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Updating workflows/microbiome/metagenomic-genes-catalogue from 1.3 to 1.4 - #1333

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Updating workflows/microbiome/metagenomic-genes-catalogue from 1.3 to 1.4 #1333
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galaxyproject:mainfrom
planemo-autoupdate:workflows/microbiome/metagenomic-genes-catalogue

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@gxydevbot

@gxydevbot gxydevbot commented Aug 3, 2026

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Hello! This is an automated update of the following workflow: workflows/microbiome/metagenomic-genes-catalogue. I created this PR because I think one or more of the component tools are out of date, i.e. there is a newer version available on the ToolShed.

By comparing with the latest versions available on the ToolShed, it seems the following tools are outdated:

  • toolshed.g2.bx.psu.edu/repos/iuc/amrfinderplus/amrfinderplus/3.12.8+galaxy0 should be updated to toolshed.g2.bx.psu.edu/repos/iuc/amrfinderplus/amrfinderplus/4.2.7+galaxy0
  • toolshed.g2.bx.psu.edu/repos/iuc/coverm_contig/coverm_contig/0.8.0+galaxy0 should be updated to toolshed.g2.bx.psu.edu/repos/iuc/coverm_contig/coverm_contig/0.8.0+galaxy1
  • toolshed.g2.bx.psu.edu/repos/iuc/multiqc/multiqc/1.35+galaxy1 should be updated to toolshed.g2.bx.psu.edu/repos/iuc/multiqc/multiqc/1.35+galaxy2

The workflow release number has been updated from 1.3 to 1.4.

If you want to skip this change, close this PR without deleting the branch. It will be reopened if another change is detected.
Any commit from another author than 'planemo-autoupdate' will prevent more auto-updates.
To ignore manual changes and allow autoupdates, delete the branch.

@gxydevbot
gxydevbot requested a review from hugolefeuvre as a code owner August 3, 2026 09:35
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github-actions Bot commented Aug 3, 2026

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Test Results (powered by Planemo)

Test Summary

Test State Count
Total 1
Passed 0
Error 1
Failure 0
Skipped 0
Errored Tests
  • ❌ metagenomic-genes-catalogue.ga_0

    Execution Problem:

    • Failed to run workflow, invocation ended in [failed] state.

    Workflow invocation details

    • Invocation Messages

      • Invocation scheduling failed because step 28 requires a dataset, but dataset entered a failed state.
    • Steps

      • Step 1: Metagenomics Trimmed reads:

        • step_state: scheduled

      • Step 2: AMR genes detection database:

        • step_state: scheduled

      • Step 3: Full genes catalogue:

        • step_state: scheduled

      • Step 4: Virulence genes detection database:

        • step_state: scheduled

      • Step 5: starAMR database:

        • step_state: scheduled

      • Step 6: mmseqs2 taxonomy DB:

        • step_state: scheduled

      • Step 7: eggNOG database:

        • step_state: scheduled

      • Step 8: Unlabelled step (toolshed.g2.bx.psu.edu/repos/iuc/megahit/megahit/1.2.9+galaxy2):

        • step_state: scheduled

        • Jobs

          • Job 1:

            • Job state is ok

            Container:

            • quay.io/biocontainers/megahit:1.2.9--haf24da9_8

            Command Line:

            • if [[ -n "$GALAXY_MEMORY_MB" ]]; then MEMORY="-m $((GALAXY_MEMORY_MB * 1024))"; fi;  megahit --num-cpu-threads ${GALAXY_SLOTS:-4}  -1 '/tmp/tmpy96jvlqm/files/8/9/5/dataset_89502fc5-67c8-40c6-82bf-e0370d0a8cf7.dat' -2 '/tmp/tmpy96jvlqm/files/5/4/a/dataset_54a460a2-e6ce-4524-9b4e-98bcf19898f8.dat' --min-count '2' --k-list '21,29,39,59,79,99,119,141'  --bubble-level '2' --merge-level '20,0.95' --prune-level '2' --prune-depth '2' --disconnect-ratio '0.1' --low-local-ratio '0.2' --cleaning-rounds '5'   --min-contig-len '200' $MEMORY

            Exit Code:

            • 0

            Standard Error:

            • 2026-08-03 09:47:39 - MEGAHIT v1.2.9
2026-08-03 09:47:39 - Using megahit_core with POPCNT and BMI2 support
2026-08-03 09:47:39 - Convert reads to binary library
2026-08-03 09:47:40 - b'INFO  sequence/io/sequence_lib.cpp  :   75 - Lib 0 (/tmp/tmpy96jvlqm/files/8/9/5/dataset_89502fc5-67c8-40c6-82bf-e0370d0a8cf7.dat,/tmp/tmpy96jvlqm/files/5/4/a/dataset_54a460a2-e6ce-4524-9b4e-98bcf19898f8.dat): pe, 500000 reads, 101 max length'
2026-08-03 09:47:40 - b'INFO  utils/utils.h                 :  152 - Real: 0.6523\tuser: 0.6180\tsys: 0.0350\tmaxrss: 29776'
2026-08-03 09:47:40 - Start assembly. Number of CPU threads 1 
2026-08-03 09:47:40 - k list: 21,29,39,59,79,99,119,141 
2026-08-03 09:47:40 - Memory used: 15093680947
2026-08-03 09:47:40 - Extract solid (k+1)-mers for k = 21 
2026-08-03 09:47:48 - Build graph for k = 21 
2026-08-03 09:47:56 - Assemble contigs from SdBG for k = 21
2026-08-03 09:48:21 - Local assembly for k = 21
2026-08-03 09:48:24 - Extract iterative edges from k = 21 to 29 
2026-08-03 09:48:26 - Build graph for k = 29 
2026-08-03 09:48:29 - Assemble contigs from SdBG for k = 29
2026-08-03 09:48:46 - Local assembly for k = 29
2026-08-03 09:48:49 - Extract iterative edges from k = 29 to 39 
2026-08-03 09:48:50 - Build graph for k = 39 
2026-08-03 09:48:52 - Assemble contigs from SdBG for k = 39
2026-08-03 09:49:04 - Local assembly for k = 39
2026-08-03 09:49:08 - Extract iterative edges from k = 39 to 59 
2026-08-03 09:49:09 - Build graph for k = 59 
2026-08-03 09:49:10 - Assemble contigs from SdBG for k = 59
2026-08-03 09:49:18 - Local assembly for k = 59
2026-08-03 09:49:21 - Extract iterative edges from k = 59 to 79 
2026-08-03 09:49:21 - Build graph for k = 79 
2026-08-03 09:49:22 - Assemble contigs from SdBG for k = 79
2026-08-03 09:49:28 - Local assembly for k = 79
2026-08-03 09:49:30 - Extract iterative edges from k = 79 to 99 
2026-08-03 09:49:31 - Build graph for k = 99 
2026-08-03 09:49:32 - Assemble contigs from SdBG for k = 99
2026-08-03 09:49:36 - Local assembly for k = 99
2026-08-03 09:49:38 - Extract iterative edges from k = 99 to 119 
2026-08-03 09:49:38 - Build graph for k = 119 
2026-08-03 09:49:39 - Assemble contigs from SdBG for k = 119
2026-08-03 09:49:42 - Local assembly for k = 119
2026-08-03 09:49:44 - Extract iterative edges from k = 119 to 141 
2026-08-03 09:49:44 - Build graph for k = 141 
2026-08-03 09:49:45 - Assemble contigs from SdBG for k = 141
2026-08-03 09:49:48 - Merging to output final contigs 
2026-08-03 09:49:48 - 3785 contigs, total 1759217 bp, min 243 bp, max 10133 bp, avg 464 bp, N50 449 bp
2026-08-03 09:49:48 - ALL DONE. Time elapsed: 128.612513 seconds

            Traceback:

            • 

              • 

            

            Job Parameters:
            

              

            • 

              


              
Job parameter
Parameter value

              
              


              
__input_ext
"fastqsanger.gz"

              

              
__workflow_invocation_uuid__
"52ab5fa08f2011f194246045bddb4fd3"

              

              
advanced_section
{"bubble_level": "2", "cleaning_rounds": "5", "disconnect_ratio": "0.1", "kmin1pass": false, "low_local_ratio": "0.2", "merge_level": "20,0.95", "nolocal": false, "nomercy": false, "prune_depth": "2", "prune_level": "2"}

              

              
basic_section
{"k_mer": {"__current_case__": 0, "k_list": "21,29,39,59,79,99,119,141", "k_mer_method": "klist_method"}, "min_count": "2"}

              

              
chromInfo
"/tmp/tmpy96jvlqm/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"

              

              
dbkey
"?"

              

              
input_option
{"__current_case__": 3, "batchmode": {"__current_case__": 0, "pair_input": {"values": [{"id": 1, "src": "dce"}]}, "processmode": "individual"}, "choice": "paired_collection"}

              

              
output_section
{"log_file": true, "min_contig_len": "200", "show_intermediate_contigs": false}

              
              

              

              • 

            

            • 

          

          

          • 

        

        • 

      • 

        Step 9: Unlabelled step (toolshed.g2.bx.psu.edu/repos/iuc/pick_value/pick_value/0.2.0):
        

          

        • 

          step_state: scheduled
          

          • 

        • 

          Jobs

            

          • 

            Job 1:
            

              

            • Job state is skipped
              • 

            

            Traceback:
            

              

            • 

              

              • 

            

            Job Parameters:
            

              

            • 

              


              
Job parameter
Parameter value

              
              


              
__input_ext
"input"

              

              
__workflow_invocation_uuid__
"52ab5fa08f2011f194246045bddb4fd3"

              

              
chromInfo
"/tmp/tmpy96jvlqm/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"

              

              
dbkey
"?"

              

              
style_cond
{"__current_case__": 1, "pick_style": "first_or_default", "type_cond": {"__current_case__": 3, "default_value": true, "param_type": "boolean", "pick_from": [{"__index__": 0, "value": false}]}}

              
              

              

              • 

            

            • 

          

          

          • 

        

        • 

      • 

        Step 10: Unlabelled step (toolshed.g2.bx.psu.edu/repos/devteam/fasta_to_tabular/fasta2tab/1.1.1):
        

          

        • 

          step_state: scheduled
          

          • 

        • 

          Jobs

            

          • 

            Job 1:
            

              

            • Job state is ok
              • 

            

            Container:
            

              

            • 

              quay.io/biocontainers/python:3.7--1
              

              • 

            

            Command Line:
            

              

            • 

              python '/tmp/shed_data/shed_tools/toolshed.g2.bx.psu.edu/repos/devteam/fasta_to_tabular/e7ed3c310b74/fasta_to_tabular/fasta_to_tabular.py' '/tmp/tmpy96jvlqm/files/5/7/3/dataset_57305f03-dbf4-438b-a90e-7598c7f79c13.dat' '/tmp/tmpy96jvlqm/job_working_directory/000/5/outputs/dataset_ec214bf9-4ec5-4596-93fc-5733657ff5d5.dat' 0 1
              

              • 

            

            Exit Code:
            

              

            • 

              0
              

              • 

            

            Traceback:
            

              

            • 

              

              • 

            

            Job Parameters:
            

              

            • 

              


              
Job parameter
Parameter value

              
              


              
__input_ext
"input"

              

              
__workflow_invocation_uuid__
"52ab5fa08f2011f194246045bddb4fd3"

              

              
chromInfo
"/tmp/tmpy96jvlqm/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"

              

              
dbkey
"?"

              

              
descr_columns
"1"

              

              
keep_first
"0"

              
              

              

              • 

            

            • 

          

          

          • 

        

        • 

      • 

        Step 11: Unlabelled step (toolshed.g2.bx.psu.edu/repos/iuc/quast/quast/5.3.0+galaxy1):
        

          

        • 

          step_state: scheduled
          

          • 

        • 

          Jobs

            

          • 

            Job 1:
            

              

            • Job state is ok
              • 

            

            Container:
            

              

            • 

              quay.io/biocontainers/mulled-v2-754a47f7005ac2c33e46ba3a97ef68abb6ef71f8:aac2489b1179db17f28c2868c3a8e41d4474683a-0
              

              • 

            

            Command Line:
            

              

            • 

              echo genes_catalogue_test &&   ln -s '/tmp/tmpy96jvlqm/files/8/9/5/dataset_89502fc5-67c8-40c6-82bf-e0370d0a8cf7.dat' 'pe1-genes_catalogue_test.fastqsanger.gz' && ln -s '/tmp/tmpy96jvlqm/files/5/4/a/dataset_54a460a2-e6ce-4524-9b4e-98bcf19898f8.dat' 'pe2-genes_catalogue_test.fastqsanger.gz' &&  metaquast  --pe1 'pe1-genes_catalogue_test.fastqsanger.gz' --pe2 'pe2-genes_catalogue_test.fastqsanger.gz' --labels 'genes_catalogue_test' -o 'outputdir'  --max-ref-num 0  --min-identity 95.0 --min-contig 1500        --min-alignment 65 --ambiguity-usage 'one' --ambiguity-score 0.99   --local-mis-size 200   --contig-thresholds '0,1000,5000,10000,25000,50000'  --extensive-mis-size 1000 --scaffold-gap-max-size 10000 --unaligned-part-size 500   --x-for-Nx 90  '/tmp/tmpy96jvlqm/files/5/7/3/dataset_57305f03-dbf4-438b-a90e-7598c7f79c13.dat' --threads ${GALAXY_SLOTS:-1}  --no-krona  && if [[ -f "outputdir/report.tsv" ]]; then mkdir -p "outputdir/combined_reference/" && cp "outputdir/report.tsv" "outputdir/combined_reference/report.tsv"; fi && if [[ -f "outputdir/report.html" ]]; then mkdir -p "outputdir/combined_reference/" && cp outputdir/*.html "outputdir/combined_reference/"; fi && mkdir -p '/tmp/tmpy96jvlqm/job_working_directory/000/6/outputs/dataset_bb4c81b5-323a-424a-a30f-5c37cdc77642_files' && cp outputdir/combined_reference/*.html '/tmp/tmpy96jvlqm/job_working_directory/000/6/outputs/dataset_bb4c81b5-323a-424a-a30f-5c37cdc77642_files' && if [[ -d "outputdir/icarus_viewers" ]]; then cp -R outputdir/icarus_viewers 'outputdir/combined_reference/'; fi && if [[ -d "outputdir/combined_reference/icarus_viewers" ]]; then cp -R outputdir/combined_reference/icarus_viewers '/tmp/tmpy96jvlqm/job_working_directory/000/6/outputs/dataset_bb4c81b5-323a-424a-a30f-5c37cdc77642_files'; fi && if [[ -d "outputdir/krona_charts/" ]]; then mkdir -p 'None' && cp outputdir/krona_charts/*.html 'None'; fi
              

              • 

            

            Exit Code:
            

              

            • 

              0
              

              • 

            

            Standard Output:
            

              

            • 

              genes_catalogue_test
/usr/local/opt/quast-5.3.0/metaquast.py --pe1 pe1-genes_catalogue_test.fastqsanger.gz --pe2 pe2-genes_catalogue_test.fastqsanger.gz --labels genes_catalogue_test -o outputdir --max-ref-num 0 --min-identity 95.0 --min-contig 1500 --min-alignment 65 --ambiguity-usage one --ambiguity-score 0.99 --local-mis-size 200 --contig-thresholds 0,1000,5000,10000,25000,50000 --extensive-mis-size 1000 --scaffold-gap-max-size 10000 --unaligned-part-size 500 --x-for-Nx 90 /tmp/tmpy96jvlqm/files/5/7/3/dataset_57305f03-dbf4-438b-a90e-7598c7f79c13.dat --threads 1 --no-krona

Version: 5.3.0

System information:
  OS: Linux-6.17.0-1020-azure-x86_64-with-glibc2.36 (linux_64)
  Python version: 3.12.3
  CPUs number: 4

Started: 2026-08-03 09:50:48

Logging to /tmp/tmpy96jvlqm/job_working_directory/000/6/working/outputdir/metaquast.log
WARNING: --ambiguity-usage was set to 'all' because not default --ambiguity-score was specified
INFO	generated new fontManager
INFO	generated new fontManager

Contigs:
  Pre-processing...
  /tmp/tmpy96jvlqm/files/5/7/3/dataset_57305f03-dbf4-438b-a90e-7598c7f79c13.dat ==> genes_catalogue_test

NOTICE: Maximum number of references (--max-ref-number) is set to 0, search in SILVA 16S rRNA database is disabled

NOTICE: No references are provided, starting regular QUAST with MetaGeneMark gene finder
/usr/local/opt/quast-5.3.0/quast.py --pe1 pe1-genes_catalogue_test.fastqsanger.gz --pe2 pe2-genes_catalogue_test.fastqsanger.gz --min-identity 95.0 --min-contig 1500 --min-alignment 65 --ambiguity-usage one --ambiguity-score 0.99 --local-mis-size 200 --contig-thresholds 0,1000,5000,10000,25000,50000 --extensive-mis-size 1000 --scaffold-gap-max-size 10000 --unaligned-part-size 500 --x-for-Nx 90 --threads 1 --no-krona /tmp/tmpy96jvlqm/files/5/7/3/dataset_57305f03-dbf4-438b-a90e-7598c7f79c13.dat -o /tmp/tmpy96jvlqm/job_working_directory/000/6/working/outputdir --labels genes_catalogue_test

Version: 5.3.0

System information:
  OS: Linux-6.17.0-1020-azure-x86_64-with-glibc2.36 (linux_64)
  Python version: 3.12.3
  CPUs number: 4

Started: 2026-08-03 09:50:48

Logging to /tmp/tmpy96jvlqm/job_working_directory/000/6/working/outputdir/quast.log
NOTICE: Output directory already exists and looks like a QUAST output dir. Existing results can be reused (e.g. previously generated alignments)!
WARNING: --ambiguity-usage was set to 'all' because not default --ambiguity-score was specified

CWD: /tmp/tmpy96jvlqm/job_working_directory/000/6/working
Main parameters: 
  MODE: meta, threads: 1, min contig length: 1500, min alignment length: 65, min alignment IDY: 95.0, \
  ambiguity: all, min local misassembly length: 200, min extensive misassembly length: 1000

Contigs:
  Pre-processing...
  /tmp/tmpy96jvlqm/files/5/7/3/dataset_57305f03-dbf4-438b-a90e-7598c7f79c13.dat ==> genes_catalogue_test

2026-08-03 09:50:48
Running Reads analyzer...
NOTICE: Permission denied accessing /usr/local/lib/python3.12/site-packages/quast_libs/gridss. GRIDSS will be downloaded to home directory /tmp/tmpy96jvlqm/job_working_directory/000/6/home/.quast
Downloading gridss (file: gridss-1.4.1.jar)...
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gridss successfully downloaded!
  Logging to files /tmp/tmpy96jvlqm/job_working_directory/000/6/working/outputdir/reads_stats/reads_stats.log and /tmp/tmpy96jvlqm/job_working_directory/000/6/working/outputdir/reads_stats/reads_stats.err...
  Pre-processing reads...
  Running BWA...
  Done.
  Sorting SAM-file...
  Analysis is finished.
  Creating total report...
    saved to /tmp/tmpy96jvlqm/job_working_directory/000/6/working/outputdir/reads_stats/reads_report.txt, reads_report.tsv, and reads_report.tex
Done.

2026-08-03 09:51:27
Running Basic statistics processor...
  Contig files: 
    genes_catalogue_test
  Calculating N50 and L50...
    genes_catalogue_test, N50 = 2144, L50 = 11, auN = 3480.3, Total length = 73179, GC % = 41.99, # N's per 100 kbp =  0.00
  Drawing Nx plot...
    saved to /tmp/tmpy96jvlqm/job_working_directory/000/6/working/outputdir/basic_stats/Nx_plot.pdf
  Drawing cumulative plot...
    saved to /tmp/tmpy96jvlqm/job_working_directory/000/6/working/outputdir/basic_stats/cumulative_plot.pdf
  Drawing GC content plot...
    saved to /tmp/tmpy96jvlqm/job_working_directory/000/6/working/outputdir/basic_stats/GC_content_plot.pdf
  Drawing genes_catalogue_test GC content plot...
    saved to /tmp/tmpy96jvlqm/job_working_directory/000/6/working/outputdir/basic_stats/genes_catalogue_test_GC_content_plot.pdf
Done.

NOTICE: Genes are not predicted by default. Use --gene-finding or --glimmer option to enable it.

2026-08-03 09:51:28
Creating large visual summaries...
This may take a while: press Ctrl-C to skip this step..
  1 of 2: Creating PDF with all tables and plots...
  2 of 2: Creating Icarus viewers...
Done

2026-08-03 09:51:28
RESULTS:
  Text versions of total report are saved to /tmp/tmpy96jvlqm/job_working_directory/000/6/working/outputdir/report.txt, report.tsv, and report.tex
  Text versions of transposed total report are saved to /tmp/tmpy96jvlqm/job_working_directory/000/6/working/outputdir/transposed_report.txt, transposed_report.tsv, and transposed_report.tex
  HTML version (interactive tables and plots) is saved to /tmp/tmpy96jvlqm/job_working_directory/000/6/working/outputdir/report.html
  PDF version (tables and plots) is saved to /tmp/tmpy96jvlqm/job_working_directory/000/6/working/outputdir/report.pdf
  Icarus (contig browser) is saved to /tmp/tmpy96jvlqm/job_working_directory/000/6/working/outputdir/icarus.html
  Log is saved to /tmp/tmpy96jvlqm/job_working_directory/000/6/working/outputdir/quast.log

Finished: 2026-08-03 09:51:28
Elapsed time: 0:00:39.919329
NOTICEs: 3; WARNINGs: 1; non-fatal ERRORs: 0

Thank you for using QUAST!

              

              • 

            

            Traceback:
            

              

            • 

              

              • 

            

            Job Parameters:
            

              

            • 

              


              
Job parameter
Parameter value

              
              


              
__input_ext
"input"

              

              
__workflow_invocation_uuid__
"52ab5fa08f2011f194246045bddb4fd3"

              

              
advanced
{"contig_thresholds": "0,1000,5000,10000,25000,50000", "extensive_mis_size": "1000", "fragmented_max_indent": null, "report_all_metrics": false, "scaffold_gap_max_size": "10000", "skip_unaligned_mis_contigs": true, "strict_NA": false, "unaligned_part_size": "500", "x_for_Nx": "90"}

              

              
alignments
{"ambiguity_score": "0.99", "ambiguity_usage": "one", "fragmented": false, "local_mis_size": "200", "min_alignment": "65", "upper_bound_assembly": false, "upper_bound_min_con": null, "use_all_alignments": false}

              

              
assembly
{"__current_case__": 1, "min_identity": "95.0", "ref": {"__current_case__": 0, "max_ref_num": "0", "origin": "silva"}, "reuse_combined_alignments": false, "type": "metagenome"}

              

              
chromInfo
"/tmp/tmpy96jvlqm/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"

              

              
dbkey
"?"

              

              
genes
{"conserved_genes_finding": false, "gene_finding": {"__current_case__": 0, "tool": "none"}, "rna_finding": false}

              

              
large
false

              

              
min_contig
"1500"

              

              
mode
{"__current_case__": 0, "in": {"__current_case__": 1, "custom": "false", "inputs": {"values": [{"id": 4, "src": "dce"}]}}, "mode": "individual", "reads": {"__current_case__": 3, "input_1": {"values": [{"id": 1, "src": "dce"}]}, "reads_option": "paired_collection"}}

              

              
output_files
["html", "pdf", "tabular", "log", "summary"]

              

              
split_scaffolds
false

              
              

              

              • 

            

            • 

          

          

          • 

        

        • 

      • 

        Step 12: Unlabelled step (toolshed.g2.bx.psu.edu/repos/iuc/pick_value/pick_value/0.2.0):
        

          

        • 

          step_state: scheduled
          

          • 

        • 

          Jobs

            

          • 

            Job 1:
            

              

            • Job state is ok
              • 

            

            Command Line:
            

              

            • 

              cd ../; python _evaluate_expression_.py
              

              • 

            

            Exit Code:
            

              

            • 

              0
              

              • 

            

            Traceback:
            

              

            • 

              

              • 

            

            Job Parameters:
            

              

            • 

              


              
Job parameter
Parameter value

              
              


              
__input_ext
"input"

              

              
__workflow_invocation_uuid__
"52ab5fa08f2011f194246045bddb4fd3"

              

              
chromInfo
"/tmp/tmpy96jvlqm/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"

              

              
dbkey
"?"

              

              
style_cond
{"__current_case__": 1, "pick_style": "first_or_default", "type_cond": {"__current_case__": 3, "default_value": true, "param_type": "boolean", "pick_from": [{"__index__": 0, "value": null}]}}

              
              

              

              • 

            

            • 

          

          

          • 

        

        • 

      • 

        Step 13: Unlabelled step (toolshed.g2.bx.psu.edu/repos/mvdbeek/add_input_name_as_column/addName/0.3.0):
        

          

        • 

          step_state: scheduled
          

          • 

        • 

          Jobs

            

          • 

            Job 1:
            

              

            • Job state is ok
              • 

            

            Container:
            

              

            • 

              quay.io/biocontainers/python:3.13.7
              

              • 

            

            Command Line:
            

              

            • 

              python '/tmp/shed_data/shed_tools/toolshed.g2.bx.psu.edu/repos/mvdbeek/add_input_name_as_column/8a19efbd2178/add_input_name_as_column/add_input_name_as_column.py' --input '/tmp/tmpy96jvlqm/files/e/c/2/dataset_ec214bf9-4ec5-4596-93fc-5733657ff5d5.dat' --label 'genes_catalogue_test' --output '/tmp/tmpy96jvlqm/job_working_directory/000/8/outputs/dataset_a38b23e0-f04c-42e4-9e2c-b32a49de03eb.dat' --prepend
              

              • 

            

            Exit Code:
            

              

            • 

              0
              

              • 

            

            Traceback:
            

              

            • 

              

              • 

            

            Job Parameters:
            

              

            • 

              


              
Job parameter
Parameter value

              
              


              
__input_ext
"input"

              

              
__workflow_invocation_uuid__
"52ab5fa08f2011f194246045bddb4fd3"

              

              
chromInfo
"/tmp/tmpy96jvlqm/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"

              

              
dbkey
"?"

              

              
header
{"__current_case__": 1, "contains_header": "no"}

              

              
prepend
true

              
              

              

              • 

            

            • 

          

          

          • 

        

        • 

      • 

        Step 14: Unlabelled step (toolshed.g2.bx.psu.edu/repos/devteam/tabular_to_fasta/tab2fasta/1.1.1):
        

          

        • 

          step_state: scheduled
          

          • 

        • 

          Jobs

            

          • 

            Job 1:
            

              

            • Job state is ok
              • 

            

            Container:
            

              

            • 

              quay.io/biocontainers/python:3.7--1
              

              • 

            

            Command Line:
            

              

            • 

              python '/tmp/shed_data/shed_tools/toolshed.g2.bx.psu.edu/repos/devteam/tabular_to_fasta/0a7799698fe5/tabular_to_fasta/tabular_to_fasta.py' '/tmp/tmpy96jvlqm/files/a/3/8/dataset_a38b23e0-f04c-42e4-9e2c-b32a49de03eb.dat' 1,2 3 '/tmp/tmpy96jvlqm/job_working_directory/000/9/outputs/dataset_6b549a60-cafe-4737-b064-e02aa8aca1f6.dat'
              

              • 

            

            Exit Code:
            

              

            • 

              0
              

              • 

            

            Traceback:
            

              

            • 

              

              • 

            

            Job Parameters:
            

              

            • 

              


              
Job parameter
Parameter value

              
              


              
__input_ext
"input"

              

              
__workflow_invocation_uuid__
"52ab5fa08f2011f194246045bddb4fd3"

              

              
chromInfo
"/tmp/tmpy96jvlqm/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"

              

              
dbkey
"?"

              

              
seq_col
"3"

              

              
title_col
["1", "2"]

              
              

              

              • 

            

            • 

          

          

          • 

        

        • 

      • 

        Step 15: Unlabelled step (toolshed.g2.bx.psu.edu/repos/iuc/prodigal/prodigal/2.6.3+galaxy0):
        

          

        • 

          step_state: scheduled
          

          • 

        • 

          Jobs

            

          • 

            Job 1:
            

              

            • Job state is ok
              • 

            

            Container:
            

              

            • 

              quay.io/biocontainers/prodigal:2.6.3--h577a1d6_11
              

              • 

            

            Command Line:
            

              

            • 

              prodigal -i '/tmp/tmpy96jvlqm/files/6/b/5/dataset_6b549a60-cafe-4737-b064-e02aa8aca1f6.dat' -o '/tmp/tmpy96jvlqm/job_working_directory/000/10/outputs/dataset_c0ed92d6-1729-417f-8caf-d7792ec167fc.dat' -f 'gbk' -p 'meta' -g '11' -a '/tmp/tmpy96jvlqm/job_working_directory/000/10/outputs/dataset_fa955743-b8df-4656-a4a5-96fbbab9f8b0.dat' -d '/tmp/tmpy96jvlqm/job_working_directory/000/10/outputs/dataset_c7acf1b1-f967-4ca4-b29b-1946e69db694.dat' -s '/tmp/tmpy96jvlqm/job_working_directory/000/10/outputs/dataset_4a6a5d04-6030-4c71-baa3-99612b6768f9.dat'
              

              • 

            

            Exit Code:
            

              

            • 

              0
              

              • 

            

            Standard Error:
            

              

            • 

              -------------------------------------
PRODIGAL v2.6.3 [February, 2016]         
Univ of Tenn / Oak Ridge National Lab
Doug Hyatt, Loren Hauser, et al.     
-------------------------------------
Request:  Metagenomic, Phase:  Training
Initializing training files...done!
-------------------------------------
Request:  Metagenomic, Phase:  Gene Finding
Finding genes in sequence #1 (502 bp)...done!
Finding genes in sequence #2 (781 bp)...done!
Finding genes in sequence #3 (580 bp)...done!
Finding genes in sequence #4 (418 bp)...done!
Finding genes in sequence #5 (891 bp)...done!
Finding genes in sequence #6 (573 bp)...done!
Finding genes in sequence #7 (500 bp)...done!
Finding genes in sequence #8 (445 bp)...done!
Finding genes in sequence #9 (317 bp)...done!
Finding genes in sequence #10 (481 bp)...done!
Finding genes in sequence #11 (357 bp)...done!
Finding genes in sequence #12 (487 bp)...done!
Finding genes in sequence #13 (639 bp)...done!
Finding genes in sequence #14 (346 bp)...done!
Finding genes in sequence #15 (421 bp)...done!
Finding genes in sequence #16 (402 bp)...done!
Finding genes in sequence #17 (452 bp)...done!
Finding genes in sequence #18 (326 bp)...done!
Finding genes in sequence #19 (491 bp)...done!
Finding genes in sequence #20 (326 bp)...done!
Finding genes in sequence #21 (492 bp)...done!
Finding genes in sequence #22 (336 bp)...done!
Finding genes in sequence #23 (571 bp)...done!
Finding genes in sequence #24 (306 bp)...done!
Finding genes in sequence #25 (340 bp)...done!
Finding genes in sequence #26 (370 bp)...done!
Finding genes in sequence #27 (347 bp)...done!
Finding genes in sequence #28 (315 bp)...done!
Finding genes in sequence #29 (350 bp)...done!
Finding genes in sequence #30 (355 bp)...done!
Finding genes in sequence #31 (414 bp)...done!
Finding genes in sequence #32 (341 bp)...done!
Finding genes in sequence #33 (677 bp)...done!
Finding genes in sequence #34 (347 bp)...done!
Finding genes in sequence #35 (307 bp)...done!
Finding genes in sequence #36 (396 bp)...done!
Finding genes in sequence #37 (317 bp)...done!
Finding genes in sequence #38 (750 bp)...done!
Finding genes in sequence #39 (538 bp)...done!
Finding genes in sequence #40 (335 bp)...done!
Finding genes in sequence #41 (348 bp)...done!
Finding genes in sequence #42 (364 bp)...done!
Finding genes in sequence #43 (345 bp)...done!
Finding genes in sequence #44 (332 bp)...done!
Finding genes in sequence #45 (374 bp)...done!
Finding genes in sequence #46 (397 bp)...done!
Finding genes in sequence #47 (391 bp)...done!
Finding genes in sequence #48 (626 bp)...done!
Finding genes in sequence #49 (484 bp)...done!
Finding genes in sequence #50 (351 bp)...done!
Finding genes in sequence #51 (536 bp)...done!
Finding genes in sequence #52 (400 bp)...done!
Finding genes in sequence #53 (417 bp)...done!
Finding genes in sequence #54 (574 bp)...done!
Finding genes in sequence #55 (392 bp)...done!
Finding genes in sequence #56 (960 bp)...done!
Finding genes in sequence #57 (557 bp)...done!
Finding genes in sequence #58 (365 bp)...done!
Finding genes in sequence #59 (352 bp)...done!
Finding genes in sequence #60 (640 bp)...done!
Finding genes in sequence #61 (443 bp)...done!
Finding genes in sequence #62 (334 bp)...done!
Finding genes in sequence #63 (517 bp)...done!
Finding genes in sequence #64 (385 bp)...done!
Finding genes in sequence #65 (463 bp)...done!
Finding genes in sequence #66 (606 bp)...done!
Finding genes in sequence #67 (307 bp)...done!
Finding genes in sequence #68 (319 bp)...done!
Finding genes in sequence #69 (308 bp)...done!
Finding genes in sequence #70 (446 bp)...done!
Finding genes in sequence #71 (358 bp)...done!
Finding genes in sequence #72 (484 bp)...done!
Finding genes in sequence #73 (424 bp)...done!
Finding genes in sequence #74 (571 bp)...done!
Finding genes in sequence #75 (525 bp)...done!
Finding genes in sequence #76 (490 bp)...done!
Finding genes in sequence #77 (373 bp)...done!
Finding genes in sequence #78 (434 bp)...done!
Finding genes in sequence #79 (463 bp)...done!
Finding genes in sequence #80 (522 bp)...done!
Finding genes in sequence #81 (492 bp)...done!
Finding genes in sequence #82 (544 bp)...done!
Finding genes in sequence #83 (472 bp)...done!
Finding genes in sequence #84 (423 bp)...done!
Finding genes in sequence #85 (395 bp)...done!
Finding genes in sequence #86 (337 bp)...done!
Finding genes in sequence #87 (442 bp)...done!
Finding genes in sequence #88 (446 bp)...done!
Finding genes in sequence #89 (310 bp)...done!
Finding genes in sequence #90 (464 bp)...done!
Finding genes in sequence #91 (311 bp)...done!
Finding genes in sequence #92 (636 bp)...done!
Finding genes in sequence #93 (444 bp)...done!
Finding genes in sequence #94 (615 bp)...done!
Finding genes in sequence #95 (599 bp)...done!
Finding genes in sequence #96 (684 bp)...done!
Finding genes in sequence #97 (461 bp)...done!
Finding genes in sequence #98 (544 bp)...done!
Finding genes in sequence #99 (616 bp)...done!
Finding genes in sequence #100 (485 bp)...done!
Finding genes in sequence #101 (303 bp)...done!
Finding genes in sequence #102 (439 bp)...done!
Finding genes in sequence #103 (367 bp)...done!
Finding genes in sequence #104 (418 bp)...done!
Finding genes in sequence #105 (302 bp)...done!
Finding genes in sequence #106 (533 bp)...done!
Finding genes in sequence #107 (355 bp)...done!
Finding genes in sequence #108 (390 bp)...done!
Finding genes in sequence #109 (520 bp)...done!
Finding genes in sequence #110 (529 bp)...done!
Finding genes in sequence #111 (379 bp)...done!
Finding genes in sequence #112 (341 bp)...done!
Finding genes in sequence #113 (1222 bp)...done!
Finding genes in sequence #114 (338 bp)...done!
Finding genes in sequence #115 (305 bp)...done!
Finding genes in sequence #116 (500 bp)...done!
Finding genes in sequence #117 (357 bp)...done!
Finding genes in sequence #118 (458 bp)...done!
Finding genes in sequence #119 (637 bp)...done!
Finding genes in sequence #120 (357 bp)...done!
Finding genes in sequence #121 (347 bp)...done!
Finding genes in sequence #122 (350 bp)...done!
Finding genes in sequence #123 (584 bp)...done!
Finding genes in sequence #124 (522 bp)...done!
Finding genes in sequence #125 (354 bp)...done!
Finding genes in sequence #126 (549 bp)...done!
Finding genes in sequence #127 (311 bp)...done!
Finding genes in sequence #128 (455 bp)...done!
Finding genes in sequence #129 (368 bp)...done!
Finding genes in sequence #130 (728 bp)...done!
Finding genes in sequence #131 (385 bp)...done!
Finding genes in sequence #132 (506 bp)...done!
Finding genes in sequence #133 (319 bp)...done!
Finding genes in sequence #134 (303 bp)...done!
Finding genes in sequence #135 (311 bp)...done!
Finding genes in sequence #136 (308 bp)...done!
Finding genes in sequence #137 (319 bp)...done!
Finding genes in sequence #138 (653 bp)...done!
Finding genes in sequence #139 (303 bp)...done!
Finding genes in sequence #140 (480 bp)...done!
Finding genes in sequence #141 (451 bp)...done!
Finding genes in sequence #142 (696 bp)...done!
Finding genes in sequence #143 (394 bp)...done!
Finding genes in sequence #144 (869 bp)...done!
Finding genes in sequence #145 (501 bp)...done!
Finding genes in sequence #146 (305 bp)...done!
Finding genes in sequence #147 (406 bp)...done!
Finding genes in sequence #148 (697 bp)...done!
Finding genes in sequence #149 (326 bp)...done!
Finding genes in sequence #150 (495 bp)...done!
Finding genes in sequence #151 (474 bp)...done!
Finding genes in sequence #152 (617 bp)...done!
Finding genes in sequence #153 (325 bp)...done!
Finding genes in sequence #154 (304 bp)...done!
Finding genes in sequence #155 (430 bp)...done!
Finding genes in sequence #156 (319 bp)...done!
Finding genes in sequence #157 (343 bp)...done!
Finding genes in sequence #158 (453 bp)...done!
Finding genes in sequence #159 (397 bp)...done!
Finding genes in sequence #160 (413 bp)...done!
Finding genes in sequence #161 (305 bp)...done!
Finding genes in sequence #162 (434 bp)...done!
Finding genes in sequence #163 (313 bp)...done!
Finding genes in sequence #164 (313 bp)...done!
Finding genes in sequence #165 (312 bp)...done!
Finding genes in sequence #166 (379 bp)...done!
Finding genes in sequence #167 (314 bp)...done!
Finding genes in sequence #168 (404 bp)...done!
Finding genes in sequence #169 (353 bp)...done!
Finding genes in sequence #170 (306 bp)...done!
Finding genes in sequence #171 (525 bp)...done!
Finding genes in sequence #172 (428 bp)...done!
Finding genes in sequence #173 (598 bp)...done!
Finding genes in sequence #174 (309 bp)...done!
Finding genes in sequence #175 (324 bp)...done!
Finding genes in sequence #176 (353 bp)...done!
Finding genes in sequence #177 (627 bp)...done!
Finding genes in sequence #178 (364 bp)...done!
Finding genes in sequence #179 (348 bp)...done!
Finding genes in sequence #180 (331 bp)...done!
Finding genes in sequence #181 (478 bp)...done!
Finding genes in sequence #182 (316 bp)...done!
Finding genes in sequence #183 (327 bp)...done!
Finding genes in sequence #184 (649 bp)...done!
Finding genes in sequence #185 (357 bp)...done!
Finding genes in sequence #186 (384 bp)...done!
Finding genes in sequence #187 (414 bp)...done!
Finding genes in sequence #188 (406 bp)...done!
Finding genes in sequence #189 (725 bp)...done!
Finding genes in sequence #190 (305 bp)...done!
Finding genes in sequence #191 (939 bp)...done!
Finding genes in sequence #192 (392 bp)...done!
Finding genes in sequence #193 (467 bp)...done!
Finding genes in sequence #194 (347 bp)...done!
Finding genes in sequence #195 (350 bp)...done!
Finding genes in sequence #196 (904 bp)...done!
Finding genes in sequence #197 (724 bp)...done!
Finding genes in sequence #198 (455 bp)...done!
Finding genes in sequence #199 (348 bp)...done!
Finding genes in sequence #200 (805 bp)...done!
Finding genes in sequence #201 (323 bp)...done!
Finding genes in sequence #202 (424 bp)...done!
Finding genes in sequence #203 (321 bp)...done!
Finding genes in sequence #204 (794 bp)...done!
Finding genes in sequence #205 (533 bp)...done!
Finding genes in sequence #206 (458 bp)...done!
Finding genes in sequence #207 (336 bp)...done!
Finding genes in sequence #208 (506 bp)...done!
Finding genes in sequence #209 (577 bp)...done!
Finding genes in sequence #210 (347 bp)...done!
Finding genes in sequence #211 (433 bp)...done!
Finding genes in sequence #212 (568 bp)...done!
Finding genes in sequence #213 (378 bp)...done!
Finding genes in sequence #214 (583 bp)...done!
Finding genes in sequence #215 (303 bp)...done!
Finding genes in sequence #216 (624 bp)...done!
Finding genes in sequence #217 (575 bp)...done!
Finding genes in sequence #218 (362 bp)...done!
Finding genes in sequence #219 (779 bp)...done!
Finding genes in sequence #220 (306 bp)...done!
Finding genes in sequence #221 (378 bp)...done!
Finding genes in sequence #222 (554 bp)...done!
Finding genes in sequence #223 (514 bp)...done!
Finding genes in sequence #224 (378 bp)...done!
Finding genes in sequence #225 (474 bp)...done!
Finding genes in sequence #226 (392 bp)...done!
Finding genes in sequence #227 (455 bp)...done!
Finding genes in sequence #228 (469 bp)...done!
Finding genes in sequence #229 (562 bp)...done!
Finding genes in sequence #230 (365 bp)...done!
Finding genes in sequence #231 (345 bp)...done!
Finding genes in sequence #232 (387 bp)...done!
Finding genes in sequence #233 (467 bp)...done!
Finding genes in sequence #234 (409 bp)...done!
Finding genes in sequence #235 (335 bp)...done!
Finding genes in sequence #236 (488 bp)...done!
Finding genes in sequence #237 (323 bp)...done!
Finding genes in sequence #238 (438 bp)...done!
Finding genes in sequence #239 (305 bp)...done!
Finding genes in sequence #240 (319 bp)...done!
Finding genes in sequence #241 (904 bp)...done!
Finding genes in sequence #242 (612 bp)...done!
Finding genes in sequence #243 (332 bp)...done!
Finding genes in sequence #244 (353 bp)...done!
Finding genes in sequence #245 (315 bp)...done!
Finding genes in sequence #246 (785 bp)...done!
Finding genes in sequence #247 (350 bp)...done!
Finding genes in sequence #248 (822 bp)...done!
Finding genes in sequence #249 (243 bp)...done!
Finding genes in sequence #250 (511 bp)...done!
Finding genes in sequence #251 (532 bp)...done!
Finding genes in sequence #252 (365 bp)...done!
Finding genes in sequence #253 (305 bp)...done!
Finding genes in sequence #254 (394 bp)...done!
Finding genes in sequence #255 (315 bp)...done!
Finding genes in sequence #256 (357 bp)...done!
Finding genes in sequence #257 (508 bp)...done!
Finding genes in sequence #258 (322 bp)...done!
Finding genes in sequence #259 (357 bp)...done!
Finding genes in sequence #260 (415 bp)...done!
Finding genes in sequence #261 (488 bp)...done!
Finding genes in sequence #262 (489 bp)...done!
Finding genes in sequence #263 (412 bp)...done!
Finding genes in sequence #264 (357 bp)...done!
Finding genes in sequence #265 (330 bp)...done!
Finding genes in sequence #266 (800 bp)...done!
Finding genes in sequence #267 (309 bp)...done!
Finding genes in sequence #268 (312 bp)...done!
Finding genes in sequence #269 (321 bp)...done!
Finding genes in sequence #270 (635 bp)...done!
Finding genes in sequence #271 (467 bp)...done!
Finding genes in sequence #272 (380 bp)...done!
Finding genes in sequence #273 (487 bp)...done!
Finding genes in sequence #274 (384 bp)...done!
Finding genes in sequence #275 (1374 bp)...done!
Finding genes in sequence #276 (374 bp)...done!
Finding genes in sequence #277 (364 bp)...done!
Finding genes in sequence #278 (415 bp)...done!
Finding genes in sequence #279 (594 bp)...done!
Finding genes in sequence #280 (355 bp)...done!
Finding genes in sequence #281 (328 bp)...done!
Finding genes in sequence #282 (339 bp)...done!
Finding genes in sequence #283 (334 bp)...done!
Finding genes in sequence #284 (521 bp)...done!
Finding genes in sequence #285 (391 bp)...done!
Finding genes in sequence #286 (573 bp)...done!
Finding genes in sequence #287 (444 bp)...done!
Finding genes in sequence #288 (349 bp)...done!
Finding genes in sequence #289 (329 bp)...done!
Finding genes in sequence #290 (393 bp)...done!
Finding genes in sequence #291 (468 bp)...done!
Finding genes in sequence #292 (2347 bp)...done!
Finding genes in sequence #293 (619 bp)...done!
Finding genes in sequence #294 (401 bp)...done!
Finding genes in sequence #295 (354 bp)...done!
Finding genes in sequence #296 (520 bp)...done!
Finding genes in sequence #297 (332 bp)...done!
Finding genes in sequence #298 (504 bp)...done!
Finding genes in sequence #299 (322 bp)...done!
Finding genes in sequence #300 (628 bp)...done!
Finding genes in sequence #301 (576 bp)...done!
Finding genes in sequence #302 (350 bp)...done!
Finding genes in sequence #303 (384 bp)...done!
Finding genes in sequence #304 (624 bp)...done!
Finding genes in sequence #305 (809 bp)...done!
Finding genes in sequence #306 (402 bp)...done!
Finding genes in sequence #307 (306 bp)...done!
Finding genes in sequence #308 (365 bp)...done!
Finding genes in sequence #309 (310 bp)...done!
Finding genes in sequence #310 (404 bp)...done!
Finding genes in sequence #311 (436 bp)...done!
Finding genes in sequence #312 (309 bp)...done!
Finding genes in sequence #313 (412 bp)...done!
Finding genes in sequence #314 (340 bp)...done!
Finding genes in sequence #315 (449 bp)...done!
Finding genes in sequence #316 (338 bp)...done!
Finding genes in sequence #317 (336 bp)...done!
Finding genes in sequence #318 (352 bp)...done!
Finding genes in sequence #319 (395 bp)...done!
Finding genes in sequence #320 (1014 bp)...done!
Finding genes in sequence #321 (386 bp)...done!
Finding genes in sequence #322 (401 bp)...done!
Finding genes in sequence #323 (337 bp)...done!
Finding genes in sequence #324 (310 bp)...done!
Finding genes in sequence #325 (464 bp)...done!
Finding genes in sequence #326 (450 bp)...done!
Finding genes in sequence #327 (332 bp)...done!
Finding genes in sequence #328 (311 bp)...done!
Finding genes in sequence #329 (424 bp)...done!
Finding genes in sequence #330 (345 bp)...done!
Finding genes in sequence #331 (541 bp)...done!
Finding genes in sequence #332 (432 bp)...done!
Finding genes in sequence #333 (576 bp)...done!
Finding genes in sequence #334 (348 bp)...done!
Finding genes in sequence #335 (420 bp)...done!
Finding genes in sequence #336 (383 bp)...done!
Findin
..
ne!
Finding genes in sequence #3452 (311 bp)...done!
Finding genes in sequence #3453 (620 bp)...done!
Finding genes in sequence #3454 (354 bp)...done!
Finding genes in sequence #3455 (485 bp)...done!
Finding genes in sequence #3456 (338 bp)...done!
Finding genes in sequence #3457 (715 bp)...done!
Finding genes in sequence #3458 (372 bp)...done!
Finding genes in sequence #3459 (438 bp)...done!
Finding genes in sequence #3460 (707 bp)...done!
Finding genes in sequence #3461 (417 bp)...done!
Finding genes in sequence #3462 (403 bp)...done!
Finding genes in sequence #3463 (452 bp)...done!
Finding genes in sequence #3464 (317 bp)...done!
Finding genes in sequence #3465 (312 bp)...done!
Finding genes in sequence #3466 (499 bp)...done!
Finding genes in sequence #3467 (322 bp)...done!
Finding genes in sequence #3468 (326 bp)...done!
Finding genes in sequence #3469 (397 bp)...done!
Finding genes in sequence #3470 (308 bp)...done!
Finding genes in sequence #3471 (412 bp)...done!
Finding genes in sequence #3472 (566 bp)...done!
Finding genes in sequence #3473 (361 bp)...done!
Finding genes in sequence #3474 (355 bp)...done!
Finding genes in sequence #3475 (370 bp)...done!
Finding genes in sequence #3476 (368 bp)...done!
Finding genes in sequence #3477 (498 bp)...done!
Finding genes in sequence #3478 (346 bp)...done!
Finding genes in sequence #3479 (338 bp)...done!
Finding genes in sequence #3480 (476 bp)...done!
Finding genes in sequence #3481 (900 bp)...done!
Finding genes in sequence #3482 (470 bp)...done!
Finding genes in sequence #3483 (304 bp)...done!
Finding genes in sequence #3484 (310 bp)...done!
Finding genes in sequence #3485 (347 bp)...done!
Finding genes in sequence #3486 (394 bp)...done!
Finding genes in sequence #3487 (344 bp)...done!
Finding genes in sequence #3488 (350 bp)...done!
Finding genes in sequence #3489 (727 bp)...done!
Finding genes in sequence #3490 (483 bp)...done!
Finding genes in sequence #3491 (325 bp)...done!
Finding genes in sequence #3492 (707 bp)...done!
Finding genes in sequence #3493 (330 bp)...done!
Finding genes in sequence #3494 (391 bp)...done!
Finding genes in sequence #3495 (391 bp)...done!
Finding genes in sequence #3496 (414 bp)...done!
Finding genes in sequence #3497 (807 bp)...done!
Finding genes in sequence #3498 (423 bp)...done!
Finding genes in sequence #3499 (340 bp)...done!
Finding genes in sequence #3500 (698 bp)...done!
Finding genes in sequence #3501 (373 bp)...done!
Finding genes in sequence #3502 (324 bp)...done!
Finding genes in sequence #3503 (339 bp)...done!
Finding genes in sequence #3504 (392 bp)...done!
Finding genes in sequence #3505 (350 bp)...done!
Finding genes in sequence #3506 (377 bp)...done!
Finding genes in sequence #3507 (482 bp)...done!
Finding genes in sequence #3508 (399 bp)...done!
Finding genes in sequence #3509 (533 bp)...done!
Finding genes in sequence #3510 (342 bp)...done!
Finding genes in sequence #3511 (324 bp)...done!
Finding genes in sequence #3512 (433 bp)...done!
Finding genes in sequence #3513 (644 bp)...done!
Finding genes in sequence #3514 (323 bp)...done!
Finding genes in sequence #3515 (652 bp)...done!
Finding genes in sequence #3516 (406 bp)...done!
Finding genes in sequence #3517 (526 bp)...done!
Finding genes in sequence #3518 (354 bp)...done!
Finding genes in sequence #3519 (392 bp)...done!
Finding genes in sequence #3520 (544 bp)...done!
Finding genes in sequence #3521 (393 bp)...done!
Finding genes in sequence #3522 (342 bp)...done!
Finding genes in sequence #3523 (449 bp)...done!
Finding genes in sequence #3524 (310 bp)...done!
Finding genes in sequence #3525 (406 bp)...done!
Finding genes in sequence #3526 (401 bp)...done!
Finding genes in sequence #3527 (1019 bp)...done!
Finding genes in sequence #3528 (335 bp)...done!
Finding genes in sequence #3529 (333 bp)...done!
Finding genes in sequence #3530 (725 bp)...done!
Finding genes in sequence #3531 (570 bp)...done!
Finding genes in sequence #3532 (324 bp)...done!
Finding genes in sequence #3533 (383 bp)...done!
Finding genes in sequence #3534 (499 bp)...done!
Finding genes in sequence #3535 (342 bp)...done!
Finding genes in sequence #3536 (311 bp)...done!
Finding genes in sequence #3537 (312 bp)...done!
Finding genes in sequence #3538 (357 bp)...done!
Finding genes in sequence #3539 (335 bp)...done!
Finding genes in sequence #3540 (337 bp)...done!
Finding genes in sequence #3541 (318 bp)...done!
Finding genes in sequence #3542 (353 bp)...done!
Finding genes in sequence #3543 (698 bp)...done!
Finding genes in sequence #3544 (325 bp)...done!
Finding genes in sequence #3545 (585 bp)...done!
Finding genes in sequence #3546 (503 bp)...done!
Finding genes in sequence #3547 (542 bp)...done!
Finding genes in sequence #3548 (499 bp)...done!
Finding genes in sequence #3549 (625 bp)...done!
Finding genes in sequence #3550 (335 bp)...done!
Finding genes in sequence #3551 (520 bp)...done!
Finding genes in sequence #3552 (892 bp)...done!
Finding genes in sequence #3553 (634 bp)...done!
Finding genes in sequence #3554 (472 bp)...done!
Finding genes in sequence #3555 (350 bp)...done!
Finding genes in sequence #3556 (420 bp)...done!
Finding genes in sequence #3557 (397 bp)...done!
Finding genes in sequence #3558 (663 bp)...done!
Finding genes in sequence #3559 (2276 bp)...done!
Finding genes in sequence #3560 (407 bp)...done!
Finding genes in sequence #3561 (368 bp)...done!
Finding genes in sequence #3562 (405 bp)...done!
Finding genes in sequence #3563 (556 bp)...done!
Finding genes in sequence #3564 (699 bp)...done!
Finding genes in sequence #3565 (324 bp)...done!
Finding genes in sequence #3566 (542 bp)...done!
Finding genes in sequence #3567 (536 bp)...done!
Finding genes in sequence #3568 (573 bp)...done!
Finding genes in sequence #3569 (330 bp)...done!
Finding genes in sequence #3570 (315 bp)...done!
Finding genes in sequence #3571 (313 bp)...done!
Finding genes in sequence #3572 (345 bp)...done!
Finding genes in sequence #3573 (330 bp)...done!
Finding genes in sequence #3574 (388 bp)...done!
Finding genes in sequence #3575 (315 bp)...done!
Finding genes in sequence #3576 (336 bp)...done!
Finding genes in sequence #3577 (333 bp)...done!
Finding genes in sequence #3578 (307 bp)...done!
Finding genes in sequence #3579 (362 bp)...done!
Finding genes in sequence #3580 (347 bp)...done!
Finding genes in sequence #3581 (359 bp)...done!
Finding genes in sequence #3582 (442 bp)...done!
Finding genes in sequence #3583 (357 bp)...done!
Finding genes in sequence #3584 (361 bp)...done!
Finding genes in sequence #3585 (604 bp)...done!
Finding genes in sequence #3586 (351 bp)...done!
Finding genes in sequence #3587 (433 bp)...done!
Finding genes in sequence #3588 (394 bp)...done!
Finding genes in sequence #3589 (450 bp)...done!
Finding genes in sequence #3590 (330 bp)...done!
Finding genes in sequence #3591 (319 bp)...done!
Finding genes in sequence #3592 (309 bp)...done!
Finding genes in sequence #3593 (736 bp)...done!
Finding genes in sequence #3594 (437 bp)...done!
Finding genes in sequence #3595 (301 bp)...done!
Finding genes in sequence #3596 (331 bp)...done!
Finding genes in sequence #3597 (666 bp)...done!
Finding genes in sequence #3598 (348 bp)...done!
Finding genes in sequence #3599 (585 bp)...done!
Finding genes in sequence #3600 (301 bp)...done!
Finding genes in sequence #3601 (500 bp)...done!
Finding genes in sequence #3602 (337 bp)...done!
Finding genes in sequence #3603 (327 bp)...done!
Finding genes in sequence #3604 (515 bp)...done!
Finding genes in sequence #3605 (671 bp)...done!
Finding genes in sequence #3606 (371 bp)...done!
Finding genes in sequence #3607 (848 bp)...done!
Finding genes in sequence #3608 (425 bp)...done!
Finding genes in sequence #3609 (350 bp)...done!
Finding genes in sequence #3610 (351 bp)...done!
Finding genes in sequence #3611 (1005 bp)...done!
Finding genes in sequence #3612 (1118 bp)...done!
Finding genes in sequence #3613 (439 bp)...done!
Finding genes in sequence #3614 (351 bp)...done!
Finding genes in sequence #3615 (328 bp)...done!
Finding genes in sequence #3616 (364 bp)...done!
Finding genes in sequence #3617 (493 bp)...done!
Finding genes in sequence #3618 (441 bp)...done!
Finding genes in sequence #3619 (652 bp)...done!
Finding genes in sequence #3620 (322 bp)...done!
Finding genes in sequence #3621 (601 bp)...done!
Finding genes in sequence #3622 (407 bp)...done!
Finding genes in sequence #3623 (462 bp)...done!
Finding genes in sequence #3624 (947 bp)...done!
Finding genes in sequence #3625 (473 bp)...done!
Finding genes in sequence #3626 (401 bp)...done!
Finding genes in sequence #3627 (715 bp)...done!
Finding genes in sequence #3628 (616 bp)...done!
Finding genes in sequence #3629 (342 bp)...done!
Finding genes in sequence #3630 (313 bp)...done!
Finding genes in sequence #3631 (487 bp)...done!
Finding genes in sequence #3632 (511 bp)...done!
Finding genes in sequence #3633 (320 bp)...done!
Finding genes in sequence #3634 (330 bp)...done!
Finding genes in sequence #3635 (353 bp)...done!
Finding genes in sequence #3636 (465 bp)...done!
Finding genes in sequence #3637 (516 bp)...done!
Finding genes in sequence #3638 (411 bp)...done!
Finding genes in sequence #3639 (597 bp)...done!
Finding genes in sequence #3640 (301 bp)...done!
Finding genes in sequence #3641 (581 bp)...done!
Finding genes in sequence #3642 (421 bp)...done!
Finding genes in sequence #3643 (367 bp)...done!
Finding genes in sequence #3644 (433 bp)...done!
Finding genes in sequence #3645 (391 bp)...done!
Finding genes in sequence #3646 (357 bp)...done!
Finding genes in sequence #3647 (316 bp)...done!
Finding genes in sequence #3648 (415 bp)...done!
Finding genes in sequence #3649 (364 bp)...done!
Finding genes in sequence #3650 (522 bp)...done!
Finding genes in sequence #3651 (614 bp)...done!
Finding genes in sequence #3652 (357 bp)...done!
Finding genes in sequence #3653 (348 bp)...done!
Finding genes in sequence #3654 (430 bp)...done!
Finding genes in sequence #3655 (340 bp)...done!
Finding genes in sequence #3656 (313 bp)...done!
Finding genes in sequence #3657 (328 bp)...done!
Finding genes in sequence #3658 (569 bp)...done!
Finding genes in sequence #3659 (607 bp)...done!
Finding genes in sequence #3660 (437 bp)...done!
Finding genes in sequence #3661 (354 bp)...done!
Finding genes in sequence #3662 (382 bp)...done!
Finding genes in sequence #3663 (354 bp)...done!
Finding genes in sequence #3664 (541 bp)...done!
Finding genes in sequence #3665 (346 bp)...done!
Finding genes in sequence #3666 (314 bp)...done!
Finding genes in sequence #3667 (332 bp)...done!
Finding genes in sequence #3668 (367 bp)...done!
Finding genes in sequence #3669 (632 bp)...done!
Finding genes in sequence #3670 (304 bp)...done!
Finding genes in sequence #3671 (373 bp)...done!
Finding genes in sequence #3672 (1327 bp)...done!
Finding genes in sequence #3673 (488 bp)...done!
Finding genes in sequence #3674 (860 bp)...done!
Finding genes in sequence #3675 (482 bp)...done!
Finding genes in sequence #3676 (349 bp)...done!
Finding genes in sequence #3677 (383 bp)...done!
Finding genes in sequence #3678 (343 bp)...done!
Finding genes in sequence #3679 (437 bp)...done!
Finding genes in sequence #3680 (1384 bp)...done!
Finding genes in sequence #3681 (485 bp)...done!
Finding genes in sequence #3682 (472 bp)...done!
Finding genes in sequence #3683 (315 bp)...done!
Finding genes in sequence #3684 (397 bp)...done!
Finding genes in sequence #3685 (406 bp)...done!
Finding genes in sequence #3686 (411 bp)...done!
Finding genes in sequence #3687 (498 bp)...done!
Finding genes in sequence #3688 (452 bp)...done!
Finding genes in sequence #3689 (376 bp)...done!
Finding genes in sequence #3690 (503 bp)...done!
Finding genes in sequence #3691 (333 bp)...done!
Finding genes in sequence #3692 (335 bp)...done!
Finding genes in sequence #3693 (369 bp)...done!
Finding genes in sequence #3694 (361 bp)...done!
Finding genes in sequence #3695 (304 bp)...done!
Finding genes in sequence #3696 (427 bp)...done!
Finding genes in sequence #3697 (442 bp)...done!
Finding genes in sequence #3698 (355 bp)...done!
Finding genes in sequence #3699 (347 bp)...done!
Finding genes in sequence #3700 (410 bp)...done!
Finding genes in sequence #3701 (414 bp)...done!
Finding genes in sequence #3702 (314 bp)...done!
Finding genes in sequence #3703 (338 bp)...done!
Finding genes in sequence #3704 (363 bp)...done!
Finding genes in sequence #3705 (343 bp)...done!
Finding genes in sequence #3706 (780 bp)...done!
Finding genes in sequence #3707 (441 bp)...done!
Finding genes in sequence #3708 (311 bp)...done!
Finding genes in sequence #3709 (307 bp)...done!
Finding genes in sequence #3710 (403 bp)...done!
Finding genes in sequence #3711 (610 bp)...done!
Finding genes in sequence #3712 (523 bp)...done!
Finding genes in sequence #3713 (670 bp)...done!
Finding genes in sequence #3714 (535 bp)...done!
Finding genes in sequence #3715 (337 bp)...done!
Finding genes in sequence #3716 (346 bp)...done!
Finding genes in sequence #3717 (623 bp)...done!
Finding genes in sequence #3718 (312 bp)...done!
Finding genes in sequence #3719 (341 bp)...done!
Finding genes in sequence #3720 (506 bp)...done!
Finding genes in sequence #3721 (373 bp)...done!
Finding genes in sequence #3722 (325 bp)...done!
Finding genes in sequence #3723 (578 bp)...done!
Finding genes in sequence #3724 (416 bp)...done!
Finding genes in sequence #3725 (2267 bp)...done!
Finding genes in sequence #3726 (546 bp)...done!
Finding genes in sequence #3727 (378 bp)...done!
Finding genes in sequence #3728 (309 bp)...done!
Finding genes in sequence #3729 (363 bp)...done!
Finding genes in sequence #3730 (359 bp)...done!
Finding genes in sequence #3731 (731 bp)...done!
Finding genes in sequence #3732 (340 bp)...done!
Finding genes in sequence #3733 (412 bp)...done!
Finding genes in sequence #3734 (488 bp)...done!
Finding genes in sequence #3735 (500 bp)...done!
Finding genes in sequence #3736 (526 bp)...done!
Finding genes in sequence #3737 (1476 bp)...done!
Finding genes in sequence #3738 (376 bp)...done!
Finding genes in sequence #3739 (319 bp)...done!
Finding genes in sequence #3740 (430 bp)...done!
Finding genes in sequence #3741 (426 bp)...done!
Finding genes in sequence #3742 (422 bp)...done!
Finding genes in sequence #3743 (358 bp)...done!
Finding genes in sequence #3744 (419 bp)...done!
Finding genes in sequence #3745 (697 bp)...done!
Finding genes in sequence #3746 (460 bp)...done!
Finding genes in sequence #3747 (580 bp)...done!
Finding genes in sequence #3748 (345 bp)...done!
Finding genes in sequence #3749 (735 bp)...done!
Finding genes in sequence #3750 (348 bp)...done!
Finding genes in sequence #3751 (402 bp)...done!
Finding genes in sequence #3752 (650 bp)...done!
Finding genes in sequence #3753 (572 bp)...done!
Finding genes in sequence #3754 (651 bp)...done!
Finding genes in sequence #3755 (470 bp)...done!
Finding genes in sequence #3756 (702 bp)...done!
Finding genes in sequence #3757 (582 bp)...done!
Finding genes in sequence #3758 (356 bp)...done!
Finding genes in sequence #3759 (313 bp)...done!
Finding genes in sequence #3760 (764 bp)...done!
Finding genes in sequence #3761 (499 bp)...done!
Finding genes in sequence #3762 (330 bp)...done!
Finding genes in sequence #3763 (359 bp)...done!
Finding genes in sequence #3764 (332 bp)...done!
Finding genes in sequence #3765 (656 bp)...done!
Finding genes in sequence #3766 (337 bp)...done!
Finding genes in sequence #3767 (367 bp)...done!
Finding genes in sequence #3768 (455 bp)...done!
Finding genes in sequence #3769 (337 bp)...done!
Finding genes in sequence #3770 (376 bp)...done!
Finding genes in sequence #3771 (1218 bp)...done!
Finding genes in sequence #3772 (304 bp)...done!
Finding genes in sequence #3773 (306 bp)...done!
Finding genes in sequence #3774 (472 bp)...done!
Finding genes in sequence #3775 (551 bp)...done!
Finding genes in sequence #3776 (574 bp)...done!
Finding genes in sequence #3777 (413 bp)...done!
Finding genes in sequence #3778 (400 bp)...done!
Finding genes in sequence #3779 (362 bp)...done!
Finding genes in sequence #3780 (5734 bp)...done!
Finding genes in sequence #3781 (1440 bp)...done!
Finding genes in sequence #3782 (317 bp)...done!
Finding genes in sequence #3783 (369 bp)...done!
Finding genes in sequence #3784 (269 bp)...done!
Finding genes in sequence #3785 (1935 bp)...done!

              

              • 

            

            Traceback:
            

              

            • 

              

              • 

            

            Job Parameters:
            

              

            • 

              


              
Job parameter
Parameter value

              
              


              
__input_ext
"input"

              

              
__workflow_invocation_uuid__
"52ab5fa08f2011f194246045bddb4fd3"

              

              
chromInfo
"/tmp/tmpy96jvlqm/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"

              

              
closed
false

              

              
dbkey
"?"

              

              
force_nonsd
false

              

              
input_train
None

              

              
masked_seq
false

              

              
out_format
"gbk"

              

              
procedure
"meta"

              

              
trans_table
"11"

              
              

              

              • 

            

            • 

          

          

          • 

        

        • 

      • 

        Step 16: Unlabelled step (toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_cat/9.5+galaxy3):
        

          

        • 

          step_state: scheduled
          

          • 

        • 

          Jobs

            

          • 

            Job 1:
            

              

            • Job state is ok
              • 

            

            Container:
            

              

            • 

              quay.io/biocontainers/coreutils:9.5
              

              • 

            

            Command Line:
            

              

            • 

              cat '/tmp/tmpy96jvlqm/files/c/7/a/dataset_c7acf1b1-f967-4ca4-b29b-1946e69db694.dat' >> '/tmp/tmpy96jvlqm/job_working_directory/000/11/outputs/dataset_76d5cf94-7447-4bf5-8dd8-733f3a5d9c2b.dat' && exit 0
              

              • 

            

            Exit Code:
            

              

            • 

              0
              

              • 

            

            Traceback:
            

              

            • 

              

              • 

            

            Job Parameters:
            

              

            • 

              


              
Job parameter
Parameter value

              
              


              
__input_ext
"input"

              

              
__workflow_invocation_uuid__
"52ab5fa08f2011f194246045bddb4fd3"

              

              
chromInfo
"/tmp/tmpy96jvlqm/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"

              

              
dbkey
"?"

              

              
queries
[]

              
              

              

              • 

            

            • 

          

          

          • 

        

        • 

      • 

        Step 17: MMseqs2 full catalogue Sequence Clustering (toolshed.g2.bx.psu.edu/repos/iuc/mmseqs2_easy_linclust_clustering/mmseqs2_easy_linclust_clustering/17-b804f+galaxy1):
        

          

        • 

          step_state: scheduled
          

          • 

        • 

          Jobs

            

          • 

            Job 1:
            

              

            • Job state is skipped
              • 

            

            Traceback:
            

              

            • 

              

              • 

            

            Job Parameters:
            

              

            • 

              


              
Job parameter
Parameter value

              
              


              
__input_ext
"input"

              

              
__workflow_invocation_uuid__
"52ab5fa08f2011f194246045bddb4fd3"

              

              
align
{"alignment_mode": "0", "alignment_output_mode": "0", "alt_ali": "0", "convertalis": false, "corr_score_weight": "0.0", "evalue": "0.001", "max_accept": "2147483647", "max_rejected": "2147483647", "min_aln_len": "0", "realign": false, "realign_max_seqs": "2147483647", "realign_score_bias": "-0.2", "score_bias": "0.0", "seq_id_mode": "0", "wrapped_scoring": false}

              

              
alph_type
{"__current_case__": 0, "dbtype": "0"}

              

              
chromInfo
"/tmp/tmpy96jvlqm/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"

              

              
cluster
{"cluster_mode": "0", "max_iterations": "1000", "similarity_type": "2"}

              

              
common
{"max_seq_len": "65535"}

              

              
cov
"0.8"

              

              
cov_mode
"0"

              

              
dbkey
"?"

              

              
expert
{"filter_hits": false, "sort_results": "0"}

              

              
kmermatcher
{"cluster_weight_threshold": "0.9", "hash_shift": "67", "ignore_multi_kmer": false, "include_only_extendable": false, "kmer_per_seq": "21"}

              

              
min_seq_id
"0.95"

              

              
misc
{"id_offset": "0", "rescore_mode": "0", "shuffle": true}

              

              
output_files
{"output_selection": ["file_rep_seq", "file_all_seq", "file_cluster_tsv"]}

              

              
prefilter
{"add_self_matches": false, "kmer_length": "0", "mask": "1", "mask_lower_case": "0", "mask_n_repeat": "0", "mask_prob": "0.9", "spaced_kmer_mode": "0"}

              
              

              

              • 

            

            • 

          

          

          • 

        

        • 

      • 

        Step 18: Unlabelled step (toolshed.g2.bx.psu.edu/repos/iuc/pick_value/pick_value/0.2.0):
        

          

        • 

          step_state: scheduled
          

          • 

        • 

          Jobs

            

          • 

            Job 1:
            

              

            • Job state is ok
              • 

            

            Command Line:
            

              

            • 

              cd ../; python _evaluate_expression_.py
              

              • 

            

            Exit Code:
            

              

            • 

              0
              

              • 

            

            Traceback:
            

              

            • 

              

              • 

            

            Job Parameters:
            

              

            • 

              


              
Job parameter
Parameter value

              
              


              
__input_ext
"input"

              

              
__workflow_invocation_uuid__
"52ab5fa08f2011f194246045bddb4fd3"

              

              
chromInfo
"/tmp/tmpy96jvlqm/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"

              

              
dbkey
"?"

              

              
style_cond
{"__current_case__": 1, "pick_style": "first_or_default", "type_cond": {"__current_case__": 4, "default_value": {"values": [{"id": 16, "src": "dce"}]}, "param_type": "data", "pick_from": [{"__index__": 0, "value": {"values": [{"id": 18, "src": "hda"}]}}]}}

              
              

              

              • 

            

            • 

          

          

          • 

        

        • 

      • 

        Step 19: Unlabelled step (toolshed.g2.bx.psu.edu/repos/iuc/amrfinderplus/amrfinderplus/4.2.7+galaxy0):
        

          

        • 

          step_state: scheduled
          

          • 

        • 

          Jobs

            

          • 

            Job 1:
            

              

            • Job state is error
              • 

            

            Traceback:
            

              

            • 

              

              • 

            

            Job Parameters:
            

              

            • 

              


              
Job parameter
Parameter value

              
              


              
__input_ext
"input"

              

              
__workflow_invocation_uuid__
"52ab5fa08f2011f194246045bddb4fd3"

              

              
chromInfo
"/tmp/tmpy96jvlqm/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"

              

              
dbkey
"?"

              

              
input_option
{"amrfinder_db_select": "amrfinderplus_V3.12_2024-05-02.2", "input_mode": {"__current_case__": 0, "input_select": "nucleotide", "nucleotide_flank5_size": "0", "nucleotide_input": {"values": [{"id": 18, "src": "dce"}]}}}

              

              
options
{"add_version_columns": false, "coverage_min": "0.5", "ident_min": "-1.0", "name": null, "plus": false, "print_node": false, "report_all_equal": false, "translation_table": "11"}

              

              
organism_options
{"organism_conditionnal": {"__current_case__": 1, "organism_select": ""}}

              
              

              

              • 

            

            • 

          

          

          • 

        

        • 

      • 

        Step 20: Unlabelled step (toolshed.g2.bx.psu.edu/repos/iuc/abricate/abricate/1.4.0):
        

          

        • 

          step_state: scheduled
          

          • 

        • 

          Jobs

            

          • 

            Job 1:
            

              

            • Job state is ok
              • 

            

            Container:
            

              

            • 

              quay.io/biocontainers/abricate:1.4.0--h05cac1d_0
              

              • 

            

            Command Line:
            

              

            • 

              ln -sf '/tmp/tmpy96jvlqm/files/c/7/a/dataset_c7acf1b1-f967-4ca4-b29b-1946e69db694.dat' genes_catalogue_test &&  abricate genes_catalogue_test  --minid=80.0 --mincov=80.0 --db=resfinder > '/tmp/tmpy96jvlqm/job_working_directory/000/15/outputs/dataset_1f244ccb-90e3-4498-8af8-b7f6537214d4.dat'
              

              • 

            

            Exit Code:
            

              

            • 

              0
              

              • 

            

            Standard Error:
            

              

            • 

              Using nucl database resfinder:  3206 sequences -  2026-Apr-3
Processing: genes_catalogue_test
Found 1 genes in genes_catalogue_test
Tip: you can use the --summary option to combine reports in a presence/absence matrix.
Done.

              

              • 

            

            Traceback:
            

              

            • 

              

              • 

            

            Job Parameters:
            

              

            • 

              


              
Job parameter
Parameter value

              
              


              
__input_ext
"input"

              

              
__workflow_invocation_uuid__
"52ab5fa08f2011f194246045bddb4fd3"

              

              
adv
{"db": "resfinder", "min_cov": "80.0", "min_dna_id": "80.0", "no_header": false}

              

              
chromInfo
"/tmp/tmpy96jvlqm/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"

              

              
dbkey
"?"

              
              

              

              • 

            

            • 

          

          

          • 

        

        • 

      • 

        Step 21: Unlabelled step (toolshed.g2.bx.psu.edu/repos/iuc/staramr/staramr_search/0.12.3+galaxy0):
        

          

        • 

          step_state: scheduled
          

          • 

        • 

          Jobs

            

          • 

            Job 1:
            

              

            • Job state is ok
              • 

            

            Container:
            

              

            • 

              quay.io/biocontainers/mulled-v2-30758c5e2be407d6bbf2570c832fb245e8488634:554912fb4663b66a7db92472d73ef2d27ab8ae27-0
              

              • 

            

            Command Line:
            

              

            • 

              ln -s '/tmp/tmpy96jvlqm/files/c/7/a/dataset_c7acf1b1-f967-4ca4-b29b-1946e69db694.dat' genes_catalogue_test.fasta &&  export GIT_CONFIG_COUNT=1 GIT_CONFIG_KEY_0=safe.directory GIT_CONFIG_VALUE_0=* &&  staramr search  -d '/cvmfs/data.galaxyproject.org/byhand/staramr/resfinder_d1e607b_pointfinder_694919f_plasmidfinder_3e77502' --nprocs "${GALAXY_SLOTS:-1}"  --genome-size-lower-bound 4000000 --genome-size-upper-bound 6000000 --minimum-N50-value 10000 --minimum-contig-length 300 --unacceptable-number-contigs 1000  --pid-threshold 98.0 --percent-length-overlap-resfinder 60.0 --percent-length-overlap-plasmidfinder 60.0 --percent-length-overlap-pointfinder 95.0          --output-summary '/tmp/tmpy96jvlqm/job_working_directory/000/16/outputs/dataset_c4c5fe2c-4ae2-43ea-be22-0b29f2c7c1a8.dat' --output-detailed-summary '/tmp/tmpy96jvlqm/job_working_directory/000/16/outputs/dataset_b863f4a0-9303-4f89-9157-ec08b67e72b7.dat' --output-resfinder '/tmp/tmpy96jvlqm/job_working_directory/000/16/outputs/dataset_df3f6a6e-5f4e-4649-9c39-33004ce2a432.dat' --output-plasmidfinder '/tmp/tmpy96jvlqm/job_working_directory/000/16/outputs/dataset_683de87f-04e2-449b-bc5c-f460fd53b285.dat' --output-settings 'XXXX' --output-excel results.xlsx --output-mlst '/tmp/tmpy96jvlqm/job_working_directory/000/16/outputs/dataset_8e2315eb-d750-44f0-9924-7e4fe22235a8.dat'  --output-hits-dir staramr_hits   genes_catalogue_test.fasta
              

              • 

            

            Exit Code:
            

              

            • 

              0
              

              • 

            

            Standard Error:
            

              

            • 

              2026-08-03 09:54:12 WARNING: Using non-default ResFinder/PointFinder. This may lead to differences in the detected AMR genes depending on how the database files are structured.
2026-08-03 09:54:12 INFO: No --pointfinder-organism specified. Will not search the PointFinder databases
2026-08-03 09:54:12 INFO: No --plasmidfinder-database-type specified. Will search the entire PlasmidFinder database
2026-08-03 09:54:12 INFO: --output-dir not set. Files will be output to the respective --output-[type] setting
2026-08-03 09:54:12 INFO: Will exclude ResFinder/PointFinder genes listed in [/usr/local/lib/python3.14/site-packages/staramr/databases/exclude/data/genes_to_exclude.tsv]. Use --no-exclude-genes to disable
2026-08-03 09:54:12 INFO: Will report complex mutations listed in [/usr/local/lib/python3.14/site-packages/staramr/databases/resistance/pointfinder/complex/data/complex_mutations.tsv]
2026-08-03 09:54:12 INFO: Making BLAST databases for input files
2026-08-03 09:54:12 INFO: Scheduling blasts and MLST for genes_catalogue_test.fasta
2026-08-03 09:54:17 WARNING: No drug found for drug_class=all, gene=cfxA_1, accession=U38243
2026-08-03 09:54:18 INFO: Finished. Took 0.10 minutes.
2026-08-03 09:54:19 INFO: Predicting AMR resistance phenotypes is enabled. The predictions are for microbiological resistance and *not* clinical resistance. These results are continually being improved and we welcome any feedback.
2026-08-03 09:54:19 INFO: Writing resfinder to [/tmp/tmpy96jvlqm/job_working_directory/000/16/outputs/dataset_df3f6a6e-5f4e-4649-9c39-33004ce2a432.dat]
2026-08-03 09:54:19 INFO: --output-dir or --output-pointfinder unset. No pointfinder file will be written
2026-08-03 09:54:19 INFO: Writing plasmidfinder to [/tmp/tmpy96jvlqm/job_working_directory/000/16/outputs/dataset_683de87f-04e2-449b-bc5c-f460fd53b285.dat]
2026-08-03 09:54:19 INFO: Writing summary to [/tmp/tmpy96jvlqm/job_working_directory/000/16/outputs/dataset_c4c5fe2c-4ae2-43ea-be22-0b29f2c7c1a8.dat]
2026-08-03 09:54:19 INFO: Writing MLST summary to [/tmp/tmpy96jvlqm/job_working_directory/000/16/outputs/dataset_8e2315eb-d750-44f0-9924-7e4fe22235a8.dat]
2026-08-03 09:54:19 INFO: Writing detailed summary to [/tmp/tmpy96jvlqm/job_working_directory/000/16/outputs/dataset_b863f4a0-9303-4f89-9157-ec08b67e72b7.dat]
2026-08-03 09:54:19 INFO: Writing settings to [XXXX]
2026-08-03 09:54:19 INFO: Writing Excel to [results.xlsx]
2026-08-03 09:54:19 INFO: BLAST hits are stored in [staramr_hits]

              

              • 

            

            Traceback:
            

              

            • 

              

              • 

            

            Job Parameters:
            

              

            • 

              


              
Job parameter
Parameter value

              
              


              
__input_ext
"input"

              

              
__workflow_invocation_uuid__
"52ab5fa08f2011f194246045bddb4fd3"

              

              
advanced
{"complex_mutations_file": null, "exclude_genes": {"__current_case__": 0, "exclude_genes_condition": "default"}, "exclude_negatives": false, "exclude_resistance_phenotypes": false, "genome_size_lower_bound": "4000000", "genome_size_upper_bound": "6000000", "minimum_N50_value": "10000", "minimum_contig_length": "300", "mlst_scheme": "auto", "percent_length_overlap_plasmidfinder": "60.0", "percent_length_overlap_pointfinder": "95.0", "percent_length_overlap_resfinder": "60.0", "pid_threshold": "98.0", "plasmidfinder_type": "include_all", "report_all_blast": false, "unacceptable_number_contigs": "1000"}

              

              
chromInfo
"/tmp/tmpy96jvlqm/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"

              

              
dbkey
"?"

              

              
hide_db_build
""

              

              
output_files
{"output_selection": ["mlst_table", "summary_table", "detailed_summary_table", "resfinder_table", "plasmidfinder_table", "pointfinder_table"]}

              

              
pointfinder_organism
"disabled"

              

              
staramr_db_select
"staramr_downloaded_07042025_resfinder_d1e607b_pointfinder_694919f_plasmidfinder_3e77502"

              
              

              

              • 

            

            • 

          

          

          • 

        

        • 

      • 

        Step 22: Unlabelled step (toolshed.g2.bx.psu.edu/repos/nml/collapse_collections/collapse_dataset/5.1.0):
        

          

        • 

          step_state: scheduled
          

          • 

        • 

          Jobs

            

          • 

            Job 1:
            

              

            • Job state is paused
              • 

            

            Traceback:
            

              

            • 

              

              • 

            

            Job Parameters:
            

              

            • 

              


              
Job parameter
Parameter value

              
              


              
__input_ext
"input"

              

              
__workflow_invocation_uuid__
"52ab5fa08f2011f194246045bddb4fd3"

              

              
chromInfo
"/tmp/tmpy96jvlqm/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"

              

              
dbkey
"?"

              

              
filename
{"__current_case__": 1, "add_name": false}

              

              
one_header
true

              
              

              

              • 

            

            • 

          

          

          • 

        

        • 

      • 

        Step 23: Unlabelled step (toolshed.g2.bx.psu.edu/repos/nml/collapse_collections/collapse_dataset/5.1.0):
        

          

        • 

          step_state: scheduled
          

          • 

        • 

          Jobs

            

          • 

            Job 1:
            

              

            • Job state is ok
              • 

            

            Container:
            

              

            • 

              quay.io/biocontainers/gawk:5.1.0--2
              

              • 

            

            Command Line:
            

              

            • 

              ( awk '{if (NR==1) {print}}' "/tmp/tmpy96jvlqm/files/1/f/2/dataset_1f244ccb-90e3-4498-8af8-b7f6537214d4.dat";   awk '{if (NR!=1) {print}}' "/tmp/tmpy96jvlqm/files/1/f/2/dataset_1f244ccb-90e3-4498-8af8-b7f6537214d4.dat";   ) > /tmp/tmpy96jvlqm/job_working_directory/000/18/outputs/dataset_f82fc17a-2187-4fcd-ba44-c9d1a1107e47.dat
              

              • 

            

            Exit Code:
            

              

            • 

              0
              

              • 

            

            Traceback:
            

              

            • 

              

              • 

            

            Job Parameters:
            

              

            • 

              


              
Job parameter
Parameter value

              
              


              
__input_ext
"input"

              

              
__workflow_invocation_uuid__
"52ab5fa08f2011f194246045bddb4fd3"

              

              
chromInfo
"/tmp/tmpy96jvlqm/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"

              

              
dbkey
"?"

              

              
filename
{"__current_case__": 1, "add_name": false}

              

              
one_header
true

              
              

              

              • 

            

            • 

          

          

          • 

        

        • 

      • 

        Step 24: Unlabelled step (toolshed.g2.bx.psu.edu/repos/iuc/column_remove_by_header/column_remove_by_header/1.0):
        

          

        • 

          step_state: scheduled
          

          • 

        • 

          Jobs

            

          • 

            Job 1:
            

              

            • Job state is queued
              • 

            

            Command Line:
            

              

            • 

              python '/tmp/shed_data/shed_tools/toolshed.g2.bx.psu.edu/repos/iuc/column_remove_by_header/6428adb323eb/column_remove_by_header/column_remove_by_header.py' -i '/tmp/tmpy96jvlqm/files/b/8/6/dataset_b863f4a0-9303-4f89-9157-ec08b67e72b7.dat' -o '/tmp/tmpy96jvlqm/job_working_directory/000/19/outputs/dataset_6b2e0e1b-25c1-42eb-8512-754b4cc4bf49.dat' -d '	'  -s '#' --unicode-escaped-cols --columns 'Isolate ID'
              

              • 

            

            Traceback:
            

              

            • 

              

              • 

            

            Job Parameters:
            

              

            • 

              


              
Job parameter
Parameter value

              
              


              
__input_ext
"tabular"

              

              
__workflow_invocation_uuid__
"52ab5fa08f2011f194246045bddb4fd3"

              

              
chromInfo
"/tmp/tmpy96jvlqm/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"

              

              
dbkey
"?"

              

              
headers
[{"__index__": 0, "name": "Isolate ID"}]

              

              
keep_columns
false

              

              
strip_characters
"#"

              
              

              

              • 

            

            • 

          

          

          • 

        

        • 

      • 

        Step 25: Unlabelled step (toolshed.g2.bx.psu.edu/repos/iuc/argnorm/argnorm/1.0.0+galaxy0):
        

          

        • 

          step_state: scheduled
          

          • 

        • 

          Jobs

            

          • 

            Job 1:
            

              

            • Job state is paused
              • 

            

            Traceback:
            

              

            • 

              

              • 

            

            Job Parameters:
            

              

            • 

              


              
Job parameter
Parameter value

              
              


              
__input_ext
"input"

              

              
__workflow_invocation_uuid__
"52ab5fa08f2011f194246045bddb4fd3"

              

              
choose_tool
{"__current_case__": 4, "tool": "amrfinderplus"}

              

              
chromInfo
"/tmp/tmpy96jvlqm/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"

              

              
dbkey
"?"

              
              

              

              • 

            

            • 

          

          

          • 

        

        • 

      • 

        Step 26: Unlabelled step (toolshed.g2.bx.psu.edu/repos/iuc/column_remove_by_header/column_remove_by_header/1.0):
        

          

        • 

          step_state: scheduled
          

          • 

        • 

          Jobs

            

          • 

            Job 1:
            

              

            • Job state is paused
              • 

            

            Traceback:
            

              

            • 

              

              • 

            

            Job Parameters:
            

              

            • 

              


              
Job parameter
Parameter value

              
              


              
__input_ext
"tabular"

              

              
__workflow_invocation_uuid__
"52ab5fa08f2011f194246045bddb4fd3"

              

              
chromInfo
"/tmp/tmpy96jvlqm/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"

              

              
dbkey
"?"

              

              
headers
[{"__index__": 0, "name": "Protein identifier"}]

              

              
keep_columns
false

              

              
strip_characters
"#"

              
              

              

              • 

            

            • 

          

          

          • 

        

        • 

      • 

        Step 27: Unlabelled step (toolshed.g2.bx.psu.edu/repos/recetox/table_pandas_rename_column/table_pandas_rename_column/3.0.2+galaxy0):
        

          

        • 

          step_state: scheduled
          

          • 

        • 

          Jobs

            

          • 

            Job 1:
            

              

            • Job state is queued
              • 

            

            Traceback:
            

              

            • 

              

              • 

            

            Job Parameters:
            

              

            • 

              


              
Job parameter
Parameter value

              
              


              
__input_ext
"input"

              

              
__workflow_invocation_uuid__
"52ab5fa08f2011f194246045bddb4fd3"

              

              
chromInfo
"/tmp/tmpy96jvlqm/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"

              

              
columns_selection
[{"__index__": 0, "column": "1", "new_name": "FILE"}]

              

              
dbkey
"?"

              
              

              

              • 

            

            • 

          

          

          • 

        

        • 

      • 

        Step 28: Unlabelled step:
        

          

        • 

          step_state: new
          

          • 

        • 

          Subworkflow Steps
 
          

          • 

        

        • 

      • 

        Step 29: Unlabelled step (toolshed.g2.bx.psu.edu/repos/iuc/column_remove_by_header/column_remove_by_header/1.0):
        

          

        • 

          step_state: scheduled
          

          • 

        • 

          Jobs

            

          • 

            Job 1:
            

              

            • Job state is new
              • 

            

            Traceback:
            

              

            • 

              

              • 

            

            Job Parameters:
            

              

            • 

              


              
Job parameter
Parameter value

              
              


              
__input_ext
"tabular"

              

              
__workflow_invocation_uuid__
"52ab5fa08f2011f194246045bddb4fd3"

              

              
chromInfo
"/tmp/tmpy96jvlqm/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"

              

              
dbkey
"?"

              

              
headers
[{"__index__": 0, "name": "FILE"}]

              

              
keep_columns
false

              

              
strip_characters
"#"

              
              

              

              • 

            

            • 

          

          

          • 

        

        • 

      • 

        Step 30: Unlabelled step:
        

          

        • step_state: new
          • 

        

        • 

      • 

        Step 31: Unlabelled step:
        

          

        • step_state: new
          • 

        

        • 

      • 

        Step 32: Unlabelled step:
        

          

        • step_state: new
          • 

        

        • 

      • 

        Step 33: MMseqs2 ARGs Sequence Clustering:
        

          

        • step_state: new
          • 

        

        • 

      • 

        Step 34: Unlabelled step:
        

          

        • step_state: new
          • 

        

        • 

      • 

        Step 35: Unlabelled step:
        

          

        • step_state: new
          • 

        

        • 

      • 

        Step 36: Unlabelled step:
        

          

        • step_state: new
          • 

        

        • 

      • 

        Step 37: Unlabelled step:
        

          

        • step_state: new
          • 

        

        • 

      • 

        Step 38: Unlabelled step:
        

          

        • step_state: new
          • 

        

        • 

      • 

        Step 39: Unlabelled step:
        

          

        • step_state: new
          • 

        

        • 

      • 

        Step 40: Unlabelled step:
        

          

        • step_state: new
          • 

        

        • 

      • 

        Step 41: Unlabelled step:
        

          

        • step_state: new
          • 

        

        • 

      • 

        Step 42: Unlabelled step:
        

          

        • step_state: new
          • 

        

        • 

      • 

        Step 43: Unlabelled step:
        

          

        • step_state: new
          • 

        

        • 

      
 
      

      • 

    • 

      Other invocation details

        

      • 

        error_message
        

          

        • Failed to run workflow, invocation ended in [failed] state.
          • 

        

        • 

      • 

        history_id
        

          

        • b201198e2d586b26
          • 

        

        • 

      • 

        history_state
        

          

        • queued
          • 

        

        • 

      • 

        invocation_id
        

          

        • b201198e2d586b26
          • 

        

        • 

      • 

        invocation_state
        

          

        • failed
          • 

        

        • 

      • 

        messages
        

          

        • [{'dependent_workflow_step_id': None, 'hda_id': '706248f5e3722abb', 'reason': 'dataset_failed', 'workflow_step_id': 27, 'workflow_step_index_path': [27]}]
          • 

        

        • 

      • 

        workflow_id
        

          

        • 699c81bf682da0de
          • 

        

        • 

      

      

      • 

    
  
    

    • 





      		
    

  





        

            

            

              
            

        

      


      

            
  
  

    
  
    
    

  

  

  


    












      

  
        





      

  
          

  
  

  
    

        

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        August 10, 2026 09:36        
        
      

    





    

    

      
    

    


      


          @gxydevbot
gxydevbot




        changed the title
Updating workflows/microbiome/metagenomic-genes-catalogue from 1.3 to 1.4

Updating workflows/microbiome/metagenomic-genes-catalogue from 1.3 to 1.4 


      Aug 10, 2026

    

  








      

  
      



  

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        Aug 10, 2026



      
    


  


  

    

      

          
    
    

  


        
            
  
      
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There are new updates, they have been integrated to the PR, check the file diff.


      		
    

  





        

            

            

              
            

        

      


      

            
  
  

    
  
    
    

  

  

  


    












      

  
      



  

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Test Results (powered by Planemo)


Test Summary



  

  

  

  

  

  








Test State
Count






Total
1




Passed
0




Error
1




Failure
0




Skipped
0






Errored Tests

    

  • 

    ❌ metagenomic-genes-catalogue.ga_0
    

    Execution Problem:
    

      

    • 

      Failed to run workflow, invocation ended in [failed] state.

      

      • 

    

    Workflow invocation details
    

      

    • 

      Invocation Messages
      

        

      • Invocation scheduling failed because step 28 requires a dataset, but dataset entered a failed state.
        • 

      

      • 

    • 

      Steps

        

      • 

        Step 1: Metagenomics Trimmed reads:
        

          

        • step_state: scheduled
          • 

        

        • 

      • 

        Step 2: AMR genes detection database:
        

          

        • step_state: scheduled
          • 

        

        • 

      • 

        Step 3: Full genes catalogue:
        

          

        • step_state: scheduled
          • 

        

        • 

      • 

        Step 4: Virulence genes detection database:
        

          

        • step_state: scheduled
          • 

        

        • 

      • 

        Step 5: starAMR database:
        

          

        • step_state: scheduled
          • 

        

        • 

      • 

        Step 6: mmseqs2 taxonomy DB:
        

          

        • step_state: scheduled
          • 

        

        • 

      • 

        Step 7: eggNOG database:
        

          

        • step_state: scheduled
          • 

        

        • 

      • 

        Step 8: Unlabelled step (toolshed.g2.bx.psu.edu/repos/iuc/megahit/megahit/1.2.9+galaxy2):
        

          

        • 

          step_state: scheduled
          

          • 

        • 

          Jobs

            

          • 

            Job 1:
            

              

            • Job state is ok
              • 

            

            Container:
            

              

            • 

              quay.io/biocontainers/megahit:1.2.9--haf24da9_8
              

              • 

            

            Command Line:
            

              

            • 

              if [[ -n "$GALAXY_MEMORY_MB" ]]; then MEMORY="-m $((GALAXY_MEMORY_MB * 1024))"; fi;  megahit --num-cpu-threads ${GALAXY_SLOTS:-4}  -1 '/tmp/tmpmaxbzsnl/files/b/f/7/dataset_bf74af05-127a-4746-ae2c-3c539b422924.dat' -2 '/tmp/tmpmaxbzsnl/files/6/4/3/dataset_64302efd-72c8-4833-b8b4-dddbbd6d0794.dat' --min-count '2' --k-list '21,29,39,59,79,99,119,141'  --bubble-level '2' --merge-level '20,0.95' --prune-level '2' --prune-depth '2' --disconnect-ratio '0.1' --low-local-ratio '0.2' --cleaning-rounds '5'   --min-contig-len '200' $MEMORY
              

              • 

            

            Exit Code:
            

              

            • 

              0
              

              • 

            

            Standard Error:
            

              

            • 

              2026-08-10 09:50:17 - MEGAHIT v1.2.9
2026-08-10 09:50:17 - Using megahit_core with POPCNT and BMI2 support
2026-08-10 09:50:17 - Convert reads to binary library
2026-08-10 09:50:18 - b'INFO  sequence/io/sequence_lib.cpp  :   75 - Lib 0 (/tmp/tmpmaxbzsnl/files/b/f/7/dataset_bf74af05-127a-4746-ae2c-3c539b422924.dat,/tmp/tmpmaxbzsnl/files/6/4/3/dataset_64302efd-72c8-4833-b8b4-dddbbd6d0794.dat): pe, 500000 reads, 101 max length'
2026-08-10 09:50:18 - b'INFO  utils/utils.h                 :  152 - Real: 0.6668\tuser: 0.6386\tsys: 0.0280\tmaxrss: 28780'
2026-08-10 09:50:18 - Start assembly. Number of CPU threads 1 
2026-08-10 09:50:18 - k list: 21,29,39,59,79,99,119,141 
2026-08-10 09:50:18 - Memory used: 15089784422
2026-08-10 09:50:18 - Extract solid (k+1)-mers for k = 21 
2026-08-10 09:50:28 - Build graph for k = 21 
2026-08-10 09:50:37 - Assemble contigs from SdBG for k = 21
2026-08-10 09:51:08 - Local assembly for k = 21
2026-08-10 09:51:11 - Extract iterative edges from k = 21 to 29 
2026-08-10 09:51:13 - Build graph for k = 29 
2026-08-10 09:51:16 - Assemble contigs from SdBG for k = 29
2026-08-10 09:51:36 - Local assembly for k = 29
2026-08-10 09:51:40 - Extract iterative edges from k = 29 to 39 
2026-08-10 09:51:41 - Build graph for k = 39 
2026-08-10 09:51:43 - Assemble contigs from SdBG for k = 39
2026-08-10 09:51:57 - Local assembly for k = 39
2026-08-10 09:52:00 - Extract iterative edges from k = 39 to 59 
2026-08-10 09:52:02 - Build graph for k = 59 
2026-08-10 09:52:03 - Assemble contigs from SdBG for k = 59
2026-08-10 09:52:11 - Local assembly for k = 59
2026-08-10 09:52:15 - Extract iterative edges from k = 59 to 79 
2026-08-10 09:52:15 - Build graph for k = 79 
2026-08-10 09:52:16 - Assemble contigs from SdBG for k = 79
2026-08-10 09:52:22 - Local assembly for k = 79
2026-08-10 09:52:25 - Extract iterative edges from k = 79 to 99 
2026-08-10 09:52:26 - Build graph for k = 99 
2026-08-10 09:52:27 - Assemble contigs from SdBG for k = 99
2026-08-10 09:52:31 - Local assembly for k = 99
2026-08-10 09:52:34 - Extract iterative edges from k = 99 to 119 
2026-08-10 09:52:34 - Build graph for k = 119 
2026-08-10 09:52:35 - Assemble contigs from SdBG for k = 119
2026-08-10 09:52:38 - Local assembly for k = 119
2026-08-10 09:52:41 - Extract iterative edges from k = 119 to 141 
2026-08-10 09:52:41 - Build graph for k = 141 
2026-08-10 09:52:41 - Assemble contigs from SdBG for k = 141
2026-08-10 09:52:44 - Merging to output final contigs 
2026-08-10 09:52:44 - 3785 contigs, total 1759217 bp, min 243 bp, max 10133 bp, avg 464 bp, N50 449 bp
2026-08-10 09:52:44 - ALL DONE. Time elapsed: 146.823895 seconds 

              

              • 

            

            Traceback:
            

              

            • 

              

              • 

            

            Job Parameters:
            

              

            • 

              


              
Job parameter
Parameter value

              
              


              
__input_ext
"fastqsanger.gz"

              

              
__workflow_invocation_uuid__
"d3be488e94a011f194247c1e52f4ef47"

              

              
advanced_section
{"bubble_level": "2", "cleaning_rounds": "5", "disconnect_ratio": "0.1", "kmin1pass": false, "low_local_ratio": "0.2", "merge_level": "20,0.95", "nolocal": false, "nomercy": false, "prune_depth": "2", "prune_level": "2"}

              

              
basic_section
{"k_mer": {"__current_case__": 0, "k_list": "21,29,39,59,79,99,119,141", "k_mer_method": "klist_method"}, "min_count": "2"}

              

              
chromInfo
"/tmp/tmpmaxbzsnl/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"

              

              
dbkey
"?"

              

              
input_option
{"__current_case__": 3, "batchmode": {"__current_case__": 0, "pair_input": {"values": [{"id": 1, "src": "dce"}]}, "processmode": "individual"}, "choice": "paired_collection"}

              

              
output_section
{"log_file": true, "min_contig_len": "200", "show_intermediate_contigs": false}

              
              

              

              • 

            

            • 

          

          

          • 

        

        • 

      • 

        Step 9: Unlabelled step (toolshed.g2.bx.psu.edu/repos/iuc/pick_value/pick_value/0.2.0):
        

          

        • 

          step_state: scheduled
          

          • 

        • 

          Jobs

            

          • 

            Job 1:
            

              

            • Job state is skipped
              • 

            

            Traceback:
            

              

            • 

              

              • 

            

            Job Parameters:
            

              

            • 

              


              
Job parameter
Parameter value

              
              


              
__input_ext
"input"

              

              
__workflow_invocation_uuid__
"d3be488e94a011f194247c1e52f4ef47"

              

              
chromInfo
"/tmp/tmpmaxbzsnl/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"

              

              
dbkey
"?"

              

              
style_cond
{"__current_case__": 1, "pick_style": "first_or_default", "type_cond": {"__current_case__": 3, "default_value": true, "param_type": "boolean", "pick_from": [{"__index__": 0, "value": false}]}}

              
              

              

              • 

            

            • 

          

          

          • 

        

        • 

      • 

        Step 10: Unlabelled step (toolshed.g2.bx.psu.edu/repos/devteam/fasta_to_tabular/fasta2tab/1.1.1):
        

          

        • 

          step_state: scheduled
          

          • 

        • 

          Jobs

            

          • 

            Job 1:
            

              

            • Job state is ok
              • 

            

            Container:
            

              

            • 

              quay.io/biocontainers/python:3.7--1
              

              • 

            

            Command Line:
            

              

            • 

              python '/tmp/shed_data/shed_tools/toolshed.g2.bx.psu.edu/repos/devteam/fasta_to_tabular/e7ed3c310b74/fasta_to_tabular/fasta_to_tabular.py' '/tmp/tmpmaxbzsnl/files/f/6/a/dataset_f6adf6f8-1749-44ba-bf42-85bdd2db4bbb.dat' '/tmp/tmpmaxbzsnl/job_working_directory/000/5/outputs/dataset_27a375ce-0a14-467f-8751-c2303088e300.dat' 0 1
              

              • 

            

            Exit Code:
            

              

            • 

              0
              

              • 

            

            Traceback:
            

              

            • 

              

              • 

            

            Job Parameters:
            

              

            • 

              


              
Job parameter
Parameter value

              
              


              
__input_ext
"input"

              

              
__workflow_invocation_uuid__
"d3be488e94a011f194247c1e52f4ef47"

              

              
chromInfo
"/tmp/tmpmaxbzsnl/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"

              

              
dbkey
"?"

              

              
descr_columns
"1"

              

              
keep_first
"0"

              
              

              

              • 

            

            • 

          

          

          • 

        

        • 

      • 

        Step 11: Unlabelled step (toolshed.g2.bx.psu.edu/repos/iuc/quast/quast/5.3.0+galaxy1):
        

          

        • 

          step_state: scheduled
          

          • 

        • 

          Jobs

            

          • 

            Job 1:
            

              

            • Job state is ok
              • 

            

            Container:
            

              

            • 

              quay.io/biocontainers/mulled-v2-754a47f7005ac2c33e46ba3a97ef68abb6ef71f8:aac2489b1179db17f28c2868c3a8e41d4474683a-0
              

              • 

            

            Command Line:
            

              

            • 

              echo genes_catalogue_test &&   ln -s '/tmp/tmpmaxbzsnl/files/b/f/7/dataset_bf74af05-127a-4746-ae2c-3c539b422924.dat' 'pe1-genes_catalogue_test.fastqsanger.gz' && ln -s '/tmp/tmpmaxbzsnl/files/6/4/3/dataset_64302efd-72c8-4833-b8b4-dddbbd6d0794.dat' 'pe2-genes_catalogue_test.fastqsanger.gz' &&  metaquast  --pe1 'pe1-genes_catalogue_test.fastqsanger.gz' --pe2 'pe2-genes_catalogue_test.fastqsanger.gz' --labels 'genes_catalogue_test' -o 'outputdir'  --max-ref-num 0  --min-identity 95.0 --min-contig 1500        --min-alignment 65 --ambiguity-usage 'one' --ambiguity-score 0.99   --local-mis-size 200   --contig-thresholds '0,1000,5000,10000,25000,50000'  --extensive-mis-size 1000 --scaffold-gap-max-size 10000 --unaligned-part-size 500   --x-for-Nx 90  '/tmp/tmpmaxbzsnl/files/f/6/a/dataset_f6adf6f8-1749-44ba-bf42-85bdd2db4bbb.dat' --threads ${GALAXY_SLOTS:-1}  --no-krona  && if [[ -f "outputdir/report.tsv" ]]; then mkdir -p "outputdir/combined_reference/" && cp "outputdir/report.tsv" "outputdir/combined_reference/report.tsv"; fi && if [[ -f "outputdir/report.html" ]]; then mkdir -p "outputdir/combined_reference/" && cp outputdir/*.html "outputdir/combined_reference/"; fi && mkdir -p '/tmp/tmpmaxbzsnl/job_working_directory/000/6/outputs/dataset_5a6bea47-9ebc-46fd-9e1a-2d50d85890a2_files' && cp outputdir/combined_reference/*.html '/tmp/tmpmaxbzsnl/job_working_directory/000/6/outputs/dataset_5a6bea47-9ebc-46fd-9e1a-2d50d85890a2_files' && if [[ -d "outputdir/icarus_viewers" ]]; then cp -R outputdir/icarus_viewers 'outputdir/combined_reference/'; fi && if [[ -d "outputdir/combined_reference/icarus_viewers" ]]; then cp -R outputdir/combined_reference/icarus_viewers '/tmp/tmpmaxbzsnl/job_working_directory/000/6/outputs/dataset_5a6bea47-9ebc-46fd-9e1a-2d50d85890a2_files'; fi && if [[ -d "outputdir/krona_charts/" ]]; then mkdir -p 'None' && cp outputdir/krona_charts/*.html 'None'; fi
              

              • 

            

            Exit Code:
            

              

            • 

              0
              

              • 

            

            Standard Output:
            

              

            • 

              genes_catalogue_test
/usr/local/opt/quast-5.3.0/metaquast.py --pe1 pe1-genes_catalogue_test.fastqsanger.gz --pe2 pe2-genes_catalogue_test.fastqsanger.gz --labels genes_catalogue_test -o outputdir --max-ref-num 0 --min-identity 95.0 --min-contig 1500 --min-alignment 65 --ambiguity-usage one --ambiguity-score 0.99 --local-mis-size 200 --contig-thresholds 0,1000,5000,10000,25000,50000 --extensive-mis-size 1000 --scaffold-gap-max-size 10000 --unaligned-part-size 500 --x-for-Nx 90 /tmp/tmpmaxbzsnl/files/f/6/a/dataset_f6adf6f8-1749-44ba-bf42-85bdd2db4bbb.dat --threads 1 --no-krona

Version: 5.3.0

System information:
  OS: Linux-6.17.0-1020-azure-x86_64-with-glibc2.36 (linux_64)
  Python version: 3.12.3
  CPUs number: 4

Started: 2026-08-10 09:53:43

Logging to /tmp/tmpmaxbzsnl/job_working_directory/000/6/working/outputdir/metaquast.log
WARNING: --ambiguity-usage was set to 'all' because not default --ambiguity-score was specified
INFO	generated new fontManager
INFO	generated new fontManager

Contigs:
  Pre-processing...
  /tmp/tmpmaxbzsnl/files/f/6/a/dataset_f6adf6f8-1749-44ba-bf42-85bdd2db4bbb.dat ==> genes_catalogue_test

NOTICE: Maximum number of references (--max-ref-number) is set to 0, search in SILVA 16S rRNA database is disabled

NOTICE: No references are provided, starting regular QUAST with MetaGeneMark gene finder
/usr/local/opt/quast-5.3.0/quast.py --pe1 pe1-genes_catalogue_test.fastqsanger.gz --pe2 pe2-genes_catalogue_test.fastqsanger.gz --min-identity 95.0 --min-contig 1500 --min-alignment 65 --ambiguity-usage one --ambiguity-score 0.99 --local-mis-size 200 --contig-thresholds 0,1000,5000,10000,25000,50000 --extensive-mis-size 1000 --scaffold-gap-max-size 10000 --unaligned-part-size 500 --x-for-Nx 90 --threads 1 --no-krona /tmp/tmpmaxbzsnl/files/f/6/a/dataset_f6adf6f8-1749-44ba-bf42-85bdd2db4bbb.dat -o /tmp/tmpmaxbzsnl/job_working_directory/000/6/working/outputdir --labels genes_catalogue_test

Version: 5.3.0

System information:
  OS: Linux-6.17.0-1020-azure-x86_64-with-glibc2.36 (linux_64)
  Python version: 3.12.3
  CPUs number: 4

Started: 2026-08-10 09:53:44

Logging to /tmp/tmpmaxbzsnl/job_working_directory/000/6/working/outputdir/quast.log
NOTICE: Output directory already exists and looks like a QUAST output dir. Existing results can be reused (e.g. previously generated alignments)!
WARNING: --ambiguity-usage was set to 'all' because not default --ambiguity-score was specified

CWD: /tmp/tmpmaxbzsnl/job_working_directory/000/6/working
Main parameters: 
  MODE: meta, threads: 1, min contig length: 1500, min alignment length: 65, min alignment IDY: 95.0, \
  ambiguity: all, min local misassembly length: 200, min extensive misassembly length: 1000

Contigs:
  Pre-processing...
  /tmp/tmpmaxbzsnl/files/f/6/a/dataset_f6adf6f8-1749-44ba-bf42-85bdd2db4bbb.dat ==> genes_catalogue_test

2026-08-10 09:53:44
Running Reads analyzer...
NOTICE: Permission denied accessing /usr/local/lib/python3.12/site-packages/quast_libs/gridss. GRIDSS will be downloaded to home directory /tmp/tmpmaxbzsnl/job_working_directory/000/6/home/.quast
Downloading gridss (file: gridss-1.4.1.jar)...
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gridss successfully downloaded!
  Logging to files /tmp/tmpmaxbzsnl/job_working_directory/000/6/working/outputdir/reads_stats/reads_stats.log and /tmp/tmpmaxbzsnl/job_working_directory/000/6/working/outputdir/reads_stats/reads_stats.err...
  Pre-processing reads...
  Running BWA...
  Done.
  Sorting SAM-file...
  Analysis is finished.
  Creating total report...
    saved to /tmp/tmpmaxbzsnl/job_working_directory/000/6/working/outputdir/reads_stats/reads_report.txt, reads_report.tsv, and reads_report.tex
Done.

2026-08-10 09:54:24
Running Basic statistics processor...
  Contig files: 
    genes_catalogue_test
  Calculating N50 and L50...
    genes_catalogue_test, N50 = 2144, L50 = 11, auN = 3480.3, Total length = 73179, GC % = 41.99, # N's per 100 kbp =  0.00
  Drawing Nx plot...
    saved to /tmp/tmpmaxbzsnl/job_working_directory/000/6/working/outputdir/basic_stats/Nx_plot.pdf
  Drawing cumulative plot...
    saved to /tmp/tmpmaxbzsnl/job_working_directory/000/6/working/outputdir/basic_stats/cumulative_plot.pdf
  Drawing GC content plot...
    saved to /tmp/tmpmaxbzsnl/job_working_directory/000/6/working/outputdir/basic_stats/GC_content_plot.pdf
  Drawing genes_catalogue_test GC content plot...
    saved to /tmp/tmpmaxbzsnl/job_working_directory/000/6/working/outputdir/basic_stats/genes_catalogue_test_GC_content_plot.pdf
Done.

NOTICE: Genes are not predicted by default. Use --gene-finding or --glimmer option to enable it.

2026-08-10 09:54:25
Creating large visual summaries...
This may take a while: press Ctrl-C to skip this step..
  1 of 2: Creating PDF with all tables and plots...
  2 of 2: Creating Icarus viewers...
Done

2026-08-10 09:54:25
RESULTS:
  Text versions of total report are saved to /tmp/tmpmaxbzsnl/job_working_directory/000/6/working/outputdir/report.txt, report.tsv, and report.tex
  Text versions of transposed total report are saved to /tmp/tmpmaxbzsnl/job_working_directory/000/6/working/outputdir/transposed_report.txt, transposed_report.tsv, and transposed_report.tex
  HTML version (interactive tables and plots) is saved to /tmp/tmpmaxbzsnl/job_working_directory/000/6/working/outputdir/report.html
  PDF version (tables and plots) is saved to /tmp/tmpmaxbzsnl/job_working_directory/000/6/working/outputdir/report.pdf
  Icarus (contig browser) is saved to /tmp/tmpmaxbzsnl/job_working_directory/000/6/working/outputdir/icarus.html
  Log is saved to /tmp/tmpmaxbzsnl/job_working_directory/000/6/working/outputdir/quast.log

Finished: 2026-08-10 09:54:25
Elapsed time: 0:00:41.608378
NOTICEs: 3; WARNINGs: 1; non-fatal ERRORs: 0

Thank you for using QUAST!

              

              • 

            

            Traceback:
            

              

            • 

              

              • 

            

            Job Parameters:
            

              

            • 

              


              
Job parameter
Parameter value

              
              


              
__input_ext
"input"

              

              
__workflow_invocation_uuid__
"d3be488e94a011f194247c1e52f4ef47"

              

              
advanced
{"contig_thresholds": "0,1000,5000,10000,25000,50000", "extensive_mis_size": "1000", "fragmented_max_indent": null, "report_all_metrics": false, "scaffold_gap_max_size": "10000", "skip_unaligned_mis_contigs": true, "strict_NA": false, "unaligned_part_size": "500", "x_for_Nx": "90"}

              

              
alignments
{"ambiguity_score": "0.99", "ambiguity_usage": "one", "fragmented": false, "local_mis_size": "200", "min_alignment": "65", "upper_bound_assembly": false, "upper_bound_min_con": null, "use_all_alignments": false}

              

              
assembly
{"__current_case__": 1, "min_identity": "95.0", "ref": {"__current_case__": 0, "max_ref_num": "0", "origin": "silva"}, "reuse_combined_alignments": false, "type": "metagenome"}

              

              
chromInfo
"/tmp/tmpmaxbzsnl/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"

              

              
dbkey
"?"

              

              
genes
{"conserved_genes_finding": false, "gene_finding": {"__current_case__": 0, "tool": "none"}, "rna_finding": false}

              

              
large
false

              

              
min_contig
"1500"

              

              
mode
{"__current_case__": 0, "in": {"__current_case__": 1, "custom": "false", "inputs": {"values": [{"id": 4, "src": "dce"}]}}, "mode": "individual", "reads": {"__current_case__": 3, "input_1": {"values": [{"id": 1, "src": "dce"}]}, "reads_option": "paired_collection"}}

              

              
output_files
["html", "pdf", "tabular", "log", "summary"]

              

              
split_scaffolds
false

              
              

              

              • 

            

            • 

          

          

          • 

        

        • 

      • 

        Step 12: Unlabelled step (toolshed.g2.bx.psu.edu/repos/iuc/pick_value/pick_value/0.2.0):
        

          

        • 

          step_state: scheduled
          

          • 

        • 

          Jobs

            

          • 

            Job 1:
            

              

            • Job state is ok
              • 

            

            Command Line:
            

              

            • 

              cd ../; python _evaluate_expression_.py
              

              • 

            

            Exit Code:
            

              

            • 

              0
              

              • 

            

            Traceback:
            

              

            • 

              

              • 

            

            Job Parameters:
            

              

            • 

              


              
Job parameter
Parameter value

              
              


              
__input_ext
"input"

              

              
__workflow_invocation_uuid__
"d3be488e94a011f194247c1e52f4ef47"

              

              
chromInfo
"/tmp/tmpmaxbzsnl/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"

              

              
dbkey
"?"

              

              
style_cond
{"__current_case__": 1, "pick_style": "first_or_default", "type_cond": {"__current_case__": 3, "default_value": true, "param_type": "boolean", "pick_from": [{"__index__": 0, "value": null}]}}

              
              

              

              • 

            

            • 

          

          

          • 

        

        • 

      • 

        Step 13: Unlabelled step (toolshed.g2.bx.psu.edu/repos/mvdbeek/add_input_name_as_column/addName/0.3.0):
        

          

        • 

          step_state: scheduled
          

          • 

        • 

          Jobs

            

          • 

            Job 1:
            

              

            • Job state is ok
              • 

            

            Container:
            

              

            • 

              quay.io/biocontainers/python:3.13.7
              

              • 

            

            Command Line:
            

              

            • 

              python '/tmp/shed_data/shed_tools/toolshed.g2.bx.psu.edu/repos/mvdbeek/add_input_name_as_column/8a19efbd2178/add_input_name_as_column/add_input_name_as_column.py' --input '/tmp/tmpmaxbzsnl/files/2/7/a/dataset_27a375ce-0a14-467f-8751-c2303088e300.dat' --label 'genes_catalogue_test' --output '/tmp/tmpmaxbzsnl/job_working_directory/000/8/outputs/dataset_d33fb0bc-bef8-4a39-ae42-a1b5895e9102.dat' --prepend
              

              • 

            

            Exit Code:
            

              

            • 

              0
              

              • 

            

            Traceback:
            

              

            • 

              

              • 

            

            Job Parameters:
            

              

            • 

              


              
Job parameter
Parameter value

              
              


              
__input_ext
"input"

              

              
__workflow_invocation_uuid__
"d3be488e94a011f194247c1e52f4ef47"

              

              
chromInfo
"/tmp/tmpmaxbzsnl/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"

              

              
dbkey
"?"

              

              
header
{"__current_case__": 1, "contains_header": "no"}

              

              
prepend
true

              
              

              

              • 

            

            • 

          

          

          • 

        

        • 

      • 

        Step 14: Unlabelled step (toolshed.g2.bx.psu.edu/repos/devteam/tabular_to_fasta/tab2fasta/1.1.1):
        

          

        • 

          step_state: scheduled
          

          • 

        • 

          Jobs

            

          • 

            Job 1:
            

              

            • Job state is ok
              • 

            

            Container:
            

              

            • 

              quay.io/biocontainers/python:3.7--1
              

              • 

            

            Command Line:
            

              

            • 

              python '/tmp/shed_data/shed_tools/toolshed.g2.bx.psu.edu/repos/devteam/tabular_to_fasta/0a7799698fe5/tabular_to_fasta/tabular_to_fasta.py' '/tmp/tmpmaxbzsnl/files/d/3/3/dataset_d33fb0bc-bef8-4a39-ae42-a1b5895e9102.dat' 1,2 3 '/tmp/tmpmaxbzsnl/job_working_directory/000/9/outputs/dataset_00fec3a8-375d-43f9-a34e-a01e6811a8b6.dat'
              

              • 

            

            Exit Code:
            

              

            • 

              0
              

              • 

            

            Traceback:
            

              

            • 

              

              • 

            

            Job Parameters:
            

              

            • 

              


              
Job parameter
Parameter value

              
              


              
__input_ext
"input"

              

              
__workflow_invocation_uuid__
"d3be488e94a011f194247c1e52f4ef47"

              

              
chromInfo
"/tmp/tmpmaxbzsnl/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"

              

              
dbkey
"?"

              

              
seq_col
"3"

              

              
title_col
["1", "2"]

              
              

              

              • 

            

            • 

          

          

          • 

        

        • 

      • 

        Step 15: Unlabelled step (toolshed.g2.bx.psu.edu/repos/iuc/prodigal/prodigal/2.6.3+galaxy0):
        

          

        • 

          step_state: scheduled
          

          • 

        • 

          Jobs

            

          • 

            Job 1:
            

              

            • Job state is ok
              • 

            

            Container:
            

              

            • 

              quay.io/biocontainers/prodigal:2.6.3--h577a1d6_11
              

              • 

            

            Command Line:
            

              

            • 

              prodigal -i '/tmp/tmpmaxbzsnl/files/0/0/f/dataset_00fec3a8-375d-43f9-a34e-a01e6811a8b6.dat' -o '/tmp/tmpmaxbzsnl/job_working_directory/000/10/outputs/dataset_47d1ddef-35ee-4dc7-a2ac-ad34a72d9ee9.dat' -f 'gbk' -p 'meta' -g '11' -a '/tmp/tmpmaxbzsnl/job_working_directory/000/10/outputs/dataset_d9fe9bea-ea21-4422-b39e-655581238155.dat' -d '/tmp/tmpmaxbzsnl/job_working_directory/000/10/outputs/dataset_e8c78468-0f35-477b-b855-d357bf970f19.dat' -s '/tmp/tmpmaxbzsnl/job_working_directory/000/10/outputs/dataset_ef306394-c852-49d9-9de7-5c790f122cd9.dat'
              

              • 

            

            Exit Code:
            

              

            • 

              0
              

              • 

            

            Standard Error:
            

              

            • 

              -------------------------------------
PRODIGAL v2.6.3 [February, 2016]         
Univ of Tenn / Oak Ridge National Lab
Doug Hyatt, Loren Hauser, et al.     
-------------------------------------
Request:  Metagenomic, Phase:  Training
Initializing training files...done!
-------------------------------------
Request:  Metagenomic, Phase:  Gene Finding
Finding genes in sequence #1 (502 bp)...done!
Finding genes in sequence #2 (781 bp)...done!
Finding genes in sequence #3 (580 bp)...done!
Finding genes in sequence #4 (418 bp)...done!
Finding genes in sequence #5 (891 bp)...done!
Finding genes in sequence #6 (573 bp)...done!
Finding genes in sequence #7 (500 bp)...done!
Finding genes in sequence #8 (445 bp)...done!
Finding genes in sequence #9 (317 bp)...done!
Finding genes in sequence #10 (481 bp)...done!
Finding genes in sequence #11 (357 bp)...done!
Finding genes in sequence #12 (487 bp)...done!
Finding genes in sequence #13 (639 bp)...done!
Finding genes in sequence #14 (346 bp)...done!
Finding genes in sequence #15 (421 bp)...done!
Finding genes in sequence #16 (402 bp)...done!
Finding genes in sequence #17 (452 bp)...done!
Finding genes in sequence #18 (326 bp)...done!
Finding genes in sequence #19 (491 bp)...done!
Finding genes in sequence #20 (326 bp)...done!
Finding genes in sequence #21 (492 bp)...done!
Finding genes in sequence #22 (336 bp)...done!
Finding genes in sequence #23 (571 bp)...done!
Finding genes in sequence #24 (306 bp)...done!
Finding genes in sequence #25 (340 bp)...done!
Finding genes in sequence #26 (370 bp)...done!
Finding genes in sequence #27 (347 bp)...done!
Finding genes in sequence #28 (315 bp)...done!
Finding genes in sequence #29 (350 bp)...done!
Finding genes in sequence #30 (355 bp)...done!
Finding genes in sequence #31 (414 bp)...done!
Finding genes in sequence #32 (341 bp)...done!
Finding genes in sequence #33 (677 bp)...done!
Finding genes in sequence #34 (347 bp)...done!
Finding genes in sequence #35 (307 bp)...done!
Finding genes in sequence #36 (396 bp)...done!
Finding genes in sequence #37 (317 bp)...done!
Finding genes in sequence #38 (750 bp)...done!
Finding genes in sequence #39 (538 bp)...done!
Finding genes in sequence #40 (335 bp)...done!
Finding genes in sequence #41 (348 bp)...done!
Finding genes in sequence #42 (364 bp)...done!
Finding genes in sequence #43 (345 bp)...done!
Finding genes in sequence #44 (332 bp)...done!
Finding genes in sequence #45 (374 bp)...done!
Finding genes in sequence #46 (397 bp)...done!
Finding genes in sequence #47 (391 bp)...done!
Finding genes in sequence #48 (626 bp)...done!
Finding genes in sequence #49 (484 bp)...done!
Finding genes in sequence #50 (351 bp)...done!
Finding genes in sequence #51 (536 bp)...done!
Finding genes in sequence #52 (400 bp)...done!
Finding genes in sequence #53 (417 bp)...done!
Finding genes in sequence #54 (574 bp)...done!
Finding genes in sequence #55 (392 bp)...done!
Finding genes in sequence #56 (960 bp)...done!
Finding genes in sequence #57 (557 bp)...done!
Finding genes in sequence #58 (365 bp)...done!
Finding genes in sequence #59 (352 bp)...done!
Finding genes in sequence #60 (640 bp)...done!
Finding genes in sequence #61 (443 bp)...done!
Finding genes in sequence #62 (334 bp)...done!
Finding genes in sequence #63 (517 bp)...done!
Finding genes in sequence #64 (385 bp)...done!
Finding genes in sequence #65 (463 bp)...done!
Finding genes in sequence #66 (606 bp)...done!
Finding genes in sequence #67 (307 bp)...done!
Finding genes in sequence #68 (319 bp)...done!
Finding genes in sequence #69 (308 bp)...done!
Finding genes in sequence #70 (446 bp)...done!
Finding genes in sequence #71 (358 bp)...done!
Finding genes in sequence #72 (484 bp)...done!
Finding genes in sequence #73 (424 bp)...done!
Finding genes in sequence #74 (571 bp)...done!
Finding genes in sequence #75 (525 bp)...done!
Finding genes in sequence #76 (490 bp)...done!
Finding genes in sequence #77 (373 bp)...done!
Finding genes in sequence #78 (434 bp)...done!
Finding genes in sequence #79 (463 bp)...done!
Finding genes in sequence #80 (522 bp)...done!
Finding genes in sequence #81 (492 bp)...done!
Finding genes in sequence #82 (544 bp)...done!
Finding genes in sequence #83 (472 bp)...done!
Finding genes in sequence #84 (423 bp)...done!
Finding genes in sequence #85 (395 bp)...done!
Finding genes in sequence #86 (337 bp)...done!
Finding genes in sequence #87 (442 bp)...done!
Finding genes in sequence #88 (446 bp)...done!
Finding genes in sequence #89 (310 bp)...done!
Finding genes in sequence #90 (464 bp)...done!
Finding genes in sequence #91 (311 bp)...done!
Finding genes in sequence #92 (636 bp)...done!
Finding genes in sequence #93 (444 bp)...done!
Finding genes in sequence #94 (615 bp)...done!
Finding genes in sequence #95 (599 bp)...done!
Finding genes in sequence #96 (684 bp)...done!
Finding genes in sequence #97 (461 bp)...done!
Finding genes in sequence #98 (544 bp)...done!
Finding genes in sequence #99 (616 bp)...done!
Finding genes in sequence #100 (485 bp)...done!
Finding genes in sequence #101 (303 bp)...done!
Finding genes in sequence #102 (439 bp)...done!
Finding genes in sequence #103 (367 bp)...done!
Finding genes in sequence #104 (418 bp)...done!
Finding genes in sequence #105 (302 bp)...done!
Finding genes in sequence #106 (533 bp)...done!
Finding genes in sequence #107 (355 bp)...done!
Finding genes in sequence #108 (390 bp)...done!
Finding genes in sequence #109 (520 bp)...done!
Finding genes in sequence #110 (529 bp)...done!
Finding genes in sequence #111 (379 bp)...done!
Finding genes in sequence #112 (341 bp)...done!
Finding genes in sequence #113 (1222 bp)...done!
Finding genes in sequence #114 (338 bp)...done!
Finding genes in sequence #115 (305 bp)...done!
Finding genes in sequence #116 (500 bp)...done!
Finding genes in sequence #117 (357 bp)...done!
Finding genes in sequence #118 (458 bp)...done!
Finding genes in sequence #119 (637 bp)...done!
Finding genes in sequence #120 (357 bp)...done!
Finding genes in sequence #121 (347 bp)...done!
Finding genes in sequence #122 (350 bp)...done!
Finding genes in sequence #123 (584 bp)...done!
Finding genes in sequence #124 (522 bp)...done!
Finding genes in sequence #125 (354 bp)...done!
Finding genes in sequence #126 (549 bp)...done!
Finding genes in sequence #127 (311 bp)...done!
Finding genes in sequence #128 (455 bp)...done!
Finding genes in sequence #129 (368 bp)...done!
Finding genes in sequence #130 (728 bp)...done!
Finding genes in sequence #131 (385 bp)...done!
Finding genes in sequence #132 (506 bp)...done!
Finding genes in sequence #133 (319 bp)...done!
Finding genes in sequence #134 (303 bp)...done!
Finding genes in sequence #135 (311 bp)...done!
Finding genes in sequence #136 (308 bp)...done!
Finding genes in sequence #137 (319 bp)...done!
Finding genes in sequence #138 (653 bp)...done!
Finding genes in sequence #139 (303 bp)...done!
Finding genes in sequence #140 (480 bp)...done!
Finding genes in sequence #141 (451 bp)...done!
Finding genes in sequence #142 (696 bp)...done!
Finding genes in sequence #143 (394 bp)...done!
Finding genes in sequence #144 (869 bp)...done!
Finding genes in sequence #145 (501 bp)...done!
Finding genes in sequence #146 (305 bp)...done!
Finding genes in sequence #147 (406 bp)...done!
Finding genes in sequence #148 (697 bp)...done!
Finding genes in sequence #149 (326 bp)...done!
Finding genes in sequence #150 (495 bp)...done!
Finding genes in sequence #151 (474 bp)...done!
Finding genes in sequence #152 (617 bp)...done!
Finding genes in sequence #153 (325 bp)...done!
Finding genes in sequence #154 (304 bp)...done!
Finding genes in sequence #155 (430 bp)...done!
Finding genes in sequence #156 (319 bp)...done!
Finding genes in sequence #157 (343 bp)...done!
Finding genes in sequence #158 (453 bp)...done!
Finding genes in sequence #159 (397 bp)...done!
Finding genes in sequence #160 (413 bp)...done!
Finding genes in sequence #161 (305 bp)...done!
Finding genes in sequence #162 (434 bp)...done!
Finding genes in sequence #163 (313 bp)...done!
Finding genes in sequence #164 (313 bp)...done!
Finding genes in sequence #165 (312 bp)...done!
Finding genes in sequence #166 (379 bp)...done!
Finding genes in sequence #167 (314 bp)...done!
Finding genes in sequence #168 (404 bp)...done!
Finding genes in sequence #169 (353 bp)...done!
Finding genes in sequence #170 (306 bp)...done!
Finding genes in sequence #171 (525 bp)...done!
Finding genes in sequence #172 (428 bp)...done!
Finding genes in sequence #173 (598 bp)...done!
Finding genes in sequence #174 (309 bp)...done!
Finding genes in sequence #175 (324 bp)...done!
Finding genes in sequence #176 (353 bp)...done!
Finding genes in sequence #177 (627 bp)...done!
Finding genes in sequence #178 (364 bp)...done!
Finding genes in sequence #179 (348 bp)...done!
Finding genes in sequence #180 (331 bp)...done!
Finding genes in sequence #181 (478 bp)...done!
Finding genes in sequence #182 (316 bp)...done!
Finding genes in sequence #183 (327 bp)...done!
Finding genes in sequence #184 (649 bp)...done!
Finding genes in sequence #185 (357 bp)...done!
Finding genes in sequence #186 (384 bp)...done!
Finding genes in sequence #187 (414 bp)...done!
Finding genes in sequence #188 (406 bp)...done!
Finding genes in sequence #189 (725 bp)...done!
Finding genes in sequence #190 (305 bp)...done!
Finding genes in sequence #191 (939 bp)...done!
Finding genes in sequence #192 (392 bp)...done!
Finding genes in sequence #193 (467 bp)...done!
Finding genes in sequence #194 (347 bp)...done!
Finding genes in sequence #195 (350 bp)...done!
Finding genes in sequence #196 (904 bp)...done!
Finding genes in sequence #197 (724 bp)...done!
Finding genes in sequence #198 (455 bp)...done!
Finding genes in sequence #199 (348 bp)...done!
Finding genes in sequence #200 (805 bp)...done!
Finding genes in sequence #201 (323 bp)...done!
Finding genes in sequence #202 (424 bp)...done!
Finding genes in sequence #203 (321 bp)...done!
Finding genes in sequence #204 (794 bp)...done!
Finding genes in sequence #205 (533 bp)...done!
Finding genes in sequence #206 (458 bp)...done!
Finding genes in sequence #207 (336 bp)...done!
Finding genes in sequence #208 (506 bp)...done!
Finding genes in sequence #209 (577 bp)...done!
Finding genes in sequence #210 (347 bp)...done!
Finding genes in sequence #211 (433 bp)...done!
Finding genes in sequence #212 (568 bp)...done!
Finding genes in sequence #213 (378 bp)...done!
Finding genes in sequence #214 (583 bp)...done!
Finding genes in sequence #215 (303 bp)...done!
Finding genes in sequence #216 (624 bp)...done!
Finding genes in sequence #217 (575 bp)...done!
Finding genes in sequence #218 (362 bp)...done!
Finding genes in sequence #219 (779 bp)...done!
Finding genes in sequence #220 (306 bp)...done!
Finding genes in sequence #221 (378 bp)...done!
Finding genes in sequence #222 (554 bp)...done!
Finding genes in sequence #223 (514 bp)...done!
Finding genes in sequence #224 (378 bp)...done!
Finding genes in sequence #225 (474 bp)...done!
Finding genes in sequence #226 (392 bp)...done!
Finding genes in sequence #227 (455 bp)...done!
Finding genes in sequence #228 (469 bp)...done!
Finding genes in sequence #229 (562 bp)...done!
Finding genes in sequence #230 (365 bp)...done!
Finding genes in sequence #231 (345 bp)...done!
Finding genes in sequence #232 (387 bp)...done!
Finding genes in sequence #233 (467 bp)...done!
Finding genes in sequence #234 (409 bp)...done!
Finding genes in sequence #235 (335 bp)...done!
Finding genes in sequence #236 (488 bp)...done!
Finding genes in sequence #237 (323 bp)...done!
Finding genes in sequence #238 (438 bp)...done!
Finding genes in sequence #239 (305 bp)...done!
Finding genes in sequence #240 (319 bp)...done!
Finding genes in sequence #241 (904 bp)...done!
Finding genes in sequence #242 (612 bp)...done!
Finding genes in sequence #243 (332 bp)...done!
Finding genes in sequence #244 (353 bp)...done!
Finding genes in sequence #245 (315 bp)...done!
Finding genes in sequence #246 (785 bp)...done!
Finding genes in sequence #247 (350 bp)...done!
Finding genes in sequence #248 (822 bp)...done!
Finding genes in sequence #249 (243 bp)...done!
Finding genes in sequence #250 (511 bp)...done!
Finding genes in sequence #251 (532 bp)...done!
Finding genes in sequence #252 (365 bp)...done!
Finding genes in sequence #253 (305 bp)...done!
Finding genes in sequence #254 (394 bp)...done!
Finding genes in sequence #255 (315 bp)...done!
Finding genes in sequence #256 (357 bp)...done!
Finding genes in sequence #257 (508 bp)...done!
Finding genes in sequence #258 (322 bp)...done!
Finding genes in sequence #259 (357 bp)...done!
Finding genes in sequence #260 (415 bp)...done!
Finding genes in sequence #261 (488 bp)...done!
Finding genes in sequence #262 (489 bp)...done!
Finding genes in sequence #263 (412 bp)...done!
Finding genes in sequence #264 (357 bp)...done!
Finding genes in sequence #265 (330 bp)...done!
Finding genes in sequence #266 (800 bp)...done!
Finding genes in sequence #267 (309 bp)...done!
Finding genes in sequence #268 (312 bp)...done!
Finding genes in sequence #269 (321 bp)...done!
Finding genes in sequence #270 (635 bp)...done!
Finding genes in sequence #271 (467 bp)...done!
Finding genes in sequence #272 (380 bp)...done!
Finding genes in sequence #273 (487 bp)...done!
Finding genes in sequence #274 (384 bp)...done!
Finding genes in sequence #275 (1374 bp)...done!
Finding genes in sequence #276 (374 bp)...done!
Finding genes in sequence #277 (364 bp)...done!
Finding genes in sequence #278 (415 bp)...done!
Finding genes in sequence #279 (594 bp)...done!
Finding genes in sequence #280 (355 bp)...done!
Finding genes in sequence #281 (328 bp)...done!
Finding genes in sequence #282 (339 bp)...done!
Finding genes in sequence #283 (334 bp)...done!
Finding genes in sequence #284 (521 bp)...done!
Finding genes in sequence #285 (391 bp)...done!
Finding genes in sequence #286 (573 bp)...done!
Finding genes in sequence #287 (444 bp)...done!
Finding genes in sequence #288 (349 bp)...done!
Finding genes in sequence #289 (329 bp)...done!
Finding genes in sequence #290 (393 bp)...done!
Finding genes in sequence #291 (468 bp)...done!
Finding genes in sequence #292 (2347 bp)...done!
Finding genes in sequence #293 (619 bp)...done!
Finding genes in sequence #294 (401 bp)...done!
Finding genes in sequence #295 (354 bp)...done!
Finding genes in sequence #296 (520 bp)...done!
Finding genes in sequence #297 (332 bp)...done!
Finding genes in sequence #298 (504 bp)...done!
Finding genes in sequence #299 (322 bp)...done!
Finding genes in sequence #300 (628 bp)...done!
Finding genes in sequence #301 (576 bp)...done!
Finding genes in sequence #302 (350 bp)...done!
Finding genes in sequence #303 (384 bp)...done!
Finding genes in sequence #304 (624 bp)...done!
Finding genes in sequence #305 (809 bp)...done!
Finding genes in sequence #306 (402 bp)...done!
Finding genes in sequence #307 (306 bp)...done!
Finding genes in sequence #308 (365 bp)...done!
Finding genes in sequence #309 (310 bp)...done!
Finding genes in sequence #310 (404 bp)...done!
Finding genes in sequence #311 (436 bp)...done!
Finding genes in sequence #312 (309 bp)...done!
Finding genes in sequence #313 (412 bp)...done!
Finding genes in sequence #314 (340 bp)...done!
Finding genes in sequence #315 (449 bp)...done!
Finding genes in sequence #316 (338 bp)...done!
Finding genes in sequence #317 (336 bp)...done!
Finding genes in sequence #318 (352 bp)...done!
Finding genes in sequence #319 (395 bp)...done!
Finding genes in sequence #320 (1014 bp)...done!
Finding genes in sequence #321 (386 bp)...done!
Finding genes in sequence #322 (401 bp)...done!
Finding genes in sequence #323 (337 bp)...done!
Finding genes in sequence #324 (310 bp)...done!
Finding genes in sequence #325 (464 bp)...done!
Finding genes in sequence #326 (450 bp)...done!
Finding genes in sequence #327 (332 bp)...done!
Finding genes in sequence #328 (311 bp)...done!
Finding genes in sequence #329 (424 bp)...done!
Finding genes in sequence #330 (345 bp)...done!
Finding genes in sequence #331 (541 bp)...done!
Finding genes in sequence #332 (432 bp)...done!
Finding genes in sequence #333 (576 bp)...done!
Finding genes in sequence #334 (348 bp)...done!
Finding genes in sequence #335 (420 bp)...done!
Finding genes in sequence #336 (383 bp)...done!
Findin
..
ne!
Finding genes in sequence #3452 (311 bp)...done!
Finding genes in sequence #3453 (620 bp)...done!
Finding genes in sequence #3454 (354 bp)...done!
Finding genes in sequence #3455 (485 bp)...done!
Finding genes in sequence #3456 (338 bp)...done!
Finding genes in sequence #3457 (715 bp)...done!
Finding genes in sequence #3458 (372 bp)...done!
Finding genes in sequence #3459 (438 bp)...done!
Finding genes in sequence #3460 (707 bp)...done!
Finding genes in sequence #3461 (417 bp)...done!
Finding genes in sequence #3462 (403 bp)...done!
Finding genes in sequence #3463 (452 bp)...done!
Finding genes in sequence #3464 (317 bp)...done!
Finding genes in sequence #3465 (312 bp)...done!
Finding genes in sequence #3466 (499 bp)...done!
Finding genes in sequence #3467 (322 bp)...done!
Finding genes in sequence #3468 (326 bp)...done!
Finding genes in sequence #3469 (397 bp)...done!
Finding genes in sequence #3470 (308 bp)...done!
Finding genes in sequence #3471 (412 bp)...done!
Finding genes in sequence #3472 (566 bp)...done!
Finding genes in sequence #3473 (361 bp)...done!
Finding genes in sequence #3474 (355 bp)...done!
Finding genes in sequence #3475 (370 bp)...done!
Finding genes in sequence #3476 (368 bp)...done!
Finding genes in sequence #3477 (498 bp)...done!
Finding genes in sequence #3478 (346 bp)...done!
Finding genes in sequence #3479 (338 bp)...done!
Finding genes in sequence #3480 (476 bp)...done!
Finding genes in sequence #3481 (900 bp)...done!
Finding genes in sequence #3482 (470 bp)...done!
Finding genes in sequence #3483 (304 bp)...done!
Finding genes in sequence #3484 (310 bp)...done!
Finding genes in sequence #3485 (347 bp)...done!
Finding genes in sequence #3486 (394 bp)...done!
Finding genes in sequence #3487 (344 bp)...done!
Finding genes in sequence #3488 (350 bp)...done!
Finding genes in sequence #3489 (727 bp)...done!
Finding genes in sequence #3490 (483 bp)...done!
Finding genes in sequence #3491 (325 bp)...done!
Finding genes in sequence #3492 (707 bp)...done!
Finding genes in sequence #3493 (330 bp)...done!
Finding genes in sequence #3494 (391 bp)...done!
Finding genes in sequence #3495 (391 bp)...done!
Finding genes in sequence #3496 (414 bp)...done!
Finding genes in sequence #3497 (807 bp)...done!
Finding genes in sequence #3498 (423 bp)...done!
Finding genes in sequence #3499 (340 bp)...done!
Finding genes in sequence #3500 (698 bp)...done!
Finding genes in sequence #3501 (373 bp)...done!
Finding genes in sequence #3502 (324 bp)...done!
Finding genes in sequence #3503 (339 bp)...done!
Finding genes in sequence #3504 (392 bp)...done!
Finding genes in sequence #3505 (350 bp)...done!
Finding genes in sequence #3506 (377 bp)...done!
Finding genes in sequence #3507 (482 bp)...done!
Finding genes in sequence #3508 (399 bp)...done!
Finding genes in sequence #3509 (533 bp)...done!
Finding genes in sequence #3510 (342 bp)...done!
Finding genes in sequence #3511 (324 bp)...done!
Finding genes in sequence #3512 (433 bp)...done!
Finding genes in sequence #3513 (644 bp)...done!
Finding genes in sequence #3514 (323 bp)...done!
Finding genes in sequence #3515 (652 bp)...done!
Finding genes in sequence #3516 (406 bp)...done!
Finding genes in sequence #3517 (526 bp)...done!
Finding genes in sequence #3518 (354 bp)...done!
Finding genes in sequence #3519 (392 bp)...done!
Finding genes in sequence #3520 (544 bp)...done!
Finding genes in sequence #3521 (393 bp)...done!
Finding genes in sequence #3522 (342 bp)...done!
Finding genes in sequence #3523 (449 bp)...done!
Finding genes in sequence #3524 (310 bp)...done!
Finding genes in sequence #3525 (406 bp)...done!
Finding genes in sequence #3526 (401 bp)...done!
Finding genes in sequence #3527 (1019 bp)...done!
Finding genes in sequence #3528 (335 bp)...done!
Finding genes in sequence #3529 (333 bp)...done!
Finding genes in sequence #3530 (725 bp)...done!
Finding genes in sequence #3531 (570 bp)...done!
Finding genes in sequence #3532 (324 bp)...done!
Finding genes in sequence #3533 (383 bp)...done!
Finding genes in sequence #3534 (499 bp)...done!
Finding genes in sequence #3535 (342 bp)...done!
Finding genes in sequence #3536 (311 bp)...done!
Finding genes in sequence #3537 (312 bp)...done!
Finding genes in sequence #3538 (357 bp)...done!
Finding genes in sequence #3539 (335 bp)...done!
Finding genes in sequence #3540 (337 bp)...done!
Finding genes in sequence #3541 (318 bp)...done!
Finding genes in sequence #3542 (353 bp)...done!
Finding genes in sequence #3543 (698 bp)...done!
Finding genes in sequence #3544 (325 bp)...done!
Finding genes in sequence #3545 (585 bp)...done!
Finding genes in sequence #3546 (503 bp)...done!
Finding genes in sequence #3547 (542 bp)...done!
Finding genes in sequence #3548 (499 bp)...done!
Finding genes in sequence #3549 (625 bp)...done!
Finding genes in sequence #3550 (335 bp)...done!
Finding genes in sequence #3551 (520 bp)...done!
Finding genes in sequence #3552 (892 bp)...done!
Finding genes in sequence #3553 (634 bp)...done!
Finding genes in sequence #3554 (472 bp)...done!
Finding genes in sequence #3555 (350 bp)...done!
Finding genes in sequence #3556 (420 bp)...done!
Finding genes in sequence #3557 (397 bp)...done!
Finding genes in sequence #3558 (663 bp)...done!
Finding genes in sequence #3559 (2276 bp)...done!
Finding genes in sequence #3560 (407 bp)...done!
Finding genes in sequence #3561 (368 bp)...done!
Finding genes in sequence #3562 (405 bp)...done!
Finding genes in sequence #3563 (556 bp)...done!
Finding genes in sequence #3564 (699 bp)...done!
Finding genes in sequence #3565 (324 bp)...done!
Finding genes in sequence #3566 (542 bp)...done!
Finding genes in sequence #3567 (536 bp)...done!
Finding genes in sequence #3568 (573 bp)...done!
Finding genes in sequence #3569 (330 bp)...done!
Finding genes in sequence #3570 (315 bp)...done!
Finding genes in sequence #3571 (313 bp)...done!
Finding genes in sequence #3572 (345 bp)...done!
Finding genes in sequence #3573 (330 bp)...done!
Finding genes in sequence #3574 (388 bp)...done!
Finding genes in sequence #3575 (315 bp)...done!
Finding genes in sequence #3576 (336 bp)...done!
Finding genes in sequence #3577 (333 bp)...done!
Finding genes in sequence #3578 (307 bp)...done!
Finding genes in sequence #3579 (362 bp)...done!
Finding genes in sequence #3580 (347 bp)...done!
Finding genes in sequence #3581 (359 bp)...done!
Finding genes in sequence #3582 (442 bp)...done!
Finding genes in sequence #3583 (357 bp)...done!
Finding genes in sequence #3584 (361 bp)...done!
Finding genes in sequence #3585 (604 bp)...done!
Finding genes in sequence #3586 (351 bp)...done!
Finding genes in sequence #3587 (433 bp)...done!
Finding genes in sequence #3588 (394 bp)...done!
Finding genes in sequence #3589 (450 bp)...done!
Finding genes in sequence #3590 (330 bp)...done!
Finding genes in sequence #3591 (319 bp)...done!
Finding genes in sequence #3592 (309 bp)...done!
Finding genes in sequence #3593 (736 bp)...done!
Finding genes in sequence #3594 (437 bp)...done!
Finding genes in sequence #3595 (301 bp)...done!
Finding genes in sequence #3596 (331 bp)...done!
Finding genes in sequence #3597 (666 bp)...done!
Finding genes in sequence #3598 (348 bp)...done!
Finding genes in sequence #3599 (585 bp)...done!
Finding genes in sequence #3600 (301 bp)...done!
Finding genes in sequence #3601 (500 bp)...done!
Finding genes in sequence #3602 (337 bp)...done!
Finding genes in sequence #3603 (327 bp)...done!
Finding genes in sequence #3604 (515 bp)...done!
Finding genes in sequence #3605 (671 bp)...done!
Finding genes in sequence #3606 (371 bp)...done!
Finding genes in sequence #3607 (848 bp)...done!
Finding genes in sequence #3608 (425 bp)...done!
Finding genes in sequence #3609 (350 bp)...done!
Finding genes in sequence #3610 (351 bp)...done!
Finding genes in sequence #3611 (1005 bp)...done!
Finding genes in sequence #3612 (1118 bp)...done!
Finding genes in sequence #3613 (439 bp)...done!
Finding genes in sequence #3614 (351 bp)...done!
Finding genes in sequence #3615 (328 bp)...done!
Finding genes in sequence #3616 (364 bp)...done!
Finding genes in sequence #3617 (493 bp)...done!
Finding genes in sequence #3618 (441 bp)...done!
Finding genes in sequence #3619 (652 bp)...done!
Finding genes in sequence #3620 (322 bp)...done!
Finding genes in sequence #3621 (601 bp)...done!
Finding genes in sequence #3622 (407 bp)...done!
Finding genes in sequence #3623 (462 bp)...done!
Finding genes in sequence #3624 (947 bp)...done!
Finding genes in sequence #3625 (473 bp)...done!
Finding genes in sequence #3626 (401 bp)...done!
Finding genes in sequence #3627 (715 bp)...done!
Finding genes in sequence #3628 (616 bp)...done!
Finding genes in sequence #3629 (342 bp)...done!
Finding genes in sequence #3630 (313 bp)...done!
Finding genes in sequence #3631 (487 bp)...done!
Finding genes in sequence #3632 (511 bp)...done!
Finding genes in sequence #3633 (320 bp)...done!
Finding genes in sequence #3634 (330 bp)...done!
Finding genes in sequence #3635 (353 bp)...done!
Finding genes in sequence #3636 (465 bp)...done!
Finding genes in sequence #3637 (516 bp)...done!
Finding genes in sequence #3638 (411 bp)...done!
Finding genes in sequence #3639 (597 bp)...done!
Finding genes in sequence #3640 (301 bp)...done!
Finding genes in sequence #3641 (581 bp)...done!
Finding genes in sequence #3642 (421 bp)...done!
Finding genes in sequence #3643 (367 bp)...done!
Finding genes in sequence #3644 (433 bp)...done!
Finding genes in sequence #3645 (391 bp)...done!
Finding genes in sequence #3646 (357 bp)...done!
Finding genes in sequence #3647 (316 bp)...done!
Finding genes in sequence #3648 (415 bp)...done!
Finding genes in sequence #3649 (364 bp)...done!
Finding genes in sequence #3650 (522 bp)...done!
Finding genes in sequence #3651 (614 bp)...done!
Finding genes in sequence #3652 (357 bp)...done!
Finding genes in sequence #3653 (348 bp)...done!
Finding genes in sequence #3654 (430 bp)...done!
Finding genes in sequence #3655 (340 bp)...done!
Finding genes in sequence #3656 (313 bp)...done!
Finding genes in sequence #3657 (328 bp)...done!
Finding genes in sequence #3658 (569 bp)...done!
Finding genes in sequence #3659 (607 bp)...done!
Finding genes in sequence #3660 (437 bp)...done!
Finding genes in sequence #3661 (354 bp)...done!
Finding genes in sequence #3662 (382 bp)...done!
Finding genes in sequence #3663 (354 bp)...done!
Finding genes in sequence #3664 (541 bp)...done!
Finding genes in sequence #3665 (346 bp)...done!
Finding genes in sequence #3666 (314 bp)...done!
Finding genes in sequence #3667 (332 bp)...done!
Finding genes in sequence #3668 (367 bp)...done!
Finding genes in sequence #3669 (632 bp)...done!
Finding genes in sequence #3670 (304 bp)...done!
Finding genes in sequence #3671 (373 bp)...done!
Finding genes in sequence #3672 (1327 bp)...done!
Finding genes in sequence #3673 (488 bp)...done!
Finding genes in sequence #3674 (860 bp)...done!
Finding genes in sequence #3675 (482 bp)...done!
Finding genes in sequence #3676 (349 bp)...done!
Finding genes in sequence #3677 (383 bp)...done!
Finding genes in sequence #3678 (343 bp)...done!
Finding genes in sequence #3679 (437 bp)...done!
Finding genes in sequence #3680 (1384 bp)...done!
Finding genes in sequence #3681 (485 bp)...done!
Finding genes in sequence #3682 (472 bp)...done!
Finding genes in sequence #3683 (315 bp)...done!
Finding genes in sequence #3684 (397 bp)...done!
Finding genes in sequence #3685 (406 bp)...done!
Finding genes in sequence #3686 (411 bp)...done!
Finding genes in sequence #3687 (498 bp)...done!
Finding genes in sequence #3688 (452 bp)...done!
Finding genes in sequence #3689 (376 bp)...done!
Finding genes in sequence #3690 (503 bp)...done!
Finding genes in sequence #3691 (333 bp)...done!
Finding genes in sequence #3692 (335 bp)...done!
Finding genes in sequence #3693 (369 bp)...done!
Finding genes in sequence #3694 (361 bp)...done!
Finding genes in sequence #3695 (304 bp)...done!
Finding genes in sequence #3696 (427 bp)...done!
Finding genes in sequence #3697 (442 bp)...done!
Finding genes in sequence #3698 (355 bp)...done!
Finding genes in sequence #3699 (347 bp)...done!
Finding genes in sequence #3700 (410 bp)...done!
Finding genes in sequence #3701 (414 bp)...done!
Finding genes in sequence #3702 (314 bp)...done!
Finding genes in sequence #3703 (338 bp)...done!
Finding genes in sequence #3704 (363 bp)...done!
Finding genes in sequence #3705 (343 bp)...done!
Finding genes in sequence #3706 (780 bp)...done!
Finding genes in sequence #3707 (441 bp)...done!
Finding genes in sequence #3708 (311 bp)...done!
Finding genes in sequence #3709 (307 bp)...done!
Finding genes in sequence #3710 (403 bp)...done!
Finding genes in sequence #3711 (610 bp)...done!
Finding genes in sequence #3712 (523 bp)...done!
Finding genes in sequence #3713 (670 bp)...done!
Finding genes in sequence #3714 (535 bp)...done!
Finding genes in sequence #3715 (337 bp)...done!
Finding genes in sequence #3716 (346 bp)...done!
Finding genes in sequence #3717 (623 bp)...done!
Finding genes in sequence #3718 (312 bp)...done!
Finding genes in sequence #3719 (341 bp)...done!
Finding genes in sequence #3720 (506 bp)...done!
Finding genes in sequence #3721 (373 bp)...done!
Finding genes in sequence #3722 (325 bp)...done!
Finding genes in sequence #3723 (578 bp)...done!
Finding genes in sequence #3724 (416 bp)...done!
Finding genes in sequence #3725 (2267 bp)...done!
Finding genes in sequence #3726 (546 bp)...done!
Finding genes in sequence #3727 (378 bp)...done!
Finding genes in sequence #3728 (309 bp)...done!
Finding genes in sequence #3729 (363 bp)...done!
Finding genes in sequence #3730 (359 bp)...done!
Finding genes in sequence #3731 (731 bp)...done!
Finding genes in sequence #3732 (340 bp)...done!
Finding genes in sequence #3733 (412 bp)...done!
Finding genes in sequence #3734 (488 bp)...done!
Finding genes in sequence #3735 (500 bp)...done!
Finding genes in sequence #3736 (526 bp)...done!
Finding genes in sequence #3737 (1476 bp)...done!
Finding genes in sequence #3738 (376 bp)...done!
Finding genes in sequence #3739 (319 bp)...done!
Finding genes in sequence #3740 (430 bp)...done!
Finding genes in sequence #3741 (426 bp)...done!
Finding genes in sequence #3742 (422 bp)...done!
Finding genes in sequence #3743 (358 bp)...done!
Finding genes in sequence #3744 (419 bp)...done!
Finding genes in sequence #3745 (697 bp)...done!
Finding genes in sequence #3746 (460 bp)...done!
Finding genes in sequence #3747 (580 bp)...done!
Finding genes in sequence #3748 (345 bp)...done!
Finding genes in sequence #3749 (735 bp)...done!
Finding genes in sequence #3750 (348 bp)...done!
Finding genes in sequence #3751 (402 bp)...done!
Finding genes in sequence #3752 (650 bp)...done!
Finding genes in sequence #3753 (572 bp)...done!
Finding genes in sequence #3754 (651 bp)...done!
Finding genes in sequence #3755 (470 bp)...done!
Finding genes in sequence #3756 (702 bp)...done!
Finding genes in sequence #3757 (582 bp)...done!
Finding genes in sequence #3758 (356 bp)...done!
Finding genes in sequence #3759 (313 bp)...done!
Finding genes in sequence #3760 (764 bp)...done!
Finding genes in sequence #3761 (499 bp)...done!
Finding genes in sequence #3762 (330 bp)...done!
Finding genes in sequence #3763 (359 bp)...done!
Finding genes in sequence #3764 (332 bp)...done!
Finding genes in sequence #3765 (656 bp)...done!
Finding genes in sequence #3766 (337 bp)...done!
Finding genes in sequence #3767 (367 bp)...done!
Finding genes in sequence #3768 (455 bp)...done!
Finding genes in sequence #3769 (337 bp)...done!
Finding genes in sequence #3770 (376 bp)...done!
Finding genes in sequence #3771 (1218 bp)...done!
Finding genes in sequence #3772 (304 bp)...done!
Finding genes in sequence #3773 (306 bp)...done!
Finding genes in sequence #3774 (472 bp)...done!
Finding genes in sequence #3775 (551 bp)...done!
Finding genes in sequence #3776 (574 bp)...done!
Finding genes in sequence #3777 (413 bp)...done!
Finding genes in sequence #3778 (400 bp)...done!
Finding genes in sequence #3779 (362 bp)...done!
Finding genes in sequence #3780 (5734 bp)...done!
Finding genes in sequence #3781 (1440 bp)...done!
Finding genes in sequence #3782 (317 bp)...done!
Finding genes in sequence #3783 (369 bp)...done!
Finding genes in sequence #3784 (269 bp)...done!
Finding genes in sequence #3785 (1935 bp)...done!

              

              • 

            

            Traceback:
            

              

            • 

              

              • 

            

            Job Parameters:
            

              

            • 

              


              
Job parameter
Parameter value

              
              


              
__input_ext
"input"

              

              
__workflow_invocation_uuid__
"d3be488e94a011f194247c1e52f4ef47"

              

              
chromInfo
"/tmp/tmpmaxbzsnl/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"

              

              
closed
false

              

              
dbkey
"?"

              

              
force_nonsd
false

              

              
input_train
None

              

              
masked_seq
false

              

              
out_format
"gbk"

              

              
procedure
"meta"

              

              
trans_table
"11"

              
              

              

              • 

            

            • 

          

          

          • 

        

        • 

      • 

        Step 16: Unlabelled step (toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_cat/9.5+galaxy3):
        

          

        • 

          step_state: scheduled
          

          • 

        • 

          Jobs

            

          • 

            Job 1:
            

              

            • Job state is ok
              • 

            

            Container:
            

              

            • 

              quay.io/biocontainers/coreutils:9.5
              

              • 

            

            Command Line:
            

              

            • 

              cat '/tmp/tmpmaxbzsnl/files/e/8/c/dataset_e8c78468-0f35-477b-b855-d357bf970f19.dat' >> '/tmp/tmpmaxbzsnl/job_working_directory/000/11/outputs/dataset_eff79722-a549-4eff-a6da-cc7f0850257c.dat' && exit 0
              

              • 

            

            Exit Code:
            

              

            • 

              0
              

              • 

            

            Traceback:
            

              

            • 

              

              • 

            

            Job Parameters:
            

              

            • 

              


              
Job parameter
Parameter value

              
              


              
__input_ext
"input"

              

              
__workflow_invocation_uuid__
"d3be488e94a011f194247c1e52f4ef47"

              

              
chromInfo
"/tmp/tmpmaxbzsnl/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"

              

              
dbkey
"?"

              

              
queries
[]

              
              

              

              • 

            

            • 

          

          

          • 

        

        • 

      • 

        Step 17: MMseqs2 full catalogue Sequence Clustering (toolshed.g2.bx.psu.edu/repos/iuc/mmseqs2_easy_linclust_clustering/mmseqs2_easy_linclust_clustering/17-b804f+galaxy1):
        

          

        • 

          step_state: scheduled
          

          • 

        • 

          Jobs

            

          • 

            Job 1:
            

              

            • Job state is skipped
              • 

            

            Traceback:
            

              

            • 

              

              • 

            

            Job Parameters:
            

              

            • 

              


              
Job parameter
Parameter value

              
              


              
__input_ext
"input"

              

              
__workflow_invocation_uuid__
"d3be488e94a011f194247c1e52f4ef47"

              

              
align
{"alignment_mode": "0", "alignment_output_mode": "0", "alt_ali": "0", "convertalis": false, "corr_score_weight": "0.0", "evalue": "0.001", "max_accept": "2147483647", "max_rejected": "2147483647", "min_aln_len": "0", "realign": false, "realign_max_seqs": "2147483647", "realign_score_bias": "-0.2", "score_bias": "0.0", "seq_id_mode": "0", "wrapped_scoring": false}

              

              
alph_type
{"__current_case__": 0, "dbtype": "0"}

              

              
chromInfo
"/tmp/tmpmaxbzsnl/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"

              

              
cluster
{"cluster_mode": "0", "max_iterations": "1000", "similarity_type": "2"}

              

              
common
{"max_seq_len": "65535"}

              

              
cov
"0.8"

              

              
cov_mode
"0"

              

              
dbkey
"?"

              

              
expert
{"filter_hits": false, "sort_results": "0"}

              

              
kmermatcher
{"cluster_weight_threshold": "0.9", "hash_shift": "67", "ignore_multi_kmer": false, "include_only_extendable": false, "kmer_per_seq": "21"}

              

              
min_seq_id
"0.95"

              

              
misc
{"id_offset": "0", "rescore_mode": "0", "shuffle": true}

              

              
output_files
{"output_selection": ["file_rep_seq", "file_all_seq", "file_cluster_tsv"]}

              

              
prefilter
{"add_self_matches": false, "kmer_length": "0", "mask": "1", "mask_lower_case": "0", "mask_n_repeat": "0", "mask_prob": "0.9", "spaced_kmer_mode": "0"}

              
              

              

              • 

            

            • 

          

          

          • 

        

        • 

      • 

        Step 18: Unlabelled step (toolshed.g2.bx.psu.edu/repos/iuc/pick_value/pick_value/0.2.0):
        

          

        • 

          step_state: scheduled
          

          • 

        • 

          Jobs

            

          • 

            Job 1:
            

              

            • Job state is ok
              • 

            

            Command Line:
            

              

            • 

              cd ../; python _evaluate_expression_.py
              

              • 

            

            Exit Code:
            

              

            • 

              0
              

              • 

            

            Traceback:
            

              

            • 

              

              • 

            

            Job Parameters:
            

              

            • 

              


              
Job parameter
Parameter value

              
              


              
__input_ext
"input"

              

              
__workflow_invocation_uuid__
"d3be488e94a011f194247c1e52f4ef47"

              

              
chromInfo
"/tmp/tmpmaxbzsnl/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"

              

              
dbkey
"?"

              

              
style_cond
{"__current_case__": 1, "pick_style": "first_or_default", "type_cond": {"__current_case__": 4, "default_value": {"values": [{"id": 16, "src": "dce"}]}, "param_type": "data", "pick_from": [{"__index__": 0, "value": {"values": [{"id": 18, "src": "hda"}]}}]}}

              
              

              

              • 

            

            • 

          

          

          • 

        

        • 

      • 

        Step 19: Unlabelled step (toolshed.g2.bx.psu.edu/repos/iuc/amrfinderplus/amrfinderplus/4.2.7+galaxy0):
        

          

        • 

          step_state: scheduled
          

          • 

        • 

          Jobs

            

          • 

            Job 1:
            

              

            • Job state is error
              • 

            

            Traceback:
            

              

            • 

              

              • 

            

            Job Parameters:
            

              

            • 

              


              
Job parameter
Parameter value

              
              


              
__input_ext
"input"

              

              
__workflow_invocation_uuid__
"d3be488e94a011f194247c1e52f4ef47"

              

              
chromInfo
"/tmp/tmpmaxbzsnl/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"

              

              
dbkey
"?"

              

              
input_option
{"amrfinder_db_select": "amrfinderplus_V3.12_2024-05-02.2", "input_mode": {"__current_case__": 0, "input_select": "nucleotide", "nucleotide_flank5_size": "0", "nucleotide_input": {"values": [{"id": 18, "src": "dce"}]}}}

              

              
options
{"add_version_columns": false, "coverage_min": "0.5", "ident_min": "-1.0", "name": null, "plus": false, "print_node": false, "report_all_equal": false, "translation_table": "11"}

              

              
organism_options
{"organism_conditionnal": {"__current_case__": 1, "organism_select": ""}}

              
              

              

              • 

            

            • 

          

          

          • 

        

        • 

      • 

        Step 20: Unlabelled step (toolshed.g2.bx.psu.edu/repos/iuc/abricate/abricate/1.4.0+galaxy1):
        

          

        • 

          step_state: scheduled
          

          • 

        • 

          Jobs

            

          • 

            Job 1:
            

              

            • Job state is ok
              • 

            

            Container:
            

              

            • 

              quay.io/biocontainers/abricate:1.4.0--h05cac1d_0
              

              • 

            

            Command Line:
            

              

            • 

              ln -sf '/tmp/tmpmaxbzsnl/files/e/8/c/dataset_e8c78468-0f35-477b-b855-d357bf970f19.dat' genes_catalogue_test &&  abricate genes_catalogue_test  --minid=80.0 --mincov=80.0 --db=resfinder > '/tmp/tmpmaxbzsnl/job_working_directory/000/15/outputs/dataset_be3ac2f1-f197-4e04-aede-6e157c996a11.dat'
              

              • 

            

            Exit Code:
            

              

            • 

              0
              

              • 

            

            Standard Error:
            

              

            • 

              Using nucl database resfinder:  3206 sequences -  2026-Apr-3
Processing: genes_catalogue_test
Found 1 genes in genes_catalogue_test
Tip: found a bug in abricate? Post it at https://github.com/tseemann/abricate/issues.
Done.

              

              • 

            

            Traceback:
            

              

            • 

              

              • 

            

            Job Parameters:
            

              

            • 

              


              
Job parameter
Parameter value

              
              


              
__input_ext
"input"

              

              
__workflow_invocation_uuid__
"d3be488e94a011f194247c1e52f4ef47"

              

              
adv
{"db": "resfinder", "min_cov": "80.0", "min_dna_id": "80.0", "no_header": false}

              

              
chromInfo
"/tmp/tmpmaxbzsnl/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"

              

              
dbkey
"?"

              
              

              

              • 

            

            • 

          

          

          • 

        

        • 

      • 

        Step 21: Unlabelled step (toolshed.g2.bx.psu.edu/repos/iuc/staramr/staramr_search/0.12.3+galaxy0):
        

          

        • 

          step_state: scheduled
          

          • 

        • 

          Jobs

            

          • 

            Job 1:
            

              

            • Job state is ok
              • 

            

            Container:
            

              

            • 

              quay.io/biocontainers/mulled-v2-30758c5e2be407d6bbf2570c832fb245e8488634:554912fb4663b66a7db92472d73ef2d27ab8ae27-0
              

              • 

            

            Command Line:
            

              

            • 

              ln -s '/tmp/tmpmaxbzsnl/files/e/8/c/dataset_e8c78468-0f35-477b-b855-d357bf970f19.dat' genes_catalogue_test.fasta &&  export GIT_CONFIG_COUNT=1 GIT_CONFIG_KEY_0=safe.directory GIT_CONFIG_VALUE_0=* &&  staramr search  -d '/cvmfs/data.galaxyproject.org/byhand/staramr/resfinder_d1e607b_pointfinder_694919f_plasmidfinder_3e77502' --nprocs "${GALAXY_SLOTS:-1}"  --genome-size-lower-bound 4000000 --genome-size-upper-bound 6000000 --minimum-N50-value 10000 --minimum-contig-length 300 --unacceptable-number-contigs 1000  --pid-threshold 98.0 --percent-length-overlap-resfinder 60.0 --percent-length-overlap-plasmidfinder 60.0 --percent-length-overlap-pointfinder 95.0          --output-summary '/tmp/tmpmaxbzsnl/job_working_directory/000/16/outputs/dataset_c2197c24-9e1a-4c1f-ac5d-37465acb3fc0.dat' --output-detailed-summary '/tmp/tmpmaxbzsnl/job_working_directory/000/16/outputs/dataset_a8e0850f-2f2e-44ff-b174-775380c3c3f5.dat' --output-resfinder '/tmp/tmpmaxbzsnl/job_working_directory/000/16/outputs/dataset_19382bab-0573-4171-8b2b-314e35684cf1.dat' --output-plasmidfinder '/tmp/tmpmaxbzsnl/job_working_directory/000/16/outputs/dataset_2c5324cf-1bff-433d-9949-996afa4d90b8.dat' --output-settings 'XXXX' --output-excel results.xlsx --output-mlst '/tmp/tmpmaxbzsnl/job_working_directory/000/16/outputs/dataset_1c8a50dd-330e-48c4-a8eb-99b9bfddc19b.dat'  --output-hits-dir staramr_hits   genes_catalogue_test.fasta
              

              • 

            

            Exit Code:
            

              

            • 

              0
              

              • 

            

            Standard Error:
            

              

            • 

              2026-08-10 09:57:25 WARNING: Using non-default ResFinder/PointFinder. This may lead to differences in the detected AMR genes depending on how the database files are structured.
2026-08-10 09:57:25 INFO: No --pointfinder-organism specified. Will not search the PointFinder databases
2026-08-10 09:57:25 INFO: No --plasmidfinder-database-type specified. Will search the entire PlasmidFinder database
2026-08-10 09:57:25 INFO: --output-dir not set. Files will be output to the respective --output-[type] setting
2026-08-10 09:57:25 INFO: Will exclude ResFinder/PointFinder genes listed in [/usr/local/lib/python3.14/site-packages/staramr/databases/exclude/data/genes_to_exclude.tsv]. Use --no-exclude-genes to disable
2026-08-10 09:57:25 INFO: Will report complex mutations listed in [/usr/local/lib/python3.14/site-packages/staramr/databases/resistance/pointfinder/complex/data/complex_mutations.tsv]
2026-08-10 09:57:25 INFO: Making BLAST databases for input files
2026-08-10 09:57:25 INFO: Scheduling blasts and MLST for genes_catalogue_test.fasta
2026-08-10 09:57:36 WARNING: No drug found for drug_class=all, gene=cfxA_1, accession=U38243
2026-08-10 09:57:39 INFO: Finished. Took 0.24 minutes.
2026-08-10 09:57:44 INFO: Predicting AMR resistance phenotypes is enabled. The predictions are for microbiological resistance and *not* clinical resistance. These results are continually being improved and we welcome any feedback.
2026-08-10 09:57:44 INFO: Writing resfinder to [/tmp/tmpmaxbzsnl/job_working_directory/000/16/outputs/dataset_19382bab-0573-4171-8b2b-314e35684cf1.dat]
2026-08-10 09:57:44 INFO: --output-dir or --output-pointfinder unset. No pointfinder file will be written
2026-08-10 09:57:44 INFO: Writing plasmidfinder to [/tmp/tmpmaxbzsnl/job_working_directory/000/16/outputs/dataset_2c5324cf-1bff-433d-9949-996afa4d90b8.dat]
2026-08-10 09:57:44 INFO: Writing summary to [/tmp/tmpmaxbzsnl/job_working_directory/000/16/outputs/dataset_c2197c24-9e1a-4c1f-ac5d-37465acb3fc0.dat]
2026-08-10 09:57:44 INFO: Writing MLST summary to [/tmp/tmpmaxbzsnl/job_working_directory/000/16/outputs/dataset_1c8a50dd-330e-48c4-a8eb-99b9bfddc19b.dat]
2026-08-10 09:57:44 INFO: Writing detailed summary to [/tmp/tmpmaxbzsnl/job_working_directory/000/16/outputs/dataset_a8e0850f-2f2e-44ff-b174-775380c3c3f5.dat]
2026-08-10 09:57:44 INFO: Writing settings to [XXXX]
2026-08-10 09:57:44 INFO: Writing Excel to [results.xlsx]
2026-08-10 09:57:44 INFO: BLAST hits are stored in [staramr_hits]

              

              • 

            

            Traceback:
            

              

            • 

              

              • 

            

            Job Parameters:
            

              

            • 

              


              
Job parameter
Parameter value

              
              


              
__input_ext
"input"

              

              
__workflow_invocation_uuid__
"d3be488e94a011f194247c1e52f4ef47"

              

              
advanced
{"complex_mutations_file": null, "exclude_genes": {"__current_case__": 0, "exclude_genes_condition": "default"}, "exclude_negatives": false, "exclude_resistance_phenotypes": false, "genome_size_lower_bound": "4000000", "genome_size_upper_bound": "6000000", "minimum_N50_value": "10000", "minimum_contig_length": "300", "mlst_scheme": "auto", "percent_length_overlap_plasmidfinder": "60.0", "percent_length_overlap_pointfinder": "95.0", "percent_length_overlap_resfinder": "60.0", "pid_threshold": "98.0", "plasmidfinder_type": "include_all", "report_all_blast": false, "unacceptable_number_contigs": "1000"}

              

              
chromInfo
"/tmp/tmpmaxbzsnl/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"

              

              
dbkey
"?"

              

              
hide_db_build
""

              

              
output_files
{"output_selection": ["mlst_table", "summary_table", "detailed_summary_table", "resfinder_table", "plasmidfinder_table", "pointfinder_table"]}

              

              
pointfinder_organism
"disabled"

              

              
staramr_db_select
"staramr_downloaded_07042025_resfinder_d1e607b_pointfinder_694919f_plasmidfinder_3e77502"

              
              

              

              • 

            

            • 

          

          

          • 

        

        • 

      • 

        Step 22: Unlabelled step (toolshed.g2.bx.psu.edu/repos/nml/collapse_collections/collapse_dataset/5.1.0):
        

          

        • 

          step_state: scheduled
          

          • 

        • 

          Jobs

            

          • 

            Job 1:
            

              

            • Job state is paused
              • 

            

            Traceback:
            

              

            • 

              

              • 

            

            Job Parameters:
            

              

            • 

              


              
Job parameter
Parameter value

              
              


              
__input_ext
"input"

              

              
__workflow_invocation_uuid__
"d3be488e94a011f194247c1e52f4ef47"

              

              
chromInfo
"/tmp/tmpmaxbzsnl/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"

              

              
dbkey
"?"

              

              
filename
{"__current_case__": 1, "add_name": false}

              

              
one_header
true

              
              

              

              • 

            

            • 

          

          

          • 

        

        • 

      • 

        Step 23: Unlabelled step (toolshed.g2.bx.psu.edu/repos/nml/collapse_collections/collapse_dataset/5.1.0):
        

          

        • 

          step_state: scheduled
          

          • 

        • 

          Jobs

            

          • 

            Job 1:
            

              

            • Job state is ok
              • 

            

            Container:
            

              

            • 

              quay.io/biocontainers/gawk:5.1.0--2
              

              • 

            

            Command Line:
            

              

            • 

              ( awk '{if (NR==1) {print}}' "/tmp/tmpmaxbzsnl/files/b/e/3/dataset_be3ac2f1-f197-4e04-aede-6e157c996a11.dat";   awk '{if (NR!=1) {print}}' "/tmp/tmpmaxbzsnl/files/b/e/3/dataset_be3ac2f1-f197-4e04-aede-6e157c996a11.dat";   ) > /tmp/tmpmaxbzsnl/job_working_directory/000/18/outputs/dataset_7ed2e162-9cd5-4552-8c10-47ab5cc06c4b.dat
              

              • 

            

            Exit Code:
            

              

            • 

              0
              

              • 

            

            Traceback:
            

              

            • 

              

              • 

            

            Job Parameters:
            

              

            • 

              


              
Job parameter
Parameter value

              
              


              
__input_ext
"input"

              

              
__workflow_invocation_uuid__
"d3be488e94a011f194247c1e52f4ef47"

              

              
chromInfo
"/tmp/tmpmaxbzsnl/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"

              

              
dbkey
"?"

              

              
filename
{"__current_case__": 1, "add_name": false}

              

              
one_header
true

              
              

              

              • 

            

            • 

          

          

          • 

        

        • 

      • 

        Step 24: Unlabelled step (toolshed.g2.bx.psu.edu/repos/iuc/column_remove_by_header/column_remove_by_header/1.0):
        

          

        • 

          step_state: scheduled
          

          • 

        • 

          Jobs

            

          • 

            Job 1:
            

              

            • Job state is queued
              • 

            

            Command Line:
            

              

            • 

              python '/tmp/shed_data/shed_tools/toolshed.g2.bx.psu.edu/repos/iuc/column_remove_by_header/6428adb323eb/column_remove_by_header/column_remove_by_header.py' -i '/tmp/tmpmaxbzsnl/files/a/8/e/dataset_a8e0850f-2f2e-44ff-b174-775380c3c3f5.dat' -o '/tmp/tmpmaxbzsnl/job_working_directory/000/19/outputs/dataset_f3beb2e1-834d-4a51-8fd7-9663f4b3312f.dat' -d '	'  -s '#' --unicode-escaped-cols --columns 'Isolate ID'
              

              • 

            

            Traceback:
            

              

            • 

              

              • 

            

            Job Parameters:
            

              

            • 

              


              
Job parameter
Parameter value

              
              


              
__input_ext
"tabular"

              

              
__workflow_invocation_uuid__
"d3be488e94a011f194247c1e52f4ef47"

              

              
chromInfo
"/tmp/tmpmaxbzsnl/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"

              

              
dbkey
"?"

              

              
headers
[{"__index__": 0, "name": "Isolate ID"}]

              

              
keep_columns
false

              

              
strip_characters
"#"

              
              

              

              • 

            

            • 

          

          

          • 

        

        • 

      • 

        Step 25: Unlabelled step (toolshed.g2.bx.psu.edu/repos/iuc/argnorm/argnorm/1.0.0+galaxy0):
        

          

        • 

          step_state: scheduled
          

          • 

        • 

          Jobs

            

          • 

            Job 1:
            

              

            • Job state is paused
              • 

            

            Traceback:
            

              

            • 

              

              • 

            

            Job Parameters:
            

              

            • 

              


              
Job parameter
Parameter value

              
              


              
__input_ext
"input"

              

              
__workflow_invocation_uuid__
"d3be488e94a011f194247c1e52f4ef47"

              

              
choose_tool
{"__current_case__": 4, "tool": "amrfinderplus"}

              

              
chromInfo
"/tmp/tmpmaxbzsnl/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"

              

              
dbkey
"?"

              
              

              

              • 

            

            • 

          

          

          • 

        

        • 

      • 

        Step 26: Unlabelled step (toolshed.g2.bx.psu.edu/repos/iuc/column_remove_by_header/column_remove_by_header/1.0):
        

          

        • 

          step_state: scheduled
          

          • 

        • 

          Jobs

            

          • 

            Job 1:
            

              

            • Job state is paused
              • 

            

            Traceback:
            

              

            • 

              

              • 

            

            Job Parameters:
            

              

            • 

              


              
Job parameter
Parameter value

              
              


              
__input_ext
"tabular"

              

              
__workflow_invocation_uuid__
"d3be488e94a011f194247c1e52f4ef47"

              

              
chromInfo
"/tmp/tmpmaxbzsnl/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"

              

              
dbkey
"?"

              

              
headers
[{"__index__": 0, "name": "Protein identifier"}]

              

              
keep_columns
false

              

              
strip_characters
"#"

              
              

              

              • 

            

            • 

          

          

          • 

        

        • 

      • 

        Step 27: Unlabelled step (toolshed.g2.bx.psu.edu/repos/recetox/table_pandas_rename_column/table_pandas_rename_column/3.0.2+galaxy0):
        

          

        • 

          step_state: scheduled
          

          • 

        • 

          Jobs

            

          • 

            Job 1:
            

              

            • Job state is queued
              • 

            

            Traceback:
            

              

            • 

              

              • 

            

            Job Parameters:
            

              

            • 

              


              
Job parameter
Parameter value

              
              


              
__input_ext
"input"

              

              
__workflow_invocation_uuid__
"d3be488e94a011f194247c1e52f4ef47"

              

              
chromInfo
"/tmp/tmpmaxbzsnl/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"

              

              
columns_selection
[{"__index__": 0, "column": "1", "new_name": "FILE"}]

              

              
dbkey
"?"

              
              

              

              • 

            

            • 

          

          

          • 

        

        • 

      • 

        Step 28: Unlabelled step:
        

          

        • 

          step_state: new
          

          • 

        • 

          Subworkflow Steps
 
          

          • 

        

        • 

      • 

        Step 29: Unlabelled step (toolshed.g2.bx.psu.edu/repos/iuc/column_remove_by_header/column_remove_by_header/1.0):
        

          

        • 

          step_state: scheduled
          

          • 

        • 

          Jobs

            

          • 

            Job 1:
            

              

            • Job state is new
              • 

            

            Traceback:
            

              

            • 

              

              • 

            

            Job Parameters:
            

              

            • 

              


              
Job parameter
Parameter value

              
              


              
__input_ext
"tabular"

              

              
__workflow_invocation_uuid__
"d3be488e94a011f194247c1e52f4ef47"

              

              
chromInfo
"/tmp/tmpmaxbzsnl/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"

              

              
dbkey
"?"

              

              
headers
[{"__index__": 0, "name": "FILE"}]

              

              
keep_columns
false

              

              
strip_characters
"#"

              
              

              

              • 

            

            • 

          

          

          • 

        

        • 

      • 

        Step 30: Unlabelled step:
        

          

        • step_state: new
          • 

        

        • 

      • 

        Step 31: Unlabelled step:
        

          

        • step_state: new
          • 

        

        • 

      • 

        Step 32: Unlabelled step:
        

          

        • step_state: new
          • 

        

        • 

      • 

        Step 33: MMseqs2 ARGs Sequence Clustering:
        

          

        • step_state: new
          • 

        

        • 

      • 

        Step 34: Unlabelled step:
        

          

        • step_state: new
          • 

        

        • 

      • 

        Step 35: Unlabelled step:
        

          

        • step_state: new
          • 

        

        • 

      • 

        Step 36: Unlabelled step:
        

          

        • step_state: new
          • 

        

        • 

      • 

        Step 37: Unlabelled step:
        

          

        • step_state: new
          • 

        

        • 

      • 

        Step 38: Unlabelled step:
        

          

        • step_state: new
          • 

        

        • 

      • 

        Step 39: Unlabelled step:
        

          

        • step_state: new
          • 

        

        • 

      • 

        Step 40: Unlabelled step:
        

          

        • step_state: new
          • 

        

        • 

      • 

        Step 41: Unlabelled step:
        

          

        • step_state: new
          • 

        

        • 

      • 

        Step 42: Unlabelled step:
        

          

        • step_state: new
          • 

        

        • 

      • 

        Step 43: Unlabelled step:
        

          

        • step_state: new
          • 

        

        • 

      
 
      

      • 

    • 

      Other invocation details

        

      • 

        error_message
        

          

        • Failed to run workflow, invocation ended in [failed] state.
          • 

        

        • 

      • 

        history_id
        

          

        • 6f5ff52556bf2a04
          • 

        

        • 

      • 

        history_state
        

          

        • new
          • 

        

        • 

      • 

        invocation_id
        

          

        • 6f5ff52556bf2a04
          • 

        

        • 

      • 

        invocation_state
        

          

        • failed
          • 

        

        • 

      • 

        messages
        

          

        • [{'dependent_workflow_step_id': None, 'hda_id': '8d9bdbceea54c3c3', 'reason': 'dataset_failed', 'workflow_step_id': 27, 'workflow_step_index_path': [27]}]
          • 

        

        • 

      • 

        workflow_id
        

          

        • ca8c1eead876a493
          • 

        

        • 

      

      

      • 

    
  
    

    • 





      		
    

  





        

            

            

              
            

        

      


      

            
  
  

    
  
    
    

  

  

  


    
















  
  

    

      

  










  








  
      

  
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    hugolefeuvre


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