| Feature detection: | |
| o Peak picking performed on MS1. | |
| o Scan range limited to 1 - 1485 | |
| Profile settings: method = bin | |
| step = 0.1 | |
| Memory usage: 0.364 MB | |
| DONE | |
| ``` | |
| **Traceback:** | |
| * ```console | |
| ``` | |
| **Job Parameters:** | |
| * | Job parameter | Parameter value | | |
| | ------------- | --------------- | | |
| | \_\_input\_ext | ` "input" ` | | |
| | \_\_workflow\_invocation\_uuid\_\_ | ` "b39b8d62114e11f189517ced8d633c14" ` | | |
| | chromInfo | ` "/tmp/tmpni2hmxgh/galaxy-dev/tool-data/shared/ucsc/chrom/?.len" ` | | |
| | dbkey | ` "?" ` | | |
| | file\_load\_section | ` {"file_load_conditional": {"__current_case__": 0, "file_load_select": "no"}} ` | | |
| | filterSection | ` {"filterAcquisitionNum": "", "filterMz": "", "filterRt": ""} ` | | |
| | methods | ` {"CentWaveAdv": {"CentWaveAdvROI": {"firstBaselineCheck": true, "roiList": null, "roiScales": ""}, "fitgauss": false, "integrate": "1", "mzCenterFun": "wMean", "mzdiff": "-0.001", "noise": "1000", "peaklist": false, "prefilter": "3,5000", "snthresh": "10", "verboseColumns": false}, "__current_case__": 0, "method": "CentWave", "peakwidth": "5,20", "ppm": "3.0"} ` | | |
| - **Job 12:** | |
| * Job state is ok | |
| **Container:** | |
| * ```console | |
| quay.io/biocontainers/mulled-v2-007db2e42e47018763bae6b2bd1e69345120fe7f:ffab248635d36a246a435f3341c896269df9943c-2 | |
| ``` | |
| **Command Line:** | |
| * ```console | |
| LC_ALL=C Rscript /tmp/shed_dir/toolshed.g2.bx.psu.edu/repos/lecorguille/xcms_xcmsset/3990a65b45a4/xcms_xcmsset/xcms_xcmsSet.r image '/tmp/tmpni2hmxgh/files/1/9/0/dataset_19048e68-7357-4058-baf8-816307779515.dat' BPPARAM ${GALAXY_SLOTS:-1} method CentWave ppm 3.0 peakwidth "c(5,20)" snthresh 10 prefilter "c(3,5000)" mzCenterFun wMean integrate 1 mzdiff -0.001 fitgauss FALSE noise 1000 verboseColumns FALSE peaklist FALSE ; return=$?; cat 'log.txt'; sh -c "exit $return" | |
| ``` | |
| **Exit Code:** | |
| * ```console | |
| 0 | |
| ``` | |
| **Standard Error:** | |
| * ```console | |
| Detecting mass traces at 3 ppm ... OK | |
| Detecting chromatographic peaks in 8700 regions of interest ... OK: 3327 found. | |
| Note: you might want to set/adjust the 'sampclass' of the returned xcmSet object before proceeding with the analysis. | |
| ``` | |
| **Standard Output:** | |
| * ```console | |
| SESSION INFO | |
| R version 4.0.5 (2021-03-31) | |
| Main packages: | |
| batch 1.1.5 xcms 3.12.0 MSnbase 2.16.1 ProtGenerics 1.22.0 S4Vectors 0.28.1 mzR 2.24.1 Rcpp 1.0.6 BiocParallel 1.24.1 Biobase 2.50.0 BiocGenerics 0.36.0 | |
| Other loaded packages: | |
| SummarizedExperiment 1.20.0 lattice 0.20.44 colorspace 2.0.1 vctrs 0.3.8 vsn 3.58.0 utf8 1.2.1 XML 3.99.0.6 rlang 0.4.11 pillar 1.6.0 glue 1.4.2 affy 1.68.0 RColorBrewer 1.1.2 affyio 1.60.0 matrixStats 0.58.0 GenomeInfoDbData 1.2.4 foreach 1.5.1 lifecycle 1.0.0 plyr 1.8.6 mzID 1.28.0 robustbase 0.93.7 zlibbioc 1.36.0 MatrixGenerics 1.2.1 munsell 0.5.0 pcaMethods 1.82.0 gtable 0.3.0 codetools 0.2.18 IRanges 2.24.1 doParallel 1.0.16 GenomeInfoDb 1.26.4 MassSpecWavelet 1.56.0 fansi 0.4.2 preprocessCore 1.52.1 DEoptimR 1.0.8 scales 1.1.1 BiocManager 1.30.15 DelayedArray 0.16.3 limma 3.46.0 XVector 0.30.0 MsCoreUtils 1.2.0 RANN 2.6.1 impute 1.64.0 ggplot2 3.3.3 digest 0.6.27 ncdf4 1.17 GenomicRanges 1.42.0 grid 4.0.5 tools 4.0.5 bitops 1.0.7 magrittr 2.0.1 RCurl 1.98.1.3 tibble 3.1.1 crayon 1.4.1 pkgconfig 2.0.3 Matrix 1.3.2 MASS 7.3.54 ellipsis 0.3.2 iterators 1.0.13 R6 2.5.0 MALDIquant 1.19.3 compiler 4.0.5 | |
| ARGUMENTS INFO | |
| image /tmp/tmpni2hmxgh/files/1/9/0/dataset_19048e68-7357-4058-baf8-816307779515.dat | |
| BPPARAM 1 | |
| method CentWave | |
| ppm 3 | |
| peakwidth c(5, 20) | |
| snthresh 10 | |
| prefilter c(3, 5000) | |
| mzCenterFun wMean | |
| integrate 1 | |
| mzdiff -0.001 | |
| fitgauss FALSE | |
| noise 1000 | |
| verboseColumns FALSE | |
| peaklist FALSE | |
| ARGUMENTS PROCESSING INFO | |
| INFILE PROCESSING INFO | |
| MAIN PROCESSING INFO | |
| COMPUTE | |
| Apply filter[s] (if asked) | |
| Chromatographic peak detection | |
| Object of class: CentWaveParam | |
| Parameters: | |
| ppm: 3 | |
| peakwidth: 5, 20 | |
| snthresh: 10 | |
| prefilter: 3, 5000 | |
| mzCenterFun: wMean | |
| integrate: 1 | |
| mzdiff: -0.001 | |
| fitgauss: FALSE | |
| noise: 1000 | |
| verboseColumns: FALSE | |
| roiList length: 0 | |
| firstBaselineCheck TRUE | |
| roiScales length: 0 | |
| Creating the sampleMetadata file... | |
| Error in R_nc4_open: NetCDF: Unknown file format | |
| XCMSnExp OBJECT INFO | |
| MSn experiment data ("XCMSnExp") | |
| Object size in memory: 0.79 Mb | |
| - - - Spectra data - - - | |
| MS level(s): 1 | |
| Number of spectra: 2039 | |
| MSn retention times: 0:1 - 18:60 minutes | |
| - - - Processing information - - - | |
| Data loaded [Tue Feb 24 07:03:17 2026] | |
| MSnbase version: 2.16.1 | |
| - - - Meta data - - - | |
| phenoData | |
| rowNames: QC1_002.mzML | |
| varLabels: sample_name sample_group | |
| varMetadata: labelDescription | |
| Loaded from: | |
| QC1_002.mzML | |
| protocolData: none | |
| featureData | |
| featureNames: F1.S0001 F1.S0002 ... F1.S2039 (2039 total) | |
| fvarLabels: fileIdx spIdx ... spectrum (35 total) | |
| fvarMetadata: labelDescription | |
| experimentData: use 'experimentData(object)' | |
| - - - xcms preprocessing - - - | |
| Chromatographic peak detection: | |
| method: centWave | |
| 3327 peaks identified in 1 samples. | |
| On average 3327 chromatographic peaks per sample. | |
| xcmsSet OBJECT INFO | |
| An "xcmsSet" object with 1 samples | |
| Time range: 4-1139.1 seconds (0.1-19 minutes) | |
| Mass range: 50.0321-963.0398 m/z | |
| Peaks: 3327 (about 3327 per sample) | |
| Peak Groups: 0 | |
| Sample classes: . | |
| Feature detection: | |
| o Peak picking performed on MS1. | |
| o Scan range limited to 1 - 2039 | |
| Profile settings: method = bin | |
| step = 0.1 | |
| Memory usage: 0.808 MB | |
| DONE | |
| ``` | |
| **Traceback:** | |
| * ```console | |
| ``` | |
| **Job Parameters:** | |
| * | Job parameter | Parameter value | | |
| | ------------- | --------------- | | |
| | \_\_input\_ext | ` "input" ` | | |
| | \_\_workflow\_invocation\_uuid\_\_ | ` "b39b8d62114e11f189517ced8d633c14" ` | | |
| | chromInfo | ` "/tmp/tmpni2hmxgh/galaxy-dev/tool-data/shared/ucsc/chrom/?.len" ` | | |
| | dbkey | ` "?" ` | | |
| | file\_load\_section | ` {"file_load_conditional": {"__current_case__": 0, "file_load_select": "no"}} ` | | |
| | filterSection | ` {"filterAcquisitionNum": "", "filterMz": "", "filterRt": ""} ` | | |
| | methods | ` {"CentWaveAdv": {"CentWaveAdvROI": {"firstBaselineCheck": true, "roiList": null, "roiScales": ""}, "fitgauss": false, "integrate": "1", "mzCenterFun": "wMean", "mzdiff": "-0.001", "noise": "1000", "peaklist": false, "prefilter": "3,5000", "snthresh": "10", "verboseColumns": false}, "__current_case__": 0, "method": "CentWave", "peakwidth": "5,20", "ppm": "3.0"} ` | | |
| </details> | |
| - **Step 6: Unlabelled step (toolshed.g2.bx.psu.edu/repos/lecorguille/xcms\_merge/xcms\_merge/3.12.0+galaxy3)**: | |
| * step_state: scheduled | |
| * <details><summary>Jobs</summary> | |
| - **Job 1:** | |
| * Job state is ok | |
| **Container:** | |
| * ```console | |
| quay.io/biocontainers/mulled-v2-007db2e42e47018763bae6b2bd1e69345120fe7f:ffab248635d36a246a435f3341c896269df9943c-2 | |
| ``` | |
| **Command Line:** | |
| * ```console | |
| LC_ALL=C Rscript /tmp/shed_dir/toolshed.g2.bx.psu.edu/repos/lecorguille/xcms_merge/ae28a753a6f8/xcms_merge/xcms_merge.r images 'c("/tmp/tmpni2hmxgh/files/e/4/8/dataset_e48bc30a-61e5-41c9-bdab-80d7ac5e8f28.dat","/tmp/tmpni2hmxgh/files/5/5/5/dataset_5552ece6-062d-4a5e-8d91-6369b8996a61.dat","/tmp/tmpni2hmxgh/files/d/3/f/dataset_d3fe4368-91e4-4ba6-88d8-2c037fe0e97a.dat","/tmp/tmpni2hmxgh/files/4/4/f/dataset_44f165fa-fbd1-49ff-a637-fa500a258e55.dat","/tmp/tmpni2hmxgh/files/f/2/5/dataset_f254a497-8ec7-40d8-9952-adda107af6d3.dat","/tmp/tmpni2hmxgh/files/2/4/0/dataset_240b4e06-d64b-4240-accf-e289380ad700.dat","/tmp/tmpni2hmxgh/files/2/3/b/dataset_23bc59c1-cecc-45b0-b876-fc3086987826.dat","/tmp/tmpni2hmxgh/files/5/d/a/dataset_5da84344-e9a8-4ad5-97fb-58b9d69e66f8.dat","/tmp/tmpni2hmxgh/files/7/a/4/dataset_7a4e9d8e-fc0e-4d43-a836-fae4df723a7c.dat","/tmp/tmpni2hmxgh/files/7/c/d/dataset_7cd4334c-c941-4d85-9dbd-54405b0dec83.dat","/tmp/tmpni2hmxgh/files/b/8/f/dataset_b8f8eea7-8b0a-4df4-9840-abcd535ccbf8.dat","/tmp/tmpni2hmxgh/files/7/9/e/dataset_79ee46ec-262d-480c-9eae-3ca75ceb0df4.dat")' sampleMetadata '/tmp/tmpni2hmxgh/files/9/a/6/dataset_9a642ccc-4da5-4a7e-8b38-ba2e1b5a4979.dat' | |
| ``` | |
| **Exit Code:** | |
| * ```console | |
| 0 | |
| ``` | |
| **Standard Error:** | |
| * ```console | |
| Note: you might want to set/adjust the 'sampclass' of the returned xcmSet object before proceeding with the analysis. | |
| ``` | |
| **Standard Output:** | |
| * ```console | |
| R version 4.0.5 (2021-03-31) | |
| Main packages: | |
| batch 1.1.5 xcms 3.12.0 MSnbase 2.16.1 ProtGenerics 1.22.0 S4Vectors 0.28.1 mzR 2.24.1 Rcpp 1.0.6 BiocParallel 1.24.1 Biobase 2.50.0 BiocGenerics 0.36.0 | |
| Other loaded packages: | |
| SummarizedExperiment 1.20.0 lattice 0.20.44 colorspace 2.0.1 vctrs 0.3.8 vsn 3.58.0 utf8 1.2.1 XML 3.99.0.6 rlang 0.4.11 pillar 1.6.0 glue 1.4.2 affy 1.68.0 RColorBrewer 1.1.2 affyio 1.60.0 matrixStats 0.58.0 GenomeInfoDbData 1.2.4 foreach 1.5.1 lifecycle 1.0.0 plyr 1.8.6 mzID 1.28.0 robustbase 0.93.7 zlibbioc 1.36.0 MatrixGenerics 1.2.1 munsell 0.5.0 pcaMethods 1.82.0 gtable 0.3.0 codetools 0.2.18 IRanges 2.24.1 doParallel 1.0.16 GenomeInfoDb 1.26.4 MassSpecWavelet 1.56.0 fansi 0.4.2 preprocessCore 1.52.1 DEoptimR 1.0.8 scales 1.1.1 BiocManager 1.30.15 DelayedArray 0.16.3 limma 3.46.0 XVector 0.30.0 MsCoreUtils 1.2.0 RANN 2.6.1 impute 1.64.0 ggplot2 3.3.3 digest 0.6.27 ncdf4 1.17 GenomicRanges 1.42.0 grid 4.0.5 tools 4.0.5 bitops 1.0.7 magrittr 2.0.1 RCurl 1.98.1.3 tibble 3.1.1 crayon 1.4.1 pkgconfig 2.0.3 Matrix 1.3.2 MASS 7.3.54 ellipsis 0.3.2 iterators 1.0.13 R6 2.5.0 MALDIquant 1.19.3 compiler 4.0.5 | |
| XSET MERGING... | |
| Blanc05 | |
| Blanc10 | |
| Blanc16 | |
| HU_neg_048 | |
| HU_neg_090 | |
| HU_neg_123 | |
| HU_neg_157 | |
| HU_neg_173 | |
| HU_neg_192 | |
| QC1_002 | |
| QC1_008 | |
| QC1_014 | |
| XSET PHENODATA SETTING... | |
| Creating the sampleMetadata file... | |
| Error in R_nc4_open: NetCDF: Unknown file format | |
| Error in R_nc4_open: NetCDF: Unknown file format | |
| Error in R_nc4_open: NetCDF: Unknown file format | |
| Error in R_nc4_open: NetCDF: Unknown file format | |
| Error in R_nc4_open: NetCDF: Unknown file format | |
| Error in R_nc4_open: NetCDF: Unknown file format | |
| Error in R_nc4_open: NetCDF: Unknown file format | |
| Error in R_nc4_open: NetCDF: Unknown file format | |
| Error in R_nc4_open: NetCDF: Unknown file format | |
| Error in R_nc4_open: NetCDF: Unknown file format | |
| Error in R_nc4_open: NetCDF: Unknown file format | |
| Error in R_nc4_open: NetCDF: Unknown file format | |
| XCMSnExp OBJECT INFO | |
| sample_name sample_group | |
| Blanc05.mzML Blanc05 blk | |
| Blanc10.mzML Blanc10 blk | |
| Blanc16.mzML Blanc16 blk | |
| HU_neg_048.mzML HU_neg_048 sample | |
| HU_neg_090.mzML HU_neg_090 sample | |
| HU_neg_123.mzML HU_neg_123 sample | |
| HU_neg_157.mzML HU_neg_157 sample | |
| HU_neg_173.mzML HU_neg_173 sample | |
| HU_neg_192.mzML HU_neg_192 sample | |
| QC1_002.mzML QC1_002 QC | |
| QC1_008.mzML QC1_008 QC | |
| QC1_014.mzML QC1_014 QC | |
| MSn experiment data ("XCMSnExp") | |
| Object size in memory: 6.31 Mb | |
| - - - Spectra data - - - | |
| MS level(s): 1 | |
| Number of spectra: 21878 | |
| MSn retention times: 0:1 - 18:60 minutes | |
| - - - Processing information - - - | |
| Concatenated [Tue Feb 24 07:06:25 2026] | |
| MSnbase version: 2.16.1 | |
| - - - Meta data - - - | |
| phenoData | |
| rowNames: Blanc05.mzML Blanc10.mzML ... QC1_014.mzML (12 total) | |
| varLabels: sample_name sample_group | |
| varMetadata: labelDescription | |
| Loaded from: | |
| [1] Blanc05.mzML... [12] QC1_014.mzML | |
| Use 'fileNames(.)' to see all files. | |
| protocolData: none | |
| featureData | |
| featureNames: F1.S0001 F1.S0002 ... F12.S1533 (21878 total) | |
| fvarLabels: fileIdx spIdx ... spectrum (35 total) | |
| fvarMetadata: labelDescription | |
| experimentData: use 'experimentData(object)' | |
| - - - xcms preprocessing - - - | |
| Chromatographic peak detection: | |
| method: centWave | |
| 34716 peaks identified in 12 samples. | |
| On average 2893 chromatographic peaks per sample. | |
| xcmsSet OBJECT INFO | |
| sample_name sample_group class | |
| Blanc05.mzML Blanc05 blk blk | |
| Blanc10.mzML Blanc10 blk blk | |
| Blanc16.mzML Blanc16 blk blk | |
| HU_neg_048.mzML HU_neg_048 sample sample | |
| HU_neg_090.mzML HU_neg_090 sample sample | |
| HU_neg_123.mzML HU_neg_123 sample sample | |
| HU_neg_157.mzML HU_neg_157 sample sample | |
| HU_neg_173.mzML HU_neg_173 sample sample | |
| HU_neg_192.mzML HU_neg_192 sample sample | |
| QC1_002.mzML QC1_002 QC QC | |
| QC1_008.mzML QC1_008 QC QC | |
| QC1_014.mzML QC1_014 QC QC | |
| An "xcmsSet" object with 12 samples | |
| Time range: 2-1139.5 seconds (0-19 minutes) | |
| Mass range: 50.025-989.2024 m/z | |
| Peaks: 34716 (about 2893 per sample) | |
| Peak Groups: 0 | |
| Sample classes: blk, sample, QC | |
| Feature detection: | |
| o Peak picking performed on MS1. | |
| o Scan range limited to 1 - 2039 | |
| Profile settings: method = bin | |
| step = 0.1 | |
| Memory usage: 8.47 MB | |
| SAVE RData | |
| ``` | |
| **Traceback:** | |
| * ```console | |
| ``` | |
| **Job Parameters:** | |
| * | Job parameter | Parameter value | | |
| | ------------- | --------------- | | |
| | \_\_input\_ext | ` "input" ` | | |
| | \_\_workflow\_invocation\_uuid\_\_ | ` "b39b8d62114e11f189517ced8d633c14" ` | | |
| | chromInfo | ` "/tmp/tmpni2hmxgh/galaxy-dev/tool-data/shared/ucsc/chrom/?.len" ` | | |
| | dbkey | ` "?" ` | | |
| | file\_load\_section | ` {"file_load_conditional": {"__current_case__": 0, "file_load_select": "no"}} ` | | |
| </details> | |
| - **Step 7: Unlabelled step (toolshed.g2.bx.psu.edu/repos/lecorguille/xcms\_group/abims\_xcms\_group/3.12.0+galaxy3)**: | |
| * step_state: scheduled | |
| * <details><summary>Jobs</summary> | |
| - **Job 1:** | |
| * Job state is ok | |
| **Container:** | |
| * ```console | |
| quay.io/biocontainers/mulled-v2-007db2e42e47018763bae6b2bd1e69345120fe7f:ffab248635d36a246a435f3341c896269df9943c-2 | |
| ``` | |
| **Command Line:** | |
| * ```console | |
| LC_ALL=C Rscript /tmp/shed_dir/toolshed.g2.bx.psu.edu/repos/lecorguille/xcms_group/3820e3f3b1cb/xcms_group/xcms_group.r image '/tmp/tmpni2hmxgh/files/6/c/1/dataset_6c1053c1-871f-4018-b9b3-f81793838315.dat' method PeakDensity bw 5.0 minFraction 0.9 minSamples 1 binSize 0.01 maxFeatures 50 convertRTMinute FALSE numDigitsMZ 4 numDigitsRT 0 intval into naTOzero TRUE ; return=$?; cat 'log.txt'; sh -c "exit $return" | |
| ``` | |
| **Exit Code:** | |
| * ```console | |
| 0 | |
| ``` | |
| **Standard Error:** | |
| * ```console | |
| Processing 187837 mz slices ... OK | |
| There were 50 or more warnings (use warnings() to see the first 50) | |
| Note: you might want to set/adjust the 'sampclass' of the returned xcmSet object before proceeding with the analysis. | |
| ``` | |
| **Standard Output:** | |
| * ```console | |
| SESSION INFO | |
| R version 4.0.5 (2021-03-31) | |
| Main packages: | |
| RColorBrewer 1.1.2 batch 1.1.5 xcms 3.12.0 MSnbase 2.16.1 ProtGenerics 1.22.0 S4Vectors 0.28.1 mzR 2.24.1 Rcpp 1.0.6 BiocParallel 1.24.1 Biobase 2.50.0 BiocGenerics 0.36.0 | |
| Other loaded packages: | |
| SummarizedExperiment 1.20.0 lattice 0.20.44 colorspace 2.0.1 vctrs 0.3.8 vsn 3.58.0 utf8 1.2.1 XML 3.99.0.6 rlang 0.4.11 pillar 1.6.0 glue 1.4.2 affy 1.68.0 affyio 1.60.0 matrixStats 0.58.0 GenomeInfoDbData 1.2.4 foreach 1.5.1 lifecycle 1.0.0 plyr 1.8.6 mzID 1.28.0 robustbase 0.93.7 zlibbioc 1.36.0 MatrixGenerics 1.2.1 munsell 0.5.0 pcaMethods 1.82.0 gtable 0.3.0 codetools 0.2.18 IRanges 2.24.1 doParallel 1.0.16 GenomeInfoDb 1.26.4 MassSpecWavelet 1.56.0 fansi 0.4.2 preprocessCore 1.52.1 DEoptimR 1.0.8 scales 1.1.1 BiocManager 1.30.15 DelayedArray 0.16.3 limma 3.46.0 XVector 0.30.0 MsCoreUtils 1.2.0 RANN 2.6.1 impute 1.64.0 ggplot2 3.3.3 digest 0.6.27 ncdf4 1.17 GenomicRanges 1.42.0 grid 4.0.5 tools 4.0.5 bitops 1.0.7 magrittr 2.0.1 RCurl 1.98.1.3 tibble 3.1.1 crayon 1.4.1 pkgconfig 2.0.3 Matrix 1.3.2 MASS 7.3.54 ellipsis 0.3.2 iterators 1.0.13 R6 2.5.0 MALDIquant 1.19.3 compiler 4.0.5 | |
| ARGUMENTS INFO | |
| image /tmp/tmpni2hmxgh/files/6/c/1/dataset_6c1053c1-871f-4018-b9b3-f81793838315.dat | |
| method PeakDensity | |
| bw 5 | |
| minFraction 0.9 | |
| minSamples 1 | |
| binSize 0.01 | |
| maxFeatures 50 | |
| convertRTMinute FALSE | |
| numDigitsMZ 4 | |
| numDigitsRT 0 | |
| intval into | |
| naTOzero TRUE | |
| ARGUMENTS PROCESSING INFO | |
| INFILE PROCESSING INFO | |
| MAIN PROCESSING INFO | |
| COMPUTE | |
| Perform the correspondence | |
| Object of class: PeakDensityParam | |
| Parameters: | |
| sampleGroups: character of length 12 | |
| bw: 5 | |
| minFraction: 0.9 | |
| minSamples: 1 | |
| binSize: 0.01 | |
| maxFeatures: 50 | |
| DRAW GRAPHICS | |
| null device | |
| 1 | |
| XCMSnExp OBJECT INFO | |
| MSn experiment data ("XCMSnExp") | |
| Object size in memory: 6.31 Mb | |
| - - - Spectra data - - - | |
| MS level(s): 1 | |
| Number of spectra: 21878 | |
| MSn retention times: 0:1 - 18:60 minutes | |
| - - - Processing information - - - | |
| Concatenated [Tue Feb 24 07:06:25 2026] | |
| MSnbase version: 2.16.1 | |
| - - - Meta data - - - | |
| phenoData | |
| rowNames: Blanc05.mzML Blanc10.mzML ... QC1_014.mzML (12 total) | |
| varLabels: sample_name sample_group | |
| varMetadata: labelDescription | |
| Loaded from: | |
| [1] Blanc05.mzML... [12] QC1_014.mzML | |
| Use 'fileNames(.)' to see all files. | |
| protocolData: none | |
| featureData | |
| featureNames: F1.S0001 F1.S0002 ... F12.S1533 (21878 total) | |
| fvarLabels: fileIdx spIdx ... spectrum (35 total) | |
| fvarMetadata: labelDescription | |
| experimentData: use 'experimentData(object)' | |
| - - - xcms preprocessing - - - | |
| Chromatographic peak detection: | |
| method: centWave | |
| 34716 peaks identified in 12 samples. | |
| On average 2893 chromatographic peaks per sample. | |
| Correspondence: | |
| method: chromatographic peak density | |
| 2228 features identified. | |
| Median mz range of features: 0.00028788 | |
| Median rt range of features: 1.747 | |
| xcmsSet OBJECT INFO | |
| An "xcmsSet" object with 12 samples | |
| Time range: 2-1139.5 seconds (0-19 minutes) | |
| Mass range: 50.025-989.2024 m/z | |
| Peaks: 34716 (about 2893 per sample) | |
| Peak Groups: 2228 | |
| Sample classes: blk, sample, QC | |
| Feature detection: | |
| o Peak picking performed on MS1. | |
| o Scan range limited to 1 - 2039 | |
| Profile settings: method = bin | |
| step = 0.1 | |
| Memory usage: 8.98 MB | |
| DONE | |
| ``` | |
| **Traceback:** | |
| * ```console | |
| ``` | |
| **Job Parameters:** | |
| * | Job parameter | Parameter value | | |
| | ------------- | --------------- | | |
| | \_\_input\_ext | ` "input" ` | | |
| | \_\_workflow\_invocation\_uuid\_\_ | ` "b39b8d62114e11f189517ced8d633c14" ` | | |
| | chromInfo | ` "/tmp/tmpni2hmxgh/galaxy-dev/tool-data/shared/ucsc/chrom/?.len" ` | | |
| | dbkey | ` "?" ` | | |
| | file\_load\_section | ` {"file_load_conditional": {"__current_case__": 0, "file_load_select": "no"}} ` | | |
| | methods | ` {"PeakDensityAdv": {"maxFeatures": "50"}, "__current_case__": 0, "binSize": "0.01", "bw": "5.0", "method": "PeakDensity", "minFraction": "0.9", "minSamples": "1"} ` | | |
| | peaklist | ` {"__current_case__": 0, "convertRTMinute": false, "intval": "into", "naTOzero": true, "numDigitsMZ": "4", "numDigitsRT": "0", "peaklistBool": "true"} ` | | |
| </details> | |
| - **Step 8: Unlabelled step (toolshed.g2.bx.psu.edu/repos/lecorguille/xcms\_retcor/abims\_xcms\_retcor/3.12.0+galaxy3)**: | |
| * step_state: scheduled | |
| * <details><summary>Jobs</summary> | |
| - **Job 1:** | |
| * Job state is ok | |
| **Container:** | |
| * ```console | |
| quay.io/biocontainers/mulled-v2-007db2e42e47018763bae6b2bd1e69345120fe7f:ffab248635d36a246a435f3341c896269df9943c-2 | |
| ``` | |
| **Command Line:** | |
| * ```console | |
| LC_ALL=C Rscript /tmp/shed_dir/toolshed.g2.bx.psu.edu/repos/lecorguille/xcms_retcor/33c0ca93f3ee/xcms_retcor/xcms_retcor.r image '/tmp/tmpni2hmxgh/files/d/e/4/dataset_de4ee60e-eff8-4f73-b3e7-4f97489bec5d.dat' method PeakGroups minFraction 0.7 extraPeaks 1 smooth loess span 0.2 family gaussian ; return=$?; cat 'log.txt'; sh -c "exit $return" | |
| ``` | |
| **Exit Code:** | |
| * ```console | |
| 0 | |
| ``` | |
| **Standard Error:** | |
| * ```console | |
| Performing retention time correction using 673 peak groups. | |
| Applying retention time adjustment to the identified chromatographic peaks ... OK | |
| Warning message: | |
| Adjusted retention times had to be re-adjusted for some files to ensure them being in the same order than the raw retention times. A call to 'dropAdjustedRtime' might thus fail to restore retention times of chromatographic peaks to their original values. Eventually consider to increase the value of the 'span' parameter. | |
| Note: you might want to set/adjust the 'sampclass' of the returned xcmSet object before proceeding with the analysis. | |
| ``` | |
| **Standard Output:** | |
| * ```console | |
| SESSION INFO | |
| R version 4.0.5 (2021-03-31) | |
| Main packages: | |
| RColorBrewer 1.1.2 batch 1.1.5 xcms 3.12.0 MSnbase 2.16.1 ProtGenerics 1.22.0 S4Vectors 0.28.1 mzR 2.24.1 Rcpp 1.0.6 BiocParallel 1.24.1 Biobase 2.50.0 BiocGenerics 0.36.0 | |
| Other loaded packages: | |
| SummarizedExperiment 1.20.0 lattice 0.20.44 colorspace 2.0.1 vctrs 0.3.8 vsn 3.58.0 utf8 1.2.1 XML 3.99.0.6 rlang 0.4.11 pillar 1.6.0 glue 1.4.2 affy 1.68.0 affyio 1.60.0 matrixStats 0.58.0 GenomeInfoDbData 1.2.4 foreach 1.5.1 lifecycle 1.0.0 plyr 1.8.6 mzID 1.28.0 robustbase 0.93.7 zlibbioc 1.36.0 MatrixGenerics 1.2.1 munsell 0.5.0 pcaMethods 1.82.0 gtable 0.3.0 codetools 0.2.18 IRanges 2.24.1 doParallel 1.0.16 GenomeInfoDb 1.26.4 MassSpecWavelet 1.56.0 fansi 0.4.2 preprocessCore 1.52.1 DEoptimR 1.0.8 scales 1.1.1 BiocManager 1.30.15 DelayedArray 0.16.3 limma 3.46.0 XVector 0.30.0 MsCoreUtils 1.2.0 RANN 2.6.1 impute 1.64.0 ggplot2 3.3.3 digest 0.6.27 ncdf4 1.17 GenomicRanges 1.42.0 grid 4.0.5 tools 4.0.5 bitops 1.0.7 magrittr 2.0.1 RCurl 1.98.1.3 tibble 3.1.1 crayon 1.4.1 pkgconfig 2.0.3 Matrix 1.3.2 MASS 7.3.54 ellipsis 0.3.2 iterators 1.0.13 R6 2.5.0 MALDIquant 1.19.3 compiler 4.0.5 | |
| ARGUMENTS INFO | |
| image /tmp/tmpni2hmxgh/files/d/e/4/dataset_de4ee60e-eff8-4f73-b3e7-4f97489bec5d.dat | |
| method PeakGroups | |
| minFraction 0.7 | |
| extraPeaks 1 | |
| smooth loess | |
| span 0.2 | |
| family gaussian | |
| ARGUMENTS PROCESSING INFO | |
| INFILE PROCESSING INFO | |
| MAIN PROCESSING INFO | |
| COMPUTE | |
| Alignment/Retention Time correction | |
| Object of class: PeakGroupsParam | |
| Parameters: | |
| minFraction: 0.7 | |
| extraPeaks: 1 | |
| smooth: loess | |
| span: 0.2 | |
| family: gaussian | |
| subset: | |
| DRAW GRAPHICS | |
| null device | |
| 1 | |
| XCMSnExp OBJECT INFO | |
| MSn experiment data ("XCMSnExp") | |
| Object size in memory: 6.42 Mb | |
| - - - Spectra data - - - | |
| MS level(s): 1 | |
| Number of spectra: 21878 | |
| MSn retention times: -1:58 - 19:2 minutes | |
| - - - Processing information - - - | |
| Concatenated [Tue Feb 24 07:06:25 2026] | |
| MSnbase version: 2.16.1 | |
| - - - Meta data - - - | |
| phenoData | |
| rowNames: Blanc05.mzML Blanc10.mzML ... QC1_014.mzML (12 total) | |
| varLabels: sample_name sample_group | |
| varMetadata: labelDescription | |
| Loaded from: | |
| [1] Blanc05.mzML... [12] QC1_014.mzML | |
| Use 'fileNames(.)' to see all files. | |
| protocolData: none | |
| featureData | |
| featureNames: F1.S0001 F1.S0002 ... F12.S1533 (21878 total) | |
| fvarLabels: fileIdx spIdx ... spectrum (35 total) | |
| fvarMetadata: labelDescription | |
| experimentData: use 'experimentData(object)' | |
| - - - xcms preprocessing - - - | |
| Chromatographic peak detection: | |
| method: centWave | |
| 34716 peaks identified in 12 samples. | |
| On average 2893 chromatographic peaks per sample. | |
| Alignment/retention time adjustment: | |
| method: peak groups | |
| xcmsSet OBJECT INFO | |
| An "xcmsSet" object with 12 samples | |
| Time range: 1.1-1141.8 seconds (0-19 minutes) | |
| Mass range: 50.025-989.2024 m/z | |
| Peaks: 34716 (about 2893 per sample) | |
| Peak Groups: 0 | |
| Sample classes: blk, sample, QC | |
| Feature detection: | |
| o Peak picking performed on MS1. | |
| o Scan range limited to 1 - 2039 | |
| Profile settings: method = bin | |
| step = 0.1 | |
| Memory usage: 8.58 MB | |
| DONE | |
| ``` | |
| **Traceback:** | |
| * ```console | |
| ``` | |
| **Job Parameters:** | |
| * | Job parameter | Parameter value | | |
| | ------------- | --------------- | | |
| | \_\_input\_ext | ` "input" ` | | |
| | \_\_workflow\_invocation\_uuid\_\_ | ` "b39b8d62114e11f189517ced8d633c14" ` | | |
| | chromInfo | ` "/tmp/tmpni2hmxgh/galaxy-dev/tool-data/shared/ucsc/chrom/?.len" ` | | |
| | dbkey | ` "?" ` | | |
| | file\_load\_section | ` {"file_load_conditional": {"__current_case__": 0, "file_load_select": "no"}} ` | | |
| | methods | ` {"__current_case__": 0, "extraPeaks": "1", "method": "PeakGroups", "minFraction": "0.7", "smooth_cond": {"PeakGroupsSmoothLoessAdv": {"family": "gaussian", "span": "0.2"}, "__current_case__": 0, "smooth": "loess"}} ` | | |
| </details> | |
| - **Step 9: Unlabelled step (toolshed.g2.bx.psu.edu/repos/ethevenot/checkformat/checkFormat/3.0.0)**: | |
| * step_state: scheduled | |
| * <details><summary>Jobs</summary> | |
| - **Job 1:** | |
| * Job state is ok | |
| **Container:** | |
| * ```console | |
| quay.io/biocontainers/r-batch:1.1_4--r3.3.2_1 | |
| ``` | |
| **Command Line:** | |
| * ```console | |
| Rscript /tmp/shed_dir/toolshed.g2.bx.psu.edu/repos/ethevenot/checkformat/e7c5811ec12f/checkformat/checkformat_wrapper.R dataMatrix_in "/tmp/tmpni2hmxgh/files/f/c/1/dataset_fc1bad60-f56d-4d49-9dae-e1f9a0c1640a.dat" sampleMetadata_in "/tmp/tmpni2hmxgh/files/9/a/6/dataset_9a642ccc-4da5-4a7e-8b38-ba2e1b5a4979.dat" variableMetadata_in "/tmp/tmpni2hmxgh/files/e/4/f/dataset_e4fd1485-fda6-464b-aae4-c5a8ed6f00e9.dat" makeNameL "FALSE" dataMatrix_out "/tmp/tmpni2hmxgh/job_working_directory/000/42/outputs/dataset_9f2d75b6-43d3-4196-b284-8e8aa72248aa.dat" sampleMetadata_out "/tmp/tmpni2hmxgh/job_working_directory/000/42/outputs/dataset_fb3e9cec-92e5-44b4-97b9-4a98bc401d73.dat" variableMetadata_out "/tmp/tmpni2hmxgh/job_working_directory/000/42/outputs/dataset_113c0ca0-aba2-4d9b-9d4f-9cd11e03d502.dat" information "/tmp/tmpni2hmxgh/job_working_directory/000/42/outputs/dataset_ce78e5c7-6ca6-4872-8705-b97ff02a670c.dat" | |
| ``` | |
| **Exit Code:** | |
| * ```console | |
| 0 | |
| ``` | |
| **Traceback:** | |
| * ```console | |
| ``` | |
| **Job Parameters:** | |
| * | Job parameter | Parameter value | | |
| | ------------- | --------------- | | |
| | \_\_input\_ext | ` "tabular" ` | | |
| | \_\_workflow\_invocation\_uuid\_\_ | ` "b39b8d62114e11f189517ced8d633c14" ` | | |
| | chromInfo | ` "/tmp/tmpni2hmxgh/galaxy-dev/tool-data/shared/ucsc/chrom/?.len" ` | | |
| | dbkey | ` "?" ` | | |
| | makeNameL | ` "FALSE" ` | | |
| </details> | |
| - **Step 10: Unlabelled step (toolshed.g2.bx.psu.edu/repos/lecorguille/xcms\_plot\_chromatogram/xcms\_plot\_chromatogram/3.12.0+galaxy3)**: | |
| * step_state: scheduled | |
| * <details><summary>Jobs</summary> | |
| - **Job 1:** | |
| * Job state is ok | |
| **Container:** | |
| * ```console | |
| quay.io/biocontainers/mulled-v2-007db2e42e47018763bae6b2bd1e69345120fe7f:ffab248635d36a246a435f3341c896269df9943c-2 | |
| ``` | |
| **Command Line:** | |
| * ```console | |
| LC_ALL=C Rscript /tmp/shed_dir/toolshed.g2.bx.psu.edu/repos/lecorguille/xcms_plot_chromatogram/9291271ec4d9/xcms_plot_chromatogram/xcms_plot_chromatogram.r images 'c("/tmp/tmpni2hmxgh/files/8/e/b/dataset_8eb0856a-e316-4a7f-a2fe-f39cfea14dfe.dat")' sampleMetadata '/tmp/tmpni2hmxgh/files/9/a/6/dataset_9a642ccc-4da5-4a7e-8b38-ba2e1b5a4979.dat' | |
| ``` | |
| **Exit Code:** | |
| * ```console | |
| 0 | |
| ``` | |
| **Standard Output:** | |
| * ```console | |
| SESSION INFO | |
| R version 4.0.5 (2021-03-31) | |
| Main packages: | |
| RColorBrewer 1.1.2 batch 1.1.5 xcms 3.12.0 MSnbase 2.16.1 ProtGenerics 1.22.0 S4Vectors 0.28.1 mzR 2.24.1 Rcpp 1.0.6 BiocParallel 1.24.1 Biobase 2.50.0 BiocGenerics 0.36.0 | |
| Other loaded packages: | |
| SummarizedExperiment 1.20.0 lattice 0.20.44 colorspace 2.0.1 vctrs 0.3.8 vsn 3.58.0 utf8 1.2.1 XML 3.99.0.6 rlang 0.4.11 pillar 1.6.0 glue 1.4.2 affy 1.68.0 affyio 1.60.0 matrixStats 0.58.0 GenomeInfoDbData 1.2.4 foreach 1.5.1 lifecycle 1.0.0 plyr 1.8.6 mzID 1.28.0 robustbase 0.93.7 zlibbioc 1.36.0 MatrixGenerics 1.2.1 munsell 0.5.0 pcaMethods 1.82.0 gtable 0.3.0 codetools 0.2.18 IRanges 2.24.1 doParallel 1.0.16 GenomeInfoDb 1.26.4 MassSpecWavelet 1.56.0 fansi 0.4.2 preprocessCore 1.52.1 DEoptimR 1.0.8 scales 1.1.1 BiocManager 1.30.15 DelayedArray 0.16.3 limma 3.46.0 XVector 0.30.0 MsCoreUtils 1.2.0 RANN 2.6.1 impute 1.64.0 ggplot2 3.3.3 digest 0.6.27 ncdf4 1.17 GenomicRanges 1.42.0 grid 4.0.5 tools 4.0.5 bitops 1.0.7 magrittr 2.0.1 RCurl 1.98.1.3 tibble 3.1.1 crayon 1.4.1 pkgconfig 2.0.3 Matrix 1.3.2 MASS 7.3.54 ellipsis 0.3.2 iterators 1.0.13 R6 2.5.0 MALDIquant 1.19.3 compiler 4.0.5 | |
| ARGUMENTS INFO | |
| images /tmp/tmpni2hmxgh/files/8/e/b/dataset_8eb0856a-e316-4a7f-a2fe-f39cfea14dfe.dat | |
| sampleMetadata /tmp/tmpni2hmxgh/files/9/a/6/dataset_9a642ccc-4da5-4a7e-8b38-ba2e1b5a4979.dat | |
| ARGUMENTS PROCESSING INFO | |
| INFILE PROCESSING INFO | |
| Blanc05 Blanc10 Blanc16 HU_neg_048 HU_neg_090 HU_neg_123 HU_neg_157 HU_neg_173 HU_neg_192 QC1_002 QC1_008 QC1_014 | |
| XSET PHENODATA SETTING... | |
| MAIN PROCESSING INFO | |
| DRAW GRAPHICS | |
| Compute TIC | |
| Compute BPI | |
| null device | |
| 1 | |
| null device | |
| 1 | |
| XCMSnExp OBJECT INFO | |
| MSn experiment data ("XCMSnExp") | |
| Object size in memory: 6.42 Mb | |
| - - - Spectra data - - - | |
| MS level(s): 1 | |
| Number of spectra: 21878 | |
| MSn retention times: -1:58 - 19:2 minutes | |
| - - - Processing information - - - | |
| Concatenated [Tue Feb 24 07:06:25 2026] | |
| MSnbase version: 2.16.1 | |
| - - - Meta data - - - | |
| phenoData | |
| rowNames: Blanc05.mzML Blanc10.mzML ... QC1_014.mzML (12 total) | |
| varLabels: sample_name sample_group | |
| varMetadata: labelDescription | |
| Loaded from: | |
| [1] Blanc05.mzML... [12] QC1_014.mzML | |
| Use 'fileNames(.)' to see all files. | |
| protocolData: none | |
| featureData | |
| featureNames: F1.S0001 F1.S0002 ... F12.S1533 (21878 total) | |
| fvarLabels: fileIdx spIdx ... spectrum (35 total) | |
| fvarMetadata: labelDescription | |
| experimentData: use 'experimentData(object)' | |
| - - - xcms preprocessing - - - | |
| Chromatographic peak detection: | |
| method: centWave | |
| 34716 peaks identified in 12 samples. | |
| On average 2893 chromatographic peaks per sample. | |
| Alignment/retention time adjustment: | |
| method: peak groups | |
| DONE | |
| ``` | |
| **Traceback:** | |
| * ```console | |
| ``` | |
| **Job Parameters:** | |
| * | Job parameter | Parameter value | | |
| | ------------- | --------------- | | |
| | \_\_input\_ext | ` "input" ` | | |
| | \_\_workflow\_invocation\_uuid\_\_ | ` "b39b8d62114e11f189517ced8d633c14" ` | | |
| | chromInfo | ` "/tmp/tmpni2hmxgh/galaxy-dev/tool-data/shared/ucsc/chrom/?.len" ` | | |
| | dbkey | ` "?" ` | | |
| | file\_load\_section | ` {"file_load_conditional": {"__current_case__": 0, "file_load_select": "no"}} ` | | |
| </details> | |
| - **Step 11: Unlabelled step (toolshed.g2.bx.psu.edu/repos/lecorguille/xcms\_group/abims\_xcms\_group/3.12.0+galaxy3)**: | |
| * step_state: scheduled | |
| * <details><summary>Jobs</summary> | |
| - **Job 1:** | |
| * Job state is ok | |
| **Container:** | |
| * ```console | |
| quay.io/biocontainers/mulled-v2-007db2e42e47018763bae6b2bd1e69345120fe7f:ffab248635d36a246a435f3341c896269df9943c-2 | |
| ``` | |
| **Command Line:** | |
| * ```console | |
| LC_ALL=C Rscript /tmp/shed_dir/toolshed.g2.bx.psu.edu/repos/lecorguille/xcms_group/3820e3f3b1cb/xcms_group/xcms_group.r image '/tmp/tmpni2hmxgh/files/8/e/b/dataset_8eb0856a-e316-4a7f-a2fe-f39cfea14dfe.dat' method PeakDensity bw 5.0 minFraction 0.9 minSamples 1 binSize 0.01 maxFeatures 50 convertRTMinute FALSE numDigitsMZ 4 numDigitsRT 0 intval into naTOzero TRUE ; return=$?; cat 'log.txt'; sh -c "exit $return" | |
| ``` | |
| **Exit Code:** | |
| * ```console | |
| 0 | |
| ``` | |
| **Standard Error:** | |
| * ```console | |
| Processing 187837 mz slices ... OK | |
| There were 50 or more warnings (use warnings() to see the first 50) | |
| Note: you might want to set/adjust the 'sampclass' of the returned xcmSet object before proceeding with the analysis. | |
| ``` | |
| **Standard Output:** | |
| * ```console | |
| SESSION INFO | |
| R version 4.0.5 (2021-03-31) | |
| Main packages: | |
| RColorBrewer 1.1.2 batch 1.1.5 xcms 3.12.0 MSnbase 2.16.1 ProtGenerics 1.22.0 S4Vectors 0.28.1 mzR 2.24.1 Rcpp 1.0.6 BiocParallel 1.24.1 Biobase 2.50.0 BiocGenerics 0.36.0 | |
| Other loaded packages: | |
| SummarizedExperiment 1.20.0 lattice 0.20.44 colorspace 2.0.1 vctrs 0.3.8 vsn 3.58.0 utf8 1.2.1 XML 3.99.0.6 rlang 0.4.11 pillar 1.6.0 glue 1.4.2 affy 1.68.0 affyio 1.60.0 matrixStats 0.58.0 GenomeInfoDbData 1.2.4 foreach 1.5.1 lifecycle 1.0.0 plyr 1.8.6 mzID 1.28.0 robustbase 0.93.7 zlibbioc 1.36.0 MatrixGenerics 1.2.1 munsell 0.5.0 pcaMethods 1.82.0 gtable 0.3.0 codetools 0.2.18 IRanges 2.24.1 doParallel 1.0.16 GenomeInfoDb 1.26.4 MassSpecWavelet 1.56.0 fansi 0.4.2 preprocessCore 1.52.1 DEoptimR 1.0.8 scales 1.1.1 BiocManager 1.30.15 DelayedArray 0.16.3 limma 3.46.0 XVector 0.30.0 MsCoreUtils 1.2.0 RANN 2.6.1 impute 1.64.0 ggplot2 3.3.3 digest 0.6.27 ncdf4 1.17 GenomicRanges 1.42.0 grid 4.0.5 tools 4.0.5 bitops 1.0.7 magrittr 2.0.1 RCurl 1.98.1.3 tibble 3.1.1 crayon 1.4.1 pkgconfig 2.0.3 Matrix 1.3.2 MASS 7.3.54 ellipsis 0.3.2 iterators 1.0.13 R6 2.5.0 MALDIquant 1.19.3 compiler 4.0.5 | |
| ARGUMENTS INFO | |
| image /tmp/tmpni2hmxgh/files/8/e/b/dataset_8eb0856a-e316-4a7f-a2fe-f39cfea14dfe.dat | |
| method PeakDensity | |
| bw 5 | |
| minFraction 0.9 | |
| minSamples 1 | |
| binSize 0.01 | |
| maxFeatures 50 | |
| convertRTMinute FALSE | |
| numDigitsMZ 4 | |
| numDigitsRT 0 | |
| intval into | |
| naTOzero TRUE | |
| ARGUMENTS PROCESSING INFO | |
| INFILE PROCESSING INFO | |
| MAIN PROCESSING INFO | |
| COMPUTE | |
| Perform the correspondence | |
| Object of class: PeakDensityParam | |
| Parameters: | |
| sampleGroups: character of length 12 | |
| bw: 5 | |
| minFraction: 0.9 | |
| minSamples: 1 | |
| binSize: 0.01 | |
| maxFeatures: 50 | |
| DRAW GRAPHICS | |
| null device | |
| 1 | |
| XCMSnExp OBJECT INFO | |
| MSn experiment data ("XCMSnExp") | |
| Object size in memory: 6.43 Mb | |
| - - - Spectra data - - - | |
| MS level(s): 1 | |
| Number of spectra: 21878 | |
| MSn retention times: -1:58 - 19:2 minutes | |
| - - - Processing information - - - | |
| Concatenated [Tue Feb 24 07:06:25 2026] | |
| MSnbase version: 2.16.1 | |
| - - - Meta data - - - | |
| phenoData | |
| rowNames: Blanc05.mzML Blanc10.mzML ... QC1_014.mzML (12 total) | |
| varLabels: sample_name sample_group | |
| varMetadata: labelDescription | |
| Loaded from: | |
| [1] Blanc05.mzML... [12] QC1_014.mzML | |
| Use 'fileNames(.)' to see all files. | |
| protocolData: none | |
| featureData | |
| featureNames: F1.S0001 F1.S0002 ... F12.S1533 (21878 total) | |
| fvarLabels: fileIdx spIdx ... spectrum (35 total) | |
| fvarMetadata: labelDescription | |
| experimentData: use 'experimentData(object)' | |
| - - - xcms preprocessing - - - | |
| Chromatographic peak detection: | |
| method: centWave | |
| 34716 peaks identified in 12 samples. | |
| On average 2893 chromatographic peaks per sample. | |
| Alignment/retention time adjustment: | |
| method: peak groups | |
| Correspondence: | |
| method: chromatographic peak density | |
| 2230 features identified. | |
| Median mz range of features: 0.00028742 | |
| Median rt range of features: 1.6196 | |
| xcmsSet OBJECT INFO | |
| An "xcmsSet" object with 12 samples | |
| Time range: 1.1-1141.8 seconds (0-19 minutes) | |
| Mass range: 50.025-989.2024 m/z | |
| Peaks: 34716 (about 2893 per sample) | |
| Peak Groups: 2230 | |
| Sample classes: blk, sample, QC | |
| Feature detection: | |
| o Peak picking performed on MS1. | |
| o Scan range limited to 1 - 2039 | |
| Profile settings: method = bin | |
| step = 0.1 | |
| Memory usage: 9.09 MB | |
| DONE | |
| ``` | |
| **Traceback:** | |
| * ```console | |
| ``` | |
| **Job Parameters:** | |
| * | Job parameter | Parameter value | | |
| | ------------- | --------------- | | |
| | \_\_input\_ext | ` "input" ` | | |
| | \_\_workflow\_invocation\_uuid\_\_ | ` "b39b8d62114e11f189517ced8d633c14" ` | | |
| | chromInfo | ` "/tmp/tmpni2hmxgh/galaxy-dev/tool-data/shared/ucsc/chrom/?.len" ` | | |
| | dbkey | ` "?" ` | | |
| | file\_load\_section | ` {"file_load_conditional": {"__current_case__": 0, "file_load_select": "no"}} ` | | |
| | methods | ` {"PeakDensityAdv": {"maxFeatures": "50"}, "__current_case__": 0, "binSize": "0.01", "bw": "5.0", "method": "PeakDensity", "minFraction": "0.9", "minSamples": "1"} ` | | |
| | peaklist | ` {"__current_case__": 0, "convertRTMinute": false, "intval": "into", "naTOzero": true, "numDigitsMZ": "4", "numDigitsRT": "0", "peaklistBool": "true"} ` | | |
| </details> | |
| - **Step 12: Unlabelled step (toolshed.g2.bx.psu.edu/repos/melpetera/intensity\_checks/intens\_check/1.3.0)**: | |
| * step_state: scheduled | |
| * <details><summary>Jobs</summary> | |
| - **Job 1:** | |
| * Job state is ok | |
| **Container:** | |
| * ```console | |
| quay.io/biocontainers/r-base:4.2.1 | |
| ``` | |
| **Command Line:** | |
| * ```console | |
| Rscript /tmp/shed_dir/toolshed.g2.bx.psu.edu/repos/melpetera/intensity_checks/ec75de7f1e08/intensity_checks/Intchecks/wrapper_intensity_check.R dataMatrix_in "/tmp/tmpni2hmxgh/files/9/f/2/dataset_9f2d75b6-43d3-4196-b284-8e8aa72248aa.dat" sampleMetadata_in "/tmp/tmpni2hmxgh/files/f/b/3/dataset_fb3e9cec-92e5-44b4-97b9-4a98bc401d73.dat" variableMetadata_in "/tmp/tmpni2hmxgh/files/1/1/3/dataset_113c0ca0-aba2-4d9b-9d4f-9cd11e03d502.dat" method "each_class" chosen_stat "NA" class_col "class" test_fold "No" variableMetadata_out "/tmp/tmpni2hmxgh/job_working_directory/000/45/outputs/dataset_2645060b-4ada-4d66-90f4-3eeafe89c96e.dat" graphs_out "/tmp/tmpni2hmxgh/job_working_directory/000/45/outputs/dataset_7e2c6ccc-5227-42d4-b7ec-96949f5a07f5.dat" | |
| ``` | |
| **Exit Code:** | |
| * ```console | |
| 0 | |
| ``` | |
| **Standard Output:** | |
| * ```console | |
| Job starting time: | |
| Tue 24 Feb 2026 07:08:13 | |
| -------------------------------------------------------------------- | |
| Intensity Check parameters: | |
| $dataMatrix_in | |
| [1] "/tmp/tmpni2hmxgh/files/9/f/2/dataset_9f2d75b6-43d3-4196-b284-8e8aa72248aa.dat" | |
| $sampleMetadata_in | |
| [1] "/tmp/tmpni2hmxgh/files/f/b/3/dataset_fb3e9cec-92e5-44b4-97b9-4a98bc401d73.dat" | |
| $variableMetadata_in | |
| [1] "/tmp/tmpni2hmxgh/files/1/1/3/dataset_113c0ca0-aba2-4d9b-9d4f-9cd11e03d502.dat" | |
| $method | |
| [1] "each_class" | |
| $chosen_stat | |
| [1] "NA" | |
| $class_col | |
| [1] "class" | |
| $test_fold | |
| [1] "No" | |
| $variableMetadata_out | |
| [1] "/tmp/tmpni2hmxgh/job_working_directory/000/45/outputs/dataset_2645060b-4ada-4d66-90f4-3eeafe89c96e.dat" | |
| $graphs_out | |
| [1] "/tmp/tmpni2hmxgh/job_working_directory/000/45/outputs/dataset_7e2c6ccc-5227-42d4-b7ec-96949f5a07f5.dat" | |
| -------------------------------------------------------------------- | |
| Data Matrix contains no NA. | |
| null device | |
| 1 | |
| -------------------------------------------------------------------- | |
| Information about R (version, Operating System, attached or loaded packages): | |
| R version 4.2.1 (2022-06-23) | |
| Platform: x86_64-conda-linux-gnu (64-bit) | |
| Running under: Debian GNU/Linux 10 (buster) | |
| Matrix products: default | |
| BLAS/LAPACK: /usr/local/lib/libopenblasp-r0.3.21.so | |
| locale: | |
| [1] LC_CTYPE=C.UTF-8 LC_NUMERIC=C LC_TIME=C.UTF-8 | |
| [4] LC_COLLATE=C.UTF-8 LC_MONETARY=C.UTF-8 LC_MESSAGES=C.UTF-8 | |
| [7] LC_PAPER=C.UTF-8 LC_NAME=C LC_ADDRESS=C | |
| [10] LC_TELEPHONE=C LC_MEASUREMENT=C.UTF-8 LC_IDENTIFICATION=C | |
| attached base packages: | |
| [1] stats graphics grDevices utils datasets methods base | |
| loaded via a namespace (and not attached): | |
| [1] compiler_4.2.1 | |
| -------------------------------------------------------------------- | |
| Job ending time: | |
| Tue 24 Feb 2026 07:08:14 | |
| ``` | |
| **Traceback:** | |
| * ```console | |
| ``` | |
| **Job Parameters:** | |
| * | Job parameter | Parameter value | | |
| | ------------- | --------------- | | |
| | \_\_input\_ext | ` "tabular" ` | | |
| | \_\_workflow\_invocation\_uuid\_\_ | ` "b39b8d62114e11f189517ced8d633c14" ` | | |
| | chromInfo | ` "/tmp/tmpni2hmxgh/galaxy-dev/tool-data/shared/ucsc/chrom/?.len" ` | | |
| | dbkey | ` "?" ` | | |
| | method\_cond | ` {"__current_case__": 1, "chosen_stat": ["NA"], "class_col": "class", "method": "each_class", "test_fold_cond": {"__current_case__": 1, "test_fold": "No"}} ` | | |
| </details> | |
| - **Step 13: Unlabelled step (toolshed.g2.bx.psu.edu/repos/lecorguille/xcms\_fillpeaks/abims\_xcms\_fillPeaks/3.12.0+galaxy3)**: | |
| * step_state: scheduled | |
| * <details><summary>Jobs</summary> | |
| - **Job 1:** | |
| * Job state is ok | |
| **Container:** | |
| * ```console | |
| quay.io/biocontainers/mulled-v2-007db2e42e47018763bae6b2bd1e69345120fe7f:ffab248635d36a246a435f3341c896269df9943c-2 | |
| ``` | |
| **Command Line:** | |
| * ```console | |
| LC_ALL=C Rscript /tmp/shed_dir/toolshed.g2.bx.psu.edu/repos/lecorguille/xcms_fillpeaks/a8d866a71ba1/xcms_fillpeaks/xcms_fillpeaks.r image '/tmp/tmpni2hmxgh/files/0/f/f/dataset_0ff2dca4-d671-49da-b75b-0599a101d129.dat' expandMz 0 expandRt 0 ppm 0 convertRTMinute FALSE numDigitsMZ 4 numDigitsRT 0 intval into naTOzero TRUE ; return=$?; cat 'log.txt'; sh -c "exit $return" | |
| ``` | |
| **Exit Code:** | |
| * ```console | |
| 0 | |
| ``` | |
| **Standard Error:** | |
| * ```console | |
| Defining peak areas for filling-in .... OK | |
| Start integrating peak areas from original files | |
| Requesting 1955 peaks from Blanc05.mzML ... got 82. | |
| Requesting 1942 peaks from Blanc10.mzML ... got 86. | |
| Requesting 1927 peaks from Blanc16.mzML ... got 147. | |
| Requesting 622 peaks from HU_neg_048.mzML ... got 316. | |
| Requesting 509 peaks from HU_neg_090.mzML ... got 315. | |
| Requesting 576 peaks from HU_neg_123.mzML ... got 342. | |
| Requesting 514 peaks from HU_neg_157.mzML ... got 331. | |
| Requesting 847 peaks from HU_neg_173.mzML ... got 426. | |
| Requesting 510 peaks from HU_neg_192.mzML ... got 313. | |
| Requesting 123 peaks from QC1_002.mzML ... got 103. | |
| Requesting 110 peaks from QC1_008.mzML ... got 95. | |
| Requesting 132 peaks from QC1_014.mzML ... got 111. | |
| Note: you might want to set/adjust the 'sampclass' of the returned xcmSet object before proceeding with the analysis. | |
| ``` | |
| **Standard Output:** | |
| * ```console | |
| SESSION INFO | |
| R version 4.0.5 (2021-03-31) | |
| Main packages: | |
| batch 1.1.5 xcms 3.12.0 MSnbase 2.16.1 ProtGenerics 1.22.0 S4Vectors 0.28.1 mzR 2.24.1 Rcpp 1.0.6 BiocParallel 1.24.1 Biobase 2.50.0 BiocGenerics 0.36.0 | |
| Other loaded packages: | |
| SummarizedExperiment 1.20.0 lattice 0.20.44 colorspace 2.0.1 vctrs 0.3.8 vsn 3.58.0 utf8 1.2.1 XML 3.99.0.6 rlang 0.4.11 pillar 1.6.0 glue 1.4.2 affy 1.68.0 RColorBrewer 1.1.2 affyio 1.60.0 matrixStats 0.58.0 GenomeInfoDbData 1.2.4 foreach 1.5.1 lifecycle 1.0.0 plyr 1.8.6 mzID 1.28.0 robustbase 0.93.7 zlibbioc 1.36.0 MatrixGenerics 1.2.1 munsell 0.5.0 pcaMethods 1.82.0 gtable 0.3.0 codetools 0.2.18 IRanges 2.24.1 doParallel 1.0.16 GenomeInfoDb 1.26.4 MassSpecWavelet 1.56.0 fansi 0.4.2 preprocessCore 1.52.1 DEoptimR 1.0.8 scales 1.1.1 BiocManager 1.30.15 DelayedArray 0.16.3 limma 3.46.0 XVector 0.30.0 MsCoreUtils 1.2.0 RANN 2.6.1 impute 1.64.0 ggplot2 3.3.3 digest 0.6.27 ncdf4 1.17 GenomicRanges 1.42.0 grid 4.0.5 tools 4.0.5 bitops 1.0.7 magrittr 2.0.1 RCurl 1.98.1.3 tibble 3.1.1 crayon 1.4.1 pkgconfig 2.0.3 Matrix 1.3.2 MASS 7.3.54 ellipsis 0.3.2 iterators 1.0.13 R6 2.5.0 MALDIquant 1.19.3 compiler 4.0.5 | |
| ARGUMENTS INFO | |
| image /tmp/tmpni2hmxgh/files/0/f/f/dataset_0ff2dca4-d671-49da-b75b-0599a101d129.dat | |
| expandMz 0 | |
| expandRt 0 | |
| ppm 0 | |
| convertRTMinute FALSE | |
| numDigitsMZ 4 | |
| numDigitsRT 0 | |
| intval into | |
| naTOzero TRUE | |
| ARGUMENTS PROCESSING INFO | |
| INFILE PROCESSING INFO | |
| MAIN PROCESSING INFO | |
| COMPUTE | |
| Filling missing peaks using default settings | |
| Object of class: FillChromPeaksParam | |
| Parameters: | |
| expandMz: 0 | |
| expandRt: 0 | |
| ppm: 0 | |
| XCMSnExp OBJECT INFO | |
| MSn experiment data ("XCMSnExp") | |
| Object size in memory: 6.44 Mb | |
| - - - Spectra data - - - | |
| MS level(s): 1 | |
| Number of spectra: 21878 | |
| MSn retention times: -1:58 - 19:2 minutes | |
| - - - Processing information - - - | |
| Concatenated [Tue Feb 24 07:06:25 2026] | |
| MSnbase version: 2.16.1 | |
| - - - Meta data - - - | |
| phenoData | |
| rowNames: Blanc05.mzML Blanc10.mzML ... QC1_014.mzML (12 total) | |
| varLabels: sample_name sample_group | |
| varMetadata: labelDescription | |
| Loaded from: | |
| [1] Blanc05.mzML... [12] QC1_014.mzML | |
| Use 'fileNames(.)' to see all files. | |
| protocolData: none | |
| featureData | |
| featureNames: F1.S0001 F1.S0002 ... F12.S1533 (21878 total) | |
| fvarLabels: fileIdx spIdx ... spectrum (35 total) | |
| fvarMetadata: labelDescription | |
| experimentData: use 'experimentData(object)' | |
| - - - xcms preprocessing - - - | |
| Chromatographic peak detection: | |
| method: centWave | |
| 37383 peaks identified in 12 samples. | |
| On average 3115 chromatographic peaks per sample. | |
| Alignment/retention time adjustment: | |
| method: peak groups | |
| Correspondence: | |
| method: chromatographic peak density | |
| 2230 features identified. | |
| Median mz range of features: 0.00028742 | |
| Median rt range of features: 1.6196 | |
| 2667 filled peaks (on average 222.25 per sample). | |
| xcmsSet OBJECT INFO | |
| An "xcmsSet" object with 12 samples | |
| Time range: 1.1-1141.8 seconds (0-19 minutes) | |
| Mass range: 50.025-989.2024 m/z | |
| Peaks: 37383 (about 3115 per sample) | |
| Peak Groups: 2230 | |
| Sample classes: blk, sample, QC | |
| Feature detection: | |
| o Peak picking performed on MS1. | |
| o Scan range limited to 1 - 2039 | |
| Profile settings: method = bin | |
| step = 0.1 | |
| Memory usage: 9.53 MB | |
| DONE | |
| ``` | |
| **Traceback:** | |
| * ```console | |
| ``` | |
| **Job Parameters:** | |
| * | Job parameter | Parameter value | | |
| | ------------- | --------------- | | |
| | Adv | ` {"expandMz": "0", "expandRt": "0", "ppm": "0"} ` | | |
| | \_\_input\_ext | ` "input" ` | | |
| | \_\_workflow\_invocation\_uuid\_\_ | ` "b39b8d62114e11f189517ced8d633c14" ` | | |
| | chromInfo | ` "/tmp/tmpni2hmxgh/galaxy-dev/tool-data/shared/ucsc/chrom/?.len" ` | | |
| | dbkey | ` "?" ` | | |
| | file\_load\_section | ` {"file_load_conditional": {"__current_case__": 0, "file_load_select": "no"}} ` | | |
| | peaklist | ` {"convertRTMinute": false, "intval": "into", "naTOzero": true, "numDigitsMZ": "4", "numDigitsRT": "0", "peaklistBool": "true"} ` | | |
| </details> | |
| - **Step 14: Unlabelled step (toolshed.g2.bx.psu.edu/repos/lecorguille/camera\_annotate/abims\_CAMERA\_annotateDiffreport/2.2.7+camera1.48.0-galaxy1)**: | |
| * step_state: scheduled | |
| * <details><summary>Jobs</summary> | |
| - **Job 1:** | |
| * Job state is ok | |
| **Container:** | |
| * ```console | |
| quay.io/biocontainers/mulled-v2-ceb396848bd4205fab17b9a25292063db3e0bd2c:28fa3a0848d6f0d93bded373cf994654a25e377a-0 | |
| ``` | |
| **Command Line:** | |
| * ```console | |
| LC_ALL=C Rscript /tmp/shed_dir/toolshed.g2.bx.psu.edu/repos/lecorguille/camera_annotate/75a1b3f7bacc/camera_annotate//CAMERA_annotateDiffreport.r image '/tmp/tmpni2hmxgh/files/4/b/5/dataset_4b560d68-1ae3-4b8c-950d-21d0d5c3d12b.dat' nSlaves ${GALAXY_SLOTS:-1} sigma 6 perfwhm 0.6 ppm 5 mzabs 0.015 maxcharge 2 maxiso 4 minfrac 0.5 quick TRUE convertRTMinute TRUE numDigitsMZ 4 numDigitsRT 2 intval into | |
| ``` | |
| **Exit Code:** | |
| * ```console | |
| 0 | |
| ``` | |
| **Standard Error:** | |
| * ```console | |
| Note: you might want to set/adjust the 'sampclass' of the returned xcmSet object before proceeding with the analysis. | |
| ``` | |
| **Standard Output:** | |
| * ```console | |
| SESSION INFO | |
| R version 4.1.0 (2021-05-18) | |
| Main packages: | |
| batch 1.1.5 multtest 2.48.0 CAMERA 1.48.0 xcms 3.14.0 MSnbase 2.18.0 ProtGenerics 1.24.0 S4Vectors 0.30.0 mzR 2.26.0 Rcpp 1.0.6 BiocParallel 1.26.0 Biobase 2.52.0 BiocGenerics 0.38.0 | |
| Other loaded packages: | |
| bitops 1.0.7 matrixStats 0.59.0 doParallel 1.0.16 RColorBrewer 1.1.2 GenomeInfoDb 1.28.0 tools 4.1.0 backports 1.2.1 utf8 1.2.1 R6 2.5.0 affyio 1.62.0 rpart 4.1.15 Hmisc 4.5.0 colorspace 2.0.2 nnet 7.3.16 gridExtra 2.3 compiler 4.1.0 MassSpecWavelet 1.58.0 preprocessCore 1.54.0 graph 1.70.0 htmlTable 2.2.1 DelayedArray 0.18.0 scales 1.1.1 checkmate 2.0.0 DEoptimR 1.0.9 robustbase 0.93.8 affy 1.70.0 RBGL 1.68.0 stringr 1.4.0 digest 0.6.27 foreign 0.8.81 XVector 0.32.0 base64enc 0.1.3 jpeg 0.1.8.1 pkgconfig 2.0.3 htmltools 0.5.1.1 MatrixGenerics 1.4.0 limma 3.48.0 htmlwidgets 1.5.3 rlang 0.4.11 rstudioapi 0.13 impute 1.66.0 mzID 1.30.0 RCurl 1.98.1.3 magrittr 2.0.1 GenomeInfoDbData 1.2.6 Formula 1.2.4 MALDIquant 1.19.3 Matrix 1.3.4 munsell 0.5.0 fansi 0.4.2 MsCoreUtils 1.4.0 lifecycle 1.0.0 vsn 3.60.0 stringi 1.6.2 MASS 7.3.54 SummarizedExperiment 1.22.0 zlibbioc 1.38.0 plyr 1.8.6 grid 4.1.0 crayon 1.4.1 lattice 0.20.44 splines 4.1.0 knitr 1.33 pillar 1.6.1 igraph 1.2.6 GenomicRanges 1.44.0 codetools 0.2.18 XML 3.99.0.6 glue 1.4.2 latticeExtra 0.6.29 data.table 1.14.0 pcaMethods 1.84.0 BiocManager 1.30.16 vctrs 0.3.8 png 0.1.7 foreach 1.5.1 gtable 0.3.0 RANN 2.6.1 clue 0.3.59 ggplot2 3.3.5 xfun 0.24 ncdf4 1.17 survival 3.2.11 tibble 3.1.2 iterators 1.0.13 IRanges 2.26.0 cluster 2.1.2 ellipsis 0.3.2 | |
| ARGUMENTS INFO | |
| image /tmp/tmpni2hmxgh/files/4/b/5/dataset_4b560d68-1ae3-4b8c-950d-21d0d5c3d12b.dat | |
| nSlaves 1 | |
| sigma 6 | |
| perfwhm 0.6 | |
| ppm 5 | |
| mzabs 0.015 | |
| maxcharge 2 | |
| maxiso 4 | |
| minfrac 0.5 | |
| quick TRUE | |
| convertRTMinute TRUE | |
| numDigitsMZ 4 | |
| numDigitsRT 2 | |
| intval into | |
| INFILE PROCESSING INFO | |
| ARGUMENTS PROCESSING INFO | |
| MAIN PROCESSING INFO | |
| Start grouping after retention time. | |
| Created 313 pseudospectra. | |
| Generating peak matrix! | |
| Run isotope peak annotation | |
| % finished: 10 20 30 40 50 60 70 80 90 100 | |
| Found isotopes: 304 | |
| [1] "converting the retention times into minutes in the variableMetadata" | |
| XSET OBJECT INFO | |
| An "xsAnnotate" object! | |
| With 313 groups (pseudospectra) | |
| With 12 samples and 2230 peaks | |
| Polarity mode is set to: | |
| Using automatic sample selection | |
| Annotated isotopes: 304 | |
| Memory usage: 10.7 MB | |
| DONE | |
| ``` | |
| **Traceback:** | |
| * ```console | |
| ``` | |
| **Job Parameters:** | |
| * | Job parameter | Parameter value | | |
| | ------------- | --------------- | | |
| | \_\_input\_ext | ` "rdata.xcms.fillpeaks" ` | | |
| | \_\_workflow\_invocation\_uuid\_\_ | ` "b39b8d62114e11f189517ced8d633c14" ` | | |
| | chromInfo | ` "/tmp/tmpni2hmxgh/galaxy-dev/tool-data/shared/ucsc/chrom/?.len" ` | | |
| | dbkey | ` "?" ` | | |
| | diffreport | ` {"options": {"__current_case__": 1, "option": "hide"}} ` | | |
| | export | ` {"convertRTMinute": true, "intval": "into", "numDigitsMZ": "4", "numDigitsRT": "2"} ` | | |
| | file\_load\_section | ` {"file_load_conditional": {"__current_case__": 0, "file_load_select": "no"}} ` | | |
| | findgeneral | ` {"mzabs": "0.015", "ppm": "5"} ` | | |
| | findisotopes | ` {"maxcharge": "2", "maxiso": "4", "minfrac": "0.5"} ` | | |
| | groupfwhm | ` {"perfwhm": "0.6", "sigma": "6"} ` | | |
| | quick\_block | ` {"__current_case__": 1, "polarity": "quick", "quick": "TRUE"} ` | | |
| </details> | |
| </details> | |
| * <details><summary>Other invocation details</summary> | |
| - **history_id** | |
| * 9a7fa22158f45d81 | |
| - **history_state** | |
| * ok | |
| - **invocation_id** | |
| * 9a7fa22158f45d81 | |
| - **invocation_state** | |
| * scheduled | |
| - **workflow_id** | |
| * 9a7fa22158f45d81 | |
| </details> | |
| </div></details> | |
| * <details class="rcorners light-red"><summary class="light-red">❌ goseq-go-kegg-enrichment-analsis.ga_0</summary><div class="padded"> | |
| **Problems**: | |
| * ``` | |
| Output with path /tmp/tmpv9d71nv9/goseq Top Categories plot (Cellular Component)__a4a62f81-807a-4f66-ac9f-dbd16542b765.pdf different than expected | |
| Expected file size of 7078+-0 found 7060 | |
| ``` | |
| #### Workflow invocation details | |
| * Invocation Messages | |
| * <details><summary>Steps</summary> | |
| - **Step 1: Select genome to use**: | |
| * step_state: scheduled | |
| - **Step 2: Differential expression result**: | |
| * step_state: scheduled | |
| - **Step 3: Select gene ID format**: | |
| * step_state: scheduled | |
| - **Step 4: gene length**: | |
| * step_state: scheduled | |
| - **Step 5: KEGG pathways**: | |
| * step_state: scheduled | |
| - **Step 6: goseq - Cellular Component (toolshed.g2.bx.psu.edu/repos/iuc/goseq/goseq/1.50.0+galaxy0)**: | |
| * step_state: scheduled | |
| * <details><summary>Jobs</summary> | |
| - **Job 1:** | |
| * Job state is ok | |
| **Container:** | |
| * ```console | |
| quay.io/biocontainers/mulled-v2-a363682a95427ff51dddd9ac3110099eb1069b4d:14721b9daa3e3a72e3b400a32eef6dfa2e4a2313-0 | |
| ``` | |
| **Command Line:** | |
| * ```console | |
| Rscript '/tmp/shed_dir/toolshed.g2.bx.psu.edu/repos/iuc/goseq/602de62d995b/goseq/goseq.r' --dge_file '/tmp/tmp5r6fv9wg/files/4/c/a/dataset_4ca64b4c-eae6-41bc-9651-b2f6c672c227.dat' --length_file '/tmp/tmp5r6fv9wg/files/a/4/4/dataset_a4404e6e-39d1-4844-b378-5e91d9ec80be.dat' --genome mm10 --gene_id ensGene --fetch_cats 'GO:CC' --wallenius_tab '/tmp/tmp5r6fv9wg/job_working_directory/000/26/outputs/dataset_dfcdc069-7cfd-4616-a633-d5d5948fb5c6.dat' --repcnt 0 --p_adj_method 'BH' --use_genes_without_cat 'false' --top_plot '/tmp/tmp5r6fv9wg/job_working_directory/000/26/outputs/dataset_a4a62f81-807a-4f66-ac9f-dbd16542b765.dat' --categories_genes_out_fp '/tmp/tmp5r6fv9wg/job_working_directory/000/26/outputs/dataset_ee2a633c-df40-4773-ac22-f441ecf1c13d.dat' | |
| ``` | |
| **Exit Code:** | |
| * ```console | |
| 0 | |
| ``` | |
| **Standard Error:** | |
| * ```console | |
| Warning message: | |
| In Sys.setlocale("LC_MESSAGES", "en_US.UTF-8") : | |
| OS reports request to set locale to "en_US.UTF-8" cannot be honored | |
| Warning message: | |
| In pcls(G) : initial point very close to some inequality constraints | |
| Loading required package: AnnotationDbi | |
| Loading required package: stats4 | |
| Loading required package: BiocGenerics | |
| Attaching package: ‘BiocGenerics’ | |
| The following objects are masked from ‘package:dplyr’: | |
| combine, intersect, setdiff, union | |
| The following objects are masked from ‘package:stats’: | |
| IQR, mad, sd, var, xtabs | |
| The following objects are masked from ‘package:base’: | |
| anyDuplicated, aperm, append, as.data.frame, basename, cbind, | |
| colnames, dirname, do.call, duplicated, eval, evalq, Filter, Find, | |
| get, grep, grepl, intersect, is.unsorted, lapply, Map, mapply, | |
| match, mget, order, paste, pmax, pmax.int, pmin, pmin.int, | |
| Position, rank, rbind, Reduce, rownames, sapply, setdiff, sort, | |
| table, tapply, union, unique, unsplit, which.max, which.min | |
| Loading required package: Biobase | |
| Welcome to Bioconductor | |
| Vignettes contain introductory material; view with | |
| 'browseVignettes()'. To cite Bioconductor, see | |
| 'citation("Biobase")', and for packages 'citation("pkgname")'. | |
| Loading required package: IRanges | |
| Loading required package: S4Vectors | |
| Attaching package: ‘S4Vectors’ | |
| The following objects are masked from ‘package:dplyr’: | |
| first, rename | |
| The following object is masked from ‘package:geneLenDataBase’: | |
| unfactor | |
| The following objects are masked from ‘package:base’: | |
| expand.grid, I, unname | |
| Attaching package: ‘IRanges’ | |
| The following objects are masked from ‘package:dplyr’: | |
| collapse, desc, slice | |
| Attaching package: ‘AnnotationDbi’ | |
| The following object is masked from ‘package:dplyr’: | |
| select | |
| Using manually entered categories. | |
| For 1658 genes, we could not find any categories. These genes will be excluded. | |
| To force their use, please run with use_genes_without_cat=TRUE (see documentation). | |
| This was the default behavior for version 1.15.1 and earlier. | |
| Calculating the p-values... | |
| 'select()' returned 1:1 mapping between keys and columns | |
| ``` | |
| **Standard Output:** | |
| * ```console | |
| R version 4.2.2 (2022-10-31) | |
| Platform: x86_64-conda-linux-gnu (64-bit) | |
| Running under: Debian GNU/Linux 10 (buster) | |
| Matrix products: default | |
| BLAS/LAPACK: /usr/local/lib/libopenblasp-r0.3.21.so | |
| locale: | |
| [1] LC_CTYPE=C.UTF-8 LC_NUMERIC=C LC_TIME=C.UTF-8 | |
| [4] LC_COLLATE=C.UTF-8 LC_MONETARY=C.UTF-8 LC_MESSAGES=C.UTF-8 | |
| [7] LC_PAPER=C.UTF-8 LC_NAME=C LC_ADDRESS=C | |
| [10] LC_TELEPHONE=C LC_MEASUREMENT=C.UTF-8 LC_IDENTIFICATION=C | |
| attached base packages: | |
| [1] stats graphics grDevices utils datasets methods base | |
| other attached packages: | |
| [1] ggplot2_3.4.0 dplyr_1.0.10 optparse_1.7.3 | |
| [4] goseq_1.50.0 geneLenDataBase_1.34.0 BiasedUrn_2.0.8 | |
| loaded via a namespace (and not attached): | |
| [1] MatrixGenerics_1.10.0 Biobase_2.58.0 | |
| [3] httr_1.4.4 bit64_4.0.5 | |
| [5] splines_4.2.2 assertthat_0.2.1 | |
| [7] stats4_4.2.2 BiocFileCache_2.6.0 | |
| [9] blob_1.2.3 GenomeInfoDbData_1.2.9 | |
| [11] Rsamtools_2.14.0 yaml_2.3.6 | |
| [13] progress_1.2.2 pillar_1.8.1 | |
| [15] RSQLite_2.2.20 lattice_0.20-45 | |
| [17] glue_1.6.2 digest_0.6.31 | |
| [19] GenomicRanges_1.50.0 XVector_0.38.0 | |
| [21] colorspace_2.0-3 Matrix_1.5-3 | |
| [23] XML_3.99-0.13 pkgconfig_2.0.3 | |
| [25] biomaRt_2.54.0 zlibbioc_1.44.0 | |
| [27] GO.db_3.16.0 scales_1.2.1 | |
| [29] getopt_1.20.3 BiocParallel_1.32.5 | |
| [31] tibble_3.1.8 KEGGREST_1.38.0 | |
| [33] mgcv_1.8-41 generics_0.1.3 | |
| [35] IRanges_2.32.0 ellipsis_0.3.2 | |
| [37] withr_2.5.0 cachem_1.0.6 | |
| [39] SummarizedExperiment_1.28.0 GenomicFeatures_1.50.2 | |
| [41] BiocGenerics_0.44.0 cli_3.6.0 | |
| [43] magrittr_2.0.3 crayon_1.5.2 | |
| [45] memoise_2.0.1 fansi_1.0.3 | |
| [47] nlme_3.1-161 xml2_1.3.3 | |
| [49] tools_4.2.2 prettyunits_1.1.1 | |
| [51] hms_1.1.2 BiocIO_1.8.0 | |
| [53] lifecycle_1.0.3 matrixStats_0.63.0 | |
| [55] stringr_1.5.0 S4Vectors_0.36.0 | |
| [57] munsell_0.5.0 DelayedArray_0.24.0 | |
| [59] AnnotationDbi_1.60.0 Biostrings_2.66.0 | |
| [61] compiler_4.2.2 GenomeInfoDb_1.34.1 | |
| [63] rlang_1.0.6 grid_4.2.2 | |
| [65] RCurl_1.98-1.9 rjson_0.2.21 | |
| [67] rappdirs_0.3.3 bitops_1.0-7 | |
| [69] restfulr_0.0.15 gtable_0.3.1 | |
| [71] codetools_0.2-18 DBI_1.1.3 | |
| [73] curl_4.3.3 R6_2.5.1 | |
| [75] GenomicAlignments_1.34.0 rtracklayer_1.58.0 | |
| [77] fastmap_1.1.0 bit_4.0.5 | |
| [79] utf8_1.2.2 filelock_1.0.2 | |
| [81] stringi_1.7.12 parallel_4.2.2 | |
| [83] Rcpp_1.0.9 vctrs_0.5.1 | |
| [85] png_0.1-8 dbplyr_2.2.1 | |
| [87] tidyselect_1.2.0 | |
| null device | |
| 1 | |
| ``` | |
| **Traceback:** | |
| * ```console | |
| ``` | |
| **Job Parameters:** | |
| * | Job parameter | Parameter value | | |
| | ------------- | --------------- | | |
| | \_\_input\_ext | ` "input" ` | | |
| | \_\_workflow\_invocation\_uuid\_\_ | ` "f2ca22b4114e11f189516045bd079be9" ` | | |
| | adv | ` {"p_adj_method": "BH", "use_genes_without_cat": false} ` | | |
| | categorySource | ` {"__current_case__": 0, "catSource": "getgo", "fetchcats": ["GO:CC"], "gene_id": "ensGene", "genome": "mm10"} ` | | |
| | chromInfo | ` "/tmp/tmp5r6fv9wg/galaxy-dev/tool-data/shared/ucsc/chrom/?.len" ` | | |
| | dbkey | ` "?" ` | | |
| | methods | ` {"hypergeometric": false, "repcnt": "0", "wallenius": true} ` | | |
| | out | ` {"cat_genes": true, "make_plots": false, "rdata_out": false, "topgo_plot": true} ` | | |
| </details> | |
| - **Step 7: goseq - Biological Process (toolshed.g2.bx.psu.edu/repos/iuc/goseq/goseq/1.50.0+galaxy0)**: | |
| * step_state: scheduled | |
| * <details><summary>Jobs</summary> | |
| - **Job 1:** | |
| * Job state is ok | |
| **Container:** | |
| * ```console | |
| quay.io/biocontainers/mulled-v2-a363682a95427ff51dddd9ac3110099eb1069b4d:14721b9daa3e3a72e3b400a32eef6dfa2e4a2313-0 | |
| ``` | |
| **Command Line:** | |
| * ```console | |
| Rscript '/tmp/shed_dir/toolshed.g2.bx.psu.edu/repos/iuc/goseq/602de62d995b/goseq/goseq.r' --dge_file '/tmp/tmp5r6fv9wg/files/4/c/a/dataset_4ca64b4c-eae6-41bc-9651-b2f6c672c227.dat' --length_file '/tmp/tmp5r6fv9wg/files/a/4/4/dataset_a4404e6e-39d1-4844-b378-5e91d9ec80be.dat' --genome mm10 --gene_id ensGene --fetch_cats 'GO:BP' --wallenius_tab '/tmp/tmp5r6fv9wg/job_working_directory/000/27/outputs/dataset_5a79d7c9-57da-4e07-a13d-54fc12649fa3.dat' --repcnt 0 --p_adj_method 'BH' --use_genes_without_cat 'false' --top_plot '/tmp/tmp5r6fv9wg/job_working_directory/000/27/outputs/dataset_71be683b-4429-4616-8ad2-b1a4f9a85b52.dat' --categories_genes_out_fp '/tmp/tmp5r6fv9wg/job_working_directory/000/27/outputs/dataset_c66785c3-71d3-4f7d-a116-60cb9e26aaf0.dat' | |
| ``` | |
| **Exit Code:** | |
| * ```console | |
| 0 | |
| ``` | |
| **Standard Error:** | |
| * ```console | |
| Warning message: | |
| In Sys.setlocale("LC_MESSAGES", "en_US.UTF-8") : | |
| OS reports request to set locale to "en_US.UTF-8" cannot be honored | |
| Warning message: | |
| In pcls(G) : initial point very close to some inequality constraints | |
| Loading required package: AnnotationDbi | |
| Loading required package: stats4 | |
| Loading required package: BiocGenerics | |
| Attaching package: ‘BiocGenerics’ | |
| The following objects are masked from ‘package:dplyr’: | |
| combine, intersect, setdiff, union | |
| The following objects are masked from ‘package:stats’: | |
| IQR, mad, sd, var, xtabs | |
| The following objects are masked from ‘package:base’: | |
| anyDuplicated, aperm, append, as.data.frame, basename, cbind, | |
| colnames, dirname, do.call, duplicated, eval, evalq, Filter, Find, | |
| get, grep, grepl, intersect, is.unsorted, lapply, Map, mapply, | |
| match, mget, order, paste, pmax, pmax.int, pmin, pmin.int, | |
| Position, rank, rbind, Reduce, rownames, sapply, setdiff, sort, | |
| table, tapply, union, unique, unsplit, which.max, which.min | |
| Loading required package: Biobase | |
| Welcome to Bioconductor | |
| Vignettes contain introductory material; view with | |
| 'browseVignettes()'. To cite Bioconductor, see | |
| 'citation("Biobase")', and for packages 'citation("pkgname")'. | |
| Loading required package: IRanges | |
| Loading required package: S4Vectors | |
| Attaching package: ‘S4Vectors’ | |
| The following objects are masked from ‘package:dplyr’: | |
| first, rename | |
| The following object is masked from ‘package:geneLenDataBase’: | |
| unfactor | |
| The following objects are masked from ‘package:base’: | |
| expand.grid, I, unname | |
| Attaching package: ‘IRanges’ | |
| The following objects are masked from ‘package:dplyr’: | |
| collapse, desc, slice | |
| Attaching package: ‘AnnotationDbi’ | |
| The following object is masked from ‘package:dplyr’: | |
| select | |
| Using manually entered categories. | |
| For 1658 genes, we could not find any categories. These genes will be excluded. | |
| To force their use, please run with use_genes_without_cat=TRUE (see documentation). | |
| This was the default behavior for version 1.15.1 and earlier. | |
| Calculating the p-values... | |
| 'select()' returned 1:1 mapping between keys and columns | |
| ``` | |
| **Standard Output:** | |
| * ```console | |
| R version 4.2.2 (2022-10-31) | |
| Platform: x86_64-conda-linux-gnu (64-bit) | |
| Running under: Debian GNU/Linux 10 (buster) | |
| Matrix products: default | |
| BLAS/LAPACK: /usr/local/lib/libopenblasp-r0.3.21.so | |
| locale: | |
| [1] LC_CTYPE=C.UTF-8 LC_NUMERIC=C LC_TIME=C.UTF-8 | |
| [4] LC_COLLATE=C.UTF-8 LC_MONETARY=C.UTF-8 LC_MESSAGES=C.UTF-8 | |
| [7] LC_PAPER=C.UTF-8 LC_NAME=C LC_ADDRESS=C | |
| [10] LC_TELEPHONE=C LC_MEASUREMENT=C.UTF-8 LC_IDENTIFICATION=C | |
| attached base packages: | |
| [1] stats graphics grDevices utils datasets methods base | |
| other attached packages: | |
| [1] ggplot2_3.4.0 dplyr_1.0.10 optparse_1.7.3 | |
| [4] goseq_1.50.0 geneLenDataBase_1.34.0 BiasedUrn_2.0.8 | |
| loaded via a namespace (and not attached): | |
| [1] MatrixGenerics_1.10.0 Biobase_2.58.0 | |
| [3] httr_1.4.4 bit64_4.0.5 | |
| [5] splines_4.2.2 assertthat_0.2.1 | |
| [7] stats4_4.2.2 BiocFileCache_2.6.0 | |
| [9] blob_1.2.3 GenomeInfoDbData_1.2.9 | |
| [11] Rsamtools_2.14.0 yaml_2.3.6 | |
| [13] progress_1.2.2 pillar_1.8.1 | |
| [15] RSQLite_2.2.20 lattice_0.20-45 | |
| [17] glue_1.6.2 digest_0.6.31 | |
| [19] GenomicRanges_1.50.0 XVector_0.38.0 | |
| [21] colorspace_2.0-3 Matrix_1.5-3 | |
| [23] XML_3.99-0.13 pkgconfig_2.0.3 | |
| [25] biomaRt_2.54.0 zlibbioc_1.44.0 | |
| [27] GO.db_3.16.0 scales_1.2.1 | |
| [29] getopt_1.20.3 BiocParallel_1.32.5 | |
| [31] tibble_3.1.8 KEGGREST_1.38.0 | |
| [33] mgcv_1.8-41 generics_0.1.3 | |
| [35] IRanges_2.32.0 ellipsis_0.3.2 | |
| [37] withr_2.5.0 cachem_1.0.6 | |
| [39] SummarizedExperiment_1.28.0 GenomicFeatures_1.50.2 | |
| [41] BiocGenerics_0.44.0 cli_3.6.0 | |
| [43] magrittr_2.0.3 crayon_1.5.2 | |
| [45] memoise_2.0.1 fansi_1.0.3 | |
| [47] nlme_3.1-161 xml2_1.3.3 | |
| [49] tools_4.2.2 prettyunits_1.1.1 | |
| [51] hms_1.1.2 BiocIO_1.8.0 | |
| [53] lifecycle_1.0.3 matrixStats_0.63.0 | |
| [55] stringr_1.5.0 S4Vectors_0.36.0 | |
| [57] munsell_0.5.0 DelayedArray_0.24.0 | |
| [59] AnnotationDbi_1.60.0 Biostrings_2.66.0 | |
| [61] compiler_4.2.2 GenomeInfoDb_1.34.1 | |
| [63] rlang_1.0.6 grid_4.2.2 | |
| [65] RCurl_1.98-1.9 rjson_0.2.21 | |
| [67] rappdirs_0.3.3 bitops_1.0-7 | |
| [69] restfulr_0.0.15 gtable_0.3.1 | |
| [71] codetools_0.2-18 DBI_1.1.3 | |
| [73] curl_4.3.3 R6_2.5.1 | |
| [75] GenomicAlignments_1.34.0 rtracklayer_1.58.0 | |
| [77] fastmap_1.1.0 bit_4.0.5 | |
| [79] utf8_1.2.2 filelock_1.0.2 | |
| [81] stringi_1.7.12 parallel_4.2.2 | |
| [83] Rcpp_1.0.9 vctrs_0.5.1 | |
| [85] png_0.1-8 dbplyr_2.2.1 | |
| [87] tidyselect_1.2.0 | |
| null device | |
| 1 | |
| ``` | |
| **Traceback:** | |
| * ```console | |
| ``` | |
| **Job Parameters:** | |
| * | Job parameter | Parameter value | | |
| | ------------- | --------------- | | |
| | \_\_input\_ext | ` "input" ` | | |
| | \_\_workflow\_invocation\_uuid\_\_ | ` "f2ca22b4114e11f189516045bd079be9" ` | | |
| | adv | ` {"p_adj_method": "BH", "use_genes_without_cat": false} ` | | |
| | categorySource | ` {"__current_case__": 0, "catSource": "getgo", "fetchcats": ["GO:BP"], "gene_id": "ensGene", "genome": "mm10"} ` | | |
| | chromInfo | ` "/tmp/tmp5r6fv9wg/galaxy-dev/tool-data/shared/ucsc/chrom/?.len" ` | | |
| | dbkey | ` "?" ` | | |
| | methods | ` {"hypergeometric": false, "repcnt": "0", "wallenius": true} ` | | |
| | out | ` {"cat_genes": true, "make_plots": false, "rdata_out": false, "topgo_plot": true} ` | | |
| </details> | |
| - **Step 8: goseq - Molecular Function (toolshed.g2.bx.psu.edu/repos/iuc/goseq/goseq/1.50.0+galaxy0)**: | |
| * step_state: scheduled | |
| * <details><summary>Jobs</summary> | |
| - **Job 1:** | |
| * Job state is ok | |
| **Container:** | |
| * ```console | |
| quay.io/biocontainers/mulled-v2-a363682a95427ff51dddd9ac3110099eb1069b4d:14721b9daa3e3a72e3b400a32eef6dfa2e4a2313-0 | |
| ``` | |
| **Command Line:** | |
| * ```console | |
| Rscript '/tmp/shed_dir/toolshed.g2.bx.psu.edu/repos/iuc/goseq/602de62d995b/goseq/goseq.r' --dge_file '/tmp/tmp5r6fv9wg/files/4/c/a/dataset_4ca64b4c-eae6-41bc-9651-b2f6c672c227.dat' --length_file '/tmp/tmp5r6fv9wg/files/a/4/4/dataset_a4404e6e-39d1-4844-b378-5e91d9ec80be.dat' --genome mm10 --gene_id ensGene --fetch_cats 'GO:MF' --wallenius_tab '/tmp/tmp5r6fv9wg/job_working_directory/000/28/outputs/dataset_4d507a72-04e5-4c06-a1ec-3beb782cfaba.dat' --repcnt 0 --p_adj_method 'BH' --use_genes_without_cat 'false' --top_plot '/tmp/tmp5r6fv9wg/job_working_directory/000/28/outputs/dataset_4a2c23a6-8f3d-4ad1-adec-9da58ca8f142.dat' --categories_genes_out_fp '/tmp/tmp5r6fv9wg/job_working_directory/000/28/outputs/dataset_451e9a2c-4489-4d08-957e-255c34a04592.dat' | |
| ``` | |
| **Exit Code:** | |
| * ```console | |
| 0 | |
| ``` | |
| **Standard Error:** | |
| * ```console | |
| Warning message: | |
| In Sys.setlocale("LC_MESSAGES", "en_US.UTF-8") : | |
| OS reports request to set locale to "en_US.UTF-8" cannot be honored | |
| Warning message: | |
| In pcls(G) : initial point very close to some inequality constraints | |
| Loading required package: AnnotationDbi | |
| Loading required package: stats4 | |
| Loading required package: BiocGenerics | |
| Attaching package: ‘BiocGenerics’ | |
| The following objects are masked from ‘package:dplyr’: | |
| combine, intersect, setdiff, union | |
| The following objects are masked from ‘package:stats’: | |
| IQR, mad, sd, var, xtabs | |
| The following objects are masked from ‘package:base’: | |
| anyDuplicated, aperm, append, as.data.frame, basename, cbind, | |
| colnames, dirname, do.call, duplicated, eval, evalq, Filter, Find, | |
| get, grep, grepl, intersect, is.unsorted, lapply, Map, mapply, | |
| match, mget, order, paste, pmax, pmax.int, pmin, pmin.int, | |
| Position, rank, rbind, Reduce, rownames, sapply, setdiff, sort, | |
| table, tapply, union, unique, unsplit, which.max, which.min | |
| Loading required package: Biobase | |
| Welcome to Bioconductor | |
| Vignettes contain introductory material; view with | |
| 'browseVignettes()'. To cite Bioconductor, see | |
| 'citation("Biobase")', and for packages 'citation("pkgname")'. | |
| Loading required package: IRanges | |
| Loading required package: S4Vectors | |
| Attaching package: ‘S4Vectors’ | |
| The following objects are masked from ‘package:dplyr’: | |
| first, rename | |
| The following object is masked from ‘package:geneLenDataBase’: | |
| unfactor | |
| The following objects are masked from ‘package:base’: | |
| expand.grid, I, unname | |
| Attaching package: ‘IRanges’ | |
| The following objects are masked from ‘package:dplyr’: | |
| collapse, desc, slice | |
| Attaching package: ‘AnnotationDbi’ | |
| The following object is masked from ‘package:dplyr’: | |
| select | |
| Using manually entered categories. | |
| For 1658 genes, we could not find any categories. These genes will be excluded. | |
| To force their use, please run with use_genes_without_cat=TRUE (see documentation). | |
| This was the default behavior for version 1.15.1 and earlier. | |
| Calculating the p-values... | |
| 'select()' returned 1:1 mapping between keys and columns | |
| ``` | |
| **Standard Output:** | |
| * ```console | |
| R version 4.2.2 (2022-10-31) | |
| Platform: x86_64-conda-linux-gnu (64-bit) | |
| Running under: Debian GNU/Linux 10 (buster) | |
| Matrix products: default | |
| BLAS/LAPACK: /usr/local/lib/libopenblasp-r0.3.21.so | |
| locale: | |
| [1] LC_CTYPE=C.UTF-8 LC_NUMERIC=C LC_TIME=C.UTF-8 | |
| [4] LC_COLLATE=C.UTF-8 LC_MONETARY=C.UTF-8 LC_MESSAGES=C.UTF-8 | |
| [7] LC_PAPER=C.UTF-8 LC_NAME=C LC_ADDRESS=C | |
| [10] LC_TELEPHONE=C LC_MEASUREMENT=C.UTF-8 LC_IDENTIFICATION=C | |
| attached base packages: | |
| [1] stats graphics grDevices utils datasets methods base | |
| other attached packages: | |
| [1] ggplot2_3.4.0 dplyr_1.0.10 optparse_1.7.3 | |
| [4] goseq_1.50.0 geneLenDataBase_1.34.0 BiasedUrn_2.0.8 | |
| loaded via a namespace (and not attached): | |
| [1] MatrixGenerics_1.10.0 Biobase_2.58.0 | |
| [3] httr_1.4.4 bit64_4.0.5 | |
| [5] splines_4.2.2 assertthat_0.2.1 | |
| [7] stats4_4.2.2 BiocFileCache_2.6.0 | |
| [9] blob_1.2.3 GenomeInfoDbData_1.2.9 | |
| [11] Rsamtools_2.14.0 yaml_2.3.6 | |
| [13] progress_1.2.2 pillar_1.8.1 | |
| [15] RSQLite_2.2.20 lattice_0.20-45 | |
| [17] glue_1.6.2 digest_0.6.31 | |
| [19] GenomicRanges_1.50.0 XVector_0.38.0 | |
| [21] colorspace_2.0-3 Matrix_1.5-3 | |
| [23] XML_3.99-0.13 pkgconfig_2.0.3 | |
| [25] biomaRt_2.54.0 zlibbioc_1.44.0 | |
| [27] GO.db_3.16.0 scales_1.2.1 | |
| [29] getopt_1.20.3 BiocParallel_1.32.5 | |
| [31] tibble_3.1.8 KEGGREST_1.38.0 | |
| [33] mgcv_1.8-41 generics_0.1.3 | |
| [35] IRanges_2.32.0 ellipsis_0.3.2 | |
| [37] withr_2.5.0 cachem_1.0.6 | |
| [39] SummarizedExperiment_1.28.0 GenomicFeatures_1.50.2 | |
| [41] BiocGenerics_0.44.0 cli_3.6.0 | |
| [43] magrittr_2.0.3 crayon_1.5.2 | |
| [45] memoise_2.0.1 fansi_1.0.3 | |
| [47] nlme_3.1-161 xml2_1.3.3 | |
| [49] tools_4.2.2 prettyunits_1.1.1 | |
| [51] hms_1.1.2 BiocIO_1.8.0 | |
| [53] lifecycle_1.0.3 matrixStats_0.63.0 | |
| [55] stringr_1.5.0 S4Vectors_0.36.0 | |
| [57] munsell_0.5.0 DelayedArray_0.24.0 | |
| [59] AnnotationDbi_1.60.0 Biostrings_2.66.0 | |
| [61] compiler_4.2.2 GenomeInfoDb_1.34.1 | |
| [63] rlang_1.0.6 grid_4.2.2 | |
| [65] RCurl_1.98-1.9 rjson_0.2.21 | |
| [67] rappdirs_0.3.3 bitops_1.0-7 | |
| [69] restfulr_0.0.15 gtable_0.3.1 | |
| [71] codetools_0.2-18 DBI_1.1.3 | |
| [73] curl_4.3.3 R6_2.5.1 | |
| [75] GenomicAlignments_1.34.0 rtracklayer_1.58.0 | |
| [77] fastmap_1.1.0 bit_4.0.5 | |
| [79] utf8_1.2.2 filelock_1.0.2 | |
| [81] stringi_1.7.12 parallel_4.2.2 | |
| [83] Rcpp_1.0.9 vctrs_0.5.1 | |
| [85] png_0.1-8 dbplyr_2.2.1 | |
| [87] tidyselect_1.2.0 | |
| null device | |
| 1 | |
| ``` | |
| **Traceback:** | |
| * ```console | |
| ``` | |
| **Job Parameters:** | |
| * | Job parameter | Parameter value | | |
| | ------------- | --------------- | | |
| | \_\_input\_ext | ` "input" ` | | |
| | \_\_workflow\_invocation\_uuid\_\_ | ` "f2ca22b4114e11f189516045bd079be9" ` | | |
| | adv | ` {"p_adj_method": "BH", "use_genes_without_cat": false} ` | | |
| | categorySource | ` {"__current_case__": 0, "catSource": "getgo", "fetchcats": ["GO:MF"], "gene_id": "ensGene", "genome": "mm10"} ` | | |
| | chromInfo | ` "/tmp/tmp5r6fv9wg/galaxy-dev/tool-data/shared/ucsc/chrom/?.len" ` | | |
| | dbkey | ` "?" ` | | |
| | methods | ` {"hypergeometric": false, "repcnt": "0", "wallenius": true} ` | | |
| | out | ` {"cat_genes": true, "make_plots": false, "rdata_out": false, "topgo_plot": true} ` | | |
| </details> | |
| - **Step 9: goseq - KEGG (toolshed.g2.bx.psu.edu/repos/iuc/goseq/goseq/1.50.0+galaxy0)**: | |
| * step_state: scheduled | |
| * <details><summary>Jobs</summary> | |
| - **Job 1:** | |
| * Job state is ok | |
| **Container:** | |
| * ```console | |
| quay.io/biocontainers/mulled-v2-a363682a95427ff51dddd9ac3110099eb1069b4d:14721b9daa3e3a72e3b400a32eef6dfa2e4a2313-0 | |
| ``` | |
| **Command Line:** | |
| * ```console | |
| Rscript '/tmp/shed_dir/toolshed.g2.bx.psu.edu/repos/iuc/goseq/602de62d995b/goseq/goseq.r' --dge_file '/tmp/tmp5r6fv9wg/files/4/c/a/dataset_4ca64b4c-eae6-41bc-9651-b2f6c672c227.dat' --length_file '/tmp/tmp5r6fv9wg/files/a/4/4/dataset_a4404e6e-39d1-4844-b378-5e91d9ec80be.dat' --genome mm10 --gene_id ensGene --fetch_cats 'KEGG' --wallenius_tab '/tmp/tmp5r6fv9wg/job_working_directory/000/29/outputs/dataset_b9434f24-9c6e-4047-8734-e14bfdd9167b.dat' --repcnt 0 --p_adj_method 'BH' --use_genes_without_cat 'false' --categories_genes_out_fp '/tmp/tmp5r6fv9wg/job_working_directory/000/29/outputs/dataset_fbd40b28-2c22-455a-9ce7-dd21379c571e.dat' | |
| ``` | |
| **Exit Code:** | |
| * ```console | |
| 0 | |
| ``` | |
| **Standard Error:** | |
| * ```console | |
| Warning message: | |
| In Sys.setlocale("LC_MESSAGES", "en_US.UTF-8") : | |
| OS reports request to set locale to "en_US.UTF-8" cannot be honored | |
| Warning message: | |
| In pcls(G) : initial point very close to some inequality constraints | |
| Loading required package: AnnotationDbi | |
| Loading required package: stats4 | |
| Loading required package: BiocGenerics | |
| Attaching package: ‘BiocGenerics’ | |
| The following objects are masked from ‘package:dplyr’: | |
| combine, intersect, setdiff, union | |
| The following objects are masked from ‘package:stats’: | |
| IQR, mad, sd, var, xtabs | |
| The following objects are masked from ‘package:base’: | |
| anyDuplicated, aperm, append, as.data.frame, basename, cbind, | |
| colnames, dirname, do.call, duplicated, eval, evalq, Filter, Find, | |
| get, grep, grepl, intersect, is.unsorted, lapply, Map, mapply, | |
| match, mget, order, paste, pmax, pmax.int, pmin, pmin.int, | |
| Position, rank, rbind, Reduce, rownames, sapply, setdiff, sort, | |
| table, tapply, union, unique, unsplit, which.max, which.min | |
| Loading required package: Biobase | |
| Welcome to Bioconductor | |
| Vignettes contain introductory material; view with | |
| 'browseVignettes()'. To cite Bioconductor, see | |
| 'citation("Biobase")', and for packages 'citation("pkgname")'. | |
| Loading required package: IRanges | |
| Loading required package: S4Vectors | |
| Attaching package: ‘S4Vectors’ | |
| The following objects are masked from ‘package:dplyr’: | |
| first, rename | |
| The following object is masked from ‘package:geneLenDataBase’: | |
| unfactor | |
| The following objects are masked from ‘package:base’: | |
| expand.grid, I, unname | |
| Attaching package: ‘IRanges’ | |
| The following objects are masked from ‘package:dplyr’: | |
| collapse, desc, slice | |
| Attaching package: ‘AnnotationDbi’ | |
| The following object is masked from ‘package:dplyr’: | |
| select | |
| Using manually entered categories. | |
| For 10338 genes, we could not find any categories. These genes will be excluded. | |
| To force their use, please run with use_genes_without_cat=TRUE (see documentation). | |
| This was the default behavior for version 1.15.1 and earlier. | |
| Calculating the p-values... | |
| ``` | |
| **Standard Output:** | |
| * ```console | |
| R version 4.2.2 (2022-10-31) | |
| Platform: x86_64-conda-linux-gnu (64-bit) | |
| Running under: Debian GNU/Linux 10 (buster) | |
| Matrix products: default | |
| BLAS/LAPACK: /usr/local/lib/libopenblasp-r0.3.21.so | |
| locale: | |
| [1] LC_CTYPE=C.UTF-8 LC_NUMERIC=C LC_TIME=C.UTF-8 | |
| [4] LC_COLLATE=C.UTF-8 LC_MONETARY=C.UTF-8 LC_MESSAGES=C.UTF-8 | |
| [7] LC_PAPER=C.UTF-8 LC_NAME=C LC_ADDRESS=C | |
| [10] LC_TELEPHONE=C LC_MEASUREMENT=C.UTF-8 LC_IDENTIFICATION=C | |
| attached base packages: | |
| [1] stats graphics grDevices utils datasets methods base | |
| other attached packages: | |
| [1] ggplot2_3.4.0 dplyr_1.0.10 optparse_1.7.3 | |
| [4] goseq_1.50.0 geneLenDataBase_1.34.0 BiasedUrn_2.0.8 | |
| loaded via a namespace (and not attached): | |
| [1] MatrixGenerics_1.10.0 Biobase_2.58.0 | |
| [3] httr_1.4.4 bit64_4.0.5 | |
| [5] splines_4.2.2 assertthat_0.2.1 | |
| [7] stats4_4.2.2 BiocFileCache_2.6.0 | |
| [9] blob_1.2.3 GenomeInfoDbData_1.2.9 | |
| [11] Rsamtools_2.14.0 yaml_2.3.6 | |
| [13] progress_1.2.2 pillar_1.8.1 | |
| [15] RSQLite_2.2.20 lattice_0.20-45 | |
| [17] glue_1.6.2 digest_0.6.31 | |
| [19] GenomicRanges_1.50.0 XVector_0.38.0 | |
| [21] colorspace_2.0-3 Matrix_1.5-3 | |
| [23] XML_3.99-0.13 pkgconfig_2.0.3 | |
| [25] biomaRt_2.54.0 zlibbioc_1.44.0 | |
| [27] GO.db_3.16.0 scales_1.2.1 | |
| [29] getopt_1.20.3 BiocParallel_1.32.5 | |
| [31] tibble_3.1.8 KEGGREST_1.38.0 | |
| [33] mgcv_1.8-41 generics_0.1.3 | |
| [35] IRanges_2.32.0 ellipsis_0.3.2 | |
| [37] withr_2.5.0 cachem_1.0.6 | |
| [39] SummarizedExperiment_1.28.0 GenomicFeatures_1.50.2 | |
| [41] BiocGenerics_0.44.0 cli_3.6.0 | |
| [43] magrittr_2.0.3 crayon_1.5.2 | |
| [45] memoise_2.0.1 fansi_1.0.3 | |
| [47] nlme_3.1-161 xml2_1.3.3 | |
| [49] tools_4.2.2 prettyunits_1.1.1 | |
| [51] hms_1.1.2 BiocIO_1.8.0 | |
| [53] lifecycle_1.0.3 matrixStats_0.63.0 | |
| [55] stringr_1.5.0 S4Vectors_0.36.0 | |
| [57] munsell_0.5.0 DelayedArray_0.24.0 | |
| [59] AnnotationDbi_1.60.0 Biostrings_2.66.0 | |
| [61] compiler_4.2.2 GenomeInfoDb_1.34.1 | |
| [63] rlang_1.0.6 grid_4.2.2 | |
| [65] RCurl_1.98-1.9 rjson_0.2.21 | |
| [67] rappdirs_0.3.3 bitops_1.0-7 | |
| [69] restfulr_0.0.15 gtable_0.3.1 | |
| [71] codetools_0.2-18 DBI_1.1.3 | |
| [73] curl_4.3.3 R6_2.5.1 | |
| [75] GenomicAlignments_1.34.0 rtracklayer_1.58.0 | |
| [77] fastmap_1.1.0 bit_4.0.5 | |
| [79] utf8_1.2.2 filelock_1.0.2 | |
| [81] stringi_1.7.12 parallel_4.2.2 | |
| [83] Rcpp_1.0.9 vctrs_0.5.1 | |
| [85] png_0.1-8 dbplyr_2.2.1 | |
| [87] tidyselect_1.2.0 | |
| ``` | |
| **Traceback:** | |
| * ```console | |
| ``` | |
| **Job Parameters:** | |
| * | Job parameter | Parameter value | | |
| | ------------- | --------------- | | |
| | \_\_input\_ext | ` "input" ` | | |
| | \_\_workflow\_invocation\_uuid\_\_ | ` "f2ca22b4114e11f189516045bd079be9" ` | | |
| | adv | ` {"p_adj_method": "BH", "use_genes_without_cat": false} ` | | |
| | categorySource | ` {"__current_case__": 0, "catSource": "getgo", "fetchcats": ["KEGG"], "gene_id": "ensGene", "genome": "mm10"} ` | | |
| | chromInfo | ` "/tmp/tmp5r6fv9wg/galaxy-dev/tool-data/shared/ucsc/chrom/?.len" ` | | |
| | dbkey | ` "?" ` | | |
| | methods | ` {"hypergeometric": false, "repcnt": "0", "wallenius": true} ` | | |
| | out | ` {"cat_genes": true, "make_plots": false, "rdata_out": false, "topgo_plot": false} ` | | |
| </details> | |
| - **Step 10: Unlabelled step (join1)**: | |
| * step_state: scheduled | |
| * <details><summary>Jobs</summary> | |
| - **Job 1:** | |
| * Job state is ok | |
| **Container:** | |
| * ```console | |
| quay.io/biocontainers/galaxy-util:25.0.2 | |
| ``` | |
| **Command Line:** | |
| * ```console | |
| python '/tmp/tmp5r6fv9wg/galaxy-dev/tools/filters/join.py' '/tmp/tmp5r6fv9wg/files/b/9/4/dataset_b9434f24-9c6e-4047-8734-e14bfdd9167b.dat' '/tmp/tmp5r6fv9wg/files/4/a/0/dataset_4a0e655c-7502-41a5-a54b-6a223a1d3cb0.dat' 1 1 '/tmp/tmp5r6fv9wg/job_working_directory/000/30/outputs/dataset_159a3253-7f7c-4f17-bdeb-fd6ea934c315.dat' -u -p --index_depth=3 --buffer=50000000 --fill_options_file=/tmp/tmp5r6fv9wg/job_working_directory/000/30/configs/tmpinale92h -H | |
| ``` | |
| **Exit Code:** | |
| * ```console | |
| 0 | |
| ``` | |
| **Traceback:** | |
| * ```console | |
| ``` | |
| **Job Parameters:** | |
| * | Job parameter | Parameter value | | |
| | ------------- | --------------- | | |
| | \_\_input\_ext | ` "input" ` | | |
| | \_\_workflow\_invocation\_uuid\_\_ | ` "f2ca22b4114e11f189516045bd079be9" ` | | |
| | chromInfo | ` "/tmp/tmp5r6fv9wg/galaxy-dev/tool-data/shared/ucsc/chrom/?.len" ` | | |
| | dbkey | ` "?" ` | | |
| | field1 | ` "1" ` | | |
| | field2 | ` "1" ` | | |
| | fill\_empty\_columns | ` {"__current_case__": 0, "fill_empty_columns_switch": "no_fill"} ` | | |
| | header | ` "-H" ` | | |
| | partial | ` "-p" ` | | |
| | unmatched | ` "-u" ` | | |
| </details> | |
| </details> | |
| * <details><summary>Other invocation details</summary> | |
| - **history_id** | |
| * e0caa649c13f0fb1 | |
| - **history_state** | |
| * ok | |
| - **invocation_id** | |
| * c02e613da20afb17 | |
| - **invocation_state** | |
| * scheduled | |
| - **workflow_id** | |
| * c02e613da20afb17 | |
| </details> | |
| </div></details> | |
| * <details class="rcorners light-red"><summary class="light-red">❌ kmer-profiling-hifi-trio-VGP2.ga_0</summary><div class="padded"> | |
| **Problems**: | |
| * ``` | |
| Output with path /tmp/tmpj_qrz4v0/Meryl on dataset 1, 2, and others and collection 3, 6, and 8 read-db.meryldb__8995837b-f365-4163-87a3-676dc865f113.meryldb different than expected | |
| Expected file size of 205051+-1000 found 221919 | |
| ``` | |
| * ``` | |
| Output with path /tmp/tmphmnxw9sa/Meryl on dataset 1, 2, and others and collection 3, 6, and 8 pat.meryldb__f2c92e5a-9d4c-42a0-8a61-1c8c5db46516.meryldb different than expected | |
| Expected file size of 40338+-1000 found 44523 | |
| ``` | |
| * ``` | |
| Output with path /tmp/tmpg6q82iqm/Meryl on dataset 1, 2, and others and collection 3, 6, and 8 mat.meryldb__f265e791-6647-4985-94d7-62bf846eb1d4.meryldb different than expected | |
| Expected file size of 49534+-1000 found 54340 | |
| ``` | |
| #### Workflow invocation details | |
| * Invocation Messages | |
| * <details><summary>Steps</summary> | |
| - **Step 1: Pacbio Hifi reads**: | |
| * step_state: scheduled | |
| - **Step 2: Paternal reads**: | |
| * step_state: scheduled | |
| - **Step 3: Maternal reads**: | |
| * step_state: scheduled | |
| - **Step 4: K-mer length**: | |
| * step_state: scheduled | |
| - **Step 5: Ploidy**: | |
| * step_state: scheduled | |
| - **Step 6: Unlabelled step (toolshed.g2.bx.psu.edu/repos/iuc/pick\_value/pick\_value/0.2.0)**: | |
| * step_state: scheduled | |
| * <details><summary>Jobs</summary> | |
| - **Job 1:** | |
| * Job state is ok | |
| **Command Line:** | |
| * ```console | |
| cd ../; python _evaluate_expression_.py | |
| ``` | |
| **Exit Code:** | |
| * ```console | |
| 0 | |
| ``` | |
| **Traceback:** | |
| * ```console | |
| ``` | |
| **Job Parameters:** | |
| * | Job parameter | Parameter value | | |
| | ------------- | --------------- | | |
| | \_\_input\_ext | ` "input" ` | | |
| | \_\_workflow\_invocation\_uuid\_\_ | ` "a9e9fe4a115611f189517ced8dc21a23" ` | | |
| | chromInfo | ` "/tmp/tmp3sfjay_q/galaxy-dev/tool-data/shared/ucsc/chrom/?.len" ` | | |
| | dbkey | ` "?" ` | | |
| | style\_cond | ` {"__current_case__": 1, "pick_style": "first_or_default", "type_cond": {"__current_case__": 1, "default_value": "21", "param_type": "integer", "pick_from": [{"__index__": 0, "value": "9"}]}} ` | | |
| </details> | |
| - **Step 7: Unlabelled step (toolshed.g2.bx.psu.edu/repos/iuc/meryl\_count\_kmers/meryl\_count\_kmers/1.3+galaxy7)**: | |
| * step_state: scheduled | |
| * <details><summary>Jobs</summary> | |
| - **Job 1:** | |
| * Job state is ok | |
| **Container:** | |
| * ```console | |
| quay.io/biocontainers/mulled-v2-ba0fa2569b9c1d280d7fb3b1bf2ad3c0c72d9296:34d0c765d43a43f8968b3d9ffb3ceb9a8cdf6a69-0 | |
| ``` | |
| **Command Line:** | |
| * ```console | |
| export GALAXY_MEMORY_GB=$((${GALAXY_MEMORY_MB:-8192}/1024)) && ln -s '/tmp/tmp3sfjay_q/files/e/e/6/dataset_ee60b813-9038-43b8-a5b5-fc02f017f4bf.dat' ./input.fastqsanger && meryl count k=9 memory=$GALAXY_MEMORY_GB threads=${GALAXY_SLOTS:-1} ./input.fastqsanger output read-db.meryl && echo 'K-mer size: 9' && tar -cf read-db.meryldb --use-compress-program="pigz -p ${GALAXY_SLOTS:-1}" read-db.meryl | |
| ``` | |
| **Exit Code:** | |
| * ```console | |
| 0 | |
| ``` | |
| **Standard Error:** | |
| * ```console | |
| Found 1 command tree. | |
| Counting 1797 (estimated) thousand canonical 9-mers from 1 input file: | |
| sequence-file: ./input.fastqsanger | |
| SIMPLE MODE | |
| ----------- | |
| 9-mers | |
| -> 262144 entries for counts up to 65535. | |
| -> 4096 kbits memory used | |
| 1841136 input bases | |
| -> expected max count of 7364, needing 0 extra bits. | |
| -> no memory used | |
| 512 kB memory needed | |
| COMPLEX MODE | |
| ------------ | |
| prefix # of struct kmers/ segs/ min data total | |
| bits prefix memory prefix prefix memory memory memory | |
| ------ ------- ------- ------- ------- ------- ------- ------- | |
| 1 2 P 10 kB 449 kM 239 S 8192 B 1912 kB 1922 kB | |
| 2 4 P 16 kB 224 kM 113 S 16 kB 1808 kB 1824 kB | |
| 3 8 P 28 kB 112 kM 53 S 32 kB 1696 kB 1724 kB | |
| 4 16 P 53 kB 56 kM 25 S 64 kB 1600 kB 1653 kB | |
| 5 32 P 104 kB 28 kM 12 S 128 kB 1536 kB 1640 kB | |
| 6 64 P 205 kB 14 kM 6 S 256 kB 1536 kB 1741 kB | |
| 7 128 P 407 kB 7192 M 3 S 512 kB 1536 kB 1943 kB | |
| 8 256 P 812 kB 3596 M 2 S 1024 kB 2048 kB 2860 kB | |
| 9 512 P 1620 kB 1798 M 1 S 2048 kB 2048 kB 3668 kB | |
| 10 1024 P 3240 kB 899 M 1 S 4096 kB 4096 kB 7336 kB Best Value! | |
| 11 2048 P 6480 kB 450 M 1 S 8192 kB 8192 kB 14 MB | |
| 12 4096 P 12 MB 225 M 1 S 16 MB 16 MB 28 MB | |
| 13 8192 P 25 MB 113 M 1 S 32 MB 32 MB 57 MB | |
| 14 16 kP 50 MB 57 M 1 S 64 MB 64 MB 114 MB | |
| 15 32 kP 101 MB 29 M 1 S 128 MB 128 MB 229 MB | |
| FINAL CONFIGURATION | |
| ------------------- | |
| Estimated to require 512 kB memory out of 8192 MB allowed. | |
| Estimated to require 2 batches. | |
| Configured simple mode for 0.000 GB memory per batch, and up to 2 batches. | |
| Start counting with SIMPLE method. | |
| Loading kmers from './input.fastqsanger' into buckets. | |
| Writing results to 'read-db.meryl', using 1 threads. | |
| [ file ][ prefix ][ suffix ][ count-suffix ] | |
| widths [ 6 ][ 0 ][ 12 ][ 0 ] | |
| number [ 64 ][ 1 ][ 4096 ][ ] | |
| thread 0 working on block 0x00000000<0x00000000<0x00000000 4096 kmers between 0x0000000000000000 and 0x0000000000000fff | |
| thread 0 working on block 0x00000001<0x00000001<0x00000001 4096 kmers between 0x0000000000001000 and 0x0000000000001fff | |
| thread 0 working on block 0x00000002<0x00000002<0x00000002 4096 kmers between 0x0000000000002000 and 0x0000000000002fff | |
| thread 0 working on block 0x00000003<0x00000003<0x00000003 4096 kmers between 0x0000000000003000 and 0x0000000000003fff | |
| thread 0 working on block 0x00000004<0x00000004<0x00000004 4096 kmers between 0x0000000000004000 and 0x0000000000004fff | |
| thread 0 working on block 0x00000005<0x00000005<0x00000005 4096 kmers between 0x0000000000005000 and 0x0000000000005fff | |
| thread 0 working on block 0x00000006<0x00000006<0x00000006 4096 kmers between 0x0000000000006000 and 0x0000000000006fff | |
| thread 0 working on block 0x00000007<0x00000007<0x00000007 4096 kmers between 0x0000000000007000 and 0x0000000000007fff | |
| thread 0 working on block 0x00000008<0x00000008<0x00000008 4096 kmers between 0x0000000000008000 and 0x0000000000008fff | |
| thread 0 working on block 0x00000009<0x00000009<0x00000009 4096 kmers between 0x0000000000009000 and 0x0000000000009fff | |
| thread 0 working on block 0x0000000a<0x0000000a<0x0000000a 4096 kmers between 0x000000000000a000 and 0x000000000000afff | |
| thread 0 working on block 0x0000000b<0x0000000b<0x0000000b 4096 kmers between 0x000000000000b000 and 0x000000000000bfff | |
| thread 0 working on block 0x0000000c<0x0000000c<0x0000000c 4096 kmers between 0x000000000000c000 and 0x000000000000cfff | |
| thread 0 working on block 0x0000000d<0x0000000d<0x0000000d 4096 kmers between 0x000000000000d000 and 0x000000000000dfff | |
| thread 0 working on block 0x0000000e<0x0000000e<0x0000000e 4096 kmers between 0x000000000000e000 and 0x000000000000efff | |
| thread 0 working on block 0x0000000f<0x0000000f<0x0000000f 4096 kmers between 0x000000000000f000 and 0x000000000000ffff | |
| thread 0 working on block 0x00000010<0x00000010<0x00000010 4096 kmers between 0x0000000000010000 and 0x0000000000010fff | |
| thread 0 working on block 0x00000011<0x00000011<0x00000011 4096 kmers between 0x0000000000011000 and 0x0000000000011fff | |
| thread 0 working on block 0x00000012<0x00000012<0x00000012 4096 kmers between 0x0000000000012000 and 0x0000000000012fff | |
| thread 0 working on block 0x00000013<0x00000013<0x00000013 4096 kmers between 0x0000000000013000 and 0x0000000000013fff | |
| thread 0 working on block 0x00000014<0x00000014<0x00000014 4096 kmers between 0x0000000000014000 and 0x0000000000014fff | |
| thread 0 working on block 0x00000015<0x00000015<0x00000015 4096 kmers between 0x0000000000015000 and 0x0000000000015fff | |
| thread 0 working on block 0x00000016<0x00000016<0x00000016 4096 kmers between 0x0000000000016000 and 0x0000000000016fff | |
| thread 0 working on block 0x00000017<0x00000017<0x00000017 4096 kmers between 0x0000000000017000 and 0x0000000000017fff | |
| thread 0 working on block 0x00000018<0x00000018<0x00000018 4096 kmers between 0x0000000000018000 and 0x0000000000018fff | |
| thread 0 working on block 0x00000019<0x00000019<0x00000019 4096 kmers between 0x0000000000019000 and 0x0000000000019fff | |
| thread 0 working on block 0x0000001a<0x0000001a<0x0000001a 4096 kmers between 0x000000000001a000 and 0x000000000001afff | |
| thread 0 working on block 0x0000001b<0x0000001b<0x0000001b 4096 kmers between 0x000000000001b000 and 0x000000000001bfff | |
| thread 0 working on block 0x0000001c<0x0000001c<0x0000001c 4096 kmers between 0x000000000001c000 and 0x000000000001cfff | |
| thread 0 working on block 0x0000001d<0x0000001d<0x0000001d 4096 kmers between 0x000000000001d000 and 0x000000000001dfff | |
| thread 0 working on block 0x0000001e<0x0000001e<0x0000001e 4096 kmers between 0x000000000001e000 and 0x000000000001efff | |
| thread 0 working on block 0x0000001f<0x0000001f<0x0000001f 4096 kmers between 0x000000000001f000 and 0x000000000001ffff | |
| thread 0 working on block 0x00000020<0x00000020<0x00000020 4096 kmers between 0x0000000000020000 and 0x0000000000020fff | |
| thread 0 working on block 0x00000021<0x00000021<0x00000021 4096 kmers between 0x0000000000021000 and 0x0000000000021fff | |
| thread 0 working on block 0x00000022<0x00000022<0x00000022 4096 kmers between 0x0000000000022000 and 0x0000000000022fff | |
| thread 0 working on block 0x00000023<0x00000023<0x00000023 4096 kmers between 0x0000000000023000 and 0x0000000000023fff | |
| thread 0 working on block 0x00000024<0x00000024<0x00000024 4096 kmers between 0x0000000000024000 and 0x0000000000024fff | |
| thread 0 working on block 0x00000025<0x00000025<0x00000025 4096 kmers between 0x0000000000025000 and 0x0000000000025fff | |
| thread 0 working on block 0x00000026<0x00000026<0x00000026 4096 kmers between 0x0000000000026000 and 0x0000000000026fff | |
| thread 0 working on block 0x00000027<0x00000027<0x00000027 4096 kmers between 0x0000000000027000 and 0x0000000000027fff | |
| thread 0 working on block 0x00000028<0x00000028<0x00000028 4096 kmers between 0x0000000000028000 and 0x0000000000028fff | |
| thread 0 working on block 0x00000029<0x00000029<0x00000029 4096 kmers between 0x0000000000029000 and 0x0000000000029fff | |
| thread 0 working on block 0x0000002a<0x0000002a<0x0000002a 4096 kmers between 0x000000000002a000 and 0x000000000002afff | |
| thread 0 working on block 0x0000002b<0x0000002b<0x0000002b 4096 kmers between 0x000000000002b000 and 0x000000000002bfff | |
| thread 0 working on block 0x0000002c<0x0000002c<0x0000002c 4096 kmers between 0x000000000002c000 and 0x000000000002cfff | |
| thread 0 working on block 0x0000002d<0x0000002d<0x0000002d 4096 kmers between 0x000000000002d000 and 0x000000000002dfff | |
| thread 0 working on block 0x0000002e<0x0000002e<0x0000002e 4096 kmers between 0x000000000002e000 and 0x000000000002efff | |
| thread 0 working on block 0x0000002f<0x0000002f<0x0000002f 4096 kmers between 0x000000000002f000 and 0x000000000002ffff | |
| thread 0 working on block 0x00000030<0x00000030<0x00000030 4096 kmers between 0x0000000000030000 and 0x0000000000030fff | |
| thread 0 working on block 0x00000031<0x00000031<0x00000031 4096 kmers between 0x0000000000031000 and 0x0000000000031fff | |
| thread 0 working on block 0x00000032<0x00000032<0x00000032 4096 kmers between 0x0000000000032000 and 0x0000000000032fff | |
| thread 0 working on block 0x00000033<0x00000033<0x00000033 4096 kmers between 0x0000000000033000 and 0x0000000000033fff | |
| thread 0 working on block 0x00000034<0x00000034<0x00000034 4096 kmers between 0x0000000000034000 and 0x0000000000034fff | |
| thread 0 working on block 0x00000035<0x00000035<0x00000035 4096 kmers between 0x0000000000035000 and 0x0000000000035fff | |
| thread 0 working on block 0x00000036<0x00000036<0x00000036 4096 kmers between 0x0000000000036000 and 0x0000000000036fff | |
| thread 0 working on block 0x00000037<0x00000037<0x00000037 4096 kmers between 0x0000000000037000 and 0x0000000000037fff | |
| thread 0 working on block 0x00000038<0x00000038<0x00000038 4096 kmers between 0x0000000000038000 and 0x0000000000038fff | |
| thread 0 working on block 0x00000039<0x00000039<0x00000039 4096 kmers between 0x0000000000039000 and 0x0000000000039fff | |
| thread 0 working on block 0x0000003a<0x0000003a<0x0000003a 4096 kmers between 0x000000000003a000 and 0x000000000003afff | |
| thread 0 working on block 0x0000003b<0x0000003b<0x0000003b 4096 kmers between 0x000000000003b000 and 0x000000000003bfff | |
| thread 0 working on block 0x0000003c<0x0000003c<0x0000003c 4096 kmers between 0x000000000003c000 and 0x000000000003cfff | |
| thread 0 working on block 0x0000003d<0x0000003d<0x0000003d 4096 kmers between 0x000000000003d000 and 0x000000000003dfff | |
| thread 0 working on block 0x0000003e<0x0000003e<0x0000003e 4096 kmers between 0x000000000003e000 and 0x000000000003efff | |
| thread 0 working on block 0x0000003f<0x0000003f<0x0000003f 4096 kmers between 0x000000000003f000 and 0x000000000003ffff | |
| finishIteration()-- | |
| Cleaning up. | |
| Bye. | |
| ``` | |
| **Standard Output:** | |
| * ```console | |
| K-mer size: 9 | |
| ``` | |
| **Traceback:** | |
| * ```console | |
| ``` | |
| **Job Parameters:** | |
| * | Job parameter | Parameter value | | |
| | ------------- | --------------- | | |
| | \_\_input\_ext | ` "input" ` | | |
| | \_\_workflow\_invocation\_uuid\_\_ | ` "a9e9fe4a115611f189517ced8dc21a23" ` | | |
| | chromInfo | ` "/tmp/tmp3sfjay_q/galaxy-dev/tool-data/shared/ucsc/chrom/?.len" ` | | |
| | count\_operation | ` "count" ` | | |
| | dbkey | ` "?" ` | | |
| | options\_kmer\_size | ` {"__current_case__": 0, "input_kmer_size": "9", "kmer_size": "provide"} ` | | |
| - **Job 2:** | |
| * Job state is ok | |
| **Container:** | |
| * ```console | |
| quay.io/biocontainers/mulled-v2-ba0fa2569b9c1d280d7fb3b1bf2ad3c0c72d9296:34d0c765d43a43f8968b3d9ffb3ceb9a8cdf6a69-0 | |
| ``` | |
| **Command Line:** | |
| * ```console | |
| export GALAXY_MEMORY_GB=$((${GALAXY_MEMORY_MB:-8192}/1024)) && ln -s '/tmp/tmp3sfjay_q/files/0/b/2/dataset_0b245fcc-3813-42ce-b6d6-3cdcd60bca01.dat' ./input.fastqsanger && meryl count k=9 memory=$GALAXY_MEMORY_GB threads=${GALAXY_SLOTS:-1} ./input.fastqsanger output read-db.meryl && echo 'K-mer size: 9' && tar -cf read-db.meryldb --use-compress-program="pigz -p ${GALAXY_SLOTS:-1}" read-db.meryl | |
| ``` | |
| **Exit Code:** | |
| * ```console | |
| 0 | |
| ``` | |
| **Standard Error:** | |
| * ```console | |
| Found 1 command tree. | |
| Counting 1797 (estimated) thousand canonical 9-mers from 1 input file: | |
| sequence-file: ./input.fastqsanger | |
| SIMPLE MODE | |
| ----------- | |
| 9-mers | |
| -> 262144 entries for counts up to 65535. | |
| -> 4096 kbits memory used | |
| 1841136 input bases | |
| -> expected max count of 7364, needing 0 extra bits. | |
| -> no memory used | |
| 512 kB memory needed | |
| COMPLEX MODE | |
| ------------ | |
| prefix # of struct kmers/ segs/ min data total | |
| bits prefix memory prefix prefix memory memory memory | |
| ------ ------- ------- ------- ------- ------- ------- ------- | |
| 1 2 P 10 kB 449 kM 239 S 8192 B 1912 kB 1922 kB | |
| 2 4 P 16 kB 224 kM 113 S 16 kB 1808 kB 1824 kB | |
| 3 8 P 28 kB 112 kM 53 S 32 kB 1696 kB 1724 kB | |
| 4 16 P 53 kB 56 kM 25 S 64 kB 1600 kB 1653 kB | |
| 5 32 P 104 kB 28 kM 12 S 128 kB 1536 kB 1640 kB | |
| 6 64 P 205 kB 14 kM 6 S 256 kB 1536 kB 1741 kB | |
| 7 128 P 407 kB 7192 M 3 S 512 kB 1536 kB 1943 kB | |
| 8 256 P 812 kB 3596 M 2 S 1024 kB 2048 kB 2860 kB | |
| 9 512 P 1620 kB 1798 M 1 S 2048 kB 2048 kB 3668 kB | |
| 10 1024 P 3240 kB 899 M 1 S 4096 kB 4096 kB 7336 kB Best Value! | |
| 11 2048 P 6480 kB 450 M 1 S 8192 kB 8192 kB 14 MB | |
| 12 4096 P 12 MB 225 M 1 S 16 MB 16 MB 28 MB | |
| 13 8192 P 25 MB 113 M 1 S 32 MB 32 MB 57 MB | |
| 14 16 kP 50 MB 57 M 1 S 64 MB 64 MB 114 MB | |
| 15 32 kP 101 MB 29 M 1 S 128 MB 128 MB 229 MB | |
| FINAL CONFIGURATION | |
| ------------------- | |
| Estimated to require 512 kB memory out of 8192 MB allowed. | |
| Estimated to require 2 batches. | |
| Configured simple mode for 0.000 GB memory per batch, and up to 2 batches. | |
| Start counting with SIMPLE method. | |
| Loading kmers from './input.fastqsanger' into buckets. | |
| Writing results to 'read-db.meryl', using 1 threads. | |
| [ file ][ prefix ][ suffix ][ count-suffix ] | |
| widths [ 6 ][ 0 ][ 12 ][ 0 ] | |
| number [ 64 ][ 1 ][ 4096 ][ ] | |
| thread 0 working on block 0x00000000<0x00000000<0x00000000 4096 kmers between 0x0000000000000000 and 0x0000000000000fff | |
| thread 0 working on block 0x00000001<0x00000001<0x00000001 4096 kmers between 0x0000000000001000 and 0x0000000000001fff | |
| thread 0 working on block 0x00000002<0x00000002<0x00000002 4096 kmers between 0x0000000000002000 and 0x0000000000002fff | |
| thread 0 working on block 0x00000003<0x00000003<0x00000003 4096 kmers between 0x0000000000003000 and 0x0000000000003fff | |
| thread 0 working on block 0x00000004<0x00000004<0x00000004 4096 kmers between 0x0000000000004000 and 0x0000000000004fff | |
| thread 0 working on block 0x00000005<0x00000005<0x00000005 4096 kmers between 0x0000000000005000 and 0x0000000000005fff | |
| thread 0 working on block 0x00000006<0x00000006<0x00000006 4096 kmers between 0x0000000000006000 and 0x0000000000006fff | |
| thread 0 working on block 0x00000007<0x00000007<0x00000007 4096 kmers between 0x0000000000007000 and 0x0000000000007fff | |
| thread 0 working on block 0x00000008<0x00000008<0x00000008 4096 kmers between 0x0000000000008000 and 0x0000000000008fff | |
| thread 0 working on block 0x00000009<0x00000009<0x00000009 4096 kmers between 0x0000000000009000 and 0x0000000000009fff | |
| thread 0 working on block 0x0000000a<0x0000000a<0x0000000a 4096 kmers between 0x000000000000a000 and 0x000000000000afff | |
| thread 0 working on block 0x0000000b<0x0000000b<0x0000000b 4096 kmers between 0x000000000000b000 and 0x000000000000bfff | |
| thread 0 working on block 0x0000000c<0x0000000c<0x0000000c 4096 kmers between 0x000000000000c000 and 0x000000000000cfff | |
| thread 0 working on block 0x0000000d<0x0000000d<0x0000000d 4096 kmers between 0x000000000000d000 and 0x000000000000dfff | |
| thread 0 working on block 0x0000000e<0x0000000e<0x0000000e 4096 kmers between 0x000000000000e000 and 0x000000000000efff | |
| thread 0 working on block 0x0000000f<0x0000000f<0x0000000f 4096 kmers between 0x000000000000f000 and 0x000000000000ffff | |
| thread 0 working on block 0x00000010<0x00000010<0x00000010 4096 kmers between 0x0000000000010000 and 0x0000000000010fff | |
| thread 0 working on block 0x00000011<0x00000011<0x00000011 4096 kmers between 0x0000000000011000 and 0x0000000000011fff | |
| thread 0 working on block 0x00000012<0x00000012<0x00000012 4096 kmers between 0x0000000000012000 and 0x0000000000012fff | |
| thread 0 working on block 0x00000013<0x00000013<0x00000013 4096 kmers between 0x0000000000013000 and 0x0000000000013fff | |
| thread 0 working on block 0x00000014<0x00000014<0x00000014 4096 kmers between 0x0000000000014000 and 0x0000000000014fff | |
| thread 0 working on block 0x00000015<0x00000015<0x00000015 4096 kmers between 0x0000000000015000 and 0x0000000000015fff | |
| thread 0 working on block 0x00000016<0x00000016<0x00000016 4096 kmers between 0x0000000000016000 and 0x0000000000016fff | |
| thread 0 working on block 0x00000017<0x00000017<0x00000017 4096 kmers between 0x0000000000017000 and 0x0000000000017fff | |
| thread 0 working on block 0x00000018<0x00000018<0x00000018 4096 kmers between 0x0000000000018000 and 0x0000000000018fff | |
| thread 0 working on block 0x00000019<0x00000019<0x00000019 4096 kmers between 0x0000000000019000 and 0x0000000000019fff | |
| thread 0 working on block 0x0000001a<0x0000001a<0x0000001a 4096 kmers between 0x000000000001a000 and 0x000000000001afff | |
| thread 0 working on block 0x0000001b<0x0000001b<0x0000001b 4096 kmers between 0x000000000001b000 and 0x000000000001bfff | |
| thread 0 working on block 0x0000001c<0x0000001c<0x0000001c 4096 kmers between 0x000000000001c000 and 0x000000000001cfff | |
| thread 0 working on block 0x0000001d<0x0000001d<0x0000001d 4096 kmers between 0x000000000001d000 and 0x000000000001dfff | |
| thread 0 working on block 0x0000001e<0x0000001e<0x0000001e 4096 kmers between 0x000000000001e000 and 0x000000000001efff | |
| thread 0 working on block 0x0000001f<0x0000001f<0x0000001f 4096 kmers between 0x000000000001f000 and 0x000000000001ffff | |
| thread 0 working on block 0x00000020<0x00000020<0x00000020 4096 kmers between 0x0000000000020000 and 0x0000000000020fff | |
| thread 0 working on block 0x00000021<0x00000021<0x00000021 4096 kmers between 0x0000000000021000 and 0x0000000000021fff | |
| thread 0 working on block 0x00000022<0x00000022<0x00000022 4096 kmers between 0x0000000000022000 and 0x0000000000022fff | |
| thread 0 working on block 0x00000023<0x00000023<0x00000023 4096 kmers between 0x0000000000023000 and 0x0000000000023fff | |
| thread 0 working on block 0x00000024<0x00000024<0x00000024 4096 kmers between 0x0000000000024000 and 0x0000000000024fff | |
| thread 0 working on block 0x00000025<0x00000025<0x00000025 4096 kmers between 0x0000000000025000 and 0x0000000000025fff | |
| thread 0 working on block 0x00000026<0x00000026<0x00000026 4096 kmers between 0x0000000000026000 and 0x0000000000026fff | |
| thread 0 working on block 0x00000027<0x00000027<0x00000027 4096 kmers between 0x0000000000027000 and 0x0000000000027fff | |
| thread 0 working on block 0x00000028<0x00000028<0x00000028 4096 kmers between 0x0000000000028000 and 0x0000000000028fff | |
| thread 0 working on block 0x00000029<0x00000029<0x00000029 4096 kmers between 0x0000000000029000 and 0x0000000000029fff | |
| thread 0 working on block 0x0000002a<0x0000002a<0x0000002a 4096 kmers between 0x000000000002a000 and 0x000000000002afff | |
| thread 0 working on block 0x0000002b<0x0000002b<0x0000002b 4096 kmers between 0x000000000002b000 and 0x000000000002bfff | |
| thread 0 working on block 0x0000002c<0x0000002c<0x0000002c 4096 kmers between 0x000000000002c000 and 0x000000000002cfff | |
| thread 0 working on block 0x0000002d<0x0000002d<0x0000002d 4096 kmers between 0x000000000002d000 and 0x000000000002dfff | |
| thread 0 working on block 0x0000002e<0x0000002e<0x0000002e 4096 kmers between 0x000000000002e000 and 0x000000000002efff | |
| thread 0 working on block 0x0000002f<0x0000002f<0x0000002f 4096 kmers between 0x000000000002f000 and 0x000000000002ffff | |
| thread 0 working on block 0x00000030<0x00000030<0x00000030 4096 kmers between 0x0000000000030000 and 0x0000000000030fff | |
| thread 0 working on block 0x00000031<0x00000031<0x00000031 4096 kmers between 0x0000000000031000 and 0x0000000000031fff | |
| thread 0 working on block 0x00000032<0x00000032<0x00000032 4096 kmers between 0x0000000000032000 and 0x0000000000032fff | |
| thread 0 working on block 0x00000033<0x00000033<0x00000033 4096 kmers between 0x0000000000033000 and 0x0000000000033fff | |
| thread 0 working on block 0x00000034<0x00000034<0x00000034 4096 kmers between 0x0000000000034000 and 0x0000000000034fff | |
| thread 0 working on block 0x00000035<0x00000035<0x00000035 4096 kmers between 0x0000000000035000 and 0x0000000000035fff | |
| thread 0 working on block 0x00000036<0x00000036<0x00000036 4096 kmers between 0x0000000000036000 and 0x0000000000036fff | |
| thread 0 working on block 0x00000037<0x00000037<0x00000037 4096 kmers between 0x0000000000037000 and 0x0000000000037fff | |
| thread 0 working on block 0x00000038<0x00000038<0x00000038 4096 kmers between 0x0000000000038000 and 0x0000000000038fff | |
| thread 0 working on block 0x00000039<0x00000039<0x00000039 4096 kmers between 0x0000000000039000 and 0x0000000000039fff | |
| thread 0 working on block 0x0000003a<0x0000003a<0x0000003a 4096 kmers between 0x000000000003a000 and 0x000000000003afff | |
| thread 0 working on block 0x0000003b<0x0000003b<0x0000003b 4096 kmers between 0x000000000003b000 and 0x000000000003bfff | |
| thread 0 working on block 0x0000003c<0x0000003c<0x0000003c 4096 kmers between 0x000000000003c000 and 0x000000000003cfff | |
| thread 0 working on block 0x0000003d<0x0000003d<0x0000003d 4096 kmers between 0x000000000003d000 and 0x000000000003dfff | |
| thread 0 working on block 0x0000003e<0x0000003e<0x0000003e 4096 kmers between 0x000000000003e000 and 0x000000000003efff | |
| thread 0 working on block 0x0000003f<0x0000003f<0x0000003f 4096 kmers between 0x000000000003f000 and 0x000000000003ffff | |
| finishIteration()-- | |
| Cleaning up. | |
| Bye. | |
| ``` | |
| **Standard Output:** | |
| * ```console | |
| K-mer size: 9 | |
| ``` | |
| **Traceback:** | |
| * ```console | |
| ``` | |
| **Job Parameters:** | |
| * | Job parameter | Parameter value | | |
| | ------------- | --------------- | | |
| | \_\_input\_ext | ` "input" ` | | |
| | \_\_workflow\_invocation\_uuid\_\_ | ` "a9e9fe4a115611f189517ced8dc21a23" ` | | |
| | chromInfo | ` "/tmp/tmp3sfjay_q/galaxy-dev/tool-data/shared/ucsc/chrom/?.len" ` | | |
| | count\_operation | ` "count" ` | | |
| | dbkey | ` "?" ` | | |
| | options\_kmer\_size | ` {"__current_case__": 0, "input_kmer_size": "9", "kmer_size": "provide"} ` | | |
| </details> | |
| - **Step 8: Unlabelled step (toolshed.g2.bx.psu.edu/repos/iuc/meryl/meryl/1.3+galaxy6)**: | |
| * step_state: scheduled | |
| * <details><summary>Jobs</summary> | |
| - **Job 1:** | |
| * Job state is ok | |
| **Container:** | |
| * ```console | |
| quay.io/biocontainers/mulled-v2-007a380c92d33c31a26a58d858982829eeafd842:9c2cffc8866024837770aedcc2c77c7a7f9bc1f7-2 | |
| ``` | |
| **Command Line:** | |
| * ```console | |
| export GALAXY_MEMORY_GB=$((${GALAXY_MEMORY_MB:-8192}/1024)) && ln -s '/tmp/tmp3sfjay_q/files/4/8/6/dataset_4869b36d-36e7-4b32-b2fc-0abdb07e06ec.dat' ./input.fastqsanger && meryl count k=9 memory=$GALAXY_MEMORY_GB threads=${GALAXY_SLOTS:-1} ./input.fastqsanger output read-db.meryl && echo 'K-mer size: 9' && tar -zcf read-db.meryldb read-db.meryl | |
| ``` | |
| **Exit Code:** | |
| * ```console | |
| 0 | |
| ``` | |
| **Standard Error:** | |
| * ```console | |
| Found 1 command tree. | |
| Counting 1896 (estimated) thousand canonical 9-mers from 1 input file: | |
| sequence-file: ./input.fastqsanger | |
| SIMPLE MODE | |
| ----------- | |
| 9-mers | |
| -> 262144 entries for counts up to 65535. | |
| -> 4096 kbits memory used | |
| 1941665 input bases | |
| -> expected max count of 7766, needing 0 extra bits. | |
| -> no memory used | |
| 512 kB memory needed | |
| COMPLEX MODE | |
| ------------ | |
| prefix # of struct kmers/ segs/ min data total | |
| bits prefix memory prefix prefix memory memory memory | |
| ------ ------- ------- ------- ------- ------- ------- ------- | |
| 1 2 P 10 kB 474 kM 252 S 8192 B 2016 kB 2026 kB | |
| 2 4 P 16 kB 237 kM 119 S 16 kB 1904 kB 1920 kB | |
| 3 8 P 28 kB 118 kM 56 S 32 kB 1792 kB 1820 kB | |
| 4 16 P 53 kB 59 kM 26 S 64 kB 1664 kB 1717 kB | |
| 5 32 P 104 kB 29 kM 13 S 128 kB 1664 kB 1768 kB | |
| 6 64 P 205 kB 14 kM 6 S 256 kB 1536 kB 1741 kB | |
| 7 128 P 407 kB 7585 M 3 S 512 kB 1536 kB 1943 kB | |
| 8 256 P 812 kB 3793 M 2 S 1024 kB 2048 kB 2860 kB | |
| 9 512 P 1620 kB 1897 M 1 S 2048 kB 2048 kB 3668 kB | |
| 10 1024 P 3240 kB 949 M 1 S 4096 kB 4096 kB 7336 kB Best Value! | |
| 11 2048 P 6480 kB 475 M 1 S 8192 kB 8192 kB 14 MB | |
| 12 4096 P 12 MB 238 M 1 S 16 MB 16 MB 28 MB | |
| 13 8192 P 25 MB 119 M 1 S 32 MB 32 MB 57 MB | |
| 14 16 kP 50 MB 60 M 1 S 64 MB 64 MB 114 MB | |
| 15 32 kP 101 MB 30 M 1 S 128 MB 128 MB 229 MB | |
| FINAL CONFIGURATION | |
| ------------------- | |
| Estimated to require 512 kB memory out of 8192 MB allowed. | |
| Estimated to require 2 batches. | |
| Configured simple mode for 0.000 GB memory per batch, and up to 2 batches. | |
| Start counting with SIMPLE method. | |
| Loading kmers from './input.fastqsanger' into buckets. | |
| Writing results to 'read-db.meryl', using 1 threads. | |
| [ file ][ prefix ][ suffix ][ count-suffix ] | |
| widths [ 6 ][ 0 ][ 12 ][ 0 ] | |
| number [ 64 ][ 1 ][ 4096 ][ ] | |
| thread 0 working on block 0x00000000<0x00000000<0x00000000 4096 kmers between 0x0000000000000000 and 0x0000000000000fff | |
| thread 0 working on block 0x00000001<0x00000001<0x00000001 4096 kmers between 0x0000000000001000 and 0x0000000000001fff | |
| thread 0 working on block 0x00000002<0x00000002<0x00000002 4096 kmers between 0x0000000000002000 and 0x0000000000002fff | |
| thread 0 working on block 0x00000003<0x00000003<0x00000003 4096 kmers between 0x0000000000003000 and 0x0000000000003fff | |
| thread 0 working on block 0x00000004<0x00000004<0x00000004 4096 kmers between 0x0000000000004000 and 0x0000000000004fff | |
| thread 0 working on block 0x00000005<0x00000005<0x00000005 4096 kmers between 0x0000000000005000 and 0x0000000000005fff | |
| thread 0 working on block 0x00000006<0x00000006<0x00000006 4096 kmers between 0x0000000000006000 and 0x0000000000006fff | |
| thread 0 working on block 0x00000007<0x00000007<0x00000007 4096 kmers between 0x0000000000007000 and 0x0000000000007fff | |
| thread 0 working on block 0x00000008<0x00000008<0x00000008 4096 kmers between 0x0000000000008000 and 0x0000000000008fff | |
| thread 0 working on block 0x00000009<0x00000009<0x00000009 4096 kmers between 0x0000000000009000 and 0x0000000000009fff | |
| thread 0 working on block 0x0000000a<0x0000000a<0x0000000a 4096 kmers between 0x000000000000a000 and 0x000000000000afff | |
| thread 0 working on block 0x0000000b<0x0000000b<0x0000000b 4096 kmers between 0x000000000000b000 and 0x000000000000bfff | |
| thread 0 working on block 0x0000000c<0x0000000c<0x0000000c 4096 kmers between 0x000000000000c000 and 0x000000000000cfff | |
| thread 0 working on block 0x0000000d<0x0000000d<0x0000000d 4096 kmers between 0x000000000000d000 and 0x000000000000dfff | |
| thread 0 working on block 0x0000000e<0x0000000e<0x0000000e 4096 kmers between 0x000000000000e000 and 0x000000000000efff | |
| thread 0 working on block 0x0000000f<0x0000000f<0x0000000f 4096 kmers between 0x000000000000f000 and 0x000000000000ffff | |
| thread 0 working on block 0x00000010<0x00000010<0x00000010 4096 kmers between 0x0000000000010000 and 0x0000000000010fff | |
| thread 0 working on block 0x00000011<0x00000011<0x00000011 4096 kmers between 0x0000000000011000 and 0x0000000000011fff | |
| thread 0 working on block 0x00000012<0x00000012<0x00000012 4096 kmers between 0x0000000000012000 and 0x0000000000012fff | |
| thread 0 working on block 0x00000013<0x00000013<0x00000013 4096 kmers between 0x0000000000013000 and 0x0000000000013fff | |
| thread 0 working on block 0x00000014<0x00000014<0x00000014 4096 kmers between 0x0000000000014000 and 0x0000000000014fff | |
| thread 0 working on block 0x00000015<0x00000015<0x00000015 4096 kmers between 0x0000000000015000 and 0x0000000000015fff | |
| thread 0 working on block 0x00000016<0x00000016<0x00000016 4096 kmers between 0x0000000000016000 and 0x0000000000016fff | |
| thread 0 working on block 0x00000017<0x00000017<0x00000017 4096 kmers between 0x0000000000017000 and 0x0000000000017fff | |
| thread 0 working on block 0x00000018<0x00000018<0x00000018 4096 kmers between 0x0000000000018000 and 0x0000000000018fff | |
| thread 0 working on block 0x00000019<0x00000019<0x00000019 4096 kmers between 0x0000000000019000 and 0x0000000000019fff | |
| thread 0 working on block 0x0000001a<0x0000001a<0x0000001a 4096 kmers between 0x000000000001a000 and 0x000000000001afff | |
| thread 0 working on block 0x0000001b<0x0000001b<0x0000001b 4096 kmers between 0x000000000001b000 and 0x000000000001bfff | |
| thread 0 working on block 0x0000001c<0x0000001c<0x0000001c 4096 kmers between 0x000000000001c000 and 0x000000000001cfff | |
| thread 0 working on block 0x0000001d<0x0000001d<0x0000001d 4096 kmers between 0x000000000001d000 and 0x000000000001dfff | |
| thread 0 working on block 0x0000001e<0x0000001e<0x0000001e 4096 kmers between 0x000000000001e000 and 0x000000000001efff | |
| thread 0 working on block 0x0000001f<0x0000001f<0x0000001f 4096 kmers between 0x000000000001f000 and 0x000000000001ffff | |
| thread 0 working on block 0x00000020<0x00000020<0x00000020 4096 kmers between 0x0000000000020000 and 0x0000000000020fff | |
| thread 0 working on block 0x00000021<0x00000021<0x00000021 4096 kmers between 0x0000000000021000 and 0x0000000000021fff | |
| thread 0 working on block 0x00000022<0x00000022<0x00000022 4096 kmers between 0x0000000000022000 and 0x0000000000022fff | |
| thread 0 working on block 0x00000023<0x00000023<0x00000023 4096 kmers between 0x0000000000023000 and 0x0000000000023fff | |
| thread 0 working on block 0x00000024<0x00000024<0x00000024 4096 kmers between 0x0000000000024000 and 0x0000000000024fff | |
| thread 0 working on block 0x00000025<0x00000025<0x00000025 4096 kmers between 0x0000000000025000 and 0x0000000000025fff | |
| thread 0 working on block 0x00000026<0x00000026<0x00000026 4096 kmers between 0x0000000000026000 and 0x0000000000026fff | |
| thread 0 working on block 0x00000027<0x00000027<0x00000027 4096 kmers between 0x0000000000027000 and 0x0000000000027fff | |
| thread 0 working on block 0x00000028<0x00000028<0x00000028 4096 kmers between 0x0000000000028000 and 0x0000000000028fff | |
| thread 0 working on block 0x00000029<0x00000029<0x00000029 4096 kmers between 0x0000000000029000 and 0x0000000000029fff | |
| thread 0 working on block 0x0000002a<0x0000002a<0x0000002a 4096 kmers between 0x000000000002a000 and 0x000000000002afff | |
| thread 0 working on block 0x0000002b<0x0000002b<0x0000002b 4096 kmers between 0x000000000002b000 and 0x000000000002bfff | |
| thread 0 working on block 0x0000002c<0x0000002c<0x0000002c 4096 kmers between 0x000000000002c000 and 0x000000000002cfff | |
| thread 0 working on block 0x0000002d<0x0000002d<0x0000002d 4096 kmers between 0x000000000002d000 and 0x000000000002dfff | |
| thread 0 working on block 0x0000002e<0x0000002e<0x0000002e 4096 kmers between 0x000000000002e000 and 0x000000000002efff | |
| thread 0 working on block 0x0000002f<0x0000002f<0x0000002f 4096 kmers between 0x000000000002f000 and 0x000000000002ffff | |
| thread 0 working on block 0x00000030<0x00000030<0x00000030 4096 kmers between 0x0000000000030000 and 0x0000000000030fff | |
| thread 0 working on block 0x00000031<0x00000031<0x00000031 4096 kmers between 0x0000000000031000 and 0x0000000000031fff | |
| thread 0 working on block 0x00000032<0x00000032<0x00000032 4096 kmers between 0x0000000000032000 and 0x0000000000032fff | |
| thread 0 working on block 0x00000033<0x00000033<0x00000033 4096 kmers between 0x0000000000033000 and 0x0000000000033fff | |
| thread 0 working on block 0x00000034<0x00000034<0x00000034 4096 kmers between 0x0000000000034000 and 0x0000000000034fff | |
| thread 0 working on block 0x00000035<0x00000035<0x00000035 4096 kmers between 0x0000000000035000 and 0x0000000000035fff | |
| thread 0 working on block 0x00000036<0x00000036<0x00000036 4096 kmers between 0x0000000000036000 and 0x0000000000036fff | |
| thread 0 working on block 0x00000037<0x00000037<0x00000037 4096 kmers between 0x0000000000037000 and 0x0000000000037fff | |
| thread 0 working on block 0x00000038<0x00000038<0x00000038 4096 kmers between 0x0000000000038000 and 0x0000000000038fff | |
| thread 0 working on block 0x00000039<0x00000039<0x00000039 4096 kmers between 0x0000000000039000 and 0x0000000000039fff | |
| thread 0 working on block 0x0000003a<0x0000003a<0x0000003a 4096 kmers between 0x000000000003a000 and 0x000000000003afff | |
| thread 0 working on block 0x0000003b<0x0000003b<0x0000003b 4096 kmers between 0x000000000003b000 and 0x000000000003bfff | |
| thread 0 working on block 0x0000003c<0x0000003c<0x0000003c 4096 kmers between 0x000000000003c000 and 0x000000000003cfff | |
| thread 0 working on block 0x0000003d<0x0000003d<0x0000003d 4096 kmers between 0x000000000003d000 and 0x000000000003dfff | |
| thread 0 working on block 0x0000003e<0x0000003e<0x0000003e 4096 kmers between 0x000000000003e000 and 0x000000000003efff | |
| thread 0 working on block 0x0000003f<0x0000003f<0x0000003f 4096 kmers between 0x000000000003f000 and 0x000000000003ffff | |
| finishIteration()-- | |
| Cleaning up. | |
| Bye. | |
| ``` | |
| **Standard Output:** | |
| * ```console | |
| K-mer size: 9 | |
| ``` | |
| **Traceback:** | |
| * ```console | |
| ``` | |
| **Job Parameters:** | |
| * | Job parameter | Parameter value | | |
| | ------------- | --------------- | | |
| | \_\_input\_ext | ` "input" ` | | |
| | \_\_workflow\_invocation\_uuid\_\_ | ` "a9e9fe4a115611f189517ced8dc21a23" ` | | |
| | chromInfo | ` "/tmp/tmp3sfjay_q/galaxy-dev/tool-data/shared/ucsc/chrom/?.len" ` | | |
| | dbkey | ` "?" ` | | |
| | operation\_type | ` {"__current_case__": 0, "command_type": "count-kmers", "count_operations": "count", "input_reads": {"values": [{"id": 118, "src": "dce"}]}, "options_kmer_size": {"__current_case__": 0, "input_kmer_size": "9", "kmer_size": "provide"}} ` | | |
| - **Job 2:** | |
| * Job state is ok | |
| **Container:** | |
| * ```console | |
| quay.io/biocontainers/mulled-v2-007a380c92d33c31a26a58d858982829eeafd842:9c2cffc8866024837770aedcc2c77c7a7f9bc1f7-2 | |
| ``` | |
| **Command Line:** | |
| * ```console | |
| export GALAXY_MEMORY_GB=$((${GALAXY_MEMORY_MB:-8192}/1024)) && ln -s '/tmp/tmp3sfjay_q/files/c/3/4/dataset_c34d005d-d417-4a87-a2d5-ac64b7af5191.dat' ./input.fastqsanger && meryl count k=9 memory=$GALAXY_MEMORY_GB threads=${GALAXY_SLOTS:-1} ./input.fastqsanger output read-db.meryl && echo 'K-mer size: 9' && tar -zcf read-db.meryldb read-db.meryl | |
| ``` | |
| **Exit Code:** | |
| * ```console | |
| 0 | |
| ``` | |
| **Standard Error:** | |
| * ```console | |
| Found 1 command tree. | |
| Counting 1896 (estimated) thousand canonical 9-mers from 1 input file: | |
| sequence-file: ./input.fastqsanger | |
| SIMPLE MODE | |
| ----------- | |
| 9-mers | |
| -> 262144 entries for counts up to 65535. | |
| -> 4096 kbits memory used | |
| 1941665 input bases | |
| -> expected max count of 7766, needing 0 extra bits. | |
| -> no memory used | |
| 512 kB memory needed | |
| COMPLEX MODE | |
| ------------ | |
| prefix # of struct kmers/ segs/ min data total | |
| bits prefix memory prefix prefix memory memory memory | |
| ------ ------- ------- ------- ------- ------- ------- ------- | |
| 1 2 P 10 kB 474 kM 252 S 8192 B 2016 kB 2026 kB | |
| 2 4 P 16 kB 237 kM 119 S 16 kB 1904 kB 1920 kB | |
| 3 8 P 28 kB 118 kM 56 S 32 kB 1792 kB 1820 kB | |
| 4 16 P 53 kB 59 kM 26 S 64 kB 1664 kB 1717 kB | |
| 5 32 P 104 kB 29 kM 13 S 128 kB 1664 kB 1768 kB | |
| 6 64 P 205 kB 14 kM 6 S 256 kB 1536 kB 1741 kB | |
| 7 128 P 407 kB 7585 M 3 S 512 kB 1536 kB 1943 kB | |
| 8 256 P 812 kB 3793 M 2 S 1024 kB 2048 kB 2860 kB | |
| 9 512 P 1620 kB 1897 M 1 S 2048 kB 2048 kB 3668 kB | |
| 10 1024 P 3240 kB 949 M 1 S 4096 kB 4096 kB 7336 kB Best Value! | |
| 11 2048 P 6480 kB 475 M 1 S 8192 kB 8192 kB 14 MB | |
| 12 4096 P 12 MB 238 M 1 S 16 MB 16 MB 28 MB | |
| 13 8192 P 25 MB 119 M 1 S 32 MB 32 MB 57 MB | |
| 14 16 kP 50 MB 60 M 1 S 64 MB 64 MB 114 MB | |
| 15 32 kP 101 MB 30 M 1 S 128 MB 128 MB 229 MB | |
| FINAL CONFIGURATION | |
| ------------------- | |
| Estimated to require 512 kB memory out of 8192 MB allowed. | |
| Estimated to require 2 batches. | |
| Configured simple mode for 0.000 GB memory per batch, and up to 2 batches. | |
| Start counting with SIMPLE method. | |
| Loading kmers from './input.fastqsanger' into buckets. | |
| Writing results to 'read-db.meryl', using 1 threads. | |
| [ file ][ prefix ][ suffix ][ count-suffix ] | |
| widths [ 6 ][ 0 ][ 12 ][ 0 ] | |
| number [ 64 ][ 1 ][ 4096 ][ ] | |
| thread 0 working on block 0x00000000<0x00000000<0x00000000 4096 kmers between 0x0000000000000000 and 0x0000000000000fff | |
| thread 0 working on block 0x00000001<0x00000001<0x00000001 4096 kmers between 0x0000000000001000 and 0x0000000000001fff | |
| thread 0 working on block 0x00000002<0x00000002<0x00000002 4096 kmers between 0x0000000000002000 and 0x0000000000002fff | |
| thread 0 working on block 0x00000003<0x00000003<0x00000003 4096 kmers between 0x0000000000003000 and 0x0000000000003fff | |
| thread 0 working on block 0x00000004<0x00000004<0x00000004 4096 kmers between 0x0000000000004000 and 0x0000000000004fff | |
| thread 0 working on block 0x00000005<0x00000005<0x00000005 4096 kmers between 0x0000000000005000 and 0x0000000000005fff | |
| thread 0 working on block 0x00000006<0x00000006<0x00000006 4096 kmers between 0x0000000000006000 and 0x0000000000006fff | |
| thread 0 working on block 0x00000007<0x00000007<0x00000007 4096 kmers between 0x0000000000007000 and 0x0000000000007fff | |
| thread 0 working on block 0x00000008<0x00000008<0x00000008 4096 kmers between 0x0000000000008000 and 0x0000000000008fff | |
| thread 0 working on block 0x00000009<0x00000009<0x00000009 4096 kmers between 0x0000000000009000 and 0x0000000000009fff | |
| thread 0 working on block 0x0000000a<0x0000000a<0x0000000a 4096 kmers between 0x000000000000a000 and 0x000000000000afff | |
| thread 0 working on block 0x0000000b<0x0000000b<0x0000000b 4096 kmers between 0x000000000000b000 and 0x000000000000bfff | |
| thread 0 working on block 0x0000000c<0x0000000c<0x0000000c 4096 kmers between 0x000000000000c000 and 0x000000000000cfff | |
| thread 0 working on block 0x0000000d<0x0000000d<0x0000000d 4096 kmers between 0x000000000000d000 and 0x000000000000dfff | |
| thread 0 working on block 0x0000000e<0x0000000e<0x0000000e 4096 kmers between 0x000000000000e000 and 0x000000000000efff | |
| thread 0 working on block 0x0000000f<0x0000000f<0x0000000f 4096 kmers between 0x000000000000f000 and 0x000000000000ffff | |
| thread 0 working on block 0x00000010<0x00000010<0x00000010 4096 kmers between 0x0000000000010000 and 0x0000000000010fff | |
| thread 0 working on block 0x00000011<0x00000011<0x00000011 4096 kmers between 0x0000000000011000 and 0x0000000000011fff | |
| thread 0 working on block 0x00000012<0x00000012<0x00000012 4096 kmers between 0x0000000000012000 and 0x0000000000012fff | |
| thread 0 working on block 0x00000013<0x00000013<0x00000013 4096 kmers between 0x0000000000013000 and 0x0000000000013fff | |
| thread 0 working on block 0x00000014<0x00000014<0x00000014 4096 kmers between 0x0000000000014000 and 0x0000000000014fff | |
| thread 0 working on block 0x00000015<0x00000015<0x00000015 4096 kmers between 0x0000000000015000 and 0x0000000000015fff | |
| thread 0 working on block 0x00000016<0x00000016<0x00000016 4096 kmers between 0x0000000000016000 and 0x0000000000016fff | |
| thread 0 working on block 0x00000017<0x00000017<0x00000017 4096 kmers between 0x0000000000017000 and 0x0000000000017fff | |
| thread 0 working on block 0x00000018<0x00000018<0x00000018 4096 kmers between 0x0000000000018000 and 0x0000000000018fff | |
| thread 0 working on block 0x00000019<0x00000019<0x00000019 4096 kmers between 0x0000000000019000 and 0x0000000000019fff | |
| thread 0 working on block 0x0000001a<0x0000001a<0x0000001a 4096 kmers between 0x000000000001a000 and 0x000000000001afff | |
| thread 0 working on block 0x0000001b<0x0000001b<0x0000001b 4096 kmers between 0x000000000001b000 and 0x000000000001bfff | |
| thread 0 working on block 0x0000001c<0x0000001c<0x0000001c 4096 kmers between 0x000000000001c000 and 0x000000000001cfff | |
| thread 0 working on block 0x0000001d<0x0000001d<0x0000001d 4096 kmers between 0x000000000001d000 and 0x000000000001dfff | |
| thread 0 working on block 0x0000001e<0x0000001e<0x0000001e 4096 kmers between 0x000000000001e000 and 0x000000000001efff | |
| thread 0 working on block 0x0000001f<0x0000001f<0x0000001f 4096 kmers between 0x000000000001f000 and 0x000000000001ffff | |
| thread 0 working on block 0x00000020<0x00000020<0x00000020 4096 kmers between 0x0000000000020000 and 0x0000000000020fff | |
| thread 0 working on block 0x00000021<0x00000021<0x00000021 4096 kmers between 0x0000000000021000 and 0x0000000000021fff | |
| thread 0 working on block 0x00000022<0x00000022<0x00000022 4096 kmers between 0x0000000000022000 and 0x0000000000022fff | |
| thread 0 working on block 0x00000023<0x00000023<0x00000023 4096 kmers between 0x0000000000023000 and 0x0000000000023fff | |
| thread 0 working on block 0x00000024<0x00000024<0x00000024 4096 kmers between 0x0000000000024000 and 0x0000000000024fff | |
| thread 0 working on block 0x00000025<0x00000025<0x00000025 4096 kmers between 0x0000000000025000 and 0x0000000000025fff | |
| thread 0 working on block 0x00000026<0x00000026<0x00000026 4096 kmers between 0x0000000000026000 and 0x0000000000026fff | |
| thread 0 working on block 0x00000027<0x00000027<0x00000027 4096 kmers between 0x0000000000027000 and 0x0000000000027fff | |
| thread 0 working on block 0x00000028<0x00000028<0x00000028 4096 kmers between 0x0000000000028000 and 0x0000000000028fff | |
| thread 0 working on block 0x00000029<0x00000029<0x00000029 4096 kmers between 0x0000000000029000 and 0x0000000000029fff | |
| thread 0 working on block 0x0000002a<0x0000002a<0x0000002a 4096 kmers between 0x000000000002a000 and 0x000000000002afff | |
| thread 0 working on block 0x0000002b<0x0000002b<0x0000002b 4096 kmers between 0x000000000002b000 and 0x000000000002bfff | |
| thread 0 working on block 0x0000002c<0x0000002c<0x0000002c 4096 kmers between 0x000000000002c000 and 0x000000000002cfff | |
| thread 0 working on block 0x0000002d<0x0000002d<0x0000002d 4096 kmers between 0x000000000002d000 and 0x000000000002dfff | |
| thread 0 working on block 0x0000002e<0x0000002e<0x0000002e 4096 kmers between 0x000000000002e000 and 0x000000000002efff | |
| thread 0 working on block 0x0000002f<0x0000002f<0x0000002f 4096 kmers between 0x000000000002f000 and 0x000000000002ffff | |
| thread 0 working on block 0x00000030<0x00000030<0x00000030 4096 kmers between 0x0000000000030000 and 0x0000000000030fff | |
| thread 0 working on block 0x00000031<0x00000031<0x00000031 4096 kmers between 0x0000000000031000 and 0x0000000000031fff | |
| thread 0 working on block 0x00000032<0x00000032<0x00000032 4096 kmers between 0x0000000000032000 and 0x0000000000032fff | |
| thread 0 working on block 0x00000033<0x00000033<0x00000033 4096 kmers between 0x0000000000033000 and 0x0000000000033fff | |
| thread 0 working on block 0x00000034<0x00000034<0x00000034 4096 kmers between 0x0000000000034000 and 0x0000000000034fff | |
| thread 0 working on block 0x00000035<0x00000035<0x00000035 4096 kmers between 0x0000000000035000 and 0x0000000000035fff | |
| thread 0 working on block 0x00000036<0x00000036<0x00000036 4096 kmers between 0x0000000000036000 and 0x0000000000036fff | |
| thread 0 working on block 0x00000037<0x00000037<0x00000037 4096 kmers between 0x0000000000037000 and 0x0000000000037fff | |
| thread 0 working on block 0x00000038<0x00000038<0x00000038 4096 kmers between 0x0000000000038000 and 0x0000000000038fff | |
| thread 0 working on block 0x00000039<0x00000039<0x00000039 4096 kmers between 0x0000000000039000 and 0x0000000000039fff | |
| thread 0 working on block 0x0000003a<0x0000003a<0x0000003a 4096 kmers between 0x000000000003a000 and 0x000000000003afff | |
| thread 0 working on block 0x0000003b<0x0000003b<0x0000003b 4096 kmers between 0x000000000003b000 and 0x000000000003bfff | |
| thread 0 working on block 0x0000003c<0x0000003c<0x0000003c 4096 kmers between 0x000000000003c000 and 0x000000000003cfff | |
| thread 0 working on block 0x0000003d<0x0000003d<0x0000003d 4096 kmers between 0x000000000003d000 and 0x000000000003dfff | |
| thread 0 working on block 0x0000003e<0x0000003e<0x0000003e 4096 kmers between 0x000000000003e000 and 0x000000000003efff | |
| thread 0 working on block 0x0000003f<0x0000003f<0x0000003f 4096 kmers between 0x000000000003f000 and 0x000000000003ffff | |
| finishIteration()-- | |
| Cleaning up. | |
| Bye. | |
| ``` | |
| **Standard Output:** | |
| * ```console | |
| K-mer size: 9 | |
| ``` | |
| **Traceback:** | |
| * ```console | |
| ``` | |
| **Job Parameters:** | |
| * | Job parameter | Parameter value | | |
| | ------------- | --------------- | | |
| | \_\_input\_ext | ` "input" ` | | |
| | \_\_workflow\_invocation\_uuid\_\_ | ` "a9e9fe4a115611f189517ced8dc21a23" ` | | |
| | chromInfo | ` "/tmp/tmp3sfjay_q/galaxy-dev/tool-data/shared/ucsc/chrom/?.len" ` | | |
| | dbkey | ` "?" ` | | |
| | operation\_type | ` {"__current_case__": 0, "command_type": "count-kmers", "count_operations": "count", "input_reads": {"values": [{"id": 117, "src": "dce"}]}, "options_kmer_size": {"__current_case__": 0, "input_kmer_size": "9", "kmer_size": "provide"}} ` | | |
| </details> | |
| - **Step 9: Unlabelled step (toolshed.g2.bx.psu.edu/repos/iuc/meryl/meryl/1.3+galaxy6)**: | |
| * step_state: scheduled | |
| * <details><summary>Jobs</summary> | |
| - **Job 1:** | |
| * Job state is ok | |
| **Container:** | |
| * ```console | |
| quay.io/biocontainers/mulled-v2-007a380c92d33c31a26a58d858982829eeafd842:9c2cffc8866024837770aedcc2c77c7a7f9bc1f7-2 | |
| ``` | |
| **Command Line:** | |
| * ```console | |
| export GALAXY_MEMORY_GB=$((${GALAXY_MEMORY_MB:-8192}/1024)) && export MERQURY=$(dirname $(command -v merqury.sh))/../share/merqury/ && mkdir 'paternal0.meryl' && ln -s '/tmp/tmp3sfjay_q/files/e/e/6/dataset_ee60b813-9038-43b8-a5b5-fc02f017f4bf.dat' ./input_paternal_0.fastqsanger && meryl count k=9 memory=$GALAXY_MEMORY_GB threads=${GALAXY_SLOTS:-1} ./input_paternal_0.fastqsanger output 'paternal0.meryl' && mkdir 'paternal1.meryl' && ln -s '/tmp/tmp3sfjay_q/files/0/b/2/dataset_0b245fcc-3813-42ce-b6d6-3cdcd60bca01.dat' ./input_paternal_1.fastqsanger && meryl count k=9 memory=$GALAXY_MEMORY_GB threads=${GALAXY_SLOTS:-1} ./input_paternal_1.fastqsanger output 'paternal1.meryl' && meryl union-sum paternal*.meryl output pat.meryl && mkdir 'maternal0.meryl' && ln -s '/tmp/tmp3sfjay_q/files/c/3/4/dataset_c34d005d-d417-4a87-a2d5-ac64b7af5191.dat' ./input_maternal_0.fastqsanger && meryl count k=9 memory=$GALAXY_MEMORY_GB threads=${GALAXY_SLOTS:-1} ./input_maternal_0.fastqsanger output 'maternal0.meryl' && mkdir 'maternal1.meryl' && ln -s '/tmp/tmp3sfjay_q/files/4/8/6/dataset_4869b36d-36e7-4b32-b2fc-0abdb07e06ec.dat' ./input_maternal_1.fastqsanger && meryl count k=9 memory=$GALAXY_MEMORY_GB threads=${GALAXY_SLOTS:-1} ./input_maternal_1.fastqsanger output 'maternal1.meryl' && meryl union-sum maternal*.meryl output mat.meryl && mkdir 'child0.meryl' && ln -s '/tmp/tmp3sfjay_q/files/5/e/a/dataset_5eaf073d-bdb6-40ba-beaa-aa5b880b521e.dat' ./input_child_0.fastqsanger && meryl count k=9 memory=$GALAXY_MEMORY_GB threads=${GALAXY_SLOTS:-1} ./input_child_0.fastqsanger output 'child0.meryl' && meryl union-sum child*.meryl output child.meryl && meryl histogram child.meryl > read-db.hist && tar -czf 'read-db.meryldb' child.meryl && meryl difference mat.meryl pat.meryl output mat.only.meryl && meryl histogram mat.only.meryl > mat.only.hist && java -jar -Xmx1g $MERQURY/eval/kmerHistToPloidyDepth.jar mat.only.hist > mat.only.ploidy && VAR=`sed -n 2p mat.only.ploidy | awk '{print $NF}'` && meryl greater-than $VAR output mat.only.filt.meryl mat.only.meryl && meryl difference pat.meryl mat.meryl output pat.only.meryl && meryl histogram pat.only.meryl > pat.only.hist && java -jar -Xmx1g $MERQURY/eval/kmerHistToPloidyDepth.jar pat.only.hist > pat.only.ploidy && VAR=`sed -n 2p pat.only.ploidy | awk '{print $NF}'` && meryl greater-than $VAR output pat.only.filt.meryl pat.only.meryl && meryl intersect output shared.meryl mat.meryl pat.meryl && meryl intersect output mat.inherited.meryl child.meryl mat.only.filt.meryl && meryl histogram mat.inherited.meryl > mat.inherited.hist && java -jar -Xmx1g $MERQURY/eval/kmerHistToPloidyDepth.jar mat.inherited.hist > mat.inherited.ploidy && VAR=`sed -n 2p mat.inherited.ploidy | awk '{print $NF}'` && meryl greater-than $VAR output mat.hapmer.meryl mat.inherited.meryl && tar -czf 'mat.meryldb' mat.hapmer.meryl && meryl intersect output pat.inherited.meryl child.meryl pat.only.filt.meryl && meryl histogram pat.inherited.meryl > pat.inherited.hist && java -jar -Xmx1g $MERQURY/eval/kmerHistToPloidyDepth.jar pat.inherited.hist > pat.inherited.ploidy && VAR=`sed -n 2p pat.inherited.ploidy | awk '{print $NF}'` && meryl greater-than $VAR output pat.hapmer.meryl pat.inherited.meryl && tar -czf 'pat.meryldb' pat.hapmer.meryl && echo 'K-mer size: 9' | |
| ``` | |
| **Exit Code:** | |
| * ```console | |
| 0 | |
| ``` | |
| **Standard Error:** | |
| * ```console | |
| Found 1 command tree. | |
| Counting 1797 (estimated) thousand canonical 9-mers from 1 input file: | |
| sequence-file: ./input_paternal_0.fastqsanger | |
| SIMPLE MODE | |
| ----------- | |
| 9-mers | |
| -> 262144 entries for counts up to 65535. | |
| -> 4096 kbits memory used | |
| 1841136 input bases | |
| -> expected max count of 7364, needing 0 extra bits. | |
| -> no memory used | |
| 512 kB memory needed | |
| COMPLEX MODE | |
| ------------ | |
| prefix # of struct kmers/ segs/ min data total | |
| bits prefix memory prefix prefix memory memory memory | |
| ------ ------- ------- ------- ------- ------- ------- ------- | |
| 1 2 P 10 kB 449 kM 239 S 8192 B 1912 kB 1922 kB | |
| 2 4 P 16 kB 224 kM 113 S 16 kB 1808 kB 1824 kB | |
| 3 8 P 28 kB 112 kM 53 S 32 kB 1696 kB 1724 kB | |
| 4 16 P 53 kB 56 kM 25 S 64 kB 1600 kB 1653 kB | |
| 5 32 P 104 kB 28 kM 12 S 128 kB 1536 kB 1640 kB | |
| 6 64 P 205 kB 14 kM 6 S 256 kB 1536 kB 1741 kB | |
| 7 128 P 407 kB 7192 M 3 S 512 kB 1536 kB 1943 kB | |
| 8 256 P 812 kB 3596 M 2 S 1024 kB 2048 kB 2860 kB | |
| 9 512 P 1620 kB 1798 M 1 S 2048 kB 2048 kB 3668 kB | |
| 10 1024 P 3240 kB 899 M 1 S 4096 kB 4096 kB 7336 kB Best Value! | |
| 11 2048 P 6480 kB 450 M 1 S 8192 kB 8192 kB 14 MB | |
| 12 4096 P 12 MB 225 M 1 S 16 MB 16 MB 28 MB | |
| 13 8192 P 25 MB 113 M 1 S 32 MB 32 MB 57 MB | |
| 14 16 kP 50 MB 57 M 1 S 64 MB 64 MB 114 MB | |
| 15 32 kP 101 MB 29 M 1 S 128 MB 128 MB 229 MB | |
| FINAL CONFIGURATION | |
| ------------------- | |
| Estimated to require 512 kB memory out of 8192 MB allowed. | |
| Estimated to require 2 batches. | |
| Configured simple mode for 0.000 GB memory per batch, and up to 2 batches. | |
| Start counting with SIMPLE method. | |
| Loading kmers from './input_paternal_0.fastqsanger' into buckets. | |
| Writing results to 'paternal0.meryl', using 1 threads. | |
| [ file ][ prefix ][ suffix ][ count-suffix ] | |
| widths [ 6 ][ 0 ][ 12 ][ 0 ] | |
| number [ 64 ][ 1 ][ 4096 ][ ] | |
| thread 0 working on block 0x00000000<0x00000000<0x00000000 4096 kmers between 0x0000000000000000 and 0x0000000000000fff | |
| thread 0 working on block 0x00000001<0x00000001<0x00000001 4096 kmers between 0x0000000000001000 and 0x0000000000001fff | |
| thread 0 working on block 0x00000002<0x00000002<0x00000002 4096 kmers between 0x0000000000002000 and 0x0000000000002fff | |
| thread 0 working on block 0x00000003<0x00000003<0x00000003 4096 kmers between 0x0000000000003000 and 0x0000000000003fff | |
| thread 0 working on block 0x00000004<0x00000004<0x00000004 4096 kmers between 0x0000000000004000 and 0x0000000000004fff | |
| thread 0 working on block 0x00000005<0x00000005<0x00000005 4096 kmers between 0x0000000000005000 and 0x0000000000005fff | |
| thread 0 working on block 0x00000006<0x00000006<0x00000006 4096 kmers between 0x0000000000006000 and 0x0000000000006fff | |
| thread 0 working on block 0x00000007<0x00000007<0x00000007 4096 kmers between 0x0000000000007000 and 0x0000000000007fff | |
| thread 0 working on block 0x00000008<0x00000008<0x00000008 4096 kmers between 0x0000000000008000 and 0x0000000000008fff | |
| thread 0 working on block 0x00000009<0x00000009<0x00000009 4096 kmers between 0x0000000000009000 and 0x0000000000009fff | |
| thread 0 working on block 0x0000000a<0x0000000a<0x0000000a 4096 kmers between 0x000000000000a000 and 0x000000000000afff | |
| thread 0 working on block 0x0000000b<0x0000000b<0x0000000b 4096 kmers between 0x000000000000b000 and 0x000000000000bfff | |
| thread 0 working on block 0x0000000c<0x0000000c<0x0000000c 4096 kmers between 0x000000000000c000 and 0x000000000000cfff | |
| thread 0 working on block 0x0000000d<0x0000000d<0x0000000d 4096 kmers between 0x000000000000d000 and 0x000000000000dfff | |
| thread 0 working on block 0x0000000e<0x0000000e<0x0000000e 4096 kmers between 0x000000000000e000 and 0x000000000000efff | |
| thread 0 working on block 0x0000000f<0x0000000f<0x0000000f 4096 kmers between 0x000000000000f000 and 0x000000000000ffff | |
| thread 0 working on block 0x00000010<0x00000010<0x00000010 4096 kmers between 0x0000000000010000 and 0x0000000000010fff | |
| thread 0 working on block 0x00000011<0x00000011<0x00000011 4096 kmers between 0x0000000000011000 and 0x0000000000011fff | |
| thread 0 working on block 0x00000012<0x00000012<0x00000012 4096 kmers between 0x0000000000012000 and 0x0000000000012fff | |
| thread 0 working on block 0x00000013<0x00000013<0x00000013 4096 kmers between 0x0000000000013000 and 0x0000000000013fff | |
| thread 0 working on block 0x00000014<0x00000014<0x00000014 4096 kmers between 0x0000000000014000 and 0x0000000000014fff | |
| thread 0 working on block 0x00000015<0x00000015<0x00000015 4096 kmers between 0x0000000000015000 and 0x0000000000015fff | |
| thread 0 working on block 0x00000016<0x00000016<0x00000016 4096 kmers between 0x0000000000016000 and 0x0000000000016fff | |
| thread 0 working on block 0x00000017<0x00000017<0x00000017 4096 kmers between 0x0000000000017000 and 0x0000000000017fff | |
| thread 0 working on block 0x00000018<0x00000018<0x00000018 4096 kmers between 0x0000000000018000 and 0x0000000000018fff | |
| thread 0 working on block 0x00000019<0x00000019<0x00000019 4096 kmers between 0x0000000000019000 and 0x0000000000019fff | |
| thread 0 working on block 0x0000001a<0x0000001a<0x0000001a 4096 kmers between 0x000000000001a000 and 0x000000000001afff | |
| thread 0 working on block 0x0000001b<0x0000001b<0x0000001b 4096 kmers between 0x000000000001b000 and 0x000000000001bfff | |
| thread 0 working on block 0x0000001c<0x0000001c<0x0000001c 4096 kmers between 0x000000000001c000 and 0x000000000001cfff | |
| thread 0 working on block 0x0000001d<0x0000001d<0x0000001d 4096 kmers between 0x000000000001d000 and 0x000000000001dfff | |
| thread 0 working on block 0x0000001e<0x0000001e<0x0000001e 4096 kmers between 0x000000000001e000 and 0x000000000001efff | |
| thread 0 working on block 0x0000001f<0x0000001f<0x0000001f 4096 kmers between 0x000000000001f000 and 0x000000000001ffff | |
| thread 0 working on block 0x00000020<0x00000020<0x00000020 4096 kmers between 0x0000000000020000 and 0x0000000000020fff | |
| thread 0 working on block 0x00000021<0x00000021<0x00000021 4096 kmers between 0x0000000000021000 and 0x0000000000021fff | |
| thread 0 working on block 0x00000022<0x00000022<0x00000022 4096 kmers between 0x0000000000022000 and 0x0000000000022fff | |
| thread 0 working on block 0x00000023<0x00000023<0x00000023 4096 kmers between 0x0000000000023000 and 0x0000000000023fff | |
| thread 0 working on block 0x00000024<0x00000024<0x00000024 4096 kmers between 0x0000000000024000 and 0x0000000000024fff | |
| thread 0 working on block 0x00000025<0x00000025<0x00000025 4096 kmers between 0x0000000000025000 and 0x0000000000025fff | |
| thread 0 working on block 0x00000026<0x00000026<0x00000026 4096 kmers between 0x0000000000026000 and 0x0000000000026fff | |
| thread 0 working on block 0x00000027<0x00000027<0x00000027 4096 kmers between 0x0000000000027000 and 0x0000000000027fff | |
| thread 0 working on block 0x00000028<0x00000028<0x00000028 4096 kmers between 0x0000000000028000 and 0x0000000000028fff | |
| thread 0 working on block 0x00000029<0x00000029<0x00000029 4096 kmers between 0x0000000000029000 and 0x0000000000029fff | |
| thread 0 working on block 0x0000002a<0x0000002a<0x0000002a 4096 kmers between 0x000000000002a000 and 0x000000000002afff | |
| thread 0 working on block 0x0000002b<0x0000002b<0x0000002b 4096 kmers between 0x000000000002b000 and 0x000000000002bfff | |
| thread 0 working on block 0x0000002c<0x0000002c<0x0000002c 4096 kmers between 0x000000000002c000 and 0x000000000002cfff | |
| thread 0 working on block 0x0000002d<0x0000002d<0x0000002d 4096 kmers between 0x000000000002d000 and 0x000000000002dfff | |
| thread 0 working on block 0x0000002e<0x0000002e<0x0000002e 4096 kmers between 0x000000000002e000 and 0x000000000002efff | |
| thread 0 working on block 0x0000002f<0x0000002f<0x0000002f 4096 kmers between 0x000000000002f000 and 0x000000000002ffff | |
| thread 0 working on block 0x00000030<0x00000030<0x00000030 4096 kmers between 0x0000000000030000 and 0x0000000000030fff | |
| thread 0 working on block 0x00000031<0x00000031<0x00000031 4096 kmers between 0x0000000000031000 and 0x0000000000031fff | |
| thread 0 working on block 0x00000032<0x00000032<0x00000032 4096 kmers between 0x0000000000032000 and 0x0000000000032fff | |
| thread 0 working on block 0x00000033<0x00000033<0x00000033 4096 kmers between 0x0000000000033000 and 0x0000000000033fff | |
| thread 0 working on block 0x00000034<0x00000034<0x00000034 4096 kmers between 0x0000000000034000 and 0x0000000000034fff | |
| thread 0 working on block 0x00000035<0x00000035<0x00000035 4096 kmers between 0x0000000000035000 and 0x0000000000035fff | |
| thread 0 working on block 0x00000036<0x00000036<0x00000036 4096 kmers between 0x0000000000036000 and 0x0000000000036fff | |
| thread 0 working on block 0x00000037<0x00000037<0x00000037 4096 kmers between 0x0000000000037000 and 0x0000000000037fff | |
| thread 0 working on block 0x00000038<0x00000038<0x00000038 4096 kmers between 0x0000000000038000 and 0x0000000000038fff | |
| thread 0 working on block 0x00000039<0x00000039<0x00000039 4096 kmers between 0x0000000000039000 and 0x0000000000039fff | |
| thread 0 working on block 0x0000003a<0x0000003a<0x0000003a 4096 kmers between 0x000000000003a000 and 0x000000000003afff | |
| thread 0 working on block 0x0000003b<0x0000003b<0x0000003b 4096 kmers between 0x000000000003b000 and 0x000000000003bfff | |
| thread 0 working on block 0x0000003c<0x0000003c<0x0000003c 4096 kmers between 0x000000000003c000 and 0x000000000003cfff | |
| thread 0 working on block 0x0000003d<0x0000003d<0x0000003d 4096 kmers between 0x000000000003d000 and 0x000000000003dfff | |
| thread 0 working on block 0x0000003e<0x0000003e<0x0000003e 4096 kmers between 0x000000000003e000 and 0x000000000003efff | |
| thread 0 working on block 0x0000003f<0x0000003f<0x0000003f 4096 kmers between 0x000000000003f000 and 0x000000000003ffff | |
| finishIteration()-- | |
| Cleaning up. | |
| Bye. | |
| Found 1 command tree. | |
| Counting 1797 (estimated) thousand canonical 9-mers from 1 input file: | |
| sequence-file: ./input_paternal_1.fastqsanger | |
| SIMPLE MODE | |
| ----------- | |
| 9-mers | |
| -> 262144 entries for counts up to 65535. | |
| -> 4096 kbits memory used | |
| 1841136 input bases | |
| -> expected max count of 7364, needing 0 extra bits. | |
| -> no memory used | |
| 512 kB memory needed | |
| COMPLEX MODE | |
| ------------ | |
| prefix # of struct kmers/ segs/ min data total | |
| bits prefix memory prefix prefix memory memory memory | |
| ------ ------- ------- ------- ------- ------- ------- ------- | |
| 1 2 P 10 kB 449 kM 239 S 8192 B 1912 kB 1922 kB | |
| 2 4 P 16 kB 224 kM 113 S 16 kB 1808 kB 1824 kB | |
| 3 8 P 28 kB 112 kM 53 S 32 kB 1696 kB 1724 kB | |
| 4 16 P 53 kB 56 kM 25 S 64 kB 1600 kB 1653 kB | |
| 5 32 P 104 kB 28 kM 12 S 128 kB 1536 kB 1640 kB | |
| 6 64 P 205 kB 14 kM 6 S 256 kB 1536 kB 1741 kB | |
| 7 128 P 407 kB 7192 M 3 S 512 kB 1536 kB 1943 kB | |
| 8 256 P 812 kB 3596 M 2 S 1024 kB 2048 kB 2860 kB | |
| 9 512 P 1620 kB 1798 M 1 S 2048 kB 2048 kB 3668 kB | |
| 10 1024 P 3240 kB 899 M 1 S 4096 kB 4096 kB 7336 kB Best Value! | |
| 11 2048 P 6480 kB 450 M 1 S 8192 kB 8192 kB 14 MB | |
| 12 4096 P 12 MB 225 M 1 S 16 MB 16 MB 28 MB | |
| 13 8192 P 25 MB 113 M 1 S 32 MB 32 MB 57 MB | |
| 14 16 kP 50 MB 57 M 1 S 64 MB 64 MB 114 MB | |
| 15 32 kP 101 MB 29 M 1 S 128 MB 128 MB 229 MB | |
| FINAL CONFIGURATION | |
| ------------------- | |
| Estimated to require 512 kB memory out of 8192 MB allowed. | |
| Estimated to require 2 batches. | |
| Configured simple mode for 0.000 GB memory per batch, and up to 2 batches. | |
| Start counting with SIMPLE method. | |
| Loading kmers from './input_paternal_1.fastqsanger' into buckets. | |
| Writing results to 'paternal1.meryl', using 1 threads. | |
| [ file ][ prefix ][ suffix ][ count-suffix ] | |
| widths [ 6 ][ 0 ][ 12 ][ 0 ] | |
| number [ 64 ][ 1 ][ 4096 ][ ] | |
| thread 0 working on block 0x00000000<0x00000000<0x00000000 4096 kmers between 0x0000000000000000 and 0x0000000000000fff | |
| thread 0 working on block 0x00000001<0x00000001<0x00000001 4096 kmers between 0x0000000000001000 and 0x0000000000001fff | |
| thread 0 working on block 0x00000002<0x00000002<0x00000002 4096 kmers between 0x0000000000002000 and 0x0000000000002fff | |
| thread 0 working on block 0x00000003<0x00000003<0x00000003 4096 kmers between 0x0000000000003000 and 0x0000000000003fff | |
| thread 0 working on block 0x00000004<0x00000004<0x00000004 4096 kmers between 0x0000000000004000 and 0x0000000000004fff | |
| thread 0 working on block 0x00000005<0x00000005<0x00000005 4096 kmers between 0x0000000000005000 and 0x0000000000005fff | |
| thread 0 working on block 0x00000006<0x00000006<0x00000006 4096 kmers between 0x0000000000006000 and 0x0000000000006fff | |
| thread 0 working on block 0x00000007<0x00000007<0x00000007 4096 kmers between 0x0000000000007000 and 0x0000000000007fff | |
| thread 0 working on block 0x00000008<0x00000008<0x00000008 4096 kmers between 0x0000000000008000 and 0x0000000000008fff | |
| thread 0 working on block 0x00000009<0x00000009<0x00000009 4096 kmers between 0x0000000000009000 and 0x0000000000009fff | |
| thread 0 working on block 0x0000000a<0x0000000a<0x0000000a 4096 kmers between 0x000000000000a000 and 0x000000000000afff | |
| thread 0 working on block 0x0000000b<0x0000000b<0x0000000b 4096 kmers between 0x000000000000b000 and 0x000000000000bfff | |
| thread 0 working on block 0x0000000c<0x0000000c<0x0000000c 4096 kmers between 0x000000000000c000 and 0x000000000000cfff | |
| thread 0 working on block 0x0000000d<0x0000000d<0x0000000d 4096 kmers between 0x000000000000d000 and 0x000000000000dfff | |
| thread 0 working on block 0x0000000e<0x0000000e<0x0000000e 4096 kmers between 0x000000000000e000 and 0x000000000000efff | |
| thread 0 working on block 0x0000000f<0x0000000f<0x0000000f 4096 kmers between 0x000000000000f000 and 0x000000000000ffff | |
| thread 0 working on block 0x00000010<0x00000010<0x00000010 4096 kmers between 0x0000000000010000 and 0x0000000000010fff | |
| thread 0 working on block 0x00000011<0x00000011<0x00000011 4096 kmers between 0x0000000000011000 and 0x0000000000011fff | |
| thread 0 working on block 0x00000012<0x00000012<0x00000012 4096 kmers between 0x0000000000012000 and 0x0000000000012fff | |
| thread 0 working on block 0x00000013<0x00000013<0x00000013 4096 kmers between 0x0000000000013000 and 0x0000000000013fff | |
| thread 0 working on block 0x00000014<0x00000014<0x00000014 4096 kmers between 0x0000000000014000 and 0x0000000000014fff | |
| thread 0 working on block 0x00000015<0x00000015<0x00000015 4096 kmers between 0x0000000000015000 and 0x0000000000015fff | |
| thread 0 working on block 0x00000016<0x00000016<0x00000016 4096 kmers between 0x0000000000016000 and 0x0000000000016fff | |
| thread 0 working on block 0x00000017<0x00000017<0x00000017 4096 kmers between 0x0000000000017000 and 0x0000000000017fff | |
| thread 0 working on block 0x00000018<0x00000018<0x00000018 4096 kmers between 0x0000000000018000 and 0x0000000000018fff | |
| thread 0 working on block 0x00000019<0x00000019<0x00000019 4096 kmers between 0x0000000000019000 and 0x0000000000019fff | |
| thread 0 working on block 0x0000001a<0x0000001a<0x0000001a 4096 kmers between 0x000000000001a000 and 0x000000000001afff | |
| thread 0 working on block 0x0000001b<0x0000001b<0x0000001b 4096 kmers between 0x000000000001b000 and 0x000000000001bfff | |
| thread 0 working on block 0x0000001c<0x0000001c<0x0000001c 4096 kmers between 0x000000000001c000 and 0x000000000001cfff | |
| thread 0 working on block 0x0000001d<0x0000001d<0x0000001d 4096 kmers between 0x000000000001d000 and 0x000000000001dfff | |
| thread 0 working on block 0x0000001e<0x0000001e<0x0000001e 4096 kmers between 0x000000000001e000 and 0x000000000001efff | |
| .. | |
| een 0x0000000000021000 and 0x0000000000021fff | |
| thread 0 working on block 0x00000022<0x00000022<0x00000022 4096 kmers between 0x0000000000022000 and 0x0000000000022fff | |
| thread 0 working on block 0x00000023<0x00000023<0x00000023 4096 kmers between 0x0000000000023000 and 0x0000000000023fff | |
| thread 0 working on block 0x00000024<0x00000024<0x00000024 4096 kmers between 0x0000000000024000 and 0x0000000000024fff | |
| thread 0 working on block 0x00000025<0x00000025<0x00000025 4096 kmers between 0x0000000000025000 and 0x0000000000025fff | |
| thread 0 working on block 0x00000026<0x00000026<0x00000026 4096 kmers between 0x0000000000026000 and 0x0000000000026fff | |
| thread 0 working on block 0x00000027<0x00000027<0x00000027 4096 kmers between 0x0000000000027000 and 0x0000000000027fff | |
| thread 0 working on block 0x00000028<0x00000028<0x00000028 4096 kmers between 0x0000000000028000 and 0x0000000000028fff | |
| thread 0 working on block 0x00000029<0x00000029<0x00000029 4096 kmers between 0x0000000000029000 and 0x0000000000029fff | |
| thread 0 working on block 0x0000002a<0x0000002a<0x0000002a 4096 kmers between 0x000000000002a000 and 0x000000000002afff | |
| thread 0 working on block 0x0000002b<0x0000002b<0x0000002b 4096 kmers between 0x000000000002b000 and 0x000000000002bfff | |
| thread 0 working on block 0x0000002c<0x0000002c<0x0000002c 4096 kmers between 0x000000000002c000 and 0x000000000002cfff | |
| thread 0 working on block 0x0000002d<0x0000002d<0x0000002d 4096 kmers between 0x000000000002d000 and 0x000000000002dfff | |
| thread 0 working on block 0x0000002e<0x0000002e<0x0000002e 4096 kmers between 0x000000000002e000 and 0x000000000002efff | |
| thread 0 working on block 0x0000002f<0x0000002f<0x0000002f 4096 kmers between 0x000000000002f000 and 0x000000000002ffff | |
| thread 0 working on block 0x00000030<0x00000030<0x00000030 4096 kmers between 0x0000000000030000 and 0x0000000000030fff | |
| thread 0 working on block 0x00000031<0x00000031<0x00000031 4096 kmers between 0x0000000000031000 and 0x0000000000031fff | |
| thread 0 working on block 0x00000032<0x00000032<0x00000032 4096 kmers between 0x0000000000032000 and 0x0000000000032fff | |
| thread 0 working on block 0x00000033<0x00000033<0x00000033 4096 kmers between 0x0000000000033000 and 0x0000000000033fff | |
| thread 0 working on block 0x00000034<0x00000034<0x00000034 4096 kmers between 0x0000000000034000 and 0x0000000000034fff | |
| thread 0 working on block 0x00000035<0x00000035<0x00000035 4096 kmers between 0x0000000000035000 and 0x0000000000035fff | |
| thread 0 working on block 0x00000036<0x00000036<0x00000036 4096 kmers between 0x0000000000036000 and 0x0000000000036fff | |
| thread 0 working on block 0x00000037<0x00000037<0x00000037 4096 kmers between 0x0000000000037000 and 0x0000000000037fff | |
| thread 0 working on block 0x00000038<0x00000038<0x00000038 4096 kmers between 0x0000000000038000 and 0x0000000000038fff | |
| thread 0 working on block 0x00000039<0x00000039<0x00000039 4096 kmers between 0x0000000000039000 and 0x0000000000039fff | |
| thread 0 working on block 0x0000003a<0x0000003a<0x0000003a 4096 kmers between 0x000000000003a000 and 0x000000000003afff | |
| thread 0 working on block 0x0000003b<0x0000003b<0x0000003b 4096 kmers between 0x000000000003b000 and 0x000000000003bfff | |
| thread 0 working on block 0x0000003c<0x0000003c<0x0000003c 4096 kmers between 0x000000000003c000 and 0x000000000003cfff | |
| thread 0 working on block 0x0000003d<0x0000003d<0x0000003d 4096 kmers between 0x000000000003d000 and 0x000000000003dfff | |
| thread 0 working on block 0x0000003e<0x0000003e<0x0000003e 4096 kmers between 0x000000000003e000 and 0x000000000003efff | |
| thread 0 working on block 0x0000003f<0x0000003f<0x0000003f 4096 kmers between 0x000000000003f000 and 0x000000000003ffff | |
| finishIteration()-- | |
| Cleaning up. | |
| Bye. | |
| Found 1 command tree. | |
| PROCESSING TREE #1 using 4 threads. | |
| opUnionSum | |
| maternal0.meryl | |
| maternal1.meryl | |
| output to mat.meryl | |
| Cleaning up. | |
| Bye. | |
| Found 1 command tree. | |
| Counting 2047 (estimated) thousand canonical 9-mers from 1 input file: | |
| sequence-file: ./input_child_0.fastqsanger | |
| SIMPLE MODE | |
| ----------- | |
| 9-mers | |
| -> 262144 entries for counts up to 65535. | |
| -> 4096 kbits memory used | |
| 2096311 input bases | |
| -> expected max count of 8385, needing 0 extra bits. | |
| -> no memory used | |
| 512 kB memory needed | |
| COMPLEX MODE | |
| ------------ | |
| prefix # of struct kmers/ segs/ min data total | |
| bits prefix memory prefix prefix memory memory memory | |
| ------ ------- ------- ------- ------- ------- ------- ------- | |
| 1 2 P 10 kB 511 kM 272 S 8192 B 2176 kB 2186 kB | |
| 2 4 P 16 kB 255 kM 128 S 16 kB 2048 kB 2064 kB | |
| 3 8 P 29 kB 127 kM 60 S 32 kB 1920 kB 1949 kB | |
| 4 16 P 54 kB 63 kM 28 S 64 kB 1792 kB 1846 kB | |
| 5 32 P 104 kB 31 kM 13 S 128 kB 1664 kB 1768 kB | |
| 6 64 P 205 kB 15 kM 6 S 256 kB 1536 kB 1741 kB | |
| 7 128 P 407 kB 8189 M 3 S 512 kB 1536 kB 1943 kB | |
| 8 256 P 812 kB 4095 M 2 S 1024 kB 2048 kB 2860 kB | |
| 9 512 P 1620 kB 2048 M 1 S 2048 kB 2048 kB 3668 kB | |
| 10 1024 P 3240 kB 1024 M 1 S 4096 kB 4096 kB 7336 kB Best Value! | |
| 11 2048 P 6480 kB 512 M 1 S 8192 kB 8192 kB 14 MB | |
| 12 4096 P 12 MB 256 M 1 S 16 MB 16 MB 28 MB | |
| 13 8192 P 25 MB 128 M 1 S 32 MB 32 MB 57 MB | |
| 14 16 kP 50 MB 64 M 1 S 64 MB 64 MB 114 MB | |
| 15 32 kP 101 MB 32 M 1 S 128 MB 128 MB 229 MB | |
| FINAL CONFIGURATION | |
| ------------------- | |
| Estimated to require 512 kB memory out of 8192 MB allowed. | |
| Estimated to require 2 batches. | |
| Configured simple mode for 0.000 GB memory per batch, and up to 2 batches. | |
| Start counting with SIMPLE method. | |
| Loading kmers from './input_child_0.fastqsanger' into buckets. | |
| Writing results to 'child0.meryl', using 1 threads. | |
| [ file ][ prefix ][ suffix ][ count-suffix ] | |
| widths [ 6 ][ 0 ][ 12 ][ 0 ] | |
| number [ 64 ][ 1 ][ 4096 ][ ] | |
| thread 0 working on block 0x00000000<0x00000000<0x00000000 4096 kmers between 0x0000000000000000 and 0x0000000000000fff | |
| thread 0 working on block 0x00000001<0x00000001<0x00000001 4096 kmers between 0x0000000000001000 and 0x0000000000001fff | |
| thread 0 working on block 0x00000002<0x00000002<0x00000002 4096 kmers between 0x0000000000002000 and 0x0000000000002fff | |
| thread 0 working on block 0x00000003<0x00000003<0x00000003 4096 kmers between 0x0000000000003000 and 0x0000000000003fff | |
| thread 0 working on block 0x00000004<0x00000004<0x00000004 4096 kmers between 0x0000000000004000 and 0x0000000000004fff | |
| thread 0 working on block 0x00000005<0x00000005<0x00000005 4096 kmers between 0x0000000000005000 and 0x0000000000005fff | |
| thread 0 working on block 0x00000006<0x00000006<0x00000006 4096 kmers between 0x0000000000006000 and 0x0000000000006fff | |
| thread 0 working on block 0x00000007<0x00000007<0x00000007 4096 kmers between 0x0000000000007000 and 0x0000000000007fff | |
| thread 0 working on block 0x00000008<0x00000008<0x00000008 4096 kmers between 0x0000000000008000 and 0x0000000000008fff | |
| thread 0 working on block 0x00000009<0x00000009<0x00000009 4096 kmers between 0x0000000000009000 and 0x0000000000009fff | |
| thread 0 working on block 0x0000000a<0x0000000a<0x0000000a 4096 kmers between 0x000000000000a000 and 0x000000000000afff | |
| thread 0 working on block 0x0000000b<0x0000000b<0x0000000b 4096 kmers between 0x000000000000b000 and 0x000000000000bfff | |
| thread 0 working on block 0x0000000c<0x0000000c<0x0000000c 4096 kmers between 0x000000000000c000 and 0x000000000000cfff | |
| thread 0 working on block 0x0000000d<0x0000000d<0x0000000d 4096 kmers between 0x000000000000d000 and 0x000000000000dfff | |
| thread 0 working on block 0x0000000e<0x0000000e<0x0000000e 4096 kmers between 0x000000000000e000 and 0x000000000000efff | |
| thread 0 working on block 0x0000000f<0x0000000f<0x0000000f 4096 kmers between 0x000000000000f000 and 0x000000000000ffff | |
| thread 0 working on block 0x00000010<0x00000010<0x00000010 4096 kmers between 0x0000000000010000 and 0x0000000000010fff | |
| thread 0 working on block 0x00000011<0x00000011<0x00000011 4096 kmers between 0x0000000000011000 and 0x0000000000011fff | |
| thread 0 working on block 0x00000012<0x00000012<0x00000012 4096 kmers between 0x0000000000012000 and 0x0000000000012fff | |
| thread 0 working on block 0x00000013<0x00000013<0x00000013 4096 kmers between 0x0000000000013000 and 0x0000000000013fff | |
| thread 0 working on block 0x00000014<0x00000014<0x00000014 4096 kmers between 0x0000000000014000 and 0x0000000000014fff | |
| thread 0 working on block 0x00000015<0x00000015<0x00000015 4096 kmers between 0x0000000000015000 and 0x0000000000015fff | |
| thread 0 working on block 0x00000016<0x00000016<0x00000016 4096 kmers between 0x0000000000016000 and 0x0000000000016fff | |
| thread 0 working on block 0x00000017<0x00000017<0x00000017 4096 kmers between 0x0000000000017000 and 0x0000000000017fff | |
| thread 0 working on block 0x00000018<0x00000018<0x00000018 4096 kmers between 0x0000000000018000 and 0x0000000000018fff | |
| thread 0 working on block 0x00000019<0x00000019<0x00000019 4096 kmers between 0x0000000000019000 and 0x0000000000019fff | |
| thread 0 working on block 0x0000001a<0x0000001a<0x0000001a 4096 kmers between 0x000000000001a000 and 0x000000000001afff | |
| thread 0 working on block 0x0000001b<0x0000001b<0x0000001b 4096 kmers between 0x000000000001b000 and 0x000000000001bfff | |
| thread 0 working on block 0x0000001c<0x0000001c<0x0000001c 4096 kmers between 0x000000000001c000 and 0x000000000001cfff | |
| thread 0 working on block 0x0000001d<0x0000001d<0x0000001d 4096 kmers between 0x000000000001d000 and 0x000000000001dfff | |
| thread 0 working on block 0x0000001e<0x0000001e<0x0000001e 4096 kmers between 0x000000000001e000 and 0x000000000001efff | |
| thread 0 working on block 0x0000001f<0x0000001f<0x0000001f 4096 kmers between 0x000000000001f000 and 0x000000000001ffff | |
| thread 0 working on block 0x00000020<0x00000020<0x00000020 4096 kmers between 0x0000000000020000 and 0x0000000000020fff | |
| thread 0 working on block 0x00000021<0x00000021<0x00000021 4096 kmers between 0x0000000000021000 and 0x0000000000021fff | |
| thread 0 working on block 0x00000022<0x00000022<0x00000022 4096 kmers between 0x0000000000022000 and 0x0000000000022fff | |
| thread 0 working on block 0x00000023<0x00000023<0x00000023 4096 kmers between 0x0000000000023000 and 0x0000000000023fff | |
| thread 0 working on block 0x00000024<0x00000024<0x00000024 4096 kmers between 0x0000000000024000 and 0x0000000000024fff | |
| thread 0 working on block 0x00000025<0x00000025<0x00000025 4096 kmers between 0x0000000000025000 and 0x0000000000025fff | |
| thread 0 working on block 0x00000026<0x00000026<0x00000026 4096 kmers between 0x0000000000026000 and 0x0000000000026fff | |
| thread 0 working on block 0x00000027<0x00000027<0x00000027 4096 kmers between 0x0000000000027000 and 0x0000000000027fff | |
| thread 0 working on block 0x00000028<0x00000028<0x00000028 4096 kmers between 0x0000000000028000 and 0x0000000000028fff | |
| thread 0 working on block 0x00000029<0x00000029<0x00000029 4096 kmers between 0x0000000000029000 and 0x0000000000029fff | |
| thread 0 working on block 0x0000002a<0x0000002a<0x0000002a 4096 kmers between 0x000000000002a000 and 0x000000000002afff | |
| thread 0 working on block 0x0000002b<0x0000002b<0x0000002b 4096 kmers between 0x000000000002b000 and 0x000000000002bfff | |
| thread 0 working on block 0x0000002c<0x0000002c<0x0000002c 4096 kmers between 0x000000000002c000 and 0x000000000002cfff | |
| thread 0 working on block 0x0000002d<0x0000002d<0x0000002d 4096 kmers between 0x000000000002d000 and 0x000000000002dfff | |
| thread 0 working on block 0x0000002e<0x0000002e<0x0000002e 4096 kmers between 0x000000000002e000 and 0x000000000002efff | |
| thread 0 working on block 0x0000002f<0x0000002f<0x0000002f 4096 kmers between 0x000000000002f000 and 0x000000000002ffff | |
| thread 0 working on block 0x00000030<0x00000030<0x00000030 4096 kmers between 0x0000000000030000 and 0x0000000000030fff | |
| thread 0 working on block 0x00000031<0x00000031<0x00000031 4096 kmers between 0x0000000000031000 and 0x0000000000031fff | |
| thread 0 working on block 0x00000032<0x00000032<0x00000032 4096 kmers between 0x0000000000032000 and 0x0000000000032fff | |
| thread 0 working on block 0x00000033<0x00000033<0x00000033 4096 kmers between 0x0000000000033000 and 0x0000000000033fff | |
| thread 0 working on block 0x00000034<0x00000034<0x00000034 4096 kmers between 0x0000000000034000 and 0x0000000000034fff | |
| thread 0 working on block 0x00000035<0x00000035<0x00000035 4096 kmers between 0x0000000000035000 and 0x0000000000035fff | |
| thread 0 working on block 0x00000036<0x00000036<0x00000036 4096 kmers between 0x0000000000036000 and 0x0000000000036fff | |
| thread 0 working on block 0x00000037<0x00000037<0x00000037 4096 kmers between 0x0000000000037000 and 0x0000000000037fff | |
| thread 0 working on block 0x00000038<0x00000038<0x00000038 4096 kmers between 0x0000000000038000 and 0x0000000000038fff | |
| thread 0 working on block 0x00000039<0x00000039<0x00000039 4096 kmers between 0x0000000000039000 and 0x0000000000039fff | |
| thread 0 working on block 0x0000003a<0x0000003a<0x0000003a 4096 kmers between 0x000000000003a000 and 0x000000000003afff | |
| thread 0 working on block 0x0000003b<0x0000003b<0x0000003b 4096 kmers between 0x000000000003b000 and 0x000000000003bfff | |
| thread 0 working on block 0x0000003c<0x0000003c<0x0000003c 4096 kmers between 0x000000000003c000 and 0x000000000003cfff | |
| thread 0 working on block 0x0000003d<0x0000003d<0x0000003d 4096 kmers between 0x000000000003d000 and 0x000000000003dfff | |
| thread 0 working on block 0x0000003e<0x0000003e<0x0000003e 4096 kmers between 0x000000000003e000 and 0x000000000003efff | |
| thread 0 working on block 0x0000003f<0x0000003f<0x0000003f 4096 kmers between 0x000000000003f000 and 0x000000000003ffff | |
| finishIteration()-- | |
| Cleaning up. | |
| Bye. | |
| Found 1 command tree. | |
| PROCESSING TREE #1 using 4 threads. | |
| opUnionSum | |
| child0.meryl | |
| output to child.meryl | |
| Cleaning up. | |
| Bye. | |
| Found 1 command tree. | |
| Found 1 command tree. | |
| PROCESSING TREE #1 using 4 threads. | |
| opDifference | |
| mat.meryl | |
| pat.meryl | |
| output to mat.only.meryl | |
| Cleaning up. | |
| Bye. | |
| Found 1 command tree. | |
| Processing file mat.only.hist | |
| Running time : 0 h 0 m 0 sec | |
| Found 1 command tree. | |
| PROCESSING TREE #1 using 4 threads. | |
| opGreaterThan | |
| threshold=0 | |
| mat.only.meryl | |
| output to mat.only.filt.meryl | |
| Cleaning up. | |
| Bye. | |
| Found 1 command tree. | |
| PROCESSING TREE #1 using 4 threads. | |
| opDifference | |
| pat.meryl | |
| mat.meryl | |
| output to pat.only.meryl | |
| Cleaning up. | |
| Bye. | |
| Found 1 command tree. | |
| Processing file pat.only.hist | |
| Running time : 0 h 0 m 0 sec | |
| Found 1 command tree. | |
| PROCESSING TREE #1 using 4 threads. | |
| opGreaterThan | |
| threshold=0 | |
| pat.only.meryl | |
| output to pat.only.filt.meryl | |
| Cleaning up. | |
| Bye. | |
| Found 1 command tree. | |
| PROCESSING TREE #1 using 4 threads. | |
| opIntersect | |
| mat.meryl | |
| pat.meryl | |
| output to shared.meryl | |
| Cleaning up. | |
| Bye. | |
| Found 1 command tree. | |
| PROCESSING TREE #1 using 4 threads. | |
| opIntersect | |
| child.meryl | |
| mat.only.filt.meryl | |
| output to mat.inherited.meryl | |
| Cleaning up. | |
| Bye. | |
| Found 1 command tree. | |
| Processing file mat.inherited.hist | |
| Start sampling here: 1, 1238.0 | |
| Next max here: 2, 1486.0 | |
| Stop sampling here: 4, 1097.0 | |
| Running time : 0 h 0 m 0 sec | |
| Found 1 command tree. | |
| PROCESSING TREE #1 using 4 threads. | |
| opGreaterThan | |
| threshold=1 | |
| mat.inherited.meryl | |
| output to mat.hapmer.meryl | |
| Cleaning up. | |
| Bye. | |
| Found 1 command tree. | |
| PROCESSING TREE #1 using 4 threads. | |
| opIntersect | |
| child.meryl | |
| pat.only.filt.meryl | |
| output to pat.inherited.meryl | |
| Cleaning up. | |
| Bye. | |
| Found 1 command tree. | |
| Processing file pat.inherited.hist | |
| Start sampling here: 1, 984.0 | |
| Next max here: 2, 1166.0 | |
| Stop sampling here: 4, 772.0 | |
| Running time : 0 h 0 m 0 sec | |
| Found 1 command tree. | |
| PROCESSING TREE #1 using 4 threads. | |
| opGreaterThan | |
| threshold=1 | |
| pat.inherited.meryl | |
| output to pat.hapmer.meryl | |
| Cleaning up. | |
| Bye. | |
| ``` | |
| **Standard Output:** | |
| * ```console | |
| K-mer size: 9 | |
| ``` | |
| **Traceback:** | |
| * ```console | |
| ``` | |
| **Job Parameters:** | |
| * | Job parameter | Parameter value | | |
| | ------------- | --------------- | | |
| | \_\_input\_ext | ` "input" ` | | |
| | \_\_workflow\_invocation\_uuid\_\_ | ` "a9e9fe4a115611f189517ced8dc21a23" ` | | |
| | chromInfo | ` "/tmp/tmp3sfjay_q/galaxy-dev/tool-data/shared/ucsc/chrom/?.len" ` | | |
| | dbkey | ` "?" ` | | |
| | operation\_type | ` {"__current_case__": 6, "child_reads": {"values": [{"id": 38, "src": "hdca"}]}, "command_type": "trio-mode", "maternal_reads": {"values": [{"id": 36, "src": "hdca"}]}, "options_kmer_size": {"__current_case__": 0, "input_kmer_size": "9", "kmer_size": "provide"}, "paternal_reads": {"values": [{"id": 37, "src": "hdca"}]}} ` | | |
| </details> | |
| - **Step 10: Unlabelled step (toolshed.g2.bx.psu.edu/repos/iuc/meryl\_groups\_kmers/meryl\_groups\_kmers/1.3+galaxy7)**: | |
| * step_state: scheduled | |
| * <details><summary>Jobs</summary> | |
| - **Job 1:** | |
| * Job state is ok | |
| **Container:** | |
| * ```console | |
| quay.io/biocontainers/mulled-v2-ba0fa2569b9c1d280d7fb3b1bf2ad3c0c72d9296:34d0c765d43a43f8968b3d9ffb3ceb9a8cdf6a69-0 | |
| ``` | |
| **Command Line:** | |
| * ```console | |
| export GALAXY_MEMORY_GB=$((${GALAXY_MEMORY_MB:-8192}/1024)) && mkdir -p ./tmp_folder_0/ && tar -xmf /tmp/tmp3sfjay_q/files/9/3/1/dataset_931aa36f-3dc9-4e6c-9dec-8b88f0800964.dat --use-compress-program="pigz -p ${GALAXY_SLOTS:-1}" -C ./tmp_folder_0 && mv ./tmp_folder_0/* db_'0'.meryl && mkdir -p ./tmp_folder_1/ && tar -xmf /tmp/tmp3sfjay_q/files/3/0/2/dataset_302fcce3-4298-48bf-95f9-fce39aa25122.dat --use-compress-program="pigz -p ${GALAXY_SLOTS:-1}" -C ./tmp_folder_1 && mv ./tmp_folder_1/* db_'1'.meryl && meryl union-sum output read-db.meryl db_* && tar -cf read-db.meryldb --use-compress-program="pigz -p ${GALAXY_SLOTS:-1}" read-db.meryl | |
| ``` | |
| **Exit Code:** | |
| * ```console | |
| 0 | |
| ``` | |
| **Standard Error:** | |
| * ```console | |
| Found 1 command tree. | |
| PROCESSING TREE #1 using 4 threads. | |
| opUnionSum | |
| db_0.meryl | |
| db_1.meryl | |
| output to read-db.meryl | |
| Cleaning up. | |
| Bye. | |
| ``` | |
| **Traceback:** | |
| * ```console | |
| ``` | |
| **Job Parameters:** | |
| * | Job parameter | Parameter value | | |
| | ------------- | --------------- | | |
| | \_\_input\_ext | ` "input" ` | | |
| | \_\_workflow\_invocation\_uuid\_\_ | ` "a9e9fe4a115611f189517ced8dc21a23" ` | | |
| | chromInfo | ` "/tmp/tmp3sfjay_q/galaxy-dev/tool-data/shared/ucsc/chrom/?.len" ` | | |
| | dbkey | ` "?" ` | | |
| | groups\_operations | ` "union-sum" ` | | |
| </details> | |
| - **Step 11: Unlabelled step (toolshed.g2.bx.psu.edu/repos/iuc/meryl\_groups\_kmers/meryl\_groups\_kmers/1.3+galaxy7)**: | |
| * step_state: scheduled | |
| * <details><summary>Jobs</summary> | |
| - **Job 1:** | |
| * Job state is ok | |
| **Container:** | |
| * ```console | |
| quay.io/biocontainers/mulled-v2-ba0fa2569b9c1d280d7fb3b1bf2ad3c0c72d9296:34d0c765d43a43f8968b3d9ffb3ceb9a8cdf6a69-0 | |
| ``` | |
| **Command Line:** | |
| * ```console | |
| export GALAXY_MEMORY_GB=$((${GALAXY_MEMORY_MB:-8192}/1024)) && mkdir -p ./tmp_folder_0/ && tar -xmf /tmp/tmp3sfjay_q/files/2/0/3/dataset_203b2935-56ce-4efa-8adf-184767b0d74a.dat --use-compress-program="pigz -p ${GALAXY_SLOTS:-1}" -C ./tmp_folder_0 && mv ./tmp_folder_0/* db_'0'.meryl && mkdir -p ./tmp_folder_1/ && tar -xmf /tmp/tmp3sfjay_q/files/3/2/5/dataset_325150c2-e9c9-4966-9259-60cd04103129.dat --use-compress-program="pigz -p ${GALAXY_SLOTS:-1}" -C ./tmp_folder_1 && mv ./tmp_folder_1/* db_'1'.meryl && meryl union-sum output read-db.meryl db_* && tar -cf read-db.meryldb --use-compress-program="pigz -p ${GALAXY_SLOTS:-1}" read-db.meryl | |
| ``` | |
| **Exit Code:** | |
| * ```console | |
| 0 | |
| ``` | |
| **Standard Error:** | |
| * ```console | |
| Found 1 command tree. | |
| PROCESSING TREE #1 using 4 threads. | |
| opUnionSum | |
| db_0.meryl | |
| db_1.meryl | |
| output to read-db.meryl | |
| Cleaning up. | |
| Bye. | |
| ``` | |
| **Traceback:** | |
| * ```console | |
| ``` | |
| **Job Parameters:** | |
| * | Job parameter | Parameter value | | |
| | ------------- | --------------- | | |
| | \_\_input\_ext | ` "input" ` | | |
| | \_\_workflow\_invocation\_uuid\_\_ | ` "a9e9fe4a115611f189517ced8dc21a23" ` | | |
| | chromInfo | ` "/tmp/tmp3sfjay_q/galaxy-dev/tool-data/shared/ucsc/chrom/?.len" ` | | |
| | dbkey | ` "?" ` | | |
| | groups\_operations | ` "union-sum" ` | | |
| </details> | |
| - **Step 12: Unlabelled step (toolshed.g2.bx.psu.edu/repos/iuc/genomescope/genomescope/2.0.1+galaxy0)**: | |
| * step_state: scheduled | |
| * <details><summary>Jobs</summary> | |
| - **Job 1:** | |
| * Job state is ok | |
| **Container:** | |
| * ```console | |
| quay.io/biocontainers/genomescope2:2.0.1--py313r44hdfd78af_1 | |
| ``` | |
| **Command Line:** | |
| * ```console | |
| genomescope2 --input '/tmp/tmp3sfjay_q/files/f/9/e/dataset_f9eeba4c-1f2a-428b-ad4f-7235281685fc.dat' --output . --kmer_length 9 --testing --ploidy 1 | |
| ``` | |
| **Exit Code:** | |
| * ```console | |
| 0 | |
| ``` | |
| **Standard Output:** | |
| * ```console | |
| GenomeScope analyzing /tmp/tmp3sfjay_q/files/f/9/e/dataset_f9eeba4c-1f2a-428b-ad4f-7235281685fc.dat p=1 k=9 outdir=. | |
| a:100% | |
| Model converged het:0 kcov:12.1 err:0.05 model fit:0.898 len:54082 | |
| ``` | |
| **Traceback:** | |
| * ```console | |
| ``` | |
| **Job Parameters:** | |
| * | Job parameter | Parameter value | | |
| | ------------- | --------------- | | |
| | \_\_input\_ext | ` "input" ` | | |
| | \_\_workflow\_invocation\_uuid\_\_ | ` "a9e9fe4a115611f189517ced8dc21a23" ` | | |
| | advanced\_options | ` {"initial_heterozygosities": "", "initial_repetitiveness": null, "num_rounds": null, "testing": true, "topology": null, "trace_flag": false, "transform_exp": null, "true_params": ""} ` | | |
| | chromInfo | ` "/tmp/tmp3sfjay_q/galaxy-dev/tool-data/shared/ucsc/chrom/?.len" ` | | |
| | dbkey | ` "?" ` | | |
| | kmer\_length | ` "9" ` | | |
| | lambda | ` None ` | | |
| | max\_kmercov | ` None ` | | |
| | output\_options | ` {"no_unique_sequence": false, "output_files": ["model_output", "summary_output"]} ` | | |
| | ploidy | ` "1" ` | | |
| </details> | |
| - **Step 13: Unlabelled step (toolshed.g2.bx.psu.edu/repos/iuc/meryl\_histogram\_kmers/meryl\_histogram\_kmers/1.3+galaxy7)**: | |
| * step_state: scheduled | |
| * <details><summary>Jobs</summary> | |
| - **Job 1:** | |
| * Job state is ok | |
| **Container:** | |
| * ```console | |
| quay.io/biocontainers/mulled-v2-ba0fa2569b9c1d280d7fb3b1bf2ad3c0c72d9296:34d0c765d43a43f8968b3d9ffb3ceb9a8cdf6a69-0 | |
| ``` | |
| **Command Line:** | |
| * ```console | |
| export GALAXY_MEMORY_GB=$((${GALAXY_MEMORY_MB:-8192}/1024)) && mkdir -p ./temp_db/ && tar -xmf /tmp/tmp3sfjay_q/files/b/3/1/dataset_b311a84c-4dd0-4e2d-9c99-4f3bfa08bc5f.dat --use-compress-program="pigz -p ${GALAXY_SLOTS:-1}" -C ./temp_db/ && mv ./temp_db/* tmp.meryl && meryl histogram tmp.meryl > read-db.hist | |
| ``` | |
| **Exit Code:** | |
| * ```console | |
| 0 | |
| ``` | |
| **Standard Error:** | |
| * ```console | |
| Found 1 command tree. | |
| ``` | |
| **Traceback:** | |
| * ```console | |
| ``` | |
| **Job Parameters:** | |
| * | Job parameter | Parameter value | | |
| | ------------- | --------------- | | |
| | \_\_input\_ext | ` "input" ` | | |
| | \_\_workflow\_invocation\_uuid\_\_ | ` "a9e9fe4a115611f189517ced8dc21a23" ` | | |
| | chromInfo | ` "/tmp/tmp3sfjay_q/galaxy-dev/tool-data/shared/ucsc/chrom/?.len" ` | | |
| | dbkey | ` "?" ` | | |
| </details> | |
| - **Step 14: Unlabelled step (toolshed.g2.bx.psu.edu/repos/iuc/meryl\_histogram\_kmers/meryl\_histogram\_kmers/1.3+galaxy7)**: | |
| * step_state: scheduled | |
| * <details><summary>Jobs</summary> | |
| - **Job 1:** | |
| * Job state is ok | |
| **Container:** | |
| * ```console | |
| quay.io/biocontainers/mulled-v2-ba0fa2569b9c1d280d7fb3b1bf2ad3c0c72d9296:34d0c765d43a43f8968b3d9ffb3ceb9a8cdf6a69-0 | |
| ``` | |
| **Command Line:** | |
| * ```console | |
| export GALAXY_MEMORY_GB=$((${GALAXY_MEMORY_MB:-8192}/1024)) && mkdir -p ./temp_db/ && tar -xmf /tmp/tmp3sfjay_q/files/a/b/8/dataset_ab8e2e9f-eae2-4e32-af70-aaaeb4c7dae9.dat --use-compress-program="pigz -p ${GALAXY_SLOTS:-1}" -C ./temp_db/ && mv ./temp_db/* tmp.meryl && meryl histogram tmp.meryl > read-db.hist | |
| ``` | |
| **Exit Code:** | |
| * ```console | |
| 0 | |
| ``` | |
| **Standard Error:** | |
| * ```console | |
| Found 1 command tree. | |
| ``` | |
| **Traceback:** | |
| * ```console | |
| ``` | |
| **Job Parameters:** | |
| * | Job parameter | Parameter value | | |
| | ------------- | --------------- | | |
| | \_\_input\_ext | ` "input" ` | | |
| | \_\_workflow\_invocation\_uuid\_\_ | ` "a9e9fe4a115611f189517ced8dc21a23" ` | | |
| | chromInfo | ` "/tmp/tmp3sfjay_q/galaxy-dev/tool-data/shared/ucsc/chrom/?.len" ` | | |
| | dbkey | ` "?" ` | | |
| </details> | |
| - **Step 15: Genomescope on paternal haplotype (toolshed.g2.bx.psu.edu/repos/iuc/genomescope/genomescope/2.0.1+galaxy0)**: | |
| * step_state: scheduled | |
| * <details><summary>Jobs</summary> | |
| - **Job 1:** | |
| * Job state is ok | |
| **Container:** | |
| * ```console | |
| quay.io/biocontainers/genomescope2:2.0.1--py313r44hdfd78af_1 | |
| ``` | |
| **Command Line:** | |
| * ```console | |
| genomescope2 --input '/tmp/tmp3sfjay_q/files/f/2/1/dataset_f21f2c50-8e37-47ee-bfb7-7badbe73c84c.dat' --output . --kmer_length 9 --ploidy 1 | |
| ``` | |
| **Exit Code:** | |
| * ```console | |
| 0 | |
| ``` | |
| **Standard Output:** | |
| * ```console | |
| GenomeScope analyzing /tmp/tmp3sfjay_q/files/f/2/1/dataset_f21f2c50-8e37-47ee-bfb7-7badbe73c84c.dat p=1 k=9 outdir=. | |
| a:100% | |
| Model converged het:0 kcov:23.6 err:0.0752 model fit:2.86 len:29941 | |
| ``` | |
| **Traceback:** | |
| * ```console | |
| ``` | |
| **Job Parameters:** | |
| * | Job parameter | Parameter value | | |
| | ------------- | --------------- | | |
| | \_\_input\_ext | ` "input" ` | | |
| | \_\_workflow\_invocation\_uuid\_\_ | ` "a9e9fe4a115611f189517ced8dc21a23" ` | | |
| | advanced\_options | ` {"initial_heterozygosities": "", "initial_repetitiveness": null, "num_rounds": null, "testing": false, "topology": null, "trace_flag": false, "transform_exp": null, "true_params": ""} ` | | |
| | chromInfo | ` "/tmp/tmp3sfjay_q/galaxy-dev/tool-data/shared/ucsc/chrom/?.len" ` | | |
| | dbkey | ` "?" ` | | |
| | kmer\_length | ` "9" ` | | |
| | lambda | ` None ` | | |
| | max\_kmercov | ` None ` | | |
| | output\_options | ` {"no_unique_sequence": false, "output_files": ["model_output", "summary_output"]} ` | | |
| | ploidy | ` "1" ` | | |
| </details> | |
| - **Step 16: Genomescope on maternal haplotype (toolshed.g2.bx.psu.edu/repos/iuc/genomescope/genomescope/2.0.1+galaxy0)**: | |
| * step_state: scheduled | |
| * <details><summary>Jobs</summary> | |
| - **Job 1:** | |
| * Job state is ok | |
| **Container:** | |
| * ```console | |
| quay.io/biocontainers/genomescope2:2.0.1--py313r44hdfd78af_1 | |
| ``` | |
| **Command Line:** | |
| * ```console | |
| genomescope2 --input '/tmp/tmp3sfjay_q/files/e/5/9/dataset_e59b841c-d57f-4874-959e-52096753689b.dat' --output . --kmer_length 9 --ploidy 1 | |
| ``` | |
| **Exit Code:** | |
| * ```console | |
| 0 | |
| ``` | |
| **Standard Output:** | |
| * ```console | |
| GenomeScope analyzing /tmp/tmp3sfjay_q/files/e/5/9/dataset_e59b841c-d57f-4874-959e-52096753689b.dat p=1 k=9 outdir=. | |
| a:100% | |
| Model converged het:0 kcov:26.7 err:0.0685 model fit:2.9 len:33838 | |
| ``` | |
| **Traceback:** | |
| * ```console | |
| ``` | |
| **Job Parameters:** | |
| * | Job parameter | Parameter value | | |
| | ------------- | --------------- | | |
| | \_\_input\_ext | ` "input" ` | | |
| | \_\_workflow\_invocation\_uuid\_\_ | ` "a9e9fe4a115611f189517ced8dc21a23" ` | | |
| | advanced\_options | ` {"initial_heterozygosities": "", "initial_repetitiveness": null, "num_rounds": null, "testing": false, "topology": null, "trace_flag": false, "transform_exp": null, "true_params": ""} ` | | |
| | chromInfo | ` "/tmp/tmp3sfjay_q/galaxy-dev/tool-data/shared/ucsc/chrom/?.len" ` | | |
| | dbkey | ` "?" ` | | |
| | kmer\_length | ` "9" ` | | |
| | lambda | ` None ` | | |
| | max\_kmercov | ` None ` | | |
| | output\_options | ` {"no_unique_sequence": false, "output_files": ["model_output", "summary_output"]} ` | | |
| | ploidy | ` "1" ` | | |
| </details> | |
| </details> | |
| * <details><summary>Other invocation details</summary> | |
| - **history_id** | |
| * 8a84ee7fd8b02fa3 | |
| - **history_state** | |
| * ok | |
| - **invocation_id** | |
| * 50357bb3220f36dd | |
| - **invocation_state** | |
| * scheduled | |
| - **workflow_id** | |
| * 50357bb3220f36dd | |
| </details> | |
| </div></details> | |
| * <details class="rcorners light-red"><summary class="light-red">❌ pe-wgs-variation.ga_0</summary><div class="padded"> | |
| **Problems**: | |
| * ``` | |
| Output with path /tmp/tmpdkd69rf5/Final (SnpEff-)annotated variants__5ae0e8f3-49b9-49c1-8641-6151cec8b609.vcf different than expected, difference (using diff): | |
| ( /home/runner/work/iwc/iwc/workflows/sars-cov-2-variant-calling/sars-cov-2-pe-illumina-wgs-variant-calling/test-data/final_snpeff_annotated_variants.vcf v. /tmp/tmpfd9cew4lfinal_snpeff_annotated_variants.vcf ) | |
| --- local_file | |
| +++ history_data | |
| @@ -1,6 +1,7 @@ | |
| ##fileformat=VCFv4.0 | |
| -##fileDate=20210221 | |
| -##source=lofreq call --verbose --ref reference.fa --call-indels --min-cov 5 --max-depth 1000000 --min-bq 30 --min-alt-bq 30 --min-mq 20 --max-mq 255 --min-jq 0 --min-alt-jq 0 --def-alt-jq 0 --sig 0.0005 --bonf dynamic --no-default-filter --no-default-filter -r NC_045512.2:1-14951 -o /tmp/lofreq2_call_parallelxh3mih1k/0.vcf.gz reads.bam | |
| +##FILTER=<ID=PASS,Description="All filters passed"> | |
| +##fileDate=20260224 | |
| +##source=lofreq call --verbose --ref reference.fa --call-indels --min-cov 5 --max-depth 1000000 --min-bq 30 --min-alt-bq 30 --min-mq 20 --max-mq 255 --min-jq 0 --min-alt-jq 0 --def-alt-jq 0 --sig 0.0005 --bonf dynamic --no-default-filter --no-default-filter -r NC_045512.2:1-14951 -o /tmp/tmpddk24pce/job_working_directory/000/12/tmp/lofreq2_call_parallel64zcre5b/0.vcf.gz reads.bam | |
| ##reference=reference.fa | |
| ##INFO=<ID=DP,Number=1,Type=Integer,Description="Raw Depth"> | |
| ##INFO=<ID=AF,Number=1,Type=Float,Description="Allele Frequency"> | |
| @@ -11,11 +12,17 @@ | |
| ##INFO=<ID=HRUN,Number=1,Type=Integer,Description="Homopolymer length to the right of report indel position"> | |
| ##FILTER=<ID=min_snvqual_68,Description="Minimum SNV Quality (Phred) 68"> | |
| ##FILTER=<ID=min_indelqual_60,Description="Minimum Indel Quality (Phred) 60"> | |
| +##contig=<ID=NC_045512.2> | |
| +##FILTER=<ID=min_snvqual_66,Description="Minimum SNV Quality (Phred) 66"> | |
| +##FILTER=<ID=min_indelqual_57,Description="Minimum Indel Quality (Phred) 57"> | |
| +##FILTER=<ID=min_indelqual_58,Description="Minimum Indel Quality (Phred) 58"> | |
| +##bcftools_concatVersion=1.21+htslib-1.21 | |
| +##bcftools_concatCommand=concat -a -O z -o /tmp/tmpddk24pce/job_working_directory/000/12/tmp/lofreq2_call_parallel64zcre5b/concat.vcf.gz /tmp/tmpddk24pce/job_working_directory/000/12/tmp/lofreq2_call_parallel64zcre5b/0.vcf.gz /tmp/tmpddk24pce/job_working_directory/000/12/tmp/lofreq2_call_parallel64zcre5b/1.vcf.gz /tmp/tmpddk24pce/job_working_directory/000/12/tmp/lofreq2_call_parallel64zcre5b/2.vcf.gz; Date=Tue Feb 24 07:00:33 2026 | |
| ##FILTER=<ID=min_snvqual_72,Description="Minimum SNV Quality (Phred) 72"> | |
| ##FILTER=<ID=min_indelqual_64,Description="Minimum Indel Quality (Phred) 64"> | |
| ##FILTER=<ID=sb_fdr,Description="Strand-Bias Multiple Testing Correction: fdr corr. pvalue > 0.001000"> | |
| ******** | |
| *SNIP * | |
| ******** | |
| NC_045512.2 1594 . C T 450.0 PASS DP=15;AF=0.866667;SB=0;DP4=0,0,4,11;EFF=SYNONYMOUS_CODING(LOW|SILENT|tcC/tcT|S443|7096|ORF1ab|protein_coding|CODING|GU280_gp01|1|T),SYNONYMOUS_CODING(LOW|SILENT|tcC/tcT|S443|4405|ORF1ab|protein_coding|CODING|GU280_gp01.2|1|T),SYNONYMOUS_CODING(LOW|SILENT|tcC/tcT|S263|637|ORF1ab|protein_coding|CODING|YP_009725298.1|1|T|WARNING_TRANSCRIPT_NO_START_CODON),SYNONYMOUS_CODING(LOW|SILENT|tcC/tcT|S263|637|ORF1ab|protein_coding|CODING|YP_009742609.1|1|T|WARNING_TRANSCRIPT_NO_START_CODON) | |
| NC_045512.2 3037 . C T 3073.0 PASS DP=108;AF=0.842593;SB=13;DP4=7,4,30,67;EFF=SYNONYMOUS_CODING(LOW|SILENT|ttC/ttT|F924|7096|ORF1ab|protein_coding|CODING|GU280_gp01|1|T),SYNONYMOUS_CODING(LOW|SILENT|ttC/ttT|F924|4405|ORF1ab|protein_coding|CODING|GU280_gp01.2|1|T),SYNONYMOUS_CODING(LOW|SILENT|ttC/ttT|F106|1944|ORF1ab|protein_coding|CODING|YP_009725299.1|1|T|WARNING_TRANSCRIPT_NO_START_CODON),SYNONYMOUS_CODING(LOW|SILENT|ttC/ttT|F106|1944|ORF1ab|protein_coding|CODING|YP_009742610.1|1|T|WARNING_TRANSCRIPT_NO_START_CODON) | |
| -NC_045512.2 3177 . C T 133.0 PASS DP=64;AF=0.093750;SB=1;DP4=20,38,1,5;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|cCt/cTt|P971L|7096|ORF1ab|protein_coding|CODING|GU280_gp01|1|T),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|cCt/cTt|P971L|4405|ORF1ab|protein_coding|CODING|GU280_gp01.2|1|T),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|cCt/cTt|P153L|1944|ORF1ab|protein_coding|CODING|YP_009725299.1|1|T|WARNING_TRANSCRIPT_NO_START_CODON),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|cCt/cTt|P153L|1944|ORF1ab|protein_coding|CODING|YP_009742610.1|1|T|WARNING_TRANSCRIPT_NO_START_CODON) | |
| -NC_045512.2 3874 . C T 275.0 PASS DP=18;AF=0.500000;SB=0;DP4=9,0,9,0;EFF=SYNONYMOUS_CODING(LOW|SILENT|atC/atT|I1203|7096|ORF1ab|protein_coding|CODING|GU280_gp01|1|T),SYNONYMOUS_CODING(LOW|SILENT|atC/atT|I1203|4405|ORF1ab|protein_coding|CODING|GU280_gp01.2|1|T),SYNONYMOUS_CODING(LOW|SILENT|atC/atT|I385|1944|ORF1ab|protein_coding|CODING|YP_009725299.1|1|T|WARNING_TRANSCRIPT_NO_START_CODON),SYNONYMOUS_CODING(LOW|SILENT|atC/atT|I385|1944|ORF1ab|protein_coding|CODING|YP_009742610.1|1|T|WARNING_TRANSCRIPT_NO_START_CODON) | |
| +NC_045512.2 3177 . C T 133.0 PASS DP=64;AF=0.09375;SB=1;DP4=20,38,1,5;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|cCt/cTt|P971L|7096|ORF1ab|protein_coding|CODING|GU280_gp01|1|T),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|cCt/cTt|P971L|4405|ORF1ab|protein_coding|CODING|GU280_gp01.2|1|T),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|cCt/cTt|P153L|1944|ORF1ab|protein_coding|CODING|YP_009725299.1|1|T|WARNING_TRANSCRIPT_NO_START_CODON),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|cCt/cTt|P153L|1944|ORF1ab|protein_coding|CODING|YP_009742610.1|1|T|WARNING_TRANSCRIPT_NO_START_CODON) | |
| +NC_045512.2 3874 . C T 275.0 PASS DP=18;AF=0.5;SB=0;DP4=9,0,9,0;EFF=SYNONYMOUS_CODING(LOW|SILENT|atC/atT|I1203|7096|ORF1ab|protein_coding|CODING|GU280_gp01|1|T),SYNONYMOUS_CODING(LOW|SILENT|atC/atT|I1203|4405|ORF1ab|protein_coding|CODING|GU280_gp01.2|1|T),SYNONYMOUS_CODING(LOW|SILENT|atC/atT|I385|1944|ORF1ab|protein_coding|CODING|YP_009725299.1|1|T|WARNING_TRANSCRIPT_NO_START_CODON),SYNONYMOUS_CODING(LOW|SILENT|atC/atT|I385|1944|ORF1ab|protein_coding|CODING|YP_009742610.1|1|T|WARNING_TRANSCRIPT_NO_START_CODON) | |
| NC_045512.2 6285 . C T 256.0 PASS DP=13;AF=0.615385;SB=0;DP4=4,1,6,2;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|aCc/aTc|T2007I|7096|ORF1ab|protein_coding|CODING|GU280_gp01|1|T),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|aCc/aTc|T2007I|4405|ORF1ab|protein_coding|CODING|GU280_gp01.2|1|T),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|aCc/aTc|T1189I|1944|ORF1ab|protein_coding|CODING|YP_009725299.1|1|T|WARNING_TRANSCRIPT_NO_START_CODON),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|aCc/aTc|T1189I|1944|ORF1ab|protein_coding|CODING|YP_009742610.1|1|T|WARNING_TRANSCRIPT_NO_START_CODON) | |
| NC_045512.2 6696 . C CT 98.0 PASS DP=142;AF=0.028169;SB=0;DP4=43,98,1,3;INDEL;HRUN=4;EFF=FRAME_SHIFT(HIGH||ctt/Tctt|L2146S?|7096|ORF1ab|protein_coding|CODING|GU280_gp01|1|CT|INFO_REALIGN_3_PRIME),FRAME_SHIFT(HIGH||ctt/Tctt|L2146S?|4405|ORF1ab|protein_coding|CODING|GU280_gp01.2|1|CT|INFO_REALIGN_3_PRIME),FRAME_SHIFT(HIGH||ctt/Tctt|L1328S?|1944|ORF1ab|protein_coding|CODING|YP_009725299.1|1|CT|WARNING_TRANSCRIPT_NO_START_CODON&INFO_REALIGN_3_PRIME),FRAME_SHIFT(HIGH||ctt/Tctt|L1328S?|1944|ORF1ab|protein_coding|CODING|YP_009742610.1|1|CT|WARNING_TRANSCRIPT_NO_START_CODON&INFO_REALIGN_3_PRIME);LOF=(ORF1ab|GU280_gp01|28|0.14) | |
| NC_045512.2 8290 . C T 3071.0 PASS DP=109;AF=0.844037;SB=10;DP4=9,6,31,63;EFF=SYNONYMOUS_CODING(LOW|SILENT|ctC/ctT|L2675|7096|ORF1ab|protein_coding|CODING|GU280_gp01|1|T),SYNONYMOUS_CODING(LOW|SILENT|ctC/ctT|L2675|4405|ORF1ab|protein_coding|CODING|GU280_gp01.2|1|T),SYNONYMOUS_CODING(LOW|SILENT|ctC/ctT|L1857|1944|ORF1ab|protein_coding|CODING|YP_009725299.1|1|T|WARNING_TRANSCRIPT_NO_START_CODON),SYNONYMOUS_CODING(LOW|SILENT|ctC/ctT|L1857|1944|ORF1ab|protein_coding|CODING|YP_009742610.1|1|T|WARNING_TRANSCRIPT_NO_START_CODON) | |
| @@ -43,7 +50,7 @@ | |
| NC_045512.2 12662 . G A 243.0 PASS DP=2923;AF=0.008895;SB=1;DP4=749,2142,8,19;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Gcc/Acc|A4133T|7096|ORF1ab|protein_coding|CODING|GU280_gp01|1|A),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Gcc/Acc|A4133T|4405|ORF1ab|protein_coding|CODING|GU280_gp01.2|1|A),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Gcc/Acc|A191T|197|ORF1ab|protein_coding|CODING|YP_009725304.1|1|A|WARNING_TRANSCRIPT_NO_START_CODON),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Gcc/Acc|A191T|197|ORF1ab|protein_coding|CODING|YP_009742615.1|1|A|WARNING_TRANSCRIPT_NO_START_CODON) | |
| NC_045512.2 14398 . G T 124.0 PASS DP=101;AF=0.059406;SB=1;DP4=51,44,4,2;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Gtg/Ttg|V4712L|7096|ORF1ab|protein_coding|CODING|GU280_gp01|2|T),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Gtg/Ttg|V320L|931|ORF1ab|protein_coding|CODING|YP_009725307.1|2|T|WARNING_TRANSCRIPT_NO_START_CODON) | |
| NC_045512.2 14408 . C T 3058.0 PASS DP=103;AF=0.873786;SB=1;DP4=3,5,48,47;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|cCt/cTt|P4715L|7096|ORF1ab|protein_coding|CODING|GU280_gp01|2|T),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|cCt/cTt|P323L|931|ORF1ab|protein_coding|CODING|YP_009725307.1|2|T|WARNING_TRANSCRIPT_NO_START_CODON) | |
| -NC_045512.2 15960 . C T 341.0 PASS DP=127;AF=0.118110;SB=1;DP4=93,18,13,3;EFF=SYNONYMOUS_CODING(LOW|SILENT|gcC/gcT|A5232|7096|ORF1ab|protein_coding|CODING|GU280_gp01|2|T),SYNONYMOUS_CODING(LOW|SILENT|gcC/gcT|A840|931|ORF1ab|protein_coding|CODING|YP_009725307.1|2|T|WARNING_TRANSCRIPT_NO_START_CODON) | |
| +NC_045512.2 15960 . C T 341.0 PASS DP=127;AF=0.11811;SB=1;DP4=93,18,13,3;EFF=SYNONYMOUS_CODING(LOW|SILENT|gcC/gcT|A5232|7096|ORF1ab|protein_coding|CODING|GU280_gp01|2|T),SYNONYMOUS_CODING(LOW|SILENT|gcC/gcT|A840|931|ORF1ab|protein_coding|CODING|YP_009725307.1|2|T|WARNING_TRANSCRIPT_NO_START_CODON) | |
| NC_045512.2 17747 . C T 225.0 PASS DP=38;AF=0.236842;SB=12;DP4=11,18,7,2;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|cCt/cTt|P5828L|7096|ORF1ab|protein_coding|CODING|GU280_gp01|2|T),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|cCt/cTt|P504L|600|ORF1ab|protein_coding|CODING|YP_009725308.1|1|T|WARNING_TRANSCRIPT_NO_START_CODON) | |
| NC_045512.2 17858 . A G 296.0 PASS DP=28;AF=0.392857;SB=0;DP4=6,9,5,8;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|tAt/tGt|Y5865C|7096|ORF1ab|protein_coding|CODING|GU280_gp01|2|G),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|tAt/tGt|Y541C|600|ORF1ab|protein_coding|CODING|YP_009725308.1|1|G|WARNING_TRANSCRIPT_NO_START_CODON) | |
| NC_045512.2 17874 . C T 292.0 PASS DP=23;AF=0.434783;SB=0;DP4=4,8,4,7;EFF=SYNONYMOUS_CODING(LOW|SILENT|ttC/ttT|F5870|7096|ORF1ab|protein_coding|CODING|GU280_gp01|2|T),SYNONYMOUS_CODING(LOW|SILENT|ttC/ttT|F546|600|ORF1ab|protein_coding|CODING|YP_009725308.1|1|T|WARNING_TRANSCRIPT_NO_START_CODON) | |
| @@ -73,5 +80,5 @@ | |
| NC_045512.2 25563 . G T 1722.0 PASS DP=59;AF=0.847458;SB=0;DP4=0,5,4,50;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|caG/caT|Q57H|275|ORF3a|protein_coding|CODING|GU280_gp03|1|T) | |
| NC_045512.2 28077 . G C 166.0 PASS DP=93;AF=0.086022;SB=1;DP4=20,63,1,8;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Gtg/Ctg|V62L|121|ORF8|protein_coding|CODING|GU280_gp09|1|C) | |
| NC_045512.2 28214 . C CT 72.0 PASS DP=105;AF=0.028571;SB=0;DP4=85,17,3,0;INDEL;HRUN=5;EFF=FRAME_SHIFT(HIGH||tta/ttTa|L109F?|121|ORF8|protein_coding|CODING|GU280_gp09|1|CT|INFO_REALIGN_3_PRIME);LOF=(ORF8|GU280_gp09|1|1.00) | |
| -NC_045512.2 28253 . C T 145.0 PASS DP=103;AF=0.077670;SB=0;DP4=67,26,7,3;EFF=SYNONYMOUS_CODING(LOW|SILENT|ttC/ttT|F120|121|ORF8|protein_coding|CODING|GU280_gp09|1|T) | |
| +NC_045512.2 28253 . C T 145.0 PASS DP=103;AF=0.07767;SB=0;DP4=67,26,7,3;EFF=SYNONYMOUS_CODING(LOW|SILENT|ttC/ttT|F120|121|ORF8|protein_coding|CODING|GU280_gp09|1|T) | |
| NC_045512.2 29700 . A G 335.0 PASS DP=139;AF=0.107914;SB=0;DP4=45,78,5,10 | |
| ``` | |
| #### Workflow invocation details | |
| * Invocation Messages | |
| * <details><summary>Steps</summary> | |
| - **Step 1: Paired Collection**: | |
| * step_state: scheduled | |
| - **Step 2: NC_045512.2 FASTA sequence of SARS-CoV-2**: | |
| * step_state: scheduled | |
| - **Step 3: Unlabelled step (toolshed.g2.bx.psu.edu/repos/iuc/fastp/fastp/0.23.2+galaxy0)**: | |
| * step_state: scheduled | |
| * <details><summary>Jobs</summary> | |
| - **Job 1:** | |
| * Job state is ok | |
| **Container:** | |
| * ```console | |
| quay.io/biocontainers/fastp:0.23.2--hadf994f_5 | |
| ``` | |
| **Command Line:** | |
| * ```console | |
| ln -s '/tmp/tmpddk24pce/files/d/a/1/dataset_da1f4e24-7500-49c9-864a-73d5c8dc86b1.dat' 'SRR11578257.fastq.gz' && ln -s '/tmp/tmpddk24pce/files/0/4/a/dataset_04a22f63-d765-4315-97ad-3701a3bcad8a.dat' 'SRR11578257_R2.fastq.gz' && fastp --thread ${GALAXY_SLOTS:-1} --report_title 'fastp report for SRR11578257.fastq.gz' -i 'SRR11578257.fastq.gz' -o first.fastq.gz -I 'SRR11578257_R2.fastq.gz' -O second.fastq.gz --detect_adapter_for_pe && mv first.fastq.gz '/tmp/tmpddk24pce/job_working_directory/000/4/outputs/dataset_73f4fcdf-2fda-4c21-a252-f4b01f4acb14.dat' && mv second.fastq.gz '/tmp/tmpddk24pce/job_working_directory/000/4/outputs/dataset_25524dc9-4327-4360-a849-3371f660f9f9.dat' | |
| ``` | |
| **Exit Code:** | |
| * ```console | |
| 0 | |
| ``` | |
| **Standard Error:** | |
| * ```console | |
| Detecting adapter sequence for read1... | |
| ACCTTAGAATCAAGATTGTTAGAATTCCAAGCTATAACGCAGCCTGTAAAATCATCTGGT | |
| Detecting adapter sequence for read2... | |
| No adapter detected for read2 | |
| Read1 before filtering: | |
| total reads: 201367 | |
| total bases: 29302687 | |
| Q20 bases: 28139796(96.0315%) | |
| Q30 bases: 27281893(93.1037%) | |
| Read2 before filtering: | |
| total reads: 201367 | |
| total bases: 29398146 | |
| Q20 bases: 27778430(94.4904%) | |
| Q30 bases: 26748339(90.9865%) | |
| Read1 after filtering: | |
| total reads: 195579 | |
| total bases: 28439132 | |
| Q20 bases: 27427010(96.4411%) | |
| Q30 bases: 26623439(93.6155%) | |
| Read2 after filtering: | |
| total reads: 195579 | |
| total bases: 28450670 | |
| Q20 bases: 27054927(95.0942%) | |
| Q30 bases: 26092568(91.7116%) | |
| Filtering result: | |
| reads passed filter: 391158 | |
| reads failed due to low quality: 5634 | |
| reads failed due to too many N: 1164 | |
| reads failed due to too short: 4778 | |
| reads with adapter trimmed: 18954 | |
| bases trimmed due to adapters: 261387 | |
| Duplication rate: 20.2521% | |
| Insert size peak (evaluated by paired-end reads): 230 | |
| JSON report: fastp.json | |
| HTML report: fastp.html | |
| fastp --thread 1 --report_title fastp report for SRR11578257.fastq.gz -i SRR11578257.fastq.gz -o first.fastq.gz -I SRR11578257_R2.fastq.gz -O second.fastq.gz --detect_adapter_for_pe | |
| fastp v0.23.2, time used: 11 seconds | |
| ``` | |
| **Traceback:** | |
| * ```console | |
| ``` | |
| **Job Parameters:** | |
| * | Job parameter | Parameter value | | |
| | ------------- | --------------- | | |
| | \_\_input\_ext | ` "fastqsanger.gz" ` | | |
| | \_\_workflow\_invocation\_uuid\_\_ | ` "21c0cf24114e11f189517c1e52865a2d" ` | | |
| | chromInfo | ` "/tmp/tmpddk24pce/galaxy-dev/tool-data/shared/ucsc/chrom/?.len" ` | | |
| | dbkey | ` "?" ` | | |
| | filter\_options | ` {"length_filtering_options": {"disable_length_filtering": false, "length_limit": null, "length_required": null}, "low_complexity_filter": {"complexity_threshold": null, "enable_low_complexity_filter": false}, "quality_filtering_options": {"disable_quality_filtering": false, "n_base_limit": null, "qualified_quality_phred": null, "unqualified_percent_limit": null}} ` | | |
| | output\_options | ` {"report_html": true, "report_json": true} ` | | |
| | overrepresented\_sequence\_analysis | ` {"overrepresentation_analysis": false, "overrepresentation_sampling": null} ` | | |
| | read\_mod\_options | ` {"base_correction_options": {"correction": false}, "cutting_by_quality_options": {"cut_by_quality3": false, "cut_by_quality5": false, "cut_mean_quality": null, "cut_window_size": null}, "polyg_tail_trimming": {"__current_case__": 1, "poly_g_min_len": null, "trimming_select": ""}, "polyx_tail_trimming": {"__current_case__": 1, "polyx_trimming_select": ""}, "umi_processing": {"umi": false, "umi_len": null, "umi_loc": "", "umi_prefix": ""}} ` | | |
| | single\_paired | ` {"__current_case__": 2, "adapter_trimming_options": {"adapter_sequence1": "", "adapter_sequence2": "", "disable_adapter_trimming": false}, "global_trimming_options": {"trim_front1": null, "trim_front2": null, "trim_tail1": null, "trim_tail2": null}, "paired_input": {"values": [{"id": 1, "src": "dce"}]}, "single_paired_selector": "paired_collection"} ` | | |
| </details> | |
| - **Step 4: Unlabelled step (toolshed.g2.bx.psu.edu/repos/devteam/bwa/bwa\_mem/0.7.17.2)**: | |
| * step_state: scheduled | |
| * <details><summary>Jobs</summary> | |
| - **Job 1:** | |
| * Job state is ok | |
| **Container:** | |
| * ```console | |
| quay.io/biocontainers/mulled-v2-fe8faa35dbf6dc65a0f7f5d4ea12e31a79f73e40:1476e745a911a5a2ac22207311b275c51e745ba9-2 | |
| ``` | |
| **Command Line:** | |
| * ```console | |
| set -o | grep -q pipefail && set -o pipefail; ln -s '/tmp/tmpddk24pce/files/5/9/c/dataset_59cfafdc-4d7d-487e-b044-7fcd7e63abf5.dat' 'localref.fa' && bwa index 'localref.fa' && bwa mem -t "${GALAXY_SLOTS:-1}" -v 1 'localref.fa' '/tmp/tmpddk24pce/files/7/3/f/dataset_73f4fcdf-2fda-4c21-a252-f4b01f4acb14.dat' '/tmp/tmpddk24pce/files/2/5/5/dataset_25524dc9-4327-4360-a849-3371f660f9f9.dat' | samtools sort -@${GALAXY_SLOTS:-2} -T "${TMPDIR:-.}" -O bam -o '/tmp/tmpddk24pce/job_working_directory/000/5/outputs/dataset_e0083911-a912-4420-b9d0-59b9072830d1.dat' | |
| ``` | |
| **Exit Code:** | |
| * ```console | |
| 0 | |
| ``` | |
| **Standard Error:** | |
| * ```console | |
| [bwa_index] Pack FASTA... 0.00 sec | |
| [bwa_index] Construct BWT for the packed sequence... | |
| [bwa_index] 0.00 seconds elapse. | |
| [bwa_index] Update BWT... 0.00 sec | |
| [bwa_index] Pack forward-only FASTA... 0.00 sec | |
| [bwa_index] Construct SA from BWT and Occ... 0.00 sec | |
| [main] Version: 0.7.17-r1188 | |
| [main] CMD: bwa index localref.fa | |
| [main] Real time: 0.010 sec; CPU: 0.008 sec | |
| [M::mem_pestat] skip orientation FF as there are not enough pairs | |
| [M::mem_pestat] analyzing insert size distribution for orientation FR... | |
| [M::mem_pestat] (25, 50, 75) percentile: (188, 240, 293) | |
| [M::mem_pestat] low and high boundaries for computing mean and std.dev: (1, 503) | |
| [M::mem_pestat] mean and std.dev: (236.09, 72.41) | |
| [M::mem_pestat] low and high boundaries for proper pairs: (1, 608) | |
| [M::mem_pestat] skip orientation RF as there are not enough pairs | |
| [M::mem_pestat] skip orientation RR as there are not enough pairs | |
| [M::mem_pestat] skip orientation FF as there are not enough pairs | |
| [M::mem_pestat] analyzing insert size distribution for orientation FR... | |
| [M::mem_pestat] (25, 50, 75) percentile: (188, 239, 293) | |
| [M::mem_pestat] low and high boundaries for computing mean and std.dev: (1, 503) | |
| [M::mem_pestat] mean and std.dev: (235.71, 72.44) | |
| [M::mem_pestat] low and high boundaries for proper pairs: (1, 608) | |
| [M::mem_pestat] skip orientation RF as there are not enough pairs | |
| [M::mem_pestat] skip orientation RR as there are not enough pairs | |
| [M::mem_pestat] skip orientation FF as there are not enough pairs | |
| [M::mem_pestat] analyzing insert size distribution for orientation FR... | |
| [M::mem_pestat] (25, 50, 75) percentile: (186, 239, 293) | |
| [M::mem_pestat] low and high boundaries for computing mean and std.dev: (1, 507) | |
| [M::mem_pestat] mean and std.dev: (235.25, 72.64) | |
| [M::mem_pestat] low and high boundaries for proper pairs: (1, 614) | |
| [M::mem_pestat] skip orientation RF as there are not enough pairs | |
| [M::mem_pestat] skip orientation RR as there are not enough pairs | |
| [M::mem_pestat] skip orientation FF as there are not enough pairs | |
| [M::mem_pestat] analyzing insert size distribution for orientation FR... | |
| [M::mem_pestat] (25, 50, 75) percentile: (187, 240, 293) | |
| [M::mem_pestat] low and high boundaries for computing mean and std.dev: (1, 505) | |
| [M::mem_pestat] mean and std.dev: (235.77, 72.25) | |
| [M::mem_pestat] low and high boundaries for proper pairs: (1, 611) | |
| [M::mem_pestat] skip orientation RF as there are not enough pairs | |
| [M::mem_pestat] skip orientation RR as there are not enough pairs | |
| [M::mem_pestat] skip orientation FF as there are not enough pairs | |
| [M::mem_pestat] analyzing insert size distribution for orientation FR... | |
| [M::mem_pestat] (25, 50, 75) percentile: (186, 238, 292) | |
| [M::mem_pestat] low and high boundaries for computing mean and std.dev: (1, 504) | |
| [M::mem_pestat] mean and std.dev: (234.79, 72.73) | |
| [M::mem_pestat] low and high boundaries for proper pairs: (1, 610) | |
| [M::mem_pestat] skip orientation RF as there are not enough pairs | |
| [M::mem_pestat] skip orientation RR as there are not enough pairs | |
| [M::mem_pestat] skip orientation FF as there are not enough pairs | |
| [M::mem_pestat] analyzing insert size distribution for orientation FR... | |
| [M::mem_pestat] (25, 50, 75) percentile: (185, 238, 292) | |
| [M::mem_pestat] low and high boundaries for computing mean and std.dev: (1, 506) | |
| [M::mem_pestat] mean and std.dev: (234.12, 72.68) | |
| [M::mem_pestat] low and high boundaries for proper pairs: (1, 613) | |
| [M::mem_pestat] skip orientation RF as there are not enough pairs | |
| [M::mem_pestat] skip orientation RR as there are not enough pairs | |
| [main] Version: 0.7.17-r1188 | |
| [main] CMD: bwa mem -t 1 -v 1 localref.fa /tmp/tmpddk24pce/files/7/3/f/dataset_73f4fcdf-2fda-4c21-a252-f4b01f4acb14.dat /tmp/tmpddk24pce/files/2/5/5/dataset_25524dc9-4327-4360-a849-3371f660f9f9.dat | |
| [main] Real time: 11.069 sec; CPU: 10.040 sec | |
| ``` | |
| **Traceback:** | |
| * ```console | |
| ``` | |
| **Job Parameters:** | |
| * | Job parameter | Parameter value | | |
| | ------------- | --------------- | | |
| | \_\_input\_ext | ` "fasta" ` | | |
| | \_\_workflow\_invocation\_uuid\_\_ | ` "21c0cf24114e11f189517c1e52865a2d" ` | | |
| | analysis\_type | ` {"__current_case__": 0, "analysis_type_selector": "illumina"} ` | | |
| | chromInfo | ` "/tmp/tmpddk24pce/galaxy-dev/tool-data/shared/ucsc/chrom/?.len" ` | | |
| | dbkey | ` "?" ` | | |
| | fastq\_input | ` {"__current_case__": 2, "fastq_input1": {"values": [{"id": 4, "src": "dce"}]}, "fastq_input_selector": "paired_collection", "iset_stats": ""} ` | | |
| | output\_sort | ` "coordinate" ` | | |
| | reference\_source | ` {"__current_case__": 1, "index_a": "auto", "ref_file": {"values": [{"id": 1, "src": "hda"}]}, "reference_source_selector": "history"} ` | | |
| | rg | ` {"__current_case__": 3, "rg_selector": "do_not_set"} ` | | |
| </details> | |
| - **Step 5: Unlabelled step (toolshed.g2.bx.psu.edu/repos/iuc/samtools\_view/samtools\_view/1.13+galaxy2)**: | |
| * step_state: scheduled | |
| * <details><summary>Jobs</summary> | |
| - **Job 1:** | |
| * Job state is ok | |
| **Container:** | |
| * ```console | |
| quay.io/biocontainers/mulled-v2-8dd8177cf5b9476288c149088f4340b576b866e3:0e17efd831b210a161d3b4b93fd9dab3479446ba-0 | |
| ``` | |
| **Command Line:** | |
| * ```console | |
| addthreads=${GALAXY_SLOTS:-1} && (( addthreads-- )) && addmemory=${GALAXY_MEMORY_MB_PER_SLOT:-768} && ((addmemory=addmemory*75/100)) && ln -s '/tmp/tmpddk24pce/files/e/0/0/dataset_e0083911-a912-4420-b9d0-59b9072830d1.dat' infile && ln -s '/tmp/tmpddk24pce/files/_metadata_files/3/d/2/metadata_3d2b28d8-bcfe-4a1d-ab48-ce33cd8a11ff.dat' infile.bai && samtools view -@ $addthreads -b -q 20 -f 3 -F 0 -G 0 -o outfile infile | |
| ``` | |
| **Exit Code:** | |
| * ```console | |
| 0 | |
| ``` | |
| **Traceback:** | |
| * ```console | |
| ``` | |
| **Job Parameters:** | |
| * | Job parameter | Parameter value | | |
| | ------------- | --------------- | | |
| | \_\_input\_ext | ` "input" ` | | |
| | \_\_workflow\_invocation\_uuid\_\_ | ` "21c0cf24114e11f189517c1e52865a2d" ` | | |
| | addref\_cond | ` {"__current_case__": 0, "addref_select": "no"} ` | | |
| | chromInfo | ` "/tmp/tmpddk24pce/galaxy-dev/tool-data/shared/ucsc/chrom/?.len" ` | | |
| | dbkey | ` "?" ` | | |
| | mode | ` {"__current_case__": 1, "filter_config": {"cigarcons": null, "cond_region": {"__current_case__": 0, "select_region": "no"}, "cond_rg": {"__current_case__": 0, "select_rg": "no"}, "exclusive_filter": null, "exclusive_filter_all": null, "inclusive_filter": ["1", "2"], "library": "", "qname_file": null, "quality": "20", "tag": null}, "output_options": {"__current_case__": 0, "adv_output": {"collapsecigar": false, "readtags": []}, "complementary_output": false, "output_format": {"__current_case__": 2, "oformat": "bam"}, "reads_report_type": "retained"}, "outtype": "selected_reads", "subsample_config": {"subsampling_mode": {"__current_case__": 0, "factor": "1.0", "seed": null, "select_subsample": "fraction"}}} ` | | |
| </details> | |
| - **Step 6: Unlabelled step (toolshed.g2.bx.psu.edu/repos/devteam/picard/picard\_MarkDuplicates/2.18.2.3)**: | |
| * step_state: scheduled | |
| * <details><summary>Jobs</summary> | |
| - **Job 1:** | |
| * Job state is ok | |
| **Container:** | |
| * ```console | |
| quay.io/biocontainers/picard:2.18.2--py36_0 | |
| ``` | |
| **Command Line:** | |
| * ```console | |
| _JAVA_OPTIONS=${_JAVA_OPTIONS:-'-Xmx2048m -Xms256m'} && export _JAVA_OPTIONS && ln -f -s '/tmp/tmpddk24pce/files/0/f/2/dataset_0f26dde8-744a-4a67-8616-7f09c7511796.dat' 'SRR11578257' && picard MarkDuplicates INPUT='SRR11578257' OUTPUT='/tmp/tmpddk24pce/job_working_directory/000/7/outputs/dataset_e369e660-2a04-4f36-a769-a140f79403ca.dat' METRICS_FILE='/tmp/tmpddk24pce/job_working_directory/000/7/outputs/dataset_b5b5e9d4-79fa-4428-8796-0f7643382bf3.dat' REMOVE_DUPLICATES='true' ASSUME_SORTED='true' DUPLICATE_SCORING_STRATEGY='SUM_OF_BASE_QUALITIES' OPTICAL_DUPLICATE_PIXEL_DISTANCE='100' VALIDATION_STRINGENCY='LENIENT' TAGGING_POLICY=All QUIET=true VERBOSITY=ERROR `if [ -n "$TMPDIR" ] ; then echo 'TMP_DIR=$TMPDIR' ; else if [ -n "$TEMP" ] ; then echo 'TMP_DIR=$TEMP' ; fi ; fi` | |
| ``` | |
| **Exit Code:** | |
| * ```console | |
| 0 | |
| ``` | |
| **Standard Error:** | |
| * ```console | |
| /usr/local/bin/picard: line 5: warning: setlocale: LC_ALL: cannot change locale (en_US.UTF-8): No such file or directory | |
| Picked up _JAVA_OPTIONS: -Xmx2048m -Xms256m | |
| 06:59:22.574 INFO NativeLibraryLoader - Loading libgkl_compression.so from jar:file:/usr/local/share/picard-2.18.2-0/picard.jar!/com/intel/gkl/native/libgkl_compression.so | |
| ``` | |
| **Traceback:** | |
| * ```console | |
| ``` | |
| **Job Parameters:** | |
| * | Job parameter | Parameter value | | |
| | ------------- | --------------- | | |
| | \_\_input\_ext | ` "bam" ` | | |
| | \_\_workflow\_invocation\_uuid\_\_ | ` "21c0cf24114e11f189517c1e52865a2d" ` | | |
| | assume\_sorted | ` true ` | | |
| | barcode\_tag | ` "" ` | | |
| | chromInfo | ` "/tmp/tmpddk24pce/galaxy-dev/tool-data/shared/ucsc/chrom/?.len" ` | | |
| | comments | ` [] ` | | |
| | dbkey | ` "?" ` | | |
| | duplicate\_scoring\_strategy | ` "SUM_OF_BASE_QUALITIES" ` | | |
| | optical\_duplicate\_pixel\_distance | ` "100" ` | | |
| | read\_name\_regex | ` "" ` | | |
| | remove\_duplicates | ` true ` | | |
| | validation\_stringency | ` "LENIENT" ` | | |
| </details> | |
| - **Step 7: Unlabelled step (toolshed.g2.bx.psu.edu/repos/devteam/samtools\_stats/samtools\_stats/2.0.3)**: | |
| * step_state: scheduled | |
| * <details><summary>Jobs</summary> | |
| - **Job 1:** | |
| * Job state is ok | |
| **Container:** | |
| * ```console | |
| quay.io/biocontainers/samtools:1.13--h8c37831_0 | |
| ``` | |
| **Command Line:** | |
| * ```console | |
| addthreads=${GALAXY_SLOTS:-1} && (( addthreads-- )) && ln -s '/tmp/tmpddk24pce/files/0/f/2/dataset_0f26dde8-744a-4a67-8616-7f09c7511796.dat' infile && ln -s '/tmp/tmpddk24pce/files/_metadata_files/f/a/d/metadata_fad853d7-4514-4724-b4f2-e1b07360034b.dat' infile.bai && samtools stats -@ $addthreads infile > '/tmp/tmpddk24pce/job_working_directory/000/8/outputs/dataset_7210b839-4af6-4129-9aa3-a8f78632d555.dat' | |
| ``` | |
| **Exit Code:** | |
| * ```console | |
| 0 | |
| ``` | |
| **Traceback:** | |
| * ```console | |
| ``` | |
| **Job Parameters:** | |
| * | Job parameter | Parameter value | | |
| | ------------- | --------------- | | |
| | \_\_input\_ext | ` "input" ` | | |
| | \_\_workflow\_invocation\_uuid\_\_ | ` "21c0cf24114e11f189517c1e52865a2d" ` | | |
| | addref\_cond | ` {"__current_case__": 0, "addref_select": "no"} ` | | |
| | chromInfo | ` "/tmp/tmpddk24pce/galaxy-dev/tool-data/shared/ucsc/chrom/?.len" ` | | |
| | cond\_region | ` {"__current_case__": 0, "select_region": "no"} ` | | |
| | cov\_threshold | ` None ` | | |
| | coverage\_cond | ` {"__current_case__": 0, "coverage_select": "no"} ` | | |
| | dbkey | ` "?" ` | | |
| | filter\_by\_flags | ` {"__current_case__": 1, "filter_flags": "nofilter"} ` | | |
| | gc\_depth | ` None ` | | |
| | insert\_size | ` None ` | | |
| | most\_inserts | ` None ` | | |
| | read\_group | ` None ` | | |
| | read\_length | ` None ` | | |
| | remove\_dups | ` false ` | | |
| | remove\_overlaps | ` false ` | | |
| | sparse | ` false ` | | |
| | split\_output\_cond | ` {"__current_case__": 0, "split_output_selector": "no"} ` | | |
| | trim\_quality | ` None ` | | |
| </details> | |
| - **Step 8: Unlabelled step (toolshed.g2.bx.psu.edu/repos/iuc/lofreq\_viterbi/lofreq\_viterbi/2.1.5+galaxy0)**: | |
| * step_state: scheduled | |
| * <details><summary>Jobs</summary> | |
| - **Job 1:** | |
| * Job state is ok | |
| **Container:** | |
| * ```console | |
| quay.io/biocontainers/lofreq:2.1.5--py312ha5e83ca_15 | |
| ``` | |
| **Command Line:** | |
| * ```console | |
| ln -s '/tmp/tmpddk24pce/files/5/9/c/dataset_59cfafdc-4d7d-487e-b044-7fcd7e63abf5.dat' reference.fa && lofreq faidx reference.fa 2>&1 || echo "Error running samtools faidx for indexing fasta reference for lofreq" >&2 && lofreq viterbi --ref 'reference.fa' --defqual 2 --out tmp.bam '/tmp/tmpddk24pce/files/e/3/6/dataset_e369e660-2a04-4f36-a769-a140f79403ca.dat' && samtools sort --no-PG -T "${TMPDIR:-.}" -@ ${GALAXY_SLOTS:-1} -O BAM -o '/tmp/tmpddk24pce/job_working_directory/000/9/outputs/dataset_f3b2dc20-878a-48c4-b441-87e07000256f.dat' tmp.bam | |
| ``` | |
| **Exit Code:** | |
| * ```console | |
| 0 | |
| ``` | |
| **Traceback:** | |
| * ```console | |
| ``` | |
| **Job Parameters:** | |
| * | Job parameter | Parameter value | | |
| | ------------- | --------------- | | |
| | \_\_input\_ext | ` "input" ` | | |
| | \_\_workflow\_invocation\_uuid\_\_ | ` "21c0cf24114e11f189517c1e52865a2d" ` | | |
| | adv\_options | ` {"bq2_handling": {"__current_case__": 0, "defqual": "2", "replace_bq2": "keep"}, "keepflags": false} ` | | |
| | chromInfo | ` "/tmp/tmpddk24pce/galaxy-dev/tool-data/shared/ucsc/chrom/?.len" ` | | |
| | dbkey | ` "?" ` | | |
| | reference\_source | ` {"__current_case__": 1, "ref": {"values": [{"id": 1, "src": "hda"}]}, "ref_selector": "history"} ` | | |
| </details> | |
| - **Step 9: Unlabelled step (toolshed.g2.bx.psu.edu/repos/iuc/multiqc/multiqc/1.11+galaxy0)**: | |
| * step_state: scheduled | |
| * <details><summary>Jobs</summary> | |
| - **Job 1:** | |
| * Job state is ok | |
| **Container:** | |
| * ```console | |
| quay.io/biocontainers/multiqc:1.11--pyhdfd78af_0 | |
| ``` | |
| **Command Line:** | |
| * ```console | |
| die() { echo "$@" 1>&2 ; exit 1; } && mkdir multiqc_WDir && mkdir multiqc_WDir/fastp_0 && ln -s '/tmp/tmpddk24pce/files/9/2/b/dataset_92b66445-7242-46f6-8c62-8e360a1cbd03.dat' 'multiqc_WDir/fastp_0/SRR11578257fastp.json' && grep -q "report_title" 'multiqc_WDir/fastp_0/SRR11578257fastp.json' || die "'report_title' or 'report_title' not found in the file" && mkdir multiqc_WDir/samtools_1 && mkdir 'multiqc_WDir/samtools_1/stats_0' && grep -q 'This file was produced by samtools stats' /tmp/tmpddk24pce/files/7/2/1/dataset_7210b839-4af6-4129-9aa3-a8f78632d555.dat || die "Module 'samtools: 'This file was produced by samtools stats' not found in the file 'SRR11578257'" && ln -s '/tmp/tmpddk24pce/files/7/2/1/dataset_7210b839-4af6-4129-9aa3-a8f78632d555.dat' 'multiqc_WDir/samtools_1/stats_0/SRR11578257' && mkdir multiqc_WDir/picard_2 && mkdir 'multiqc_WDir/picard_2/markdups_0' && grep -q 'MarkDuplicates' /tmp/tmpddk24pce/files/b/5/b/dataset_b5b5e9d4-79fa-4428-8796-0f7643382bf3.dat || die "Module 'picard: 'MarkDuplicates' not found in the file 'SRR11578257'" && ln -s '/tmp/tmpddk24pce/files/b/5/b/dataset_b5b5e9d4-79fa-4428-8796-0f7643382bf3.dat' 'multiqc_WDir/picard_2/markdups_0/SRR11578257' && multiqc multiqc_WDir --filename 'report' | |
| ``` | |
| **Exit Code:** | |
| * ```console | |
| 0 | |
| ``` | |
| **Standard Error:** | |
| * ```console | |
| /// MultiQC 🔍 | v1.11 | |
| | multiqc | MultiQC Version v1.33 now available! | |
| | multiqc | Search path : /tmp/tmpddk24pce/job_working_directory/000/10/working/multiqc_WDir | |
| | picard | Found 1 MarkDuplicates reports | |
| | samtools | Found 1 stats reports | |
| | fastp | Found 1 reports | |
| | multiqc | Compressing plot data | |
| | multiqc | Report : report.html | |
| | multiqc | Data : report_data | |
| | multiqc | MultiQC complete | |
| ``` | |
| **Standard Output:** | |
| * ```console | |
| | searching | ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 100% 3/3 | |
| ``` | |
| **Traceback:** | |
| * ```console | |
| ``` | |
| **Job Parameters:** | |
| * | Job parameter | Parameter value | | |
| | ------------- | --------------- | | |
| | \_\_input\_ext | ` "input" ` | | |
| | \_\_workflow\_invocation\_uuid\_\_ | ` "21c0cf24114e11f189517c1e52865a2d" ` | | |
| | chromInfo | ` "/tmp/tmpddk24pce/galaxy-dev/tool-data/shared/ucsc/chrom/?.len" ` | | |
| | comment | ` "" ` | | |
| | dbkey | ` "?" ` | | |
| | export | ` false ` | | |
| | flat | ` false ` | | |
| | results | ` [{"__index__": 0, "software_cond": {"__current_case__": 7, "input": {"values": [{"id": 4, "src": "hdca"}]}, "software": "fastp"}}, {"__index__": 1, "software_cond": {"__current_case__": 24, "output": [{"__index__": 0, "type": {"__current_case__": 0, "input": {"values": [{"id": 9, "src": "hdca"}]}, "type": "stats"}}], "software": "samtools"}}, {"__index__": 2, "software_cond": {"__current_case__": 17, "output": [{"__index__": 0, "input": {"values": [{"id": 7, "src": "hdca"}]}, "type": "markdups"}], "software": "picard"}}] ` | | |
| | saveLog | ` false ` | | |
| | title | ` "" ` | | |
| </details> | |
| - **Step 10: Unlabelled step (toolshed.g2.bx.psu.edu/repos/iuc/lofreq\_indelqual/lofreq\_indelqual/2.1.5+galaxy0)**: | |
| * step_state: scheduled | |
| * <details><summary>Jobs</summary> | |
| - **Job 1:** | |
| * Job state is ok | |
| **Container:** | |
| * ```console | |
| quay.io/biocontainers/lofreq:2.1.5--py312ha5e83ca_15 | |
| ``` | |
| **Command Line:** | |
| * ```console | |
| ln -s '/tmp/tmpddk24pce/files/5/9/c/dataset_59cfafdc-4d7d-487e-b044-7fcd7e63abf5.dat' reference.fa && lofreq faidx reference.fa 2>&1 || echo "Error running samtools faidx for indexing fasta reference for lofreq" >&2 && lofreq indelqual --dindel --ref reference.fa -o output.bam /tmp/tmpddk24pce/files/f/3/b/dataset_f3b2dc20-878a-48c4-b441-87e07000256f.dat | |
| ``` | |
| **Exit Code:** | |
| * ```console | |
| 0 | |
| ``` | |
| **Traceback:** | |
| * ```console | |
| ``` | |
| **Job Parameters:** | |
| * | Job parameter | Parameter value | | |
| | ------------- | --------------- | | |
| | \_\_input\_ext | ` "input" ` | | |
| | \_\_workflow\_invocation\_uuid\_\_ | ` "21c0cf24114e11f189517c1e52865a2d" ` | | |
| | chromInfo | ` "/tmp/tmpddk24pce/galaxy-dev/tool-data/shared/ucsc/chrom/?.len" ` | | |
| | dbkey | ` "?" ` | | |
| | strategy | ` {"__current_case__": 1, "reference_source": {"__current_case__": 1, "ref": {"values": [{"id": 1, "src": "hda"}]}, "ref_selector": "history"}, "selector": "dindel"} ` | | |
| </details> | |
| - **Step 11: Unlabelled step (toolshed.g2.bx.psu.edu/repos/iuc/lofreq\_call/lofreq\_call/2.1.5+galaxy1)**: | |
| * step_state: scheduled | |
| * <details><summary>Jobs</summary> | |
| - **Job 1:** | |
| * Job state is ok | |
| **Container:** | |
| * ```console | |
| quay.io/biocontainers/lofreq:2.1.5--py312ha5e83ca_15 | |
| ``` | |
| **Command Line:** | |
| * ```console | |
| ln -s '/tmp/tmpddk24pce/files/5/9/c/dataset_59cfafdc-4d7d-487e-b044-7fcd7e63abf5.dat' reference.fa && lofreq faidx reference.fa 2>&1 || echo "Error running samtools faidx for indexing fasta reference for lofreq" >&2 && ln -s '/tmp/tmpddk24pce/files/5/d/3/dataset_5d37e156-72fc-4196-8b5f-6b92b3df6eb1.dat' reads.bam && ln -s -f '/tmp/tmpddk24pce/files/_metadata_files/6/5/1/metadata_65169a24-b9b8-4cf5-b0bb-59e359233cf3.dat' reads.bam.bai && lofreq call-parallel --pp-threads ${GALAXY_SLOTS:-1} --verbose --ref 'reference.fa' --out variants.vcf --call-indels --min-cov 5 --max-depth 1000000 --min-bq 30 --min-alt-bq 30 --min-mq 20 --max-mq 255 --min-jq 0 --min-alt-jq 0 --def-alt-jq 0 --sig 0.0005 --bonf dynamic --no-default-filter reads.bam 2>&1 || (tool_exit_code=$? && cat "$TMPDIR/lofreq2_call_parallel*/*.log" 1>&2 && exit $tool_exit_code) | |
| ``` | |
| **Exit Code:** | |
| * ```console | |
| 0 | |
| ``` | |
| **Standard Output:** | |
| * ```console | |
| INFO [2026-02-24 07:00:06,156]: Using 1 threads with following basic args: lofreq call --verbose --ref reference.fa --call-indels --min-cov 5 --max-depth 1000000 --min-bq 30 --min-alt-bq 30 --min-mq 20 --max-mq 255 --min-jq 0 --min-alt-jq 0 --def-alt-jq 0 --sig 0.0005 --bonf dynamic --no-default-filter reads.bam | |
| INFO [2026-02-24 07:00:06,165]: Adding 3 commands to mp-pool | |
| Checking the headers and starting positions of 3 files | |
| Number of substitution tests performed: 8235 | |
| Number of indel tests performed: 1170 | |
| INFO [2026-02-24 07:00:33,785]: Executing lofreq filter -i /tmp/tmpddk24pce/job_working_directory/000/12/tmp/lofreq2_call_parallel64zcre5b/concat.vcf.gz -o variants.vcf --no-defaults --snvqual-thresh 72 --indelqual-thresh 64 | |
| ``` | |
| **Traceback:** | |
| * ```console | |
| ``` | |
| **Job Parameters:** | |
| * | Job parameter | Parameter value | | |
| | ------------- | --------------- | | |
| | \_\_input\_ext | ` "input" ` | | |
| | \_\_workflow\_invocation\_uuid\_\_ | ` "21c0cf24114e11f189517c1e52865a2d" ` | | |
| | call\_control | ` {"__current_case__": 1, "align_quals": {"alnqual": {"__current_case__": 0, "alnqual_choice": {"__current_case__": 1, "alnquals_to_use": "", "extended_baq": true}, "use_alnqual": ""}}, "bc_quals": {"alt_bq": {"__current_case__": 0, "modify": ""}, "min_alt_bq": "30", "min_bq": "30"}, "coverage": {"max_depth": "1000000", "min_cov": "5"}, "joint_qual": {"def_alt_jq": "0", "min_alt_jq": "0", "min_jq": "0"}, "map_quals": {"min_mq": "20", "use_mq": {"__current_case__": 0, "max_mq": "255", "no_mq": ""}}, "pe": {"use_orphan": false}, "set_call_options": "yes", "source_qual": {"use_src_qual": {"__current_case__": 0, "src_qual": ""}}} ` | | |
| | chromInfo | ` "/tmp/tmpddk24pce/galaxy-dev/tool-data/shared/ucsc/chrom/?.len" ` | | |
| | dbkey | ` "?" ` | | |
| | filter\_control | ` {"__current_case__": 3, "bonf": "0", "filter_type": "set_custom", "others": false, "sig": "0.0005"} ` | | |
| | reference\_source | ` {"__current_case__": 1, "ref": {"values": [{"id": 1, "src": "hda"}]}, "ref_selector": "history"} ` | | |
| | regions | ` {"__current_case__": 0, "restrict_to_region": "genome"} ` | | |
| | variant\_types | ` "--call-indels" ` | | |
| </details> | |
| - **Step 12: Unlabelled step (toolshed.g2.bx.psu.edu/repos/iuc/lofreq\_filter/lofreq\_filter/2.1.5+galaxy0)**: | |
| * step_state: scheduled | |
| * <details><summary>Jobs</summary> | |
| - **Job 1:** | |
| * Job state is ok | |
| **Container:** | |
| * ```console | |
| quay.io/biocontainers/lofreq:2.1.5--py312ha5e83ca_15 | |
| ``` | |
| **Command Line:** | |
| * ```console | |
| lofreq filter -i /tmp/tmpddk24pce/files/b/a/7/dataset_ba76a9d6-b778-4ab3-8eec-86131d02affc.dat --no-defaults --verbose --print-all -v 0 -V 0 -a 0.0 -A 0.0 -b fdr -c 0.001 -o filtered.vcf | |
| ``` | |
| **Exit Code:** | |
| * ```console | |
| 0 | |
| ``` | |
| **Standard Error:** | |
| * ```console | |
| Skipping default settings | |
| At least one type of multiple testing correction requested. Doing first pass of vcf | |
| MTC application completed | |
| Successful exit. | |
| ``` | |
| **Traceback:** | |
| * ```console | |
| ``` | |
| **Job Parameters:** | |
| * | Job parameter | Parameter value | | |
| | ------------- | --------------- | | |
| | \_\_input\_ext | ` "input" ` | | |
| | \_\_workflow\_invocation\_uuid\_\_ | ` "21c0cf24114e11f189517c1e52865a2d" ` | | |
| | af | ` {"af_max": "0.0", "af_min": "0.0"} ` | | |
| | chromInfo | ` "/tmp/tmpddk24pce/galaxy-dev/tool-data/shared/ucsc/chrom/?.len" ` | | |
| | coverage | ` {"cov_max": "0", "cov_min": "0"} ` | | |
| | dbkey | ` "?" ` | | |
| | filter\_by\_type | ` {"__current_case__": 0, "keep_only": "", "qual": {"indelqual_filter": {"__current_case__": 0, "indelqual": "no"}, "snvqual_filter": {"__current_case__": 0, "snvqual": "no"}}} ` | | |
| | flag\_or\_drop | ` "--print-all" ` | | |
| | sb | ` {"sb_filter": {"__current_case__": 2, "sb_alpha": "0.001", "sb_compound": true, "sb_indels": false, "sb_mtc": "fdr", "strand_bias": "mtc"}} ` | | |
| </details> | |
| - **Step 13: SnpEff eff covid19 version (toolshed.g2.bx.psu.edu/repos/iuc/snpeff\_sars\_cov\_2/snpeff\_sars\_cov\_2/4.5covid19)**: | |
| * step_state: scheduled | |
| * <details><summary>Jobs</summary> | |
| - **Job 1:** | |
| * Job state is ok | |
| **Container:** | |
| * ```console | |
| quay.io/biocontainers/snpeff:4.5covid19--hdfd78af_2 | |
| ``` | |
| **Command Line:** | |
| * ```console | |
| snpEff -Xmx${GALAXY_MEMORY_MB:-8192}m eff -i vcf -o vcf -upDownStreamLen 0 -formatEff -classic -no-downstream -no-intergenic -no-upstream -no-utr -stats '/tmp/tmpddk24pce/job_working_directory/000/14/outputs/dataset_b8667b07-bde5-4a24-8eac-a763975ea2b2.dat' -noLog NC_045512.2 '/tmp/tmpddk24pce/files/0/e/6/dataset_0e6ad5a4-5f03-4c89-bec1-4a1409d0d0c1.dat' > '/tmp/tmpddk24pce/job_working_directory/000/14/outputs/dataset_5ae0e8f3-49b9-49c1-8641-6151cec8b609.dat' && mkdir '/tmp/tmpddk24pce/job_working_directory/000/14/outputs/dataset_b8667b07-bde5-4a24-8eac-a763975ea2b2_files' && mv '/tmp/tmpddk24pce/job_working_directory/000/14/outputs/dataset_b8667b07-bde5-4a24-8eac-a763975ea2b2.dat.genes.txt' '/tmp/tmpddk24pce/job_working_directory/000/14/outputs/dataset_b8667b07-bde5-4a24-8eac-a763975ea2b2_files/dataset_b8667b07-bde5-4a24-8eac-a763975ea2b2.dat.genes.txt' | |
| ``` | |
| **Exit Code:** | |
| * ```console | |
| 0 | |
| ``` | |
| **Traceback:** | |
| * ```console | |
| ``` | |
| **Job Parameters:** | |
| * | Job parameter | Parameter value | | |
| | ------------- | --------------- | | |
| | \_\_input\_ext | ` "vcf" ` | | |
| | \_\_workflow\_invocation\_uuid\_\_ | ` "21c0cf24114e11f189517c1e52865a2d" ` | | |
| | annotations | ` ["-formatEff", "-classic"] ` | | |
| | chr | ` "" ` | | |
| | chromInfo | ` "/tmp/tmpddk24pce/galaxy-dev/tool-data/shared/ucsc/chrom/?.len" ` | | |
| | csvStats | ` false ` | | |
| | dbkey | ` "?" ` | | |
| | filter | ` {"__current_case__": 0, "specificEffects": "no"} ` | | |
| | filterOut | ` ["-no-downstream", "-no-intergenic", "-no-upstream", "-no-utr"] ` | | |
| | generate\_stats | ` true ` | | |
| | genome\_version | ` "NC_045512.2" ` | | |
| | inputFormat | ` "vcf" ` | | |
| | intervals | ` None ` | | |
| | noLog | ` true ` | | |
| | offset | ` "default" ` | | |
| | outputConditional | ` {"__current_case__": 0, "outputFormat": "vcf"} ` | | |
| | transcripts | ` None ` | | |
| | udLength | ` "0" ` | | |
| </details> | |
| </details> | |
| * <details><summary>Other invocation details</summary> | |
| - **history_id** | |
| * bd66b97923858b65 | |
| - **history_state** | |
| * ok | |
| - **invocation_id** | |
| * bd66b97923858b65 | |
| - **invocation_state** | |
| * scheduled | |
| - **workflow_id** | |
| * bd66b97923858b65 | |
| </details> | |
| </div></details> | |
| </details> | |
| <details ><summary>Passed Tests</summary> | |
| * <details class="rcorners light-green"><summary class="light-green">✅ Allele-based-Pathogen-Identification.ga_0</summary><div class="padded"> | |
| #### Workflow invocation details | |
| * Invocation Messages | |
| * <details><summary>Steps</summary> | |
| - **Step 1: collection_of_preprocessed_samples**: | |
| * step_state: scheduled | |
| - **Step 2: samples_profile**: | |
| * step_state: scheduled | |
| - **Step 3: reference_genome_of_tested_strain**: | |
| * step_state: scheduled | |
| - **Step 4: Unlabelled step (CONVERTER\_gz\_to\_uncompressed)**: | |
| * step_state: scheduled | |
| * <details><summary>Jobs</summary> | |
| - **Job 1:** | |
| * Job state is ok | |
| **Command Line:** | |
| * ```console | |
| cp '/tmp/tmp4oiilqtb/job_working_directory/000/4/configs/tmpy2uavb7k' 'galaxy.json' && gzip -dcf '/tmp/tmp4oiilqtb/files/1/c/a/dataset_1ca47457-11fa-47e6-bbbf-af5461ec933f.dat' > '/tmp/tmp4oiilqtb/job_working_directory/000/4/outputs/dataset_dbcb3ea2-271b-49ae-aa59-5ea11693bd8e.dat' | |
| ``` | |
| **Exit Code:** | |
| * ```console | |
| 0 | |
| ``` | |
| **Traceback:** | |
| * ```console | |
| ``` | |
| **Job Parameters:** | |
| * | Job parameter | Parameter value | | |
| | ------------- | --------------- | | |
| | \_\_input\_ext | ` "input" ` | | |
| | \_\_workflow\_invocation\_uuid\_\_ | ` "2bc979b2114e11f18951000d3a5a8e28" ` | | |
| | chromInfo | ` "/tmp/tmp4oiilqtb/galaxy-dev/tool-data/shared/ucsc/chrom/?.len" ` | | |
| | dbkey | ` "?" ` | | |
| </details> | |
| - **Step 5: Unlabelled step (toolshed.g2.bx.psu.edu/repos/iuc/minimap2/minimap2/2.28+galaxy1)**: | |
| * step_state: scheduled | |
| * <details><summary>Jobs</summary> | |
| - **Job 1:** | |
| * Job state is ok | |
| **Container:** | |
| * ```console | |
| quay.io/biocontainers/mulled-v2-66534bcbb7031a148b13e2ad42583020b9cd25c4:3a70f8bc7e17b723591f6132418640cfdbc88246-0 | |
| ``` | |
| **Command Line:** | |
| * ```console | |
| ln -f -s '/tmp/tmp4oiilqtb/files/d/b/c/dataset_dbcb3ea2-271b-49ae-aa59-5ea11693bd8e.dat' reference.fa && minimap2 --q-occ-frac 0.01 -t ${GALAXY_SLOTS:-4} reference.fa '/tmp/tmp4oiilqtb/files/d/8/4/dataset_d84174d6-9a75-465c-bfc5-5b323f3a13e7.dat' -a | samtools view --no-PG -hT reference.fa | samtools sort -@${GALAXY_SLOTS:-2} -T "${TMPDIR:-.}" -O BAM -o '/tmp/tmp4oiilqtb/job_working_directory/000/6/outputs/dataset_2b421f1d-a959-4de8-9e45-52a9e14685f1.dat' | |
| ``` | |
| **Exit Code:** | |
| * ```console | |
| 0 | |
| ``` | |
| **Standard Error:** | |
| * ```console | |
| [M::mm_idx_gen::0.138*1.00] collected minimizers | |
| [M::mm_idx_gen::0.202*1.00] sorted minimizers | |
| [M::main::0.202*1.00] loaded/built the index for 2 target sequence(s) | |
| [M::mm_mapopt_update::0.214*1.00] mid_occ = 10 | |
| [M::mm_idx_stat] kmer size: 15; skip: 10; is_hpc: 0; #seq: 2 | |
| [M::mm_idx_stat::0.224*1.00] distinct minimizers: 897839 (97.82% are singletons); average occurrences: 1.031; average spacing: 5.350; total length: 4951383 | |
| [M::worker_pipeline::6.195*0.99] mapped 2700 sequences | |
| [M::main] Version: 2.28-r1209 | |
| [M::main] CMD: minimap2 --q-occ-frac 0.01 -t 1 -a reference.fa /tmp/tmp4oiilqtb/files/d/8/4/dataset_d84174d6-9a75-465c-bfc5-5b323f3a13e7.dat | |
| [M::main] Real time: 6.202 sec; CPU: 6.118 sec; Peak RSS: 0.517 GB | |
| ``` | |
| **Traceback:** | |
| * ```console | |
| ``` | |
| **Job Parameters:** | |
| * | Job parameter | Parameter value | | |
| | ------------- | --------------- | | |
| | \_\_input\_ext | ` "input" ` | | |
| | \_\_workflow\_invocation\_uuid\_\_ | ` "2bc979b2114e11f18951000d3a5a8e28" ` | | |
| | alignment\_options | ` {"A": null, "B": null, "E": null, "E2": null, "O": null, "O2": null, "no_end_flt": true, "s": null, "splicing": {"__current_case__": 0, "splice_mode": "preset"}, "z": null, "z2": null} ` | | |
| | chromInfo | ` "/tmp/tmp4oiilqtb/galaxy-dev/tool-data/shared/ucsc/chrom/?.len" ` | | |
| | dbkey | ` "?" ` | | |
| | fastq\_input | ` {"__current_case__": 0, "analysis_type_selector": null, "fastq_input1": {"values": [{"id": 2, "src": "dce"}]}, "fastq_input_selector": "single"} ` | | |
| | indexing\_options | ` {"H": false, "I": null, "k": null, "w": null} ` | | |
| | io\_options | ` {"K": null, "L": false, "Q": false, "Y": false, "c": false, "cs": null, "eqx": false, "output_format": "BAM"} ` | | |
| | mapping\_options | ` {"F": null, "N": null, "X": false, "f": null, "g": null, "kmer_ocurrence_interval": {"__current_case__": 1, "interval": ""}, "m": null, "mask_len": null, "max_chain_iter": null, "max_chain_skip": null, "min_occ_floor": null, "n": null, "p": null, "q_occ_frac": "0.01", "r": null} ` | | |
| | reference\_source | ` {"__current_case__": 1, "ref_file": {"values": [{"id": 4, "src": "hda"}]}, "reference_source_selector": "history"} ` | | |
| - **Job 2:** | |
| * Job state is ok | |
| **Container:** | |
| * ```console | |
| quay.io/biocontainers/mulled-v2-66534bcbb7031a148b13e2ad42583020b9cd25c4:3a70f8bc7e17b723591f6132418640cfdbc88246-0 | |
| ``` | |
| **Command Line:** | |
| * ```console | |
| ln -f -s '/tmp/tmp4oiilqtb/files/d/b/c/dataset_dbcb3ea2-271b-49ae-aa59-5ea11693bd8e.dat' reference.fa && minimap2 --q-occ-frac 0.01 -t ${GALAXY_SLOTS:-4} reference.fa '/tmp/tmp4oiilqtb/files/a/2/b/dataset_a2ba4c3d-d2ca-4b85-9fc2-11d6fb626a0d.dat' -a | samtools view --no-PG -hT reference.fa | samtools sort -@${GALAXY_SLOTS:-2} -T "${TMPDIR:-.}" -O BAM -o '/tmp/tmp4oiilqtb/job_working_directory/000/5/outputs/dataset_fc0c7f8e-e94e-4d7d-86b8-7ed58a4b6d23.dat' | |
| ``` | |
| **Exit Code:** | |
| * ```console | |
| 0 | |
| ``` | |
| **Standard Error:** | |
| * ```console | |
| [M::mm_idx_gen::0.142*0.95] collected minimizers | |
| [M::mm_idx_gen::0.207*0.96] sorted minimizers | |
| [M::main::0.207*0.96] loaded/built the index for 2 target sequence(s) | |
| [M::mm_mapopt_update::0.220*0.97] mid_occ = 10 | |
| [M::mm_idx_stat] kmer size: 15; skip: 10; is_hpc: 0; #seq: 2 | |
| [M::mm_idx_stat::0.229*0.97] distinct minimizers: 897839 (97.82% are singletons); average occurrences: 1.031; average spacing: 5.350; total length: 4951383 | |
| [M::worker_pipeline::6.070*0.98] mapped 8974 sequences | |
| [M::main] Version: 2.28-r1209 | |
| [M::main] CMD: minimap2 --q-occ-frac 0.01 -t 1 -a reference.fa /tmp/tmp4oiilqtb/files/a/2/b/dataset_a2ba4c3d-d2ca-4b85-9fc2-11d6fb626a0d.dat | |
| [M::main] Real time: 6.077 sec; CPU: 5.970 sec; Peak RSS: 0.506 GB | |
| ``` | |
| **Traceback:** | |
| * ```console | |
| ``` | |
| **Job Parameters:** | |
| * | Job parameter | Parameter value | | |
| | ------------- | --------------- | | |
| | \_\_input\_ext | ` "input" ` | | |
| | \_\_workflow\_invocation\_uuid\_\_ | ` "2bc979b2114e11f18951000d3a5a8e28" ` | | |
| | alignment\_options | ` {"A": null, "B": null, "E": null, "E2": null, "O": null, "O2": null, "no_end_flt": true, "s": null, "splicing": {"__current_case__": 0, "splice_mode": "preset"}, "z": null, "z2": null} ` | | |
| | chromInfo | ` "/tmp/tmp4oiilqtb/galaxy-dev/tool-data/shared/ucsc/chrom/?.len" ` | | |
| | dbkey | ` "?" ` | | |
| | fastq\_input | ` {"__current_case__": 0, "analysis_type_selector": null, "fastq_input1": {"values": [{"id": 1, "src": "dce"}]}, "fastq_input_selector": "single"} ` | | |
| | indexing\_options | ` {"H": false, "I": null, "k": null, "w": null} ` | | |
| | io\_options | ` {"K": null, "L": false, "Q": false, "Y": false, "c": false, "cs": null, "eqx": false, "output_format": "BAM"} ` | | |
| | mapping\_options | ` {"F": null, "N": null, "X": false, "f": null, "g": null, "kmer_ocurrence_interval": {"__current_case__": 1, "interval": ""}, "m": null, "mask_len": null, "max_chain_iter": null, "max_chain_skip": null, "min_occ_floor": null, "n": null, "p": null, "q_occ_frac": "0.01", "r": null} ` | | |
| | reference\_source | ` {"__current_case__": 1, "ref_file": {"values": [{"id": 4, "src": "hda"}]}, "reference_source_selector": "history"} ` | | |
| </details> | |
| - **Step 6: Unlabelled step (toolshed.g2.bx.psu.edu/repos/iuc/clair3/clair3/1.0.10+galaxy1)**: | |
| * step_state: scheduled | |
| * <details><summary>Jobs</summary> | |
| - **Job 1:** | |
| * Job state is ok | |
| **Container:** | |
| * ```console | |
| quay.io/biocontainers/clair3:1.0.10--py39hd649744_1 | |
| ``` | |
| **Command Line:** | |
| * ```console | |
| ln -s '/tmp/tmp4oiilqtb/files/d/b/c/dataset_dbcb3ea2-271b-49ae-aa59-5ea11693bd8e.dat' reference.fasta && samtools faidx reference.fasta && ln -s '/tmp/tmp4oiilqtb/files/2/b/4/dataset_2b421f1d-a959-4de8-9e45-52a9e14685f1.dat' input_reads.bam && ln -s '/tmp/tmp4oiilqtb/files/_metadata_files/9/c/c/metadata_9cc8d4ee-94b6-4565-918a-7cfbb42d0cda.dat' input_reads.bai && run_clair3.sh --bam_fn=input_reads.bam --ref_fn=reference.fasta --platform='ont' --model_path=$(dirname $(which run_clair3.sh))/models/r941_prom_hac_g360+g422 --output='.' --threads=${GALAXY_SLOTS:-2} --include_all_ctgs --snp_min_af=0.08 --indel_min_af=0.15 --haploid_precise --chunk_size=5000000 | |
| ``` | |
| **Exit Code:** | |
| * ```console | |
| 0 | |
| ``` | |
| **Standard Output:** | |
| * ```console | |
| [33m[WARNING] No absolute output path provided, using current directory as prefix[0m | |
| [INFO] CLAIR3 VERSION: v1.0.10 | |
| [INFO] BAM FILE PATH: /tmp/tmp4oiilqtb/job_working_directory/000/8/working/input_reads.bam | |
| [INFO] REFERENCE FILE PATH: /tmp/tmp4oiilqtb/job_working_directory/000/8/working/reference.fasta | |
| [INFO] MODEL PATH: /usr/local/bin/models/r941_prom_hac_g360+g422 | |
| [INFO] OUTPUT FOLDER: /tmp/tmp4oiilqtb/job_working_directory/000/8/working/. | |
| [INFO] PLATFORM: ont | |
| [INFO] THREADS: 1 | |
| [INFO] BED FILE PATH: EMPTY | |
| [INFO] VCF FILE PATH: EMPTY | |
| [INFO] CONTIGS: EMPTY | |
| [INFO] CONDA PREFIX: /usr/local | |
| [INFO] SAMTOOLS PATH: samtools | |
| [INFO] PYTHON PATH: python3 | |
| [INFO] PYPY PATH: pypy3 | |
| [INFO] PARALLEL PATH: parallel | |
| [INFO] WHATSHAP PATH: whatshap | |
| [INFO] LONGPHASE PATH: EMPTY | |
| [INFO] CHUNK SIZE: 5000000 | |
| [INFO] FULL ALIGN PROPORTION: 0.7 | |
| [INFO] FULL ALIGN REFERENCE PROPORTION: 0.1 | |
| [INFO] PHASING PROPORTION: 0.7 | |
| [INFO] MINIMUM MQ: 5 | |
| [INFO] MINIMUM COVERAGE: 2 | |
| [INFO] SNP AF THRESHOLD: 0.08 | |
| [INFO] INDEL AF THRESHOLD: 0.15 | |
| [INFO] BASE ERROR IN GVCF: 0.001 | |
| [INFO] GQ BIN SIZE IN GVCF: 5 | |
| [INFO] ENABLE FILEUP ONLY CALLING: False | |
| [INFO] ENABLE FAST MODE CALLING: False | |
| [INFO] ENABLE CALLING SNP CANDIDATES ONLY: False | |
| [INFO] ENABLE PRINTING REFERENCE CALLS: False | |
| [INFO] ENABLE OUTPUT GVCF: False | |
| [INFO] ENABLE HAPLOID PRECISE MODE: True | |
| [INFO] ENABLE HAPLOID SENSITIVE MODE: False | |
| [INFO] ENABLE INCLUDE ALL CTGS CALLING: True | |
| [INFO] ENABLE NO PHASING FOR FULL ALIGNMENT: False | |
| [INFO] ENABLE REMOVING INTERMEDIATE FILES: False | |
| [INFO] ENABLE LONGPHASE FOR INTERMEDIATE VCF PHASING: False | |
| [INFO] ENABLE PHASING FINAL VCF OUTPUT USING WHATSHAP: False | |
| [INFO] ENABLE PHASING FINAL VCF OUTPUT USING LONGPHASE: False | |
| [INFO] ENABLE HAPLOTAGGING FINAL BAM: False | |
| [INFO] ENABLE LONG INDEL CALLING: False | |
| [INFO] ENABLE C_IMPLEMENT: True | |
| + /usr/local/bin/scripts/clair3_c_impl.sh --bam_fn /tmp/tmp4oiilqtb/job_working_directory/000/8/working/input_reads.bam --ref_fn /tmp/tmp4oiilqtb/job_working_directory/000/8/working/reference.fasta --threads 1 --model_path /usr/local/bin/models/r941_prom_hac_g360+g422 --platform ont --output /tmp/tmp4oiilqtb/job_working_directory/000/8/working/. --bed_fn=EMPTY --vcf_fn=EMPTY --ctg_name=EMPTY --sample_name=SAMPLE --chunk_num=0 --chunk_size=5000000 --samtools=samtools --python=python3 --pypy=pypy3 --parallel=parallel --whatshap=whatshap --qual=2 --var_pct_full=0.7 --ref_pct_full=0.1 --var_pct_phasing=0.7 --snp_min_af=0.08 --indel_min_af=0.15 --min_mq=5 --min_coverage=2 --min_contig_size=0 --pileup_only=False --gvcf=False --base_err=0.001 --gq_bin_size=5 --fast_mode=False --call_snp_only=False --print_ref_calls=False --haploid_precise=True --haploid_sensitive=False --include_all_ctgs=True --no_phasing_for_fa=False --pileup_model_prefix=pileup --fa_model_prefix=full_alignment --remove_intermediate_dir=False --enable_phasing=False --enable_long_indel=False --keep_iupac_bases=False --use_gpu=False --longphase_for_phasing=False --longphase=EMPTY --use_whatshap_for_intermediate_phasing=True --use_longphase_for_intermediate_phasing=False --use_whatshap_for_final_output_phasing=False --use_longphase_for_final_output_phasing=False --use_whatshap_for_final_output_haplotagging=False | |
| [INFO] Check environment variables | |
| [INFO] Create folder /tmp/tmp4oiilqtb/job_working_directory/000/8/working/log | |
| [INFO] Create folder /tmp/tmp4oiilqtb/job_working_directory/000/8/working/tmp/pileup_output | |
| [INFO] Create folder /tmp/tmp4oiilqtb/job_working_directory/000/8/working/tmp/merge_output | |
| [INFO] Create folder /tmp/tmp4oiilqtb/job_working_directory/000/8/working/tmp/phase_output | |
| [INFO] Create folder /tmp/tmp4oiilqtb/job_working_directory/000/8/working/tmp/gvcf_tmp_output | |
| [INFO] Create folder /tmp/tmp4oiilqtb/job_working_directory/000/8/working/tmp/full_alignment_output | |
| [INFO] Create folder /tmp/tmp4oiilqtb/job_working_directory/000/8/working/tmp/phase_output/phase_vcf | |
| [INFO] Create folder /tmp/tmp4oiilqtb/job_working_directory/000/8/working/tmp/phase_output/phase_bam | |
| [INFO] Create folder /tmp/tmp4oiilqtb/job_working_directory/000/8/working/tmp/full_alignment_output/candidate_bed | |
| [INFO] --include_all_ctgs enabled | |
| [93m[WARNING] Please enable --no_phasing_for_fa if calling variant in non-diploid organisms[0m | |
| [INFO] Call variant in contigs: NC_003197.2 NC_003277.2 | |
| [INFO] Chunk number for each contig: 1 1 | |
| [INFO] 1/7 Call variants using pileup model | |
| Calling variants ... | |
| Total processed positions in NC_003197.2 (chunk 1/1) : 474727 | |
| Total time elapsed: 512.23 s | |
| Calling variants ... | |
| Total processed positions in NC_003277.2 (chunk 1/1) : 0 | |
| Total time elapsed: 0.02 s | |
| [INFO] No vcf output for file /tmp/tmp4oiilqtb/job_working_directory/000/8/working/./tmp/pileup_output/pileup_NC_003277.2_1.vcf, remove empty file | |
| real 8m38.336s | |
| user 8m32.319s | |
| sys 0m3.666s | |
| [INFO] 2/7 Select heterozygous SNP variants for Whatshap phasing and haplotagging | |
| [INFO] Select heterozygous pileup variants exceeding phasing quality cutoff 5 | |
| [INFO] Total heterozygous SNP positions selected: NC_003197.2: 9614 | |
| [INFO] Total heterozygous SNP positions selected: NC_003277.2: 0 | |
| real 0m1.753s | |
| user 0m1.276s | |
| sys 0m0.130s | |
| [INFO] 3/7 Phase VCF file using Whatshap | |
| This is WhatsHap 1.7 running under Python 3.9.0 | |
| Working on 1 sample from 1 family | |
| # Working on contig NC_003197.2 in individual SAMPLE | |
| Found 9614 usable heterozygous variants (0 skipped due to missing genotypes) | |
| Found 1144 reads covering 9612 variants | |
| Kept 969 reads that cover at least two variants each | |
| Selected 969 most phase-informative reads covering 9605 variants | |
| Phasing 1 sample by solving the MEC problem ... | |
| Largest block contains 1066 variants (11.1% of accessible variants) between position 1144263 and 1223703 | |
| Changed 48 genotypes while writing VCF | |
| # Resource usage | |
| Maximum memory usage: 0.059 GB | |
| Time spent reading BAM/CRAM: 0.7 s | |
| Time spent parsing VCF: 0.2 s | |
| Time spent selecting reads: 0.1 s | |
| Time spent phasing: 0.1 s | |
| Time spent writing VCF: 0.2 s | |
| Time spent finding components: 0.1 s | |
| Time spent on rest: 0.2 s | |
| Total elapsed time: 1.5 s | |
| This is WhatsHap 1.7 running under Python 3.9.0 | |
| Working on 1 sample from 1 family | |
| # Resource usage | |
| Maximum memory usage: 0.038 GB | |
| Time spent reading BAM/CRAM: 0.0 s | |
| Time spent parsing VCF: 0.0 s | |
| Time spent selecting reads: 0.0 s | |
| Time spent phasing: 0.0 s | |
| Time spent writing VCF: 0.0 s | |
| Time spent finding components: 0.0 s | |
| Time spent on rest: 0.0 s | |
| Total elapsed time: 0.0 s | |
| real 0m2.731s | |
| user 0m2.413s | |
| sys 0m0.185s | |
| [INFO] 5/7 Select candidates for full-alignment calling | |
| [INFO] Set variants quality cutoff 9.0 | |
| [INFO] Set reference calls quality cutoff 9.0 | |
| [INFO] Low quality reference calls to be processed in NC_003197.2: 33725 | |
| [INFO] Low quality variants to be processed in NC_003197.2: 96152 | |
| [93m[WARNING] Cannot find any low-quality 0/0, 0/1 or 1/1 variant in pileup output in contig NC_003277.2[0m | |
| [93m[WARNING] Copying pileup.vcf.gz to /tmp/tmp4oiilqtb/job_working_directory/000/8/working/./merge_output.vcf.gz[0m | |
| [INFO] Low quality reference calls to be processed in NC_003277.2: 0 | |
| [INFO] Low quality variants to be processed in NC_003277.2: 0 | |
| real 0m1.953s | |
| user 0m1.396s | |
| sys 0m0.182s | |
| [INFO] 6/7 Call low-quality variants using full-alignment model | |
| Calling variants ... | |
| Total processed positions in NC_003197.2 (chunk 1/13) : 10000 | |
| Total time elapsed: 67.77 s | |
| Calling variants ... | |
| Total processed positions in NC_003197.2 (chunk 2/13) : 10000 | |
| Total time elapsed: 67.36 s | |
| Calling variants ... | |
| Total processed positions in NC_003197.2 (chunk 3/13) : 10000 | |
| Total time elapsed: 68.37 s | |
| Calling variants ... | |
| Total processed positions in NC_003197.2 (chunk 4/13) : 10000 | |
| Total time elapsed: 66.11 s | |
| Calling variants ... | |
| Total processed positions in NC_003197.2 (chunk 5/13) : 10000 | |
| Total time elapsed: 65.50 s | |
| Calling variants ... | |
| Total processed positions in NC_003197.2 (chunk 6/13) : 10000 | |
| Total time elapsed: 65.97 s | |
| Calling variants ... | |
| Total processed positions in NC_003197.2 (chunk 7/13) : 10000 | |
| Total time elapsed: 66.45 s | |
| Calling variants ... | |
| Total processed positions in NC_003197.2 (chunk 8/13) : 10000 | |
| Total time elapsed: 65.68 s | |
| Calling variants ... | |
| Total processed positions in NC_003197.2 (chunk 9/13) : 10000 | |
| Total time elapsed: 66.14 s | |
| Calling variants ... | |
| Total processed positions in NC_003197.2 (chunk 10/13) : 10000 | |
| Total time elapsed: 65.58 s | |
| Calling variants ... | |
| Total processed positions in NC_003197.2 (chunk 11/13) : 10000 | |
| Total time elapsed: 65.43 s | |
| Calling variants ... | |
| Total processed positions in NC_003197.2 (chunk 12/13) : 10000 | |
| Total time elapsed: 66.35 s | |
| Calling variants ... | |
| Total processed positions in NC_003197.2 (chunk 13/13) : 9877 | |
| Total time elapsed: 64.96 s | |
| Calling variants ... | |
| Total processed positions in : 0 | |
| [93m[WARNING] No full-alignment output for file //tmp/tmp4oiilqtb/job_working_directory/000/8/working/./tmp/full_alignment_output/full_alignment_.vcf[0m | |
| Total time elapsed: 0.00 s | |
| [INFO] No vcf output for file /tmp/tmp4oiilqtb/job_working_directory/000/8/working/./tmp/full_alignment_output/full_alignment_.vcf, remove empty file | |
| real 15m0.166s | |
| user 14m28.466s | |
| sys 0m24.484s | |
| [INFO] 7/7 Merge pileup VCF and full-alignment VCF | |
| [INFO] Pileup variants processed in NC_003197.2: 41286 | |
| [INFO] Full-alignment variants processed in NC_003197.2: 79621 | |
| [INFO] Pileup variants processed in NC_003277.2: 0 | |
| [INFO] Full-alignment variants processed in NC_003277.2: 0 | |
| real 0m2.682s | |
| user 0m2.329s | |
| sys 0m0.264s | |
| [INFO] Finish calling, output file: /tmp/tmp4oiilqtb/job_working_directory/000/8/working/./merge_output.vcf.gz | |
| real 23m52.810s | |
| user 23m12.594s | |
| sys 0m29.657s | |
| ``` | |
| **Traceback:** | |
| * ```console | |
| ``` | |
| **Job Parameters:** | |
| * | Job parameter | Parameter value | | |
| | ------------- | --------------- | | |
| | \_\_input\_ext | ` "input" ` | | |
| | \_\_workflow\_invocation\_uuid\_\_ | ` "2bc979b2114e11f18951000d3a5a8e28" ` | | |
| | adv | ` {"chunk_size": "5000000", "enable_phasing": false, "indel_min_af": "0.15", "no_phasing_for_fa": false, "ploidity_model": "--haploid_precise", "print_ref_calls": false, "qual": "0", "snp_min_af": "0.08"} ` | | |
| | bed\_or\_vcf | ` {"__current_case__": 2, "bed_or_vcf_selector": "unrestricted", "include_all_ctgs": true} ` | | |
| | chromInfo | ` "/tmp/tmp4oiilqtb/galaxy-dev/tool-data/shared/ucsc/chrom/?.len" ` | | |
| | dbkey | ` "?" ` | | |
| | gvcf | ` false ` | | |
| | model\_source | ` {"__current_case__": 0, "select_built_in": "r941_prom_hac_g360+g422", "source": "built-in"} ` | | |
| | ont\_license\_agree | ` false ` | | |
| | output\_files | ` ["full_alignment", "pileup"] ` | | |
| | ref\_source | ` {"__current_case__": 0, "ref_fasta": {"values": [{"id": 4, "src": "hda"}]}, "source": "history"} ` | | |
| - **Job 2:** | |
| * Job state is ok | |
| **Container:** | |
| * ```console | |
| quay.io/biocontainers/clair3:1.0.10--py39hd649744_1 | |
| ``` | |
| **Command Line:** | |
| * ```console | |
| ln -s '/tmp/tmp4oiilqtb/files/d/b/c/dataset_dbcb3ea2-271b-49ae-aa59-5ea11693bd8e.dat' reference.fasta && samtools faidx reference.fasta && ln -s '/tmp/tmp4oiilqtb/files/f/c/0/dataset_fc0c7f8e-e94e-4d7d-86b8-7ed58a4b6d23.dat' input_reads.bam && ln -s '/tmp/tmp4oiilqtb/files/_metadata_files/0/b/7/metadata_0b71067f-c933-44c4-8c32-11ae2e7042d3.dat' input_reads.bai && run_clair3.sh --bam_fn=input_reads.bam --ref_fn=reference.fasta --platform='ont' --model_path=$(dirname $(which run_clair3.sh))/models/r941_prom_hac_g360+g422 --output='.' --threads=${GALAXY_SLOTS:-2} --include_all_ctgs --snp_min_af=0.08 --indel_min_af=0.15 --haploid_precise --chunk_size=5000000 | |
| ``` | |
| **Exit Code:** | |
| * ```console | |
| 0 | |
| ``` | |
| **Standard Output:** | |
| * ```console | |
| [33m[WARNING] No absolute output path provided, using current directory as prefix[0m | |
| [INFO] CLAIR3 VERSION: v1.0.10 | |
| [INFO] BAM FILE PATH: /tmp/tmp4oiilqtb/job_working_directory/000/7/working/input_reads.bam | |
| [INFO] REFERENCE FILE PATH: /tmp/tmp4oiilqtb/job_working_directory/000/7/working/reference.fasta | |
| [INFO] MODEL PATH: /usr/local/bin/models/r941_prom_hac_g360+g422 | |
| [INFO] OUTPUT FOLDER: /tmp/tmp4oiilqtb/job_working_directory/000/7/working/. | |
| [INFO] PLATFORM: ont | |
| [INFO] THREADS: 1 | |
| [INFO] BED FILE PATH: EMPTY | |
| [INFO] VCF FILE PATH: EMPTY | |
| [INFO] CONTIGS: EMPTY | |
| [INFO] CONDA PREFIX: /usr/local | |
| [INFO] SAMTOOLS PATH: samtools | |
| [INFO] PYTHON PATH: python3 | |
| [INFO] PYPY PATH: pypy3 | |
| [INFO] PARALLEL PATH: parallel | |
| [INFO] WHATSHAP PATH: whatshap | |
| [INFO] LONGPHASE PATH: EMPTY | |
| [INFO] CHUNK SIZE: 5000000 | |
| [INFO] FULL ALIGN PROPORTION: 0.7 | |
| [INFO] FULL ALIGN REFERENCE PROPORTION: 0.1 | |
| [INFO] PHASING PROPORTION: 0.7 | |
| [INFO] MINIMUM MQ: 5 | |
| [INFO] MINIMUM COVERAGE: 2 | |
| [INFO] SNP AF THRESHOLD: 0.08 | |
| [INFO] INDEL AF THRESHOLD: 0.15 | |
| [INFO] BASE ERROR IN GVCF: 0.001 | |
| [INFO] GQ BIN SIZE IN GVCF: 5 | |
| [INFO] ENABLE FILEUP ONLY CALLING: False | |
| [INFO] ENABLE FAST MODE CALLING: False | |
| [INFO] ENABLE CALLING SNP CANDIDATES ONLY: False | |
| [INFO] ENABLE PRINTING REFERENCE CALLS: False | |
| [INFO] ENABLE OUTPUT GVCF: False | |
| [INFO] ENABLE HAPLOID PRECISE MODE: True | |
| [INFO] ENABLE HAPLOID SENSITIVE MODE: False | |
| [INFO] ENABLE INCLUDE ALL CTGS CALLING: True | |
| [INFO] ENABLE NO PHASING FOR FULL ALIGNMENT: False | |
| [INFO] ENABLE REMOVING INTERMEDIATE FILES: False | |
| [INFO] ENABLE LONGPHASE FOR INTERMEDIATE VCF PHASING: False | |
| [INFO] ENABLE PHASING FINAL VCF OUTPUT USING WHATSHAP: False | |
| [INFO] ENABLE PHASING FINAL VCF OUTPUT USING LONGPHASE: False | |
| [INFO] ENABLE HAPLOTAGGING FINAL BAM: False | |
| [INFO] ENABLE LONG INDEL CALLING: False | |
| [INFO] ENABLE C_IMPLEMENT: True | |
| + /usr/local/bin/scripts/clair3_c_impl.sh --bam_fn /tmp/tmp4oiilqtb/job_working_directory/000/7/working/input_reads.bam --ref_fn /tmp/tmp4oiilqtb/job_working_directory/000/7/working/reference.fasta --threads 1 --model_path /usr/local/bin/models/r941_prom_hac_g360+g422 --platform ont --output /tmp/tmp4oiilqtb/job_working_directory/000/7/working/. --bed_fn=EMPTY --vcf_fn=EMPTY --ctg_name=EMPTY --sample_name=SAMPLE --chunk_num=0 --chunk_size=5000000 --samtools=samtools --python=python3 --pypy=pypy3 --parallel=parallel --whatshap=whatshap --qual=2 --var_pct_full=0.7 --ref_pct_full=0.1 --var_pct_phasing=0.7 --snp_min_af=0.08 --indel_min_af=0.15 --min_mq=5 --min_coverage=2 --min_contig_size=0 --pileup_only=False --gvcf=False --base_err=0.001 --gq_bin_size=5 --fast_mode=False --call_snp_only=False --print_ref_calls=False --haploid_precise=True --haploid_sensitive=False --include_all_ctgs=True --no_phasing_for_fa=False --pileup_model_prefix=pileup --fa_model_prefix=full_alignment --remove_intermediate_dir=False --enable_phasing=False --enable_long_indel=False --keep_iupac_bases=False --use_gpu=False --longphase_for_phasing=False --longphase=EMPTY --use_whatshap_for_intermediate_phasing=True --use_longphase_for_intermediate_phasing=False --use_whatshap_for_final_output_phasing=False --use_longphase_for_final_output_phasing=False --use_whatshap_for_final_output_haplotagging=False | |
| [INFO] Check environment variables | |
| [INFO] Create folder /tmp/tmp4oiilqtb/job_working_directory/000/7/working/log | |
| [INFO] Create folder /tmp/tmp4oiilqtb/job_working_directory/000/7/working/tmp/pileup_output | |
| [INFO] Create folder /tmp/tmp4oiilqtb/job_working_directory/000/7/working/tmp/merge_output | |
| [INFO] Create folder /tmp/tmp4oiilqtb/job_working_directory/000/7/working/tmp/phase_output | |
| [INFO] Create folder /tmp/tmp4oiilqtb/job_working_directory/000/7/working/tmp/gvcf_tmp_output | |
| [INFO] Create folder /tmp/tmp4oiilqtb/job_working_directory/000/7/working/tmp/full_alignment_output | |
| [INFO] Create folder /tmp/tmp4oiilqtb/job_working_directory/000/7/working/tmp/phase_output/phase_vcf | |
| [INFO] Create folder /tmp/tmp4oiilqtb/job_working_directory/000/7/working/tmp/phase_output/phase_bam | |
| [INFO] Create folder /tmp/tmp4oiilqtb/job_working_directory/000/7/working/tmp/full_alignment_output/candidate_bed | |
| [INFO] --include_all_ctgs enabled | |
| [93m[WARNING] Please enable --no_phasing_for_fa if calling variant in non-diploid organisms[0m | |
| [INFO] Call variant in contigs: NC_003277.2 NC_003197.2 | |
| [INFO] Chunk number for each contig: 1 1 | |
| [INFO] 1/7 Call variants using pileup model | |
| Calling variants ... | |
| Total processed positions in NC_003277.2 (chunk 1/1) : 9577 | |
| Total time elapsed: 16.63 s | |
| Calling variants ... | |
| Total processed positions in NC_003197.2 (chunk 1/1) : 523632 | |
| Total time elapsed: 723.35 s | |
| real 12m26.453s | |
| user 12m17.477s | |
| sys 0m4.885s | |
| [INFO] 2/7 Select heterozygous SNP variants for Whatshap phasing and haplotagging | |
| [INFO] Select heterozygous pileup variants exceeding phasing quality cutoff 7 | |
| [INFO] Total heterozygous SNP positions selected: NC_003277.2: 449 | |
| [INFO] Total heterozygous SNP positions selected: NC_003197.2: 64421 | |
| real 0m1.990s | |
| user 0m1.430s | |
| sys 0m0.156s | |
| [INFO] 3/7 Phase VCF file using Whatshap | |
| This is WhatsHap 1.7 running under Python 3.9.0 | |
| Working on 1 sample from 1 family | |
| # Working on contig NC_003277.2 in individual SAMPLE | |
| Found 449 usable heterozygous variants (0 skipped due to missing genotypes) | |
| Found 69 reads covering 449 variants | |
| Kept 61 reads that cover at least two variants each | |
| Selected 61 most phase-informative reads covering 449 variants | |
| Phasing 1 sample by solving the MEC problem ... | |
| Largest block contains 314 variants (69.9% of accessible variants) between position 64728 and 79939 | |
| # Resource usage | |
| Maximum memory usage: 0.039 GB | |
| Time spent reading BAM/CRAM: 0.0 s | |
| Time spent parsing VCF: 0.0 s | |
| Time spent selecting reads: 0.0 s | |
| Time spent phasing: 0.0 s | |
| Time spent writing VCF: 0.0 s | |
| Time spent finding components: 0.0 s | |
| Time spent on rest: 0.0 s | |
| Total elapsed time: 0.1 s | |
| This is WhatsHap 1.7 running under Python 3.9.0 | |
| Working on 1 sample from 1 family | |
| # Working on contig NC_003197.2 in individual SAMPLE | |
| Found 64421 usable heterozygous variants (0 skipped due to missing genotypes) | |
| Found 2271 reads covering 64418 variants | |
| Kept 1985 reads that cover at least two variants each | |
| Selected 1985 most phase-informative reads covering 64395 variants | |
| Phasing 1 sample by solving the MEC problem ... | |
| Largest block contains 8961 variants (13.9% of accessible variants) between position 2523235 and 2635600 | |
| Changed 32 genotypes while writing VCF | |
| # Resource usage | |
| Maximum memory usage: 0.167 GB | |
| Time spent reading BAM/CRAM: 3.6 s | |
| Time spent parsing VCF: 1.0 s | |
| Time spent selecting reads: 1.0 s | |
| Time spent phasing: 0.5 s | |
| Time spent writing VCF: 1.4 s | |
| Time spent finding components: 0.6 s | |
| Time spent on rest: 1.4 s | |
| Total elapsed time: 9.5 s | |
| real 0m10.691s | |
| user 0m10.383s | |
| sys 0m0.265s | |
| [INFO] 5/7 Select candidates for full-alignment calling | |
| [INFO] Set variants quality cutoff 10.0 | |
| [INFO] Set reference calls quality cutoff 7.0 | |
| [INFO] Low quality reference calls to be processed in NC_003277.2: 388 | |
| [INFO] Low quality variants to be processed in NC_003277.2: 484 | |
| [INFO] Low quality reference calls to be processed in NC_003197.2: 41432 | |
| [INFO] Low quality variants to be processed in NC_003197.2: 78699 | |
| real 0m1.951s | |
| user 0m1.359s | |
| sys 0m0.196s | |
| [INFO] 6/7 Call low-quality variants using full-alignment model | |
| Calling variants ... | |
| Total processed positions in NC_003197.2 (chunk 1/13) : 10000 | |
| Total time elapsed: 64.21 s | |
| Calling variants ... | |
| Total processed positions in NC_003197.2 (chunk 2/13) : 10000 | |
| Total time elapsed: 64.68 s | |
| Calling variants ... | |
| Total processed positions in NC_003197.2 (chunk 3/13) : 10000 | |
| Total time elapsed: 64.07 s | |
| Calling variants ... | |
| Total processed positions in NC_003197.2 (chunk 4/13) : 10000 | |
| Total time elapsed: 64.08 s | |
| Calling variants ... | |
| Total processed positions in NC_003197.2 (chunk 5/13) : 10000 | |
| Total time elapsed: 64.58 s | |
| Calling variants ... | |
| Total processed positions in NC_003197.2 (chunk 6/13) : 10000 | |
| Total time elapsed: 64.78 s | |
| Calling variants ... | |
| Total processed positions in NC_003197.2 (chunk 7/13) : 10000 | |
| Total time elapsed: 64.50 s | |
| Calling variants ... | |
| Total processed positions in NC_003197.2 (chunk 8/13) : 10000 | |
| Total time elapsed: 64.27 s | |
| Calling variants ... | |
| Total processed positions in NC_003197.2 (chunk 9/13) : 10000 | |
| Total time elapsed: 66.21 s | |
| Calling variants ... | |
| Total processed positions in NC_003197.2 (chunk 10/13) : 10000 | |
| Total time elapsed: 65.27 s | |
| Calling variants ... | |
| Total processed positions in NC_003197.2 (chunk 11/13) : 10000 | |
| Total time elapsed: 69.78 s | |
| Calling variants ... | |
| Total processed positions in NC_003197.2 (chunk 12/13) : 10000 | |
| Total time elapsed: 63.48 s | |
| Calling variants ... | |
| Total processed positions in NC_003197.2 (chunk 13/13) : 131 | |
| Total time elapsed: 1.65 s | |
| Calling variants ... | |
| Total processed positions in NC_003277.2 (chunk 1/1) : 872 | |
| Total time elapsed: 6.16 s | |
| real 13m45.232s | |
| user 13m10.302s | |
| sys 0m22.962s | |
| [INFO] 7/7 Merge pileup VCF and full-alignment VCF | |
| [INFO] Pileup variants processed in NC_003277.2: 206 | |
| [INFO] Full-alignment variants processed in NC_003277.2: 112 | |
| [INFO] Pileup variants processed in NC_003197.2: 33781 | |
| [INFO] Full-alignment variants processed in NC_003197.2: 25310 | |
| real 0m2.477s | |
| user 0m2.214s | |
| sys 0m0.212s | |
| [INFO] Finish calling, output file: /tmp/tmp4oiilqtb/job_working_directory/000/7/working/./merge_output.vcf.gz | |
| real 26m33.880s | |
| user 25m47.396s | |
| sys 0m29.477s | |
| ``` | |
| **Traceback:** | |
| * ```console | |
| ``` | |
| **Job Parameters:** | |
| * | Job parameter | Parameter value | | |
| | ------------- | --------------- | | |
| | \_\_input\_ext | ` "input" ` | | |
| | \_\_workflow\_invocation\_uuid\_\_ | ` "2bc979b2114e11f18951000d3a5a8e28" ` | | |
| | adv | ` {"chunk_size": "5000000", "enable_phasing": false, "indel_min_af": "0.15", "no_phasing_for_fa": false, "ploidity_model": "--haploid_precise", "print_ref_calls": false, "qual": "0", "snp_min_af": "0.08"} ` | | |
| | bed\_or\_vcf | ` {"__current_case__": 2, "bed_or_vcf_selector": "unrestricted", "include_all_ctgs": true} ` | | |
| | chromInfo | ` "/tmp/tmp4oiilqtb/galaxy-dev/tool-data/shared/ucsc/chrom/?.len" ` | | |
| | dbkey | ` "?" ` | | |
| | gvcf | ` false ` | | |
| | model\_source | ` {"__current_case__": 0, "select_built_in": "r941_prom_hac_g360+g422", "source": "built-in"} ` | | |
| | ont\_license\_agree | ` false ` | | |
| | output\_files | ` ["full_alignment", "pileup"] ` | | |
| | ref\_source | ` {"__current_case__": 0, "ref_fasta": {"values": [{"id": 4, "src": "hda"}]}, "source": "history"} ` | | |
| </details> | |
| - **Step 7: Unlabelled step (toolshed.g2.bx.psu.edu/repos/iuc/samtools\_depth/samtools\_depth/1.15.1+galaxy2)**: | |
| * step_state: scheduled | |
| * <details><summary>Jobs</summary> | |
| - **Job 1:** | |
| * Job state is ok | |
| **Container:** | |
| * ```console | |
| quay.io/biocontainers/samtools:1.15.1--h6899075_1 | |
| ``` | |
| **Command Line:** | |
| * ```console | |
| ln -s '/tmp/tmp4oiilqtb/files/f/c/0/dataset_fc0c7f8e-e94e-4d7d-86b8-7ed58a4b6d23.dat' '0' && ln -s '/tmp/tmp4oiilqtb/files/_metadata_files/0/b/7/metadata_0b71067f-c933-44c4-8c32-11ae2e7042d3.dat' '0.bai' && ln -s '/tmp/tmp4oiilqtb/files/2/b/4/dataset_2b421f1d-a959-4de8-9e45-52a9e14685f1.dat' '1' && ln -s '/tmp/tmp4oiilqtb/files/_metadata_files/9/c/c/metadata_9cc8d4ee-94b6-4565-918a-7cfbb42d0cda.dat' '1.bai' && samtools depth 0 1 -g 0 -G 1796 > '/tmp/tmp4oiilqtb/job_working_directory/000/9/outputs/dataset_6e8c2fbc-bdde-45a0-a014-f76dcf958ba7.dat' | |
| ``` | |
| **Exit Code:** | |
| * ```console | |
| 0 | |
| ``` | |
| **Traceback:** | |
| * ```console | |
| ``` | |
| **Job Parameters:** | |
| * | Job parameter | Parameter value | | |
| | ------------- | --------------- | | |
| | \_\_input\_ext | ` "input" ` | | |
| | \_\_workflow\_invocation\_uuid\_\_ | ` "2bc979b2114e11f18951000d3a5a8e28" ` | | |
| | additional\_options | ` {"deletions": false, "required_flags": null, "single_read": false, "skipped_flags": ["4", "256", "512", "1024"]} ` | | |
| | all | ` "" ` | | |
| | basequality | ` None ` | | |
| | chromInfo | ` "/tmp/tmp4oiilqtb/galaxy-dev/tool-data/shared/ucsc/chrom/?.len" ` | | |
| | cond\_region | ` {"__current_case__": 0, "select_region": "no"} ` | | |
| | dbkey | ` "?" ` | | |
| | mapquality | ` None ` | | |
| | maxdepth | ` None ` | | |
| | minlength | ` None ` | | |
| | output\_options | ` {"header": false} ` | | |
| </details> | |
| - **Step 8: Unlabelled step (toolshed.g2.bx.psu.edu/repos/iuc/samtools\_coverage/samtools\_coverage/1.15.1+galaxy2)**: | |
| * step_state: scheduled | |
| * <details><summary>Jobs</summary> | |
| - **Job 1:** | |
| * Job state is ok | |
| **Container:** | |
| * ```console | |
| quay.io/biocontainers/samtools:1.15.1--h6899075_1 | |
| ``` | |
| **Command Line:** | |
| * ```console | |
| ln -s '/tmp/tmp4oiilqtb/files/2/b/4/dataset_2b421f1d-a959-4de8-9e45-52a9e14685f1.dat' infile && ln -s '/tmp/tmp4oiilqtb/files/_metadata_files/9/c/c/metadata_9cc8d4ee-94b6-4565-918a-7cfbb42d0cda.dat' infile.bai && samtools coverage infile -l 0 -q 0 -Q 0 --rf 0 --ff 1796 -o '/tmp/tmp4oiilqtb/job_working_directory/000/11/outputs/dataset_57f10e24-6630-49ab-956c-32626b2e46cd.dat' | |
| ``` | |
| **Exit Code:** | |
| * ```console | |
| 0 | |
| ``` | |
| **Traceback:** | |
| * ```console | |
| ``` | |
| **Job Parameters:** | |
| * | Job parameter | Parameter value | | |
| | ------------- | --------------- | | |
| | \_\_input\_ext | ` "input" ` | | |
| | \_\_workflow\_invocation\_uuid\_\_ | ` "2bc979b2114e11f18951000d3a5a8e28" ` | | |
| | additional\_options | ` {"min_bq": "0", "min_mq": "0", "min_read_length": "0", "region": "", "required_flags": null, "skipped_flags": ["4", "256", "512", "1024"]} ` | | |
| | chromInfo | ` "/tmp/tmp4oiilqtb/galaxy-dev/tool-data/shared/ucsc/chrom/?.len" ` | | |
| | condition\_histogram | ` {"__current_case__": 1, "histogram_select": "no"} ` | | |
| | condition\_input | ` {"__current_case__": 0, "input": {"values": [{"id": 4, "src": "dce"}]}, "input_pooling": "No"} ` | | |
| | dbkey | ` "?" ` | | |
| - **Job 2:** | |
| * Job state is ok | |
| **Container:** | |
| * ```console | |
| quay.io/biocontainers/samtools:1.15.1--h6899075_1 | |
| ``` | |
| **Command Line:** | |
| * ```console | |
| ln -s '/tmp/tmp4oiilqtb/files/f/c/0/dataset_fc0c7f8e-e94e-4d7d-86b8-7ed58a4b6d23.dat' infile && ln -s '/tmp/tmp4oiilqtb/files/_metadata_files/0/b/7/metadata_0b71067f-c933-44c4-8c32-11ae2e7042d3.dat' infile.bai && samtools coverage infile -l 0 -q 0 -Q 0 --rf 0 --ff 1796 -o '/tmp/tmp4oiilqtb/job_working_directory/000/10/outputs/dataset_3700d45d-f18d-4c20-b3c0-f6c739056b39.dat' | |
| ``` | |
| **Exit Code:** | |
| * ```console | |
| 0 | |
| ``` | |
| **Traceback:** | |
| * ```console | |
| ``` | |
| **Job Parameters:** | |
| * | Job parameter | Parameter value | | |
| | ------------- | --------------- | | |
| | \_\_input\_ext | ` "input" ` | | |
| | \_\_workflow\_invocation\_uuid\_\_ | ` "2bc979b2114e11f18951000d3a5a8e28" ` | | |
| | additional\_options | ` {"min_bq": "0", "min_mq": "0", "min_read_length": "0", "region": "", "required_flags": null, "skipped_flags": ["4", "256", "512", "1024"]} ` | | |
| | chromInfo | ` "/tmp/tmp4oiilqtb/galaxy-dev/tool-data/shared/ucsc/chrom/?.len" ` | | |
| | condition\_histogram | ` {"__current_case__": 1, "histogram_select": "no"} ` | | |
| | condition\_input | ` {"__current_case__": 0, "input": {"values": [{"id": 3, "src": "dce"}]}, "input_pooling": "No"} ` | | |
| | dbkey | ` "?" ` | | |
| </details> | |
| - **Step 9: Unlabelled step (toolshed.g2.bx.psu.edu/repos/iuc/bcftools\_norm/bcftools\_norm/1.15.1+galaxy4)**: | |
| * step_state: scheduled | |
| * <details><summary>Jobs</summary> | |
| - **Job 1:** | |
| * Job state is ok | |
| **Container:** | |
| * ```console | |
| quay.io/biocontainers/mulled-v2-03d30cf7bcc23ba5d755e498a98359af8a2cd947:7b1ad5dbd0ee31d66967a1f20b4d8cd630dcec00-0 | |
| ``` | |
| **Command Line:** | |
| * ```console | |
| export BCFTOOLS_PLUGINS=`which bcftools | sed 's,bin/bcftools,libexec/bcftools,'`; ln -s '/tmp/tmp4oiilqtb/files/3/7/4/dataset_374358de-b58e-4dee-9f15-d1c74ad9cdf0.dat' input.vcf.gz && ln -s '/tmp/tmp4oiilqtb/files/_metadata_files/c/a/b/metadata_cab504d6-b070-47c0-956a-111a7ecfaaf2.dat' input.vcf.gz.tbi && ln -s '/tmp/tmp4oiilqtb/files/d/b/c/dataset_dbcb3ea2-271b-49ae-aa59-5ea11693bd8e.dat' ref.fa && samtools faidx ref.fa && awk '{ if ($0 !~ />/) {print toupper($0)} else {print $0} }' 'ref.fa' > ref_upper.fa && bcftools norm --fasta-ref ref_upper.fa --check-ref w --do-not-normalize --site-win 1000 --output-type 'v' --threads ${GALAXY_SLOTS:-4} input.vcf.gz > '/tmp/tmp4oiilqtb/job_working_directory/000/13/outputs/dataset_c5f12df5-b6aa-43ac-bacf-910dd5b1e275.dat' | |
| ``` | |
| **Exit Code:** | |
| * ```console | |
| 0 | |
| ``` | |
| **Standard Error:** | |
| * ```console | |
| Lines total/split/realigned/skipped: 100832/0/0/0 | |
| ``` | |
| **Traceback:** | |
| * ```console | |
| ``` | |
| **Job Parameters:** | |
| * | Job parameter | Parameter value | | |
| | ------------- | --------------- | | |
| | \_\_input\_ext | ` "input" ` | | |
| | \_\_workflow\_invocation\_uuid\_\_ | ` "2bc979b2114e11f18951000d3a5a8e28" ` | | |
| | atomize | ` false ` | | |
| | check\_ref | ` "w" ` | | |
| | chromInfo | ` "/tmp/tmp4oiilqtb/galaxy-dev/tool-data/shared/ucsc/chrom/?.len" ` | | |
| | dbkey | ` "?" ` | | |
| | multiallelics | ` {"__current_case__": 0, "mode": ""} ` | | |
| | normalize\_indels | ` false ` | | |
| | old\_rec\_tag | ` "" ` | | |
| | output\_type | ` "v" ` | | |
| | reference\_source | ` {"__current_case__": 1, "fasta_ref": {"values": [{"id": 4, "src": "hda"}]}, "reference_source_selector": "history"} ` | | |
| | rm\_dup | ` "" ` | | |
| | sec\_default | ` {"site_win": "1000"} ` | | |
| | sec\_restrict | ` {"regions": {"__current_case__": 0, "regions_src": "__none__"}, "regions_overlap": null, "targets": {"__current_case__": 0, "targets_src": "__none__"}, "targets_overlap": null} ` | | |
| - **Job 2:** | |
| * Job state is ok | |
| **Container:** | |
| * ```console | |
| quay.io/biocontainers/mulled-v2-03d30cf7bcc23ba5d755e498a98359af8a2cd947:7b1ad5dbd0ee31d66967a1f20b4d8cd630dcec00-0 | |
| ``` | |
| **Command Line:** | |
| * ```console | |
| export BCFTOOLS_PLUGINS=`which bcftools | sed 's,bin/bcftools,libexec/bcftools,'`; ln -s '/tmp/tmp4oiilqtb/files/8/7/d/dataset_87db06ba-eac4-4454-b301-a5e83f4ce1b3.dat' input.vcf.gz && ln -s '/tmp/tmp4oiilqtb/files/_metadata_files/b/6/f/metadata_b6fb8f50-0332-4c2f-a342-cfd5c8380995.dat' input.vcf.gz.tbi && ln -s '/tmp/tmp4oiilqtb/files/d/b/c/dataset_dbcb3ea2-271b-49ae-aa59-5ea11693bd8e.dat' ref.fa && samtools faidx ref.fa && awk '{ if ($0 !~ />/) {print toupper($0)} else {print $0} }' 'ref.fa' > ref_upper.fa && bcftools norm --fasta-ref ref_upper.fa --check-ref w --do-not-normalize --site-win 1000 --output-type 'v' --threads ${GALAXY_SLOTS:-4} input.vcf.gz > '/tmp/tmp4oiilqtb/job_working_directory/000/12/outputs/dataset_0b2a7f52-c4e1-43a7-9237-8ae82cda2024.dat' | |
| ``` | |
| **Exit Code:** | |
| * ```console | |
| 0 | |
| ``` | |
| **Standard Error:** | |
| * ```console | |
| Lines total/split/realigned/skipped: 8714/0/0/0 | |
| ``` | |
| **Traceback:** | |
| * ```console | |
| ``` | |
| **Job Parameters:** | |
| * | Job parameter | Parameter value | | |
| | ------------- | --------------- | | |
| | \_\_input\_ext | ` "input" ` | | |
| | \_\_workflow\_invocation\_uuid\_\_ | ` "2bc979b2114e11f18951000d3a5a8e28" ` | | |
| | atomize | ` false ` | | |
| | check\_ref | ` "w" ` | | |
| | chromInfo | ` "/tmp/tmp4oiilqtb/galaxy-dev/tool-data/shared/ucsc/chrom/?.len" ` | | |
| | dbkey | ` "?" ` | | |
| | multiallelics | ` {"__current_case__": 0, "mode": ""} ` | | |
| | normalize\_indels | ` false ` | | |
| | old\_rec\_tag | ` "" ` | | |
| | output\_type | ` "v" ` | | |
| | reference\_source | ` {"__current_case__": 1, "fasta_ref": {"values": [{"id": 4, "src": "hda"}]}, "reference_source_selector": "history"} ` | | |
| | rm\_dup | ` "" ` | | |
| | sec\_default | ` {"site_win": "1000"} ` | | |
| | sec\_restrict | ` {"regions": {"__current_case__": 0, "regions_src": "__none__"}, "regions_overlap": null, "targets": {"__current_case__": 0, "targets_src": "__none__"}, "targets_overlap": null} ` | | |
| </details> | |
| - **Step 10: Unlabelled step (toolshed.g2.bx.psu.edu/repos/bgruening/text\_processing/tp\_cut\_tool/9.5+galaxy0)**: | |
| * step_state: scheduled | |
| * <details><summary>Jobs</summary> | |
| - **Job 1:** | |
| * Job state is ok | |
| **Container:** | |
| * ```console | |
| quay.io/biocontainers/coreutils:9.5 | |
| ``` | |
| **Command Line:** | |
| * ```console | |
| cut --complement -f '1,2' '/tmp/tmp4oiilqtb/files/6/e/8/dataset_6e8c2fbc-bdde-45a0-a014-f76dcf958ba7.dat' > '/tmp/tmp4oiilqtb/job_working_directory/000/14/outputs/dataset_98d7eab3-89fd-419d-bbec-b44fabf8d68a.dat' | |
| ``` | |
| **Exit Code:** | |
| * ```console | |
| 0 | |
| ``` | |
| **Traceback:** | |
| * ```console | |
| ``` | |
| **Job Parameters:** | |
| * | Job parameter | Parameter value | | |
| | ------------- | --------------- | | |
| | \_\_input\_ext | ` "input" ` | | |
| | \_\_workflow\_invocation\_uuid\_\_ | ` "2bc979b2114e11f18951000d3a5a8e28" ` | | |
| | chromInfo | ` "/tmp/tmp4oiilqtb/galaxy-dev/tool-data/shared/ucsc/chrom/?.len" ` | | |
| | complement | ` "--complement" ` | | |
| | cut\_type\_options | ` {"__current_case__": 0, "colnames_option": {"__current_case__": 1, "header": "N", "list": "1,2"}, "cut_element": "-f", "delimiter": ""} ` | | |
| | dbkey | ` "?" ` | | |
| </details> | |
| - **Step 11: Unlabelled step (Remove beginning1)**: | |
| * step_state: scheduled | |
| * <details><summary>Jobs</summary> | |
| - **Job 1:** | |
| * Job state is ok | |
| **Container:** | |
| * ```console | |
| quay.io/biocontainers/coreutils:8.31--h14c3975_0 | |
| ``` | |
| **Command Line:** | |
| * ```console | |
| tail -n '+2' '/tmp/tmp4oiilqtb/files/3/7/0/dataset_3700d45d-f18d-4c20-b3c0-f6c739056b39.dat' > '/tmp/tmp4oiilqtb/job_working_directory/000/15/outputs/dataset_3f741343-6128-425e-8bf2-c549f09aa1a5.dat' | |
| ``` | |
| **Exit Code:** | |
| * ```console | |
| 0 | |
| ``` | |
| **Traceback:** | |
| * ```console | |
| ``` | |
| **Job Parameters:** | |
| * | Job parameter | Parameter value | | |
| | ------------- | --------------- | | |
| | \_\_input\_ext | ` "input" ` | | |
| | \_\_workflow\_invocation\_uuid\_\_ | ` "2bc979b2114e11f18951000d3a5a8e28" ` | | |
| | chromInfo | ` "/tmp/tmp4oiilqtb/galaxy-dev/tool-data/shared/ucsc/chrom/?.len" ` | | |
| | dbkey | ` "?" ` | | |
| | num\_lines | ` "1" ` | | |
| - **Job 2:** | |
| * Job state is ok | |
| **Container:** | |
| * ```console | |
| quay.io/biocontainers/coreutils:8.31--h14c3975_0 | |
| ``` | |
| **Command Line:** | |
| * ```console | |
| tail -n '+2' '/tmp/tmp4oiilqtb/files/5/7/f/dataset_57f10e24-6630-49ab-956c-32626b2e46cd.dat' > '/tmp/tmp4oiilqtb/job_working_directory/000/16/outputs/dataset_c5dbee66-5e25-4cfb-b1de-6bfdd7ea940d.dat' | |
| ``` | |
| **Exit Code:** | |
| * ```console | |
| 0 | |
| ``` | |
| **Traceback:** | |
| * ```console | |
| ``` | |
| **Job Parameters:** | |
| * | Job parameter | Parameter value | | |
| | ------------- | --------------- | | |
| | \_\_input\_ext | ` "input" ` | | |
| | \_\_workflow\_invocation\_uuid\_\_ | ` "2bc979b2114e11f18951000d3a5a8e28" ` | | |
| | chromInfo | ` "/tmp/tmp4oiilqtb/galaxy-dev/tool-data/shared/ucsc/chrom/?.len" ` | | |
| | dbkey | ` "?" ` | | |
| | num\_lines | ` "1" ` | | |
| </details> | |
| - **Step 12: Unlabelled step (toolshed.g2.bx.psu.edu/repos/iuc/snpsift/snpSift\_filter/4.3+t.galaxy1)**: | |
| * step_state: scheduled | |
| * <details><summary>Jobs</summary> | |
| - **Job 1:** | |
| * Job state is ok | |
| **Container:** | |
| * ```console | |
| quay.io/biocontainers/mulled-v2-76138fae381092ad1f9b99bff152a05bded7f84e:73b2e0c1767e24516c39639e6a0c3b063e927522-0 | |
| ``` | |
| **Command Line:** | |
| * ```console | |
| SnpSift -Xmx6G filter -f '/tmp/tmp4oiilqtb/files/c/5/f/dataset_c5f12df5-b6aa-43ac-bacf-910dd5b1e275.dat' -e '/tmp/tmp4oiilqtb/job_working_directory/000/18/configs/tmpf5dy2o9t' > '/tmp/tmp4oiilqtb/job_working_directory/000/18/outputs/dataset_f599ef16-4839-472b-9198-073ed9395df3.dat' | |
| ``` | |
| **Exit Code:** | |
| * ```console | |
| 0 | |
| ``` | |
| **Traceback:** | |
| * ```console | |
| ``` | |
| **Job Parameters:** | |
| * | Job parameter | Parameter value | | |
| | ------------- | --------------- | | |
| | \_\_input\_ext | ` "vcf" ` | | |
| | \_\_workflow\_invocation\_uuid\_\_ | ` "2bc979b2114e11f18951000d3a5a8e28" ` | | |
| | chromInfo | ` "/tmp/tmp4oiilqtb/galaxy-dev/tool-data/shared/ucsc/chrom/?.len" ` | | |
| | dbkey | ` "?" ` | | |
| | filter\_expression | ` {"__current_case__": 0, "expr": "(QUAL > 2)", "type": "simple"} ` | | |
| | filtering | ` {"__current_case__": 0, "mode": "entries"} ` | | |
| | inverse | ` false ` | | |
| - **Job 2:** | |
| * Job state is ok | |
| **Container:** | |
| * ```console | |
| quay.io/biocontainers/mulled-v2-76138fae381092ad1f9b99bff152a05bded7f84e:73b2e0c1767e24516c39639e6a0c3b063e927522-0 | |
| ``` | |
| **Command Line:** | |
| * ```console | |
| SnpSift -Xmx6G filter -f '/tmp/tmp4oiilqtb/files/0/b/2/dataset_0b2a7f52-c4e1-43a7-9237-8ae82cda2024.dat' -e '/tmp/tmp4oiilqtb/job_working_directory/000/17/configs/tmpur9uhmmi' > '/tmp/tmp4oiilqtb/job_working_directory/000/17/outputs/dataset_29d44ead-c37d-45f7-8d0b-e0f34f95f250.dat' | |
| ``` | |
| **Exit Code:** | |
| * ```console | |
| 0 | |
| ``` | |
| **Traceback:** | |
| * ```console | |
| ``` | |
| **Job Parameters:** | |
| * | Job parameter | Parameter value | | |
| | ------------- | --------------- | | |
| | \_\_input\_ext | ` "vcf" ` | | |
| | \_\_workflow\_invocation\_uuid\_\_ | ` "2bc979b2114e11f18951000d3a5a8e28" ` | | |
| | chromInfo | ` "/tmp/tmp4oiilqtb/galaxy-dev/tool-data/shared/ucsc/chrom/?.len" ` | | |
| | dbkey | ` "?" ` | | |
| | filter\_expression | ` {"__current_case__": 0, "expr": "(QUAL > 2)", "type": "simple"} ` | | |
| | filtering | ` {"__current_case__": 0, "mode": "entries"} ` | | |
| | inverse | ` false ` | | |
| </details> | |
| - **Step 13: Unlabelled step (toolshed.g2.bx.psu.edu/repos/iuc/table\_compute/table\_compute/1.2.4+galaxy1)**: | |
| * step_state: scheduled | |
| * <details><summary>Jobs</summary> | |
| - **Job 1:** | |
| * Job state is ok | |
| **Container:** | |
| * ```console | |
| quay.io/biocontainers/mulled-v2-344874846f44224e5f0b7b741eacdddffe895d1e:d3fff24ee1297b4c3bcef48354c2a30f0c82007a-2 | |
| ``` | |
| **Command Line:** | |
| * ```console | |
| cp '/tmp/tmp4oiilqtb/job_working_directory/000/19/configs/tmp3b5y9p11' ./userconfig.py && cp '/tmp/shed_dir/toolshed.g2.bx.psu.edu/repos/iuc/table_compute/56a8da1f2243/table_compute/scripts/safety.py' ./safety.py && cp '/tmp/shed_dir/toolshed.g2.bx.psu.edu/repos/iuc/table_compute/56a8da1f2243/table_compute/scripts/table_compute.py' ./table_compute.py && python ./table_compute.py | |
| ``` | |
| **Exit Code:** | |
| * ```console | |
| 0 | |
| ``` | |
| **Traceback:** | |
| * ```console | |
| ``` | |
| **Job Parameters:** | |
| * | Job parameter | Parameter value | | |
| | ------------- | --------------- | | |
| | \_\_input\_ext | ` "tabular" ` | | |
| | \_\_workflow\_invocation\_uuid\_\_ | ` "2bc979b2114e11f18951000d3a5a8e28" ` | | |
| | chromInfo | ` "/tmp/tmp4oiilqtb/galaxy-dev/tool-data/shared/ucsc/chrom/?.len" ` | | |
| | dbkey | ` "?" ` | | |
| | out\_opts | ` ["ignore_nas"] ` | | |
| | precision | ` "2" ` | | |
| | singtabop | ` {"__current_case__": 0, "adv": {"header": null, "nrows": null, "skip_blank_lines": true, "skipfooter": null}, "col_row_names": null, "input": {"values": [{"id": 18, "src": "hda"}]}, "use_type": "single", "user": {"__current_case__": 3, "dimension": "0", "matrixapply_func": {"__current_case__": 6, "vector_op": "mean"}, "mode": "matrixapply"}} ` | | |
| </details> | |
| - **Step 14: Unlabelled step (Cut1)**: | |
| * step_state: scheduled | |
| * <details><summary>Jobs</summary> | |
| - **Job 1:** | |
| * Job state is ok | |
| **Container:** | |
| * ```console | |
| quay.io/biocontainers/perl:5.26--2 | |
| ``` | |
| **Command Line:** | |
| * ```console | |
| perl '/tmp/tmp4oiilqtb/galaxy-dev/tools/filters/cutWrapper.pl' '/tmp/tmp4oiilqtb/files/3/f/7/dataset_3f741343-6128-425e-8bf2-c549f09aa1a5.dat' 'c6' T '/tmp/tmp4oiilqtb/job_working_directory/000/20/outputs/dataset_b592b0bb-a40e-4242-826d-84d1d81d9432.dat' | |
| ``` | |
| **Exit Code:** | |
| * ```console | |
| 0 | |
| ``` | |
| **Traceback:** | |
| * ```console | |
| ``` | |
| **Job Parameters:** | |
| * | Job parameter | Parameter value | | |
| | ------------- | --------------- | | |
| | \_\_input\_ext | ` "tabular" ` | | |
| | \_\_workflow\_invocation\_uuid\_\_ | ` "2bc979b2114e11f18951000d3a5a8e28" ` | | |
| | chromInfo | ` "/tmp/tmp4oiilqtb/galaxy-dev/tool-data/shared/ucsc/chrom/?.len" ` | | |
| | columnList | ` "c6" ` | | |
| | dbkey | ` "?" ` | | |
| | delimiter | ` "T" ` | | |
| - **Job 2:** | |
| * Job state is ok | |
| **Container:** | |
| * ```console | |
| quay.io/biocontainers/perl:5.26--2 | |
| ``` | |
| **Command Line:** | |
| * ```console | |
| perl '/tmp/tmp4oiilqtb/galaxy-dev/tools/filters/cutWrapper.pl' '/tmp/tmp4oiilqtb/files/c/5/d/dataset_c5dbee66-5e25-4cfb-b1de-6bfdd7ea940d.dat' 'c6' T '/tmp/tmp4oiilqtb/job_working_directory/000/21/outputs/dataset_63aa38db-ef4e-47eb-a8c2-959abf4797dc.dat' | |
| ``` | |
| **Exit Code:** | |
| * ```console | |
| 0 | |
| ``` | |
| **Traceback:** | |
| * ```console | |
| ``` | |
| **Job Parameters:** | |
| * | Job parameter | Parameter value | | |
| | ------------- | --------------- | | |
| | \_\_input\_ext | ` "tabular" ` | | |
| | \_\_workflow\_invocation\_uuid\_\_ | ` "2bc979b2114e11f18951000d3a5a8e28" ` | | |
| | chromInfo | ` "/tmp/tmp4oiilqtb/galaxy-dev/tool-data/shared/ucsc/chrom/?.len" ` | | |
| | columnList | ` "c6" ` | | |
| | dbkey | ` "?" ` | | |
| | delimiter | ` "T" ` | | |
| </details> | |
| - **Step 15: Unlabelled step (toolshed.g2.bx.psu.edu/repos/iuc/snpsift/snpSift\_extractFields/4.3+t.galaxy0)**: | |
| * step_state: scheduled | |
| * <details><summary>Jobs</summary> | |
| - **Job 1:** | |
| * Job state is ok | |
| **Container:** | |
| * ```console | |
| quay.io/biocontainers/mulled-v2-76138fae381092ad1f9b99bff152a05bded7f84e:73b2e0c1767e24516c39639e6a0c3b063e927522-0 | |
| ``` | |
| **Command Line:** | |
| * ```console | |
| if [ -z "$SNPSIFT_JAR_PATH" ]; then export SNPSIFT_JAR_PATH=$(dirname $(readlink -e $(which SnpSift))); fi && cat '/tmp/tmp4oiilqtb/files/2/9/d/dataset_29d44ead-c37d-45f7-8d0b-e0f34f95f250.dat' | SnpSift -Xmx6G extractFields - "CHROM" "POS" "ID" "REF" "ALT" "FILTER"> '/tmp/tmp4oiilqtb/job_working_directory/000/22/outputs/dataset_19460b34-70a3-4d38-9852-d2ccaa473fd3.dat' | |
| ``` | |
| **Exit Code:** | |
| * ```console | |
| 0 | |
| ``` | |
| **Traceback:** | |
| * ```console | |
| ``` | |
| **Job Parameters:** | |
| * | Job parameter | Parameter value | | |
| | ------------- | --------------- | | |
| | \_\_input\_ext | ` "vcf" ` | | |
| | \_\_workflow\_invocation\_uuid\_\_ | ` "2bc979b2114e11f18951000d3a5a8e28" ` | | |
| | chromInfo | ` "/tmp/tmp4oiilqtb/galaxy-dev/tool-data/shared/ucsc/chrom/?.len" ` | | |
| | dbkey | ` "?" ` | | |
| | empty\_text | ` "" ` | | |
| | extract | ` "CHROM POS ID REF ALT FILTER" ` | | |
| | one\_effect\_per\_line | ` false ` | | |
| | separator | ` "" ` | | |
| - **Job 2:** | |
| * Job state is ok | |
| **Container:** | |
| * ```console | |
| quay.io/biocontainers/mulled-v2-76138fae381092ad1f9b99bff152a05bded7f84e:73b2e0c1767e24516c39639e6a0c3b063e927522-0 | |
| ``` | |
| **Command Line:** | |
| * ```console | |
| if [ -z "$SNPSIFT_JAR_PATH" ]; then export SNPSIFT_JAR_PATH=$(dirname $(readlink -e $(which SnpSift))); fi && cat '/tmp/tmp4oiilqtb/files/f/5/9/dataset_f599ef16-4839-472b-9198-073ed9395df3.dat' | SnpSift -Xmx6G extractFields - "CHROM" "POS" "ID" "REF" "ALT" "FILTER"> '/tmp/tmp4oiilqtb/job_working_directory/000/23/outputs/dataset_fa00650e-b77e-43b0-971f-1805235abc43.dat' | |
| ``` | |
| **Exit Code:** | |
| * ```console | |
| 0 | |
| ``` | |
| **Traceback:** | |
| * ```console | |
| ``` | |
| **Job Parameters:** | |
| * | Job parameter | Parameter value | | |
| | ------------- | --------------- | | |
| | \_\_input\_ext | ` "vcf" ` | | |
| | \_\_workflow\_invocation\_uuid\_\_ | ` "2bc979b2114e11f18951000d3a5a8e28" ` | | |
| | chromInfo | ` "/tmp/tmp4oiilqtb/galaxy-dev/tool-data/shared/ucsc/chrom/?.len" ` | | |
| | dbkey | ` "?" ` | | |
| | empty\_text | ` "" ` | | |
| | extract | ` "CHROM POS ID REF ALT FILTER" ` | | |
| | one\_effect\_per\_line | ` false ` | | |
| | separator | ` "" ` | | |
| </details> | |
| - **Step 16: Unlabelled step (toolshed.g2.bx.psu.edu/repos/iuc/bcftools\_consensus/bcftools\_consensus/1.15.1+galaxy4)**: | |
| * step_state: scheduled | |
| * <details><summary>Jobs</summary> | |
| - **Job 1:** | |
| * Job state is ok | |
| **Container:** | |
| * ```console | |
| quay.io/biocontainers/mulled-v2-03d30cf7bcc23ba5d755e498a98359af8a2cd947:7b1ad5dbd0ee31d66967a1f20b4d8cd630dcec00-0 | |
| ``` | |
| **Command Line:** | |
| * ```console | |
| export BCFTOOLS_PLUGINS=`which bcftools | sed 's,bin/bcftools,libexec/bcftools,'`; bgzip -c '/tmp/tmp4oiilqtb/files/2/9/d/dataset_29d44ead-c37d-45f7-8d0b-e0f34f95f250.dat' > input.vcf.gz && bcftools index input.vcf.gz && ln -s '/tmp/tmp4oiilqtb/files/d/b/c/dataset_dbcb3ea2-271b-49ae-aa59-5ea11693bd8e.dat' ref.fa && samtools faidx ref.fa && bcftools consensus --fasta-ref ref.fa --output '/tmp/tmp4oiilqtb/job_working_directory/000/24/outputs/dataset_eb3b2bbe-bbe9-402d-b164-f7d2dd303653.dat' input.vcf.gz | |
| ``` | |
| **Exit Code:** | |
| * ```console | |
| 0 | |
| ``` | |
| **Standard Error:** | |
| * ```console | |
| Note: the --sample option not given, applying all records regardless of the genotype | |
| Applied 8310 variants | |
| ``` | |
| **Traceback:** | |
| * ```console | |
| ``` | |
| **Job Parameters:** | |
| * | Job parameter | Parameter value | | |
| | ------------- | --------------- | | |
| | \_\_input\_ext | ` "input" ` | | |
| | \_\_workflow\_invocation\_uuid\_\_ | ` "2bc979b2114e11f18951000d3a5a8e28" ` | | |
| | absent | ` "" ` | | |
| | chain | ` false ` | | |
| | chromInfo | ` "/tmp/tmp4oiilqtb/galaxy-dev/tool-data/shared/ucsc/chrom/?.len" ` | | |
| | dbkey | ` "?" ` | | |
| | reference\_source | ` {"__current_case__": 1, "fasta_ref": {"values": [{"id": 4, "src": "hda"}]}, "reference_source_selector": "history"} ` | | |
| | rename | ` false ` | | |
| | sec\_default | ` {"conditional_mask": {"__current_case__": 0, "selector": "disabled"}, "iupac_codes": false, "mark_del": "", "mark_ins": null, "mark_snv": null, "mask": null, "sample": "", "select_haplotype": null} ` | | |
| | sec\_restrict | ` {"exclude": null, "include": null} ` | | |
| - **Job 2:** | |
| * Job state is ok | |
| **Container:** | |
| * ```console | |
| quay.io/biocontainers/mulled-v2-03d30cf7bcc23ba5d755e498a98359af8a2cd947:7b1ad5dbd0ee31d66967a1f20b4d8cd630dcec00-0 | |
| ``` | |
| **Command Line:** | |
| * ```console | |
| export BCFTOOLS_PLUGINS=`which bcftools | sed 's,bin/bcftools,libexec/bcftools,'`; bgzip -c '/tmp/tmp4oiilqtb/files/f/5/9/dataset_f599ef16-4839-472b-9198-073ed9395df3.dat' > input.vcf.gz && bcftools index input.vcf.gz && ln -s '/tmp/tmp4oiilqtb/files/d/b/c/dataset_dbcb3ea2-271b-49ae-aa59-5ea11693bd8e.dat' ref.fa && samtools faidx ref.fa && bcftools consensus --fasta-ref ref.fa --output '/tmp/tmp4oiilqtb/job_working_directory/000/25/outputs/dataset_3ee96c11-5d92-4e9a-9b25-33a951db0a6c.dat' input.vcf.gz | |
| ``` | |
| **Exit Code:** | |
| * ```console | |
| 0 | |
| ``` | |
| **Standard Error:** | |
| * ```console | |
| Note: the --sample option not given, applying all records regardless of the genotype | |
| The site NC_003197.2:88220 overlaps with another variant, skipping... | |
| The site NC_003197.2:91039 overlaps with another variant, skipping... | |
| The site NC_003197.2:247269 overlaps with another variant, skipping... | |
| The site NC_003197.2:1476067 overlaps with another variant, skipping... | |
| The site NC_003197.2:1603944 overlaps with another variant, skipping... | |
| The site NC_003197.2:2055500 overlaps with another variant, skipping... | |
| The site NC_003197.2:2077326 overlaps with another variant, skipping... | |
| The site NC_003197.2:2657857 overlaps with another variant, skipping... | |
| The site NC_003197.2:2676022 overlaps with another variant, skipping... | |
| The site NC_003197.2:2995302 overlaps with another variant, skipping... | |
| The site NC_003197.2:3010808 overlaps with another variant, skipping... | |
| The site NC_003197.2:3726364 overlaps with another variant, skipping... | |
| The site NC_003197.2:4100091 overlaps with another variant, skipping... | |
| The site NC_003197.2:4101761 overlaps with another variant, skipping... | |
| The site NC_003197.2:4636377 overlaps with another variant, skipping... | |
| Applied 99817 variants | |
| ``` | |
| **Traceback:** | |
| * ```console | |
| ``` | |
| **Job Parameters:** | |
| * | Job parameter | Parameter value | | |
| | ------------- | --------------- | | |
| | \_\_input\_ext | ` "input" ` | | |
| | \_\_workflow\_invocation\_uuid\_\_ | ` "2bc979b2114e11f18951000d3a5a8e28" ` | | |
| | absent | ` "" ` | | |
| | chain | ` false ` | | |
| | chromInfo | ` "/tmp/tmp4oiilqtb/galaxy-dev/tool-data/shared/ucsc/chrom/?.len" ` | | |
| | dbkey | ` "?" ` | | |
| | reference\_source | ` {"__current_case__": 1, "fasta_ref": {"values": [{"id": 4, "src": "hda"}]}, "reference_source_selector": "history"} ` | | |
| | rename | ` false ` | | |
| | sec\_default | ` {"conditional_mask": {"__current_case__": 0, "selector": "disabled"}, "iupac_codes": false, "mark_del": "", "mark_ins": null, "mark_snv": null, "mask": null, "sample": "", "select_haplotype": null} ` | | |
| | sec\_restrict | ` {"exclude": null, "include": null} ` | | |
| </details> | |
| - **Step 17: Unlabelled step (toolshed.g2.bx.psu.edu/repos/bgruening/text\_processing/tp\_head\_tool/9.5+galaxy0)**: | |
| * step_state: scheduled | |
| * <details><summary>Jobs</summary> | |
| - **Job 1:** | |
| * Job state is ok | |
| **Container:** | |
| * ```console | |
| quay.io/biocontainers/coreutils:9.5 | |
| ``` | |
| **Command Line:** | |
| * ```console | |
| head --lines 1 '/tmp/tmp4oiilqtb/files/6/3/a/dataset_63aa38db-ef4e-47eb-a8c2-959abf4797dc.dat' > '/tmp/tmp4oiilqtb/job_working_directory/000/27/outputs/dataset_cc4563b0-9d33-4f04-8644-716f0197ed75.dat' | |
| ``` | |
| **Exit Code:** | |
| * ```console | |
| 0 | |
| ``` | |
| **Traceback:** | |
| * ```console | |
| ``` | |
| **Job Parameters:** | |
| * | Job parameter | Parameter value | | |
| | ------------- | --------------- | | |
| | \_\_input\_ext | ` "input" ` | | |
| | \_\_workflow\_invocation\_uuid\_\_ | ` "2bc979b2114e11f18951000d3a5a8e28" ` | | |
| | chromInfo | ` "/tmp/tmp4oiilqtb/galaxy-dev/tool-data/shared/ucsc/chrom/?.len" ` | | |
| | complement | ` "" ` | | |
| | count | ` "1" ` | | |
| | dbkey | ` "?" ` | | |
| - **Job 2:** | |
| * Job state is ok | |
| **Container:** | |
| * ```console | |
| quay.io/biocontainers/coreutils:9.5 | |
| ``` | |
| **Command Line:** | |
| * ```console | |
| head --lines 1 '/tmp/tmp4oiilqtb/files/b/5/9/dataset_b592b0bb-a40e-4242-826d-84d1d81d9432.dat' > '/tmp/tmp4oiilqtb/job_working_directory/000/26/outputs/dataset_f1e598a9-5a71-40c8-979e-d252f6bb7232.dat' | |
| ``` | |
| **Exit Code:** | |
| * ```console | |
| 0 | |
| ``` | |
| **Traceback:** | |
| * ```console | |
| ``` | |
| **Job Parameters:** | |
| * | Job parameter | Parameter value | | |
| | ------------- | --------------- | | |
| | \_\_input\_ext | ` "input" ` | | |
| | \_\_workflow\_invocation\_uuid\_\_ | ` "2bc979b2114e11f18951000d3a5a8e28" ` | | |
| | chromInfo | ` "/tmp/tmp4oiilqtb/galaxy-dev/tool-data/shared/ucsc/chrom/?.len" ` | | |
| | complement | ` "" ` | | |
| | count | ` "1" ` | | |
| | dbkey | ` "?" ` | | |
| </details> | |
| - **Step 18: Unlabelled step (Remove beginning1)**: | |
| * step_state: scheduled | |
| * <details><summary>Jobs</summary> | |
| - **Job 1:** | |
| * Job state is ok | |
| **Container:** | |
| * ```console | |
| quay.io/biocontainers/coreutils:8.31--h14c3975_0 | |
| ``` | |
| **Command Line:** | |
| * ```console | |
| tail -n '+2' '/tmp/tmp4oiilqtb/files/f/a/0/dataset_fa00650e-b77e-43b0-971f-1805235abc43.dat' > '/tmp/tmp4oiilqtb/job_working_directory/000/29/outputs/dataset_79ffd65b-90f9-4970-b60f-36f8a85f343f.dat' | |
| ``` | |
| **Exit Code:** | |
| * ```console | |
| 0 | |
| ``` | |
| **Traceback:** | |
| * ```console | |
| ``` | |
| **Job Parameters:** | |
| * | Job parameter | Parameter value | | |
| | ------------- | --------------- | | |
| | \_\_input\_ext | ` "input" ` | | |
| | \_\_workflow\_invocation\_uuid\_\_ | ` "2bc979b2114e11f18951000d3a5a8e28" ` | | |
| | chromInfo | ` "/tmp/tmp4oiilqtb/galaxy-dev/tool-data/shared/ucsc/chrom/?.len" ` | | |
| | dbkey | ` "?" ` | | |
| | num\_lines | ` "1" ` | | |
| - **Job 2:** | |
| * Job state is ok | |
| **Container:** | |
| * ```console | |
| quay.io/biocontainers/coreutils:8.31--h14c3975_0 | |
| ``` | |
| **Command Line:** | |
| * ```console | |
| tail -n '+2' '/tmp/tmp4oiilqtb/files/1/9/4/dataset_19460b34-70a3-4d38-9852-d2ccaa473fd3.dat' > '/tmp/tmp4oiilqtb/job_working_directory/000/28/outputs/dataset_f0317467-ca43-4a95-9584-eed79606fb68.dat' | |
| ``` | |
| **Exit Code:** | |
| * ```console | |
| 0 | |
| ``` | |
| **Traceback:** | |
| * ```console | |
| ``` | |
| **Job Parameters:** | |
| * | Job parameter | Parameter value | | |
| | ------------- | --------------- | | |
| | \_\_input\_ext | ` "input" ` | | |
| | \_\_workflow\_invocation\_uuid\_\_ | ` "2bc979b2114e11f18951000d3a5a8e28" ` | | |
| | chromInfo | ` "/tmp/tmp4oiilqtb/galaxy-dev/tool-data/shared/ucsc/chrom/?.len" ` | | |
| | dbkey | ` "?" ` | | |
| | num\_lines | ` "1" ` | | |
| </details> | |
| - **Step 19: Unlabelled step (toolshed.g2.bx.psu.edu/repos/nml/collapse\_collections/collapse\_dataset/5.1.0)**: | |
| * step_state: scheduled | |
| * <details><summary>Jobs</summary> | |
| - **Job 1:** | |
| * Job state is ok | |
| **Container:** | |
| * ```console | |
| quay.io/biocontainers/gawk:5.1.0--2 | |
| ``` | |
| **Command Line:** | |
| * ```console | |
| ( printf "nanopore_preprocessed_collection_of_all_samples_Spike3bBarcode10\t"; awk '{ print $0 } END { if (NR == 0 && NF == 0) { print "" } }' "/tmp/tmp4oiilqtb/files/f/1/e/dataset_f1e598a9-5a71-40c8-979e-d252f6bb7232.dat"; printf "nanopore_preprocessed_collection_of_all_samples_Spike3bBarcode12\t"; awk '{ print $0 } END { if (NR == 0 && NF == 0) { print "" } }' "/tmp/tmp4oiilqtb/files/c/c/4/dataset_cc4563b0-9d33-4f04-8644-716f0197ed75.dat"; ) > /tmp/tmp4oiilqtb/job_working_directory/000/30/outputs/dataset_f50f9749-e3c9-4ce0-878f-78dea43c1e5a.dat | |
| ``` | |
| **Exit Code:** | |
| * ```console | |
| 0 | |
| ``` | |
| **Traceback:** | |
| * ```console | |
| ``` | |
| **Job Parameters:** | |
| * | Job parameter | Parameter value | | |
| | ------------- | --------------- | | |
| | \_\_input\_ext | ` "input" ` | | |
| | \_\_workflow\_invocation\_uuid\_\_ | ` "2bc979b2114e11f18951000d3a5a8e28" ` | | |
| | chromInfo | ` "/tmp/tmp4oiilqtb/galaxy-dev/tool-data/shared/ucsc/chrom/?.len" ` | | |
| | dbkey | ` "?" ` | | |
| | filename | ` {"__current_case__": 0, "add_name": true, "place_name": "same_once"} ` | | |
| | one\_header | ` false ` | | |
| </details> | |
| - **Step 20: Unlabelled step (Count1)**: | |
| * step_state: scheduled | |
| * <details><summary>Jobs</summary> | |
| - **Job 1:** | |
| * Job state is ok | |
| **Container:** | |
| * ```console | |
| quay.io/biocontainers/mulled-v2-879928bcdd8adc5b4660a3f6de3703d7c7861de4:6ce96688844d469d84f94fabb34055d8dfa283c7-1 | |
| ``` | |
| **Command Line:** | |
| * ```console | |
| python '/tmp/tmp4oiilqtb/galaxy-dev/tools/filters/uniq.py' -i '/tmp/tmp4oiilqtb/files/7/9/f/dataset_79ffd65b-90f9-4970-b60f-36f8a85f343f.dat' -o '/tmp/tmp4oiilqtb/job_working_directory/000/32/outputs/dataset_15610a9c-bf81-456b-aa15-7539d016c74c.dat' -c '1' -d T -s value | |
| ``` | |
| **Exit Code:** | |
| * ```console | |
| 0 | |
| ``` | |
| **Standard Output:** | |
| * ```console | |
| Count of unique values in c1 | |
| ``` | |
| **Traceback:** | |
| * ```console | |
| ``` | |
| **Job Parameters:** | |
| * | Job parameter | Parameter value | | |
| | ------------- | --------------- | | |
| | \_\_input\_ext | ` "tabular" ` | | |
| | \_\_workflow\_invocation\_uuid\_\_ | ` "2bc979b2114e11f18951000d3a5a8e28" ` | | |
| | chromInfo | ` "/tmp/tmp4oiilqtb/galaxy-dev/tool-data/shared/ucsc/chrom/?.len" ` | | |
| | column | ` "1" ` | | |
| | dbkey | ` "?" ` | | |
| | delim | ` "T" ` | | |
| | sorting | ` "value" ` | | |
| - **Job 2:** | |
| * Job state is ok | |
| **Container:** | |
| * ```console | |
| quay.io/biocontainers/mulled-v2-879928bcdd8adc5b4660a3f6de3703d7c7861de4:6ce96688844d469d84f94fabb34055d8dfa283c7-1 | |
| ``` | |
| **Command Line:** | |
| * ```console | |
| python '/tmp/tmp4oiilqtb/galaxy-dev/tools/filters/uniq.py' -i '/tmp/tmp4oiilqtb/files/f/0/3/dataset_f0317467-ca43-4a95-9584-eed79606fb68.dat' -o '/tmp/tmp4oiilqtb/job_working_directory/000/31/outputs/dataset_24c794d0-d04d-47dc-89fd-e54d8e0d6bd0.dat' -c '1' -d T -s value | |
| ``` | |
| **Exit Code:** | |
| * ```console | |
| 0 | |
| ``` | |
| **Standard Output:** | |
| * ```console | |
| Count of unique values in c1 | |
| ``` | |
| **Traceback:** | |
| * ```console | |
| ``` | |
| **Job Parameters:** | |
| * | Job parameter | Parameter value | | |
| | ------------- | --------------- | | |
| | \_\_input\_ext | ` "tabular" ` | | |
| | \_\_workflow\_invocation\_uuid\_\_ | ` "2bc979b2114e11f18951000d3a5a8e28" ` | | |
| | chromInfo | ` "/tmp/tmp4oiilqtb/galaxy-dev/tool-data/shared/ucsc/chrom/?.len" ` | | |
| | column | ` "1" ` | | |
| | dbkey | ` "?" ` | | |
| | delim | ` "T" ` | | |
| | sorting | ` "value" ` | | |
| </details> | |
| - **Step 21: Unlabelled step (toolshed.g2.bx.psu.edu/repos/bgruening/text\_processing/tp\_cut\_tool/9.5+galaxy0)**: | |
| * step_state: scheduled | |
| * <details><summary>Jobs</summary> | |
| - **Job 1:** | |
| * Job state is ok | |
| **Container:** | |
| * ```console | |
| quay.io/biocontainers/coreutils:9.5 | |
| ``` | |
| **Command Line:** | |
| * ```console | |
| cut -f '1' '/tmp/tmp4oiilqtb/files/f/5/0/dataset_f50f9749-e3c9-4ce0-878f-78dea43c1e5a.dat' > '/tmp/tmp4oiilqtb/job_working_directory/000/33/outputs/dataset_415c1570-bbcd-4354-ac65-cc432a03d4c6.dat' | |
| ``` | |
| **Exit Code:** | |
| * ```console | |
| 0 | |
| ``` | |
| **Traceback:** | |
| * ```console | |
| ``` | |
| **Job Parameters:** | |
| * | Job parameter | Parameter value | | |
| | ------------- | --------------- | | |
| | \_\_input\_ext | ` "input" ` | | |
| | \_\_workflow\_invocation\_uuid\_\_ | ` "2bc979b2114e11f18951000d3a5a8e28" ` | | |
| | chromInfo | ` "/tmp/tmp4oiilqtb/galaxy-dev/tool-data/shared/ucsc/chrom/?.len" ` | | |
| | complement | ` "" ` | | |
| | cut\_type\_options | ` {"__current_case__": 0, "colnames_option": {"__current_case__": 1, "header": "N", "list": "1"}, "cut_element": "-f", "delimiter": ""} ` | | |
| | dbkey | ` "?" ` | | |
| </details> | |
| - **Step 22: Unlabelled step (Cut1)**: | |
| * step_state: scheduled | |
| * <details><summary>Jobs</summary> | |
| - **Job 1:** | |
| * Job state is ok | |
| **Container:** | |
| * ```console | |
| quay.io/biocontainers/perl:5.26--2 | |
| ``` | |
| **Command Line:** | |
| * ```console | |
| perl '/tmp/tmp4oiilqtb/galaxy-dev/tools/filters/cutWrapper.pl' '/tmp/tmp4oiilqtb/files/2/4/c/dataset_24c794d0-d04d-47dc-89fd-e54d8e0d6bd0.dat' 'c1' T '/tmp/tmp4oiilqtb/job_working_directory/000/34/outputs/dataset_82fb6ca8-d4b1-4938-8650-c05f52ee5bff.dat' | |
| ``` | |
| **Exit Code:** | |
| * ```console | |
| 0 | |
| ``` | |
| **Traceback:** | |
| * ```console | |
| ``` | |
| **Job Parameters:** | |
| * | Job parameter | Parameter value | | |
| | ------------- | --------------- | | |
| | \_\_input\_ext | ` "tabular" ` | | |
| | \_\_workflow\_invocation\_uuid\_\_ | ` "2bc979b2114e11f18951000d3a5a8e28" ` | | |
| | chromInfo | ` "/tmp/tmp4oiilqtb/galaxy-dev/tool-data/shared/ucsc/chrom/?.len" ` | | |
| | columnList | ` "c1" ` | | |
| | dbkey | ` "?" ` | | |
| | delimiter | ` "T" ` | | |
| - **Job 2:** | |
| * Job state is ok | |
| **Container:** | |
| * ```console | |
| quay.io/biocontainers/perl:5.26--2 | |
| ``` | |
| **Command Line:** | |
| * ```console | |
| perl '/tmp/tmp4oiilqtb/galaxy-dev/tools/filters/cutWrapper.pl' '/tmp/tmp4oiilqtb/files/1/5/6/dataset_15610a9c-bf81-456b-aa15-7539d016c74c.dat' 'c1' T '/tmp/tmp4oiilqtb/job_working_directory/000/35/outputs/dataset_6d1a680f-ff19-46d1-8fc7-50cdeaac0652.dat' | |
| ``` | |
| **Exit Code:** | |
| * ```console | |
| 0 | |
| ``` | |
| **Traceback:** | |
| * ```console | |
| ``` | |
| **Job Parameters:** | |
| * | Job parameter | Parameter value | | |
| | ------------- | --------------- | | |
| | \_\_input\_ext | ` "tabular" ` | | |
| | \_\_workflow\_invocation\_uuid\_\_ | ` "2bc979b2114e11f18951000d3a5a8e28" ` | | |
| | chromInfo | ` "/tmp/tmp4oiilqtb/galaxy-dev/tool-data/shared/ucsc/chrom/?.len" ` | | |
| | columnList | ` "c1" ` | | |
| | dbkey | ` "?" ` | | |
| | delimiter | ` "T" ` | | |
| </details> | |
| - **Step 23: Unlabelled step (Paste1)**: | |
| * step_state: scheduled | |
| * <details><summary>Jobs</summary> | |
| - **Job 1:** | |
| * Job state is ok | |
| **Container:** | |
| * ```console | |
| quay.io/biocontainers/coreutils:8.31--h14c3975_0 | |
| ``` | |
| **Command Line:** | |
| * ```console | |
| paste '/tmp/tmp4oiilqtb/files/4/1/5/dataset_415c1570-bbcd-4354-ac65-cc432a03d4c6.dat' '/tmp/tmp4oiilqtb/files/a/8/6/dataset_a86e6a7a-4c52-41b1-b8c0-44c9073cd88b.dat' > '/tmp/tmp4oiilqtb/job_working_directory/000/36/outputs/dataset_a21079a6-0e32-4d13-8fe5-ebf388987f5f.dat' | |
| ``` | |
| **Exit Code:** | |
| * ```console | |
| 0 | |
| ``` | |
| **Traceback:** | |
| * ```console | |
| ``` | |
| **Job Parameters:** | |
| * | Job parameter | Parameter value | | |
| | ------------- | --------------- | | |
| | \_\_input\_ext | ` "input" ` | | |
| | \_\_workflow\_invocation\_uuid\_\_ | ` "2bc979b2114e11f18951000d3a5a8e28" ` | | |
| | chromInfo | ` "/tmp/tmp4oiilqtb/galaxy-dev/tool-data/shared/ucsc/chrom/?.len" ` | | |
| | dbkey | ` "?" ` | | |
| | delimiter | ` "T" ` | | |
| </details> | |
| - **Step 24: Unlabelled step (toolshed.g2.bx.psu.edu/repos/bgruening/text\_processing/tp\_head\_tool/9.5+galaxy0)**: | |
| * step_state: scheduled | |
| * <details><summary>Jobs</summary> | |
| - **Job 1:** | |
| * Job state is ok | |
| **Container:** | |
| * ```console | |
| quay.io/biocontainers/coreutils:9.5 | |
| ``` | |
| **Command Line:** | |
| * ```console | |
| head --lines 1 '/tmp/tmp4oiilqtb/files/8/2/f/dataset_82fb6ca8-d4b1-4938-8650-c05f52ee5bff.dat' > '/tmp/tmp4oiilqtb/job_working_directory/000/37/outputs/dataset_902eb22b-b1f5-4a8a-804e-cc729f6bc6da.dat' | |
| ``` | |
| **Exit Code:** | |
| * ```console | |
| 0 | |
| ``` | |
| **Traceback:** | |
| * ```console | |
| ``` | |
| **Job Parameters:** | |
| * | Job parameter | Parameter value | | |
| | ------------- | --------------- | | |
| | \_\_input\_ext | ` "input" ` | | |
| | \_\_workflow\_invocation\_uuid\_\_ | ` "2bc979b2114e11f18951000d3a5a8e28" ` | | |
| | chromInfo | ` "/tmp/tmp4oiilqtb/galaxy-dev/tool-data/shared/ucsc/chrom/?.len" ` | | |
| | complement | ` "" ` | | |
| | count | ` "1" ` | | |
| | dbkey | ` "?" ` | | |
| - **Job 2:** | |
| * Job state is ok | |
| **Container:** | |
| * ```console | |
| quay.io/biocontainers/coreutils:9.5 | |
| ``` | |
| **Command Line:** | |
| * ```console | |
| head --lines 1 '/tmp/tmp4oiilqtb/files/6/d/1/dataset_6d1a680f-ff19-46d1-8fc7-50cdeaac0652.dat' > '/tmp/tmp4oiilqtb/job_working_directory/000/38/outputs/dataset_b8f2d355-ebb4-455d-b977-4beffccf0a64.dat' | |
| ``` | |
| **Exit Code:** | |
| * ```console | |
| 0 | |
| ``` | |
| **Traceback:** | |
| * ```console | |
| ``` | |
| **Job Parameters:** | |
| * | Job parameter | Parameter value | | |
| | ------------- | --------------- | | |
| | \_\_input\_ext | ` "input" ` | | |
| | \_\_workflow\_invocation\_uuid\_\_ | ` "2bc979b2114e11f18951000d3a5a8e28" ` | | |
| | chromInfo | ` "/tmp/tmp4oiilqtb/galaxy-dev/tool-data/shared/ucsc/chrom/?.len" ` | | |
| | complement | ` "" ` | | |
| | count | ` "1" ` | | |
| | dbkey | ` "?" ` | | |
| </details> | |
| - **Step 25: Unlabelled step (toolshed.g2.bx.psu.edu/repos/nml/collapse\_collections/collapse\_dataset/5.1.0)**: | |
| * step_state: scheduled | |
| * <details><summary>Jobs</summary> | |
| - **Job 1:** | |
| * Job state is ok | |
| **Container:** | |
| * ```console | |
| quay.io/biocontainers/gawk:5.1.0--2 | |
| ``` | |
| **Command Line:** | |
| * ```console | |
| ( printf "nanopore_preprocessed_collection_of_all_samples_Spike3bBarcode10\t"; awk '{ print $0 } END { if (NR == 0 && NF == 0) { print "" } }' "/tmp/tmp4oiilqtb/files/9/0/2/dataset_902eb22b-b1f5-4a8a-804e-cc729f6bc6da.dat"; printf "nanopore_preprocessed_collection_of_all_samples_Spike3bBarcode12\t"; awk '{ print $0 } END { if (NR == 0 && NF == 0) { print "" } }' "/tmp/tmp4oiilqtb/files/b/8/f/dataset_b8f2d355-ebb4-455d-b977-4beffccf0a64.dat"; ) > /tmp/tmp4oiilqtb/job_working_directory/000/39/outputs/dataset_c41ebf72-a7fd-4e4b-8e90-e902c74cb632.dat | |
| ``` | |
| **Exit Code:** | |
| * ```console | |
| 0 | |
| ``` | |
| **Traceback:** | |
| * ```console | |
| ``` | |
| **Job Parameters:** | |
| * | Job parameter | Parameter value | | |
| | ------------- | --------------- | | |
| | \_\_input\_ext | ` "input" ` | | |
| | \_\_workflow\_invocation\_uuid\_\_ | ` "2bc979b2114e11f18951000d3a5a8e28" ` | | |
| | chromInfo | ` "/tmp/tmp4oiilqtb/galaxy-dev/tool-data/shared/ucsc/chrom/?.len" ` | | |
| | dbkey | ` "?" ` | | |
| | filename | ` {"__current_case__": 0, "add_name": true, "place_name": "same_once"} ` | | |
| | one\_header | ` false ` | | |
| </details> | |
| - **Step 26: Unlabelled step (toolshed.g2.bx.psu.edu/repos/galaxyp/regex\_find\_replace/regexColumn1/1.0.3)**: | |
| * step_state: scheduled | |
| * <details><summary>Jobs</summary> | |
| - **Job 1:** | |
| * Job state is ok | |
| **Container:** | |
| * ```console | |
| quay.io/biocontainers/python:3.7--1 | |
| ``` | |
| **Command Line:** | |
| * ```console | |
| python '/tmp/shed_dir/toolshed.g2.bx.psu.edu/repos/galaxyp/regex_find_replace/503bcd6ebe4b/regex_find_replace/regex.py' --input '/tmp/tmp4oiilqtb/files/c/4/1/dataset_c41ebf72-a7fd-4e4b-8e90-e902c74cb632.dat' --output '/tmp/tmp4oiilqtb/job_working_directory/000/40/outputs/dataset_b8364093-a881-4007-81f7-4e5f3ea49314.dat' --column 2 --input_display_name 'Collapse Collection on dataset 58 and 59 and collection 57' --pattern='^$' --replacement='0' | |
| ``` | |
| **Exit Code:** | |
| * ```console | |
| 0 | |
| ``` | |
| **Traceback:** | |
| * ```console | |
| ``` | |
| **Job Parameters:** | |
| * | Job parameter | Parameter value | | |
| | ------------- | --------------- | | |
| | \_\_input\_ext | ` "input" ` | | |
| | \_\_workflow\_invocation\_uuid\_\_ | ` "2bc979b2114e11f18951000d3a5a8e28" ` | | |
| | checks | ` [{"__index__": 0, "pattern": "^$", "replacement": "0"}] ` | | |
| | chromInfo | ` "/tmp/tmp4oiilqtb/galaxy-dev/tool-data/shared/ucsc/chrom/?.len" ` | | |
| | dbkey | ` "?" ` | | |
| | field | ` "2" ` | | |
| </details> | |
| </details> | |
| * <details><summary>Other invocation details</summary> | |
| - **history_id** | |
| * 6c4fe19c772d653b | |
| - **history_state** | |
| * ok | |
| - **invocation_id** | |
| * 6c4fe19c772d653b | |
| - **invocation_state** | |
| * scheduled | |
| - **workflow_id** | |
| * 6c4fe19c772d653b | |
| </details> | |
| </div></details> | |
| * <details class="rcorners light-green"><summary class="light-green">✅ Assembly-Hifi-HiC-phasing-VGP4.ga_0</summary><div class="padded"> | |
| #### Workflow invocation details | |
| * Invocation Messages | |
| * <details><summary>Steps</summary> | |
| - **Step 1: Species Name**: | |
| * step_state: scheduled | |
| - **Step 2: Assembly Name**: | |
| * step_state: scheduled | |
| - **Step 3: Pacbio Reads**: | |
| * step_state: scheduled | |
| - **Step 4: Trim Hi-C reads?**: | |
| * step_state: scheduled | |
| - **Step 5: Hi-C reads**: | |
| * step_state: scheduled | |
| - **Step 6: Genomescope Summary**: | |
| * step_state: scheduled | |
| - **Step 7: Meryl Database**: | |
| * step_state: scheduled | |
| - **Step 8: Database for Busco Lineage**: | |
| * step_state: scheduled | |
| - **Step 9: Lineage**: | |
| * step_state: scheduled | |
| - **Step 10: Name for Haplotype 1**: | |
| * step_state: scheduled | |
| - **Step 11: Name for Haplotype 2**: | |
| * step_state: scheduled | |
| - **Step 12: Bits for bloom filter**: | |
| * step_state: scheduled | |
| - **Step 13: Homozygous Read Coverage**: | |
| * step_state: scheduled | |
| - **Step 14: Genomescope Model Parameters**: | |
| * step_state: scheduled | |
| - **Step 15: Unlabelled step (toolshed.g2.bx.psu.edu/repos/iuc/compose\_text\_param/compose\_text\_param/0.1.1)**: | |
| * step_state: scheduled | |
| * <details><summary>Jobs</summary> | |
| - **Job 1:** | |
| * Job state is ok | |
| **Command Line:** | |
| * ```console | |
| cd ../; python _evaluate_expression_.py | |
| ``` | |
| **Exit Code:** | |
| * ```console | |
| 0 | |
| ``` | |
| **Traceback:** | |
| * ```console | |
| ``` | |
| **Job Parameters:** | |
| * | Job parameter | Parameter value | | |
| | ------------- | --------------- | | |
| | \_\_input\_ext | ` "input" ` | | |
| | \_\_workflow\_invocation\_uuid\_\_ | ` "30ca0a3a114e11f189517ced8d7c0d2f" ` | | |
| | chromInfo | ` "/tmp/tmpgck0c6r3/galaxy-dev/tool-data/shared/ucsc/chrom/?.len" ` | | |
| | components | ` [{"__index__": 0, "param_type": {"__current_case__": 0, "component_value": "Random Name", "select_param_type": "text"}}] ` | | |
| | dbkey | ` "?" ` | | |
| </details> | |
| - **Step 16: Unlabelled step (toolshed.g2.bx.psu.edu/repos/iuc/compose\_text\_param/compose\_text\_param/0.1.1)**: | |
| * step_state: scheduled | |
| * <details><summary>Jobs</summary> | |
| - **Job 1:** | |
| * Job state is ok | |
| **Command Line:** | |
| * ```console | |
| cd ../; python _evaluate_expression_.py | |
| ``` | |
| **Exit Code:** | |
| * ```console | |
| 0 | |
| ``` | |
| **Traceback:** | |
| * ```console | |
| ``` | |
| **Job Parameters:** | |
| * | Job parameter | Parameter value | | |
| | ------------- | --------------- | | |
| | \_\_input\_ext | ` "input" ` | | |
| | \_\_workflow\_invocation\_uuid\_\_ | ` "30ca0a3a114e11f189517ced8d7c0d2f" ` | | |
| | chromInfo | ` "/tmp/tmpgck0c6r3/galaxy-dev/tool-data/shared/ucsc/chrom/?.len" ` | | |
| | components | ` [{"__index__": 0, "param_type": {"__current_case__": 0, "component_value": "randName4", "select_param_type": "text"}}] ` | | |
| | dbkey | ` "?" ` | | |
| </details> | |
| - **Step 17: Unlabelled step (toolshed.g2.bx.psu.edu/repos/lparsons/cutadapt/cutadapt/5.1+galaxy0)**: | |
| * step_state: scheduled | |
| * <details><summary>Jobs</summary> | |
| - **Job 1:** | |
| * Job state is ok | |
| **Container:** | |
| * ```console | |
| quay.io/biocontainers/cutadapt:5.1--py312h0fa9677_0 | |
| ``` | |
| **Command Line:** | |
| * ```console | |
| ln -f -s '/tmp/tmpgck0c6r3/files/6/0/d/dataset_60d7036c-7351-4b63-b2a8-55d97a1e916e.dat' 'yeast_reads_sub1_fastq_gz.fq.gz' && cutadapt -j=${GALAXY_SLOTS:-4} -b 'ATCTCTCTCAACAACAACAACGGAGGAGGAGGAAAAGAGAGAGAT' -b 'ATCTCTCTCTTTTCCTCCTCCTCCGTTGTTGTTGTTGAGAGAGAT' --error-rate=0.1 --times=1 --overlap=35 --action=trim --rc --discard-trimmed --minimum-length=1 --json=stats.json -o 'out1.fq.gz' 'yeast_reads_sub1_fastq_gz.fq.gz' > report.txt | |
| ``` | |
| **Exit Code:** | |
| * ```console | |
| 0 | |
| ``` | |
| **Traceback:** | |
| * ```console | |
| ``` | |
| **Job Parameters:** | |
| * | Job parameter | Parameter value | | |
| | ------------- | --------------- | | |
| | \_\_input\_ext | ` "input" ` | | |
| | \_\_workflow\_invocation\_uuid\_\_ | ` "30ca0a3a114e11f189517ced8d7c0d2f" ` | | |
| | adapter\_options | ` {"action": "trim", "error_rate": "0.1", "match_read_wildcards": false, "no_indels": false, "no_match_adapter_wildcards": true, "overlap": "35", "revcomp": true, "times": "1"} ` | | |
| | chromInfo | ` "/tmp/tmpgck0c6r3/galaxy-dev/tool-data/shared/ucsc/chrom/?.len" ` | | |
| | dbkey | ` "?" ` | | |
| | filter\_options | ` {"discard_casava": false, "discard_trimmed": true, "discard_untrimmed": false, "max_average_error_rate": null, "max_expected_errors": null, "max_n": null, "maximum_length": null, "maximum_length2": null, "minimum_length": "1", "minimum_length2": null, "pair_filter": "any"} ` | | |
| | library | ` {"__current_case__": 0, "input_1": {"values": [{"id": 4, "src": "dce"}]}, "r1": {"adapters": [], "anywhere_adapters": [{"__index__": 0, "adapter_source": {"__current_case__": 0, "adapter": "ATCTCTCTCAACAACAACAACGGAGGAGGAGGAAAAGAGAGAGAT", "adapter_name": "", "adapter_source_list": "user"}, "single_noindels": false}, {"__index__": 1, "adapter_source": {"__current_case__": 0, "adapter": "ATCTCTCTCTTTTCCTCCTCCTCCGTTGTTGTTGTTGAGAGAGAT", "adapter_name": "", "adapter_source_list": "user"}, "single_noindels": false}], "front_adapters": []}, "type": "single"} ` | | |
| | other\_trimming\_options | ` {"cut": "0", "cut2": "0", "nextseq_trim": "0", "poly_a": false, "quality_cutoff": "0", "quality_cutoff2": "", "shorten_options": {"__current_case__": 1, "shorten_values": "False"}, "shorten_options_r2": {"__current_case__": 1, "shorten_values_r2": "False"}, "trim_n": false} ` | | |
| | output\_selector | ` ["report", "json_stats"] ` | | |
| | read\_mod\_options | ` {"length_tag": "", "rename": "", "strip_suffix": "", "zero_cap": false} ` | | |
| </details> | |
| - **Step 18: Unlabelled step (toolshed.g2.bx.psu.edu/repos/lparsons/cutadapt/cutadapt/5.1+galaxy0)**: | |
| * step_state: scheduled | |
| * <details><summary>Jobs</summary> | |
| - **Job 1:** | |
| * Job state is skipped | |
| **Traceback:** | |
| * ```console | |
| ``` | |
| **Job Parameters:** | |
| * | Job parameter | Parameter value | | |
| | ------------- | --------------- | | |
| | \_\_input\_ext | ` "input" ` | | |
| | \_\_workflow\_invocation\_uuid\_\_ | ` "30ca0a3a114e11f189517ced8d7c0d2f" ` | | |
| | adapter\_options | ` {"action": "trim", "error_rate": "0.1", "match_read_wildcards": false, "no_indels": false, "no_match_adapter_wildcards": true, "overlap": "3", "revcomp": false, "times": "1"} ` | | |
| | chromInfo | ` "/tmp/tmpgck0c6r3/galaxy-dev/tool-data/shared/ucsc/chrom/?.len" ` | | |
| | dbkey | ` "?" ` | | |
| | filter\_options | ` {"discard_casava": false, "discard_trimmed": false, "discard_untrimmed": false, "max_average_error_rate": null, "max_expected_errors": null, "max_n": null, "maximum_length": null, "maximum_length2": null, "minimum_length": "1", "minimum_length2": null, "pair_filter": "any"} ` | | |
| | library | ` {"__current_case__": 2, "input_1": {"values": [{"id": 1, "src": "dce"}]}, "pair_adapters": false, "r1": {"adapters": [], "anywhere_adapters": [], "front_adapters": []}, "r2": {"adapters2": [], "anywhere_adapters2": [], "front_adapters2": []}, "type": "paired_collection"} ` | | |
| | other\_trimming\_options | ` {"cut": "5", "cut2": "5", "nextseq_trim": "0", "poly_a": false, "quality_cutoff": "0", "quality_cutoff2": "", "shorten_options": {"__current_case__": 1, "shorten_values": "False"}, "shorten_options_r2": {"__current_case__": 1, "shorten_values_r2": "False"}, "trim_n": false} ` | | |
| | output\_selector | ` None ` | | |
| | read\_mod\_options | ` {"length_tag": null, "rename": null, "strip_suffix": null, "zero_cap": false} ` | | |
| </details> | |
| - **Step 19: Unlabelled step (toolshed.g2.bx.psu.edu/repos/bgruening/text\_processing/tp\_grep\_tool/9.5+galaxy2)**: | |
| * step_state: scheduled | |
| * <details><summary>Jobs</summary> | |
| - **Job 1:** | |
| * Job state is ok | |
| **Container:** | |
| * ```console | |
| quay.io/biocontainers/mulled-v2-a8b1e1ec4fafcddd7d4c96fdaa021e5b6c1e8a67:27f652719ff0f4dfc5e3d483435124548d01020c-0 | |
| ``` | |
| **Command Line:** | |
| * ```console | |
| grep -G -A 0 -B 0 --no-group-separator -i -- 'Haploid' '/tmp/tmpgck0c6r3/files/8/4/5/dataset_8457f9df-6934-4521-88a3-dc2eb90f3f5f.dat' > '/tmp/tmpgck0c6r3/job_working_directory/000/11/outputs/dataset_b5c7d8f4-25ea-4fbc-8192-57afd6e4416c.dat' | |
| ``` | |
| **Exit Code:** | |
| * ```console | |
| 0 | |
| ``` | |
| **Traceback:** | |
| * ```console | |
| ``` | |
| **Job Parameters:** | |
| * | Job parameter | Parameter value | | |
| | ------------- | --------------- | | |
| | \_\_input\_ext | ` "input" ` | | |
| | \_\_workflow\_invocation\_uuid\_\_ | ` "30ca0a3a114e11f189517ced8d7c0d2f" ` | | |
| | case\_sensitive | ` "-i" ` | | |
| | chromInfo | ` "/tmp/tmpgck0c6r3/galaxy-dev/tool-data/shared/ucsc/chrom/?.len" ` | | |
| | color | ` "NOCOLOR" ` | | |
| | dbkey | ` "?" ` | | |
| | invert | ` "" ` | | |
| | lines\_after | ` "0" ` | | |
| | lines\_before | ` "0" ` | | |
| | regex\_type | ` "-G" ` | | |
| | url\_paste | ` "Haploid" ` | | |
| </details> | |
| - **Step 20: Unlabelled step (toolshed.g2.bx.psu.edu/repos/iuc/compose\_text\_param/compose\_text\_param/0.1.1)**: | |
| * step_state: scheduled | |
| * <details><summary>Jobs</summary> | |
| - **Job 1:** | |
| * Job state is ok | |
| **Command Line:** | |
| * ```console | |
| cd ../; python _evaluate_expression_.py | |
| ``` | |
| **Exit Code:** | |
| * ```console | |
| 0 | |
| ``` | |
| **Traceback:** | |
| * ```console | |
| ``` | |
| **Job Parameters:** | |
| * | Job parameter | Parameter value | | |
| | ------------- | --------------- | | |
| | \_\_input\_ext | ` "input" ` | | |
| | \_\_workflow\_invocation\_uuid\_\_ | ` "30ca0a3a114e11f189517ced8d7c0d2f" ` | | |
| | chromInfo | ` "/tmp/tmpgck0c6r3/galaxy-dev/tool-data/shared/ucsc/chrom/?.len" ` | | |
| | components | ` [{"__index__": 0, "param_type": {"__current_case__": 0, "component_value": "vertebrata_odb10", "select_param_type": "text"}}] ` | | |
| | dbkey | ` "?" ` | | |
| </details> | |
| - **Step 21: Unlabelled step (toolshed.g2.bx.psu.edu/repos/devteam/column\_maker/Add\_a\_column1/2.1)**: | |
| * step_state: scheduled | |
| * <details><summary>Jobs</summary> | |
| - **Job 1:** | |
| * Job state is ok | |
| **Container:** | |
| * ```console | |
| quay.io/biocontainers/mulled-v2-b1a1ba6b0445e5a9141e8becdb2ab56f8d930e41:477f302c9d587c361f49c5f5853e2f0cc6119bf4-0 | |
| ``` | |
| **Command Line:** | |
| * ```console | |
| python '/tmp/shed_dir/toolshed.g2.bx.psu.edu/repos/devteam/column_maker/aff5135563c6/column_maker/column_maker.py' --column-types float,float,float,float,float,int --file '/tmp/tmpgck0c6r3/job_working_directory/000/13/configs/tmphbsy6ig7' --fail-on-non-existent-columns --fail-on-non-computable '/tmp/tmpgck0c6r3/files/b/9/4/dataset_b9439871-5bbc-4153-873a-40ebb62b8ab1.dat' '/tmp/tmpgck0c6r3/job_working_directory/000/13/outputs/dataset_7c3ffb5c-0313-432c-8934-cb7188e9d840.dat' | |
| ``` | |
| **Exit Code:** | |
| * ```console | |
| 0 | |
| ``` | |
| **Standard Output:** | |
| * ```console | |
| c3*2 | |
| Computing 1 new columns with instructions ['c3*2;;'] | |
| Computed new column values for 100.00% of 1 lines written. | |
| ``` | |
| **Traceback:** | |
| * ```console | |
| ``` | |
| **Job Parameters:** | |
| * | Job parameter | Parameter value | | |
| | ------------- | --------------- | | |
| | \_\_input\_ext | ` "input" ` | | |
| | \_\_workflow\_invocation\_uuid\_\_ | ` "30ca0a3a114e11f189517ced8d7c0d2f" ` | | |
| | avoid\_scientific\_notation | ` false ` | | |
| | chromInfo | ` "/tmp/tmpgck0c6r3/galaxy-dev/tool-data/shared/ucsc/chrom/?.len" ` | | |
| | dbkey | ` "?" ` | | |
| | error\_handling | ` {"auto_col_types": true, "fail_on_non_existent_columns": true, "non_computable": {"__current_case__": 0, "action": "--fail-on-non-computable"}} ` | | |
| | ops | ` {"__current_case__": 0, "expressions": [{"__index__": 0, "add_column": {"__current_case__": 0, "mode": "", "pos": ""}, "cond": "c3*2"}], "header_lines_select": "no"} ` | | |
| </details> | |
| - **Step 22: Unlabelled step (toolshed.g2.bx.psu.edu/repos/iuc/multiqc/multiqc/1.27+galaxy4)**: | |
| * step_state: scheduled | |
| * <details><summary>Jobs</summary> | |
| - **Job 1:** | |
| * Job state is ok | |
| **Container:** | |
| * ```console | |
| quay.io/biocontainers/multiqc:1.27--pyhdfd78af_0 | |
| ``` | |
| **Command Line:** | |
| * ```console | |
| die() { echo "$@" 1>&2 ; exit 1; } && mkdir multiqc_WDir && mkdir multiqc_WDir/cutadapt_0 && ln -s '/tmp/tmpgck0c6r3/files/8/8/9/dataset_889fdc73-1bff-4628-a7a0-e599ac1b622d.dat' 'multiqc_WDir/cutadapt_0/yeast_reads_sub1_fastq_gz.txt' && sed -i.old 's/You are running/This is/' 'multiqc_WDir/cutadapt_0/yeast_reads_sub1_fastq_gz.txt' && grep -q "This is cutadapt" 'multiqc_WDir/cutadapt_0/yeast_reads_sub1_fastq_gz.txt' || die "'This is cutadapt' or 'You are running cutadapt' not found in the file" && multiqc multiqc_WDir --filename 'report' && mkdir -p ./plots && ls -l ./report_data/ && cp ./report_data/*plot*.txt ./plots/ | true | |
| ``` | |
| **Exit Code:** | |
| * ```console | |
| 0 | |
| ``` | |
| **Standard Error:** | |
| * ```console | |
| /// MultiQC 🔍 v1.27 | |
| version_check | MultiQC Version v1.33 now available! | |
| file_search | Search path: /tmp/tmpgck0c6r3/job_working_directory/000/14/working/multiqc_WDir | |
| cutadapt | Found 1 reports | |
| write_results | Data : report_data | |
| write_results | Report : report.html | |
| multiqc | MultiQC complete | |
| ``` | |
| **Standard Output:** | |
| * ```console | |
| total 80 | |
| -rw-r--r-- 1 1001 1001 97 Feb 24 07:00 cutadapt_filtered_reads_plot.txt | |
| -rw-r--r-- 1 1001 1001 66 Feb 24 07:00 cutadapt_trimmed_sequences_plot_default_Counts.txt | |
| -rw-r--r-- 1 1001 1001 70 Feb 24 07:00 cutadapt_trimmed_sequences_plot_default_Obs_Exp.txt | |
| -rw-r--r-- 1 1001 1001 397 Feb 24 07:00 multiqc.log | |
| -rw-r--r-- 1 1001 1001 124 Feb 24 07:00 multiqc_citations.txt | |
| -rw-r--r-- 1 1001 1001 222 Feb 24 07:00 multiqc_cutadapt.txt | |
| -rw-r--r-- 1 1001 1001 44093 Feb 24 07:00 multiqc_data.json | |
| -rw-r--r-- 1 1001 1001 79 Feb 24 07:00 multiqc_general_stats.txt | |
| -rw-r--r-- 1 1001 1001 29 Feb 24 07:00 multiqc_software_versions.txt | |
| -rw-r--r-- 1 1001 1001 194 Feb 24 07:00 multiqc_sources.txt | |
| ``` | |
| **Traceback:** | |
| * ```console | |
| ``` | |
| **Job Parameters:** | |
| * | Job parameter | Parameter value | | |
| | ------------- | --------------- | | |
| | \_\_input\_ext | ` "input" ` | | |
| | \_\_workflow\_invocation\_uuid\_\_ | ` "30ca0a3a114e11f189517ced8d7c0d2f" ` | | |
| | chromInfo | ` "/tmp/tmpgck0c6r3/galaxy-dev/tool-data/shared/ucsc/chrom/?.len" ` | | |
| | comment | ` "" ` | | |
| | dbkey | ` "?" ` | | |
| | export | ` false ` | | |
| | flat | ` false ` | | |
| | image\_content\_input | ` None ` | | |
| | png\_plots | ` false ` | | |
| | results | ` [{"__index__": 0, "software_cond": {"__current_case__": 5, "input": {"values": [{"id": 4, "src": "hdca"}]}, "software": "cutadapt"}}] ` | | |
| | title | ` "" ` | | |
| </details> | |
| - **Step 23: Pick forward 2 (toolshed.g2.bx.psu.edu/repos/iuc/pick\_value/pick\_value/0.2.0)**: | |
| * step_state: scheduled | |
| * <details><summary>Jobs</summary> | |
| - **Job 1:** | |
| * Job state is ok | |
| **Command Line:** | |
| * ```console | |
| cd ../; python _evaluate_expression_.py | |
| ``` | |
| **Exit Code:** | |
| * ```console | |
| 0 | |
| ``` | |
| **Traceback:** | |
| * ```console | |
| ``` | |
| **Job Parameters:** | |
| * | Job parameter | Parameter value | | |
| | ------------- | --------------- | | |
| | \_\_input\_ext | ` "input" ` | | |
| | \_\_workflow\_invocation\_uuid\_\_ | ` "30ca0a3a114e11f189517ced8d7c0d2f" ` | | |
| | chromInfo | ` "/tmp/tmpgck0c6r3/galaxy-dev/tool-data/shared/ucsc/chrom/?.len" ` | | |
| | dbkey | ` "?" ` | | |
| | style\_cond | ` {"__current_case__": 0, "pick_style": "first", "type_cond": {"__current_case__": 4, "param_type": "data", "pick_from": [{"__index__": 0, "value": {"values": [{"id": 9, "src": "dce"}]}}, {"__index__": 1, "value": {"values": [{"id": 2, "src": "dce"}]}}]}} ` | | |
| - **Job 2:** | |
| * Job state is ok | |
| **Command Line:** | |
| * ```console | |
| cd ../; python _evaluate_expression_.py | |
| ``` | |
| **Exit Code:** | |
| * ```console | |
| 0 | |
| ``` | |
| **Traceback:** | |
| * ```console | |
| ``` | |
| **Job Parameters:** | |
| * | Job parameter | Parameter value | | |
| | ------------- | --------------- | | |
| | \_\_input\_ext | ` "input" ` | | |
| | \_\_workflow\_invocation\_uuid\_\_ | ` "30ca0a3a114e11f189517ced8d7c0d2f" ` | | |
| | chromInfo | ` "/tmp/tmpgck0c6r3/galaxy-dev/tool-data/shared/ucsc/chrom/?.len" ` | | |
| | dbkey | ` "?" ` | | |
| | style\_cond | ` {"__current_case__": 0, "pick_style": "first", "type_cond": {"__current_case__": 4, "param_type": "data", "pick_from": [{"__index__": 0, "value": {"values": [{"id": 10, "src": "dce"}]}}, {"__index__": 1, "value": {"values": [{"id": 3, "src": "dce"}]}}]}} ` | | |
| </details> | |
| - **Step 24: Unlabelled step (toolshed.g2.bx.psu.edu/repos/bgruening/text\_processing/tp\_replace\_in\_line/9.5+galaxy2)**: | |
| * step_state: scheduled | |
| * <details><summary>Jobs</summary> | |
| - **Job 1:** | |
| * Job state is ok | |
| **Container:** | |
| * ```console | |
| quay.io/biocontainers/sed:4.8 | |
| ``` | |
| **Command Line:** | |
| * ```console | |
| sed -r --sandbox -e '' -e 's/bp//g' -e '' -e 's/,//g' -e '' -e 's/([a-z])\s+([A-Z])/\1_\2/g' '/tmp/tmpgck0c6r3/files/b/5/c/dataset_b5c7d8f4-25ea-4fbc-8192-57afd6e4416c.dat' > '/tmp/tmpgck0c6r3/job_working_directory/000/17/outputs/dataset_3061865a-b0ec-410d-a21e-e7f40604ebed.dat' | |
| ``` | |
| **Exit Code:** | |
| * ```console | |
| 0 | |
| ``` | |
| **Traceback:** | |
| * ```console | |
| ``` | |
| **Job Parameters:** | |
| * | Job parameter | Parameter value | | |
| | ------------- | --------------- | | |
| | \_\_input\_ext | ` "input" ` | | |
| | \_\_workflow\_invocation\_uuid\_\_ | ` "30ca0a3a114e11f189517ced8d7c0d2f" ` | | |
| | chromInfo | ` "/tmp/tmpgck0c6r3/galaxy-dev/tool-data/shared/ucsc/chrom/?.len" ` | | |
| | dbkey | ` "?" ` | | |
| | replacements | ` [{"__index__": 0, "find_pattern": "bp", "replace_pattern": "", "sed_options": null}, {"__index__": 1, "find_pattern": ",", "replace_pattern": "", "sed_options": null}, {"__index__": 2, "find_pattern": "([a-z])\\s+([A-Z])", "replace_pattern": "\\1_\\2", "sed_options": null}] ` | | |
| </details> | |
| - **Step 25: Unlabelled step (Cut1)**: | |
| * step_state: scheduled | |
| * <details><summary>Jobs</summary> | |
| - **Job 1:** | |
| * Job state is ok | |
| **Container:** | |
| * ```console | |
| quay.io/biocontainers/perl:5.26--2 | |
| ``` | |
| **Command Line:** | |
| * ```console | |
| perl '/tmp/tmpgck0c6r3/galaxy-dev/tools/filters/cutWrapper.pl' '/tmp/tmpgck0c6r3/files/7/c/3/dataset_7c3ffb5c-0313-432c-8934-cb7188e9d840.dat' 'c7' T '/tmp/tmpgck0c6r3/job_working_directory/000/18/outputs/dataset_089fa93a-4954-410e-acb7-7f56a6f295a1.dat' | |
| ``` | |
| **Exit Code:** | |
| * ```console | |
| 0 | |
| ``` | |
| **Traceback:** | |
| * ```console | |
| ``` | |
| **Job Parameters:** | |
| * | Job parameter | Parameter value | | |
| | ------------- | --------------- | | |
| | \_\_input\_ext | ` "tabular" ` | | |
| | \_\_workflow\_invocation\_uuid\_\_ | ` "30ca0a3a114e11f189517ced8d7c0d2f" ` | | |
| | chromInfo | ` "/tmp/tmpgck0c6r3/galaxy-dev/tool-data/shared/ucsc/chrom/?.len" ` | | |
| | columnList | ` "c7" ` | | |
| | dbkey | ` "?" ` | | |
| | delimiter | ` "T" ` | | |
| </details> | |
| - **Step 26: Unlabelled step**: | |
| * step_state: scheduled | |
| * <details><summary>Subworkflow Steps</summary> | |
| - **Step 1: Unlabelled step**: | |
| * step_state: scheduled | |
| - **Step 2: Unlabelled step (toolshed.g2.bx.psu.edu/repos/iuc/collection\_element\_identifiers/collection\_element\_identifiers/0.0.2)**: | |
| * step_state: scheduled | |
| * <details><summary>Jobs</summary> | |
| - **Job 1:** | |
| * Job state is ok | |
| **Command Line:** | |
| * ```console | |
| mv '/tmp/tmpgck0c6r3/job_working_directory/000/19/configs/tmpx9ectcti' '/tmp/tmpgck0c6r3/job_working_directory/000/19/outputs/dataset_04b00fab-05c3-4b11-8ca0-eec4f4b6c108.dat' | |
| ``` | |
| **Exit Code:** | |
| * ```console | |
| 0 | |
| ``` | |
| **Traceback:** | |
| * ```console | |
| ``` | |
| **Job Parameters:** | |
| * | Job parameter | Parameter value | | |
| | ------------- | --------------- | | |
| | \_\_input\_ext | ` "expression.json" ` | | |
| | \_\_workflow\_invocation\_uuid\_\_ | ` "30ca0a3b114e11f189517ced8d7c0d2f" ` | | |
| | chromInfo | ` "/tmp/tmpgck0c6r3/galaxy-dev/tool-data/shared/ucsc/chrom/?.len" ` | | |
| | dbkey | ` "?" ` | | |
| | input\_collection | ` {"values": [{"id": 7, "src": "hdca"}]} ` | | |
| </details> | |
| - **Step 3: Unlabelled step (wc\_gnu)**: | |
| * step_state: scheduled | |
| * <details><summary>Jobs</summary> | |
| - **Job 1:** | |
| * Job state is ok | |
| **Command Line:** | |
| * ```console | |
| echo "#lines words characters" > /tmp/tmpgck0c6r3/job_working_directory/000/20/outputs/dataset_f5ab1ba3-8e98-4d72-98c6-336111042b0d.dat && cat '/tmp/tmpgck0c6r3/files/0/4/b/dataset_04b00fab-05c3-4b11-8ca0-eec4f4b6c108.dat' | wc -l -w -m | awk '{ print $1"\t"$2"\t"$3 }' >> /tmp/tmpgck0c6r3/job_working_directory/000/20/outputs/dataset_f5ab1ba3-8e98-4d72-98c6-336111042b0d.dat | |
| ``` | |
| **Exit Code:** | |
| * ```console | |
| 0 | |
| ``` | |
| **Traceback:** | |
| * ```console | |
| ``` | |
| **Job Parameters:** | |
| * | Job parameter | Parameter value | | |
| | ------------- | --------------- | | |
| | \_\_input\_ext | ` "txt" ` | | |
| | \_\_workflow\_invocation\_uuid\_\_ | ` "30ca0a3b114e11f189517ced8d7c0d2f" ` | | |
| | chromInfo | ` "/tmp/tmpgck0c6r3/galaxy-dev/tool-data/shared/ucsc/chrom/?.len" ` | | |
| | dbkey | ` "?" ` | | |
| | include\_header | ` true ` | | |
| | options | ` ["lines", "words", "characters"] ` | | |
| </details> | |
| - **Step 4: Unlabelled step (Cut1)**: | |
| * step_state: scheduled | |
| * <details><summary>Jobs</summary> | |
| - **Job 1:** | |
| * Job state is ok | |
| **Container:** | |
| * ```console | |
| quay.io/biocontainers/perl:5.26--2 | |
| ``` | |
| **Command Line:** | |
| * ```console | |
| perl '/tmp/tmpgck0c6r3/galaxy-dev/tools/filters/cutWrapper.pl' '/tmp/tmpgck0c6r3/files/f/5/a/dataset_f5ab1ba3-8e98-4d72-98c6-336111042b0d.dat' 'c1' T '/tmp/tmpgck0c6r3/job_working_directory/000/21/outputs/dataset_de7d39de-6205-4173-9eab-ff8d2d1940bc.dat' | |
| ``` | |
| **Exit Code:** | |
| * ```console | |
| 0 | |
| ``` | |
| **Traceback:** | |
| * ```console | |
| ``` | |
| **Job Parameters:** | |
| * | Job parameter | Parameter value | | |
| | ------------- | --------------- | | |
| | \_\_input\_ext | ` "tabular" ` | | |
| | \_\_workflow\_invocation\_uuid\_\_ | ` "30ca0a3b114e11f189517ced8d7c0d2f" ` | | |
| | chromInfo | ` "/tmp/tmpgck0c6r3/galaxy-dev/tool-data/shared/ucsc/chrom/?.len" ` | | |
| | columnList | ` "c1" ` | | |
| | dbkey | ` "?" ` | | |
| | delimiter | ` "T" ` | | |
| </details> | |
| - **Step 5: Unlabelled step (param\_value\_from\_file)**: | |
| * step_state: scheduled | |
| * <details><summary>Jobs</summary> | |
| - **Job 1:** | |
| * Job state is ok | |
| **Command Line:** | |
| * ```console | |
| cd ../; python _evaluate_expression_.py | |
| ``` | |
| **Exit Code:** | |
| * ```console | |
| 0 | |
| ``` | |
| **Traceback:** | |
| * ```console | |
| ``` | |
| **Job Parameters:** | |
| * | Job parameter | Parameter value | | |
| | ------------- | --------------- | | |
| | \_\_input\_ext | ` "input" ` | | |
| | \_\_workflow\_invocation\_uuid\_\_ | ` "30ca0a3b114e11f189517ced8d7c0d2f" ` | | |
| | chromInfo | ` "/tmp/tmpgck0c6r3/galaxy-dev/tool-data/shared/ucsc/chrom/?.len" ` | | |
| | dbkey | ` "?" ` | | |
| | param\_type | ` "text" ` | | |
| | remove\_newlines | ` true ` | | |
| </details> | |
| - **Step 6: Unlabelled step (toolshed.g2.bx.psu.edu/repos/iuc/map\_param\_value/map\_param\_value/0.2.0)**: | |
| * step_state: scheduled | |
| * <details><summary>Jobs</summary> | |
| - **Job 1:** | |
| * Job state is ok | |
| **Command Line:** | |
| * ```console | |
| cd ../; python _evaluate_expression_.py | |
| ``` | |
| **Exit Code:** | |
| * ```console | |
| 0 | |
| ``` | |
| **Traceback:** | |
| * ```console | |
| ``` | |
| **Job Parameters:** | |
| * | Job parameter | Parameter value | | |
| | ------------- | --------------- | | |
| | \_\_input\_ext | ` "input" ` | | |
| | \_\_workflow\_invocation\_uuid\_\_ | ` "30ca0a3b114e11f189517ced8d7c0d2f" ` | | |
| | chromInfo | ` "/tmp/tmpgck0c6r3/galaxy-dev/tool-data/shared/ucsc/chrom/?.len" ` | | |
| | dbkey | ` "?" ` | | |
| | input\_param\_type | ` {"__current_case__": 0, "input_param": "1", "mappings": [{"__index__": 0, "from": "0", "to": "True"}], "type": "text"} ` | | |
| | output\_param\_type | ` "boolean" ` | | |
| | unmapped | ` {"__current_case__": 2, "default_value": "False", "on_unmapped": "default"} ` | | |
| </details> | |
| - **Step 7: Unlabelled step (toolshed.g2.bx.psu.edu/repos/iuc/map\_param\_value/map\_param\_value/0.2.0)**: | |
| * step_state: scheduled | |
| * <details><summary>Jobs</summary> | |
| - **Job 1:** | |
| * Job state is ok | |
| **Command Line:** | |
| * ```console | |
| cd ../; python _evaluate_expression_.py | |
| ``` | |
| **Exit Code:** | |
| * ```console | |
| 0 | |
| ``` | |
| **Traceback:** | |
| * ```console | |
| ``` | |
| **Job Parameters:** | |
| * | Job parameter | Parameter value | | |
| | ------------- | --------------- | | |
| | \_\_input\_ext | ` "input" ` | | |
| | \_\_workflow\_invocation\_uuid\_\_ | ` "30ca0a3b114e11f189517ced8d7c0d2f" ` | | |
| | chromInfo | ` "/tmp/tmpgck0c6r3/galaxy-dev/tool-data/shared/ucsc/chrom/?.len" ` | | |
| | dbkey | ` "?" ` | | |
| | input\_param\_type | ` {"__current_case__": 0, "input_param": "1", "mappings": [{"__index__": 0, "from": "1", "to": "True"}], "type": "text"} ` | | |
| | output\_param\_type | ` "boolean" ` | | |
| | unmapped | ` {"__current_case__": 2, "default_value": "False", "on_unmapped": "default"} ` | | |
| </details> | |
| - **Step 8: Unlabelled step (toolshed.g2.bx.psu.edu/repos/iuc/map\_param\_value/map\_param\_value/0.2.0)**: | |
| * step_state: scheduled | |
| * <details><summary>Jobs</summary> | |
| - **Job 1:** | |
| * Job state is ok | |
| **Command Line:** | |
| * ```console | |
| cd ../; python _evaluate_expression_.py | |
| ``` | |
| **Exit Code:** | |
| * ```console | |
| 0 | |
| ``` | |
| **Traceback:** | |
| * ```console | |
| ``` | |
| **Job Parameters:** | |
| * | Job parameter | Parameter value | | |
| | ------------- | --------------- | | |
| | \_\_input\_ext | ` "input" ` | | |
| | \_\_workflow\_invocation\_uuid\_\_ | ` "30ca0a3b114e11f189517ced8d7c0d2f" ` | | |
| | chromInfo | ` "/tmp/tmpgck0c6r3/galaxy-dev/tool-data/shared/ucsc/chrom/?.len" ` | | |
| | dbkey | ` "?" ` | | |
| | input\_param\_type | ` {"__current_case__": 0, "input_param": "1", "mappings": [{"__index__": 0, "from": "0", "to": "False"}, {"__index__": 1, "from": "1", "to": "False"}], "type": "text"} ` | | |
| | output\_param\_type | ` "boolean" ` | | |
| | unmapped | ` {"__current_case__": 2, "default_value": "True", "on_unmapped": "default"} ` | | |
| </details> | |
| </details> | |
| - **Step 27: Unlabelled step (\_\_UNZIP\_COLLECTION\_\_)**: | |
| * step_state: scheduled | |
| * <details><summary>Jobs</summary> | |
| - **Job 1:** | |
| * Job state is ok | |
| **Traceback:** | |
| * ```console | |
| ``` | |
| **Job Parameters:** | |
| * | Job parameter | Parameter value | | |
| | ------------- | --------------- | | |
| | \_\_workflow\_invocation\_uuid\_\_ | ` "30ca0a3a114e11f189517ced8d7c0d2f" ` | | |
| | input | ` {"values": [{"id": 11, "src": "dce"}]} ` | | |
| </details> | |
| - **Step 28: Unlabelled step (Convert characters1)**: | |
| * step_state: scheduled | |
| * <details><summary>Jobs</summary> | |
| - **Job 1:** | |
| * Job state is ok | |
| **Container:** | |
| * ```console | |
| quay.io/biocontainers/python:3.13 | |
| ``` | |
| **Command Line:** | |
| * ```console | |
| python '/tmp/tmpgck0c6r3/galaxy-dev/tools/filters/convert_characters.py' --strip --condense '/tmp/tmpgck0c6r3/files/3/0/6/dataset_3061865a-b0ec-410d-a21e-e7f40604ebed.dat' 's' '/tmp/tmpgck0c6r3/job_working_directory/000/24/outputs/dataset_8ce8ec6d-abcb-4f79-8162-02a5c8d03c17.dat' | |
| ``` | |
| **Exit Code:** | |
| * ```console | |
| 0 | |
| ``` | |
| **Traceback:** | |
| * ```console | |
| ``` | |
| **Job Parameters:** | |
| * | Job parameter | Parameter value | | |
| | ------------- | --------------- | | |
| | \_\_input\_ext | ` "input" ` | | |
| | \_\_workflow\_invocation\_uuid\_\_ | ` "30ca0a3a114e11f189517ced8d7c0d2f" ` | | |
| | chromInfo | ` "/tmp/tmpgck0c6r3/galaxy-dev/tool-data/shared/ucsc/chrom/?.len" ` | | |
| | condense | ` true ` | | |
| | convert\_from | ` "s" ` | | |
| | dbkey | ` "?" ` | | |
| | strip | ` true ` | | |
| </details> | |
| - **Step 29: Estimated homozygous read coverage (param\_value\_from\_file)**: | |
| * step_state: scheduled | |
| * <details><summary>Jobs</summary> | |
| - **Job 1:** | |
| * Job state is ok | |
| **Command Line:** | |
| * ```console | |
| cd ../; python _evaluate_expression_.py | |
| ``` | |
| **Exit Code:** | |
| * ```console | |
| 0 | |
| ``` | |
| **Traceback:** | |
| * ```console | |
| ``` | |
| **Job Parameters:** | |
| * | Job parameter | Parameter value | | |
| | ------------- | --------------- | | |
| | \_\_input\_ext | ` "input" ` | | |
| | \_\_workflow\_invocation\_uuid\_\_ | ` "30ca0a3a114e11f189517ced8d7c0d2f" ` | | |
| | chromInfo | ` "/tmp/tmpgck0c6r3/galaxy-dev/tool-data/shared/ucsc/chrom/?.len" ` | | |
| | dbkey | ` "?" ` | | |
| | param\_type | ` "integer" ` | | |
| | remove\_newlines | ` true ` | | |
| </details> | |
| - **Step 30: Extract Hic forward (\_\_EXTRACT\_DATASET\_\_)**: | |
| * step_state: scheduled | |
| * <details><summary>Jobs</summary> | |
| - **Job 1:** | |
| * Job state is ok | |
| **Traceback:** | |
| * ```console | |
| ``` | |
| **Job Parameters:** | |
| * | Job parameter | Parameter value | | |
| | ------------- | --------------- | | |
| | \_\_workflow\_invocation\_uuid\_\_ | ` "30ca0a3a114e11f189517ced8d7c0d2f" ` | | |
| | input | ` {"values": [{"id": 8, "src": "hdca"}]} ` | | |
| | which | ` {"__current_case__": 0, "which_dataset": "first"} ` | | |
| </details> | |
| - **Step 31: Extract Hic reverse (\_\_EXTRACT\_DATASET\_\_)**: | |
| * step_state: scheduled | |
| * <details><summary>Jobs</summary> | |
| - **Job 1:** | |
| * Job state is ok | |
| **Traceback:** | |
| * ```console | |
| ``` | |
| **Job Parameters:** | |
| * | Job parameter | Parameter value | | |
| | ------------- | --------------- | | |
| | \_\_workflow\_invocation\_uuid\_\_ | ` "30ca0a3a114e11f189517ced8d7c0d2f" ` | | |
| | input | ` {"values": [{"id": 9, "src": "hdca"}]} ` | | |
| | which | ` {"__current_case__": 0, "which_dataset": "first"} ` | | |
| </details> | |
| - **Step 32: Collapse forward reads (toolshed.g2.bx.psu.edu/repos/nml/collapse\_collections/collapse\_dataset/5.1.0)**: | |
| * step_state: scheduled | |
| * <details><summary>Jobs</summary> | |
| - **Job 1:** | |
| * Job state is skipped | |
| **Traceback:** | |
| * ```console | |
| ``` | |
| **Job Parameters:** | |
| * | Job parameter | Parameter value | | |
| | ------------- | --------------- | | |
| | \_\_input\_ext | ` "input" ` | | |
| | \_\_workflow\_invocation\_uuid\_\_ | ` "30ca0a3a114e11f189517ced8d7c0d2f" ` | | |
| | chromInfo | ` "/tmp/tmpgck0c6r3/galaxy-dev/tool-data/shared/ucsc/chrom/?.len" ` | | |
| | dbkey | ` "?" ` | | |
| | filename | ` {"__current_case__": 1, "add_name": false} ` | | |
| | one\_header | ` false ` | | |
| </details> | |
| - **Step 33: Collapse reverse reads (toolshed.g2.bx.psu.edu/repos/nml/collapse\_collections/collapse\_dataset/5.1.0)**: | |
| * step_state: scheduled | |
| * <details><summary>Jobs</summary> | |
| - **Job 1:** | |
| * Job state is skipped | |
| **Traceback:** | |
| * ```console | |
| ``` | |
| **Job Parameters:** | |
| * | Job parameter | Parameter value | | |
| | ------------- | --------------- | | |
| | \_\_input\_ext | ` "input" ` | | |
| | \_\_workflow\_invocation\_uuid\_\_ | ` "30ca0a3a114e11f189517ced8d7c0d2f" ` | | |
| | chromInfo | ` "/tmp/tmpgck0c6r3/galaxy-dev/tool-data/shared/ucsc/chrom/?.len" ` | | |
| | dbkey | ` "?" ` | | |
| | filename | ` {"__current_case__": 1, "add_name": false} ` | | |
| | one\_header | ` false ` | | |
| </details> | |
| - **Step 34: Unlabelled step (Cut1)**: | |
| * step_state: scheduled | |
| * <details><summary>Jobs</summary> | |
| - **Job 1:** | |
| * Job state is ok | |
| **Container:** | |
| * ```console | |
| quay.io/biocontainers/perl:5.26--2 | |
| ``` | |
| **Command Line:** | |
| * ```console | |
| perl '/tmp/tmpgck0c6r3/galaxy-dev/tools/filters/cutWrapper.pl' '/tmp/tmpgck0c6r3/files/8/c/e/dataset_8ce8ec6d-abcb-4f79-8162-02a5c8d03c17.dat' 'c3' T '/tmp/tmpgck0c6r3/job_working_directory/000/26/outputs/dataset_c9b2437a-a6f6-4e16-aef0-e5fdba7d7211.dat' | |
| ``` | |
| **Exit Code:** | |
| * ```console | |
| 0 | |
| ``` | |
| **Traceback:** | |
| * ```console | |
| ``` | |
| **Job Parameters:** | |
| * | Job parameter | Parameter value | | |
| | ------------- | --------------- | | |
| | \_\_input\_ext | ` "tabular" ` | | |
| | \_\_workflow\_invocation\_uuid\_\_ | ` "30ca0a3a114e11f189517ced8d7c0d2f" ` | | |
| | chromInfo | ` "/tmp/tmpgck0c6r3/galaxy-dev/tool-data/shared/ucsc/chrom/?.len" ` | | |
| | columnList | ` "c3" ` | | |
| | dbkey | ` "?" ` | | |
| | delimiter | ` "T" ` | | |
| </details> | |
| - **Step 35: Homozygous read coverage for Hifiasm (toolshed.g2.bx.psu.edu/repos/iuc/pick\_value/pick\_value/0.2.0)**: | |
| * step_state: scheduled | |
| * <details><summary>Jobs</summary> | |
| - **Job 1:** | |
| * Job state is ok | |
| **Command Line:** | |
| * ```console | |
| cd ../; python _evaluate_expression_.py | |
| ``` | |
| **Exit Code:** | |
| * ```console | |
| 0 | |
| ``` | |
| **Traceback:** | |
| * ```console | |
| ``` | |
| **Job Parameters:** | |
| * | Job parameter | Parameter value | | |
| | ------------- | --------------- | | |
| | \_\_input\_ext | ` "input" ` | | |
| | \_\_workflow\_invocation\_uuid\_\_ | ` "30ca0a3a114e11f189517ced8d7c0d2f" ` | | |
| | chromInfo | ` "/tmp/tmpgck0c6r3/galaxy-dev/tool-data/shared/ucsc/chrom/?.len" ` | | |
| | dbkey | ` "?" ` | | |
| | style\_cond | ` {"__current_case__": 0, "pick_style": "first", "type_cond": {"__current_case__": 1, "param_type": "integer", "pick_from": [{"__index__": 0, "value": null}, {"__index__": 1, "value": "21"}]}} ` | | |
| </details> | |
| - **Step 36: Hi-C forward reads (toolshed.g2.bx.psu.edu/repos/iuc/pick\_value/pick\_value/0.2.0)**: | |
| * step_state: scheduled | |
| * <details><summary>Jobs</summary> | |
| - **Job 1:** | |
| * Job state is ok | |
| **Command Line:** | |
| * ```console | |
| cd ../; python _evaluate_expression_.py | |
| ``` | |
| **Exit Code:** | |
| * ```console | |
| 0 | |
| ``` | |
| **Traceback:** | |
| * ```console | |
| ``` | |
| **Job Parameters:** | |
| * | Job parameter | Parameter value | | |
| | ------------- | --------------- | | |
| | \_\_input\_ext | ` "input" ` | | |
| | \_\_workflow\_invocation\_uuid\_\_ | ` "30ca0a3a114e11f189517ced8d7c0d2f" ` | | |
| | chromInfo | ` "/tmp/tmpgck0c6r3/galaxy-dev/tool-data/shared/ucsc/chrom/?.len" ` | | |
| | dbkey | ` "?" ` | | |
| | style\_cond | ` {"__current_case__": 0, "pick_style": "first", "type_cond": {"__current_case__": 4, "param_type": "data", "pick_from": [{"__index__": 0, "value": {"values": [{"id": 39, "src": "hda"}]}}, {"__index__": 1, "value": {"values": [{"id": 37, "src": "hda"}]}}]}} ` | | |
| </details> | |
| - **Step 37: Hi-C reverse reads (toolshed.g2.bx.psu.edu/repos/iuc/pick\_value/pick\_value/0.2.0)**: | |
| * step_state: scheduled | |
| * <details><summary>Jobs</summary> | |
| - **Job 1:** | |
| * Job state is ok | |
| **Command Line:** | |
| * ```console | |
| cd ../; python _evaluate_expression_.py | |
| ``` | |
| **Exit Code:** | |
| * ```console | |
| 0 | |
| ``` | |
| **Traceback:** | |
| * ```console | |
| ``` | |
| **Job Parameters:** | |
| * | Job parameter | Parameter value | | |
| | ------------- | --------------- | | |
| | \_\_input\_ext | ` "input" ` | | |
| | \_\_workflow\_invocation\_uuid\_\_ | ` "30ca0a3a114e11f189517ced8d7c0d2f" ` | | |
| | chromInfo | ` "/tmp/tmpgck0c6r3/galaxy-dev/tool-data/shared/ucsc/chrom/?.len" ` | | |
| | dbkey | ` "?" ` | | |
| | style\_cond | ` {"__current_case__": 0, "pick_style": "first", "type_cond": {"__current_case__": 4, "param_type": "data", "pick_from": [{"__index__": 0, "value": {"values": [{"id": 40, "src": "hda"}]}}, {"__index__": 1, "value": {"values": [{"id": 38, "src": "hda"}]}}]}} ` | | |
| </details> | |
| - **Step 38: Estimated genome size (param\_value\_from\_file)**: | |
| * step_state: scheduled | |
| * <details><summary>Jobs</summary> | |
| - **Job 1:** | |
| * Job state is ok | |
| **Command Line:** | |
| * ```console | |
| cd ../; python _evaluate_expression_.py | |
| ``` | |
| **Exit Code:** | |
| * ```console | |
| 0 | |
| ``` | |
| **Traceback:** | |
| * ```console | |
| ``` | |
| **Job Parameters:** | |
| * | Job parameter | Parameter value | | |
| | ------------- | --------------- | | |
| | \_\_input\_ext | ` "input" ` | | |
| | \_\_workflow\_invocation\_uuid\_\_ | ` "30ca0a3a114e11f189517ced8d7c0d2f" ` | | |
| | chromInfo | ` "/tmp/tmpgck0c6r3/galaxy-dev/tool-data/shared/ucsc/chrom/?.len" ` | | |
| | dbkey | ` "?" ` | | |
| | param\_type | ` "integer" ` | | |
| | remove\_newlines | ` true ` | | |
| </details> | |
| - **Step 39: Hifiasm (toolshed.g2.bx.psu.edu/repos/bgruening/hifiasm/hifiasm/0.25.0+galaxy0)**: | |
| * step_state: scheduled | |
| * <details><summary>Jobs</summary> | |
| - **Job 1:** | |
| * Job state is ok | |
| **Container:** | |
| * ```console | |
| quay.io/biocontainers/mulled-v2-36ba0d5590c58fd8485272d70f458149cdb6dd94:1301b5b2d7a262e3260acaef4392863cb62ec20f-0 | |
| ``` | |
| **Command Line:** | |
| * ```console | |
| ln -s '/tmp/tmpgck0c6r3/files/2/3/2/dataset_2320363f-e509-45ed-96dd-6904d97f0b79.dat' input_0.fastq.gz && mkdir HiCF HiCR && ln -s '/tmp/tmpgck0c6r3/files/4/7/f/dataset_47fb3015-e379-43c7-a4f9-396fe42f9469.dat' ./HiCF/input_0.fastqsanger.gz && ln -s '/tmp/tmpgck0c6r3/files/8/2/5/dataset_825722e9-9d28-4976-b51b-702cfbe24de7.dat' ./HiCR/input_0.fastqsanger.gz && hifiasm -t ${GALAXY_SLOTS:-1} -o output -f 32 -a 4 -z 0 -m 10000000 -p 100000 -n 3 -x 0.8 -y 0.2 --hom-cov 21 --h1 './HiCF/input_0.fastqsanger.gz' --h2 './HiCR/input_0.fastqsanger.gz' --l-msjoin 500000 --primary input_0.fastq.gz 2> output.log && mkdir noseq_files && mv *.noseq.gfa noseq_files && mkdir bin_files && mv *.bin bin_files | |
| ``` | |
| **Exit Code:** | |
| * ```console | |
| 0 | |
| ``` | |
| **Traceback:** | |
| * ```console | |
| ``` | |
| **Job Parameters:** | |
| * | Job parameter | Parameter value | | |
| | ------------- | --------------- | | |
| | \_\_input\_ext | ` "fastq.gz" ` | | |
| | \_\_workflow\_invocation\_uuid\_\_ | ` "30ca0a3a114e11f189517ced8d7c0d2f" ` | | |
| | advanced\_options | ` {"__current_case__": 0, "advanced_selector": "blank"} ` | | |
| | assembly\_options | ` {"__current_case__": 1, "adapter_length": "0", "assembly_selector": "set", "cleaning_rounds": "4", "disable_post_join": false, "hom_cov": "21", "ignore_error_corrected": false, "max_overlap": "0.8", "min_overlap": "0.2", "pop_contigs": "10000000", "pop_unitigs": "100000", "remove_tips": "3"} ` | | |
| | bins\_out | ` true ` | | |
| | chromInfo | ` "/tmp/tmpgck0c6r3/galaxy-dev/tool-data/shared/ucsc/chrom/?.len" ` | | |
| | dbkey | ` "?" ` | | |
| | filter\_bits | ` "32" ` | | |
| | hic\_partition | ` {"__current_case__": 1, "f_perturb": null, "h1": {"values": [{"id": 41, "src": "hda"}]}, "h2": {"values": [{"id": 42, "src": "hda"}]}, "hic_partition_selector": "set", "l_msjoin": "500000", "n_perturb": null, "n_weight": null, "seed": null} ` | | |
| | log\_out | ` true ` | | |
| | mode | ` {"__current_case__": 0, "mode_selector": "standard", "reads": {"values": [{"id": 3, "src": "hdca"}]}} ` | | |
| | ont\_integration | ` {"__current_case__": 0, "ont_integration_selector": "blank"} ` | | |
| | purge\_options | ` {"__current_case__": 0, "purge_selector": "blank"} ` | | |
| | scaffolding\_options | ` {"__current_case__": 0, "scaffold_selector": "blank"} ` | | |
| </details> | |
| - **Step 40: Unlabelled step (toolshed.g2.bx.psu.edu/repos/bgruening/gfastats/gfastats/1.3.11+galaxy0)**: | |
| * step_state: scheduled | |
| * <details><summary>Jobs</summary> | |
| - **Job 1:** | |
| * Job state is ok | |
| **Container:** | |
| * ```console | |
| quay.io/biocontainers/gfastats:1.3.11--h077b44d_0 | |
| ``` | |
| **Command Line:** | |
| * ```console | |
| gfastats '/tmp/tmpgck0c6r3/files/2/f/7/dataset_2f7b64ca-7850-4736-8ea3-0600db0f18d7.dat' 2288021 --nstar-report --locale en_US.UTF-8 --discover-paths --tabular > '/tmp/tmpgck0c6r3/job_working_directory/000/39/outputs/dataset_83218544-a578-473d-be4f-7625e30aa8bb.dat' --threads ${GALAXY_SLOTS:-8} | |
| ``` | |
| **Exit Code:** | |
| * ```console | |
| 0 | |
| ``` | |
| **Traceback:** | |
| * ```console | |
| ``` | |
| **Job Parameters:** | |
| * | Job parameter | Parameter value | | |
| | ------------- | --------------- | | |
| | \_\_input\_ext | ` "input" ` | | |
| | \_\_workflow\_invocation\_uuid\_\_ | ` "30ca0a3a114e11f189517ced8d7c0d2f" ` | | |
| | chromInfo | ` "/tmp/tmpgck0c6r3/galaxy-dev/tool-data/shared/ucsc/chrom/?.len" ` | | |
| | dbkey | ` "?" ` | | |
| | mode\_condition | ` {"__current_case__": 1, "discover_paths": true, "locale": true, "selector": "statistics", "statistics_condition": {"__current_case__": 2, "expected_genomesize": "2288021", "selector": "assembly"}, "tabular": true} ` | | |
| | target\_condition | ` {"__current_case__": 0, "target_option": "false"} ` | | |
| </details> | |
| - **Step 41: Unlabelled step (toolshed.g2.bx.psu.edu/repos/bgruening/gfastats/gfastats/1.3.11+galaxy0)**: | |
| * step_state: scheduled | |
| * <details><summary>Jobs</summary> | |
| - **Job 1:** | |
| * Job state is ok | |
| **Container:** | |
| * ```console | |
| quay.io/biocontainers/gfastats:1.3.11--h077b44d_0 | |
| ``` | |
| **Command Line:** | |
| * ```console | |
| gfastats '/tmp/tmpgck0c6r3/files/8/1/b/dataset_81b287d4-8420-4d66-b390-dbdb0b735038.dat' 2288021 --nstar-report --locale en_US.UTF-8 --discover-paths --tabular > '/tmp/tmpgck0c6r3/job_working_directory/000/40/outputs/dataset_931d6a99-69cc-46b9-aa68-54e8fd18d923.dat' --threads ${GALAXY_SLOTS:-8} | |
| ``` | |
| **Exit Code:** | |
| * ```console | |
| 0 | |
| ``` | |
| **Traceback:** | |
| * ```console | |
| ``` | |
| **Job Parameters:** | |
| * | Job parameter | Parameter value | | |
| | ------------- | --------------- | | |
| | \_\_input\_ext | ` "input" ` | | |
| | \_\_workflow\_invocation\_uuid\_\_ | ` "30ca0a3a114e11f189517ced8d7c0d2f" ` | | |
| | chromInfo | ` "/tmp/tmpgck0c6r3/galaxy-dev/tool-data/shared/ucsc/chrom/?.len" ` | | |
| | dbkey | ` "?" ` | | |
| | mode\_condition | ` {"__current_case__": 1, "discover_paths": true, "locale": true, "selector": "statistics", "statistics_condition": {"__current_case__": 2, "expected_genomesize": "2288021", "selector": "assembly"}, "tabular": true} ` | | |
| | target\_condition | ` {"__current_case__": 0, "target_option": "false"} ` | | |
| </details> | |
| - **Step 42: Raw Unitig Image (toolshed.g2.bx.psu.edu/repos/iuc/bandage/bandage\_image/2022.09+galaxy4)**: | |
| * step_state: scheduled | |
| * <details><summary>Jobs</summary> | |
| - **Job 1:** | |
| * Job state is ok | |
| **Container:** | |
| * ```console | |
| quay.io/biocontainers/bandage_ng:2022.09--h60d1f2b_4 | |
| ``` | |
| **Command Line:** | |
| * ```console | |
| ln -s '/tmp/tmpgck0c6r3/files/4/4/c/dataset_44c6b6cd-dff9-4413-8c90-796831f139a3.dat' input.gfa && export QT_QPA_PLATFORM='offscreen' && Bandage image input.gfa 'out.png' --height '2000' --nodewidth '25.0' | |
| ``` | |
| **Exit Code:** | |
| * ```console | |
| 0 | |
| ``` | |
| **Traceback:** | |
| * ```console | |
| ``` | |
| **Job Parameters:** | |
| * | Job parameter | Parameter value | | |
| | ------------- | --------------- | | |
| | \_\_input\_ext | ` "input" ` | | |
| | \_\_workflow\_invocation\_uuid\_\_ | ` "30ca0a3a114e11f189517ced8d7c0d2f" ` | | |
| | chromInfo | ` "/tmp/tmpgck0c6r3/galaxy-dev/tool-data/shared/ucsc/chrom/?.len" ` | | |
| | dbkey | ` "?" ` | | |
| | fontsize | ` None ` | | |
| | height | ` "2000" ` | | |
| | lengths | ` false ` | | |
| | names | ` false ` | | |
| | nodewidth | ` "25.0" ` | | |
| | output\_format | ` "png" ` | | |
| | width | ` None ` | | |
| </details> | |
| - **Step 43: Unlabelled step (toolshed.g2.bx.psu.edu/repos/bgruening/gfastats/gfastats/1.3.11+galaxy0)**: | |
| * step_state: scheduled | |
| * <details><summary>Jobs</summary> | |
| - **Job 1:** | |
| * Job state is ok | |
| **Container:** | |
| * ```console | |
| quay.io/biocontainers/gfastats:1.3.11--h077b44d_0 | |
| ``` | |
| **Command Line:** | |
| * ```console | |
| gfastats '/tmp/tmpgck0c6r3/files/2/f/7/dataset_2f7b64ca-7850-4736-8ea3-0600db0f18d7.dat' --out-size c --discover-paths --tabular > '/tmp/tmpgck0c6r3/job_working_directory/000/42/outputs/dataset_20b16557-8e60-4859-a828-7a54fb86d977.dat' --threads ${GALAXY_SLOTS:-8} | |
| ``` | |
| **Exit Code:** | |
| * ```console | |
| 0 | |
| ``` | |
| **Traceback:** | |
| * ```console | |
| ``` | |
| **Job Parameters:** | |
| * | Job parameter | Parameter value | | |
| | ------------- | --------------- | | |
| | \_\_input\_ext | ` "input" ` | | |
| | \_\_workflow\_invocation\_uuid\_\_ | ` "30ca0a3a114e11f189517ced8d7c0d2f" ` | | |
| | chromInfo | ` "/tmp/tmpgck0c6r3/galaxy-dev/tool-data/shared/ucsc/chrom/?.len" ` | | |
| | dbkey | ` "?" ` | | |
| | mode\_condition | ` {"__current_case__": 1, "discover_paths": true, "locale": false, "selector": "statistics", "statistics_condition": {"__current_case__": 0, "out_size": "c", "selector": "size"}, "tabular": true} ` | | |
| | target\_condition | ` {"__current_case__": 0, "target_option": "false"} ` | | |
| </details> | |
| - **Step 44: gfastats gfa hap2 no sequences (toolshed.g2.bx.psu.edu/repos/bgruening/gfastats/gfastats/1.3.11+galaxy0)**: | |
| * step_state: scheduled | |
| * <details><summary>Jobs</summary> | |
| - **Job 1:** | |
| * Job state is ok | |
| **Container:** | |
| * ```console | |
| quay.io/biocontainers/gfastats:1.3.11--h077b44d_0 | |
| ``` | |
| **Command Line:** | |
| * ```console | |
| gfastats '/tmp/tmpgck0c6r3/files/2/f/7/dataset_2f7b64ca-7850-4736-8ea3-0600db0f18d7.dat' --discover-paths -o dataset.gfa --no-sequence --threads ${GALAXY_SLOTS:-8} && mv dataset* output_dataset | |
| ``` | |
| **Exit Code:** | |
| * ```console | |
| 0 | |
| ``` | |
| **Standard Output:** | |
| * ```console | |
| +++Assembly summary+++: | |
| # scaffolds: 51 | |
| Total scaffold length: 1351178 | |
| Average scaffold length: 26493.69 | |
| Scaffold N50: 23338 | |
| Scaffold auN: 40651.78 | |
| Scaffold L50: 16 | |
| Largest scaffold: 132684 | |
| Smallest scaffold: 16240 | |
| # contigs: 51 | |
| Total contig length: 1351178 | |
| Average contig length: 26493.69 | |
| Contig N50: 23338 | |
| Contig auN: 40651.78 | |
| Contig L50: 16 | |
| Largest contig: 132684 | |
| Smallest contig: 16240 | |
| # gaps in scaffolds: 0 | |
| Total gap length in scaffolds: 0 | |
| Average gap length in scaffolds: 0.00 | |
| Gap N50 in scaffolds: 0 | |
| Gap auN in scaffolds: 0.00 | |
| Gap L50 in scaffolds: 0 | |
| Largest gap in scaffolds: 0 | |
| Smallest gap in scaffolds: 0 | |
| Base composition (A:C:G:T): 409637:263447:265494:412600 | |
| GC content %: 39.15 | |
| # soft-masked bases: 0 | |
| # segments: 51 | |
| Total segment length: 1351178 | |
| Average segment length: 26493.69 | |
| # gaps: 0 | |
| # paths: 51 | |
| ``` | |
| **Traceback:** | |
| * ```console | |
| ``` | |
| **Job Parameters:** | |
| * | Job parameter | Parameter value | | |
| | ------------- | --------------- | | |
| | \_\_input\_ext | ` "input" ` | | |
| | \_\_workflow\_invocation\_uuid\_\_ | ` "30ca0a3a114e11f189517ced8d7c0d2f" ` | | |
| | chromInfo | ` "/tmp/tmpgck0c6r3/galaxy-dev/tool-data/shared/ucsc/chrom/?.len" ` | | |
| | dbkey | ` "?" ` | | |
| | mode\_condition | ` {"__current_case__": 0, "discover_paths": true, "homopolymer_compress": null, "output_condition": {"__current_case__": 4, "no_sequence": true, "out_format": "gfa", "terminal_overlaps_condition": {"__current_case__": 0, "terminal_overlaps_select": "no"}}, "remove_terminal_gaps": false, "selector": "manipulation", "sort": "", "swiss_army_knife": null} ` | | |
| | target\_condition | ` {"__current_case__": 0, "target_option": "false"} ` | | |
| </details> | |
| - **Step 45: Unlabelled step (toolshed.g2.bx.psu.edu/repos/bgruening/gfastats/gfastats/1.3.11+galaxy0)**: | |
| * step_state: scheduled | |
| * <details><summary>Jobs</summary> | |
| - **Job 1:** | |
| * Job state is ok | |
| **Container:** | |
| * ```console | |
| quay.io/biocontainers/gfastats:1.3.11--h077b44d_0 | |
| ``` | |
| **Command Line:** | |
| * ```console | |
| gfastats '/tmp/tmpgck0c6r3/files/8/1/b/dataset_81b287d4-8420-4d66-b390-dbdb0b735038.dat' --out-size c --discover-paths --tabular > '/tmp/tmpgck0c6r3/job_working_directory/000/44/outputs/dataset_a5ec6afd-3143-456a-9be9-c36d55ef4c29.dat' --threads ${GALAXY_SLOTS:-8} | |
| ``` | |
| **Exit Code:** | |
| * ```console | |
| 0 | |
| ``` | |
| **Traceback:** | |
| * ```console | |
| ``` | |
| **Job Parameters:** | |
| * | Job parameter | Parameter value | | |
| | ------------- | --------------- | | |
| | \_\_input\_ext | ` "input" ` | | |
| | \_\_workflow\_invocation\_uuid\_\_ | ` "30ca0a3a114e11f189517ced8d7c0d2f" ` | | |
| | chromInfo | ` "/tmp/tmpgck0c6r3/galaxy-dev/tool-data/shared/ucsc/chrom/?.len" ` | | |
| | dbkey | ` "?" ` | | |
| | mode\_condition | ` {"__current_case__": 1, "discover_paths": true, "locale": false, "selector": "statistics", "statistics_condition": {"__current_case__": 0, "out_size": "c", "selector": "size"}, "tabular": true} ` | | |
| | target\_condition | ` {"__current_case__": 0, "target_option": "false"} ` | | |
| </details> | |
| - **Step 46: gfastats gfa hap1 (toolshed.g2.bx.psu.edu/repos/bgruening/gfastats/gfastats/1.3.11+galaxy0)**: | |
| * step_state: scheduled | |
| * <details><summary>Jobs</summary> | |
| - **Job 1:** | |
| * Job state is ok | |
| **Container:** | |
| * ```console | |
| quay.io/biocontainers/gfastats:1.3.11--h077b44d_0 | |
| ``` | |
| **Command Line:** | |
| * ```console | |
| gfastats '/tmp/tmpgck0c6r3/files/8/1/b/dataset_81b287d4-8420-4d66-b390-dbdb0b735038.dat' --discover-paths -o dataset.gfa --threads ${GALAXY_SLOTS:-8} && mv dataset* output_dataset | |
| ``` | |
| **Exit Code:** | |
| * ```console | |
| 0 | |
| ``` | |
| **Standard Output:** | |
| * ```console | |
| +++Assembly summary+++: | |
| # scaffolds: 57 | |
| Total scaffold length: 1473565 | |
| Average scaffold length: 25852.02 | |
| Scaffold N50: 23819 | |
| Scaffold auN: 38682.45 | |
| Scaffold L50: 20 | |
| Largest scaffold: 132684 | |
| Smallest scaffold: 15406 | |
| # contigs: 57 | |
| Total contig length: 1473565 | |
| Average contig length: 25852.02 | |
| Contig N50: 23819 | |
| Contig auN: 38682.45 | |
| Contig L50: 20 | |
| Largest contig: 132684 | |
| Smallest contig: 15406 | |
| # gaps in scaffolds: 0 | |
| Total gap length in scaffolds: 0 | |
| Average gap length in scaffolds: 0.00 | |
| Gap N50 in scaffolds: 0 | |
| Gap auN in scaffolds: 0.00 | |
| Gap L50 in scaffolds: 0 | |
| Largest gap in scaffolds: 0 | |
| Smallest gap in scaffolds: 0 | |
| Base composition (A:C:G:T): 448657:285670:288915:450323 | |
| GC content %: 38.99 | |
| # soft-masked bases: 0 | |
| # segments: 57 | |
| Total segment length: 1473565 | |
| Average segment length: 25852.02 | |
| # gaps: 0 | |
| # paths: 57 | |
| # edges: 4 | |
| Average degree: 0.07 | |
| # connected components: 1 | |
| Largest connected component length: 89366 | |
| # dead ends: 111 | |
| # disconnected components: 54 | |
| Total length disconnected components: 1384199 | |
| # separated components: 55 | |
| # bubbles: 0 | |
| # circular segments: 0 | |
| # circular paths: 0 | |
| ``` | |
| **Traceback:** | |
| * ```console | |
| ``` | |
| **Job Parameters:** | |
| * | Job parameter | Parameter value | | |
| | ------------- | --------------- | | |
| | \_\_input\_ext | ` "input" ` | | |
| | \_\_workflow\_invocation\_uuid\_\_ | ` "30ca0a3a114e11f189517ced8d7c0d2f" ` | | |
| | chromInfo | ` "/tmp/tmpgck0c6r3/galaxy-dev/tool-data/shared/ucsc/chrom/?.len" ` | | |
| | dbkey | ` "?" ` | | |
| | mode\_condition | ` {"__current_case__": 0, "discover_paths": true, "homopolymer_compress": null, "output_condition": {"__current_case__": 4, "no_sequence": false, "out_format": "gfa", "terminal_overlaps_condition": {"__current_case__": 0, "terminal_overlaps_select": "no"}}, "remove_terminal_gaps": false, "selector": "manipulation", "sort": "", "swiss_army_knife": null} ` | | |
| | target\_condition | ` {"__current_case__": 0, "target_option": "false"} ` | | |
| </details> | |
| - **Step 47: gfastats gfa hap2 (toolshed.g2.bx.psu.edu/repos/bgruening/gfastats/gfastats/1.3.11+galaxy0)**: | |
| * step_state: scheduled | |
| * <details><summary>Jobs</summary> | |
| - **Job 1:** | |
| * Job state is ok | |
| **Container:** | |
| * ```console | |
| quay.io/biocontainers/gfastats:1.3.11--h077b44d_0 | |
| ``` | |
| **Command Line:** | |
| * ```console | |
| gfastats '/tmp/tmpgck0c6r3/files/2/f/7/dataset_2f7b64ca-7850-4736-8ea3-0600db0f18d7.dat' --discover-paths -o dataset.gfa --threads ${GALAXY_SLOTS:-8} && mv dataset* output_dataset | |
| ``` | |
| **Exit Code:** | |
| * ```console | |
| 0 | |
| ``` | |
| **Standard Output:** | |
| * ```console | |
| +++Assembly summary+++: | |
| # scaffolds: 51 | |
| Total scaffold length: 1351178 | |
| Average scaffold length: 26493.69 | |
| Scaffold N50: 23338 | |
| Scaffold auN: 40651.78 | |
| Scaffold L50: 16 | |
| Largest scaffold: 132684 | |
| Smallest scaffold: 16240 | |
| # contigs: 51 | |
| Total contig length: 1351178 | |
| Average contig length: 26493.69 | |
| Contig N50: 23338 | |
| Contig auN: 40651.78 | |
| Contig L50: 16 | |
| Largest contig: 132684 | |
| Smallest contig: 16240 | |
| # gaps in scaffolds: 0 | |
| Total gap length in scaffolds: 0 | |
| Average gap length in scaffolds: 0.00 | |
| Gap N50 in scaffolds: 0 | |
| Gap auN in scaffolds: 0.00 | |
| Gap L50 in scaffolds: 0 | |
| Largest gap in scaffolds: 0 | |
| Smallest gap in scaffolds: 0 | |
| Base composition (A:C:G:T): 409637:263447:265494:412600 | |
| GC content %: 39.15 | |
| # soft-masked bases: 0 | |
| # segments: 51 | |
| Total segment length: 1351178 | |
| Average segment length: 26493.69 | |
| # gaps: 0 | |
| # paths: 51 | |
| ``` | |
| **Traceback:** | |
| * ```console | |
| ``` | |
| **Job Parameters:** | |
| * | Job parameter | Parameter value | | |
| | ------------- | --------------- | | |
| | \_\_input\_ext | ` "input" ` | | |
| | \_\_workflow\_invocation\_uuid\_\_ | ` "30ca0a3a114e11f189517ced8d7c0d2f" ` | | |
| | chromInfo | ` "/tmp/tmpgck0c6r3/galaxy-dev/tool-data/shared/ucsc/chrom/?.len" ` | | |
| | dbkey | ` "?" ` | | |
| | mode\_condition | ` {"__current_case__": 0, "discover_paths": true, "homopolymer_compress": null, "output_condition": {"__current_case__": 4, "no_sequence": false, "out_format": "gfa", "terminal_overlaps_condition": {"__current_case__": 0, "terminal_overlaps_select": "no"}}, "remove_terminal_gaps": false, "selector": "manipulation", "sort": "", "swiss_army_knife": null} ` | | |
| | target\_condition | ` {"__current_case__": 0, "target_option": "false"} ` | | |
| </details> | |
| - **Step 48: Unlabelled step (toolshed.g2.bx.psu.edu/repos/bgruening/gfastats/gfastats/1.3.11+galaxy0)**: | |
| * step_state: scheduled | |
| * <details><summary>Jobs</summary> | |
| - **Job 1:** | |
| * Job state is ok | |
| **Container:** | |
| * ```console | |
| quay.io/biocontainers/gfastats:1.3.11--h077b44d_0 | |
| ``` | |
| **Command Line:** | |
| * ```console | |
| gfastats '/tmp/tmpgck0c6r3/files/2/f/7/dataset_2f7b64ca-7850-4736-8ea3-0600db0f18d7.dat' --discover-paths -o dataset.fasta --threads ${GALAXY_SLOTS:-8} && mv dataset* output_dataset | |
| ``` | |
| **Exit Code:** | |
| * ```console | |
| 0 | |
| ``` | |
| **Standard Output:** | |
| * ```console | |
| +++Assembly summary+++: | |
| # scaffolds: 51 | |
| Total scaffold length: 1351178 | |
| Average scaffold length: 26493.69 | |
| Scaffold N50: 23338 | |
| Scaffold auN: 40651.78 | |
| Scaffold L50: 16 | |
| Largest scaffold: 132684 | |
| Smallest scaffold: 16240 | |
| # contigs: 51 | |
| Total contig length: 1351178 | |
| Average contig length: 26493.69 | |
| Contig N50: 23338 | |
| Contig auN: 40651.78 | |
| Contig L50: 16 | |
| Largest contig: 132684 | |
| Smallest contig: 16240 | |
| # gaps in scaffolds: 0 | |
| Total gap length in scaffolds: 0 | |
| Average gap length in scaffolds: 0.00 | |
| Gap N50 in scaffolds: 0 | |
| Gap auN in scaffolds: 0.00 | |
| Gap L50 in scaffolds: 0 | |
| Largest gap in scaffolds: 0 | |
| Smallest gap in scaffolds: 0 | |
| Base composition (A:C:G:T): 409637:263447:265494:412600 | |
| GC content %: 39.15 | |
| # soft-masked bases: 0 | |
| # segments: 51 | |
| Total segment length: 1351178 | |
| Average segment length: 26493.69 | |
| # gaps: 0 | |
| # paths: 51 | |
| ``` | |
| **Traceback:** | |
| * ```console | |
| ``` | |
| **Job Parameters:** | |
| * | Job parameter | Parameter value | | |
| | ------------- | --------------- | | |
| | \_\_input\_ext | ` "input" ` | | |
| | \_\_workflow\_invocation\_uuid\_\_ | ` "30ca0a3a114e11f189517ced8d7c0d2f" ` | | |
| | chromInfo | ` "/tmp/tmpgck0c6r3/galaxy-dev/tool-data/shared/ucsc/chrom/?.len" ` | | |
| | dbkey | ` "?" ` | | |
| | mode\_condition | ` {"__current_case__": 0, "discover_paths": true, "homopolymer_compress": null, "output_condition": {"__current_case__": 0, "line_length": null, "out_format": "fasta"}, "remove_terminal_gaps": false, "selector": "manipulation", "sort": "", "swiss_army_knife": null} ` | | |
| | target\_condition | ` {"__current_case__": 0, "target_option": "false"} ` | | |
| </details> | |
| - **Step 49: gfastats gfa hap1 no sequences (toolshed.g2.bx.psu.edu/repos/bgruening/gfastats/gfastats/1.3.11+galaxy0)**: | |
| * step_state: scheduled | |
| * <details><summary>Jobs</summary> | |
| - **Job 1:** | |
| * Job state is ok | |
| **Container:** | |
| * ```console | |
| quay.io/biocontainers/gfastats:1.3.11--h077b44d_0 | |
| ``` | |
| **Command Line:** | |
| * ```console | |
| gfastats '/tmp/tmpgck0c6r3/files/8/1/b/dataset_81b287d4-8420-4d66-b390-dbdb0b735038.dat' --discover-paths -o dataset.gfa --no-sequence --threads ${GALAXY_SLOTS:-8} && mv dataset* output_dataset | |
| ``` | |
| **Exit Code:** | |
| * ```console | |
| 0 | |
| ``` | |
| **Standard Output:** | |
| * ```console | |
| +++Assembly summary+++: | |
| # scaffolds: 57 | |
| Total scaffold length: 1473565 | |
| Average scaffold length: 25852.02 | |
| Scaffold N50: 23819 | |
| Scaffold auN: 38682.45 | |
| Scaffold L50: 20 | |
| Largest scaffold: 132684 | |
| Smallest scaffold: 15406 | |
| # contigs: 57 | |
| Total contig length: 1473565 | |
| Average contig length: 25852.02 | |
| Contig N50: 23819 | |
| Contig auN: 38682.45 | |
| Contig L50: 20 | |
| Largest contig: 132684 | |
| Smallest contig: 15406 | |
| # gaps in scaffolds: 0 | |
| Total gap length in scaffolds: 0 | |
| Average gap length in scaffolds: 0.00 | |
| Gap N50 in scaffolds: 0 | |
| Gap auN in scaffolds: 0.00 | |
| Gap L50 in scaffolds: 0 | |
| Largest gap in scaffolds: 0 | |
| Smallest gap in scaffolds: 0 | |
| Base composition (A:C:G:T): 448657:285670:288915:450323 | |
| GC content %: 38.99 | |
| # soft-masked bases: 0 | |
| # segments: 57 | |
| Total segment length: 1473565 | |
| Average segment length: 25852.02 | |
| # gaps: 0 | |
| # paths: 57 | |
| # edges: 4 | |
| Average degree: 0.07 | |
| # connected components: 1 | |
| Largest connected component length: 89366 | |
| # dead ends: 111 | |
| # disconnected components: 54 | |
| Total length disconnected components: 1384199 | |
| # separated components: 55 | |
| # bubbles: 0 | |
| # circular segments: 0 | |
| # circular paths: 0 | |
| ``` | |
| **Traceback:** | |
| * ```console | |
| ``` | |
| **Job Parameters:** | |
| * | Job parameter | Parameter value | | |
| | ------------- | --------------- | | |
| | \_\_input\_ext | ` "input" ` | | |
| | \_\_workflow\_invocation\_uuid\_\_ | ` "30ca0a3a114e11f189517ced8d7c0d2f" ` | | |
| | chromInfo | ` "/tmp/tmpgck0c6r3/galaxy-dev/tool-data/shared/ucsc/chrom/?.len" ` | | |
| | dbkey | ` "?" ` | | |
| | mode\_condition | ` {"__current_case__": 0, "discover_paths": true, "homopolymer_compress": null, "output_condition": {"__current_case__": 4, "no_sequence": true, "out_format": "gfa", "terminal_overlaps_condition": {"__current_case__": 0, "terminal_overlaps_select": "no"}}, "remove_terminal_gaps": false, "selector": "manipulation", "sort": "", "swiss_army_knife": null} ` | | |
| | target\_condition | ` {"__current_case__": 0, "target_option": "false"} ` | | |
| </details> | |
| - **Step 50: Unlabelled step (toolshed.g2.bx.psu.edu/repos/bgruening/gfastats/gfastats/1.3.11+galaxy0)**: | |
| * step_state: scheduled | |
| * <details><summary>Jobs</summary> | |
| - **Job 1:** | |
| * Job state is ok | |
| **Container:** | |
| * ```console | |
| quay.io/biocontainers/gfastats:1.3.11--h077b44d_0 | |
| ``` | |
| **Command Line:** | |
| * ```console | |
| gfastats '/tmp/tmpgck0c6r3/files/8/1/b/dataset_81b287d4-8420-4d66-b390-dbdb0b735038.dat' --discover-paths -o dataset.fasta --threads ${GALAXY_SLOTS:-8} && mv dataset* output_dataset | |
| ``` | |
| **Exit Code:** | |
| * ```console | |
| 0 | |
| ``` | |
| **Standard Output:** | |
| * ```console | |
| +++Assembly summary+++: | |
| # scaffolds: 57 | |
| Total scaffold length: 1473565 | |
| Average scaffold length: 25852.02 | |
| Scaffold N50: 23819 | |
| Scaffold auN: 38682.45 | |
| Scaffold L50: 20 | |
| Largest scaffold: 132684 | |
| Smallest scaffold: 15406 | |
| # contigs: 57 | |
| Total contig length: 1473565 | |
| Average contig length: 25852.02 | |
| Contig N50: 23819 | |
| Contig auN: 38682.45 | |
| Contig L50: 20 | |
| Largest contig: 132684 | |
| Smallest contig: 15406 | |
| # gaps in scaffolds: 0 | |
| Total gap length in scaffolds: 0 | |
| Average gap length in scaffolds: 0.00 | |
| Gap N50 in scaffolds: 0 | |
| Gap auN in scaffolds: 0.00 | |
| Gap L50 in scaffolds: 0 | |
| Largest gap in scaffolds: 0 | |
| Smallest gap in scaffolds: 0 | |
| Base composition (A:C:G:T): 448657:285670:288915:450323 | |
| GC content %: 38.99 | |
| # soft-masked bases: 0 | |
| # segments: 57 | |
| Total segment length: 1473565 | |
| Average segment length: 25852.02 | |
| # gaps: 0 | |
| # paths: 57 | |
| # edges: 4 | |
| Average degree: 0.07 | |
| # connected components: 1 | |
| Largest connected component length: 89366 | |
| # dead ends: 111 | |
| # disconnected components: 54 | |
| Total length disconnected components: 1384199 | |
| # separated components: 55 | |
| # bubbles: 0 | |
| # circular segments: 0 | |
| # circular paths: 0 | |
| ``` | |
| **Traceback:** | |
| * ```console | |
| ``` | |
| **Job Parameters:** | |
| * | Job parameter | Parameter value | | |
| | ------------- | --------------- | | |
| | \_\_input\_ext | ` "input" ` | | |
| | \_\_workflow\_invocation\_uuid\_\_ | ` "30ca0a3a114e11f189517ced8d7c0d2f" ` | | |
| | chromInfo | ` "/tmp/tmpgck0c6r3/galaxy-dev/tool-data/shared/ucsc/chrom/?.len" ` | | |
| | dbkey | ` "?" ` | | |
| | mode\_condition | ` {"__current_case__": 0, "discover_paths": true, "homopolymer_compress": null, "output_condition": {"__current_case__": 0, "line_length": null, "out_format": "fasta"}, "remove_terminal_gaps": false, "selector": "manipulation", "sort": "", "swiss_army_knife": null} ` | | |
| | target\_condition | ` {"__current_case__": 0, "target_option": "false"} ` | | |
| </details> | |
| - **Step 51: Unlabelled step (toolshed.g2.bx.psu.edu/repos/bgruening/text\_processing/tp\_awk\_tool/9.5+galaxy2)**: | |
| * step_state: scheduled | |
| * <details><summary>Jobs</summary> | |
| - **Job 1:** | |
| * Job state is ok | |
| **Container:** | |
| * ```console | |
| quay.io/biocontainers/gawk:5.3.1 | |
| ``` | |
| **Command Line:** | |
| * ```console | |
| env -i $(which awk) --sandbox -v FS=' ' -v OFS=' ' --re-interval -f '/tmp/tmpgck0c6r3/job_working_directory/000/50/configs/tmp_t1nmpoo' '/tmp/tmpgck0c6r3/files/8/3/2/dataset_83218544-a578-473d-be4f-7625e30aa8bb.dat' > '/tmp/tmpgck0c6r3/job_working_directory/000/50/outputs/dataset_222f1751-b711-4c1a-8df6-42a7bddf1e25.dat' | |
| ``` | |
| **Exit Code:** | |
| * ```console | |
| 0 | |
| ``` | |
| **Traceback:** | |
| * ```console | |
| ``` | |
| **Job Parameters:** | |
| * | Job parameter | Parameter value | | |
| | ------------- | --------------- | | |
| | \_\_input\_ext | ` "input" ` | | |
| | \_\_workflow\_invocation\_uuid\_\_ | ` "30ca0a3a114e11f189517ced8d7c0d2f" ` | | |
| | chromInfo | ` "/tmp/tmpgck0c6r3/galaxy-dev/tool-data/shared/ucsc/chrom/?.len" ` | | |
| | code | ` "BEGIN{print \"Metric\\thap2\"}; {print}; " ` | | |
| | dbkey | ` "?" ` | | |
| | variables | ` [] ` | | |
| </details> | |
| - **Step 52: Unlabelled step (toolshed.g2.bx.psu.edu/repos/bgruening/text\_processing/tp\_awk\_tool/9.5+galaxy2)**: | |
| * step_state: scheduled | |
| * <details><summary>Jobs</summary> | |
| - **Job 1:** | |
| * Job state is ok | |
| **Container:** | |
| * ```console | |
| quay.io/biocontainers/gawk:5.3.1 | |
| ``` | |
| **Command Line:** | |
| * ```console | |
| env -i $(which awk) --sandbox -v FS=' ' -v OFS=' ' --re-interval -f '/tmp/tmpgck0c6r3/job_working_directory/000/51/configs/tmpymvk7hrd' '/tmp/tmpgck0c6r3/files/9/3/1/dataset_931d6a99-69cc-46b9-aa68-54e8fd18d923.dat' > '/tmp/tmpgck0c6r3/job_working_directory/000/51/outputs/dataset_ed328b3d-a609-48a9-a972-44dc73f39800.dat' | |
| ``` | |
| **Exit Code:** | |
| * ```console | |
| 0 | |
| ``` | |
| **Traceback:** | |
| * ```console | |
| ``` | |
| **Job Parameters:** | |
| * | Job parameter | Parameter value | | |
| | ------------- | --------------- | | |
| | \_\_input\_ext | ` "input" ` | | |
| | \_\_workflow\_invocation\_uuid\_\_ | ` "30ca0a3a114e11f189517ced8d7c0d2f" ` | | |
| | chromInfo | ` "/tmp/tmpgck0c6r3/galaxy-dev/tool-data/shared/ucsc/chrom/?.len" ` | | |
| | code | ` "BEGIN{print \"Metric\\thap1\"}; {print}; " ` | | |
| | dbkey | ` "?" ` | | |
| | variables | ` [] ` | | |
| </details> | |
| - **Step 53: Data Prep Hap2**: | |
| * step_state: scheduled | |
| * <details><summary>Subworkflow Steps</summary> | |
| - **Step 1: gfa_stats**: | |
| * step_state: scheduled | |
| - **Step 2: Unlabelled step (sort1)**: | |
| * step_state: scheduled | |
| * <details><summary>Jobs</summary> | |
| - **Job 1:** | |
| * Job state is ok | |
| **Container:** | |
| * ```console | |
| quay.io/biocontainers/mulled-v2-f44eb8f8fd694df8f5d103351c6e7f6816bd9bb1:a06a12e18332de5a030bf1ab1353c17d8448cd90-0 | |
| ``` | |
| **Command Line:** | |
| * ```console | |
| grep '^#' '/tmp/tmpgck0c6r3/files/2/0/b/dataset_20b16557-8e60-4859-a828-7a54fb86d977.dat' >> '/tmp/tmpgck0c6r3/job_working_directory/000/52/outputs/dataset_588bfa7d-a3fa-4e73-8987-cae722065c0c.dat'; < '/tmp/tmpgck0c6r3/files/2/0/b/dataset_20b16557-8e60-4859-a828-7a54fb86d977.dat' grep '^[^#]' | sort -f -t $'\t' -k 2,2nr >> '/tmp/tmpgck0c6r3/job_working_directory/000/52/outputs/dataset_588bfa7d-a3fa-4e73-8987-cae722065c0c.dat' | |
| ``` | |
| **Exit Code:** | |
| * ```console | |
| 0 | |
| ``` | |
| **Traceback:** | |
| * ```console | |
| ``` | |
| **Job Parameters:** | |
| * | Job parameter | Parameter value | | |
| | ------------- | --------------- | | |
| | \_\_input\_ext | ` "input" ` | | |
| | \_\_workflow\_invocation\_uuid\_\_ | ` "30ca0a3c114e11f189517ced8d7c0d2f" ` | | |
| | chromInfo | ` "/tmp/tmpgck0c6r3/galaxy-dev/tool-data/shared/ucsc/chrom/?.len" ` | | |
| | column | ` "2" ` | | |
| | column\_set | ` [] ` | | |
| | dbkey | ` "?" ` | | |
| | header\_lines | ` "0" ` | | |
| | order | ` "DESC" ` | | |
| | style | ` "num" ` | | |
| </details> | |
| - **Step 3: Unlabelled step (toolshed.g2.bx.psu.edu/repos/bgruening/text\_processing/tp\_awk\_tool/9.5+galaxy2)**: | |
| * step_state: scheduled | |
| * <details><summary>Jobs</summary> | |
| - **Job 1:** | |
| * Job state is ok | |
| **Container:** | |
| * ```console | |
| quay.io/biocontainers/gawk:5.3.1 | |
| ``` | |
| **Command Line:** | |
| * ```console | |
| env -i $(which awk) --sandbox -v FS=' ' -v OFS=' ' --re-interval -f '/tmp/tmpgck0c6r3/job_working_directory/000/53/configs/tmp63hzv2eg' '/tmp/tmpgck0c6r3/files/5/8/8/dataset_588bfa7d-a3fa-4e73-8987-cae722065c0c.dat' > '/tmp/tmpgck0c6r3/job_working_directory/000/53/outputs/dataset_1e6a8041-5d11-4c19-8b68-f53f4a104cf6.dat' | |
| ``` | |
| **Exit Code:** | |
| * ```console | |
| 0 | |
| ``` | |
| **Traceback:** | |
| * ```console | |
| ``` | |
| **Job Parameters:** | |
| * | Job parameter | Parameter value | | |
| | ------------- | --------------- | | |
| | \_\_input\_ext | ` "input" ` | | |
| | \_\_workflow\_invocation\_uuid\_\_ | ` "30ca0a3c114e11f189517ced8d7c0d2f" ` | | |
| | chromInfo | ` "/tmp/tmpgck0c6r3/galaxy-dev/tool-data/shared/ucsc/chrom/?.len" ` | | |
| | code | ` "{total += $2; $3 = total}1" ` | | |
| | dbkey | ` "?" ` | | |
| | variables | ` [] ` | | |
| </details> | |
| - **Step 4: Unlabelled step (toolshed.g2.bx.psu.edu/repos/iuc/datamash\_ops/datamash\_ops/1.9+galaxy0)**: | |
| * step_state: scheduled | |
| * <details><summary>Jobs</summary> | |
| - **Job 1:** | |
| * Job state is ok | |
| **Container:** | |
| * ```console | |
| quay.io/biocontainers/datamash:1.9 | |
| ``` | |
| **Command Line:** | |
| * ```console | |
| datamash absmax 3 < /tmp/tmpgck0c6r3/files/1/e/6/dataset_1e6a8041-5d11-4c19-8b68-f53f4a104cf6.dat > '/tmp/tmpgck0c6r3/job_working_directory/000/54/outputs/dataset_c7dd1788-8f08-48e5-bf01-f525c0d58f73.dat' | |
| ``` | |
| **Exit Code:** | |
| * ```console | |
| 0 | |
| ``` | |
| **Traceback:** | |
| * ```console | |
| ``` | |
| **Job Parameters:** | |
| * | Job parameter | Parameter value | | |
| | ------------- | --------------- | | |
| | \_\_input\_ext | ` "input" ` | | |
| | \_\_workflow\_invocation\_uuid\_\_ | ` "30ca0a3c114e11f189517ced8d7c0d2f" ` | | |
| | chromInfo | ` "/tmp/tmpgck0c6r3/galaxy-dev/tool-data/shared/ucsc/chrom/?.len" ` | | |
| | dbkey | ` "?" ` | | |
| | grouping | ` "" ` | | |
| | header\_in | ` false ` | | |
| | header\_out | ` false ` | | |
| | ignore\_case | ` false ` | | |
| | narm | ` false ` | | |
| | need\_sort | ` false ` | | |
| | operations | ` [{"__index__": 0, "op_column": "3", "op_name": "absmax"}] ` | | |
| | print\_full\_line | ` false ` | | |
| </details> | |
| - **Step 5: Unlabelled step (toolshed.g2.bx.psu.edu/repos/devteam/add\_value/addValue/1.0.1)**: | |
| * step_state: scheduled | |
| * <details><summary>Jobs</summary> | |
| - **Job 1:** | |
| * Job state is ok | |
| **Container:** | |
| * ```console | |
| quay.io/biocontainers/perl:5.26--2 | |
| ``` | |
| **Command Line:** | |
| * ```console | |
| perl /tmp/shed_dir/toolshed.g2.bx.psu.edu/repos/devteam/add_value/023f0a3760b3/add_value/fixedValueColumn.pl "/tmp/tmpgck0c6r3/files/1/e/6/dataset_1e6a8041-5d11-4c19-8b68-f53f4a104cf6.dat" "/tmp/tmpgck0c6r3/job_working_directory/000/55/outputs/dataset_4981158a-4e9c-4c32-b006-244aea9fc034.dat" "1" "yes" | |
| ``` | |
| **Exit Code:** | |
| * ```console | |
| 0 | |
| ``` | |
| **Traceback:** | |
| * ```console | |
| ``` | |
| **Job Parameters:** | |
| * | Job parameter | Parameter value | | |
| | ------------- | --------------- | | |
| | \_\_input\_ext | ` "input" ` | | |
| | \_\_workflow\_invocation\_uuid\_\_ | ` "30ca0a3c114e11f189517ced8d7c0d2f" ` | | |
| | chromInfo | ` "/tmp/tmpgck0c6r3/galaxy-dev/tool-data/shared/ucsc/chrom/?.len" ` | | |
| | dbkey | ` "?" ` | | |
| | exp | ` "1" ` | | |
| | iterate | ` "yes" ` | | |
| </details> | |
| - **Step 6: Unlabelled step (param\_value\_from\_file)**: | |
| * step_state: scheduled | |
| * <details><summary>Jobs</summary> | |
| - **Job 1:** | |
| * Job state is ok | |
| **Command Line:** | |
| * ```console | |
| cd ../; python _evaluate_expression_.py | |
| ``` | |
| **Exit Code:** | |
| * ```console | |
| 0 | |
| ``` | |
| **Traceback:** | |
| * ```console | |
| ``` | |
| **Job Parameters:** | |
| * | Job parameter | Parameter value | | |
| | ------------- | --------------- | | |
| | \_\_input\_ext | ` "input" ` | | |
| | \_\_workflow\_invocation\_uuid\_\_ | ` "30ca0a3c114e11f189517ced8d7c0d2f" ` | | |
| | chromInfo | ` "/tmp/tmpgck0c6r3/galaxy-dev/tool-data/shared/ucsc/chrom/?.len" ` | | |
| | dbkey | ` "?" ` | | |
| | param\_type | ` "integer" ` | | |
| | remove\_newlines | ` true ` | | |
| </details> | |
| - **Step 7: Unlabelled step (toolshed.g2.bx.psu.edu/repos/iuc/compose\_text\_param/compose\_text\_param/0.1.1)**: | |
| * step_state: scheduled | |
| * <details><summary>Jobs</summary> | |
| - **Job 1:** | |
| * Job state is ok | |
| **Command Line:** | |
| * ```console | |
| cd ../; python _evaluate_expression_.py | |
| ``` | |
| **Exit Code:** | |
| * ```console | |
| 0 | |
| ``` | |
| **Traceback:** | |
| * ```console | |
| ``` | |
| **Job Parameters:** | |
| * | Job parameter | Parameter value | | |
| | ------------- | --------------- | | |
| | \_\_input\_ext | ` "input" ` | | |
| | \_\_workflow\_invocation\_uuid\_\_ | ` "30ca0a3c114e11f189517ced8d7c0d2f" ` | | |
| | chromInfo | ` "/tmp/tmpgck0c6r3/galaxy-dev/tool-data/shared/ucsc/chrom/?.len" ` | | |
| | components | ` [{"__index__": 0, "param_type": {"__current_case__": 0, "component_value": "c3/", "select_param_type": "text"}}, {"__index__": 1, "param_type": {"__current_case__": 1, "component_value": "1351178", "select_param_type": "integer"}}] ` | | |
| | dbkey | ` "?" ` | | |
| </details> | |
| - **Step 8: Unlabelled step (toolshed.g2.bx.psu.edu/repos/devteam/column\_maker/Add\_a\_column1/2.1)**: | |
| * step_state: scheduled | |
| * <details><summary>Jobs</summary> | |
| - **Job 1:** | |
| * Job state is ok | |
| **Container:** | |
| * ```console | |
| quay.io/biocontainers/mulled-v2-b1a1ba6b0445e5a9141e8becdb2ab56f8d930e41:477f302c9d587c361f49c5f5853e2f0cc6119bf4-0 | |
| ``` | |
| **Command Line:** | |
| * ```console | |
| python '/tmp/shed_dir/toolshed.g2.bx.psu.edu/repos/devteam/column_maker/aff5135563c6/column_maker/column_maker.py' --column-types str,int,int,int --file '/tmp/tmpgck0c6r3/job_working_directory/000/83/configs/tmpa2vkpl2_' --fail-on-non-existent-columns --fail-on-non-computable '/tmp/tmpgck0c6r3/files/4/9/8/dataset_4981158a-4e9c-4c32-b006-244aea9fc034.dat' '/tmp/tmpgck0c6r3/job_working_directory/000/83/outputs/dataset_0605f299-2f5c-4b18-bd96-64968433909f.dat' | |
| ``` | |
| **Exit Code:** | |
| * ```console | |
| 0 | |
| ``` | |
| **Standard Output:** | |
| * ```console | |
| c3/1351178 | |
| c2/1000000 | |
| c3/1000000 | |
| Computing 3 new columns with instructions ['c3/1351178;;', 'c2/1000000;;', 'c3/1000000;;'] | |
| Computed new column values for 100.00% of 51 lines written. | |
| ``` | |
| **Traceback:** | |
| * ```console | |
| ``` | |
| **Job Parameters:** | |
| * | Job parameter | Parameter value | | |
| | ------------- | --------------- | | |
| | \_\_input\_ext | ` "input" ` | | |
| | \_\_workflow\_invocation\_uuid\_\_ | ` "30ca0a3c114e11f189517ced8d7c0d2f" ` | | |
| | avoid\_scientific\_notation | ` false ` | | |
| | chromInfo | ` "/tmp/tmpgck0c6r3/galaxy-dev/tool-data/shared/ucsc/chrom/?.len" ` | | |
| | dbkey | ` "?" ` | | |
| | error\_handling | ` {"auto_col_types": true, "fail_on_non_existent_columns": true, "non_computable": {"__current_case__": 0, "action": "--fail-on-non-computable"}} ` | | |
| | ops | ` {"__current_case__": 0, "expressions": [{"__index__": 0, "add_column": {"__current_case__": 0, "mode": "", "pos": ""}, "cond": "c3/1351178"}, {"__index__": 1, "add_column": {"__current_case__": 0, "mode": "", "pos": ""}, "cond": "c2/1000000"}, {"__index__": 2, "add_column": {"__current_case__": 0, "mode": "", "pos": ""}, "cond": "c3/1000000"}], "header_lines_select": "no"} ` | | |
| </details> | |
| </details> | |
| - **Step 54: Data Prep Hap1**: | |
| * step_state: scheduled | |
| * <details><summary>Subworkflow Steps</summary> | |
| - **Step 1: gfa_stats**: | |
| * step_state: scheduled | |
| - **Step 2: Unlabelled step (sort1)**: | |
| * step_state: scheduled | |
| * <details><summary>Jobs</summary> | |
| - **Job 1:** | |
| * Job state is ok | |
| **Container:** | |
| * ```console | |
| quay.io/biocontainers/mulled-v2-f44eb8f8fd694df8f5d103351c6e7f6816bd9bb1:a06a12e18332de5a030bf1ab1353c17d8448cd90-0 | |
| ``` | |
| **Command Line:** | |
| * ```console | |
| grep '^#' '/tmp/tmpgck0c6r3/files/a/5/e/dataset_a5ec6afd-3143-456a-9be9-c36d55ef4c29.dat' >> '/tmp/tmpgck0c6r3/job_working_directory/000/57/outputs/dataset_7a157da9-db79-4dac-8d7f-8bb52f90497c.dat'; < '/tmp/tmpgck0c6r3/files/a/5/e/dataset_a5ec6afd-3143-456a-9be9-c36d55ef4c29.dat' grep '^[^#]' | sort -f -t $'\t' -k 2,2nr >> '/tmp/tmpgck0c6r3/job_working_directory/000/57/outputs/dataset_7a157da9-db79-4dac-8d7f-8bb52f90497c.dat' | |
| ``` | |
| **Exit Code:** | |
| * ```console | |
| 0 | |
| ``` | |
| **Traceback:** | |
| * ```console | |
| ``` | |
| **Job Parameters:** | |
| * | Job parameter | Parameter value | | |
| | ------------- | --------------- | | |
| | \_\_input\_ext | ` "input" ` | | |
| | \_\_workflow\_invocation\_uuid\_\_ | ` "30ca0a3d114e11f189517ced8d7c0d2f" ` | | |
| | chromInfo | ` "/tmp/tmpgck0c6r3/galaxy-dev/tool-data/shared/ucsc/chrom/?.len" ` | | |
| | column | ` "2" ` | | |
| | column\_set | ` [] ` | | |
| | dbkey | ` "?" ` | | |
| | header\_lines | ` "0" ` | | |
| | order | ` "DESC" ` | | |
| | style | ` "num" ` | | |
| </details> | |
| - **Step 3: Unlabelled step (toolshed.g2.bx.psu.edu/repos/bgruening/text\_processing/tp\_awk\_tool/9.5+galaxy2)**: | |
| * step_state: scheduled | |
| * <details><summary>Jobs</summary> | |
| - **Job 1:** | |
| * Job state is ok | |
| **Container:** | |
| * ```console | |
| quay.io/biocontainers/gawk:5.3.1 | |
| ``` | |
| **Command Line:** | |
| * ```console | |
| env -i $(which awk) --sandbox -v FS=' ' -v OFS=' ' --re-interval -f '/tmp/tmpgck0c6r3/job_working_directory/000/58/configs/tmpp80zzuxo' '/tmp/tmpgck0c6r3/files/7/a/1/dataset_7a157da9-db79-4dac-8d7f-8bb52f90497c.dat' > '/tmp/tmpgck0c6r3/job_working_directory/000/58/outputs/dataset_2b131501-ad05-4424-a6dc-c6ca993b226f.dat' | |
| ``` | |
| **Exit Code:** | |
| * ```console | |
| 0 | |
| ``` | |
| **Traceback:** | |
| * ```console | |
| ``` | |
| **Job Parameters:** | |
| * | Job parameter | Parameter value | | |
| | ------------- | --------------- | | |
| | \_\_input\_ext | ` "input" ` | | |
| | \_\_workflow\_invocation\_uuid\_\_ | ` "30ca0a3d114e11f189517ced8d7c0d2f" ` | | |
| | chromInfo | ` "/tmp/tmpgck0c6r3/galaxy-dev/tool-data/shared/ucsc/chrom/?.len" ` | | |
| | code | ` "{total += $2; $3 = total}1" ` | | |
| | dbkey | ` "?" ` | | |
| | variables | ` [] ` | | |
| </details> | |
| - **Step 4: Unlabelled step (toolshed.g2.bx.psu.edu/repos/iuc/datamash\_ops/datamash\_ops/1.9+galaxy0)**: | |
| * step_state: scheduled | |
| * <details><summary>Jobs</summary> | |
| - **Job 1:** | |
| * Job state is ok | |
| **Container:** | |
| * ```console | |
| quay.io/biocontainers/datamash:1.9 | |
| ``` | |
| **Command Line:** | |
| * ```console | |
| datamash absmax 3 < /tmp/tmpgck0c6r3/files/2/b/1/dataset_2b131501-ad05-4424-a6dc-c6ca993b226f.dat > '/tmp/tmpgck0c6r3/job_working_directory/000/59/outputs/dataset_c3b26ebd-760d-4a88-b110-f3cfbd0ea223.dat' | |
| ``` | |
| **Exit Code:** | |
| * ```console | |
| 0 | |
| ``` | |
| **Traceback:** | |
| * ```console | |
| ``` | |
| **Job Parameters:** | |
| * | Job parameter | Parameter value | | |
| | ------------- | --------------- | | |
| | \_\_input\_ext | ` "input" ` | | |
| | \_\_workflow\_invocation\_uuid\_\_ | ` "30ca0a3d114e11f189517ced8d7c0d2f" ` | | |
| | chromInfo | ` "/tmp/tmpgck0c6r3/galaxy-dev/tool-data/shared/ucsc/chrom/?.len" ` | | |
| | dbkey | ` "?" ` | | |
| | grouping | ` "" ` | | |
| | header\_in | ` false ` | | |
| | header\_out | ` false ` | | |
| | ignore\_case | ` false ` | | |
| | narm | ` false ` | | |
| | need\_sort | ` false ` | | |
| | operations | ` [{"__index__": 0, "op_column": "3", "op_name": "absmax"}] ` | | |
| | print\_full\_line | ` false ` | | |
| </details> | |
| - **Step 5: Unlabelled step (toolshed.g2.bx.psu.edu/repos/devteam/add\_value/addValue/1.0.1)**: | |
| * step_state: scheduled | |
| * <details><summary>Jobs</summary> | |
| - **Job 1:** | |
| * Job state is ok | |
| **Container:** | |
| * ```console | |
| quay.io/biocontainers/perl:5.26--2 | |
| ``` | |
| **Command Line:** | |
| * ```console | |
| perl /tmp/shed_dir/toolshed.g2.bx.psu.edu/repos/devteam/add_value/023f0a3760b3/add_value/fixedValueColumn.pl "/tmp/tmpgck0c6r3/files/2/b/1/dataset_2b131501-ad05-4424-a6dc-c6ca993b226f.dat" "/tmp/tmpgck0c6r3/job_working_directory/000/60/outputs/dataset_0cc7cc4b-725c-4e8a-a387-c819a56b90eb.dat" "1" "yes" | |
| ``` | |
| **Exit Code:** | |
| * ```console | |
| 0 | |
| ``` | |
| **Traceback:** | |
| * ```console | |
| ``` | |
| **Job Parameters:** | |
| * | Job parameter | Parameter value | | |
| | ------------- | --------------- | | |
| | \_\_input\_ext | ` "input" ` | | |
| | \_\_workflow\_invocation\_uuid\_\_ | ` "30ca0a3d114e11f189517ced8d7c0d2f" ` | | |
| | chromInfo | ` "/tmp/tmpgck0c6r3/galaxy-dev/tool-data/shared/ucsc/chrom/?.len" ` | | |
| | dbkey | ` "?" ` | | |
| | exp | ` "1" ` | | |
| | iterate | ` "yes" ` | | |
| </details> | |
| - **Step 6: Unlabelled step (param\_value\_from\_file)**: | |
| * step_state: scheduled | |
| * <details><summary>Jobs</summary> | |
| - **Job 1:** | |
| * Job state is ok | |
| **Command Line:** | |
| * ```console | |
| cd ../; python _evaluate_expression_.py | |
| ``` | |
| **Exit Code:** | |
| * ```console | |
| 0 | |
| ``` | |
| **Traceback:** | |
| * ```console | |
| ``` | |
| **Job Parameters:** | |
| * | Job parameter | Parameter value | | |
| | ------------- | --------------- | | |
| | \_\_input\_ext | ` "input" ` | | |
| | \_\_workflow\_invocation\_uuid\_\_ | ` "30ca0a3d114e11f189517ced8d7c0d2f" ` | | |
| | chromInfo | ` "/tmp/tmpgck0c6r3/galaxy-dev/tool-data/shared/ucsc/chrom/?.len" ` | | |
| | dbkey | ` "?" ` | | |
| | param\_type | ` "integer" ` | | |
| | remove\_newlines | ` true ` | | |
| </details> | |
| - **Step 7: Unlabelled step (toolshed.g2.bx.psu.edu/repos/iuc/compose\_text\_param/compose\_text\_param/0.1.1)**: | |
| * step_state: scheduled | |
| * <details><summary>Jobs</summary> | |
| - **Job 1:** | |
| * Job state is ok | |
| **Command Line:** | |
| * ```console | |
| cd ../; python _evaluate_expression_.py | |
| ``` | |
| **Exit Code:** | |
| * ```console | |
| 0 | |
| ``` | |
| **Traceback:** | |
| * ```console | |
| ``` | |
| **Job Parameters:** | |
| * | Job parameter | Parameter value | | |
| | ------------- | --------------- | | |
| | \_\_input\_ext | ` "input" ` | | |
| | \_\_workflow\_invocation\_uuid\_\_ | ` "30ca0a3d114e11f189517ced8d7c0d2f" ` | | |
| | chromInfo | ` "/tmp/tmpgck0c6r3/galaxy-dev/tool-data/shared/ucsc/chrom/?.len" ` | | |
| | components | ` [{"__index__": 0, "param_type": {"__current_case__": 0, "component_value": "c3/", "select_param_type": "text"}}, {"__index__": 1, "param_type": {"__current_case__": 1, "component_value": "1473565", "select_param_type": "integer"}}] ` | | |
| | dbkey | ` "?" ` | | |
| </details> | |
| - **Step 8: Unlabelled step (toolshed.g2.bx.psu.edu/repos/devteam/column\_maker/Add\_a\_column1/2.1)**: | |
| * step_state: scheduled | |
| * <details><summary>Jobs</summary> | |
| - **Job 1:** | |
| * Job state is ok | |
| **Container:** | |
| * ```console | |
| quay.io/biocontainers/mulled-v2-b1a1ba6b0445e5a9141e8becdb2ab56f8d930e41:477f302c9d587c361f49c5f5853e2f0cc6119bf4-0 | |
| ``` | |
| **Command Line:** | |
| * ```console | |
| python '/tmp/shed_dir/toolshed.g2.bx.psu.edu/repos/devteam/column_maker/aff5135563c6/column_maker/column_maker.py' --column-types str,int,int,int --file '/tmp/tmpgck0c6r3/job_working_directory/000/84/configs/tmpvzgp14d7' --fail-on-non-existent-columns --fail-on-non-computable '/tmp/tmpgck0c6r3/files/0/c/c/dataset_0cc7cc4b-725c-4e8a-a387-c819a56b90eb.dat' '/tmp/tmpgck0c6r3/job_working_directory/000/84/outputs/dataset_0f7ffce6-65c1-4abb-97ae-d54c2138bac6.dat' | |
| ``` | |
| **Exit Code:** | |
| * ```console | |
| 0 | |
| ``` | |
| **Standard Output:** | |
| * ```console | |
| c3/1473565 | |
| c2/1000000 | |
| c3/1000000 | |
| Computing 3 new columns with instructions ['c3/1473565;;', 'c2/1000000;;', 'c3/1000000;;'] | |
| Computed new column values for 100.00% of 57 lines written. | |
| ``` | |
| **Traceback:** | |
| * ```console | |
| ``` | |
| **Job Parameters:** | |
| * | Job parameter | Parameter value | | |
| | ------------- | --------------- | | |
| | \_\_input\_ext | ` "input" ` | | |
| | \_\_workflow\_invocation\_uuid\_\_ | ` "30ca0a3d114e11f189517ced8d7c0d2f" ` | | |
| | avoid\_scientific\_notation | ` false ` | | |
| | chromInfo | ` "/tmp/tmpgck0c6r3/galaxy-dev/tool-data/shared/ucsc/chrom/?.len" ` | | |
| | dbkey | ` "?" ` | | |
| | error\_handling | ` {"auto_col_types": true, "fail_on_non_existent_columns": true, "non_computable": {"__current_case__": 0, "action": "--fail-on-non-computable"}} ` | | |
| | ops | ` {"__current_case__": 0, "expressions": [{"__index__": 0, "add_column": {"__current_case__": 0, "mode": "", "pos": ""}, "cond": "c3/1473565"}, {"__index__": 1, "add_column": {"__current_case__": 0, "mode": "", "pos": ""}, "cond": "c2/1000000"}, {"__index__": 2, "add_column": {"__current_case__": 0, "mode": "", "pos": ""}, "cond": "c3/1000000"}], "header_lines_select": "no"} ` | | |
| </details> | |
| </details> | |
| - **Step 55: Unlabelled step (toolshed.g2.bx.psu.edu/repos/bgruening/text\_processing/tp\_sed\_tool/9.5+galaxy2)**: | |
| * step_state: scheduled | |
| * <details><summary>Jobs</summary> | |
| - **Job 1:** | |
| * Job state is ok | |
| **Container:** | |
| * ```console | |
| quay.io/biocontainers/sed:4.8 | |
| ``` | |
| **Command Line:** | |
| * ```console | |
| sed --sandbox -r -f '/tmp/tmpgck0c6r3/job_working_directory/000/62/configs/tmp_kdfwtao' '/tmp/tmpgck0c6r3/files/6/e/9/dataset_6e93e448-1c9e-418a-84c9-4619919760ab.dat' > '/tmp/tmpgck0c6r3/job_working_directory/000/62/outputs/dataset_ec30905f-b6ab-4141-959f-bc2d87fcd32c.dat' | |
| ``` | |
| **Exit Code:** | |
| * ```console | |
| 0 | |
| ``` | |
| **Traceback:** | |
| * ```console | |
| ``` | |
| **Job Parameters:** | |
| * | Job parameter | Parameter value | | |
| | ------------- | --------------- | | |
| | \_\_input\_ext | ` "input" ` | | |
| | \_\_workflow\_invocation\_uuid\_\_ | ` "30ca0a3a114e11f189517ced8d7c0d2f" ` | | |
| | adv\_opts | ` {"__current_case__": 0, "adv_opts_selector": "basic"} ` | | |
| | chromInfo | ` "/tmp/tmpgck0c6r3/galaxy-dev/tool-data/shared/ucsc/chrom/?.len" ` | | |
| | code | ` "s/_path//g" ` | | |
| | dbkey | ` "?" ` | | |
| </details> | |
| - **Step 56: Unlabelled step (toolshed.g2.bx.psu.edu/repos/bgruening/text\_processing/tp\_sed\_tool/9.5+galaxy2)**: | |
| * step_state: scheduled | |
| * <details><summary>Jobs</summary> | |
| - **Job 1:** | |
| * Job state is ok | |
| **Container:** | |
| * ```console | |
| quay.io/biocontainers/sed:4.8 | |
| ``` | |
| **Command Line:** | |
| * ```console | |
| sed --sandbox -r -f '/tmp/tmpgck0c6r3/job_working_directory/000/63/configs/tmp3mbi8qww' '/tmp/tmpgck0c6r3/files/6/9/a/dataset_69a96cf1-2a76-41f8-bf15-761a6c4ffcab.dat' > '/tmp/tmpgck0c6r3/job_working_directory/000/63/outputs/dataset_3fc83f7a-c80b-48d6-8838-2821fe73129e.dat' | |
| ``` | |
| **Exit Code:** | |
| * ```console | |
| 0 | |
| ``` | |
| **Traceback:** | |
| * ```console | |
| ``` | |
| **Job Parameters:** | |
| * | Job parameter | Parameter value | | |
| | ------------- | --------------- | | |
| | \_\_input\_ext | ` "input" ` | | |
| | \_\_workflow\_invocation\_uuid\_\_ | ` "30ca0a3a114e11f189517ced8d7c0d2f" ` | | |
| | adv\_opts | ` {"__current_case__": 0, "adv_opts_selector": "basic"} ` | | |
| | chromInfo | ` "/tmp/tmpgck0c6r3/galaxy-dev/tool-data/shared/ucsc/chrom/?.len" ` | | |
| | code | ` "s/_path//g" ` | | |
| | dbkey | ` "?" ` | | |
| </details> | |
| - **Step 57: Unlabelled step (join1)**: | |
| * step_state: scheduled | |
| * <details><summary>Jobs</summary> | |
| - **Job 1:** | |
| * Job state is ok | |
| **Container:** | |
| * ```console | |
| quay.io/biocontainers/galaxy-util:25.0.2 | |
| ``` | |
| **Command Line:** | |
| * ```console | |
| python '/tmp/tmpgck0c6r3/galaxy-dev/tools/filters/join.py' '/tmp/tmpgck0c6r3/files/e/d/3/dataset_ed328b3d-a609-48a9-a972-44dc73f39800.dat' '/tmp/tmpgck0c6r3/files/2/2/2/dataset_222f1751-b711-4c1a-8df6-42a7bddf1e25.dat' 1 1 '/tmp/tmpgck0c6r3/job_working_directory/000/64/outputs/dataset_0be521f0-0a98-477f-952e-380e42eda70b.dat' -u -p --index_depth=3 --buffer=50000000 --fill_options_file=/tmp/tmpgck0c6r3/job_working_directory/000/64/configs/tmpfgtafs_a | |
| ``` | |
| **Exit Code:** | |
| * ```console | |
| 0 | |
| ``` | |
| **Traceback:** | |
| * ```console | |
| ``` | |
| **Job Parameters:** | |
| * | Job parameter | Parameter value | | |
| | ------------- | --------------- | | |
| | \_\_input\_ext | ` "input" ` | | |
| | \_\_workflow\_invocation\_uuid\_\_ | ` "30ca0a3a114e11f189517ced8d7c0d2f" ` | | |
| | chromInfo | ` "/tmp/tmpgck0c6r3/galaxy-dev/tool-data/shared/ucsc/chrom/?.len" ` | | |
| | dbkey | ` "?" ` | | |
| | field1 | ` "1" ` | | |
| | field2 | ` "1" ` | | |
| | fill\_empty\_columns | ` {"__current_case__": 1, "do_fill_empty_columns": {"__current_case__": 0, "column_fill_type": "single_fill_value", "fill_value": "."}, "fill_columns_by": "fill_unjoined_only", "fill_empty_columns_switch": "fill_empty"} ` | | |
| | header | ` "" ` | | |
| | partial | ` "-p" ` | | |
| | unmatched | ` "-u" ` | | |
| </details> | |
| - **Step 58: Plot Data**: | |
| * step_state: scheduled | |
| * <details><summary>Subworkflow Steps</summary> | |
| - **Step 1: Primary data**: | |
| * step_state: scheduled | |
| - **Step 2: Alternate data**: | |
| * step_state: scheduled | |
| - **Step 3: Name of primary assembly**: | |
| * step_state: scheduled | |
| - **Step 4: Name of alternate assembly**: | |
| * step_state: scheduled | |
| - **Step 5: Unlabelled step (toolshed.g2.bx.psu.edu/repos/devteam/add\_value/addValue/1.0.1)**: | |
| * step_state: scheduled | |
| * <details><summary>Jobs</summary> | |
| - **Job 1:** | |
| * Job state is ok | |
| **Container:** | |
| * ```console | |
| quay.io/biocontainers/perl:5.26--2 | |
| ``` | |
| **Command Line:** | |
| * ```console | |
| perl /tmp/shed_dir/toolshed.g2.bx.psu.edu/repos/devteam/add_value/023f0a3760b3/add_value/fixedValueColumn.pl "/tmp/tmpgck0c6r3/files/0/f/7/dataset_0f7ffce6-65c1-4abb-97ae-d54c2138bac6.dat" "/tmp/tmpgck0c6r3/job_working_directory/000/85/outputs/dataset_767747d4-de5b-47e7-8757-4089a169cdc4.dat" "Hap1" "no" | |
| ``` | |
| **Exit Code:** | |
| * ```console | |
| 0 | |
| ``` | |
| **Traceback:** | |
| * ```console | |
| ``` | |
| **Job Parameters:** | |
| * | Job parameter | Parameter value | | |
| | ------------- | --------------- | | |
| | \_\_input\_ext | ` "input" ` | | |
| | \_\_workflow\_invocation\_uuid\_\_ | ` "30ca0a3e114e11f189517ced8d7c0d2f" ` | | |
| | chromInfo | ` "/tmp/tmpgck0c6r3/galaxy-dev/tool-data/shared/ucsc/chrom/?.len" ` | | |
| | dbkey | ` "?" ` | | |
| | exp | ` "Hap1" ` | | |
| | iterate | ` "no" ` | | |
| </details> | |
| - **Step 6: Unlabelled step (toolshed.g2.bx.psu.edu/repos/devteam/add\_value/addValue/1.0.1)**: | |
| * step_state: scheduled | |
| * <details><summary>Jobs</summary> | |
| - **Job 1:** | |
| * Job state is ok | |
| **Container:** | |
| * ```console | |
| quay.io/biocontainers/perl:5.26--2 | |
| ``` | |
| **Command Line:** | |
| * ```console | |
| perl /tmp/shed_dir/toolshed.g2.bx.psu.edu/repos/devteam/add_value/023f0a3760b3/add_value/fixedValueColumn.pl "/tmp/tmpgck0c6r3/files/0/6/0/dataset_0605f299-2f5c-4b18-bd96-64968433909f.dat" "/tmp/tmpgck0c6r3/job_working_directory/000/86/outputs/dataset_7757ade7-5eb5-4190-b0a3-327c267de9ee.dat" "Hap2" "no" | |
| ``` | |
| **Exit Code:** | |
| * ```console | |
| 0 | |
| ``` | |
| **Traceback:** | |
| * ```console | |
| ``` | |
| **Job Parameters:** | |
| * | Job parameter | Parameter value | | |
| | ------------- | --------------- | | |
| | \_\_input\_ext | ` "input" ` | | |
| | \_\_workflow\_invocation\_uuid\_\_ | ` "30ca0a3e114e11f189517ced8d7c0d2f" ` | | |
| | chromInfo | ` "/tmp/tmpgck0c6r3/galaxy-dev/tool-data/shared/ucsc/chrom/?.len" ` | | |
| | dbkey | ` "?" ` | | |
| | exp | ` "Hap2" ` | | |
| | iterate | ` "no" ` | | |
| </details> | |
| - **Step 7: Unlabelled step (toolshed.g2.bx.psu.edu/repos/bgruening/text\_processing/tp\_cat/9.5+galaxy2)**: | |
| * step_state: scheduled | |
| * <details><summary>Jobs</summary> | |
| - **Job 1:** | |
| * Job state is ok | |
| **Container:** | |
| * ```console | |
| quay.io/biocontainers/coreutils:9.5 | |
| ``` | |
| **Command Line:** | |
| * ```console | |
| cat '/tmp/tmpgck0c6r3/files/7/6/7/dataset_767747d4-de5b-47e7-8757-4089a169cdc4.dat' >> '/tmp/tmpgck0c6r3/job_working_directory/000/87/outputs/dataset_b34fa442-f108-47a2-b4f4-3df63b410a99.dat' && cat '/tmp/tmpgck0c6r3/files/7/7/5/dataset_7757ade7-5eb5-4190-b0a3-327c267de9ee.dat' >> '/tmp/tmpgck0c6r3/job_working_directory/000/87/outputs/dataset_b34fa442-f108-47a2-b4f4-3df63b410a99.dat' && exit 0 | |
| ``` | |
| **Exit Code:** | |
| * ```console | |
| 0 | |
| ``` | |
| **Traceback:** | |
| * ```console | |
| ``` | |
| **Job Parameters:** | |
| * | Job parameter | Parameter value | | |
| | ------------- | --------------- | | |
| | \_\_input\_ext | ` "input" ` | | |
| | \_\_workflow\_invocation\_uuid\_\_ | ` "30ca0a3e114e11f189517ced8d7c0d2f" ` | | |
| | chromInfo | ` "/tmp/tmpgck0c6r3/galaxy-dev/tool-data/shared/ucsc/chrom/?.len" ` | | |
| | dbkey | ` "?" ` | | |
| | queries | ` [{"__index__": 0, "inputs2": {"values": [{"id": 139, "src": "hda"}]}}] ` | | |
| </details> | |
| - **Step 8: Unlabelled step (Cut1)**: | |
| * step_state: scheduled | |
| * <details><summary>Jobs</summary> | |
| - **Job 1:** | |
| * Job state is ok | |
| **Container:** | |
| * ```console | |
| quay.io/biocontainers/perl:5.26--2 | |
| ``` | |
| **Command Line:** | |
| * ```console | |
| perl '/tmp/tmpgck0c6r3/galaxy-dev/tools/filters/cutWrapper.pl' '/tmp/tmpgck0c6r3/files/b/3/4/dataset_b34fa442-f108-47a2-b4f4-3df63b410a99.dat' 'c8,c5,c6' T '/tmp/tmpgck0c6r3/job_working_directory/000/88/outputs/dataset_f68f9fc0-ed3c-43bd-8bca-624c9da7b851.dat' | |
| ``` | |
| **Exit Code:** | |
| * ```console | |
| 0 | |
| ``` | |
| **Traceback:** | |
| * ```console | |
| ``` | |
| **Job Parameters:** | |
| * | Job parameter | Parameter value | | |
| | ------------- | --------------- | | |
| | \_\_input\_ext | ` "tabular" ` | | |
| | \_\_workflow\_invocation\_uuid\_\_ | ` "30ca0a3e114e11f189517ced8d7c0d2f" ` | | |
| | chromInfo | ` "/tmp/tmpgck0c6r3/galaxy-dev/tool-data/shared/ucsc/chrom/?.len" ` | | |
| | columnList | ` "c8,c5,c6" ` | | |
| | dbkey | ` "?" ` | | |
| | delimiter | ` "T" ` | | |
| </details> | |
| - **Step 9: Unlabelled step (Cut1)**: | |
| * step_state: scheduled | |
| * <details><summary>Jobs</summary> | |
| - **Job 1:** | |
| * Job state is ok | |
| **Container:** | |
| * ```console | |
| quay.io/biocontainers/perl:5.26--2 | |
| ``` | |
| **Command Line:** | |
| * ```console | |
| perl '/tmp/tmpgck0c6r3/galaxy-dev/tools/filters/cutWrapper.pl' '/tmp/tmpgck0c6r3/files/b/3/4/dataset_b34fa442-f108-47a2-b4f4-3df63b410a99.dat' 'c8,c4,c7' T '/tmp/tmpgck0c6r3/job_working_directory/000/89/outputs/dataset_b8960a79-a29a-4068-b572-00699f6c9ed2.dat' | |
| ``` | |
| **Exit Code:** | |
| * ```console | |
| 0 | |
| ``` | |
| **Traceback:** | |
| * ```console | |
| ``` | |
| **Job Parameters:** | |
| * | Job parameter | Parameter value | | |
| | ------------- | --------------- | | |
| | \_\_input\_ext | ` "tabular" ` | | |
| | \_\_workflow\_invocation\_uuid\_\_ | ` "30ca0a3e114e11f189517ced8d7c0d2f" ` | | |
| | chromInfo | ` "/tmp/tmpgck0c6r3/galaxy-dev/tool-data/shared/ucsc/chrom/?.len" ` | | |
| | columnList | ` "c8,c4,c7" ` | | |
| | dbkey | ` "?" ` | | |
| | delimiter | ` "T" ` | | |
| </details> | |
| - **Step 10: Nx Plot (toolshed.g2.bx.psu.edu/repos/iuc/ggplot2\_point/ggplot2\_point/3.5.1+galaxy2)**: | |
| * step_state: scheduled | |
| * <details><summary>Jobs</summary> | |
| - **Job 1:** | |
| * Job state is ok | |
| **Container:** | |
| * ```console | |
| quay.io/biocontainers/mulled-v2-c07fe12ea1e24392c0b08ab611fa35b7c2dd3fd7:f9b597df47fe575d793bf1c7c3ae2b137fb49807-0 | |
| ``` | |
| **Command Line:** | |
| * ```console | |
| cat '/tmp/tmpgck0c6r3/job_working_directory/000/90/configs/tmp2_62l4ov' && Rscript '/tmp/tmpgck0c6r3/job_working_directory/000/90/configs/tmp2_62l4ov' | |
| ``` | |
| **Exit Code:** | |
| * ```console | |
| 0 | |
| ``` | |
| **Standard Error:** | |
| * ```console | |
| Warning message: | |
| In Sys.setlocale("LC_MESSAGES", "en_US.UTF-8") : | |
| OS reports request to set locale to "en_US.UTF-8" cannot be honored | |
| Warning message: | |
| Using `size` aesthetic for lines was deprecated in ggplot2 3.4.0. | |
| ℹ Please use `linewidth` instead. | |
| Warning message: | |
| `aes_string()` was deprecated in ggplot2 3.0.0. | |
| ℹ Please use tidy evaluation idioms with `aes()`. | |
| ℹ See also `vignette("ggplot2-in-packages")` for more information. | |
| ``` | |
| **Standard Output:** | |
| * ```console | |
| options(show.error.messages=F, error=function(){cat(geterrmessage(), file=stderr()); q("no",1,F)}) | |
| loc <- Sys.setlocale("LC_MESSAGES", "en_US.UTF-8") | |
| library(ggplot2) | |
| #Choose between automatically scaled x and y axis or user defined | |
| gg_scalex = NULL | |
| gg_scaley = NULL | |
| gg_theme = theme_bw() | |
| gg_legend = theme(legend.position="right") | |
| input <- read.csv('/tmp/tmpgck0c6r3/files/f/6/8/dataset_f68f9fc0-ed3c-43bd-8bca-624c9da7b851.dat', sep='\t') | |
| names(input)[2] <- "xcol" | |
| names(input)[3] <- "ycol" | |
| gg_facet = NULL | |
| gg_factor = aes(colour=factor(factor)) | |
| gg_line = geom_line(size=1, alpha=1, gg_factor) | |
| color_scale = scale_color_brewer(palette='Set1', direction='1') | |
| names(input)[1] <- "factor" | |
| gg_axistitle = theme(axis.title = element_text(color = NULL, size = NULL, face = NULL)) | |
| gg_axistext = theme(axis.text = element_text(color = NULL, size = NULL, face = NULL)) | |
| gg_plottitle = theme(plot.title = element_text(color = NULL, size = NULL, face = NULL)) | |
| gg_gridline = NULL | |
| gg_point = NULL | |
| #this is the actual ggplot command to make the final plot(s) | |
| plot_out <- ggplot(input, aes_string(x=names(input)[2], y=names(input)[3])) + gg_point + gg_line + gg_facet + | |
| gg_theme + gg_scalex + gg_scaley + color_scale + gg_legend + ggtitle('Nx Plot') + xlab('x') + ylab('Nx (Mb)')+ | |
| gg_axistitle + gg_axistext + gg_plottitle + gg_gridline | |
| gg_width <- as.double('6.0') | |
| gg_height <- as.double('4.0') | |
| gg_unit <- 'in' | |
| gg_dpi <- as.double('300.0') | |
| gg_add_device <- 'none' | |
| output1 <- '/tmp/tmpgck0c6r3/job_working_directory/000/90/outputs/dataset_b826d8a4-1feb-4522-8bf7-45f61e88d881.dat' | |
| output2 <- 'XXXX' | |
| ggsave(filename = output1, plot = plot_out, width = gg_width, height = gg_height, units = gg_unit, dpi = gg_dpi, device = "png") | |
| if(gg_add_device != "none"){ | |
| ggsave(filename = output2, plot = plot_out, width = gg_width, height = gg_height, units = gg_unit, dpi = gg_dpi, device = gg_add_device) | |
| } | |
| ``` | |
| **Traceback:** | |
| * ```console | |
| ``` | |
| **Job Parameters:** | |
| * | Job parameter | Parameter value | | |
| | ------------- | --------------- | | |
| | \_\_input\_ext | ` "input" ` | | |
| | \_\_workflow\_invocation\_uuid\_\_ | ` "30ca0a3e114e11f189517ced8d7c0d2f" ` | | |
| | adv | ` {"axis_text_customization": {"__current_case__": 0, "axis_customization": "default"}, "axis_title_customization": {"__current_case__": 0, "axis_customization": "default"}, "factor": {"__current_case__": 1, "colororder": "1", "colors": "Set1", "factorcol": "1", "factoring": "Single"}, "gridlinecust": "default", "legend": "yes", "plot_title_customization": {"__current_case__": 0, "axis_customization": "default"}, "scaling": {"__current_case__": 0, "plot_scaling": "Automatic"}, "theme": "bw", "transform": "none", "type_conditional": {"__current_case__": 2, "type_options": "lines"}} ` | | |
| | chromInfo | ` "/tmp/tmpgck0c6r3/galaxy-dev/tool-data/shared/ucsc/chrom/?.len" ` | | |
| | cols | ` {"__current_case__": 0, "header": "yes", "xplot": "2", "yplot": "3"} ` | | |
| | dbkey | ` "?" ` | | |
| | out | ` {"additional_output_format": "none", "dpi_output_dim": "300.0", "height_output_dim": "4.0", "unit_output_dim": "in", "width_output_dim": "6.0"} ` | | |
| | title | ` "Nx Plot" ` | | |
| | xlab | ` "x" ` | | |
| | ylab | ` "Nx (Mb)" ` | | |
| </details> | |
| - **Step 11: Size Plot (toolshed.g2.bx.psu.edu/repos/iuc/ggplot2\_point/ggplot2\_point/3.5.1+galaxy2)**: | |
| * step_state: scheduled | |
| * <details><summary>Jobs</summary> | |
| - **Job 1:** | |
| * Job state is ok | |
| **Container:** | |
| * ```console | |
| quay.io/biocontainers/mulled-v2-c07fe12ea1e24392c0b08ab611fa35b7c2dd3fd7:f9b597df47fe575d793bf1c7c3ae2b137fb49807-0 | |
| ``` | |
| **Command Line:** | |
| * ```console | |
| cat '/tmp/tmpgck0c6r3/job_working_directory/000/91/configs/tmpujuvr3h6' && Rscript '/tmp/tmpgck0c6r3/job_working_directory/000/91/configs/tmpujuvr3h6' | |
| ``` | |
| **Exit Code:** | |
| * ```console | |
| 0 | |
| ``` | |
| **Standard Error:** | |
| * ```console | |
| Warning message: | |
| In Sys.setlocale("LC_MESSAGES", "en_US.UTF-8") : | |
| OS reports request to set locale to "en_US.UTF-8" cannot be honored | |
| Warning message: | |
| Using `size` aesthetic for lines was deprecated in ggplot2 3.4.0. | |
| ℹ Please use `linewidth` instead. | |
| Warning message: | |
| `aes_string()` was deprecated in ggplot2 3.0.0. | |
| ℹ Please use tidy evaluation idioms with `aes()`. | |
| ℹ See also `vignette("ggplot2-in-packages")` for more information. | |
| ``` | |
| **Standard Output:** | |
| * ```console | |
| options(show.error.messages=F, error=function(){cat(geterrmessage(), file=stderr()); q("no",1,F)}) | |
| loc <- Sys.setlocale("LC_MESSAGES", "en_US.UTF-8") | |
| library(ggplot2) | |
| #Choose between automatically scaled x and y axis or user defined | |
| gg_scalex = NULL | |
| gg_scaley = NULL | |
| gg_theme = theme_bw() | |
| gg_legend = theme(legend.position="right") | |
| input <- read.csv('/tmp/tmpgck0c6r3/files/b/8/9/dataset_b8960a79-a29a-4068-b572-00699f6c9ed2.dat', sep='\t') | |
| names(input)[2] <- "xcol" | |
| names(input)[3] <- "ycol" | |
| gg_facet = NULL | |
| gg_factor = aes(colour=factor(factor)) | |
| gg_line = geom_line(size=1, alpha=1, gg_factor) | |
| color_scale = scale_color_brewer(palette='Set1', direction='1') | |
| names(input)[1] <- "factor" | |
| gg_axistitle = theme(axis.title = element_text(color = NULL, size = NULL, face = NULL)) | |
| gg_axistext = theme(axis.text = element_text(color = NULL, size = NULL, face = NULL)) | |
| gg_plottitle = theme(plot.title = element_text(color = NULL, size = NULL, face = NULL)) | |
| gg_gridline = NULL | |
| gg_point = NULL | |
| #this is the actual ggplot command to make the final plot(s) | |
| plot_out <- ggplot(input, aes_string(x=names(input)[2], y=names(input)[3])) + gg_point + gg_line + gg_facet + | |
| gg_theme + gg_scalex + gg_scaley + color_scale + gg_legend + ggtitle('Size Plot') + xlab('Scaffold number') + ylab('Cumulative Size (Mb)')+ | |
| gg_axistitle + gg_axistext + gg_plottitle + gg_gridline | |
| gg_width <- as.double('6.0') | |
| gg_height <- as.double('4.0') | |
| gg_unit <- 'in' | |
| gg_dpi <- as.double('300.0') | |
| gg_add_device <- 'none' | |
| output1 <- '/tmp/tmpgck0c6r3/job_working_directory/000/91/outputs/dataset_10ec65b5-7c06-41e9-81a8-3322c3708087.dat' | |
| output2 <- 'XXXX' | |
| ggsave(filename = output1, plot = plot_out, width = gg_width, height = gg_height, units = gg_unit, dpi = gg_dpi, device = "png") | |
| if(gg_add_device != "none"){ | |
| ggsave(filename = output2, plot = plot_out, width = gg_width, height = gg_height, units = gg_unit, dpi = gg_dpi, device = gg_add_device) | |
| } | |
| ``` | |
| **Traceback:** | |
| * ```console | |
| ``` | |
| **Job Parameters:** | |
| * | Job parameter | Parameter value | | |
| | ------------- | --------------- | | |
| | \_\_input\_ext | ` "input" ` | | |
| | \_\_workflow\_invocation\_uuid\_\_ | ` "30ca0a3e114e11f189517ced8d7c0d2f" ` | | |
| | adv | ` {"axis_text_customization": {"__current_case__": 0, "axis_customization": "default"}, "axis_title_customization": {"__current_case__": 0, "axis_customization": "default"}, "factor": {"__current_case__": 1, "colororder": "1", "colors": "Set1", "factorcol": "1", "factoring": "Single"}, "gridlinecust": "default", "legend": "yes", "plot_title_customization": {"__current_case__": 0, "axis_customization": "default"}, "scaling": {"__current_case__": 0, "plot_scaling": "Automatic"}, "theme": "bw", "transform": "none", "type_conditional": {"__current_case__": 2, "type_options": "lines"}} ` | | |
| | chromInfo | ` "/tmp/tmpgck0c6r3/galaxy-dev/tool-data/shared/ucsc/chrom/?.len" ` | | |
| | cols | ` {"__current_case__": 0, "header": "yes", "xplot": "2", "yplot": "3"} ` | | |
| | dbkey | ` "?" ` | | |
| | out | ` {"additional_output_format": "none", "dpi_output_dim": "300.0", "height_output_dim": "4.0", "unit_output_dim": "in", "width_output_dim": "6.0"} ` | | |
| | title | ` "Size Plot" ` | | |
| | xlab | ` "Scaffold number" ` | | |
| | ylab | ` "Cumulative Size (Mb)" ` | | |
| </details> | |
| </details> | |
| - **Step 59: Compleasm Hap2 (toolshed.g2.bx.psu.edu/repos/iuc/compleasm/compleasm/0.2.6+galaxy3)**: | |
| * step_state: scheduled | |
| * <details><summary>Jobs</summary> | |
| - **Job 1:** | |
| * Job state is ok | |
| **Container:** | |
| * ```console | |
| quay.io/biocontainers/compleasm:0.2.6--pyh7cba7a3_0 | |
| ``` | |
| **Command Line:** | |
| * ```console | |
| mkdir -p 'galaxy_db/' && ln -s '/cvmfs/data.galaxyproject.org/byhand/busco/v5/lineages/vertebrata_odb10/' 'galaxy_db/vertebrata_odb10' && touch 'galaxy_db/vertebrata_odb10.done' && compleasm run -a '/tmp/tmpgck0c6r3/files/e/c/3/dataset_ec30905f-b6ab-4141-959f-bc2d87fcd32c.dat' -o galaxy_output --mode busco -L 'galaxy_db' -l 'vertebrata_odb10' -t "${GALAXY_SLOTS:-1}" | |
| ``` | |
| **Exit Code:** | |
| * ```console | |
| 0 | |
| ``` | |
| **Standard Error:** | |
| * ```console | |
| [M::mp_ntseq_read@0.008*0.97] read 1351178 bases in 51 contigs | |
| [M::mp_idx_build@0.009*0.93] 10608 blocks | |
| [M::mp_idx_build@0.074*0.77] collected syncmers | |
| [M::mp_idx_build@0.118*0.85] 629339 kmer-block pairs | |
| [M::mp_mapopt_set_max_intron] set max intron size to 10000 | |
| [M::mp_idx_print_stat] 328535 distinct k-mers; mean occ of infrequent k-mers: 1.92; 0 frequent k-mers accounting for 0 occurrences | |
| [M::worker_pipeline::6.596*0.93] mapped 3408 sequences | |
| [M::worker_pipeline::12.547*0.93] mapped 3404 sequences | |
| [M::worker_pipeline::18.454*0.93] mapped 3357 sequences | |
| [M::worker_pipeline::24.305*0.93] mapped 3488 sequences | |
| [M::worker_pipeline::30.427*0.93] mapped 3573 sequences | |
| [M::worker_pipeline::36.251*0.94] mapped 3161 sequences | |
| [M::worker_pipeline::41.850*0.94] mapped 3178 sequences | |
| [M::worker_pipeline::47.490*0.95] mapped 3277 sequences | |
| [M::worker_pipeline::53.058*0.95] mapped 3290 sequences | |
| [M::worker_pipeline::58.751*0.95] mapped 3415 sequences | |
| [M::worker_pipeline::64.206*0.96] mapped 3273 sequences | |
| [M::worker_pipeline::69.786*0.96] mapped 3297 sequences | |
| [M::worker_pipeline::75.812*0.96] mapped 3366 sequences | |
| [M::worker_pipeline::81.651*0.96] mapped 3526 sequences | |
| [M::worker_pipeline::87.483*0.96] mapped 3363 sequences | |
| [M::worker_pipeline::93.068*0.96] mapped 3386 sequences | |
| [M::worker_pipeline::98.610*0.97] mapped 3472 sequences | |
| [M::worker_pipeline::103.986*0.97] mapped 3375 sequences | |
| [M::worker_pipeline::109.694*0.97] mapped 3337 sequences | |
| [M::worker_pipeline::114.815*0.96] mapped 3452 sequences | |
| [M::worker_pipeline::120.449*0.96] mapped 3598 sequences | |
| [M::worker_pipeline::126.048*0.96] mapped 3363 sequences | |
| [M::worker_pipeline::132.487*0.96] mapped 3385 sequences | |
| [M::worker_pipeline::138.420*0.96] mapped 3335 sequences | |
| [M::worker_pipeline::144.525*0.96] mapped 3434 sequences | |
| [M::worker_pipeline::150.811*0.96] mapped 3323 sequences | |
| [M::worker_pipeline::156.562*0.96] mapped 3415 sequences | |
| [M::worker_pipeline::162.899*0.96] mapped 3310 sequences | |
| [M::worker_pipeline::169.151*0.96] mapped 3376 sequences | |
| [M::worker_pipeline::175.159*0.96] mapped 3489 sequences | |
| [M::worker_pipeline::181.617*0.96] mapped 3313 sequences | |
| [M::worker_pipeline::187.651*0.96] mapped 3450 sequences | |
| [M::worker_pipeline::193.711*0.96] mapped 3456 sequences | |
| [M::worker_pipeline::199.817*0.96] mapped 3301 sequences | |
| [M::worker_pipeline::205.930*0.96] mapped 3463 sequences | |
| [M::worker_pipeline::211.232*0.96] mapped 3439 sequences | |
| [M::worker_pipeline::216.410*0.96] mapped 3267 sequences | |
| [M::worker_pipeline::221.719*0.96] mapped 3484 sequences | |
| [M::worker_pipeline::227.367*0.96] mapped 3767 sequences | |
| [M::worker_pipeline::232.990*0.96] mapped 3506 sequences | |
| [M::worker_pipeline::237.784*0.96] mapped 3561 sequences | |
| [M::worker_pipeline::243.597*0.97] mapped 3335 sequences | |
| [M::worker_pipeline::249.085*0.97] mapped 3436 sequences | |
| [M::worker_pipeline::254.642*0.97] mapped 3410 sequences | |
| [M::worker_pipeline::260.908*0.97] mapped 3504 sequences | |
| [M::worker_pipeline::266.515*0.97] mapped 3821 sequences | |
| [M::worker_pipeline::272.219*0.97] mapped 3426 sequences | |
| [M::worker_pipeline::278.048*0.97] mapped 3341 sequences | |
| [M::worker_pipeline::283.311*0.97] mapped 3484 sequences | |
| [M::worker_pipeline::288.989*0.97] mapped 3276 sequences | |
| [M::worker_pipeline::293.365*0.97] mapped 3314 sequences | |
| [M::worker_pipeline::297.700*0.97] mapped 3277 sequences | |
| [M::worker_pipeline::301.986*0.97] mapped 3697 sequences | |
| [M::worker_pipeline::306.637*0.97] mapped 3334 sequences | |
| [M::worker_pipeline::310.903*0.97] mapped 3323 sequences | |
| [M::worker_pipeline::315.167*0.97] mapped 3927 sequences | |
| [M::worker_pipeline::319.602*0.97] mapped 3655 sequences | |
| [M::worker_pipeline::323.632*0.97] mapped 3385 sequences | |
| [M::worker_pipeline::327.976*0.97] mapped 3395 sequences | |
| [M::worker_pipeline::332.095*0.97] mapped 3382 sequences | |
| [M::worker_pipeline::336.313*0.97] mapped 3341 sequences | |
| [M::worker_pipeline::340.406*0.97] mapped 3366 sequences | |
| [M::worker_pipeline::344.350*0.97] mapped 3334 sequences | |
| [M::worker_pipeline::349.032*0.97] mapped 3281 sequences | |
| [M::worker_pipeline::353.734*0.97] mapped 3362 sequences | |
| [M::worker_pipeline::357.831*0.97] mapped 3686 sequences | |
| [M::worker_pipeline::361.723*0.97] mapped 3406 sequences | |
| [M::worker_pipeline::366.114*0.97] mapped 3262 sequences | |
| [M::worker_pipeline::370.500*0.97] mapped 3312 sequences | |
| [M::worker_pipeline::374.853*0.97] mapped 3308 sequences | |
| [M::worker_pipeline::379.389*0.97] mapped 3392 sequences | |
| [M::worker_pipeline::383.938*0.98] mapped 3346 sequences | |
| [M::worker_pipeline::388.173*0.98] mapped 3408 sequences | |
| [M::worker_pipeline::392.314*0.98] mapped 3200 sequences | |
| [M::worker_pipeline::396.984*0.98] mapped 3425 sequences | |
| [M::worker_pipeline::400.924*0.98] mapped 3425 sequences | |
| [M::worker_pipeline::405.079*0.98] mapped 3367 sequences | |
| [M::worker_pipeline::409.300*0.98] mapped 3464 sequences | |
| [M::worker_pipeline::413.415*0.98] mapped 3250 sequences | |
| [M::worker_pipeline::417.627*0.98] mapped 3312 sequences | |
| [M::worker_pipeline::421.951*0.98] mapped 3806 sequences | |
| [M::worker_pipeline::426.673*0.98] mapped 3475 sequences | |
| [M::worker_pipeline::431.037*0.98] mapped 3685 sequences | |
| [M::worker_pipeline::435.369*0.98] mapped 3335 sequences | |
| [M::worker_pipeline::439.645*0.98] mapped 3353 sequences | |
| [M::worker_pipeline::443.986*0.98] mapped 3356 sequences | |
| [M::worker_pipeline::448.631*0.98] mapped 3291 sequences | |
| [M::worker_pipeline::452.882*0.98] mapped 3309 sequences | |
| [M::worker_pipeline::457.638*0.98] mapped 3204 sequences | |
| [M::worker_pipeline::461.749*0.98] mapped 3319 sequences | |
| [M::worker_pipeline::465.868*0.98] mapped 3381 sequences | |
| [M::worker_pipeline::470.340*0.98] mapped 3312 sequences | |
| [M::worker_pipeline::474.518*0.98] mapped 3247 sequences | |
| [M::worker_pipeline::478.917*0.98] mapped 3342 sequences | |
| [M::worker_pipeline::483.571*0.98] mapped 3305 sequences | |
| [M::worker_pipeline::487.955*0.98] mapped 3425 sequences | |
| [M::worker_pipeline::492.302*0.98] mapped 3646 sequences | |
| [M::worker_pipeline::497.049*0.98] mapped 3250 sequences | |
| [M::worker_pipeline::501.291*0.98] mapped 3404 sequences | |
| [M::worker_pipeline::505.580*0.98] mapped 3324 sequences | |
| [M::worker_pipeline::509.678*0.98] mapped 3530 sequences | |
| [M::worker_pipeline::514.002*0.98] mapped 3330 sequences | |
| [M::worker_pipeline::518.663*0.98] mapped 3432 sequences | |
| [M::worker_pipeline::522.969*0.98] mapped 3830 sequences | |
| [M::worker_pipeline::527.171*0.98] mapped 3937 sequences | |
| [M::worker_pipeline::531.787*0.98] mapped 3391 sequences | |
| [M::worker_pipeline::536.387*0.98] mapped 3562 sequences | |
| [M::worker_pipeline::540.963*0.98] mapped 3605 sequences | |
| [M::worker_pipeline::545.419*0.98] mapped 3897 sequences | |
| [M::worker_pipeline::549.392*0.98] mapped 4068 sequences | |
| [M::worker_pipeline::553.432*0.98] mapped 3511 sequences | |
| [M::worker_pipeline::557.455*0.98] mapped 3324 sequences | |
| [M::worker_pipeline::561.176*0.98] mapped 3395 sequences | |
| [M::worker_pipeline::565.693*0.98] mapped 3394 sequences | |
| [M::worker_pipeline::570.048*0.98] mapped 3273 sequences | |
| [M::worker_pipeline::574.586*0.98] mapped 3211 sequences | |
| [M::worker_pipeline::578.549*0.98] mapped 3338 sequences | |
| [M::worker_pipeline::582.501*0.98] mapped 3208 sequences | |
| [M::worker_pipeline::586.575*0.98] mapped 3294 sequences | |
| [M::worker_pipeline::590.774*0.98] mapped 3415 sequences | |
| [M::worker_pipeline::595.543*0.98] mapped 3446 sequences | |
| [M::worker_pipeline::600.100*0.98] mapped 3498 sequences | |
| [M::worker_pipeline::604.408*0.98] mapped 3417 sequences | |
| [M::worker_pipeline::609.063*0.98] mapped 3417 sequences | |
| [M::worker_pipeline::613.860*0.98] mapped 3328 sequences | |
| [M::worker_pipeline::619.026*0.98] mapped 3448 sequences | |
| [M::worker_pipeline::623.870*0.98] mapped 3569 sequences | |
| [M::worker_pipeline::627.739*0.98] mapped 4045 sequences | |
| [M::worker_pipeline::632.168*0.98] mapped 3258 sequences | |
| [M::worker_pipeline::637.070*0.98] mapped 3320 sequences | |
| [M::worker_pipeline::641.758*0.99] mapped 3321 sequences | |
| [M::worker_pipeline::646.177*0.99] mapped 3223 sequences | |
| [M::worker_pipeline::651.232*0.99] mapped 3193 sequences | |
| [M::worker_pipeline::655.965*0.99] mapped 3310 sequences | |
| [M::worker_pipeline::660.799*0.99] mapped 3206 sequences | |
| [M::worker_pipeline::665.370*0.99] mapped 3287 sequences | |
| [M::worker_pipeline::670.008*0.99] mapped 3460 sequences | |
| [M::worker_pipeline::674.621*0.99] mapped 3243 sequences | |
| [M::worker_pipeline::679.280*0.99] mapped 3284 sequences | |
| [M::worker_pipeline::683.583*0.99] mapped 3268 sequences | |
| [M::worker_pipeline::688.329*0.99] mapped 3430 sequences | |
| [M::worker_pipeline::692.955*0.99] mapped 3283 sequences | |
| [M::worker_pipeline::698.241*0.99] mapped 3136 sequences | |
| [M::worker_pipeline::703.330*0.99] mapped 3340 sequences | |
| [M::worker_pipeline::707.728*0.99] mapped 4104 sequences | |
| [M::worker_pipeline::712.376*0.99] mapped 3490 sequences | |
| [M::worker_pipeline::716.966*0.99] mapped 3360 sequences | |
| [M::worker_pipeline::721.328*0.99] mapped 3363 sequences | |
| [M::worker_pipeline::725.706*0.99] mapped 3384 sequences | |
| [M::worker_pipeline::730.201*0.99] mapped 3202 sequences | |
| [M::worker_pipeline::734.459*0.99] mapped 3294 sequences | |
| [M::worker_pipeline::738.802*0.99] mapped 3435 sequences | |
| [M::worker_pipeline::743.268*0.99] mapped 3481 sequences | |
| [M::worker_pipeline::747.287*0.99] mapped 3337 sequences | |
| [M::worker_pipeline::751.978*0.99] mapped 3380 sequences | |
| [M::worker_pipeline::756.127*0.99] mapped 3308 sequences | |
| [M::worker_pipeline::760.026*0.99] mapped 3347 sequences | |
| [M::worker_pipeline::764.701*0.99] mapped 3455 sequences | |
| [M::worker_pipeline::769.038*0.99] mapped 3245 sequences | |
| [M::worker_pipeline::773.100*0.99] mapped 3481 sequences | |
| [M::worker_pipeline::777.249*0.99] mapped 3502 sequences | |
| [M::worker_pipeline::781.987*0.99] mapped 3248 sequences | |
| [M::worker_pipeline::786.107*0.99] mapped 3540 sequences | |
| [M::worker_pipeline::790.582*0.99] mapped 3491 sequences | |
| [M::worker_pipeline::795.086*0.99] mapped 3322 sequences | |
| [M::worker_pipeline::799.455*0.99] mapped 3485 sequences | |
| [M::worker_pipeline::803.649*0.99] mapped 3884 sequences | |
| [M::worker_pipeline::808.410*0.99] mapped 3447 sequences | |
| [M::worker_pipeline::812.717*0.99] mapped 3294 sequences | |
| [M::worker_pipeline::816.586*0.99] mapped 3422 sequences | |
| [M::worker_pipeline::820.784*0.99] mapped 3318 sequences | |
| [M::worker_pipeline::825.173*0.99] mapped 3210 sequences | |
| [M::worker_pipeline::829.296*0.99] mapped 3264 sequences | |
| [M::worker_pipeline::833.455*0.99] mapped 3572 sequences | |
| [M::worker_pipeline::837.621*0.99] mapped 3309 sequences | |
| [M::worker_pipeline::841.771*0.99] mapped 3235 sequences | |
| [M::worker_pipeline::846.211*0.99] mapped 3246 sequences | |
| [M::worker_pipeline::850.229*0.99] mapped 3349 sequences | |
| [M::worker_pipeline::854.312*0.99] mapped 3240 sequences | |
| [M::worker_pipeline::858.544*0.99] mapped 3161 sequences | |
| [M::worker_pipeline::862.663*0.99] mapped 3259 sequences | |
| [M::worker_pipeline::866.651*0.99] mapped 3252 sequences | |
| [M::worker_pipeline::870.845*0.99] mapped 3149 sequences | |
| [M::worker_pipeline::874.973*0.99] mapped 3595 sequences | |
| [M::worker_pipeline::878.747*0.99] mapped 3485 sequences | |
| [M::worker_pipeline::882.575*0.99] mapped 3287 sequences | |
| [M::worker_pipeline::886.618*0.99] mapped 3200 sequences | |
| [M::worker_pipeline::890.829*0.99] mapped 3249 sequences | |
| [M::worker_pipeline::894.972*0.99] mapped 3273 sequences | |
| [M::worker_pipeline::899.076*0.99] mapped 3329 sequences | |
| [M::worker_pipeline::903.380*0.99] mapped 3150 sequences | |
| [M::worker_pipeline::907.357*0.99] mapped 3282 sequences | |
| [M::worker_pipeline::911.243*0.99] mapped 3128 sequences | |
| [M::worker_pipeline::915.055*0.99] mapped 3144 sequences | |
| [M::worker_pipeline::918.927*0.99] mapped 3451 sequences | |
| [M::worker_pipeline::922.809*0.99] mapped 3466 sequences | |
| [M::worker_pipeline::927.017*0.99] mapped 3277 sequences | |
| [M::worker_pipeline::930.227*0.99] mapped 2560 sequences | |
| [M::main] Version: 0.13-r248 | |
| [M::main] CMD: /usr/local/bin/miniprot --trans -u -I --outs=0.95 -t 1 --gff /tmp/tmpgck0c6r3/files/e/c/3/dataset_ec30905f-b6ab-4141-959f-bc2d87fcd32c.dat galaxy_db/vertebrata_odb10/refseq_db.faa.gz | |
| [M::main] Real time: 930.233 sec; CPU: 920.430 sec; Peak RSS: 0.150 GB | |
| ``` | |
| **Standard Output:** | |
| * ```console | |
| Searching for miniprot in the path where compleasm.py is located | |
| Searching for miniprot in the current execution path | |
| Searching for miniprot in $PATH | |
| Searching for hmmsearch in the path where compleasm.py is located | |
| Searching for hmmsearch in the current execution path | |
| Searching for hmmsearch in $PATH | |
| miniprot execute command: | |
| /usr/local/bin/miniprot | |
| Success download from https://busco-data.ezlab.org/v5/data/file_versions.tsv | |
| Success download from https://busco-data.ezlab.org/v5/data/placement_files/list_of_reference_markers.eukaryota_odb10.2019-12-16.txt.tar.gz | |
| Placement file extraction path: galaxy_db/placement_files/list_of_reference_markers.eukaryota_odb10.2019-12-16.txt | |
| Success download from https://busco-data.ezlab.org/v5/data/placement_files/list_of_reference_markers.eukaryota_odb12.2025-01-15.txt.tar.gz | |
| Placement file extraction path: galaxy_db/placement_files/list_of_reference_markers.eukaryota_odb12.2025-01-15.txt | |
| Success download from https://busco-data.ezlab.org/v5/data/placement_files/mapping_taxid-lineage.eukaryota_odb10.2019-12-16.txt.tar.gz | |
| Placement file extraction path: galaxy_db/placement_files/mapping_taxid-lineage.eukaryota_odb10.2019-12-16.txt | |
| Success download from https://busco-data.ezlab.org/v5/data/placement_files/mapping_taxid-lineage.eukaryota_odb12.2025-01-15.txt.tar.gz | |
| Placement file extraction path: galaxy_db/placement_files/mapping_taxid-lineage.eukaryota_odb12.2025-01-15.txt | |
| Success download from https://busco-data.ezlab.org/v5/data/placement_files/mapping_taxids-busco_dataset_name.eukaryota_odb10.2019-12-16.txt.tar.gz | |
| Placement file extraction path: galaxy_db/placement_files/mapping_taxids-busco_dataset_name.eukaryota_odb10.2019-12-16.txt | |
| Success download from https://busco-data.ezlab.org/v5/data/placement_files/mapping_taxids-busco_dataset_name.eukaryota_odb12.2025-01-15.txt.tar.gz | |
| Placement file extraction path: galaxy_db/placement_files/mapping_taxids-busco_dataset_name.eukaryota_odb12.2025-01-15.txt | |
| Success download from https://busco-data.ezlab.org/v5/data/placement_files/supermatrix.aln.eukaryota_odb10.2019-12-16.faa.tar.gz | |
| Placement file extraction path: galaxy_db/placement_files/supermatrix.aln.eukaryota_odb10.2019-12-16.faa | |
| Success download from https://busco-data.ezlab.org/v5/data/placement_files/supermatrix.aln.eukaryota_odb12.2025-01-15.faa.tar.gz | |
| Placement file extraction path: galaxy_db/placement_files/supermatrix.aln.eukaryota_odb12.2025-01-15.faa | |
| Success download from https://busco-data.ezlab.org/v5/data/placement_files/tree.eukaryota_odb10.2019-12-16.nwk.tar.gz | |
| Placement file extraction path: galaxy_db/placement_files/tree.eukaryota_odb10.2019-12-16.nwk | |
| Success download from https://busco-data.ezlab.org/v5/data/placement_files/tree.eukaryota_odb12.2025-01-15.nwk.tar.gz | |
| Placement file extraction path: galaxy_db/placement_files/tree.eukaryota_odb12.2025-01-15.nwk | |
| Success download from https://busco-data.ezlab.org/v5/data/placement_files/tree_metadata.eukaryota_odb10.2019-12-16.txt.tar.gz | |
| Placement file extraction path: galaxy_db/placement_files/tree_metadata.eukaryota_odb10.2019-12-16.txt | |
| Success download from https://busco-data.ezlab.org/v5/data/placement_files/tree_metadata.eukaryota_odb12.2025-01-15.txt.tar.gz | |
| Placement file extraction path: galaxy_db/placement_files/tree_metadata.eukaryota_odb12.2025-01-15.txt | |
| Success download from https://busco-data.ezlab.org/v5/data/lineages/eukaryota_odb10.2024-01-08.tar.gz | |
| Lineage file extraction path: galaxy_db/eukaryota_odb10 | |
| lineage: vertebrata_odb10 | |
| hmmsearch execute command: | |
| /usr/local/bin/hmmsearch | |
| S:0.60%, 20 | |
| D:0.03%, 1 | |
| F:0.06%, 2 | |
| I:0.00%, 0 | |
| M:99.31%, 3331 | |
| N:3354 | |
| Warning: Given the potentially high diversity of the sample, compleasm results may not be reliable!We recommend reassessing the sample using BUSCO. | |
| ## Download lineage: 0.00(s) | |
| ## Run miniprot: 930.24(s) | |
| ## Analyze miniprot: 366.62(s) | |
| ## Total runtime: 1296.86(s) | |
| ``` | |
| **Traceback:** | |
| * ```console | |
| ``` | |
| **Job Parameters:** | |
| * | Job parameter | Parameter value | | |
| | ------------- | --------------- | | |
| | \_\_input\_ext | ` "input" ` | | |
| | \_\_workflow\_invocation\_uuid\_\_ | ` "30ca0a3a114e11f189517ced8d7c0d2f" ` | | |
| | busco\_database | ` "v5" ` | | |
| | chromInfo | ` "/tmp/tmpgck0c6r3/galaxy-dev/tool-data/shared/ucsc/chrom/?.len" ` | | |
| | dbkey | ` "?" ` | | |
| | lineage\_dataset | ` "vertebrata_odb10" ` | | |
| | mode | ` "busco" ` | | |
| | outputs | ` ["full_table_busco", "miniprot", "translated_protein", "full_table", "summary"] ` | | |
| | specified\_contigs | ` None ` | | |
| </details> | |
| - **Step 60: Compleasm Hap1 (toolshed.g2.bx.psu.edu/repos/iuc/compleasm/compleasm/0.2.6+galaxy3)**: | |
| * step_state: scheduled | |
| * <details><summary>Jobs</summary> | |
| - **Job 1:** | |
| * Job state is ok | |
| **Container:** | |
| * ```console | |
| quay.io/biocontainers/compleasm:0.2.6--pyh7cba7a3_0 | |
| ``` | |
| **Command Line:** | |
| * ```console | |
| mkdir -p 'galaxy_db/' && ln -s '/cvmfs/data.galaxyproject.org/byhand/busco/v5/lineages/vertebrata_odb10/' 'galaxy_db/vertebrata_odb10' && touch 'galaxy_db/vertebrata_odb10.done' && compleasm run -a '/tmp/tmpgck0c6r3/files/3/f/c/dataset_3fc83f7a-c80b-48d6-8838-2821fe73129e.dat' -o galaxy_output --mode busco -L 'galaxy_db' -l 'vertebrata_odb10' -t "${GALAXY_SLOTS:-1}" | |
| ``` | |
| **Exit Code:** | |
| * ```console | |
| 0 | |
| ``` | |
| **Standard Error:** | |
| * ```console | |
| [M::mp_ntseq_read@0.005*1.59] read 1473565 bases in 57 contigs | |
| [M::mp_idx_build@0.005*1.55] 11572 blocks | |
| [M::mp_idx_build@0.057*1.03] collected syncmers | |
| [M::mp_idx_build@0.118*1.00] 677833 kmer-block pairs | |
| [M::mp_mapopt_set_max_intron] set max intron size to 10000 | |
| [M::mp_idx_print_stat] 322886 distinct k-mers; mean occ of infrequent k-mers: 2.10; 0 frequent k-mers accounting for 0 occurrences | |
| [M::worker_pipeline::6.168*0.91] mapped 3408 sequences | |
| [M::worker_pipeline::11.934*0.91] mapped 3404 sequences | |
| [M::worker_pipeline::17.440*0.92] mapped 3357 sequences | |
| [M::worker_pipeline::23.207*0.92] mapped 3488 sequences | |
| [M::worker_pipeline::28.899*0.92] mapped 3573 sequences | |
| [M::worker_pipeline::34.343*0.93] mapped 3161 sequences | |
| [M::worker_pipeline::39.860*0.93] mapped 3178 sequences | |
| [M::worker_pipeline::45.099*0.93] mapped 3277 sequences | |
| [M::worker_pipeline::50.364*0.94] mapped 3290 sequences | |
| [M::worker_pipeline::55.419*0.94] mapped 3415 sequences | |
| [M::worker_pipeline::60.419*0.95] mapped 3273 sequences | |
| [M::worker_pipeline::65.808*0.95] mapped 3297 sequences | |
| [M::worker_pipeline::71.763*0.95] mapped 3366 sequences | |
| [M::worker_pipeline::77.023*0.95] mapped 3526 sequences | |
| [M::worker_pipeline::82.561*0.96] mapped 3363 sequences | |
| [M::worker_pipeline::87.966*0.96] mapped 3386 sequences | |
| [M::worker_pipeline::93.042*0.96] mapped 3472 sequences | |
| [M::worker_pipeline::98.419*0.96] mapped 3375 sequences | |
| [M::worker_pipeline::103.843*0.96] mapped 3337 sequences | |
| [M::worker_pipeline::108.849*0.96] mapped 3452 sequences | |
| [M::worker_pipeline::113.896*0.96] mapped 3598 sequences | |
| [M::worker_pipeline::119.346*0.97] mapped 3363 sequences | |
| [M::worker_pipeline::125.257*0.97] mapped 3385 sequences | |
| [M::worker_pipeline::131.215*0.97] mapped 3335 sequences | |
| [M::worker_pipeline::136.917*0.96] mapped 3434 sequences | |
| [M::worker_pipeline::142.927*0.96] mapped 3323 sequences | |
| [M::worker_pipeline::148.402*0.96] mapped 3415 sequences | |
| [M::worker_pipeline::154.265*0.96] mapped 3310 sequences | |
| [M::worker_pipeline::159.926*0.96] mapped 3376 sequences | |
| [M::worker_pipeline::165.628*0.96] mapped 3489 sequences | |
| [M::worker_pipeline::171.301*0.96] mapped 3313 sequences | |
| [M::worker_pipeline::176.701*0.96] mapped 3450 sequences | |
| [M::worker_pipeline::182.249*0.96] mapped 3456 sequences | |
| [M::worker_pipeline::188.167*0.96] mapped 3301 sequences | |
| [M::worker_pipeline::194.034*0.96] mapped 3463 sequences | |
| [M::worker_pipeline::198.711*0.96] mapped 3439 sequences | |
| [M::worker_pipeline::203.796*0.97] mapped 3267 sequences | |
| [M::worker_pipeline::209.023*0.97] mapped 3484 sequences | |
| [M::worker_pipeline::214.047*0.97] mapped 3767 sequences | |
| [M::worker_pipeline::218.989*0.97] mapped 3506 sequences | |
| [M::worker_pipeline::224.371*0.97] mapped 3561 sequences | |
| [M::worker_pipeline::230.163*0.97] mapped 3335 sequences | |
| [M::worker_pipeline::234.536*0.97] mapped 3436 sequences | |
| [M::worker_pipeline::239.328*0.97] mapped 3410 sequences | |
| [M::worker_pipeline::244.928*0.97] mapped 3504 sequences | |
| [M::worker_pipeline::249.919*0.97] mapped 3821 sequences | |
| [M::worker_pipeline::255.465*0.97] mapped 3426 sequences | |
| [M::worker_pipeline::261.405*0.97] mapped 3341 sequences | |
| [M::worker_pipeline::267.433*0.97] mapped 3484 sequences | |
| [M::worker_pipeline::273.074*0.97] mapped 3276 sequences | |
| [M::worker_pipeline::278.546*0.97] mapped 3314 sequences | |
| [M::worker_pipeline::283.967*0.97] mapped 3277 sequences | |
| [M::worker_pipeline::288.122*0.97] mapped 3697 sequences | |
| [M::worker_pipeline::292.528*0.97] mapped 3334 sequences | |
| [M::worker_pipeline::296.666*0.97] mapped 3323 sequences | |
| [M::worker_pipeline::300.746*0.97] mapped 3927 sequences | |
| [M::worker_pipeline::305.139*0.97] mapped 3655 sequences | |
| [M::worker_pipeline::309.157*0.97] mapped 3385 sequences | |
| [M::worker_pipeline::313.288*0.97] mapped 3395 sequences | |
| [M::worker_pipeline::317.015*0.97] mapped 3382 sequences | |
| [M::worker_pipeline::321.166*0.97] mapped 3341 sequences | |
| [M::worker_pipeline::324.917*0.97] mapped 3366 sequences | |
| [M::worker_pipeline::328.620*0.97] mapped 3334 sequences | |
| [M::worker_pipeline::332.850*0.97] mapped 3281 sequences | |
| [M::worker_pipeline::337.150*0.97] mapped 3362 sequences | |
| [M::worker_pipeline::340.864*0.97] mapped 3686 sequences | |
| [M::worker_pipeline::344.875*0.97] mapped 3406 sequences | |
| [M::worker_pipeline::348.876*0.97] mapped 3262 sequences | |
| [M::worker_pipeline::352.978*0.98] mapped 3312 sequences | |
| [M::worker_pipeline::357.092*0.98] mapped 3308 sequences | |
| [M::worker_pipeline::361.897*0.98] mapped 3392 sequences | |
| [M::worker_pipeline::366.285*0.98] mapped 3346 sequences | |
| [M::worker_pipeline::370.598*0.98] mapped 3408 sequences | |
| [M::worker_pipeline::374.604*0.98] mapped 3200 sequences | |
| [M::worker_pipeline::379.028*0.98] mapped 3425 sequences | |
| [M::worker_pipeline::382.725*0.98] mapped 3425 sequences | |
| [M::worker_pipeline::386.810*0.98] mapped 3367 sequences | |
| [M::worker_pipeline::390.839*0.98] mapped 3464 sequences | |
| [M::worker_pipeline::394.701*0.98] mapped 3250 sequences | |
| [M::worker_pipeline::398.602*0.98] mapped 3312 sequences | |
| [M::worker_pipeline::402.693*0.98] mapped 3806 sequences | |
| [M::worker_pipeline::406.785*0.98] mapped 3475 sequences | |
| [M::worker_pipeline::410.808*0.98] mapped 3685 sequences | |
| [M::worker_pipeline::414.977*0.98] mapped 3335 sequences | |
| [M::worker_pipeline::419.506*0.98] mapped 3353 sequences | |
| [M::worker_pipeline::423.596*0.98] mapped 3356 sequences | |
| [M::worker_pipeline::427.924*0.98] mapped 3291 sequences | |
| [M::worker_pipeline::431.938*0.98] mapped 3309 sequences | |
| [M::worker_pipeline::436.577*0.98] mapped 3204 sequences | |
| [M::worker_pipeline::440.497*0.98] mapped 3319 sequences | |
| [M::worker_pipeline::444.269*0.98] mapped 3381 sequences | |
| [M::worker_pipeline::448.523*0.98] mapped 3312 sequences | |
| [M::worker_pipeline::452.362*0.98] mapped 3247 sequences | |
| [M::worker_pipeline::456.428*0.98] mapped 3342 sequences | |
| [M::worker_pipeline::460.809*0.98] mapped 3305 sequences | |
| [M::worker_pipeline::464.816*0.98] mapped 3425 sequences | |
| [M::worker_pipeline::469.042*0.98] mapped 3646 sequences | |
| [M::worker_pipeline::473.428*0.98] mapped 3250 sequences | |
| [M::worker_pipeline::477.495*0.98] mapped 3404 sequences | |
| [M::worker_pipeline::481.590*0.98] mapped 3324 sequences | |
| [M::worker_pipeline::485.569*0.98] mapped 3530 sequences | |
| [M::worker_pipeline::489.779*0.98] mapped 3330 sequences | |
| [M::worker_pipeline::494.248*0.98] mapped 3432 sequences | |
| [M::worker_pipeline::498.178*0.98] mapped 3830 sequences | |
| [M::worker_pipeline::502.317*0.98] mapped 3937 sequences | |
| [M::worker_pipeline::506.637*0.98] mapped 3391 sequences | |
| [M::worker_pipeline::511.171*0.98] mapped 3562 sequences | |
| [M::worker_pipeline::515.385*0.98] mapped 3605 sequences | |
| [M::worker_pipeline::519.592*0.98] mapped 3897 sequences | |
| [M::worker_pipeline::523.453*0.98] mapped 4068 sequences | |
| [M::worker_pipeline::527.476*0.98] mapped 3511 sequences | |
| [M::worker_pipeline::531.407*0.98] mapped 3324 sequences | |
| [M::worker_pipeline::535.037*0.98] mapped 3395 sequences | |
| [M::worker_pipeline::539.100*0.98] mapped 3394 sequences | |
| [M::worker_pipeline::543.050*0.98] mapped 3273 sequences | |
| [M::worker_pipeline::547.396*0.98] mapped 3211 sequences | |
| [M::worker_pipeline::551.267*0.98] mapped 3338 sequences | |
| [M::worker_pipeline::555.356*0.98] mapped 3208 sequences | |
| [M::worker_pipeline::559.284*0.98] mapped 3294 sequences | |
| [M::worker_pipeline::563.176*0.98] mapped 3415 sequences | |
| [M::worker_pipeline::567.398*0.98] mapped 3446 sequences | |
| [M::worker_pipeline::571.483*0.98] mapped 3498 sequences | |
| [M::worker_pipeline::575.489*0.98] mapped 3417 sequences | |
| [M::worker_pipeline::579.701*0.98] mapped 3417 sequences | |
| [M::worker_pipeline::583.820*0.98] mapped 3328 sequences | |
| [M::worker_pipeline::588.408*0.98] mapped 3448 sequences | |
| [M::worker_pipeline::592.796*0.99] mapped 3569 sequences | |
| [M::worker_pipeline::596.655*0.99] mapped 4045 sequences | |
| [M::worker_pipeline::600.933*0.99] mapped 3258 sequences | |
| [M::worker_pipeline::605.147*0.99] mapped 3320 sequences | |
| [M::worker_pipeline::609.330*0.99] mapped 3321 sequences | |
| [M::worker_pipeline::613.306*0.99] mapped 3223 sequences | |
| [M::worker_pipeline::617.535*0.99] mapped 3193 sequences | |
| [M::worker_pipeline::621.675*0.99] mapped 3310 sequences | |
| [M::worker_pipeline::626.132*0.99] mapped 3206 sequences | |
| [M::worker_pipeline::630.115*0.99] mapped 3287 sequences | |
| [M::worker_pipeline::634.412*0.99] mapped 3460 sequences | |
| [M::worker_pipeline::638.839*0.99] mapped 3243 sequences | |
| [M::worker_pipeline::643.143*0.99] mapped 3284 sequences | |
| [M::worker_pipeline::647.017*0.99] mapped 3268 sequences | |
| [M::worker_pipeline::651.348*0.99] mapped 3430 sequences | |
| [M::worker_pipeline::655.775*0.99] mapped 3283 sequences | |
| [M::worker_pipeline::660.518*0.99] mapped 3136 sequences | |
| [M::worker_pipeline::664.949*0.99] mapped 3340 sequences | |
| [M::worker_pipeline::668.889*0.99] mapped 4104 sequences | |
| [M::worker_pipeline::672.998*0.99] mapped 3490 sequences | |
| [M::worker_pipeline::677.403*0.99] mapped 3360 sequences | |
| [M::worker_pipeline::681.666*0.99] mapped 3363 sequences | |
| [M::worker_pipeline::685.929*0.99] mapped 3384 sequences | |
| [M::worker_pipeline::690.413*0.99] mapped 3202 sequences | |
| [M::worker_pipeline::694.590*0.99] mapped 3294 sequences | |
| [M::worker_pipeline::698.581*0.99] mapped 3435 sequences | |
| [M::worker_pipeline::702.824*0.99] mapped 3481 sequences | |
| [M::worker_pipeline::706.687*0.99] mapped 3337 sequences | |
| [M::worker_pipeline::711.077*0.99] mapped 3380 sequences | |
| [M::worker_pipeline::715.168*0.99] mapped 3308 sequences | |
| [M::worker_pipeline::719.097*0.99] mapped 3347 sequences | |
| [M::worker_pipeline::723.404*0.99] mapped 3455 sequences | |
| [M::worker_pipeline::727.570*0.99] mapped 3245 sequences | |
| [M::worker_pipeline::731.659*0.99] mapped 3481 sequences | |
| [M::worker_pipeline::735.696*0.99] mapped 3502 sequences | |
| [M::worker_pipeline::740.220*0.99] mapped 3248 sequences | |
| [M::worker_pipeline::744.246*0.99] mapped 3540 sequences | |
| [M::worker_pipeline::748.357*0.99] mapped 3491 sequences | |
| [M::worker_pipeline::752.731*0.99] mapped 3322 sequences | |
| [M::worker_pipeline::756.764*0.99] mapped 3485 sequences | |
| [M::worker_pipeline::760.709*0.99] mapped 3884 sequences | |
| [M::worker_pipeline::765.158*0.99] mapped 3447 sequences | |
| [M::worker_pipeline::769.328*0.99] mapped 3294 sequences | |
| [M::worker_pipeline::772.991*0.99] mapped 3422 sequences | |
| [M::worker_pipeline::777.181*0.99] mapped 3318 sequences | |
| [M::worker_pipeline::781.248*0.99] mapped 3210 sequences | |
| [M::worker_pipeline::785.342*0.99] mapped 3264 sequences | |
| [M::worker_pipeline::789.300*0.99] mapped 3572 sequences | |
| [M::worker_pipeline::793.317*0.99] mapped 3309 sequences | |
| [M::worker_pipeline::797.400*0.99] mapped 3235 sequences | |
| [M::worker_pipeline::801.530*0.99] mapped 3246 sequences | |
| [M::worker_pipeline::805.313*0.99] mapped 3349 sequences | |
| [M::worker_pipeline::809.195*0.99] mapped 3240 sequences | |
| [M::worker_pipeline::813.351*0.99] mapped 3161 sequences | |
| [M::worker_pipeline::817.337*0.99] mapped 3259 sequences | |
| [M::worker_pipeline::821.098*0.99] mapped 3252 sequences | |
| [M::worker_pipeline::825.287*0.99] mapped 3149 sequences | |
| [M::worker_pipeline::829.483*0.99] mapped 3595 sequences | |
| [M::worker_pipeline::833.376*0.99] mapped 3485 sequences | |
| [M::worker_pipeline::836.996*0.99] mapped 3287 sequences | |
| [M::worker_pipeline::840.885*0.99] mapped 3200 sequences | |
| [M::worker_pipeline::844.820*0.99] mapped 3249 sequences | |
| [M::worker_pipeline::848.899*0.99] mapped 3273 sequences | |
| [M::worker_pipeline::852.815*0.99] mapped 3329 sequences | |
| [M::worker_pipeline::856.776*0.99] mapped 3150 sequences | |
| [M::worker_pipeline::860.711*0.99] mapped 3282 sequences | |
| [M::worker_pipeline::864.368*0.99] mapped 3128 sequences | |
| [M::worker_pipeline::868.107*0.99] mapped 3144 sequences | |
| [M::worker_pipeline::871.823*0.99] mapped 3451 sequences | |
| [M::worker_pipeline::875.528*0.99] mapped 3466 sequences | |
| [M::worker_pipeline::879.580*0.99] mapped 3277 sequences | |
| [M::worker_pipeline::882.517*0.99] mapped 2560 sequences | |
| [M::main] Version: 0.13-r248 | |
| [M::main] CMD: /usr/local/bin/miniprot --trans -u -I --outs=0.95 -t 1 --gff /tmp/tmpgck0c6r3/files/3/f/c/dataset_3fc83f7a-c80b-48d6-8838-2821fe73129e.dat galaxy_db/vertebrata_odb10/refseq_db.faa.gz | |
| [M::main] Real time: 882.524 sec; CPU: 873.553 sec; Peak RSS: 0.209 GB | |
| ``` | |
| **Standard Output:** | |
| * ```console | |
| Searching for miniprot in the path where compleasm.py is located | |
| Searching for miniprot in the current execution path | |
| Searching for miniprot in $PATH | |
| Searching for hmmsearch in the path where compleasm.py is located | |
| Searching for hmmsearch in the current execution path | |
| Searching for hmmsearch in $PATH | |
| miniprot execute command: | |
| /usr/local/bin/miniprot | |
| Success download from https://busco-data.ezlab.org/v5/data/file_versions.tsv | |
| Success download from https://busco-data.ezlab.org/v5/data/placement_files/list_of_reference_markers.eukaryota_odb10.2019-12-16.txt.tar.gz | |
| Placement file extraction path: galaxy_db/placement_files/list_of_reference_markers.eukaryota_odb10.2019-12-16.txt | |
| Success download from https://busco-data.ezlab.org/v5/data/placement_files/list_of_reference_markers.eukaryota_odb12.2025-01-15.txt.tar.gz | |
| Placement file extraction path: galaxy_db/placement_files/list_of_reference_markers.eukaryota_odb12.2025-01-15.txt | |
| Success download from https://busco-data.ezlab.org/v5/data/placement_files/mapping_taxid-lineage.eukaryota_odb10.2019-12-16.txt.tar.gz | |
| Placement file extraction path: galaxy_db/placement_files/mapping_taxid-lineage.eukaryota_odb10.2019-12-16.txt | |
| Success download from https://busco-data.ezlab.org/v5/data/placement_files/mapping_taxid-lineage.eukaryota_odb12.2025-01-15.txt.tar.gz | |
| Placement file extraction path: galaxy_db/placement_files/mapping_taxid-lineage.eukaryota_odb12.2025-01-15.txt | |
| Success download from https://busco-data.ezlab.org/v5/data/placement_files/mapping_taxids-busco_dataset_name.eukaryota_odb10.2019-12-16.txt.tar.gz | |
| Placement file extraction path: galaxy_db/placement_files/mapping_taxids-busco_dataset_name.eukaryota_odb10.2019-12-16.txt | |
| Success download from https://busco-data.ezlab.org/v5/data/placement_files/mapping_taxids-busco_dataset_name.eukaryota_odb12.2025-01-15.txt.tar.gz | |
| Placement file extraction path: galaxy_db/placement_files/mapping_taxids-busco_dataset_name.eukaryota_odb12.2025-01-15.txt | |
| Success download from https://busco-data.ezlab.org/v5/data/placement_files/supermatrix.aln.eukaryota_odb10.2019-12-16.faa.tar.gz | |
| Placement file extraction path: galaxy_db/placement_files/supermatrix.aln.eukaryota_odb10.2019-12-16.faa | |
| Success download from https://busco-data.ezlab.org/v5/data/placement_files/supermatrix.aln.eukaryota_odb12.2025-01-15.faa.tar.gz | |
| Placement file extraction path: galaxy_db/placement_files/supermatrix.aln.eukaryota_odb12.2025-01-15.faa | |
| Success download from https://busco-data.ezlab.org/v5/data/placement_files/tree.eukaryota_odb10.2019-12-16.nwk.tar.gz | |
| Placement file extraction path: galaxy_db/placement_files/tree.eukaryota_odb10.2019-12-16.nwk | |
| Success download from https://busco-data.ezlab.org/v5/data/placement_files/tree.eukaryota_odb12.2025-01-15.nwk.tar.gz | |
| Placement file extraction path: galaxy_db/placement_files/tree.eukaryota_odb12.2025-01-15.nwk | |
| Success download from https://busco-data.ezlab.org/v5/data/placement_files/tree_metadata.eukaryota_odb10.2019-12-16.txt.tar.gz | |
| Placement file extraction path: galaxy_db/placement_files/tree_metadata.eukaryota_odb10.2019-12-16.txt | |
| Success download from https://busco-data.ezlab.org/v5/data/placement_files/tree_metadata.eukaryota_odb12.2025-01-15.txt.tar.gz | |
| Placement file extraction path: galaxy_db/placement_files/tree_metadata.eukaryota_odb12.2025-01-15.txt | |
| Success download from https://busco-data.ezlab.org/v5/data/lineages/eukaryota_odb10.2024-01-08.tar.gz | |
| Lineage file extraction path: galaxy_db/eukaryota_odb10 | |
| lineage: vertebrata_odb10 | |
| hmmsearch execute command: | |
| /usr/local/bin/hmmsearch | |
| S:0.81%, 27 | |
| D:0.03%, 1 | |
| F:0.09%, 3 | |
| I:0.00%, 0 | |
| M:99.08%, 3323 | |
| N:3354 | |
| Warning: Given the potentially high diversity of the sample, compleasm results may not be reliable!We recommend reassessing the sample using BUSCO. | |
| ## Download lineage: 0.00(s) | |
| ## Run miniprot: 882.53(s) | |
| ## Analyze miniprot: 402.20(s) | |
| ## Total runtime: 1284.74(s) | |
| ``` | |
| **Traceback:** | |
| * ```console | |
| ``` | |
| **Job Parameters:** | |
| * | Job parameter | Parameter value | | |
| | ------------- | --------------- | | |
| | \_\_input\_ext | ` "input" ` | | |
| | \_\_workflow\_invocation\_uuid\_\_ | ` "30ca0a3a114e11f189517ced8d7c0d2f" ` | | |
| | busco\_database | ` "v5" ` | | |
| | chromInfo | ` "/tmp/tmpgck0c6r3/galaxy-dev/tool-data/shared/ucsc/chrom/?.len" ` | | |
| | dbkey | ` "?" ` | | |
| | lineage\_dataset | ` "vertebrata_odb10" ` | | |
| | mode | ` "busco" ` | | |
| | outputs | ` ["full_table_busco", "miniprot", "translated_protein", "full_table", "summary"] ` | | |
| | specified\_contigs | ` None ` | | |
| </details> | |
| - **Step 61: Merqury (toolshed.g2.bx.psu.edu/repos/iuc/merqury/merqury/1.3+galaxy4)**: | |
| * step_state: scheduled | |
| * <details><summary>Jobs</summary> | |
| - **Job 1:** | |
| * Job state is ok | |
| **Container:** | |
| * ```console | |
| quay.io/biocontainers/mulled-v2-18b619b415d9ff69d3a7bacbbb7b09f45ba1a215:f3370f24695c57921a5f15b5625c16e2df7f9cea-0 | |
| ``` | |
| **Command Line:** | |
| * ```console | |
| mkdir -p output_files && mkdir -p read-db.meryl && tar -zxf /tmp/tmpgck0c6r3/files/7/4/1/dataset_7415576d-9509-4ee0-82f6-4b7bd4380ce3.dat -C read-db.meryl --strip-components=1 && ln -s '/tmp/tmpgck0c6r3/files/3/f/c/dataset_3fc83f7a-c80b-48d6-8838-2821fe73129e.dat' assembly_01.fasta && ln -s '/tmp/tmpgck0c6r3/files/e/c/3/dataset_ec30905f-b6ab-4141-959f-bc2d87fcd32c.dat' assembly_02.fasta && merqury.sh read-db.meryl assembly_01.fasta assembly_02.fasta output_merqury &> /tmp/tmpgck0c6r3/job_working_directory/000/67/outputs/dataset_773977bd-31b4-4e9e-8560-8ec2cc476c1f.dat && mv output_merqury* output_files && find . -maxdepth 1 -name 'assembly_only*' -type f -print0 | xargs -0r mv -t output_files && sed -i '1s/^/assembly\tk-mer set\tsolid k-mers in assembly\tsolid k-mers in reads\tcompleteness %\n/' 'output_files/output_merqury.completeness.stats' && sed -i '1s/^/assembly\tunique k-mers\tcommon k-mers\tQV\terror rate\n/' 'output_files/output_merqury.qv' | |
| ``` | |
| **Exit Code:** | |
| * ```console | |
| 0 | |
| ``` | |
| **Traceback:** | |
| * ```console | |
| ``` | |
| **Job Parameters:** | |
| * | Job parameter | Parameter value | | |
| | ------------- | --------------- | | |
| | \_\_input\_ext | ` "input" ` | | |
| | \_\_workflow\_invocation\_uuid\_\_ | ` "30ca0a3a114e11f189517ced8d7c0d2f" ` | | |
| | chromInfo | ` "/tmp/tmpgck0c6r3/galaxy-dev/tool-data/shared/ucsc/chrom/?.len" ` | | |
| | dbkey | ` "?" ` | | |
| | label | ` "output_merqury" ` | | |
| | mode | ` {"__current_case__": 0, "assembly_options": {"__current_case__": 1, "assembly_01": {"values": [{"id": 73, "src": "hda"}]}, "assembly_02": {"values": [{"id": 72, "src": "hda"}]}, "number_assemblies": "two"}, "meryldb_F1": {"values": [{"id": 5, "src": "hda"}]}, "options": "default"} ` | | |
| | output\_add\_headers | ` true ` | | |
| | output\_selector | ` ["qv", "plots", "stats", "log", "hist"] ` | | |
| </details> | |
| - **Step 62: Unlabelled step (toolshed.g2.bx.psu.edu/repos/bgruening/text\_processing/tp\_cut\_tool/9.5+galaxy2)**: | |
| * step_state: scheduled | |
| * <details><summary>Jobs</summary> | |
| - **Job 1:** | |
| * Job state is ok | |
| **Container:** | |
| * ```console | |
| quay.io/biocontainers/coreutils:9.5 | |
| ``` | |
| **Command Line:** | |
| * ```console | |
| cut --complement -f '3' '/tmp/tmpgck0c6r3/files/0/b/e/dataset_0be521f0-0a98-477f-952e-380e42eda70b.dat' > '/tmp/tmpgck0c6r3/job_working_directory/000/68/outputs/dataset_7c88c615-2f86-434f-97c9-35117de3f9be.dat' | |
| ``` | |
| **Exit Code:** | |
| * ```console | |
| 0 | |
| ``` | |
| **Traceback:** | |
| * ```console | |
| ``` | |
| **Job Parameters:** | |
| * | Job parameter | Parameter value | | |
| | ------------- | --------------- | | |
| | \_\_input\_ext | ` "input" ` | | |
| | \_\_workflow\_invocation\_uuid\_\_ | ` "30ca0a3a114e11f189517ced8d7c0d2f" ` | | |
| | chromInfo | ` "/tmp/tmpgck0c6r3/galaxy-dev/tool-data/shared/ucsc/chrom/?.len" ` | | |
| | complement | ` "--complement" ` | | |
| | cut\_type\_options | ` {"__current_case__": 0, "colnames_option": {"__current_case__": 1, "header": "N", "list": ["3"]}, "cut_element": "-f", "delimiter": ""} ` | | |
| | dbkey | ` "?" ` | | |
| </details> | |
| - **Step 63: Unlabelled step (toolshed.g2.bx.psu.edu/repos/bgruening/imagemagick\_image\_montage/imagemagick\_image\_montage/7.1.2-2+galaxy0)**: | |
| * step_state: scheduled | |
| * <details><summary>Jobs</summary> | |
| - **Job 1:** | |
| * Job state is ok | |
| **Container:** | |
| * ```console | |
| quay.io/biocontainers/mulled-v2-7a407d02e5cdb08ceaad5b125da833026292af1a:d937d67ba578113e308814a552e9ec1b021e0a47-0 | |
| ``` | |
| **Command Line:** | |
| * ```console | |
| ln -s /tmp/tmpgck0c6r3/files/b/8/2/dataset_b826d8a4-1feb-4522-8bf7-45f61e88d881.dat "1.Nx Plot.png" && ln -s /tmp/tmpgck0c6r3/files/1/0/e/dataset_10ec65b5-7c06-41e9-81a8-3322c3708087.dat "2.Size Plot.png" && fontfile=$(fc-list | grep DejaVuSans.ttf | head -n 1 | cut -d: -f1) && magick montage -geometry +0+0 -background white -font $fontfile -pointsize 14 -tile 2x -resize 60% "1.Nx Plot.png" "2.Size Plot.png" output.png | |
| ``` | |
| **Exit Code:** | |
| * ```console | |
| 0 | |
| ``` | |
| **Traceback:** | |
| * ```console | |
| ``` | |
| **Job Parameters:** | |
| * | Job parameter | Parameter value | | |
| | ------------- | --------------- | | |
| | \_\_input\_ext | ` "input" ` | | |
| | \_\_workflow\_invocation\_uuid\_\_ | ` "30ca0a3a114e11f189517ced8d7c0d2f" ` | | |
| | chromInfo | ` "/tmp/tmpgck0c6r3/galaxy-dev/tool-data/shared/ucsc/chrom/?.len" ` | | |
| | dbkey | ` "?" ` | | |
| | images | ` [{"__index__": 0, "input": {"values": [{"id": 143, "src": "hda"}]}}, {"__index__": 1, "input": {"values": [{"id": 144, "src": "hda"}]}}] ` | | |
| | label\_options | ` {"__current_case__": 1, "label": "false"} ` | | |
| | pointsize | ` "14" ` | | |
| | resize | ` "60" ` | | |
| | title | ` None ` | | |
| | width | ` "2" ` | | |
| </details> | |
| - **Step 64: output_merqury.spectra-cn.fl (\_\_EXTRACT\_DATASET\_\_)**: | |
| * step_state: scheduled | |
| * <details><summary>Jobs</summary> | |
| - **Job 1:** | |
| * Job state is ok | |
| **Traceback:** | |
| * ```console | |
| ``` | |
| **Job Parameters:** | |
| * | Job parameter | Parameter value | | |
| | ------------- | --------------- | | |
| | \_\_workflow\_invocation\_uuid\_\_ | ` "30ca0a3a114e11f189517ced8d7c0d2f" ` | | |
| | input | ` {"values": [{"id": 13, "src": "hdca"}]} ` | | |
| | which | ` {"__current_case__": 1, "identifier": "output_merqury.spectra-cn.fl", "which_dataset": "by_identifier"} ` | | |
| </details> | |
| - **Step 65: output_merqury.spectra-asm.fl (\_\_EXTRACT\_DATASET\_\_)**: | |
| * step_state: scheduled | |
| * <details><summary>Jobs</summary> | |
| - **Job 1:** | |
| * Job state is ok | |
| **Traceback:** | |
| * ```console | |
| ``` | |
| **Job Parameters:** | |
| * | Job parameter | Parameter value | | |
| | ------------- | --------------- | | |
| | \_\_workflow\_invocation\_uuid\_\_ | ` "30ca0a3a114e11f189517ced8d7c0d2f" ` | | |
| | input | ` {"values": [{"id": 13, "src": "hdca"}]} ` | | |
| | which | ` {"__current_case__": 1, "identifier": "output_merqury.spectra-asm.fl", "which_dataset": "by_identifier"} ` | | |
| </details> | |
| - **Step 66: merqury_qv (\_\_EXTRACT\_DATASET\_\_)**: | |
| * step_state: scheduled | |
| * <details><summary>Jobs</summary> | |
| - **Job 1:** | |
| * Job state is ok | |
| **Traceback:** | |
| * ```console | |
| ``` | |
| **Job Parameters:** | |
| * | Job parameter | Parameter value | | |
| | ------------- | --------------- | | |
| | \_\_workflow\_invocation\_uuid\_\_ | ` "30ca0a3a114e11f189517ced8d7c0d2f" ` | | |
| | input | ` {"values": [{"id": 12, "src": "hdca"}]} ` | | |
| | which | ` {"__current_case__": 1, "identifier": "output_merqury", "which_dataset": "by_identifier"} ` | | |
| </details> | |
| - **Step 67: merqury_stats (\_\_EXTRACT\_DATASET\_\_)**: | |
| * step_state: scheduled | |
| * <details><summary>Jobs</summary> | |
| - **Job 1:** | |
| * Job state is ok | |
| **Traceback:** | |
| * ```console | |
| ``` | |
| **Job Parameters:** | |
| * | Job parameter | Parameter value | | |
| | ------------- | --------------- | | |
| | \_\_workflow\_invocation\_uuid\_\_ | ` "30ca0a3a114e11f189517ced8d7c0d2f" ` | | |
| | input | ` {"values": [{"id": 14, "src": "hdca"}]} ` | | |
| | which | ` {"__current_case__": 1, "identifier": "output_merqury.completeness", "which_dataset": "by_identifier"} ` | | |
| </details> | |
| - **Step 68: output_merqury.assembly_01.spectra-cn.fl (\_\_EXTRACT\_DATASET\_\_)**: | |
| * step_state: scheduled | |
| * <details><summary>Jobs</summary> | |
| - **Job 1:** | |
| * Job state is ok | |
| **Traceback:** | |
| * ```console | |
| ``` | |
| **Job Parameters:** | |
| * | Job parameter | Parameter value | | |
| | ------------- | --------------- | | |
| | \_\_workflow\_invocation\_uuid\_\_ | ` "30ca0a3a114e11f189517ced8d7c0d2f" ` | | |
| | input | ` {"values": [{"id": 13, "src": "hdca"}]} ` | | |
| | which | ` {"__current_case__": 1, "identifier": "output_merqury.assembly_01.spectra-cn.fl", "which_dataset": "by_identifier"} ` | | |
| </details> | |
| - **Step 69: output_merqury.assembly_02.spectra-cn.fl (\_\_EXTRACT\_DATASET\_\_)**: | |
| * step_state: scheduled | |
| * <details><summary>Jobs</summary> | |
| - **Job 1:** | |
| * Job state is ok | |
| **Traceback:** | |
| * ```console | |
| ``` | |
| **Job Parameters:** | |
| * | Job parameter | Parameter value | | |
| | ------------- | --------------- | | |
| | \_\_workflow\_invocation\_uuid\_\_ | ` "30ca0a3a114e11f189517ced8d7c0d2f" ` | | |
| | input | ` {"values": [{"id": 13, "src": "hdca"}]} ` | | |
| | which | ` {"__current_case__": 1, "identifier": "output_merqury.assembly_02.spectra-cn.fl", "which_dataset": "by_identifier"} ` | | |
| </details> | |
| - **Step 70: Unlabelled step (toolshed.g2.bx.psu.edu/repos/bgruening/text\_processing/tp\_uniq\_tool/9.5+galaxy2)**: | |
| * step_state: scheduled | |
| * <details><summary>Jobs</summary> | |
| - **Job 1:** | |
| * Job state is ok | |
| **Container:** | |
| * ```console | |
| quay.io/biocontainers/mulled-v2-3b62966bb5abb1228683819650478f85a768a305:d811e96fbcf8ecf6b62f09be04e8ab2bae37af16-0 | |
| ``` | |
| **Command Line:** | |
| * ```console | |
| uniq '/tmp/tmpgck0c6r3/files/7/c/8/dataset_7c88c615-2f86-434f-97c9-35117de3f9be.dat' > '/tmp/tmpgck0c6r3/job_working_directory/000/69/outputs/dataset_f6331166-f648-4914-bea7-b1fb50731da6.dat' | |
| ``` | |
| **Exit Code:** | |
| * ```console | |
| 0 | |
| ``` | |
| **Traceback:** | |
| * ```console | |
| ``` | |
| **Job Parameters:** | |
| * | Job parameter | Parameter value | | |
| | ------------- | --------------- | | |
| | \_\_input\_ext | ` "input" ` | | |
| | \_\_workflow\_invocation\_uuid\_\_ | ` "30ca0a3a114e11f189517ced8d7c0d2f" ` | | |
| | chromInfo | ` "/tmp/tmpgck0c6r3/galaxy-dev/tool-data/shared/ucsc/chrom/?.len" ` | | |
| | dbkey | ` "?" ` | | |
| | grouping | ` {"__current_case__": 0, "count": false, "grouping_select": "no", "repeated": false, "uniqueonly": false} ` | | |
| | ignorecase | ` false ` | | |
| | skipfields | ` "0" ` | | |
| </details> | |
| - **Step 71: Unlabelled step (toolshed.g2.bx.psu.edu/repos/bgruening/imagemagick\_image\_montage/imagemagick\_image\_montage/7.1.2-2+galaxy0)**: | |
| * step_state: scheduled | |
| * <details><summary>Jobs</summary> | |
| - **Job 1:** | |
| * Job state is ok | |
| **Container:** | |
| * ```console | |
| quay.io/biocontainers/mulled-v2-7a407d02e5cdb08ceaad5b125da833026292af1a:d937d67ba578113e308814a552e9ec1b021e0a47-0 | |
| ``` | |
| **Command Line:** | |
| * ```console | |
| ln -s /tmp/tmpgck0c6r3/files/8/1/a/dataset_81a15a73-1162-4100-9003-c57a53585424.dat "spectra-cn.png" && ln -s /tmp/tmpgck0c6r3/files/8/7/e/dataset_87ecfc40-ca7a-4b4e-935e-2b9ffab95aab.dat "spectra-asm.png" && fontfile=$(fc-list | grep DejaVuSans.ttf | head -n 1 | cut -d: -f1) && magick montage -geometry +0+0 -background white -font $fontfile -pointsize 20 -tile 2x -resize 60% -label "%t" -title 'Merqury plots for both haplotypes' "spectra-cn.png" "spectra-asm.png" output.png | |
| ``` | |
| **Exit Code:** | |
| * ```console | |
| 0 | |
| ``` | |
| **Traceback:** | |
| * ```console | |
| ``` | |
| **Job Parameters:** | |
| * | Job parameter | Parameter value | | |
| | ------------- | --------------- | | |
| | \_\_input\_ext | ` "input" ` | | |
| | \_\_workflow\_invocation\_uuid\_\_ | ` "30ca0a3a114e11f189517ced8d7c0d2f" ` | | |
| | chromInfo | ` "/tmp/tmpgck0c6r3/galaxy-dev/tool-data/shared/ucsc/chrom/?.len" ` | | |
| | dbkey | ` "?" ` | | |
| | images | ` [{"__index__": 0, "input": {"values": [{"id": 126, "src": "hda"}]}}, {"__index__": 1, "input": {"values": [{"id": 127, "src": "hda"}]}}] ` | | |
| | label\_options | ` {"__current_case__": 0, "label": "true", "label_indexes": false} ` | | |
| | pointsize | ` "20" ` | | |
| | resize | ` "60" ` | | |
| | title | ` "Merqury plots for both haplotypes" ` | | |
| | width | ` "2" ` | | |
| </details> | |
| - **Step 72: Unlabelled step (Show beginning1)**: | |
| * step_state: scheduled | |
| * <details><summary>Jobs</summary> | |
| - **Job 1:** | |
| * Job state is ok | |
| **Container:** | |
| * ```console | |
| quay.io/biocontainers/coreutils:8.31--h14c3975_0 | |
| ``` | |
| **Command Line:** | |
| * ```console | |
| head -n 20 '/tmp/tmpgck0c6r3/files/7/6/b/dataset_76b32962-a56c-4e5b-90c1-bf907817fa1e.dat' > '/tmp/tmpgck0c6r3/job_working_directory/000/80/outputs/dataset_f6b91f71-ea26-47ee-a0b2-05507c902645.dat' | |
| ``` | |
| **Exit Code:** | |
| * ```console | |
| 0 | |
| ``` | |
| **Traceback:** | |
| * ```console | |
| ``` | |
| **Job Parameters:** | |
| * | Job parameter | Parameter value | | |
| | ------------- | --------------- | | |
| | \_\_input\_ext | ` "input" ` | | |
| | \_\_workflow\_invocation\_uuid\_\_ | ` "30ca0a3a114e11f189517ced8d7c0d2f" ` | | |
| | chromInfo | ` "/tmp/tmpgck0c6r3/galaxy-dev/tool-data/shared/ucsc/chrom/?.len" ` | | |
| | dbkey | ` "?" ` | | |
| | header | ` false ` | | |
| | lineNum | ` "20" ` | | |
| </details> | |
| - **Step 73: Unlabelled step (Show beginning1)**: | |
| * step_state: scheduled | |
| * <details><summary>Jobs</summary> | |
| - **Job 1:** | |
| * Job state is ok | |
| **Container:** | |
| * ```console | |
| quay.io/biocontainers/coreutils:8.31--h14c3975_0 | |
| ``` | |
| **Command Line:** | |
| * ```console | |
| head -n 20 '/tmp/tmpgck0c6r3/files/c/5/b/dataset_c5bdc8f9-97fb-4282-9d23-dc04504fb611.dat' > '/tmp/tmpgck0c6r3/job_working_directory/000/81/outputs/dataset_ad08bb11-0a7c-4caa-abb3-e2d1b9da500f.dat' | |
| ``` | |
| **Exit Code:** | |
| * ```console | |
| 0 | |
| ``` | |
| **Traceback:** | |
| * ```console | |
| ``` | |
| **Job Parameters:** | |
| * | Job parameter | Parameter value | | |
| | ------------- | --------------- | | |
| | \_\_input\_ext | ` "input" ` | | |
| | \_\_workflow\_invocation\_uuid\_\_ | ` "30ca0a3a114e11f189517ced8d7c0d2f" ` | | |
| | chromInfo | ` "/tmp/tmpgck0c6r3/galaxy-dev/tool-data/shared/ucsc/chrom/?.len" ` | | |
| | dbkey | ` "?" ` | | |
| | header | ` false ` | | |
| | lineNum | ` "20" ` | | |
| </details> | |
| - **Step 74: Unlabelled step (toolshed.g2.bx.psu.edu/repos/bgruening/imagemagick\_image\_montage/imagemagick\_image\_montage/7.1.2-2+galaxy0)**: | |
| * step_state: scheduled | |
| * <details><summary>Jobs</summary> | |
| - **Job 1:** | |
| * Job state is ok | |
| **Container:** | |
| * ```console | |
| quay.io/biocontainers/mulled-v2-7a407d02e5cdb08ceaad5b125da833026292af1a:d937d67ba578113e308814a552e9ec1b021e0a47-0 | |
| ``` | |
| **Command Line:** | |
| * ```console | |
| ln -s /tmp/tmpgck0c6r3/files/b/7/1/dataset_b719017e-fe4b-4426-82e8-0d5e96879421.dat "spectra-cn for Hap1.png" && ln -s /tmp/tmpgck0c6r3/files/9/f/3/dataset_9f35bf5f-08e3-463d-a6f0-0582f92ebb44.dat "spectra-cn for Hap2.png" && fontfile=$(fc-list | grep DejaVuSans.ttf | head -n 1 | cut -d: -f1) && magick montage -geometry +0+0 -background white -font $fontfile -pointsize 20 -tile 2x -resize 60% -label "%t" -title 'Merqury plots for both haplotypes' "spectra-cn for Hap1.png" "spectra-cn for Hap2.png" output.png | |
| ``` | |
| **Exit Code:** | |
| * ```console | |
| 0 | |
| ``` | |
| **Traceback:** | |
| * ```console | |
| ``` | |
| **Job Parameters:** | |
| * | Job parameter | Parameter value | | |
| | ------------- | --------------- | | |
| | \_\_input\_ext | ` "input" ` | | |
| | \_\_workflow\_invocation\_uuid\_\_ | ` "30ca0a3a114e11f189517ced8d7c0d2f" ` | | |
| | chromInfo | ` "/tmp/tmpgck0c6r3/galaxy-dev/tool-data/shared/ucsc/chrom/?.len" ` | | |
| | dbkey | ` "?" ` | | |
| | images | ` [{"__index__": 0, "input": {"values": [{"id": 130, "src": "hda"}]}}, {"__index__": 1, "input": {"values": [{"id": 131, "src": "hda"}]}}] ` | | |
| | label\_options | ` {"__current_case__": 0, "label": "true", "label_indexes": false} ` | | |
| | pointsize | ` "20" ` | | |
| | resize | ` "60" ` | | |
| | title | ` "Merqury plots for both haplotypes" ` | | |
| | width | ` "2" ` | | |
| </details> | |
| - **Step 75: Unlabelled step (toolshed.g2.bx.psu.edu/repos/bgruening/text\_processing/tp\_find\_and\_replace/9.5+galaxy2)**: | |
| * step_state: scheduled | |
| * <details><summary>Jobs</summary> | |
| - **Job 1:** | |
| * Job state is ok | |
| **Container:** | |
| * ```console | |
| quay.io/biocontainers/perl:5.32 | |
| ``` | |
| **Command Line:** | |
| * ```console | |
| perl '/tmp/shed_dir/toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/c41d78ae5fee/text_processing/find_and_replace' -o '/tmp/tmpgck0c6r3/job_working_directory/000/70/outputs/dataset_c1e3081f-1527-4ff3-9150-d3dd9d880fbf.dat' -g '#' 'Number of' '/tmp/tmpgck0c6r3/files/f/6/3/dataset_f6331166-f648-4914-bea7-b1fb50731da6.dat' | |
| ``` | |
| **Exit Code:** | |
| * ```console | |
| 0 | |
| ``` | |
| **Traceback:** | |
| * ```console | |
| ``` | |
| **Job Parameters:** | |
| * | Job parameter | Parameter value | | |
| | ------------- | --------------- | | |
| | \_\_input\_ext | ` "input" ` | | |
| | \_\_workflow\_invocation\_uuid\_\_ | ` "30ca0a3a114e11f189517ced8d7c0d2f" ` | | |
| | chromInfo | ` "/tmp/tmpgck0c6r3/galaxy-dev/tool-data/shared/ucsc/chrom/?.len" ` | | |
| | dbkey | ` "?" ` | | |
| | find\_and\_replace | ` [{"__index__": 0, "caseinsensitive": false, "find_pattern": "#", "global": true, "is_regex": false, "replace_pattern": "Number of", "searchwhere": {"__current_case__": 0, "searchwhere_select": "line"}, "skip_first_line": false, "wholewords": false}] ` | | |
| </details> | |
| </details> | |
| * <details><summary>Other invocation details</summary> | |
| - **history_id** | |
| * a1f9de336f7322bf | |
| - **history_state** | |
| * ok | |
| - **invocation_id** | |
| * a1f9de336f7322bf | |
| - **invocation_state** | |
| * scheduled | |
| - **workflow_id** | |
| * 28d7d56e0567c3c4 | |
| </details> | |
| </div></details> | |
| * <details class="rcorners light-green"><summary class="light-green">✅ Assembly-Hifi-HiC-phasing-VGP4.ga_1</summary><div class="padded"> | |
| #### Workflow invocation details | |
| * Invocation Messages | |
| * <details><summary>Steps</summary> | |
| - **Step 1: Species Name**: | |
| * step_state: scheduled | |
| - **Step 2: Assembly Name**: | |
| * step_state: scheduled | |
| - **Step 3: Pacbio Reads**: | |
| * step_state: scheduled | |
| - **Step 4: Trim Hi-C reads?**: | |
| * step_state: scheduled | |
| - **Step 5: Hi-C reads**: | |
| * step_state: scheduled | |
| - **Step 6: Genomescope Summary**: | |
| * step_state: scheduled | |
| - **Step 7: Meryl Database**: | |
| * step_state: scheduled | |
| - **Step 8: Database for Busco Lineage**: | |
| * step_state: scheduled | |
| - **Step 9: Lineage**: | |
| * step_state: scheduled | |
| - **Step 10: Name for Haplotype 1**: | |
| * step_state: scheduled | |
| - **Step 11: Name for Haplotype 2**: | |
| * step_state: scheduled | |
| - **Step 12: Bits for bloom filter**: | |
| * step_state: scheduled | |
| - **Step 13: Homozygous Read Coverage**: | |
| * step_state: scheduled | |
| - **Step 14: Genomescope Model Parameters**: | |
| * step_state: scheduled | |
| - **Step 15: Unlabelled step (toolshed.g2.bx.psu.edu/repos/iuc/compose\_text\_param/compose\_text\_param/0.1.1)**: | |
| * step_state: scheduled | |
| * <details><summary>Jobs</summary> | |
| - **Job 1:** | |
| * Job state is ok | |
| **Command Line:** | |
| * ```console | |
| cd ../; python _evaluate_expression_.py | |
| ``` | |
| **Exit Code:** | |
| * ```console | |
| 0 | |
| ``` | |
| **Traceback:** | |
| * ```console | |
| ``` | |
| **Job Parameters:** | |
| * | Job parameter | Parameter value | | |
| | ------------- | --------------- | | |
| | \_\_input\_ext | ` "input" ` | | |
| | \_\_workflow\_invocation\_uuid\_\_ | ` "94f24bb8115211f189517ced8d7c0d2f" ` | | |
| | chromInfo | ` "/tmp/tmpgck0c6r3/galaxy-dev/tool-data/shared/ucsc/chrom/?.len" ` | | |
| | components | ` [{"__index__": 0, "param_type": {"__current_case__": 0, "component_value": "Random Name", "select_param_type": "text"}}] ` | | |
| | dbkey | ` "?" ` | | |
| </details> | |
| - **Step 16: Unlabelled step (toolshed.g2.bx.psu.edu/repos/iuc/compose\_text\_param/compose\_text\_param/0.1.1)**: | |
| * step_state: scheduled | |
| * <details><summary>Jobs</summary> | |
| - **Job 1:** | |
| * Job state is ok | |
| **Command Line:** | |
| * ```console | |
| cd ../; python _evaluate_expression_.py | |
| ``` | |
| **Exit Code:** | |
| * ```console | |
| 0 | |
| ``` | |
| **Traceback:** | |
| * ```console | |
| ``` | |
| **Job Parameters:** | |
| * | Job parameter | Parameter value | | |
| | ------------- | --------------- | | |
| | \_\_input\_ext | ` "input" ` | | |
| | \_\_workflow\_invocation\_uuid\_\_ | ` "94f24bb8115211f189517ced8d7c0d2f" ` | | |
| | chromInfo | ` "/tmp/tmpgck0c6r3/galaxy-dev/tool-data/shared/ucsc/chrom/?.len" ` | | |
| | components | ` [{"__index__": 0, "param_type": {"__current_case__": 0, "component_value": "randName4", "select_param_type": "text"}}] ` | | |
| | dbkey | ` "?" ` | | |
| </details> | |
| - **Step 17: Unlabelled step (toolshed.g2.bx.psu.edu/repos/lparsons/cutadapt/cutadapt/5.1+galaxy0)**: | |
| * step_state: scheduled | |
| * <details><summary>Jobs</summary> | |
| - **Job 1:** | |
| * Job state is ok | |
| **Container:** | |
| * ```console | |
| quay.io/biocontainers/cutadapt:5.1--py312h0fa9677_0 | |
| ``` | |
| **Command Line:** | |
| * ```console | |
| ln -f -s '/tmp/tmpgck0c6r3/files/5/6/a/dataset_56aa6e84-c47b-4cc7-b810-a9ae5d69213c.dat' 'yeast_reads_sub1_fastq_gz.fq.gz' && cutadapt -j=${GALAXY_SLOTS:-4} -b 'ATCTCTCTCAACAACAACAACGGAGGAGGAGGAAAAGAGAGAGAT' -b 'ATCTCTCTCTTTTCCTCCTCCTCCGTTGTTGTTGTTGAGAGAGAT' --error-rate=0.1 --times=1 --overlap=35 --action=trim --rc --discard-trimmed --minimum-length=1 --json=stats.json -o 'out1.fq.gz' 'yeast_reads_sub1_fastq_gz.fq.gz' > report.txt | |
| ``` | |
| **Exit Code:** | |
| * ```console | |
| 0 | |
| ``` | |
| **Traceback:** | |
| * ```console | |
| ``` | |
| **Job Parameters:** | |
| * | Job parameter | Parameter value | | |
| | ------------- | --------------- | | |
| | \_\_input\_ext | ` "input" ` | | |
| | \_\_workflow\_invocation\_uuid\_\_ | ` "94f24bb8115211f189517ced8d7c0d2f" ` | | |
| | adapter\_options | ` {"action": "trim", "error_rate": "0.1", "match_read_wildcards": false, "no_indels": false, "no_match_adapter_wildcards": true, "overlap": "35", "revcomp": true, "times": "1"} ` | | |
| | chromInfo | ` "/tmp/tmpgck0c6r3/galaxy-dev/tool-data/shared/ucsc/chrom/?.len" ` | | |
| | dbkey | ` "?" ` | | |
| | filter\_options | ` {"discard_casava": false, "discard_trimmed": true, "discard_untrimmed": false, "max_average_error_rate": null, "max_expected_errors": null, "max_n": null, "maximum_length": null, "maximum_length2": null, "minimum_length": "1", "minimum_length2": null, "pair_filter": "any"} ` | | |
| | library | ` {"__current_case__": 0, "input_1": {"values": [{"id": 57, "src": "dce"}]}, "r1": {"adapters": [], "anywhere_adapters": [{"__index__": 0, "adapter_source": {"__current_case__": 0, "adapter": "ATCTCTCTCAACAACAACAACGGAGGAGGAGGAAAAGAGAGAGAT", "adapter_name": "", "adapter_source_list": "user"}, "single_noindels": false}, {"__index__": 1, "adapter_source": {"__current_case__": 0, "adapter": "ATCTCTCTCTTTTCCTCCTCCTCCGTTGTTGTTGTTGAGAGAGAT", "adapter_name": "", "adapter_source_list": "user"}, "single_noindels": false}], "front_adapters": []}, "type": "single"} ` | | |
| | other\_trimming\_options | ` {"cut": "0", "cut2": "0", "nextseq_trim": "0", "poly_a": false, "quality_cutoff": "0", "quality_cutoff2": "", "shorten_options": {"__current_case__": 1, "shorten_values": "False"}, "shorten_options_r2": {"__current_case__": 1, "shorten_values_r2": "False"}, "trim_n": false} ` | | |
| | output\_selector | ` ["report", "json_stats"] ` | | |
| | read\_mod\_options | ` {"length_tag": "", "rename": "", "strip_suffix": "", "zero_cap": false} ` | | |
| </details> | |
| - **Step 18: Unlabelled step (toolshed.g2.bx.psu.edu/repos/lparsons/cutadapt/cutadapt/5.1+galaxy0)**: | |
| * step_state: scheduled | |
| * <details><summary>Jobs</summary> | |
| - **Job 1:** | |
| * Job state is skipped | |
| **Traceback:** | |
| * ```console | |
| ``` | |
| **Job Parameters:** | |
| * | Job parameter | Parameter value | | |
| | ------------- | --------------- | | |
| | \_\_input\_ext | ` "input" ` | | |
| | \_\_workflow\_invocation\_uuid\_\_ | ` "94f24bb8115211f189517ced8d7c0d2f" ` | | |
| | adapter\_options | ` {"action": "trim", "error_rate": "0.1", "match_read_wildcards": false, "no_indels": false, "no_match_adapter_wildcards": true, "overlap": "3", "revcomp": false, "times": "1"} ` | | |
| | chromInfo | ` "/tmp/tmpgck0c6r3/galaxy-dev/tool-data/shared/ucsc/chrom/?.len" ` | | |
| | dbkey | ` "?" ` | | |
| | filter\_options | ` {"discard_casava": false, "discard_trimmed": false, "discard_untrimmed": false, "max_average_error_rate": null, "max_expected_errors": null, "max_n": null, "maximum_length": null, "maximum_length2": null, "minimum_length": "1", "minimum_length2": null, "pair_filter": "any"} ` | | |
| | library | ` {"__current_case__": 2, "input_1": {"values": [{"id": 51, "src": "dce"}]}, "pair_adapters": false, "r1": {"adapters": [], "anywhere_adapters": [], "front_adapters": []}, "r2": {"adapters2": [], "anywhere_adapters2": [], "front_adapters2": []}, "type": "paired_collection"} ` | | |
| | other\_trimming\_options | ` {"cut": "5", "cut2": "5", "nextseq_trim": "0", "poly_a": false, "quality_cutoff": "0", "quality_cutoff2": "", "shorten_options": {"__current_case__": 1, "shorten_values": "False"}, "shorten_options_r2": {"__current_case__": 1, "shorten_values_r2": "False"}, "trim_n": false} ` | | |
| | output\_selector | ` None ` | | |
| | read\_mod\_options | ` {"length_tag": null, "rename": null, "strip_suffix": null, "zero_cap": false} ` | | |
| - **Job 2:** | |
| * Job state is skipped | |
| **Traceback:** | |
| * ```console | |
| ``` | |
| **Job Parameters:** | |
| * | Job parameter | Parameter value | | |
| | ------------- | --------------- | | |
| | \_\_input\_ext | ` "input" ` | | |
| | \_\_workflow\_invocation\_uuid\_\_ | ` "94f24bb8115211f189517ced8d7c0d2f" ` | | |
| | adapter\_options | ` {"action": "trim", "error_rate": "0.1", "match_read_wildcards": false, "no_indels": false, "no_match_adapter_wildcards": true, "overlap": "3", "revcomp": false, "times": "1"} ` | | |
| | chromInfo | ` "/tmp/tmpgck0c6r3/galaxy-dev/tool-data/shared/ucsc/chrom/?.len" ` | | |
| | dbkey | ` "?" ` | | |
| | filter\_options | ` {"discard_casava": false, "discard_trimmed": false, "discard_untrimmed": false, "max_average_error_rate": null, "max_expected_errors": null, "max_n": null, "maximum_length": null, "maximum_length2": null, "minimum_length": "1", "minimum_length2": null, "pair_filter": "any"} ` | | |
| | library | ` {"__current_case__": 2, "input_1": {"values": [{"id": 54, "src": "dce"}]}, "pair_adapters": false, "r1": {"adapters": [], "anywhere_adapters": [], "front_adapters": []}, "r2": {"adapters2": [], "anywhere_adapters2": [], "front_adapters2": []}, "type": "paired_collection"} ` | | |
| | other\_trimming\_options | ` {"cut": "5", "cut2": "5", "nextseq_trim": "0", "poly_a": false, "quality_cutoff": "0", "quality_cutoff2": "", "shorten_options": {"__current_case__": 1, "shorten_values": "False"}, "shorten_options_r2": {"__current_case__": 1, "shorten_values_r2": "False"}, "trim_n": false} ` | | |
| | output\_selector | ` None ` | | |
| | read\_mod\_options | ` {"length_tag": null, "rename": null, "strip_suffix": null, "zero_cap": false} ` | | |
| </details> | |
| - **Step 19: Unlabelled step (toolshed.g2.bx.psu.edu/repos/bgruening/text\_processing/tp\_grep\_tool/9.5+galaxy2)**: | |
| * step_state: scheduled | |
| * <details><summary>Jobs</summary> | |
| - **Job 1:** | |
| * Job state is ok | |
| **Container:** | |
| * ```console | |
| quay.io/biocontainers/mulled-v2-a8b1e1ec4fafcddd7d4c96fdaa021e5b6c1e8a67:27f652719ff0f4dfc5e3d483435124548d01020c-0 | |
| ``` | |
| **Command Line:** | |
| * ```console | |
| grep -G -A 0 -B 0 --no-group-separator -i -- 'Haploid' '/tmp/tmpgck0c6r3/files/4/4/6/dataset_44628725-462c-4f7a-9906-5485c0f40d9f.dat' > '/tmp/tmpgck0c6r3/job_working_directory/000/106/outputs/dataset_71ef77f3-b505-469f-8394-27d88e286ce8.dat' | |
| ``` | |
| **Exit Code:** | |
| * ```console | |
| 0 | |
| ``` | |
| **Traceback:** | |
| * ```console | |
| ``` | |
| **Job Parameters:** | |
| * | Job parameter | Parameter value | | |
| | ------------- | --------------- | | |
| | \_\_input\_ext | ` "input" ` | | |
| | \_\_workflow\_invocation\_uuid\_\_ | ` "94f24bb8115211f189517ced8d7c0d2f" ` | | |
| | case\_sensitive | ` "-i" ` | | |
| | chromInfo | ` "/tmp/tmpgck0c6r3/galaxy-dev/tool-data/shared/ucsc/chrom/?.len" ` | | |
| | color | ` "NOCOLOR" ` | | |
| | dbkey | ` "?" ` | | |
| | invert | ` "" ` | | |
| | lines\_after | ` "0" ` | | |
| | lines\_before | ` "0" ` | | |
| | regex\_type | ` "-G" ` | | |
| | url\_paste | ` "Haploid" ` | | |
| </details> | |
| - **Step 20: Unlabelled step (toolshed.g2.bx.psu.edu/repos/iuc/compose\_text\_param/compose\_text\_param/0.1.1)**: | |
| * step_state: scheduled | |
| * <details><summary>Jobs</summary> | |
| - **Job 1:** | |
| * Job state is ok | |
| **Command Line:** | |
| * ```console | |
| cd ../; python _evaluate_expression_.py | |
| ``` | |
| **Exit Code:** | |
| * ```console | |
| 0 | |
| ``` | |
| **Traceback:** | |
| * ```console | |
| ``` | |
| **Job Parameters:** | |
| * | Job parameter | Parameter value | | |
| | ------------- | --------------- | | |
| | \_\_input\_ext | ` "input" ` | | |
| | \_\_workflow\_invocation\_uuid\_\_ | ` "94f24bb8115211f189517ced8d7c0d2f" ` | | |
| | chromInfo | ` "/tmp/tmpgck0c6r3/galaxy-dev/tool-data/shared/ucsc/chrom/?.len" ` | | |
| | components | ` [{"__index__": 0, "param_type": {"__current_case__": 0, "component_value": "vertebrata_odb10", "select_param_type": "text"}}] ` | | |
| | dbkey | ` "?" ` | | |
| </details> | |
| - **Step 21: Unlabelled step (toolshed.g2.bx.psu.edu/repos/devteam/column\_maker/Add\_a\_column1/2.1)**: | |
| * step_state: scheduled | |
| * <details><summary>Jobs</summary> | |
| - **Job 1:** | |
| * Job state is ok | |
| **Container:** | |
| * ```console | |
| quay.io/biocontainers/mulled-v2-b1a1ba6b0445e5a9141e8becdb2ab56f8d930e41:477f302c9d587c361f49c5f5853e2f0cc6119bf4-0 | |
| ``` | |
| **Command Line:** | |
| * ```console | |
| python '/tmp/shed_dir/toolshed.g2.bx.psu.edu/repos/devteam/column_maker/aff5135563c6/column_maker/column_maker.py' --column-types float,float,float,float,float,int --file '/tmp/tmpgck0c6r3/job_working_directory/000/108/configs/tmpssrp554k' --fail-on-non-existent-columns --fail-on-non-computable '/tmp/tmpgck0c6r3/files/a/f/4/dataset_af433f2e-2dfd-4ca0-a261-3fa234f7e2ad.dat' '/tmp/tmpgck0c6r3/job_working_directory/000/108/outputs/dataset_f9c7c0fa-6be6-44fb-b6d1-6c92d4b39867.dat' | |
| ``` | |
| **Exit Code:** | |
| * ```console | |
| 0 | |
| ``` | |
| **Standard Output:** | |
| * ```console | |
| c3*2 | |
| Computing 1 new columns with instructions ['c3*2;;'] | |
| Computed new column values for 100.00% of 1 lines written. | |
| ``` | |
| **Traceback:** | |
| * ```console | |
| ``` | |
| **Job Parameters:** | |
| * | Job parameter | Parameter value | | |
| | ------------- | --------------- | | |
| | \_\_input\_ext | ` "input" ` | | |
| | \_\_workflow\_invocation\_uuid\_\_ | ` "94f24bb8115211f189517ced8d7c0d2f" ` | | |
| | avoid\_scientific\_notation | ` false ` | | |
| | chromInfo | ` "/tmp/tmpgck0c6r3/galaxy-dev/tool-data/shared/ucsc/chrom/?.len" ` | | |
| | dbkey | ` "?" ` | | |
| | error\_handling | ` {"auto_col_types": true, "fail_on_non_existent_columns": true, "non_computable": {"__current_case__": 0, "action": "--fail-on-non-computable"}} ` | | |
| | ops | ` {"__current_case__": 0, "expressions": [{"__index__": 0, "add_column": {"__current_case__": 0, "mode": "", "pos": ""}, "cond": "c3*2"}], "header_lines_select": "no"} ` | | |
| </details> | |
| - **Step 22: Unlabelled step (toolshed.g2.bx.psu.edu/repos/iuc/multiqc/multiqc/1.27+galaxy4)**: | |
| * step_state: scheduled | |
| * <details><summary>Jobs</summary> | |
| - **Job 1:** | |
| * Job state is ok | |
| **Container:** | |
| * ```console | |
| quay.io/biocontainers/multiqc:1.27--pyhdfd78af_0 | |
| ``` | |
| **Command Line:** | |
| * ```console | |
| die() { echo "$@" 1>&2 ; exit 1; } && mkdir multiqc_WDir && mkdir multiqc_WDir/cutadapt_0 && ln -s '/tmp/tmpgck0c6r3/files/7/2/b/dataset_72b6fec6-5a88-4eb0-a530-81ac1eeed3b0.dat' 'multiqc_WDir/cutadapt_0/yeast_reads_sub1_fastq_gz.txt' && sed -i.old 's/You are running/This is/' 'multiqc_WDir/cutadapt_0/yeast_reads_sub1_fastq_gz.txt' && grep -q "This is cutadapt" 'multiqc_WDir/cutadapt_0/yeast_reads_sub1_fastq_gz.txt' || die "'This is cutadapt' or 'You are running cutadapt' not found in the file" && multiqc multiqc_WDir --filename 'report' && mkdir -p ./plots && ls -l ./report_data/ && cp ./report_data/*plot*.txt ./plots/ | true | |
| ``` | |
| **Exit Code:** | |
| * ```console | |
| 0 | |
| ``` | |
| **Standard Error:** | |
| * ```console | |
| /// MultiQC 🔍 v1.27 | |
| version_check | MultiQC Version v1.33 now available! | |
| file_search | Search path: /tmp/tmpgck0c6r3/job_working_directory/000/109/working/multiqc_WDir | |
| cutadapt | Found 1 reports | |
| write_results | Data : report_data | |
| write_results | Report : report.html | |
| multiqc | MultiQC complete | |
| ``` | |
| **Standard Output:** | |
| * ```console | |
| total 80 | |
| -rw-r--r-- 1 1001 1001 97 Feb 24 07:30 cutadapt_filtered_reads_plot.txt | |
| -rw-r--r-- 1 1001 1001 66 Feb 24 07:30 cutadapt_trimmed_sequences_plot_default_Counts.txt | |
| -rw-r--r-- 1 1001 1001 70 Feb 24 07:30 cutadapt_trimmed_sequences_plot_default_Obs_Exp.txt | |
| -rw-r--r-- 1 1001 1001 398 Feb 24 07:30 multiqc.log | |
| -rw-r--r-- 1 1001 1001 124 Feb 24 07:30 multiqc_citations.txt | |
| -rw-r--r-- 1 1001 1001 222 Feb 24 07:30 multiqc_cutadapt.txt | |
| -rw-r--r-- 1 1001 1001 44096 Feb 24 07:30 multiqc_data.json | |
| -rw-r--r-- 1 1001 1001 79 Feb 24 07:30 multiqc_general_stats.txt | |
| -rw-r--r-- 1 1001 1001 29 Feb 24 07:30 multiqc_software_versions.txt | |
| -rw-r--r-- 1 1001 1001 195 Feb 24 07:30 multiqc_sources.txt | |
| ``` | |
| **Traceback:** | |
| * ```console | |
| ``` | |
| **Job Parameters:** | |
| * | Job parameter | Parameter value | | |
| | ------------- | --------------- | | |
| | \_\_input\_ext | ` "input" ` | | |
| | \_\_workflow\_invocation\_uuid\_\_ | ` "94f24bb8115211f189517ced8d7c0d2f" ` | | |
| | chromInfo | ` "/tmp/tmpgck0c6r3/galaxy-dev/tool-data/shared/ucsc/chrom/?.len" ` | | |
| | comment | ` "" ` | | |
| | dbkey | ` "?" ` | | |
| | export | ` false ` | | |
| | flat | ` false ` | | |
| | image\_content\_input | ` None ` | | |
| | png\_plots | ` false ` | | |
| | results | ` [{"__index__": 0, "software_cond": {"__current_case__": 5, "input": {"values": [{"id": 19, "src": "hdca"}]}, "software": "cutadapt"}}] ` | | |
| | title | ` "" ` | | |
| </details> | |
| - **Step 23: Pick forward 2 (toolshed.g2.bx.psu.edu/repos/iuc/pick\_value/pick\_value/0.2.0)**: | |
| * step_state: scheduled | |
| * <details><summary>Jobs</summary> | |
| - **Job 1:** | |
| * Job state is ok | |
| **Command Line:** | |
| * ```console | |
| cd ../; python _evaluate_expression_.py | |
| ``` | |
| **Exit Code:** | |
| * ```console | |
| 0 | |
| ``` | |
| **Traceback:** | |
| * ```console | |
| ``` | |
| **Job Parameters:** | |
| * | Job parameter | Parameter value | | |
| | ------------- | --------------- | | |
| | \_\_input\_ext | ` "input" ` | | |
| | \_\_workflow\_invocation\_uuid\_\_ | ` "94f24bb8115211f189517ced8d7c0d2f" ` | | |
| | chromInfo | ` "/tmp/tmpgck0c6r3/galaxy-dev/tool-data/shared/ucsc/chrom/?.len" ` | | |
| | dbkey | ` "?" ` | | |
| | style\_cond | ` {"__current_case__": 0, "pick_style": "first", "type_cond": {"__current_case__": 4, "param_type": "data", "pick_from": [{"__index__": 0, "value": {"values": [{"id": 66, "src": "dce"}]}}, {"__index__": 1, "value": {"values": [{"id": 56, "src": "dce"}]}}]}} ` | | |
| - **Job 2:** | |
| * Job state is ok | |
| **Command Line:** | |
| * ```console | |
| cd ../; python _evaluate_expression_.py | |
| ``` | |
| **Exit Code:** | |
| * ```console | |
| 0 | |
| ``` | |
| **Traceback:** | |
| * ```console | |
| ``` | |
| **Job Parameters:** | |
| * | Job parameter | Parameter value | | |
| | ------------- | --------------- | | |
| | \_\_input\_ext | ` "input" ` | | |
| | \_\_workflow\_invocation\_uuid\_\_ | ` "94f24bb8115211f189517ced8d7c0d2f" ` | | |
| | chromInfo | ` "/tmp/tmpgck0c6r3/galaxy-dev/tool-data/shared/ucsc/chrom/?.len" ` | | |
| | dbkey | ` "?" ` | | |
| | style\_cond | ` {"__current_case__": 0, "pick_style": "first", "type_cond": {"__current_case__": 4, "param_type": "data", "pick_from": [{"__index__": 0, "value": {"values": [{"id": 63, "src": "dce"}]}}, {"__index__": 1, "value": {"values": [{"id": 52, "src": "dce"}]}}]}} ` | | |
| - **Job 3:** | |
| * Job state is ok | |
| **Command Line:** | |
| * ```console | |
| cd ../; python _evaluate_expression_.py | |
| ``` | |
| **Exit Code:** | |
| * ```console | |
| 0 | |
| ``` | |
| **Traceback:** | |
| * ```console | |
| ``` | |
| **Job Parameters:** | |
| * | Job parameter | Parameter value | | |
| | ------------- | --------------- | | |
| | \_\_input\_ext | ` "input" ` | | |
| | \_\_workflow\_invocation\_uuid\_\_ | ` "94f24bb8115211f189517ced8d7c0d2f" ` | | |
| | chromInfo | ` "/tmp/tmpgck0c6r3/galaxy-dev/tool-data/shared/ucsc/chrom/?.len" ` | | |
| | dbkey | ` "?" ` | | |
| | style\_cond | ` {"__current_case__": 0, "pick_style": "first", "type_cond": {"__current_case__": 4, "param_type": "data", "pick_from": [{"__index__": 0, "value": {"values": [{"id": 64, "src": "dce"}]}}, {"__index__": 1, "value": {"values": [{"id": 53, "src": "dce"}]}}]}} ` | | |
| - **Job 4:** | |
| * Job state is ok | |
| **Command Line:** | |
| * ```console | |
| cd ../; python _evaluate_expression_.py | |
| ``` | |
| **Exit Code:** | |
| * ```console | |
| 0 | |
| ``` | |
| **Traceback:** | |
| * ```console | |
| ``` | |
| **Job Parameters:** | |
| * | Job parameter | Parameter value | | |
| | ------------- | --------------- | | |
| | \_\_input\_ext | ` "input" ` | | |
| | \_\_workflow\_invocation\_uuid\_\_ | ` "94f24bb8115211f189517ced8d7c0d2f" ` | | |
| | chromInfo | ` "/tmp/tmpgck0c6r3/galaxy-dev/tool-data/shared/ucsc/chrom/?.len" ` | | |
| | dbkey | ` "?" ` | | |
| | style\_cond | ` {"__current_case__": 0, "pick_style": "first", "type_cond": {"__current_case__": 4, "param_type": "data", "pick_from": [{"__index__": 0, "value": {"values": [{"id": 65, "src": "dce"}]}}, {"__index__": 1, "value": {"values": [{"id": 55, "src": "dce"}]}}]}} ` | | |
| </details> | |
| - **Step 24: Unlabelled step (toolshed.g2.bx.psu.edu/repos/bgruening/text\_processing/tp\_replace\_in\_line/9.5+galaxy2)**: | |
| * step_state: scheduled | |
| * <details><summary>Jobs</summary> | |
| - **Job 1:** | |
| * Job state is ok | |
| **Container:** | |
| * ```console | |
| quay.io/biocontainers/sed:4.8 | |
| ``` | |
| **Command Line:** | |
| * ```console | |
| sed -r --sandbox -e '' -e 's/bp//g' -e '' -e 's/,//g' -e '' -e 's/([a-z])\s+([A-Z])/\1_\2/g' '/tmp/tmpgck0c6r3/files/7/1/e/dataset_71ef77f3-b505-469f-8394-27d88e286ce8.dat' > '/tmp/tmpgck0c6r3/job_working_directory/000/114/outputs/dataset_a0539b91-b7f1-4d7d-b43b-c39f066bd850.dat' | |
| ``` | |
| **Exit Code:** | |
| * ```console | |
| 0 | |
| ``` | |
| **Traceback:** | |
| * ```console | |
| ``` | |
| **Job Parameters:** | |
| * | Job parameter | Parameter value | | |
| | ------------- | --------------- | | |
| | \_\_input\_ext | ` "input" ` | | |
| | \_\_workflow\_invocation\_uuid\_\_ | ` "94f24bb8115211f189517ced8d7c0d2f" ` | | |
| | chromInfo | ` "/tmp/tmpgck0c6r3/galaxy-dev/tool-data/shared/ucsc/chrom/?.len" ` | | |
| | dbkey | ` "?" ` | | |
| | replacements | ` [{"__index__": 0, "find_pattern": "bp", "replace_pattern": "", "sed_options": null}, {"__index__": 1, "find_pattern": ",", "replace_pattern": "", "sed_options": null}, {"__index__": 2, "find_pattern": "([a-z])\\s+([A-Z])", "replace_pattern": "\\1_\\2", "sed_options": null}] ` | | |
| </details> | |
| - **Step 25: Unlabelled step (Cut1)**: | |
| * step_state: scheduled | |
| * <details><summary>Jobs</summary> | |
| - **Job 1:** | |
| * Job state is ok | |
| **Container:** | |
| * ```console | |
| quay.io/biocontainers/perl:5.26--2 | |
| ``` | |
| **Command Line:** | |
| * ```console | |
| perl '/tmp/tmpgck0c6r3/galaxy-dev/tools/filters/cutWrapper.pl' '/tmp/tmpgck0c6r3/files/f/9/c/dataset_f9c7c0fa-6be6-44fb-b6d1-6c92d4b39867.dat' 'c7' T '/tmp/tmpgck0c6r3/job_working_directory/000/115/outputs/dataset_07e5a721-73b6-4ecb-9ffb-d14144768ba4.dat' | |
| ``` | |
| **Exit Code:** | |
| * ```console | |
| 0 | |
| ``` | |
| **Traceback:** | |
| * ```console | |
| ``` | |
| **Job Parameters:** | |
| * | Job parameter | Parameter value | | |
| | ------------- | --------------- | | |
| | \_\_input\_ext | ` "tabular" ` | | |
| | \_\_workflow\_invocation\_uuid\_\_ | ` "94f24bb8115211f189517ced8d7c0d2f" ` | | |
| | chromInfo | ` "/tmp/tmpgck0c6r3/galaxy-dev/tool-data/shared/ucsc/chrom/?.len" ` | | |
| | columnList | ` "c7" ` | | |
| | dbkey | ` "?" ` | | |
| | delimiter | ` "T" ` | | |
| </details> | |
| - **Step 26: Unlabelled step**: | |
| * step_state: scheduled | |
| * <details><summary>Subworkflow Steps</summary> | |
| - **Step 1: Unlabelled step**: | |
| * step_state: scheduled | |
| - **Step 2: Unlabelled step (toolshed.g2.bx.psu.edu/repos/iuc/collection\_element\_identifiers/collection\_element\_identifiers/0.0.2)**: | |
| * step_state: scheduled | |
| * <details><summary>Jobs</summary> | |
| - **Job 1:** | |
| * Job state is ok | |
| **Command Line:** | |
| * ```console | |
| mv '/tmp/tmpgck0c6r3/job_working_directory/000/116/configs/tmpz93wmxim' '/tmp/tmpgck0c6r3/job_working_directory/000/116/outputs/dataset_31d87f8f-7226-45f9-b5d4-504cfd34f03f.dat' | |
| ``` | |
| **Exit Code:** | |
| * ```console | |
| 0 | |
| ``` | |
| **Traceback:** | |
| * ```console | |
| ``` | |
| **Job Parameters:** | |
| * | Job parameter | Parameter value | | |
| | ------------- | --------------- | | |
| | \_\_input\_ext | ` "expression.json" ` | | |
| | \_\_workflow\_invocation\_uuid\_\_ | ` "94f24bb9115211f189517ced8d7c0d2f" ` | | |
| | chromInfo | ` "/tmp/tmpgck0c6r3/galaxy-dev/tool-data/shared/ucsc/chrom/?.len" ` | | |
| | dbkey | ` "?" ` | | |
| | input\_collection | ` {"values": [{"id": 22, "src": "hdca"}]} ` | | |
| </details> | |
| - **Step 3: Unlabelled step (wc\_gnu)**: | |
| * step_state: scheduled | |
| * <details><summary>Jobs</summary> | |
| - **Job 1:** | |
| * Job state is ok | |
| **Command Line:** | |
| * ```console | |
| echo "#lines words characters" > /tmp/tmpgck0c6r3/job_working_directory/000/117/outputs/dataset_0d130604-9453-4fbe-a230-8d0eacc6e088.dat && cat '/tmp/tmpgck0c6r3/files/3/1/d/dataset_31d87f8f-7226-45f9-b5d4-504cfd34f03f.dat' | wc -l -w -m | awk '{ print $1"\t"$2"\t"$3 }' >> /tmp/tmpgck0c6r3/job_working_directory/000/117/outputs/dataset_0d130604-9453-4fbe-a230-8d0eacc6e088.dat | |
| ``` | |
| **Exit Code:** | |
| * ```console | |
| 0 | |
| ``` | |
| **Traceback:** | |
| * ```console | |
| ``` | |
| **Job Parameters:** | |
| * | Job parameter | Parameter value | | |
| | ------------- | --------------- | | |
| | \_\_input\_ext | ` "txt" ` | | |
| | \_\_workflow\_invocation\_uuid\_\_ | ` "94f24bb9115211f189517ced8d7c0d2f" ` | | |
| | chromInfo | ` "/tmp/tmpgck0c6r3/galaxy-dev/tool-data/shared/ucsc/chrom/?.len" ` | | |
| | dbkey | ` "?" ` | | |
| | include\_header | ` true ` | | |
| | options | ` ["lines", "words", "characters"] ` | | |
| </details> | |
| - **Step 4: Unlabelled step (Cut1)**: | |
| * step_state: scheduled | |
| * <details><summary>Jobs</summary> | |
| - **Job 1:** | |
| * Job state is ok | |
| **Container:** | |
| * ```console | |
| quay.io/biocontainers/perl:5.26--2 | |
| ``` | |
| **Command Line:** | |
| * ```console | |
| perl '/tmp/tmpgck0c6r3/galaxy-dev/tools/filters/cutWrapper.pl' '/tmp/tmpgck0c6r3/files/0/d/1/dataset_0d130604-9453-4fbe-a230-8d0eacc6e088.dat' 'c1' T '/tmp/tmpgck0c6r3/job_working_directory/000/118/outputs/dataset_e53afb48-f39a-4216-9461-30111e264d5f.dat' | |
| ``` | |
| **Exit Code:** | |
| * ```console | |
| 0 | |
| ``` | |
| **Traceback:** | |
| * ```console | |
| ``` | |
| **Job Parameters:** | |
| * | Job parameter | Parameter value | | |
| | ------------- | --------------- | | |
| | \_\_input\_ext | ` "tabular" ` | | |
| | \_\_workflow\_invocation\_uuid\_\_ | ` "94f24bb9115211f189517ced8d7c0d2f" ` | | |
| | chromInfo | ` "/tmp/tmpgck0c6r3/galaxy-dev/tool-data/shared/ucsc/chrom/?.len" ` | | |
| | columnList | ` "c1" ` | | |
| | dbkey | ` "?" ` | | |
| | delimiter | ` "T" ` | | |
| </details> | |
| - **Step 5: Unlabelled step (param\_value\_from\_file)**: | |
| * step_state: scheduled | |
| * <details><summary>Jobs</summary> | |
| - **Job 1:** | |
| * Job state is ok | |
| **Command Line:** | |
| * ```console | |
| cd ../; python _evaluate_expression_.py | |
| ``` | |
| **Exit Code:** | |
| * ```console | |
| 0 | |
| ``` | |
| **Traceback:** | |
| * ```console | |
| ``` | |
| **Job Parameters:** | |
| * | Job parameter | Parameter value | | |
| | ------------- | --------------- | | |
| | \_\_input\_ext | ` "input" ` | | |
| | \_\_workflow\_invocation\_uuid\_\_ | ` "94f24bb9115211f189517ced8d7c0d2f" ` | | |
| | chromInfo | ` "/tmp/tmpgck0c6r3/galaxy-dev/tool-data/shared/ucsc/chrom/?.len" ` | | |
| | dbkey | ` "?" ` | | |
| | param\_type | ` "text" ` | | |
| | remove\_newlines | ` true ` | | |
| </details> | |
| - **Step 6: Unlabelled step (toolshed.g2.bx.psu.edu/repos/iuc/map\_param\_value/map\_param\_value/0.2.0)**: | |
| * step_state: scheduled | |
| * <details><summary>Jobs</summary> | |
| - **Job 1:** | |
| * Job state is ok | |
| **Command Line:** | |
| * ```console | |
| cd ../; python _evaluate_expression_.py | |
| ``` | |
| **Exit Code:** | |
| * ```console | |
| 0 | |
| ``` | |
| **Traceback:** | |
| * ```console | |
| ``` | |
| **Job Parameters:** | |
| * | Job parameter | Parameter value | | |
| | ------------- | --------------- | | |
| | \_\_input\_ext | ` "input" ` | | |
| | \_\_workflow\_invocation\_uuid\_\_ | ` "94f24bb9115211f189517ced8d7c0d2f" ` | | |
| | chromInfo | ` "/tmp/tmpgck0c6r3/galaxy-dev/tool-data/shared/ucsc/chrom/?.len" ` | | |
| | dbkey | ` "?" ` | | |
| | input\_param\_type | ` {"__current_case__": 0, "input_param": "2", "mappings": [{"__index__": 0, "from": "0", "to": "True"}], "type": "text"} ` | | |
| | output\_param\_type | ` "boolean" ` | | |
| | unmapped | ` {"__current_case__": 2, "default_value": "False", "on_unmapped": "default"} ` | | |
| </details> | |
| - **Step 7: Unlabelled step (toolshed.g2.bx.psu.edu/repos/iuc/map\_param\_value/map\_param\_value/0.2.0)**: | |
| * step_state: scheduled | |
| * <details><summary>Jobs</summary> | |
| - **Job 1:** | |
| * Job state is ok | |
| **Command Line:** | |
| * ```console | |
| cd ../; python _evaluate_expression_.py | |
| ``` | |
| **Exit Code:** | |
| * ```console | |
| 0 | |
| ``` | |
| **Traceback:** | |
| * ```console | |
| ``` | |
| **Job Parameters:** | |
| * | Job parameter | Parameter value | | |
| | ------------- | --------------- | | |
| | \_\_input\_ext | ` "input" ` | | |
| | \_\_workflow\_invocation\_uuid\_\_ | ` "94f24bb9115211f189517ced8d7c0d2f" ` | | |
| | chromInfo | ` "/tmp/tmpgck0c6r3/galaxy-dev/tool-data/shared/ucsc/chrom/?.len" ` | | |
| | dbkey | ` "?" ` | | |
| | input\_param\_type | ` {"__current_case__": 0, "input_param": "2", "mappings": [{"__index__": 0, "from": "1", "to": "True"}], "type": "text"} ` | | |
| | output\_param\_type | ` "boolean" ` | | |
| | unmapped | ` {"__current_case__": 2, "default_value": "False", "on_unmapped": "default"} ` | | |
| </details> | |
| - **Step 8: Unlabelled step (toolshed.g2.bx.psu.edu/repos/iuc/map\_param\_value/map\_param\_value/0.2.0)**: | |
| * step_state: scheduled | |
| * <details><summary>Jobs</summary> | |
| - **Job 1:** | |
| * Job state is ok | |
| **Command Line:** | |
| * ```console | |
| cd ../; python _evaluate_expression_.py | |
| ``` | |
| **Exit Code:** | |
| * ```console | |
| 0 | |
| ``` | |
| **Traceback:** | |
| * ```console | |
| ``` | |
| **Job Parameters:** | |
| * | Job parameter | Parameter value | | |
| | ------------- | --------------- | | |
| | \_\_input\_ext | ` "input" ` | | |
| | \_\_workflow\_invocation\_uuid\_\_ | ` "94f24bb9115211f189517ced8d7c0d2f" ` | | |
| | chromInfo | ` "/tmp/tmpgck0c6r3/galaxy-dev/tool-data/shared/ucsc/chrom/?.len" ` | | |
| | dbkey | ` "?" ` | | |
| | input\_param\_type | ` {"__current_case__": 0, "input_param": "2", "mappings": [{"__index__": 0, "from": "0", "to": "False"}, {"__index__": 1, "from": "1", "to": "False"}], "type": "text"} ` | | |
| | output\_param\_type | ` "boolean" ` | | |
| | unmapped | ` {"__current_case__": 2, "default_value": "True", "on_unmapped": "default"} ` | | |
| </details> | |
| </details> | |
| - **Step 27: Unlabelled step (\_\_UNZIP\_COLLECTION\_\_)**: | |
| * step_state: scheduled | |
| * <details><summary>Jobs</summary> | |
| - **Job 1:** | |
| * Job state is ok | |
| **Traceback:** | |
| * ```console | |
| ``` | |
| **Job Parameters:** | |
| * | Job parameter | Parameter value | | |
| | ------------- | --------------- | | |
| | \_\_workflow\_invocation\_uuid\_\_ | ` "94f24bb8115211f189517ced8d7c0d2f" ` | | |
| | input | ` {"values": [{"id": 67, "src": "dce"}]} ` | | |
| - **Job 2:** | |
| * Job state is ok | |
| **Traceback:** | |
| * ```console | |
| ``` | |
| **Job Parameters:** | |
| * | Job parameter | Parameter value | | |
| | ------------- | --------------- | | |
| | \_\_workflow\_invocation\_uuid\_\_ | ` "94f24bb8115211f189517ced8d7c0d2f" ` | | |
| | input | ` {"values": [{"id": 70, "src": "dce"}]} ` | | |
| </details> | |
| - **Step 28: Unlabelled step (Convert characters1)**: | |
| * step_state: scheduled | |
| * <details><summary>Jobs</summary> | |
| - **Job 1:** | |
| * Job state is ok | |
| **Container:** | |
| * ```console | |
| quay.io/biocontainers/python:3.13 | |
| ``` | |
| **Command Line:** | |
| * ```console | |
| python '/tmp/tmpgck0c6r3/galaxy-dev/tools/filters/convert_characters.py' --strip --condense '/tmp/tmpgck0c6r3/files/a/0/5/dataset_a0539b91-b7f1-4d7d-b43b-c39f066bd850.dat' 's' '/tmp/tmpgck0c6r3/job_working_directory/000/122/outputs/dataset_92cabe64-5b0b-45d9-8c3a-44a5d684260a.dat' | |
| ``` | |
| **Exit Code:** | |
| * ```console | |
| 0 | |
| ``` | |
| **Traceback:** | |
| * ```console | |
| ``` | |
| **Job Parameters:** | |
| * | Job parameter | Parameter value | | |
| | ------------- | --------------- | | |
| | \_\_input\_ext | ` "input" ` | | |
| | \_\_workflow\_invocation\_uuid\_\_ | ` "94f24bb8115211f189517ced8d7c0d2f" ` | | |
| | chromInfo | ` "/tmp/tmpgck0c6r3/galaxy-dev/tool-data/shared/ucsc/chrom/?.len" ` | | |
| | condense | ` true ` | | |
| | convert\_from | ` "s" ` | | |
| | dbkey | ` "?" ` | | |
| | strip | ` true ` | | |
| </details> | |
| - **Step 29: Estimated homozygous read coverage (param\_value\_from\_file)**: | |
| * step_state: scheduled | |
| * <details><summary>Jobs</summary> | |
| - **Job 1:** | |
| * Job state is ok | |
| **Command Line:** | |
| * ```console | |
| cd ../; python _evaluate_expression_.py | |
| ``` | |
| **Exit Code:** | |
| * ```console | |
| 0 | |
| ``` | |
| **Traceback:** | |
| * ```console | |
| ``` | |
| **Job Parameters:** | |
| * | Job parameter | Parameter value | | |
| | ------------- | --------------- | | |
| | \_\_input\_ext | ` "input" ` | | |
| | \_\_workflow\_invocation\_uuid\_\_ | ` "94f24bb8115211f189517ced8d7c0d2f" ` | | |
| | chromInfo | ` "/tmp/tmpgck0c6r3/galaxy-dev/tool-data/shared/ucsc/chrom/?.len" ` | | |
| | dbkey | ` "?" ` | | |
| | param\_type | ` "integer" ` | | |
| | remove\_newlines | ` true ` | | |
| </details> | |
| - **Step 30: Extract Hic forward (\_\_EXTRACT\_DATASET\_\_)**: | |
| * step_state: scheduled | |
| * <details><summary>Jobs</summary> | |
| - **Job 1:** | |
| * Job state is skipped | |
| **Traceback:** | |
| * ```console | |
| ``` | |
| **Job Parameters:** | |
| * | Job parameter | Parameter value | | |
| | ------------- | --------------- | | |
| | \_\_workflow\_invocation\_uuid\_\_ | ` "94f24bb8115211f189517ced8d7c0d2f" ` | | |
| | input | ` {"values": [{"id": 23, "src": "hdca"}]} ` | | |
| | which | ` {"__current_case__": 0, "which_dataset": "first"} ` | | |
| </details> | |
| - **Step 31: Extract Hic reverse (\_\_EXTRACT\_DATASET\_\_)**: | |
| * step_state: scheduled | |
| * <details><summary>Jobs</summary> | |
| - **Job 1:** | |
| * Job state is skipped | |
| **Traceback:** | |
| * ```console | |
| ``` | |
| **Job Parameters:** | |
| * | Job parameter | Parameter value | | |
| | ------------- | --------------- | | |
| | \_\_workflow\_invocation\_uuid\_\_ | ` "94f24bb8115211f189517ced8d7c0d2f" ` | | |
| | input | ` {"values": [{"id": 24, "src": "hdca"}]} ` | | |
| | which | ` {"__current_case__": 0, "which_dataset": "first"} ` | | |
| </details> | |
| - **Step 32: Collapse forward reads (toolshed.g2.bx.psu.edu/repos/nml/collapse\_collections/collapse\_dataset/5.1.0)**: | |
| * step_state: scheduled | |
| * <details><summary>Jobs</summary> | |
| - **Job 1:** | |
| * Job state is ok | |
| **Container:** | |
| * ```console | |
| quay.io/biocontainers/gawk:5.1.0--2 | |
| ``` | |
| **Command Line:** | |
| * ```console | |
| ( cat "/tmp/tmpgck0c6r3/files/1/e/b/dataset_1eb0130e-a76e-46ae-8e13-b7d9753417c2.dat" ; cat "/tmp/tmpgck0c6r3/files/a/f/f/dataset_affd8033-cce1-4956-aec6-62d4469f795a.dat" ; ) > /tmp/tmpgck0c6r3/job_working_directory/000/132/outputs/dataset_f48c6551-89e7-4f9b-9fb9-428d8b370c55.dat | |
| ``` | |
| **Exit Code:** | |
| * ```console | |
| 0 | |
| ``` | |
| **Traceback:** | |
| * ```console | |
| ``` | |
| **Job Parameters:** | |
| * | Job parameter | Parameter value | | |
| | ------------- | --------------- | | |
| | \_\_input\_ext | ` "input" ` | | |
| | \_\_workflow\_invocation\_uuid\_\_ | ` "94f24bb8115211f189517ced8d7c0d2f" ` | | |
| | chromInfo | ` "/tmp/tmpgck0c6r3/galaxy-dev/tool-data/shared/ucsc/chrom/?.len" ` | | |
| | dbkey | ` "?" ` | | |
| | filename | ` {"__current_case__": 1, "add_name": false} ` | | |
| | one\_header | ` false ` | | |
| </details> | |
| - **Step 33: Collapse reverse reads (toolshed.g2.bx.psu.edu/repos/nml/collapse\_collections/collapse\_dataset/5.1.0)**: | |
| * step_state: scheduled | |
| * <details><summary>Jobs</summary> | |
| - **Job 1:** | |
| * Job state is ok | |
| **Container:** | |
| * ```console | |
| quay.io/biocontainers/gawk:5.1.0--2 | |
| ``` | |
| **Command Line:** | |
| * ```console | |
| ( cat "/tmp/tmpgck0c6r3/files/2/9/8/dataset_298582ea-e2da-4a02-9c3b-dd61c3b9efdf.dat" ; cat "/tmp/tmpgck0c6r3/files/c/d/1/dataset_cd1f925d-2af0-47ce-953b-1113c0a21508.dat" ; ) > /tmp/tmpgck0c6r3/job_working_directory/000/133/outputs/dataset_4d5b5bf2-e69e-498c-b0ca-5f4143ed68c1.dat | |
| ``` | |
| **Exit Code:** | |
| * ```console | |
| 0 | |
| ``` | |
| **Traceback:** | |
| * ```console | |
| ``` | |
| **Job Parameters:** | |
| * | Job parameter | Parameter value | | |
| | ------------- | --------------- | | |
| | \_\_input\_ext | ` "input" ` | | |
| | \_\_workflow\_invocation\_uuid\_\_ | ` "94f24bb8115211f189517ced8d7c0d2f" ` | | |
| | chromInfo | ` "/tmp/tmpgck0c6r3/galaxy-dev/tool-data/shared/ucsc/chrom/?.len" ` | | |
| | dbkey | ` "?" ` | | |
| | filename | ` {"__current_case__": 1, "add_name": false} ` | | |
| | one\_header | ` false ` | | |
| </details> | |
| - **Step 34: Unlabelled step (Cut1)**: | |
| * step_state: scheduled | |
| * <details><summary>Jobs</summary> | |
| - **Job 1:** | |
| * Job state is ok | |
| **Container:** | |
| * ```console | |
| quay.io/biocontainers/perl:5.26--2 | |
| ``` | |
| **Command Line:** | |
| * ```console | |
| perl '/tmp/tmpgck0c6r3/galaxy-dev/tools/filters/cutWrapper.pl' '/tmp/tmpgck0c6r3/files/9/2/c/dataset_92cabe64-5b0b-45d9-8c3a-44a5d684260a.dat' 'c3' T '/tmp/tmpgck0c6r3/job_working_directory/000/124/outputs/dataset_89ce6de4-11b6-4af2-9211-37f101323611.dat' | |
| ``` | |
| **Exit Code:** | |
| * ```console | |
| 0 | |
| ``` | |
| **Traceback:** | |
| * ```console | |
| ``` | |
| **Job Parameters:** | |
| * | Job parameter | Parameter value | | |
| | ------------- | --------------- | | |
| | \_\_input\_ext | ` "tabular" ` | | |
| | \_\_workflow\_invocation\_uuid\_\_ | ` "94f24bb8115211f189517ced8d7c0d2f" ` | | |
| | chromInfo | ` "/tmp/tmpgck0c6r3/galaxy-dev/tool-data/shared/ucsc/chrom/?.len" ` | | |
| | columnList | ` "c3" ` | | |
| | dbkey | ` "?" ` | | |
| | delimiter | ` "T" ` | | |
| </details> | |
| - **Step 35: Homozygous read coverage for Hifiasm (toolshed.g2.bx.psu.edu/repos/iuc/pick\_value/pick\_value/0.2.0)**: | |
| * step_state: scheduled | |
| * <details><summary>Jobs</summary> | |
| - **Job 1:** | |
| * Job state is ok | |
| **Command Line:** | |
| * ```console | |
| cd ../; python _evaluate_expression_.py | |
| ``` | |
| **Exit Code:** | |
| * ```console | |
| 0 | |
| ``` | |
| **Traceback:** | |
| * ```console | |
| ``` | |
| **Job Parameters:** | |
| * | Job parameter | Parameter value | | |
| | ------------- | --------------- | | |
| | \_\_input\_ext | ` "input" ` | | |
| | \_\_workflow\_invocation\_uuid\_\_ | ` "94f24bb8115211f189517ced8d7c0d2f" ` | | |
| | chromInfo | ` "/tmp/tmpgck0c6r3/galaxy-dev/tool-data/shared/ucsc/chrom/?.len" ` | | |
| | dbkey | ` "?" ` | | |
| | style\_cond | ` {"__current_case__": 0, "pick_style": "first", "type_cond": {"__current_case__": 1, "param_type": "integer", "pick_from": [{"__index__": 0, "value": null}, {"__index__": 1, "value": "21"}]}} ` | | |
| </details> | |
| - **Step 36: Hi-C forward reads (toolshed.g2.bx.psu.edu/repos/iuc/pick\_value/pick\_value/0.2.0)**: | |
| * step_state: scheduled | |
| * <details><summary>Jobs</summary> | |
| - **Job 1:** | |
| * Job state is ok | |
| **Command Line:** | |
| * |
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