MAGs building workflow #769

paulzierep · 2025-03-26T12:47:59Z

FOR CONTRIBUTOR:

I have read the Adding workflows guidelines
License permits unrestricted use (educational + commercial)
Please also take note of the reviewer guidelines below to facilitate a smooth review process.

I have difficulties writing tests for this workflow. Ideally I would like to write a test that checks the created bins, but bin IDs (so the name of the fasta files in dereplicated_genomes) are randomly assigned, so the names are different every time I run the workflow. Is it possible to check e.g. the number of elements on the collection, or some other loose test. I could not find any details for test docs.
If not, is it ok to check only the mutliQC report, if any of the workflow steps does not work, the report will change significantly and the test fail.

github-actions · 2025-03-26T13:05:18Z

Test Results (powered by Planemo)

Test Summary

Test State	Count
Total	1
Passed	0
Error	1
Failure	0
Skipped	0

Errored Tests

❌ Metagenome-Assembled-Genomes-(MAGs)-generation.ga_0

Execution Problem:

Final state of invocation 6ddd0e18cc4f60be is [failed]. Failed to run workflow, at least one job is in [error] state.

Workflow invocation details

Invocation Messages
- Invocation scheduling failed because step 26 requires a dataset collection created by step 23, but dataset collection entered a failed state.

Steps

Step 1: Choose Assembler:
- step_state: scheduled
Step 2: Minimum length of contigs to output:
- step_state: scheduled
Step 11: ANI threshold for dereplication:
- step_state: scheduled
Step 12: Run Bakta on MAGs:
- step_state: scheduled

Step 13: toolshed.g2.bx.psu.edu/repos/iuc/map_param_value/map_param_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__	`"6e9b82e40a4211f08a57002248aaba0a"`
chromInfo	`"/tmp/tmpunau54_g/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
dbkey	`"?"`
input_param_type	`{"__current_case__": 0, "input_param": "MEGAHIT", "mappings": [{"__index__": 0, "from": "MEGAHIT", "to": "True"}], "type": "text"}`
output_param_type	`"boolean"`
unmapped	`{"__current_case__": 2, "default_value": "False", "on_unmapped": "default"}`

Step 14: toolshed.g2.bx.psu.edu/repos/iuc/map_param_value/map_param_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__	`"6e9b82e40a4211f08a57002248aaba0a"`
chromInfo	`"/tmp/tmpunau54_g/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
dbkey	`"?"`
input_param_type	`{"__current_case__": 0, "input_param": "MEGAHIT", "mappings": [{"__index__": 0, "from": "metaSPAdes", "to": "True"}], "type": "text"}`
output_param_type	`"boolean"`
unmapped	`{"__current_case__": 2, "default_value": "False", "on_unmapped": "default"}`

Step 15: __UNZIP_COLLECTION__:
- step_state: scheduled
- Jobs
  - Job 1:
    - Job state is ok
    Traceback:
    Job Parameters:
    - Job parameter Parameter value
      
      __workflow_invocation_uuid__ "6e9b82e40a4211f08a57002248aaba0a"
      
      input {"values": [{"id": 1, "src": "dce"}]}

Step 16: toolshed.g2.bx.psu.edu/repos/iuc/megahit/megahit/1.2.9+galaxy2:

step_state: scheduled

Jobs

Job 1:

Job state is ok

Command Line:

if [[ -n "$GALAXY_MEMORY_MB" ]]; then MEMORY="-m $((GALAXY_MEMORY_MB * 1024))"; fi;  megahit --num-cpu-threads ${GALAXY_SLOTS:-4}  -1 '/tmp/tmpunau54_g/files/6/1/8/dataset_618900d2-82f4-478e-b4de-59e697c3bf37.dat' -2 '/tmp/tmpunau54_g/files/7/3/9/dataset_739b969b-6d3d-4163-8939-56482ad4c124.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:

2025-03-26 13:02:35 - MEGAHIT v1.2.9
2025-03-26 13:02:35 - Using megahit_core with POPCNT and BMI2 support
2025-03-26 13:02:35 - Convert reads to binary library
2025-03-26 13:02:35 - b'INFO  sequence/io/sequence_lib.cpp  :   75 - Lib 0 (/tmp/tmpunau54_g/files/6/1/8/dataset_618900d2-82f4-478e-b4de-59e697c3bf37.dat,/tmp/tmpunau54_g/files/7/3/9/dataset_739b969b-6d3d-4163-8939-56482ad4c124.dat): pe, 18924 reads, 150 max length'
2025-03-26 13:02:35 - b'INFO  utils/utils.h                 :  152 - Real: 0.0419\tuser: 0.0412\tsys: 0.0020\tmaxrss: 20616'
2025-03-26 13:02:35 - Start assembly. Number of CPU threads 1 
2025-03-26 13:02:35 - k list: 21,29,39,59,79,99,119,141 
2025-03-26 13:02:35 - Memory used: 15090090393
2025-03-26 13:02:35 - Extract solid (k+1)-mers for k = 21 
2025-03-26 13:02:36 - Build graph for k = 21 
2025-03-26 13:02:36 - Assemble contigs from SdBG for k = 21
2025-03-26 13:02:37 - Local assembly for k = 21
2025-03-26 13:02:38 - Extract iterative edges from k = 21 to 29 
2025-03-26 13:02:38 - Build graph for k = 29 
2025-03-26 13:02:38 - Assemble contigs from SdBG for k = 29
2025-03-26 13:02:38 - Local assembly for k = 29
2025-03-26 13:02:39 - Extract iterative edges from k = 29 to 39 
2025-03-26 13:02:39 - Build graph for k = 39 
2025-03-26 13:02:39 - Assemble contigs from SdBG for k = 39
2025-03-26 13:02:40 - Local assembly for k = 39
2025-03-26 13:02:41 - Extract iterative edges from k = 39 to 59 
2025-03-26 13:02:41 - Build graph for k = 59 
2025-03-26 13:02:41 - Assemble contigs from SdBG for k = 59
2025-03-26 13:02:41 - Local assembly for k = 59
2025-03-26 13:02:42 - Extract iterative edges from k = 59 to 79 
2025-03-26 13:02:42 - Build graph for k = 79 
2025-03-26 13:02:42 - Assemble contigs from SdBG for k = 79
2025-03-26 13:02:42 - Local assembly for k = 79
2025-03-26 13:02:43 - Extract iterative edges from k = 79 to 99 
2025-03-26 13:02:43 - Build graph for k = 99 
2025-03-26 13:02:43 - Assemble contigs from SdBG for k = 99
2025-03-26 13:02:43 - Local assembly for k = 99
2025-03-26 13:02:43 - Extract iterative edges from k = 99 to 119 
2025-03-26 13:02:43 - Build graph for k = 119 
2025-03-26 13:02:44 - Assemble contigs from SdBG for k = 119
2025-03-26 13:02:44 - Local assembly for k = 119
2025-03-26 13:02:44 - Extract iterative edges from k = 119 to 141 
2025-03-26 13:02:44 - Build graph for k = 141 
2025-03-26 13:02:44 - Assemble contigs from SdBG for k = 141
2025-03-26 13:02:45 - Merging to output final contigs 
2025-03-26 13:02:45 - 63 contigs, total 266124 bp, min 354 bp, max 11001 bp, avg 4224 bp, N50 4877 bp
2025-03-26 13:02:45 - ALL DONE. Time elapsed: 9.625468 seconds

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"fastqsanger.gz"`
__workflow_invocation_uuid__	`"6e9b82e40a4211f08a57002248aaba0a"`
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/tmpunau54_g/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": false, "min_contig_len": "200", "show_intermediate_contigs": false}`

Step 17: toolshed.g2.bx.psu.edu/repos/nml/metaspades/metaspades/4.1.0+galaxy0:

step_state: scheduled

Jobs

Job 1:

Job state is skipped

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"input"`
__workflow_invocation_uuid__	`"6e9b82e40a4211f08a57002248aaba0a"`
additional_reads	`{"__current_case__": 1, "selector": "false"}`
arf	`{"nanopore": null, "pacbio": null}`
chromInfo	`"/tmp/tmpunau54_g/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
dbkey	`"?"`
kmer_cond	`{"__current_case__": 0, "kmer_sel": "auto"}`
library_number	`"true"`
mode_sel	`["--iontorrent"]`
optional_output	`["ag", "ags", "cn", "cs"]`
phred_offset	`"auto"`
singlePaired	`{"__current_case__": 1, "input": {"values": [{"id": 1, "src": "hdca"}]}, "orientation": "fr", "sPaired": "paired_collection", "type_paired": "pe"}`

Step 18: 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__	`"6e9b82e40a4211f08a57002248aaba0a"`
chromInfo	`"/tmp/tmpunau54_g/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
dbkey	`"?"`
style_cond	`{"__current_case__": 0, "pick_style": "first", "type_cond": {"__current_case__": 4, "param_type": "data", "pick_from": [{"__index__": 0, "value": {"values": [{"id": 12, "src": "hda"}]}}, {"__index__": 1, "value": {"values": [{"id": 9, "src": "dce"}]}}]}}`

Step 19: toolshed.g2.bx.psu.edu/repos/iuc/quast/quast/5.3.0+galaxy0:

step_state: scheduled

Jobs

Job 1:

Job state is ok

Command Line:

echo 50contig_reads &&   ln -s '/tmp/tmpunau54_g/files/6/1/8/dataset_618900d2-82f4-478e-b4de-59e697c3bf37.dat' 'pe1-50contig_reads.fastqsanger.gz' && ln -s '/tmp/tmpunau54_g/files/7/3/9/dataset_739b969b-6d3d-4163-8939-56482ad4c124.dat' 'pe2-50contig_reads.fastqsanger.gz' &&  metaquast  --pe1 'pe1-50contig_reads.fastqsanger.gz' --pe2 'pe2-50contig_reads.fastqsanger.gz' --labels '50contig_reads' -o 'outputdir'  --max-ref-num 0  --min-identity 90.0 --min-contig 500        --min-alignment 65 --ambiguity-usage 'one' --ambiguity-score 0.99   --local-mis-size 200   --contig-thresholds '0,1000'  --extensive-mis-size 1000 --scaffold-gap-max-size 1000 --unaligned-part-size 500   --x-for-Nx 90  '/tmp/tmpunau54_g/files/a/f/8/dataset_af8ab189-efe4-4cd3-a676-5e305dffe743.dat' --threads ${GALAXY_SLOTS:-1}  && 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/tmpunau54_g/job_working_directory/000/11/outputs/dataset_9988ba27-427c-42d6-b301-ca3a0bf3f8e1_files' && cp outputdir/combined_reference/*.html '/tmp/tmpunau54_g/job_working_directory/000/11/outputs/dataset_9988ba27-427c-42d6-b301-ca3a0bf3f8e1_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/tmpunau54_g/job_working_directory/000/11/outputs/dataset_9988ba27-427c-42d6-b301-ca3a0bf3f8e1_files'; fi && if [[ -d "outputdir/krona_charts/" ]]; then mkdir -p 'None' && cp outputdir/krona_charts/*.html 'None'; fi

Exit Code:

```
0
```

Standard Output:

50contig_reads
/usr/local/opt/quast-5.3.0/metaquast.py --pe1 pe1-50contig_reads.fastqsanger.gz --pe2 pe2-50contig_reads.fastqsanger.gz --labels 50contig_reads -o outputdir --max-ref-num 0 --min-identity 90.0 --min-contig 500 --min-alignment 65 --ambiguity-usage one --ambiguity-score 0.99 --local-mis-size 200 --contig-thresholds 0,1000 --extensive-mis-size 1000 --scaffold-gap-max-size 1000 --unaligned-part-size 500 --x-for-Nx 90 /tmp/tmpunau54_g/files/a/f/8/dataset_af8ab189-efe4-4cd3-a676-5e305dffe743.dat --threads 1

Version: 5.3.0

System information:
  OS: Linux-6.8.0-1021-azure-x86_64-with-glibc2.36 (linux_64)
  Python version: 3.12.3
  CPUs number: 4

Started: 2025-03-26 13:03:39

Logging to /tmp/tmpunau54_g/job_working_directory/000/11/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/tmpunau54_g/files/a/f/8/dataset_af8ab189-efe4-4cd3-a676-5e305dffe743.dat ==> 50contig_reads

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 pe1-50contig_reads.fastqsanger.gz --pe2 pe2-50contig_reads.fastqsanger.gz --min-identity 90.0 --min-contig 500 --min-alignment 65 --ambiguity-usage one --ambiguity-score 0.99 --local-mis-size 200 --contig-thresholds 0,1000 --extensive-mis-size 1000 --scaffold-gap-max-size 1000 --unaligned-part-size 500 --x-for-Nx 90 --threads 1 /tmp/tmpunau54_g/files/a/f/8/dataset_af8ab189-efe4-4cd3-a676-5e305dffe743.dat -o /tmp/tmpunau54_g/job_working_directory/000/11/working/outputdir --labels 50contig_reads

Version: 5.3.0

System information:
  OS: Linux-6.8.0-1021-azure-x86_64-with-glibc2.36 (linux_64)
  Python version: 3.12.3
  CPUs number: 4

Started: 2025-03-26 13:03:40

Logging to /tmp/tmpunau54_g/job_working_directory/000/11/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/tmpunau54_g/job_working_directory/000/11/working
Main parameters: 
  MODE: meta, threads: 1, min contig length: 500, min alignment length: 65, min alignment IDY: 90.0, \
  ambiguity: all, min local misassembly length: 200, min extensive misassembly length: 1000

Contigs:
  Pre-processing...
  /tmp/tmpunau54_g/files/a/f/8/dataset_af8ab189-efe4-4cd3-a676-5e305dffe743.dat ==> 50contig_reads

2025-03-26 13:03:40
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/tmpunau54_g/job_working_directory/000/11/home/.quast
Downloading gridss (file: gridss-1.4.1.jar)...
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gridss successfully downloaded!
  Logging to files /tmp/tmpunau54_g/job_working_directory/000/11/working/outputdir/reads_stats/reads_stats.log and /tmp/tmpunau54_g/job_working_directory/000/11/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/tmpunau54_g/job_working_directory/000/11/working/outputdir/reads_stats/reads_report.txt, reads_report.tsv, and reads_report.tex
Done.

2025-03-26 13:03:45
Running Basic statistics processor...
  Contig files: 
    50contig_reads
  Calculating N50 and L50...
    50contig_reads, N50 = 4877, L50 = 22, auN = 5187.8, Total length = 265405, GC % = 36.45, # N's per 100 kbp =  0.00
  Drawing Nx plot...
    saved to /tmp/tmpunau54_g/job_working_directory/000/11/working/outputdir/basic_stats/Nx_plot.pdf
  Drawing cumulative plot...
    saved to /tmp/tmpunau54_g/job_working_directory/000/11/working/outputdir/basic_stats/cumulative_plot.pdf
  Drawing GC content plot...
    saved to /tmp/tmpunau54_g/job_working_directory/000/11/working/outputdir/basic_stats/GC_content_plot.pdf
  Drawing 50contig_reads GC content plot...
    saved to /tmp/tmpunau54_g/job_working_directory/000/11/working/outputdir/basic_stats/50contig_reads_GC_content_plot.pdf
Done.

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

2025-03-26 13:03:46
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

2025-03-26 13:03:47
RESULTS:
  Text versions of total report are saved to /tmp/tmpunau54_g/job_working_directory/000/11/working/outputdir/report.txt, report.tsv, and report.tex
  Text versions of transposed total report are saved to /tmp/tmpunau54_g/job_working_directory/000/11/working/outputdir/transposed_report.txt, transposed_report.tsv, and transposed_report.tex
  HTML version (interactive tables and plots) is saved to /tmp/tmpunau54_g/job_working_directory/000/11/working/outputdir/report.html
  PDF version (tables and plots) is saved to /tmp/tmpunau54_g/job_working_directory/000/11/working/outputdir/report.pdf
  Icarus (contig browser) is saved to /tmp/tmpunau54_g/job_working_directory/000/11/working/outputdir/icarus.html
  Log is saved to /tmp/tmpunau54_g/job_working_directory/000/11/working/outputdir/quast.log

Finished: 2025-03-26 13:03:47
Elapsed time: 0:00:06.934427
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__	`"6e9b82e40a4211f08a57002248aaba0a"`
advanced	`{"contig_thresholds": "0,1000", "extensive_mis_size": "1000", "fragmented_max_indent": null, "report_all_metrics": false, "scaffold_gap_max_size": "1000", "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": "90.0", "ref": {"__current_case__": 0, "max_ref_num": "0", "origin": "silva"}, "reuse_combined_alignments": false, "type": "metagenome"}`
chromInfo	`"/tmp/tmpunau54_g/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	`"500"`
mode	`{"__current_case__": 0, "in": {"__current_case__": 1, "custom": "false", "inputs": {"values": [{"id": 10, "src": "dce"}]}}, "mode": "individual", "reads": {"__current_case__": 2, "input_1": {"values": [{"id": 7, "src": "dce"}]}, "input_2": {"values": [{"id": 8, "src": "dce"}]}, "reads_option": "paired"}}`
output_files	`["html", "pdf", "tabular", "log", "summary", "krona"]`
split_scaffolds	`false`

Step 20: toolshed.g2.bx.psu.edu/repos/devteam/bowtie2/bowtie2/2.5.3+galaxy1:

step_state: scheduled

Jobs

Job 1:

Job state is ok

Command Line:

set -o | grep -q pipefail && set -o pipefail; bowtie2-build --threads ${GALAXY_SLOTS:-4} '/tmp/tmpunau54_g/files/a/f/8/dataset_af8ab189-efe4-4cd3-a676-5e305dffe743.dat' genome && ln -s -f '/tmp/tmpunau54_g/files/a/f/8/dataset_af8ab189-efe4-4cd3-a676-5e305dffe743.dat' genome.fa &&   ln -f -s '/tmp/tmpunau54_g/files/6/1/8/dataset_618900d2-82f4-478e-b4de-59e697c3bf37.dat' input_f.fastq.gz &&  ln -f -s '/tmp/tmpunau54_g/files/7/3/9/dataset_739b969b-6d3d-4163-8939-56482ad4c124.dat' input_r.fastq.gz &&    THREADS=${GALAXY_SLOTS:-4} && if [ "$THREADS" -gt 1 ]; then (( THREADS-- )); fi &&   bowtie2  -p "$THREADS"  -x 'genome'   -1 'input_f.fastq.gz' -2 'input_r.fastq.gz'                2> >(tee '/tmp/tmpunau54_g/job_working_directory/000/12/outputs/dataset_fcc635a9-6816-4975-a389-52a4c4009289.dat' >&2)  | samtools sort -l 0 -T "${TMPDIR:-.}" -O bam | samtools view --no-PG -O bam -@ ${GALAXY_SLOTS:-1} -o '/tmp/tmpunau54_g/job_working_directory/000/12/outputs/dataset_0a5b7195-0d10-4a74-ba58-5e7908a309b0.dat'

Exit Code:

```
0
```

Standard Error:

Building a SMALL index
Renaming genome.3.bt2.tmp to genome.3.bt2
Renaming genome.4.bt2.tmp to genome.4.bt2
Renaming genome.1.bt2.tmp to genome.1.bt2
Renaming genome.2.bt2.tmp to genome.2.bt2
Renaming genome.rev.1.bt2.tmp to genome.rev.1.bt2
Renaming genome.rev.2.bt2.tmp to genome.rev.2.bt2
9462 reads; of these:
  9462 (100.00%) were paired; of these:
    90 (0.95%) aligned concordantly 0 times
    9300 (98.29%) aligned concordantly exactly 1 time
    72 (0.76%) aligned concordantly >1 times
    ----
    90 pairs aligned concordantly 0 times; of these:
      8 (8.89%) aligned discordantly 1 time
    ----
    82 pairs aligned 0 times concordantly or discordantly; of these:
      164 mates make up the pairs; of these:
        93 (56.71%) aligned 0 times
        70 (42.68%) aligned exactly 1 time
        1 (0.61%) aligned >1 times
99.51% overall alignment rate

Standard Output:

Settings:
  Output files: "genome.*.bt2"
  Line rate: 6 (line is 64 bytes)
  Lines per side: 1 (side is 64 bytes)
  Offset rate: 4 (one in 16)
  FTable chars: 10
  Strings: unpacked
  Max bucket size: default
  Max bucket size, sqrt multiplier: default
  Max bucket size, len divisor: 4
  Difference-cover sample period: 1024
  Endianness: little
  Actual local endianness: little
  Sanity checking: disabled
  Assertions: disabled
  Random seed: 0
  Sizeofs: void*:8, int:4, long:8, size_t:8
Input files DNA, FASTA:
  /tmp/tmpunau54_g/files/a/f/8/dataset_af8ab189-efe4-4cd3-a676-5e305dffe743.dat
Reading reference sizes
  Time reading reference sizes: 00:00:00
Calculating joined length
Writing header
Reserving space for joined string
Joining reference sequences
  Time to join reference sequences: 00:00:00
bmax according to bmaxDivN setting: 66531
Using parameters --bmax 49899 --dcv 1024
  Doing ahead-of-time memory usage test
  Passed!  Constructing with these parameters: --bmax 49899 --dcv 1024
Constructing suffix-array element generator
Building DifferenceCoverSample
  Building sPrime
  Building sPrimeOrder
  V-Sorting samples
  V-Sorting samples time: 00:00:00
  Allocating rank array
  Ranking v-sort output
  Ranking v-sort output time: 00:00:00
  Invoking Larsson-Sadakane on ranks
  Invoking Larsson-Sadakane on ranks time: 00:00:00
  Sanity-checking and returning
Building samples
Reserving space for 12 sample suffixes
Generating random suffixes
QSorting 12 sample offsets, eliminating duplicates
QSorting sample offsets, eliminating duplicates time: 00:00:00
Multikey QSorting 12 samples
  (Using difference cover)
  Multikey QSorting samples time: 00:00:00
Calculating bucket sizes
Splitting and merging
  Splitting and merging time: 00:00:00
Split 1, merged 6; iterating...
Splitting and merging
  Splitting and merging time: 00:00:00
Avg bucket size: 38016.9 (target: 49898)
Converting suffix-array elements to index image
Allocating ftab, absorbFtab
Entering Ebwt loop
Getting block 1 of 7
  Reserving size (49899) for bucket 1
  Calculating Z arrays for bucket 1
  Entering block accumulator loop for bucket 1:
  bucket 1: 10%
  bucket 1: 20%
  bucket 1: 30%
  bucket 1: 40%
  bucket 1: 50%
  bucket 1: 60%
  bucket 1: 70%
  bucket 1: 80%
  bucket 1: 90%
  bucket 1: 100%
  Sorting block of length 18323 for bucket 1
  (Using difference cover)
  Sorting block time: 00:00:00
Returning block of 18324 for bucket 1
Getting block 2 of 7
  Reserving size (49899) for bucket 2
  Calculating Z arrays for bucket 2
  Entering block accumulator loop for bucket 2:
  bucket 2: 10%
  bucket 2: 20%
  bucket 2: 30%
  bucket 2: 40%
  bucket 2: 50%
  bucket 2: 60%
  bucket 2: 70%
  bucket 2: 80%
  bucket 2: 90%
  bucket 2: 100%
  Sorting block of length 49606 for bucket 2
  (Using difference cover)
  Sorting block time: 00:00:00
Returning block of 49607 for bucket 2
Getting block 3 of 7
  Reserving size (49899) for bucket 3
  Calculating Z arrays for bucket 3
  Entering block accumulator loop for bucket 3:
  bucket 3: 10%
  bucket 3: 20%
  bucket 3: 30%
  bucket 3: 40%
  bucket 3: 50%
  bucket 3: 60%
  bucket 3: 70%
  bucket 3: 80%
  bucket 3: 90%
  bucket 3: 100%
  Sorting block of length 45151 for bucket 3
  (Using difference cover)
  Sorting block time: 00:00:00
Returning block of 45152 for bucket 3
Getting block 4 of 7
  Reserving size (49899) for bucket 4
  Calculating Z arrays for bucket 4
  Entering block accumulator loop for bucket 4:
  bucket 4: 10%
  bucket 4: 20%
  bucket 4: 30%
  bucket 4: 40%
  bucket 4: 50%
  bucket 4: 60%
  bucket 4: 70%
  bucket 4: 80%
  bucket 4: 90%
  bucket 4: 100%
  Sorting block of length 49787 for bucket 4
  (Using difference cover)
  Sorting block time: 00:00:00
Returning block of 49788 for bucket 4
Getting block 5 of 7
  Reserving size (49899) for bucket 5
  Calculating Z arrays for bucket 5
  Entering block accumulator loop for bucket 5:
  bucket 5: 10%
  bucket 5: 20%
  bucket 5: 30%
  bucket 5: 40%
  bucket 5: 50%
  bucket 5: 60%
  bucket 5: 70%
  bucket 5: 80%
  bucket 5: 90%
  bucket 5: 100%
  Sorting block of length 28638 for bucket 5
  (Using difference cover)
  Sorting block time: 00:00:00
Returning block of 28639 for bucket 5
Getting block 6 of 7
  Reserving size (49899) for bucket 6
  Calculating Z arrays for bucket 6
  Entering block accumulator loop for bucket 6:
  bucket 6: 10%
  bucket 6: 20%
  bucket 6: 30%
  bucket 6: 40%
  bucket 6: 50%
  bucket 6: 60%
  bucket 6: 70%
  bucket 6: 80%
  bucket 6: 90%
  bucket 6: 100%
  Sorting block of length 43194 for bucket 6
  (Using difference cover)
  Sorting block time: 00:00:00
Returning block of 43195 for bucket 6
Getting block 7 of 7
  Reserving size (49899) for bucket 7
  Calculating Z arrays for bucket 7
  Entering block accumulator loop for bucket 7:
  bucket 7: 10%
  bucket 7: 20%
  bucket 7: 30%
  bucket 7: 40%
  bucket 7: 50%
  bucket 7: 60%
  bucket 7: 70%
  bucket 7: 80%
  bucket 7: 90%
  bucket 7: 100%
  Sorting block of length 31419 for bucket 7
  (Using difference cover)
  Sorting block time: 00:00:00
Returning block of 31420 for bucket 7
Exited Ebwt loop
fchr[A]: 0
fchr[C]: 84325
fchr[G]: 133305
fchr[T]: 181307
fchr[$]: 266124
Exiting Ebwt::buildToDisk()
Returning from initFromVector
Wrote 4286544 bytes to primary EBWT file: genome.1.bt2.tmp
Wrote 66536 bytes to secondary EBWT file: genome.2.bt2.tmp
Re-opening _in1 and _in2 as input streams
Returning from Ebwt constructor
Headers:
    len: 266124
    bwtLen: 266125
    sz: 66531
    bwtSz: 66532
    lineRate: 6
    offRate: 4
    offMask: 0xfffffff0
    ftabChars: 10
    eftabLen: 20
    eftabSz: 80
    ftabLen: 1048577
    ftabSz: 4194308
    offsLen: 16633
    offsSz: 66532
    lineSz: 64
    sideSz: 64
    sideBwtSz: 48
    sideBwtLen: 192
    numSides: 1387
    numLines: 1387
    ebwtTotLen: 88768
    ebwtTotSz: 88768
    color: 0
    reverse: 0
Total time for call to driver() for forward index: 00:00:00
Reading reference sizes
  Time reading reference sizes: 00:00:00
Calculating joined length
Writing header
Reserving space for joined string
Joining reference sequences
  Time to join reference sequences: 00:00:00
  Time to reverse reference sequence: 00:00:00
bmax according to bmaxDivN setting: 66531
Using parameters --bmax 49899 --dcv 1024
  Doing ahead-of-time memory usage test
  Passed!  Constructing with these parameters: --bmax 49899 --dcv 1024
Constructing suffix-array element generator
Building DifferenceCoverSample
  Building sPrime
  Building sPrimeOrder
  V-Sorting samples
  V-Sorting samples time: 00:00:00
  Allocating rank array
  Ranking v-sort output
  Ranking v-sort output time: 00:00:00
  Invoking Larsson-Sadakane on ranks
  Invoking Larsson-Sadakane on ranks time: 00:00:00
  Sanity-checking and returning
Building samples
Reserving space for 12 sample suffixes
Generating random suffixes
QSorting 12 sample offsets, eliminating duplicates
QSorting sample offsets, eliminating duplicates time: 00:00:00
Multikey QSorting 12 samples
  (Using difference cover)
  Multikey QSorting samples time: 00:00:00
Calculating bucket sizes
Splitting and merging
  Splitting and merging time: 00:00:00
Split 1, merged 7; iterating...
Splitting and merging
  Splitting and merging time: 00:00:00
Avg bucket size: 44353.2 (target: 49898)
Converting suffix-array elements to index image
Allocating ftab, absorbFtab
Entering Ebwt loop
Getting block 1 of 6
  Reserving size (49899) for bucket 1
  Calculating Z arrays for bucket 1
  Entering block accumulator loop for bucket 1:
  bucket 1: 10%
  bucket 1: 20%
  bucket 1: 30%
  bucket 1: 40%
  bucket 1: 50%
  bucket 1: 60%
  bucket 1: 70%
  bucket 1: 80%
  bucket 1: 90%
  bucket 1: 100%
  Sorting block of length 47687 for bucket 1
  (Using difference cover)
  Sorting block time: 00:00:00
Returning block of 47688 for bucket 1
Getting block 2 of 6
  Reserving size (49899) for bucket 2
  Calculating Z arrays for bucket 2
  Entering block accumulator loop for bucket 2:
  bucket 2: 10%
  bucket 2: 20%
  bucket 2: 30%
  bucket 2: 40%
  bucket 2: 50%
  bucket 2: 60%
  bucket 2: 70%
  bucket 2: 80%
  bucket 2: 90%
  bucket 2: 100%
  Sorting block of length 36636 for bucket 2
  (Using difference cover)
  Sorting block time: 00:00:00
Returning block of 36637 for bucket 2
Getting block 3 of 6
  Reserving size (49899) for bucket 3
  Calculating Z arrays for bucket 3
  Entering block accumulator loop for bucket 3:
  bucket 3: 10%
  bucket 3: 20%
  bucket 3: 30%
  bucket 3: 40%
  bucket 3: 50%
  bucket 3: 60%
  bucket 3: 70%
  bucket 3: 80%
  bucket 3: 90%
  bucket 3: 100%
  Sorting block of length 49027 for bucket 3
  (Using difference cover)
  Sorting block time: 00:00:00
Returning block of 49028 for bucket 3
Getting block 4 of 6
  Reserving size (49899) for bucket 4
  Calculating Z arrays for bucket 4
  Entering block accumulator loop for bucket 4:
  bucket 4: 10%
  bucket 4: 20%
  bucket 4: 30%
  bucket 4: 40%
  bucket 4: 50%
  bucket 4: 60%
  bucket 4: 70%
  bucket 4: 80%
  bucket 4: 90%
  bucket 4: 100%
  Sorting block of length 37449 for bucket 4
  (Using difference cover)
  Sorting block time: 00:00:00
Returning block of 37450 for bucket 4
Getting block 5 of 6
  Reserving size (49899) for bucket 5
  Calculating Z arrays for bucket 5
  Entering block accumulator loop for bucket 5:
  bucket 5: 10%
  bucket 5: 20%
  bucket 5: 30%
  bucket 5: 40%
  bucket 5: 50%
  bucket 5: 60%
  bucket 5: 70%
  bucket 5: 80%
  bucket 5: 90%
  bucket 5: 100%
  Sorting block of length 47142 for bucket 5
  (Using difference cover)
  Sorting block time: 00:00:00
Returning block of 47143 for bucket 5
Getting block 6 of 6
  Reserving size (49899) for bucket 6
  Calculating Z arrays for bucket 6
  Entering block accumulator loop for bucket 6:
  bucket 6: 10%
  bucket 6: 20%
  bucket 6: 30%
  bucket 6: 40%
  bucket 6: 50%
  bucket 6: 60%
  bucket 6: 70%
  bucket 6: 80%
  bucket 6: 90%
  bucket 6: 100%
  Sorting block of length 48178 for bucket 6
  (Using difference cover)
  Sorting block time: 00:00:00
Returning block of 48179 for bucket 6
Exited Ebwt loop
fchr[A]: 0
fchr[C]: 84325
fchr[G]: 133305
fchr[T]: 181307
fchr[$]: 266124
Exiting Ebwt::buildToDisk()
Returning from initFromVector
Wrote 4286544 bytes to primary EBWT file: genome.rev.1.bt2.tmp
Wrote 66536 bytes to secondary EBWT file: genome.rev.2.bt2.tmp
Re-opening _in1 and _in2 as input streams
Returning from Ebwt constructor
Headers:
    len: 266124
    bwtLen: 266125
    sz: 66531
    bwtSz: 66532
    lineRate: 6
    offRate: 4
    offMask: 0xfffffff0
    ftabChars: 10
    eftabLen: 20
    eftabSz: 80
    ftabLen: 1048577
    ftabSz: 4194308
    offsLen: 16633
    offsSz: 66532
    lineSz: 64
    sideSz: 64
    sideBwtSz: 48
    sideBwtLen: 192
    numSides: 1387
    numLines: 1387
    ebwtTotLen: 88768
    ebwtTotSz: 88768
    color: 0
    reverse: 1
Total time for backward call to driver() for mirror index: 00:00:01

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"input"`
__workflow_invocation_uuid__	`"6e9b82e40a4211f08a57002248aaba0a"`
analysis_type	`{"__current_case__": 0, "analysis_type_selector": "simple", "presets": "no_presets"}`
chromInfo	`"/tmp/tmpunau54_g/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
dbkey	`"?"`
library	`{"__current_case__": 2, "aligned_file": false, "input_1": {"values": [{"id": 1, "src": "dce"}]}, "paired_options": {"__current_case__": 1, "paired_options_selector": "no"}, "type": "paired_collection", "unaligned_file": false}`
own_file	__identifier__
reference_genome	`{"__current_case__": 1, "own_file": {"values": [{"id": 10, "src": "dce"}]}, "source": "history"}`
rg	`{"__current_case__": 3, "rg_selector": "do_not_set"}`
sam_options	`{"__current_case__": 1, "sam_options_selector": "no"}`
save_mapping_stats	`true`

Step 3: Read length (CONCOCT):
- step_state: scheduled

Step 21: toolshed.g2.bx.psu.edu/repos/iuc/concoct_cut_up_fasta/concoct_cut_up_fasta/1.1.0+galaxy2:

step_state: scheduled

Jobs

Job 1:

Job state is ok

Command Line:

ln -s '/tmp/tmpunau54_g/files/a/f/8/dataset_af8ab189-efe4-4cd3-a676-5e305dffe743.dat' 'input.fa' &&  cut_up_fasta.py 'input.fa' --chunk_size 10000 --overlap_size 0 --merge_last --bedfile '/tmp/tmpunau54_g/job_working_directory/000/13/outputs/dataset_4432b494-d554-43e7-9fdc-c217e0dce33a.dat' > '/tmp/tmpunau54_g/job_working_directory/000/13/outputs/dataset_9236a430-6f5d-4ac9-abd3-7b0f543e479f.dat'

Exit Code:

```
0
```

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"input"`
__workflow_invocation_uuid__	`"6e9b82e40a4211f08a57002248aaba0a"`
bedfile	`true`
chromInfo	`"/tmp/tmpunau54_g/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
chunk_size	`"10000"`
dbkey	`"?"`
input_fasta	__identifier__
merge_last	`true`
overlap_size	`"0"`

Step 22: toolshed.g2.bx.psu.edu/repos/devteam/samtools_sort/samtools_sort/2.0.5:

step_state: scheduled

Jobs

Job 1:

Job state is ok

Command Line:

addthreads=${GALAXY_SLOTS:-1} && (( addthreads-- )) &&   addmemory=${GALAXY_MEMORY_MB_PER_SLOT:-768} && ((addmemory=addmemory*75/100)) &&  samtools sort -@ $addthreads -m $addmemory"M"   -O bam -T "${TMPDIR:-.}" '/tmp/tmpunau54_g/files/0/a/5/dataset_0a5b7195-0d10-4a74-ba58-5e7908a309b0.dat' > '/tmp/tmpunau54_g/job_working_directory/000/14/outputs/dataset_c9c193af-93a8-4086-8ac0-e3d6801fbe6f.dat'

Exit Code:

```
0
```

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"input"`
__workflow_invocation_uuid__	`"6e9b82e40a4211f08a57002248aaba0a"`
chromInfo	`"/tmp/tmpunau54_g/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
dbkey	`"?"`
input1	__identifier__
minhash	`false`
prim_key_cond	`{"__current_case__": 0, "prim_key_select": ""}`

Step 23: toolshed.g2.bx.psu.edu/repos/iuc/semibin/semibin/2.0.2+galaxy0:

step_state: scheduled

Jobs

Job 1:

Job state is error

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"input"`
__workflow_invocation_uuid__	`"6e9b82e40a4211f08a57002248aaba0a"`
annot	`{"ml_threshold": null}`
bin	`{"max_edges": "200", "max_node": "1.0", "minfasta_kbs": "200"}`
chromInfo	`"/tmp/tmpunau54_g/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
dbkey	`"?"`
extra_output	`["data", "coverage"]`
min_len	`{"__current_case__": 0, "method": "automatic"}`
mode	`{"__current_case__": 0, "environment": "global", "input_bam": {"values": [{"id": 20, "src": "dce"}]}, "input_fasta": {"values": [{"id": 10, "src": "dce"}]}, "ref": {"__current_case__": 0, "cached_db": "17102022", "select": "cached"}, "select": "single"}`
orf_finder	`"fast-naive"`
random_seed	`"0"`
training	`{"batch_size": "2048", "epoches": "20"}`

Step 24: toolshed.g2.bx.psu.edu/repos/iuc/concoct_coverage_table/concoct_coverage_table/1.1.0+galaxy2:

step_state: scheduled

Jobs

Job 1:

Job state is running

Command Line:

mkdir 'mapping' && ln -s '/tmp/tmpunau54_g/files/c/9/c/dataset_c9c193af-93a8-4086-8ac0-e3d6801fbe6f.dat' 'mapping/_tmp_tmpunau54_g_files_c_9_c_dataset_c9c193af-93a8-4086-8ac0-e3d6801fbe6f.dat.sorted.bam' && samtools index 'mapping/_tmp_tmpunau54_g_files_c_9_c_dataset_c9c193af-93a8-4086-8ac0-e3d6801fbe6f.dat.sorted.bam' 'mapping/_tmp_tmpunau54_g_files_c_9_c_dataset_c9c193af-93a8-4086-8ac0-e3d6801fbe6f.dat.bam.bai' && mv 'mapping/_tmp_tmpunau54_g_files_c_9_c_dataset_c9c193af-93a8-4086-8ac0-e3d6801fbe6f.dat.sorted.bam' 'mapping/_tmp_tmpunau54_g_files_c_9_c_dataset_c9c193af-93a8-4086-8ac0-e3d6801fbe6f.dat.bam' && concoct_coverage_table.py '/tmp/tmpunau54_g/files/4/4/3/dataset_4432b494-d554-43e7-9fdc-c217e0dce33a.dat' mapping/*.bam > '/tmp/tmpunau54_g/job_working_directory/000/16/outputs/dataset_a822225a-50d9-4f0b-a221-6c5832e0acda.dat'

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"input"`
__workflow_invocation_uuid__	`"6e9b82e40a4211f08a57002248aaba0a"`
bedfile	__identifier__
chromInfo	`"/tmp/tmpunau54_g/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
dbkey	`"?"`
mode	`{"__current_case__": 0, "bamfile": {"values": [{"id": 20, "src": "dce"}]}, "type": "individual"}`
mode	bamfile

Step 25: toolshed.g2.bx.psu.edu/repos/iuc/metabat2_jgi_summarize_bam_contig_depths/metabat2_jgi_summarize_bam_contig_depths/2.17+galaxy0:

step_state: scheduled

Jobs

Job 1:

Job state is queued

Command Line:

jgi_summarize_bam_contig_depths --outputDepth '/tmp/tmpunau54_g/job_working_directory/000/17/outputs/dataset_bea7c80b-39f4-4946-a286-07d18ee8053c.dat' --percentIdentity 97   --minMapQual 0 --weightMapQual 0.0  --maxEdgeBases 75 --shredLength 16000 --shredDepth 5 --minContigLength 1 --minContigDepth 0.0 '/tmp/tmpunau54_g/files/c/9/c/dataset_c9c193af-93a8-4086-8ac0-e3d6801fbe6f.dat'

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"input"`
__workflow_invocation_uuid__	`"6e9b82e40a4211f08a57002248aaba0a"`
advanced	`{"includeEdgeBases": false, "maxEdgeBases": "75", "minMapQual": "0", "noIntraDepthVariance": false, "output_paired_contigs": false, "percentIdentity": "97", "showDepth": false, "weightMapQual": "0.0"}`
bam_indiv_input	__identifier__
chromInfo	`"/tmp/tmpunau54_g/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
dbkey	`"?"`
mode	`{"__current_case__": 0, "bam_indiv_input": {"values": [{"id": 20, "src": "dce"}]}, "type": "individual", "use_reference_cond": {"__current_case__": 0, "use_reference": "no"}}`
shredding	`{"minContigDepth": "0.0", "minContigLength": "1", "shredDepth": "5", "shredLength": "16000"}`

Step 26: Unlabelled step:
- step_state: new

Step 27: toolshed.g2.bx.psu.edu/repos/iuc/concoct/concoct/1.1.0+galaxy2:

step_state: scheduled

Jobs

Job 1:

Job state is new

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"input"`
__workflow_invocation_uuid__	`"6e9b82e40a4211f08a57002248aaba0a"`
advanced	`{"clusters": "400", "iterations": "500", "kmer_length": "4", "length_threshold": "1000", "no_cov_normalization": false, "read_length": "250", "seed": "1", "total_percentage_pca": "90"}`
chromInfo	`"/tmp/tmpunau54_g/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
dbkey	`"?"`
output	`{"converge_out": false, "log": false, "no_total_coverage": false}`

Step 28: toolshed.g2.bx.psu.edu/repos/mbernt/maxbin2/maxbin2/2.2.7+galaxy6:

step_state: scheduled

Jobs

Job 1:

Job state is new

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"expression.json"`
__workflow_invocation_uuid__	`"6e9b82e40a4211f08a57002248aaba0a"`
adv	`{"max_iteration": "50", "min_contig_length": "1000", "prob_threshold": "0.5"}`
assembly	`{"__current_case__": 0, "inputs": {"__current_case__": 1, "abund": {"values": [{"id": 27, "src": "dce"}]}, "type": "abund"}, "type": "individual"}`
chromInfo	`"/tmp/tmpunau54_g/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
dbkey	`"?"`
output	`{"log": true, "marker": true, "markers": true, "markerset": "107", "plotmarker": true}`

Step 29: toolshed.g2.bx.psu.edu/repos/iuc/metabat2/metabat2/2.17+galaxy0:

step_state: scheduled

Jobs

Job 1:

Job state is new

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"input"`
__workflow_invocation_uuid__	`"6e9b82e40a4211f08a57002248aaba0a"`
advanced	`{"base_coverage_depth_cond": {"__current_case__": 1, "abdFile": {"values": [{"id": 27, "src": "dce"}]}, "base_coverage_depth": "yes", "cvExt": null}, "maxEdges": "200", "maxP": "95", "minCV": "1.0", "minCVSum": "1.0", "minContig": "1500", "minS": "60", "noAdd": false, "pTNF": "0", "seed": "0"}`
advanced	abdFile
chromInfo	`"/tmp/tmpunau54_g/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
dbkey	`"?"`
inFile	__identifier__
out	`{"extra_outputs": ["lowDepth", "tooShort", "unbinned", "log"], "minClsSize": "200000", "onlyLabel": false, "saveCls": false}`

Step 30: toolshed.g2.bx.psu.edu/repos/iuc/concoct_merge_cut_up_clustering/concoct_merge_cut_up_clustering/1.1.0+galaxy2:

step_state: scheduled

Jobs

Job 1:

Job state is new

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"input"`
__workflow_invocation_uuid__	`"6e9b82e40a4211f08a57002248aaba0a"`
chromInfo	`"/tmp/tmpunau54_g/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
cutup_clustering_result	__identifier__
dbkey	`"?"`

Step 4: Environment for the built-in model (SemiBin):
- step_state: scheduled
Step 31: Unlabelled step:
- step_state: new
Step 32: Unlabelled step:
- step_state: new

Step 33: toolshed.g2.bx.psu.edu/repos/iuc/concoct_extract_fasta_bins/concoct_extract_fasta_bins/1.1.0+galaxy2:

step_state: scheduled

Jobs

Job 1:

Job state is new

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"input"`
__workflow_invocation_uuid__	`"6e9b82e40a4211f08a57002248aaba0a"`
chromInfo	`"/tmp/tmpunau54_g/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
cluster_file	__identifier__
dbkey	`"?"`
fasta_file	__identifier__

Step 34: Unlabelled step:
- step_state: new
Step 35: Unlabelled step:
- step_state: new
Step 36: Unlabelled step:
- step_state: new
Step 37: Pool Bins from all samples:
- 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 5: Trimmed grouped paired reads:
- step_state: scheduled
Step 41: Unlabelled step:
- step_state: new
Step 42: Unlabelled step:
- step_state: new
Step 43: Unlabelled step:
- step_state: new
Step 44: Unlabelled step:
- step_state: new
Step 45: Unlabelled step:
- step_state: new
Step 46: Unlabelled step:
- step_state: new
Step 47: Unlabelled step:
- step_state: new
Step 48: Unlabelled step:
- step_state: new
Step 6: Trimmed sample paired reads:
- step_state: scheduled
Step 7: Contamination weight (Binette):
- step_state: scheduled
Step 8: Minimum MAG completeness percentage:
- step_state: scheduled
Step 9: Maximum MAG contamination percentage:
- step_state: scheduled
**Step 10: Minimum MAG length **:
- step_state: scheduled

Other invocation details
- error_message
  - Final state of invocation 6ddd0e18cc4f60be is [failed]. Failed to run workflow, at least one job is in [error] state.
- history_id
  - 6ddd0e18cc4f60be
- history_state
  - error
- invocation_id
  - 6ddd0e18cc4f60be
- invocation_state
  - failed
- messages
  - [{'dependent_workflow_step_id': 22, 'hdca_id': '6338019c8f0e24d7', 'reason': 'collection_failed', 'workflow_step_id': 25}]
- workflow_id
  - 6ddd0e18cc4f60be

github-actions · 2025-03-26T13:15:33Z

Test Results (powered by Planemo)

Test Summary

Test State	Count
Total	1
Passed	0
Error	1
Failure	0
Skipped	0

Errored Tests

❌ Metagenome-Assembled-Genomes-(MAGs)-generation.ga_0

Execution Problem:

Final state of invocation cdf6c67c360f70c6 is [failed]. Failed to run workflow, at least one job is in [error] state.

Workflow invocation details

Invocation Messages
- Invocation scheduling failed because step 26 requires a dataset collection created by step 23, but dataset collection entered a failed state.

Steps

Step 1: Choose Assembler:
- step_state: scheduled
Step 2: Minimum length of contigs to output:
- step_state: scheduled
Step 11: ANI threshold for dereplication:
- step_state: scheduled
Step 12: Run Bakta on MAGs:
- step_state: scheduled

Step 13: toolshed.g2.bx.psu.edu/repos/iuc/map_param_value/map_param_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__	`"eff2b0140a4311f08a576045bd7d7463"`
chromInfo	`"/tmp/tmp4ato2skh/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
dbkey	`"?"`
input_param_type	`{"__current_case__": 0, "input_param": "MEGAHIT", "mappings": [{"__index__": 0, "from": "MEGAHIT", "to": "True"}], "type": "text"}`
output_param_type	`"boolean"`
unmapped	`{"__current_case__": 2, "default_value": "False", "on_unmapped": "default"}`

Step 14: toolshed.g2.bx.psu.edu/repos/iuc/map_param_value/map_param_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__	`"eff2b0140a4311f08a576045bd7d7463"`
chromInfo	`"/tmp/tmp4ato2skh/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
dbkey	`"?"`
input_param_type	`{"__current_case__": 0, "input_param": "MEGAHIT", "mappings": [{"__index__": 0, "from": "metaSPAdes", "to": "True"}], "type": "text"}`
output_param_type	`"boolean"`
unmapped	`{"__current_case__": 2, "default_value": "False", "on_unmapped": "default"}`

Step 15: __UNZIP_COLLECTION__:
- step_state: scheduled
- Jobs
  - Job 1:
    - Job state is ok
    Traceback:
    Job Parameters:
    - Job parameter Parameter value
      
      __workflow_invocation_uuid__ "eff2b0140a4311f08a576045bd7d7463"
      
      input {"values": [{"id": 1, "src": "dce"}]}

Step 16: toolshed.g2.bx.psu.edu/repos/iuc/megahit/megahit/1.2.9+galaxy2:

step_state: scheduled

Jobs

Job 1:

Job state is ok

Command Line:

if [[ -n "$GALAXY_MEMORY_MB" ]]; then MEMORY="-m $((GALAXY_MEMORY_MB * 1024))"; fi;  megahit --num-cpu-threads ${GALAXY_SLOTS:-4}  -1 '/tmp/tmp4ato2skh/files/5/2/3/dataset_523a5bb5-97a6-4c1d-8c5a-154e49bfe9aa.dat' -2 '/tmp/tmp4ato2skh/files/d/a/4/dataset_da42f7ca-f21d-486d-8dbf-76967966324b.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:

2025-03-26 13:12:53 - MEGAHIT v1.2.9
2025-03-26 13:12:53 - Using megahit_core with POPCNT and BMI2 support
2025-03-26 13:12:53 - Convert reads to binary library
2025-03-26 13:12:53 - b'INFO  sequence/io/sequence_lib.cpp  :   75 - Lib 0 (/tmp/tmp4ato2skh/files/5/2/3/dataset_523a5bb5-97a6-4c1d-8c5a-154e49bfe9aa.dat,/tmp/tmp4ato2skh/files/d/a/4/dataset_da42f7ca-f21d-486d-8dbf-76967966324b.dat): pe, 18924 reads, 150 max length'
2025-03-26 13:12:53 - b'INFO  utils/utils.h                 :  152 - Real: 0.0488\tuser: 0.0468\tsys: 0.0029\tmaxrss: 20796'
2025-03-26 13:12:53 - Start assembly. Number of CPU threads 1 
2025-03-26 13:12:53 - k list: 21,29,39,59,79,99,119,141 
2025-03-26 13:12:53 - Memory used: 15090086707
2025-03-26 13:12:53 - Extract solid (k+1)-mers for k = 21 
2025-03-26 13:12:53 - Build graph for k = 21 
2025-03-26 13:12:54 - Assemble contigs from SdBG for k = 21
2025-03-26 13:12:54 - Local assembly for k = 21
2025-03-26 13:12:55 - Extract iterative edges from k = 21 to 29 
2025-03-26 13:12:55 - Build graph for k = 29 
2025-03-26 13:12:55 - Assemble contigs from SdBG for k = 29
2025-03-26 13:12:56 - Local assembly for k = 29
2025-03-26 13:12:57 - Extract iterative edges from k = 29 to 39 
2025-03-26 13:12:57 - Build graph for k = 39 
2025-03-26 13:12:57 - Assemble contigs from SdBG for k = 39
2025-03-26 13:12:57 - Local assembly for k = 39
2025-03-26 13:12:58 - Extract iterative edges from k = 39 to 59 
2025-03-26 13:12:58 - Build graph for k = 59 
2025-03-26 13:12:58 - Assemble contigs from SdBG for k = 59
2025-03-26 13:12:59 - Local assembly for k = 59
2025-03-26 13:12:59 - Extract iterative edges from k = 59 to 79 
2025-03-26 13:12:59 - Build graph for k = 79 
2025-03-26 13:12:59 - Assemble contigs from SdBG for k = 79
2025-03-26 13:13:00 - Local assembly for k = 79
2025-03-26 13:13:00 - Extract iterative edges from k = 79 to 99 
2025-03-26 13:13:00 - Build graph for k = 99 
2025-03-26 13:13:00 - Assemble contigs from SdBG for k = 99
2025-03-26 13:13:01 - Local assembly for k = 99
2025-03-26 13:13:01 - Extract iterative edges from k = 99 to 119 
2025-03-26 13:13:01 - Build graph for k = 119 
2025-03-26 13:13:01 - Assemble contigs from SdBG for k = 119
2025-03-26 13:13:01 - Local assembly for k = 119
2025-03-26 13:13:02 - Extract iterative edges from k = 119 to 141 
2025-03-26 13:13:02 - Build graph for k = 141 
2025-03-26 13:13:02 - Assemble contigs from SdBG for k = 141
2025-03-26 13:13:02 - Merging to output final contigs 
2025-03-26 13:13:02 - 63 contigs, total 266124 bp, min 354 bp, max 11001 bp, avg 4224 bp, N50 4877 bp
2025-03-26 13:13:02 - ALL DONE. Time elapsed: 9.585234 seconds

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"fastqsanger.gz"`
__workflow_invocation_uuid__	`"eff2b0140a4311f08a576045bd7d7463"`
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/tmp4ato2skh/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": false, "min_contig_len": "200", "show_intermediate_contigs": false}`

Step 17: toolshed.g2.bx.psu.edu/repos/nml/metaspades/metaspades/4.1.0+galaxy0:

step_state: scheduled

Jobs

Job 1:

Job state is skipped

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"input"`
__workflow_invocation_uuid__	`"eff2b0140a4311f08a576045bd7d7463"`
additional_reads	`{"__current_case__": 1, "selector": "false"}`
arf	`{"nanopore": null, "pacbio": null}`
chromInfo	`"/tmp/tmp4ato2skh/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
dbkey	`"?"`
kmer_cond	`{"__current_case__": 0, "kmer_sel": "auto"}`
library_number	`"true"`
mode_sel	`["--iontorrent"]`
optional_output	`["ag", "ags", "cn", "cs"]`
phred_offset	`"auto"`
singlePaired	`{"__current_case__": 1, "input": {"values": [{"id": 1, "src": "hdca"}]}, "orientation": "fr", "sPaired": "paired_collection", "type_paired": "pe"}`

Step 18: 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__	`"eff2b0140a4311f08a576045bd7d7463"`
chromInfo	`"/tmp/tmp4ato2skh/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
dbkey	`"?"`
style_cond	`{"__current_case__": 0, "pick_style": "first", "type_cond": {"__current_case__": 4, "param_type": "data", "pick_from": [{"__index__": 0, "value": {"values": [{"id": 12, "src": "hda"}]}}, {"__index__": 1, "value": {"values": [{"id": 9, "src": "dce"}]}}]}}`

Step 19: toolshed.g2.bx.psu.edu/repos/iuc/quast/quast/5.3.0+galaxy0:

step_state: scheduled

Jobs

Job 1:

Job state is running

Command Line:

echo 50contig_reads &&   ln -s '/tmp/tmp4ato2skh/files/5/2/3/dataset_523a5bb5-97a6-4c1d-8c5a-154e49bfe9aa.dat' 'pe1-50contig_reads.fastqsanger.gz' && ln -s '/tmp/tmp4ato2skh/files/d/a/4/dataset_da42f7ca-f21d-486d-8dbf-76967966324b.dat' 'pe2-50contig_reads.fastqsanger.gz' &&  metaquast  --pe1 'pe1-50contig_reads.fastqsanger.gz' --pe2 'pe2-50contig_reads.fastqsanger.gz' --labels '50contig_reads' -o 'outputdir'  --max-ref-num 0  --min-identity 90.0 --min-contig 500        --min-alignment 65 --ambiguity-usage 'one' --ambiguity-score 0.99   --local-mis-size 200   --contig-thresholds '0,1000'  --extensive-mis-size 1000 --scaffold-gap-max-size 1000 --unaligned-part-size 500   --x-for-Nx 90  '/tmp/tmp4ato2skh/files/6/f/3/dataset_6f3f0843-9fa4-4df8-882c-b0cd443710de.dat' --threads ${GALAXY_SLOTS:-1}  && 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/tmp4ato2skh/job_working_directory/000/11/outputs/dataset_bc44384c-4af8-45ca-839a-75e8a9426d98_files' && cp outputdir/combined_reference/*.html '/tmp/tmp4ato2skh/job_working_directory/000/11/outputs/dataset_bc44384c-4af8-45ca-839a-75e8a9426d98_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/tmp4ato2skh/job_working_directory/000/11/outputs/dataset_bc44384c-4af8-45ca-839a-75e8a9426d98_files'; fi && if [[ -d "outputdir/krona_charts/" ]]; then mkdir -p 'None' && cp outputdir/krona_charts/*.html 'None'; fi

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"input"`
__workflow_invocation_uuid__	`"eff2b0140a4311f08a576045bd7d7463"`
advanced	`{"contig_thresholds": "0,1000", "extensive_mis_size": "1000", "fragmented_max_indent": null, "report_all_metrics": false, "scaffold_gap_max_size": "1000", "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": "90.0", "ref": {"__current_case__": 0, "max_ref_num": "0", "origin": "silva"}, "reuse_combined_alignments": false, "type": "metagenome"}`
chromInfo	`"/tmp/tmp4ato2skh/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	`"500"`
mode	`{"__current_case__": 0, "in": {"__current_case__": 1, "custom": "false", "inputs": {"values": [{"id": 10, "src": "dce"}]}}, "mode": "individual", "reads": {"__current_case__": 2, "input_1": {"values": [{"id": 7, "src": "dce"}]}, "input_2": {"values": [{"id": 8, "src": "dce"}]}, "reads_option": "paired"}}`
output_files	`["html", "pdf", "tabular", "log", "summary", "krona"]`
split_scaffolds	`false`

Step 20: toolshed.g2.bx.psu.edu/repos/devteam/bowtie2/bowtie2/2.5.3+galaxy1:

step_state: scheduled

Jobs

Job 1:

Job state is ok

Command Line:

set -o | grep -q pipefail && set -o pipefail; bowtie2-build --threads ${GALAXY_SLOTS:-4} '/tmp/tmp4ato2skh/files/6/f/3/dataset_6f3f0843-9fa4-4df8-882c-b0cd443710de.dat' genome && ln -s -f '/tmp/tmp4ato2skh/files/6/f/3/dataset_6f3f0843-9fa4-4df8-882c-b0cd443710de.dat' genome.fa &&   ln -f -s '/tmp/tmp4ato2skh/files/5/2/3/dataset_523a5bb5-97a6-4c1d-8c5a-154e49bfe9aa.dat' input_f.fastq.gz &&  ln -f -s '/tmp/tmp4ato2skh/files/d/a/4/dataset_da42f7ca-f21d-486d-8dbf-76967966324b.dat' input_r.fastq.gz &&    THREADS=${GALAXY_SLOTS:-4} && if [ "$THREADS" -gt 1 ]; then (( THREADS-- )); fi &&   bowtie2  -p "$THREADS"  -x 'genome'   -1 'input_f.fastq.gz' -2 'input_r.fastq.gz'                2> >(tee '/tmp/tmp4ato2skh/job_working_directory/000/12/outputs/dataset_4c6c40d5-98d3-447a-bcba-d4723de04b18.dat' >&2)  | samtools sort -l 0 -T "${TMPDIR:-.}" -O bam | samtools view --no-PG -O bam -@ ${GALAXY_SLOTS:-1} -o '/tmp/tmp4ato2skh/job_working_directory/000/12/outputs/dataset_f664fa69-585e-47cb-ae50-93abcd51616d.dat'

Exit Code:

```
0
```

Standard Error:

Building a SMALL index
Renaming genome.3.bt2.tmp to genome.3.bt2
Renaming genome.4.bt2.tmp to genome.4.bt2
Renaming genome.1.bt2.tmp to genome.1.bt2
Renaming genome.2.bt2.tmp to genome.2.bt2
Renaming genome.rev.1.bt2.tmp to genome.rev.1.bt2
Renaming genome.rev.2.bt2.tmp to genome.rev.2.bt2
9462 reads; of these:
  9462 (100.00%) were paired; of these:
    90 (0.95%) aligned concordantly 0 times
    9300 (98.29%) aligned concordantly exactly 1 time
    72 (0.76%) aligned concordantly >1 times
    ----
    90 pairs aligned concordantly 0 times; of these:
      8 (8.89%) aligned discordantly 1 time
    ----
    82 pairs aligned 0 times concordantly or discordantly; of these:
      164 mates make up the pairs; of these:
        93 (56.71%) aligned 0 times
        70 (42.68%) aligned exactly 1 time
        1 (0.61%) aligned >1 times
99.51% overall alignment rate

Standard Output:

Settings:
  Output files: "genome.*.bt2"
  Line rate: 6 (line is 64 bytes)
  Lines per side: 1 (side is 64 bytes)
  Offset rate: 4 (one in 16)
  FTable chars: 10
  Strings: unpacked
  Max bucket size: default
  Max bucket size, sqrt multiplier: default
  Max bucket size, len divisor: 4
  Difference-cover sample period: 1024
  Endianness: little
  Actual local endianness: little
  Sanity checking: disabled
  Assertions: disabled
  Random seed: 0
  Sizeofs: void*:8, int:4, long:8, size_t:8
Input files DNA, FASTA:
  /tmp/tmp4ato2skh/files/6/f/3/dataset_6f3f0843-9fa4-4df8-882c-b0cd443710de.dat
Reading reference sizes
  Time reading reference sizes: 00:00:00
Calculating joined length
Writing header
Reserving space for joined string
Joining reference sequences
  Time to join reference sequences: 00:00:00
bmax according to bmaxDivN setting: 66531
Using parameters --bmax 49899 --dcv 1024
  Doing ahead-of-time memory usage test
  Passed!  Constructing with these parameters: --bmax 49899 --dcv 1024
Constructing suffix-array element generator
Building DifferenceCoverSample
  Building sPrime
  Building sPrimeOrder
  V-Sorting samples
  V-Sorting samples time: 00:00:00
  Allocating rank array
  Ranking v-sort output
  Ranking v-sort output time: 00:00:00
  Invoking Larsson-Sadakane on ranks
  Invoking Larsson-Sadakane on ranks time: 00:00:00
  Sanity-checking and returning
Building samples
Reserving space for 12 sample suffixes
Generating random suffixes
QSorting 12 sample offsets, eliminating duplicates
QSorting sample offsets, eliminating duplicates time: 00:00:00
Multikey QSorting 12 samples
  (Using difference cover)
  Multikey QSorting samples time: 00:00:00
Calculating bucket sizes
Splitting and merging
  Splitting and merging time: 00:00:00
Split 1, merged 6; iterating...
Splitting and merging
  Splitting and merging time: 00:00:00
Avg bucket size: 38016.9 (target: 49898)
Converting suffix-array elements to index image
Allocating ftab, absorbFtab
Entering Ebwt loop
Getting block 1 of 7
  Reserving size (49899) for bucket 1
  Calculating Z arrays for bucket 1
  Entering block accumulator loop for bucket 1:
  bucket 1: 10%
  bucket 1: 20%
  bucket 1: 30%
  bucket 1: 40%
  bucket 1: 50%
  bucket 1: 60%
  bucket 1: 70%
  bucket 1: 80%
  bucket 1: 90%
  bucket 1: 100%
  Sorting block of length 18323 for bucket 1
  (Using difference cover)
  Sorting block time: 00:00:00
Returning block of 18324 for bucket 1
Getting block 2 of 7
  Reserving size (49899) for bucket 2
  Calculating Z arrays for bucket 2
  Entering block accumulator loop for bucket 2:
  bucket 2: 10%
  bucket 2: 20%
  bucket 2: 30%
  bucket 2: 40%
  bucket 2: 50%
  bucket 2: 60%
  bucket 2: 70%
  bucket 2: 80%
  bucket 2: 90%
  bucket 2: 100%
  Sorting block of length 49606 for bucket 2
  (Using difference cover)
  Sorting block time: 00:00:00
Returning block of 49607 for bucket 2
Getting block 3 of 7
  Reserving size (49899) for bucket 3
  Calculating Z arrays for bucket 3
  Entering block accumulator loop for bucket 3:
  bucket 3: 10%
  bucket 3: 20%
  bucket 3: 30%
  bucket 3: 40%
  bucket 3: 50%
  bucket 3: 60%
  bucket 3: 70%
  bucket 3: 80%
  bucket 3: 90%
  bucket 3: 100%
  Sorting block of length 45151 for bucket 3
  (Using difference cover)
  Sorting block time: 00:00:00
Returning block of 45152 for bucket 3
Getting block 4 of 7
  Reserving size (49899) for bucket 4
  Calculating Z arrays for bucket 4
  Entering block accumulator loop for bucket 4:
  bucket 4: 10%
  bucket 4: 20%
  bucket 4: 30%
  bucket 4: 40%
  bucket 4: 50%
  bucket 4: 60%
  bucket 4: 70%
  bucket 4: 80%
  bucket 4: 90%
  bucket 4: 100%
  Sorting block of length 49787 for bucket 4
  (Using difference cover)
  Sorting block time: 00:00:00
Returning block of 49788 for bucket 4
Getting block 5 of 7
  Reserving size (49899) for bucket 5
  Calculating Z arrays for bucket 5
  Entering block accumulator loop for bucket 5:
  bucket 5: 10%
  bucket 5: 20%
  bucket 5: 30%
  bucket 5: 40%
  bucket 5: 50%
  bucket 5: 60%
  bucket 5: 70%
  bucket 5: 80%
  bucket 5: 90%
  bucket 5: 100%
  Sorting block of length 28638 for bucket 5
  (Using difference cover)
  Sorting block time: 00:00:00
Returning block of 28639 for bucket 5
Getting block 6 of 7
  Reserving size (49899) for bucket 6
  Calculating Z arrays for bucket 6
  Entering block accumulator loop for bucket 6:
  bucket 6: 10%
  bucket 6: 20%
  bucket 6: 30%
  bucket 6: 40%
  bucket 6: 50%
  bucket 6: 60%
  bucket 6: 70%
  bucket 6: 80%
  bucket 6: 90%
  bucket 6: 100%
  Sorting block of length 43194 for bucket 6
  (Using difference cover)
  Sorting block time: 00:00:00
Returning block of 43195 for bucket 6
Getting block 7 of 7
  Reserving size (49899) for bucket 7
  Calculating Z arrays for bucket 7
  Entering block accumulator loop for bucket 7:
  bucket 7: 10%
  bucket 7: 20%
  bucket 7: 30%
  bucket 7: 40%
  bucket 7: 50%
  bucket 7: 60%
  bucket 7: 70%
  bucket 7: 80%
  bucket 7: 90%
  bucket 7: 100%
  Sorting block of length 31419 for bucket 7
  (Using difference cover)
  Sorting block time: 00:00:00
Returning block of 31420 for bucket 7
Exited Ebwt loop
fchr[A]: 0
fchr[C]: 84325
fchr[G]: 133305
fchr[T]: 181307
fchr[$]: 266124
Exiting Ebwt::buildToDisk()
Returning from initFromVector
Wrote 4286544 bytes to primary EBWT file: genome.1.bt2.tmp
Wrote 66536 bytes to secondary EBWT file: genome.2.bt2.tmp
Re-opening _in1 and _in2 as input streams
Returning from Ebwt constructor
Headers:
    len: 266124
    bwtLen: 266125
    sz: 66531
    bwtSz: 66532
    lineRate: 6
    offRate: 4
    offMask: 0xfffffff0
    ftabChars: 10
    eftabLen: 20
    eftabSz: 80
    ftabLen: 1048577
    ftabSz: 4194308
    offsLen: 16633
    offsSz: 66532
    lineSz: 64
    sideSz: 64
    sideBwtSz: 48
    sideBwtLen: 192
    numSides: 1387
    numLines: 1387
    ebwtTotLen: 88768
    ebwtTotSz: 88768
    color: 0
    reverse: 0
Total time for call to driver() for forward index: 00:00:00
Reading reference sizes
  Time reading reference sizes: 00:00:00
Calculating joined length
Writing header
Reserving space for joined string
Joining reference sequences
  Time to join reference sequences: 00:00:00
  Time to reverse reference sequence: 00:00:00
bmax according to bmaxDivN setting: 66531
Using parameters --bmax 49899 --dcv 1024
  Doing ahead-of-time memory usage test
  Passed!  Constructing with these parameters: --bmax 49899 --dcv 1024
Constructing suffix-array element generator
Building DifferenceCoverSample
  Building sPrime
  Building sPrimeOrder
  V-Sorting samples
  V-Sorting samples time: 00:00:00
  Allocating rank array
  Ranking v-sort output
  Ranking v-sort output time: 00:00:00
  Invoking Larsson-Sadakane on ranks
  Invoking Larsson-Sadakane on ranks time: 00:00:00
  Sanity-checking and returning
Building samples
Reserving space for 12 sample suffixes
Generating random suffixes
QSorting 12 sample offsets, eliminating duplicates
QSorting sample offsets, eliminating duplicates time: 00:00:00
Multikey QSorting 12 samples
  (Using difference cover)
  Multikey QSorting samples time: 00:00:00
Calculating bucket sizes
Splitting and merging
  Splitting and merging time: 00:00:00
Split 1, merged 7; iterating...
Splitting and merging
  Splitting and merging time: 00:00:00
Avg bucket size: 44353.2 (target: 49898)
Converting suffix-array elements to index image
Allocating ftab, absorbFtab
Entering Ebwt loop
Getting block 1 of 6
  Reserving size (49899) for bucket 1
  Calculating Z arrays for bucket 1
  Entering block accumulator loop for bucket 1:
  bucket 1: 10%
  bucket 1: 20%
  bucket 1: 30%
  bucket 1: 40%
  bucket 1: 50%
  bucket 1: 60%
  bucket 1: 70%
  bucket 1: 80%
  bucket 1: 90%
  bucket 1: 100%
  Sorting block of length 47687 for bucket 1
  (Using difference cover)
  Sorting block time: 00:00:00
Returning block of 47688 for bucket 1
Getting block 2 of 6
  Reserving size (49899) for bucket 2
  Calculating Z arrays for bucket 2
  Entering block accumulator loop for bucket 2:
  bucket 2: 10%
  bucket 2: 20%
  bucket 2: 30%
  bucket 2: 40%
  bucket 2: 50%
  bucket 2: 60%
  bucket 2: 70%
  bucket 2: 80%
  bucket 2: 90%
  bucket 2: 100%
  Sorting block of length 36636 for bucket 2
  (Using difference cover)
  Sorting block time: 00:00:00
Returning block of 36637 for bucket 2
Getting block 3 of 6
  Reserving size (49899) for bucket 3
  Calculating Z arrays for bucket 3
  Entering block accumulator loop for bucket 3:
  bucket 3: 10%
  bucket 3: 20%
  bucket 3: 30%
  bucket 3: 40%
  bucket 3: 50%
  bucket 3: 60%
  bucket 3: 70%
  bucket 3: 80%
  bucket 3: 90%
  bucket 3: 100%
  Sorting block of length 49027 for bucket 3
  (Using difference cover)
  Sorting block time: 00:00:00
Returning block of 49028 for bucket 3
Getting block 4 of 6
  Reserving size (49899) for bucket 4
  Calculating Z arrays for bucket 4
  Entering block accumulator loop for bucket 4:
  bucket 4: 10%
  bucket 4: 20%
  bucket 4: 30%
  bucket 4: 40%
  bucket 4: 50%
  bucket 4: 60%
  bucket 4: 70%
  bucket 4: 80%
  bucket 4: 90%
  bucket 4: 100%
  Sorting block of length 37449 for bucket 4
  (Using difference cover)
  Sorting block time: 00:00:00
Returning block of 37450 for bucket 4
Getting block 5 of 6
  Reserving size (49899) for bucket 5
  Calculating Z arrays for bucket 5
  Entering block accumulator loop for bucket 5:
  bucket 5: 10%
  bucket 5: 20%
  bucket 5: 30%
  bucket 5: 40%
  bucket 5: 50%
  bucket 5: 60%
  bucket 5: 70%
  bucket 5: 80%
  bucket 5: 90%
  bucket 5: 100%
  Sorting block of length 47142 for bucket 5
  (Using difference cover)
  Sorting block time: 00:00:00
Returning block of 47143 for bucket 5
Getting block 6 of 6
  Reserving size (49899) for bucket 6
  Calculating Z arrays for bucket 6
  Entering block accumulator loop for bucket 6:
  bucket 6: 10%
  bucket 6: 20%
  bucket 6: 30%
  bucket 6: 40%
  bucket 6: 50%
  bucket 6: 60%
  bucket 6: 70%
  bucket 6: 80%
  bucket 6: 90%
  bucket 6: 100%
  Sorting block of length 48178 for bucket 6
  (Using difference cover)
  Sorting block time: 00:00:00
Returning block of 48179 for bucket 6
Exited Ebwt loop
fchr[A]: 0
fchr[C]: 84325
fchr[G]: 133305
fchr[T]: 181307
fchr[$]: 266124
Exiting Ebwt::buildToDisk()
Returning from initFromVector
Wrote 4286544 bytes to primary EBWT file: genome.rev.1.bt2.tmp
Wrote 66536 bytes to secondary EBWT file: genome.rev.2.bt2.tmp
Re-opening _in1 and _in2 as input streams
Returning from Ebwt constructor
Headers:
    len: 266124
    bwtLen: 266125
    sz: 66531
    bwtSz: 66532
    lineRate: 6
    offRate: 4
    offMask: 0xfffffff0
    ftabChars: 10
    eftabLen: 20
    eftabSz: 80
    ftabLen: 1048577
    ftabSz: 4194308
    offsLen: 16633
    offsSz: 66532
    lineSz: 64
    sideSz: 64
    sideBwtSz: 48
    sideBwtLen: 192
    numSides: 1387
    numLines: 1387
    ebwtTotLen: 88768
    ebwtTotSz: 88768
    color: 0
    reverse: 1
Total time for backward call to driver() for mirror index: 00:00:00

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"input"`
__workflow_invocation_uuid__	`"eff2b0140a4311f08a576045bd7d7463"`
analysis_type	`{"__current_case__": 0, "analysis_type_selector": "simple", "presets": "no_presets"}`
chromInfo	`"/tmp/tmp4ato2skh/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
dbkey	`"?"`
library	`{"__current_case__": 2, "aligned_file": false, "input_1": {"values": [{"id": 1, "src": "dce"}]}, "paired_options": {"__current_case__": 1, "paired_options_selector": "no"}, "type": "paired_collection", "unaligned_file": false}`
own_file	__identifier__
reference_genome	`{"__current_case__": 1, "own_file": {"values": [{"id": 10, "src": "dce"}]}, "source": "history"}`
rg	`{"__current_case__": 3, "rg_selector": "do_not_set"}`
sam_options	`{"__current_case__": 1, "sam_options_selector": "no"}`
save_mapping_stats	`true`

Step 3: Read length (CONCOCT):
- step_state: scheduled

Step 21: toolshed.g2.bx.psu.edu/repos/iuc/concoct_cut_up_fasta/concoct_cut_up_fasta/1.1.0+galaxy2:

step_state: scheduled

Jobs

Job 1:

Job state is ok

Command Line:

ln -s '/tmp/tmp4ato2skh/files/6/f/3/dataset_6f3f0843-9fa4-4df8-882c-b0cd443710de.dat' 'input.fa' &&  cut_up_fasta.py 'input.fa' --chunk_size 10000 --overlap_size 0 --merge_last --bedfile '/tmp/tmp4ato2skh/job_working_directory/000/13/outputs/dataset_be63c849-f2ff-4cf9-ba6d-898e0e102b80.dat' > '/tmp/tmp4ato2skh/job_working_directory/000/13/outputs/dataset_30269942-41c7-4cfe-8c8d-a963165d0e7b.dat'

Exit Code:

```
0
```

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"input"`
__workflow_invocation_uuid__	`"eff2b0140a4311f08a576045bd7d7463"`
bedfile	`true`
chromInfo	`"/tmp/tmp4ato2skh/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
chunk_size	`"10000"`
dbkey	`"?"`
input_fasta	__identifier__
merge_last	`true`
overlap_size	`"0"`

Step 22: toolshed.g2.bx.psu.edu/repos/devteam/samtools_sort/samtools_sort/2.0.5:

step_state: scheduled

Jobs

Job 1:

Job state is ok

Command Line:

addthreads=${GALAXY_SLOTS:-1} && (( addthreads-- )) &&   addmemory=${GALAXY_MEMORY_MB_PER_SLOT:-768} && ((addmemory=addmemory*75/100)) &&  samtools sort -@ $addthreads -m $addmemory"M"   -O bam -T "${TMPDIR:-.}" '/tmp/tmp4ato2skh/files/f/6/6/dataset_f664fa69-585e-47cb-ae50-93abcd51616d.dat' > '/tmp/tmp4ato2skh/job_working_directory/000/14/outputs/dataset_dd853b06-f0bc-45ba-8065-a11810c2a786.dat'

Exit Code:

```
0
```

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"input"`
__workflow_invocation_uuid__	`"eff2b0140a4311f08a576045bd7d7463"`
chromInfo	`"/tmp/tmp4ato2skh/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
dbkey	`"?"`
input1	__identifier__
minhash	`false`
prim_key_cond	`{"__current_case__": 0, "prim_key_select": ""}`

Step 23: toolshed.g2.bx.psu.edu/repos/iuc/semibin/semibin/2.0.2+galaxy0:

step_state: scheduled

Jobs

Job 1:

Job state is error

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"input"`
__workflow_invocation_uuid__	`"eff2b0140a4311f08a576045bd7d7463"`
annot	`{"ml_threshold": null}`
bin	`{"max_edges": "200", "max_node": "1.0", "minfasta_kbs": "200"}`
chromInfo	`"/tmp/tmp4ato2skh/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
dbkey	`"?"`
extra_output	`["data", "coverage"]`
min_len	`{"__current_case__": 0, "method": "automatic"}`
mode	`{"__current_case__": 0, "environment": "global", "input_bam": {"values": [{"id": 20, "src": "dce"}]}, "input_fasta": {"values": [{"id": 10, "src": "dce"}]}, "ref": {"__current_case__": 0, "cached_db": "17102022", "select": "cached"}, "select": "single"}`
orf_finder	`"fast-naive"`
random_seed	`"0"`
training	`{"batch_size": "2048", "epoches": "20"}`

Step 24: toolshed.g2.bx.psu.edu/repos/iuc/concoct_coverage_table/concoct_coverage_table/1.1.0+galaxy2:

step_state: scheduled

Jobs

Job 1:

Job state is running

Command Line:

mkdir 'mapping' && ln -s '/tmp/tmp4ato2skh/files/d/d/8/dataset_dd853b06-f0bc-45ba-8065-a11810c2a786.dat' 'mapping/_tmp_tmp4ato2skh_files_d_d_8_dataset_dd853b06-f0bc-45ba-8065-a11810c2a786.dat.sorted.bam' && samtools index 'mapping/_tmp_tmp4ato2skh_files_d_d_8_dataset_dd853b06-f0bc-45ba-8065-a11810c2a786.dat.sorted.bam' 'mapping/_tmp_tmp4ato2skh_files_d_d_8_dataset_dd853b06-f0bc-45ba-8065-a11810c2a786.dat.bam.bai' && mv 'mapping/_tmp_tmp4ato2skh_files_d_d_8_dataset_dd853b06-f0bc-45ba-8065-a11810c2a786.dat.sorted.bam' 'mapping/_tmp_tmp4ato2skh_files_d_d_8_dataset_dd853b06-f0bc-45ba-8065-a11810c2a786.dat.bam' && concoct_coverage_table.py '/tmp/tmp4ato2skh/files/b/e/6/dataset_be63c849-f2ff-4cf9-ba6d-898e0e102b80.dat' mapping/*.bam > '/tmp/tmp4ato2skh/job_working_directory/000/16/outputs/dataset_fd75bb04-5ea5-4a61-9812-be7370042a4c.dat'

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"input"`
__workflow_invocation_uuid__	`"eff2b0140a4311f08a576045bd7d7463"`
bedfile	__identifier__
chromInfo	`"/tmp/tmp4ato2skh/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
dbkey	`"?"`
mode	`{"__current_case__": 0, "bamfile": {"values": [{"id": 20, "src": "dce"}]}, "type": "individual"}`
mode	bamfile

Step 25: toolshed.g2.bx.psu.edu/repos/iuc/metabat2_jgi_summarize_bam_contig_depths/metabat2_jgi_summarize_bam_contig_depths/2.17+galaxy0:

step_state: scheduled

Jobs

Job 1:

Job state is queued

Command Line:

jgi_summarize_bam_contig_depths --outputDepth '/tmp/tmp4ato2skh/job_working_directory/000/17/outputs/dataset_7054bb38-f9a3-4358-b793-46c0eff08a53.dat' --percentIdentity 97   --minMapQual 0 --weightMapQual 0.0  --maxEdgeBases 75 --shredLength 16000 --shredDepth 5 --minContigLength 1 --minContigDepth 0.0 '/tmp/tmp4ato2skh/files/d/d/8/dataset_dd853b06-f0bc-45ba-8065-a11810c2a786.dat'

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"input"`
__workflow_invocation_uuid__	`"eff2b0140a4311f08a576045bd7d7463"`
advanced	`{"includeEdgeBases": false, "maxEdgeBases": "75", "minMapQual": "0", "noIntraDepthVariance": false, "output_paired_contigs": false, "percentIdentity": "97", "showDepth": false, "weightMapQual": "0.0"}`
bam_indiv_input	__identifier__
chromInfo	`"/tmp/tmp4ato2skh/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
dbkey	`"?"`
mode	`{"__current_case__": 0, "bam_indiv_input": {"values": [{"id": 20, "src": "dce"}]}, "type": "individual", "use_reference_cond": {"__current_case__": 0, "use_reference": "no"}}`
shredding	`{"minContigDepth": "0.0", "minContigLength": "1", "shredDepth": "5", "shredLength": "16000"}`

Step 26: Unlabelled step:
- step_state: new

Step 27: toolshed.g2.bx.psu.edu/repos/iuc/concoct/concoct/1.1.0+galaxy2:

step_state: scheduled

Jobs

Job 1:

Job state is new

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"input"`
__workflow_invocation_uuid__	`"eff2b0140a4311f08a576045bd7d7463"`
advanced	`{"clusters": "400", "iterations": "500", "kmer_length": "4", "length_threshold": "1000", "no_cov_normalization": false, "read_length": "250", "seed": "1", "total_percentage_pca": "90"}`
chromInfo	`"/tmp/tmp4ato2skh/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
dbkey	`"?"`
output	`{"converge_out": false, "log": false, "no_total_coverage": false}`

Step 28: toolshed.g2.bx.psu.edu/repos/mbernt/maxbin2/maxbin2/2.2.7+galaxy6:

step_state: scheduled

Jobs

Job 1:

Job state is new

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"expression.json"`
__workflow_invocation_uuid__	`"eff2b0140a4311f08a576045bd7d7463"`
adv	`{"max_iteration": "50", "min_contig_length": "1000", "prob_threshold": "0.5"}`
assembly	`{"__current_case__": 0, "inputs": {"__current_case__": 1, "abund": {"values": [{"id": 27, "src": "dce"}]}, "type": "abund"}, "type": "individual"}`
chromInfo	`"/tmp/tmp4ato2skh/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
dbkey	`"?"`
output	`{"log": true, "marker": true, "markers": true, "markerset": "107", "plotmarker": true}`

Step 29: toolshed.g2.bx.psu.edu/repos/iuc/metabat2/metabat2/2.17+galaxy0:

step_state: scheduled

Jobs

Job 1:

Job state is new

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"input"`
__workflow_invocation_uuid__	`"eff2b0140a4311f08a576045bd7d7463"`
advanced	`{"base_coverage_depth_cond": {"__current_case__": 1, "abdFile": {"values": [{"id": 27, "src": "dce"}]}, "base_coverage_depth": "yes", "cvExt": null}, "maxEdges": "200", "maxP": "95", "minCV": "1.0", "minCVSum": "1.0", "minContig": "1500", "minS": "60", "noAdd": false, "pTNF": "0", "seed": "0"}`
advanced	abdFile
chromInfo	`"/tmp/tmp4ato2skh/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
dbkey	`"?"`
inFile	__identifier__
out	`{"extra_outputs": ["lowDepth", "tooShort", "unbinned", "log"], "minClsSize": "200000", "onlyLabel": false, "saveCls": false}`

Step 30: toolshed.g2.bx.psu.edu/repos/iuc/concoct_merge_cut_up_clustering/concoct_merge_cut_up_clustering/1.1.0+galaxy2:

step_state: scheduled

Jobs

Job 1:

Job state is new

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"input"`
__workflow_invocation_uuid__	`"eff2b0140a4311f08a576045bd7d7463"`
chromInfo	`"/tmp/tmp4ato2skh/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
cutup_clustering_result	__identifier__
dbkey	`"?"`

Step 4: Environment for the built-in model (SemiBin):
- step_state: scheduled
Step 31: Unlabelled step:
- step_state: new
Step 32: Unlabelled step:
- step_state: new

Step 33: toolshed.g2.bx.psu.edu/repos/iuc/concoct_extract_fasta_bins/concoct_extract_fasta_bins/1.1.0+galaxy2:

step_state: scheduled

Jobs

Job 1:

Job state is new

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"input"`
__workflow_invocation_uuid__	`"eff2b0140a4311f08a576045bd7d7463"`
chromInfo	`"/tmp/tmp4ato2skh/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
cluster_file	__identifier__
dbkey	`"?"`
fasta_file	__identifier__

Step 34: Unlabelled step:
- step_state: new
Step 35: Unlabelled step:
- step_state: new
Step 36: Unlabelled step:
- step_state: new
Step 37: Pool Bins from all samples:
- 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 5: Trimmed grouped paired reads:
- step_state: scheduled
Step 41: Unlabelled step:
- step_state: new
Step 42: Unlabelled step:
- step_state: new
Step 43: Unlabelled step:
- step_state: new
Step 44: Unlabelled step:
- step_state: new
Step 45: Unlabelled step:
- step_state: new
Step 46: Unlabelled step:
- step_state: new
Step 47: Unlabelled step:
- step_state: new
Step 48: Unlabelled step:
- step_state: new
Step 6: Trimmed sample paired reads:
- step_state: scheduled
Step 7: Contamination weight (Binette):
- step_state: scheduled
Step 8: Minimum MAG completeness percentage:
- step_state: scheduled
Step 9: Maximum MAG contamination percentage:
- step_state: scheduled
**Step 10: Minimum MAG length **:
- step_state: scheduled

Other invocation details
- error_message
  - Final state of invocation cdf6c67c360f70c6 is [failed]. Failed to run workflow, at least one job is in [error] state.
- history_id
  - cdf6c67c360f70c6
- history_state
  - error
- invocation_id
  - cdf6c67c360f70c6
- invocation_state
  - failed
- messages
  - [{'dependent_workflow_step_id': 22, 'hdca_id': '5869b5b3219f70eb', 'reason': 'collection_failed', 'workflow_step_id': 25}]
- workflow_id
  - cdf6c67c360f70c6

github-actions · 2025-04-08T13:50:49Z

Test Results (powered by Planemo)

Test Summary

Test State	Count
Total	0
Passed	0
Error	0
Failure	0
Skipped	0

github-actions · 2025-04-08T13:59:47Z

Test Results (powered by Planemo)

Test Summary

Test State	Count
Total	1
Passed	0
Error	1
Failure	0
Skipped	0

Errored Tests

❌ MAGs-generation.ga_0

Execution Problem:

Unexpected HTTP status code: 500: Internal Server Error

github-actions · 2025-04-08T15:02:44Z

Test Results (powered by Planemo)

Test Summary

Test State	Count
Total	1
Passed	0
Error	1
Failure	0
Skipped	0

Errored Tests

❌ MAGs-generation.ga_0

Execution Problem:

Final state of invocation 1ed2e242fb805563 is [failed]. Failed to run workflow, at least one job is in [error] state.

Workflow invocation details

Invocation Messages
- Invocation scheduling failed because step 55 requires a dataset collection created by step 48, but dataset collection entered a failed state.

Steps

Step 1: Choose Assembler:
- step_state: scheduled
Step 2: Custom Assemblies:
- step_state: scheduled
Step 11: Maximum MAG contamination percentage:
- step_state: scheduled
Step 12: Minimum MAG length:
- step_state: scheduled
Step 13: CheckM2 Database (dRep step):
- step_state: scheduled
Step 14: ANI threshold for dereplication:
- step_state: scheduled
Step 15: CheckM2 Database (Bin step):
- step_state: scheduled
Step 16: GTDB-tk Database:
- step_state: scheduled
Step 17: Bakta Database:
- step_state: scheduled
Step 18: AMRFinderPlus Database for Bakta:
- step_state: scheduled
Step 19: Run Bakta on MAGs:
- step_state: scheduled

Step 20: toolshed.g2.bx.psu.edu/repos/iuc/map_param_value/map_param_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__	`"639edb8a148211f0aeac6045bda70f2c"`
chromInfo	`"/tmp/tmpbo76svqj/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
dbkey	`"?"`
input_param_type	`{"__current_case__": 0, "input_param": "MEGAHIT", "mappings": [{"__index__": 0, "from": "MEGAHIT", "to": "True"}], "type": "text"}`
output_param_type	`"boolean"`
unmapped	`{"__current_case__": 2, "default_value": "False", "on_unmapped": "default"}`

Step 3: Minimum length of contigs to output:
- step_state: scheduled

Step 21: toolshed.g2.bx.psu.edu/repos/iuc/map_param_value/map_param_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__	`"639edb8a148211f0aeac6045bda70f2c"`
chromInfo	`"/tmp/tmpbo76svqj/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
dbkey	`"?"`
input_param_type	`{"__current_case__": 0, "input_param": "MEGAHIT", "mappings": [{"__index__": 0, "from": "metaSPAdes", "to": "True"}], "type": "text"}`
output_param_type	`"boolean"`
unmapped	`{"__current_case__": 2, "default_value": "False", "on_unmapped": "default"}`

Step 22: __UNZIP_COLLECTION__:
- step_state: scheduled
- Jobs
  - Job 1:
    - Job state is ok
    Traceback:
    Job Parameters:
    - Job parameter Parameter value
      
      __workflow_invocation_uuid__ "639edb8a148211f0aeac6045bda70f2c"
      
      input {"values": [{"id": 1, "src": "dce"}]}

Step 23: toolshed.g2.bx.psu.edu/repos/iuc/megahit/megahit/1.2.9+galaxy2:

step_state: scheduled

Jobs

Job 1:

Job state is ok

Command Line:

if [[ -n "$GALAXY_MEMORY_MB" ]]; then MEMORY="-m $((GALAXY_MEMORY_MB * 1024))"; fi;  megahit --num-cpu-threads ${GALAXY_SLOTS:-4}  -1 '/tmp/tmpbo76svqj/files/b/2/7/dataset_b27ae4d4-9ab0-4bc6-b3d2-325dc79aa2b6.dat' -2 '/tmp/tmpbo76svqj/files/1/3/f/dataset_13fc15e4-5959-4e47-a36d-075c5894ac88.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:

2025-04-08 14:05:03 - MEGAHIT v1.2.9
2025-04-08 14:05:03 - Using megahit_core with POPCNT and BMI2 support
2025-04-08 14:05:03 - Convert reads to binary library
2025-04-08 14:05:03 - b'INFO  sequence/io/sequence_lib.cpp  :   75 - Lib 0 (/tmp/tmpbo76svqj/files/b/2/7/dataset_b27ae4d4-9ab0-4bc6-b3d2-325dc79aa2b6.dat,/tmp/tmpbo76svqj/files/1/3/f/dataset_13fc15e4-5959-4e47-a36d-075c5894ac88.dat): pe, 18924 reads, 150 max length'
2025-04-08 14:05:03 - b'INFO  utils/utils.h                 :  152 - Real: 0.0460\tuser: 0.0401\tsys: 0.0070\tmaxrss: 20616'
2025-04-08 14:05:03 - Start assembly. Number of CPU threads 1 
2025-04-08 14:05:03 - k list: 21,29,39,59,79,99,119,141 
2025-04-08 14:05:03 - Memory used: 15090086707
2025-04-08 14:05:03 - Extract solid (k+1)-mers for k = 21 
2025-04-08 14:05:04 - Build graph for k = 21 
2025-04-08 14:05:04 - Assemble contigs from SdBG for k = 21
2025-04-08 14:05:05 - Local assembly for k = 21
2025-04-08 14:05:06 - Extract iterative edges from k = 21 to 29 
2025-04-08 14:05:06 - Build graph for k = 29 
2025-04-08 14:05:06 - Assemble contigs from SdBG for k = 29
2025-04-08 14:05:06 - Local assembly for k = 29
2025-04-08 14:05:07 - Extract iterative edges from k = 29 to 39 
2025-04-08 14:05:07 - Build graph for k = 39 
2025-04-08 14:05:07 - Assemble contigs from SdBG for k = 39
2025-04-08 14:05:08 - Local assembly for k = 39
2025-04-08 14:05:09 - Extract iterative edges from k = 39 to 59 
2025-04-08 14:05:09 - Build graph for k = 59 
2025-04-08 14:05:09 - Assemble contigs from SdBG for k = 59
2025-04-08 14:05:09 - Local assembly for k = 59
2025-04-08 14:05:10 - Extract iterative edges from k = 59 to 79 
2025-04-08 14:05:10 - Build graph for k = 79 
2025-04-08 14:05:10 - Assemble contigs from SdBG for k = 79
2025-04-08 14:05:10 - Local assembly for k = 79
2025-04-08 14:05:11 - Extract iterative edges from k = 79 to 99 
2025-04-08 14:05:11 - Build graph for k = 99 
2025-04-08 14:05:11 - Assemble contigs from SdBG for k = 99
2025-04-08 14:05:11 - Local assembly for k = 99
2025-04-08 14:05:11 - Extract iterative edges from k = 99 to 119 
2025-04-08 14:05:11 - Build graph for k = 119 
2025-04-08 14:05:12 - Assemble contigs from SdBG for k = 119
2025-04-08 14:05:12 - Local assembly for k = 119
2025-04-08 14:05:12 - Extract iterative edges from k = 119 to 141 
2025-04-08 14:05:12 - Build graph for k = 141 
2025-04-08 14:05:12 - Assemble contigs from SdBG for k = 141
2025-04-08 14:05:13 - Merging to output final contigs 
2025-04-08 14:05:13 - 63 contigs, total 266124 bp, min 354 bp, max 11001 bp, avg 4224 bp, N50 4877 bp
2025-04-08 14:05:13 - ALL DONE. Time elapsed: 9.814435 seconds

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"fastqsanger.gz"`
__workflow_invocation_uuid__	`"639edb8a148211f0aeac6045bda70f2c"`
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/tmpbo76svqj/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": false, "min_contig_len": "200", "show_intermediate_contigs": false}`

Step 24: toolshed.g2.bx.psu.edu/repos/nml/metaspades/metaspades/4.1.0+galaxy0:

step_state: scheduled

Jobs

Job 1:

Job state is skipped

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"input"`
__workflow_invocation_uuid__	`"639edb8a148211f0aeac6045bda70f2c"`
additional_reads	`{"__current_case__": 1, "selector": "false"}`
arf	`{"nanopore": null, "pacbio": null}`
chromInfo	`"/tmp/tmpbo76svqj/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
dbkey	`"?"`
kmer_cond	`{"__current_case__": 0, "kmer_sel": "auto"}`
library_number	`"true"`
mode_sel	`None`
optional_output	`["ag", "ags", "cn", "cs"]`
phred_offset	`"auto"`
singlePaired	`{"__current_case__": 1, "input": {"values": [{"id": 1, "src": "hdca"}]}, "orientation": "fr", "sPaired": "paired_collection", "type_paired": "pe"}`

Step 25: 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__	`"639edb8a148211f0aeac6045bda70f2c"`
chromInfo	`"/tmp/tmpbo76svqj/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
dbkey	`"?"`
style_cond	`{"__current_case__": 0, "pick_style": "first", "type_cond": {"__current_case__": 4, "param_type": "data", "pick_from": [{"__index__": 0, "value": {"values": [{"id": 12, "src": "hda"}]}}, {"__index__": 1, "value": {"values": [{"id": 9, "src": "dce"}]}}, {"__index__": 2, "value": null}]}}`

Step 26: toolshed.g2.bx.psu.edu/repos/iuc/quast/quast/5.3.0+galaxy0:

step_state: scheduled

Jobs

Job 1:

Job state is ok

Command Line:

echo 50contig_reads &&   ln -s '/tmp/tmpbo76svqj/files/b/2/7/dataset_b27ae4d4-9ab0-4bc6-b3d2-325dc79aa2b6.dat' 'pe1-50contig_reads.fastqsanger.gz' && ln -s '/tmp/tmpbo76svqj/files/1/3/f/dataset_13fc15e4-5959-4e47-a36d-075c5894ac88.dat' 'pe2-50contig_reads.fastqsanger.gz' &&  metaquast  --pe1 'pe1-50contig_reads.fastqsanger.gz' --pe2 'pe2-50contig_reads.fastqsanger.gz' --labels '50contig_reads' -o 'outputdir'  --max-ref-num 0  --min-identity 90.0 --min-contig 500        --min-alignment 65 --ambiguity-usage 'one' --ambiguity-score 0.99   --local-mis-size 200   --contig-thresholds '0,1000'  --extensive-mis-size 1000 --scaffold-gap-max-size 1000 --unaligned-part-size 500   --x-for-Nx 90  '/tmp/tmpbo76svqj/files/1/8/b/dataset_18b41470-af6e-41fc-8ca4-51e94f07d355.dat' --threads ${GALAXY_SLOTS:-1}  && 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/tmpbo76svqj/job_working_directory/000/11/outputs/dataset_ee0c24d5-377a-4588-8297-6744fc1cabb7_files' && cp outputdir/combined_reference/*.html '/tmp/tmpbo76svqj/job_working_directory/000/11/outputs/dataset_ee0c24d5-377a-4588-8297-6744fc1cabb7_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/tmpbo76svqj/job_working_directory/000/11/outputs/dataset_ee0c24d5-377a-4588-8297-6744fc1cabb7_files'; fi && if [[ -d "outputdir/krona_charts/" ]]; then mkdir -p 'None' && cp outputdir/krona_charts/*.html 'None'; fi

Exit Code:

```
0
```

Standard Output:

50contig_reads
/usr/local/opt/quast-5.3.0/metaquast.py --pe1 pe1-50contig_reads.fastqsanger.gz --pe2 pe2-50contig_reads.fastqsanger.gz --labels 50contig_reads -o outputdir --max-ref-num 0 --min-identity 90.0 --min-contig 500 --min-alignment 65 --ambiguity-usage one --ambiguity-score 0.99 --local-mis-size 200 --contig-thresholds 0,1000 --extensive-mis-size 1000 --scaffold-gap-max-size 1000 --unaligned-part-size 500 --x-for-Nx 90 /tmp/tmpbo76svqj/files/1/8/b/dataset_18b41470-af6e-41fc-8ca4-51e94f07d355.dat --threads 1

Version: 5.3.0

System information:
  OS: Linux-6.8.0-1021-azure-x86_64-with-glibc2.36 (linux_64)
  Python version: 3.12.3
  CPUs number: 4

Started: 2025-04-08 14:06:14

Logging to /tmp/tmpbo76svqj/job_working_directory/000/11/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/tmpbo76svqj/files/1/8/b/dataset_18b41470-af6e-41fc-8ca4-51e94f07d355.dat ==> 50contig_reads

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 pe1-50contig_reads.fastqsanger.gz --pe2 pe2-50contig_reads.fastqsanger.gz --min-identity 90.0 --min-contig 500 --min-alignment 65 --ambiguity-usage one --ambiguity-score 0.99 --local-mis-size 200 --contig-thresholds 0,1000 --extensive-mis-size 1000 --scaffold-gap-max-size 1000 --unaligned-part-size 500 --x-for-Nx 90 --threads 1 /tmp/tmpbo76svqj/files/1/8/b/dataset_18b41470-af6e-41fc-8ca4-51e94f07d355.dat -o /tmp/tmpbo76svqj/job_working_directory/000/11/working/outputdir --labels 50contig_reads

Version: 5.3.0

System information:
  OS: Linux-6.8.0-1021-azure-x86_64-with-glibc2.36 (linux_64)
  Python version: 3.12.3
  CPUs number: 4

Started: 2025-04-08 14:06:15

Logging to /tmp/tmpbo76svqj/job_working_directory/000/11/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/tmpbo76svqj/job_working_directory/000/11/working
Main parameters: 
  MODE: meta, threads: 1, min contig length: 500, min alignment length: 65, min alignment IDY: 90.0, \
  ambiguity: all, min local misassembly length: 200, min extensive misassembly length: 1000

Contigs:
  Pre-processing...
  /tmp/tmpbo76svqj/files/1/8/b/dataset_18b41470-af6e-41fc-8ca4-51e94f07d355.dat ==> 50contig_reads

2025-04-08 14:06:15
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/tmpbo76svqj/job_working_directory/000/11/home/.quast
Downloading gridss (file: gridss-1.4.1.jar)...
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gridss successfully downloaded!
  Logging to files /tmp/tmpbo76svqj/job_working_directory/000/11/working/outputdir/reads_stats/reads_stats.log and /tmp/tmpbo76svqj/job_working_directory/000/11/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/tmpbo76svqj/job_working_directory/000/11/working/outputdir/reads_stats/reads_report.txt, reads_report.tsv, and reads_report.tex
Done.

2025-04-08 14:06:20
Running Basic statistics processor...
  Contig files: 
    50contig_reads
  Calculating N50 and L50...
    50contig_reads, N50 = 4877, L50 = 22, auN = 5187.8, Total length = 265405, GC % = 36.45, # N's per 100 kbp =  0.00
  Drawing Nx plot...
    saved to /tmp/tmpbo76svqj/job_working_directory/000/11/working/outputdir/basic_stats/Nx_plot.pdf
  Drawing cumulative plot...
    saved to /tmp/tmpbo76svqj/job_working_directory/000/11/working/outputdir/basic_stats/cumulative_plot.pdf
  Drawing GC content plot...
    saved to /tmp/tmpbo76svqj/job_working_directory/000/11/working/outputdir/basic_stats/GC_content_plot.pdf
  Drawing 50contig_reads GC content plot...
    saved to /tmp/tmpbo76svqj/job_working_directory/000/11/working/outputdir/basic_stats/50contig_reads_GC_content_plot.pdf
Done.

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

2025-04-08 14:06:21
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

2025-04-08 14:06:21
RESULTS:
  Text versions of total report are saved to /tmp/tmpbo76svqj/job_working_directory/000/11/working/outputdir/report.txt, report.tsv, and report.tex
  Text versions of transposed total report are saved to /tmp/tmpbo76svqj/job_working_directory/000/11/working/outputdir/transposed_report.txt, transposed_report.tsv, and transposed_report.tex
  HTML version (interactive tables and plots) is saved to /tmp/tmpbo76svqj/job_working_directory/000/11/working/outputdir/report.html
  PDF version (tables and plots) is saved to /tmp/tmpbo76svqj/job_working_directory/000/11/working/outputdir/report.pdf
  Icarus (contig browser) is saved to /tmp/tmpbo76svqj/job_working_directory/000/11/working/outputdir/icarus.html
  Log is saved to /tmp/tmpbo76svqj/job_working_directory/000/11/working/outputdir/quast.log

Finished: 2025-04-08 14:06:21
Elapsed time: 0:00:06.436382
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__	`"639edb8a148211f0aeac6045bda70f2c"`
advanced	`{"contig_thresholds": "0,1000", "extensive_mis_size": "1000", "fragmented_max_indent": null, "report_all_metrics": false, "scaffold_gap_max_size": "1000", "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": "90.0", "ref": {"__current_case__": 0, "max_ref_num": "0", "origin": "silva"}, "reuse_combined_alignments": false, "type": "metagenome"}`
chromInfo	`"/tmp/tmpbo76svqj/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	`"500"`
mode	`{"__current_case__": 0, "in": {"__current_case__": 1, "custom": "false", "inputs": {"values": [{"id": 10, "src": "dce"}]}}, "mode": "individual", "reads": {"__current_case__": 2, "input_1": {"values": [{"id": 7, "src": "dce"}]}, "input_2": {"values": [{"id": 8, "src": "dce"}]}, "reads_option": "paired"}}`
output_files	`["html", "pdf", "tabular", "log", "summary", "krona"]`
split_scaffolds	`false`

Step 27: toolshed.g2.bx.psu.edu/repos/devteam/bowtie2/bowtie2/2.5.3+galaxy1:

step_state: scheduled

Jobs

Job 1:

Job state is ok

Command Line:

set -o | grep -q pipefail && set -o pipefail; bowtie2-build --threads ${GALAXY_SLOTS:-4} '/tmp/tmpbo76svqj/files/1/8/b/dataset_18b41470-af6e-41fc-8ca4-51e94f07d355.dat' genome && ln -s -f '/tmp/tmpbo76svqj/files/1/8/b/dataset_18b41470-af6e-41fc-8ca4-51e94f07d355.dat' genome.fa &&   ln -f -s '/tmp/tmpbo76svqj/files/b/2/7/dataset_b27ae4d4-9ab0-4bc6-b3d2-325dc79aa2b6.dat' input_f.fastq.gz &&  ln -f -s '/tmp/tmpbo76svqj/files/1/3/f/dataset_13fc15e4-5959-4e47-a36d-075c5894ac88.dat' input_r.fastq.gz &&    THREADS=${GALAXY_SLOTS:-4} && if [ "$THREADS" -gt 1 ]; then (( THREADS-- )); fi &&   bowtie2  -p "$THREADS"  -x 'genome'   -1 'input_f.fastq.gz' -2 'input_r.fastq.gz'                2> >(tee '/tmp/tmpbo76svqj/job_working_directory/000/12/outputs/dataset_363c5fba-1d6a-469b-bc82-93a15630d0a4.dat' >&2)  | samtools sort -l 0 -T "${TMPDIR:-.}" -O bam | samtools view --no-PG -O bam -@ ${GALAXY_SLOTS:-1} -o '/tmp/tmpbo76svqj/job_working_directory/000/12/outputs/dataset_9ed09d4e-2d74-46b0-88c7-c9d362d8c801.dat'

Exit Code:

```
0
```

Standard Error:

Building a SMALL index
Renaming genome.3.bt2.tmp to genome.3.bt2
Renaming genome.4.bt2.tmp to genome.4.bt2
Renaming genome.1.bt2.tmp to genome.1.bt2
Renaming genome.2.bt2.tmp to genome.2.bt2
Renaming genome.rev.1.bt2.tmp to genome.rev.1.bt2
Renaming genome.rev.2.bt2.tmp to genome.rev.2.bt2
9462 reads; of these:
  9462 (100.00%) were paired; of these:
    90 (0.95%) aligned concordantly 0 times
    9300 (98.29%) aligned concordantly exactly 1 time
    72 (0.76%) aligned concordantly >1 times
    ----
    90 pairs aligned concordantly 0 times; of these:
      8 (8.89%) aligned discordantly 1 time
    ----
    82 pairs aligned 0 times concordantly or discordantly; of these:
      164 mates make up the pairs; of these:
        93 (56.71%) aligned 0 times
        70 (42.68%) aligned exactly 1 time
        1 (0.61%) aligned >1 times
99.51% overall alignment rate

Standard Output:

Settings:
  Output files: "genome.*.bt2"
  Line rate: 6 (line is 64 bytes)
  Lines per side: 1 (side is 64 bytes)
  Offset rate: 4 (one in 16)
  FTable chars: 10
  Strings: unpacked
  Max bucket size: default
  Max bucket size, sqrt multiplier: default
  Max bucket size, len divisor: 4
  Difference-cover sample period: 1024
  Endianness: little
  Actual local endianness: little
  Sanity checking: disabled
  Assertions: disabled
  Random seed: 0
  Sizeofs: void*:8, int:4, long:8, size_t:8
Input files DNA, FASTA:
  /tmp/tmpbo76svqj/files/1/8/b/dataset_18b41470-af6e-41fc-8ca4-51e94f07d355.dat
Reading reference sizes
  Time reading reference sizes: 00:00:00
Calculating joined length
Writing header
Reserving space for joined string
Joining reference sequences
  Time to join reference sequences: 00:00:00
bmax according to bmaxDivN setting: 66531
Using parameters --bmax 49899 --dcv 1024
  Doing ahead-of-time memory usage test
  Passed!  Constructing with these parameters: --bmax 49899 --dcv 1024
Constructing suffix-array element generator
Building DifferenceCoverSample
  Building sPrime
  Building sPrimeOrder
  V-Sorting samples
  V-Sorting samples time: 00:00:00
  Allocating rank array
  Ranking v-sort output
  Ranking v-sort output time: 00:00:00
  Invoking Larsson-Sadakane on ranks
  Invoking Larsson-Sadakane on ranks time: 00:00:00
  Sanity-checking and returning
Building samples
Reserving space for 12 sample suffixes
Generating random suffixes
QSorting 12 sample offsets, eliminating duplicates
QSorting sample offsets, eliminating duplicates time: 00:00:00
Multikey QSorting 12 samples
  (Using difference cover)
  Multikey QSorting samples time: 00:00:00
Calculating bucket sizes
Splitting and merging
  Splitting and merging time: 00:00:00
Split 1, merged 6; iterating...
Splitting and merging
  Splitting and merging time: 00:00:00
Avg bucket size: 38016.9 (target: 49898)
Converting suffix-array elements to index image
Allocating ftab, absorbFtab
Entering Ebwt loop
Getting block 1 of 7
  Reserving size (49899) for bucket 1
  Calculating Z arrays for bucket 1
  Entering block accumulator loop for bucket 1:
  bucket 1: 10%
  bucket 1: 20%
  bucket 1: 30%
  bucket 1: 40%
  bucket 1: 50%
  bucket 1: 60%
  bucket 1: 70%
  bucket 1: 80%
  bucket 1: 90%
  bucket 1: 100%
  Sorting block of length 18323 for bucket 1
  (Using difference cover)
  Sorting block time: 00:00:00
Returning block of 18324 for bucket 1
Getting block 2 of 7
  Reserving size (49899) for bucket 2
  Calculating Z arrays for bucket 2
  Entering block accumulator loop for bucket 2:
  bucket 2: 10%
  bucket 2: 20%
  bucket 2: 30%
  bucket 2: 40%
  bucket 2: 50%
  bucket 2: 60%
  bucket 2: 70%
  bucket 2: 80%
  bucket 2: 90%
  bucket 2: 100%
  Sorting block of length 49606 for bucket 2
  (Using difference cover)
  Sorting block time: 00:00:00
Returning block of 49607 for bucket 2
Getting block 3 of 7
  Reserving size (49899) for bucket 3
  Calculating Z arrays for bucket 3
  Entering block accumulator loop for bucket 3:
  bucket 3: 10%
  bucket 3: 20%
  bucket 3: 30%
  bucket 3: 40%
  bucket 3: 50%
  bucket 3: 60%
  bucket 3: 70%
  bucket 3: 80%
  bucket 3: 90%
  bucket 3: 100%
  Sorting block of length 45151 for bucket 3
  (Using difference cover)
  Sorting block time: 00:00:00
Returning block of 45152 for bucket 3
Getting block 4 of 7
  Reserving size (49899) for bucket 4
  Calculating Z arrays for bucket 4
  Entering block accumulator loop for bucket 4:
  bucket 4: 10%
  bucket 4: 20%
  bucket 4: 30%
  bucket 4: 40%
  bucket 4: 50%
  bucket 4: 60%
  bucket 4: 70%
  bucket 4: 80%
  bucket 4: 90%
  bucket 4: 100%
  Sorting block of length 49787 for bucket 4
  (Using difference cover)
  Sorting block time: 00:00:00
Returning block of 49788 for bucket 4
Getting block 5 of 7
  Reserving size (49899) for bucket 5
  Calculating Z arrays for bucket 5
  Entering block accumulator loop for bucket 5:
  bucket 5: 10%
  bucket 5: 20%
  bucket 5: 30%
  bucket 5: 40%
  bucket 5: 50%
  bucket 5: 60%
  bucket 5: 70%
  bucket 5: 80%
  bucket 5: 90%
  bucket 5: 100%
  Sorting block of length 28638 for bucket 5
  (Using difference cover)
  Sorting block time: 00:00:00
Returning block of 28639 for bucket 5
Getting block 6 of 7
  Reserving size (49899) for bucket 6
  Calculating Z arrays for bucket 6
  Entering block accumulator loop for bucket 6:
  bucket 6: 10%
  bucket 6: 20%
  bucket 6: 30%
  bucket 6: 40%
  bucket 6: 50%
  bucket 6: 60%
  bucket 6: 70%
  bucket 6: 80%
  bucket 6: 90%
  bucket 6: 100%
  Sorting block of length 43194 for bucket 6
  (Using difference cover)
  Sorting block time: 00:00:00
Returning block of 43195 for bucket 6
Getting block 7 of 7
  Reserving size (49899) for bucket 7
  Calculating Z arrays for bucket 7
  Entering block accumulator loop for bucket 7:
  bucket 7: 10%
  bucket 7: 20%
  bucket 7: 30%
  bucket 7: 40%
  bucket 7: 50%
  bucket 7: 60%
  bucket 7: 70%
  bucket 7: 80%
  bucket 7: 90%
  bucket 7: 100%
  Sorting block of length 31419 for bucket 7
  (Using difference cover)
  Sorting block time: 00:00:00
Returning block of 31420 for bucket 7
Exited Ebwt loop
fchr[A]: 0
fchr[C]: 84325
fchr[G]: 133305
fchr[T]: 181307
fchr[$]: 266124
Exiting Ebwt::buildToDisk()
Returning from initFromVector
Wrote 4286544 bytes to primary EBWT file: genome.1.bt2.tmp
Wrote 66536 bytes to secondary EBWT file: genome.2.bt2.tmp
Re-opening _in1 and _in2 as input streams
Returning from Ebwt constructor
Headers:
    len: 266124
    bwtLen: 266125
    sz: 66531
    bwtSz: 66532
    lineRate: 6
    offRate: 4
    offMask: 0xfffffff0
    ftabChars: 10
    eftabLen: 20
    eftabSz: 80
    ftabLen: 1048577
    ftabSz: 4194308
    offsLen: 16633
    offsSz: 66532
    lineSz: 64
    sideSz: 64
    sideBwtSz: 48
    sideBwtLen: 192
    numSides: 1387
    numLines: 1387
    ebwtTotLen: 88768
    ebwtTotSz: 88768
    color: 0
    reverse: 0
Total time for call to driver() for forward index: 00:00:00
Reading reference sizes
  Time reading reference sizes: 00:00:00
Calculating joined length
Writing header
Reserving space for joined string
Joining reference sequences
  Time to join reference sequences: 00:00:00
  Time to reverse reference sequence: 00:00:00
bmax according to bmaxDivN setting: 66531
Using parameters --bmax 49899 --dcv 1024
  Doing ahead-of-time memory usage test
  Passed!  Constructing with these parameters: --bmax 49899 --dcv 1024
Constructing suffix-array element generator
Building DifferenceCoverSample
  Building sPrime
  Building sPrimeOrder
  V-Sorting samples
  V-Sorting samples time: 00:00:00
  Allocating rank array
  Ranking v-sort output
  Ranking v-sort output time: 00:00:00
  Invoking Larsson-Sadakane on ranks
  Invoking Larsson-Sadakane on ranks time: 00:00:00
  Sanity-checking and returning
Building samples
Reserving space for 12 sample suffixes
Generating random suffixes
QSorting 12 sample offsets, eliminating duplicates
QSorting sample offsets, eliminating duplicates time: 00:00:00
Multikey QSorting 12 samples
  (Using difference cover)
  Multikey QSorting samples time: 00:00:00
Calculating bucket sizes
Splitting and merging
  Splitting and merging time: 00:00:00
Split 1, merged 7; iterating...
Splitting and merging
  Splitting and merging time: 00:00:00
Avg bucket size: 44353.2 (target: 49898)
Converting suffix-array elements to index image
Allocating ftab, absorbFtab
Entering Ebwt loop
Getting block 1 of 6
  Reserving size (49899) for bucket 1
  Calculating Z arrays for bucket 1
  Entering block accumulator loop for bucket 1:
  bucket 1: 10%
  bucket 1: 20%
  bucket 1: 30%
  bucket 1: 40%
  bucket 1: 50%
  bucket 1: 60%
  bucket 1: 70%
  bucket 1: 80%
  bucket 1: 90%
  bucket 1: 100%
  Sorting block of length 47687 for bucket 1
  (Using difference cover)
  Sorting block time: 00:00:00
Returning block of 47688 for bucket 1
Getting block 2 of 6
  Reserving size (49899) for bucket 2
  Calculating Z arrays for bucket 2
  Entering block accumulator loop for bucket 2:
  bucket 2: 10%
  bucket 2: 20%
  bucket 2: 30%
  bucket 2: 40%
  bucket 2: 50%
  bucket 2: 60%
  bucket 2: 70%
  bucket 2: 80%
  bucket 2: 90%
  bucket 2: 100%
  Sorting block of length 36636 for bucket 2
  (Using difference cover)
  Sorting block time: 00:00:00
Returning block of 36637 for bucket 2
Getting block 3 of 6
  Reserving size (49899) for bucket 3
  Calculating Z arrays for bucket 3
  Entering block accumulator loop for bucket 3:
  bucket 3: 10%
  bucket 3: 20%
  bucket 3: 30%
  bucket 3: 40%
  bucket 3: 50%
  bucket 3: 60%
  bucket 3: 70%
  bucket 3: 80%
  bucket 3: 90%
  bucket 3: 100%
  Sorting block of length 49027 for bucket 3
  (Using difference cover)
  Sorting block time: 00:00:00
Returning block of 49028 for bucket 3
Getting block 4 of 6
  Reserving size (49899) for bucket 4
  Calculating Z arrays for bucket 4
  Entering block accumulator loop for bucket 4:
  bucket 4: 10%
  bucket 4: 20%
  bucket 4: 30%
  bucket 4: 40%
  bucket 4: 50%
  bucket 4: 60%
  bucket 4: 70%
  bucket 4: 80%
  bucket 4: 90%
  bucket 4: 100%
  Sorting block of length 37449 for bucket 4
  (Using difference cover)
  Sorting block time: 00:00:00
Returning block of 37450 for bucket 4
Getting block 5 of 6
  Reserving size (49899) for bucket 5
  Calculating Z arrays for bucket 5
  Entering block accumulator loop for bucket 5:
  bucket 5: 10%
  bucket 5: 20%
  bucket 5: 30%
  bucket 5: 40%
  bucket 5: 50%
  bucket 5: 60%
  bucket 5: 70%
  bucket 5: 80%
  bucket 5: 90%
  bucket 5: 100%
  Sorting block of length 47142 for bucket 5
  (Using difference cover)
  Sorting block time: 00:00:00
Returning block of 47143 for bucket 5
Getting block 6 of 6
  Reserving size (49899) for bucket 6
  Calculating Z arrays for bucket 6
  Entering block accumulator loop for bucket 6:
  bucket 6: 10%
  bucket 6: 20%
  bucket 6: 30%
  bucket 6: 40%
  bucket 6: 50%
  bucket 6: 60%
  bucket 6: 70%
  bucket 6: 80%
  bucket 6: 90%
  bucket 6: 100%
  Sorting block of length 48178 for bucket 6
  (Using difference cover)
  Sorting block time: 00:00:00
Returning block of 48179 for bucket 6
Exited Ebwt loop
fchr[A]: 0
fchr[C]: 84325
fchr[G]: 133305
fchr[T]: 181307
fchr[$]: 266124
Exiting Ebwt::buildToDisk()
Returning from initFromVector
Wrote 4286544 bytes to primary EBWT file: genome.rev.1.bt2.tmp
Wrote 66536 bytes to secondary EBWT file: genome.rev.2.bt2.tmp
Re-opening _in1 and _in2 as input streams
Returning from Ebwt constructor
Headers:
    len: 266124
    bwtLen: 266125
    sz: 66531
    bwtSz: 66532
    lineRate: 6
    offRate: 4
    offMask: 0xfffffff0
    ftabChars: 10
    eftabLen: 20
    eftabSz: 80
    ftabLen: 1048577
    ftabSz: 4194308
    offsLen: 16633
    offsSz: 66532
    lineSz: 64
    sideSz: 64
    sideBwtSz: 48
    sideBwtLen: 192
    numSides: 1387
    numLines: 1387
    ebwtTotLen: 88768
    ebwtTotSz: 88768
    color: 0
    reverse: 1
Total time for backward call to driver() for mirror index: 00:00:00

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"input"`
__workflow_invocation_uuid__	`"639edb8a148211f0aeac6045bda70f2c"`
analysis_type	`{"__current_case__": 0, "analysis_type_selector": "simple", "presets": "no_presets"}`
chromInfo	`"/tmp/tmpbo76svqj/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
dbkey	`"?"`
library	`{"__current_case__": 2, "aligned_file": false, "input_1": {"values": [{"id": 1, "src": "dce"}]}, "paired_options": {"__current_case__": 1, "paired_options_selector": "no"}, "type": "paired_collection", "unaligned_file": false}`
own_file	__identifier__
reference_genome	`{"__current_case__": 1, "own_file": {"values": [{"id": 10, "src": "dce"}]}, "source": "history"}`
rg	`{"__current_case__": 3, "rg_selector": "do_not_set"}`
sam_options	`{"__current_case__": 1, "sam_options_selector": "no"}`
save_mapping_stats	`true`

Step 28: toolshed.g2.bx.psu.edu/repos/iuc/concoct_cut_up_fasta/concoct_cut_up_fasta/1.1.0+galaxy2:

step_state: scheduled

Jobs

Job 1:

Job state is ok

Command Line:

ln -s '/tmp/tmpbo76svqj/files/1/8/b/dataset_18b41470-af6e-41fc-8ca4-51e94f07d355.dat' 'input.fa' &&  cut_up_fasta.py 'input.fa' --chunk_size 10000 --overlap_size 0 --merge_last --bedfile '/tmp/tmpbo76svqj/job_working_directory/000/13/outputs/dataset_97c6b6c4-2bd3-4a23-8b1c-94f97d599d0e.dat' > '/tmp/tmpbo76svqj/job_working_directory/000/13/outputs/dataset_979c6b30-d621-4027-b77a-e875cc7da112.dat'

Exit Code:

```
0
```

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"input"`
__workflow_invocation_uuid__	`"639edb8a148211f0aeac6045bda70f2c"`
bedfile	`true`
chromInfo	`"/tmp/tmpbo76svqj/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
chunk_size	`"10000"`
dbkey	`"?"`
input_fasta	__identifier__
merge_last	`true`
overlap_size	`"0"`

Step 29: toolshed.g2.bx.psu.edu/repos/devteam/samtools_sort/samtools_sort/2.0.5:

step_state: scheduled

Jobs

Job 1:

Job state is ok

Command Line:

addthreads=${GALAXY_SLOTS:-1} && (( addthreads-- )) &&   addmemory=${GALAXY_MEMORY_MB_PER_SLOT:-768} && ((addmemory=addmemory*75/100)) &&  samtools sort -@ $addthreads -m $addmemory"M"   -O bam -T "${TMPDIR:-.}" '/tmp/tmpbo76svqj/files/9/e/d/dataset_9ed09d4e-2d74-46b0-88c7-c9d362d8c801.dat' > '/tmp/tmpbo76svqj/job_working_directory/000/14/outputs/dataset_7a8425b7-a209-4210-8bb2-d58c3044d20e.dat'

Exit Code:

```
0
```

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"input"`
__workflow_invocation_uuid__	`"639edb8a148211f0aeac6045bda70f2c"`
chromInfo	`"/tmp/tmpbo76svqj/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
dbkey	`"?"`
input1	__identifier__
minhash	`false`
prim_key_cond	`{"__current_case__": 0, "prim_key_select": ""}`

Step 30: toolshed.g2.bx.psu.edu/repos/iuc/semibin/semibin/2.0.2+galaxy1:

step_state: scheduled

Jobs

Job 1:

Job state is ok

Command Line:

ln -s '/tmp/tmpbo76svqj/files/7/a/8/dataset_7a8425b7-a209-4210-8bb2-d58c3044d20e.dat' '50contig_reads.bam' &&   ln -s '/tmp/tmpbo76svqj/files/1/8/b/dataset_18b41470-af6e-41fc-8ca4-51e94f07d355.dat' 'contigs.fasta' &&  SemiBin2 single_easy_bin --environment 'global' --input-fasta 'contigs.fasta' --input-bam *.bam --output 'output' --cannot-name 'cannot'   --orf-finder 'fast-naive' --random-seed 0  --epoches 20 --batch-size 2048 --max-node 1.0 --max-edges 200 --minfasta-kbs 200 --compression none --threads ${GALAXY_SLOTS:-1} --processes ${GALAXY_SLOTS:-1} && echo "output" && ls output

Exit Code:

```
0
```

Standard Error:

2025-04-08 14:07:04 7565e4633be5 SemiBin[10] INFO Binning for short_read
2025-04-08 14:07:09 7565e4633be5 SemiBin[10] INFO Did not detect GPU, using CPU.
2025-04-08 14:07:09 7565e4633be5 SemiBin[10] INFO Generating training data...
2025-04-08 14:07:10 7565e4633be5 SemiBin[10] INFO Calculating coverage for every sample.
2025-04-08 14:07:10 7565e4633be5 SemiBin[10] INFO Processed: 50contig_reads.bam
2025-04-08 14:07:11 7565e4633be5 SemiBin[10] INFO Start binning.
2025-04-08 14:07:13 7565e4633be5 SemiBin[10] INFO Number of bins prior to reclustering: 1
2025-04-08 14:07:13 7565e4633be5 SemiBin[10] INFO Running naive ORF finder
2025-04-08 14:07:14 7565e4633be5 SemiBin[10] INFO Number of bins after reclustering: 1
2025-04-08 14:07:14 7565e4633be5 SemiBin[10] INFO Binning finished

Standard Output:

If you find SemiBin useful, please cite:
        Pan, S.; Zhu, C.; Zhao, XM.; Coelho, LP. A deep siamese neural network improves metagenome-assembled genomes in microbiome datasets across different environments. Nat Commun 13, 2326 (2022). https://doi.org/10.1038/s41467-022-29843-y

        Pan, S.; Zhao, XM; Coelho, LP. SemiBin2: self-supervised contrastive learning leads to better MAGs for short- and long-read sequencing. Bioinformatics Volume 39, Issue Supplement_1, June 2023, Pages i21–i29. https://doi.org/10.1093/bioinformatics/btad209


output
50contig_reads.bam_0_data_cov.csv
SemiBinRun.log
contig_bins.tsv
data.csv
data_split.csv
output_bins
recluster_bins_info.tsv

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"input"`
__workflow_invocation_uuid__	`"639edb8a148211f0aeac6045bda70f2c"`
annot	`{"ml_threshold": null}`
bin	`{"max_edges": "200", "max_node": "1.0", "minfasta_kbs": "200"}`
chromInfo	`"/tmp/tmpbo76svqj/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
dbkey	`"?"`
extra_output	`["data", "coverage"]`
min_len	`{"__current_case__": 0, "method": "automatic"}`
mode	`{"__current_case__": 0, "environment": "global", "input_bam": {"values": [{"id": 20, "src": "dce"}]}, "input_fasta": {"values": [{"id": 10, "src": "dce"}]}, "ref": {"__current_case__": 2, "select": "ml"}, "select": "single"}`
orf_finder	`"fast-naive"`
random_seed	`"0"`
training	`{"batch_size": "2048", "epoches": "20"}`

Step 4: Read length (CONCOCT):
- step_state: scheduled

Step 31: toolshed.g2.bx.psu.edu/repos/iuc/concoct_coverage_table/concoct_coverage_table/1.1.0+galaxy2:

step_state: scheduled

Jobs

Job 1:

Job state is ok

Command Line:

mkdir 'mapping' && ln -s '/tmp/tmpbo76svqj/files/7/a/8/dataset_7a8425b7-a209-4210-8bb2-d58c3044d20e.dat' 'mapping/_tmp_tmpbo76svqj_files_7_a_8_dataset_7a8425b7-a209-4210-8bb2-d58c3044d20e.dat.sorted.bam' && samtools index 'mapping/_tmp_tmpbo76svqj_files_7_a_8_dataset_7a8425b7-a209-4210-8bb2-d58c3044d20e.dat.sorted.bam' 'mapping/_tmp_tmpbo76svqj_files_7_a_8_dataset_7a8425b7-a209-4210-8bb2-d58c3044d20e.dat.bam.bai' && mv 'mapping/_tmp_tmpbo76svqj_files_7_a_8_dataset_7a8425b7-a209-4210-8bb2-d58c3044d20e.dat.sorted.bam' 'mapping/_tmp_tmpbo76svqj_files_7_a_8_dataset_7a8425b7-a209-4210-8bb2-d58c3044d20e.dat.bam' && concoct_coverage_table.py '/tmp/tmpbo76svqj/files/9/7/c/dataset_97c6b6c4-2bd3-4a23-8b1c-94f97d599d0e.dat' mapping/*.bam > '/tmp/tmpbo76svqj/job_working_directory/000/16/outputs/dataset_2dd8d97a-0d51-4828-a323-c51ea729610b.dat'

Exit Code:

```
0
```

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"input"`
__workflow_invocation_uuid__	`"639edb8a148211f0aeac6045bda70f2c"`
bedfile	__identifier__
chromInfo	`"/tmp/tmpbo76svqj/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
dbkey	`"?"`
mode	`{"__current_case__": 0, "bamfile": {"values": [{"id": 20, "src": "dce"}]}, "type": "individual"}`
mode	bamfile

Step 32: toolshed.g2.bx.psu.edu/repos/iuc/metabat2_jgi_summarize_bam_contig_depths/metabat2_jgi_summarize_bam_contig_depths/2.17+galaxy0:

step_state: scheduled

Jobs

Job 1:

Job state is ok

Command Line:

jgi_summarize_bam_contig_depths --outputDepth '/tmp/tmpbo76svqj/job_working_directory/000/17/outputs/dataset_3baebf7c-d0ea-4486-a616-e20b7ce0cefb.dat' --percentIdentity 97   --minMapQual 0 --weightMapQual 0.0  --maxEdgeBases 75 --shredLength 16000 --shredDepth 5 --minContigLength 1 --minContigDepth 0.0 '/tmp/tmpbo76svqj/files/7/a/8/dataset_7a8425b7-a209-4210-8bb2-d58c3044d20e.dat'

Exit Code:

```
0
```

Standard Error:

Output depth matrix to /tmp/tmpbo76svqj/job_working_directory/000/17/outputs/dataset_3baebf7c-d0ea-4486-a616-e20b7ce0cefb.dat
Minimum percent identity for a mapped read: 0.97
minMapQual: 0
weightMapQual: 0
Edge bases will be included up to 75 bases
shredLength: 16000
shredDepth: 5
minContigLength: 1
minContigDepth: 0
jgi_summarize_bam_contig_depths 2.17 (Bioconda) 2024-12-15T06:34:17
Running with 4 threads to save memory you can reduce the number of threads with the OMP_NUM_THREADS variable
Output matrix to /tmp/tmpbo76svqj/job_working_directory/000/17/outputs/dataset_3baebf7c-d0ea-4486-a616-e20b7ce0cefb.dat
Opening all bam files and validating headers
Processing bam files with largest_contig=0
Thread 0 opening and reading the header for file: /tmp/tmpbo76svqj/files/7/a/8/dataset_7a8425b7-a209-4210-8bb2-d58c3044d20e.dat
Thread 0 opened the file: /tmp/tmpbo76svqj/files/7/a/8/dataset_7a8425b7-a209-4210-8bb2-d58c3044d20e.dat
Thread 0 processing bam 0: dataset_7a8425b7-a209-4210-8bb2-d58c3044d20e.dat
Thread 0 finished reading bam 0: dataset_7a8425b7-a209-4210-8bb2-d58c3044d20e.dat
Thread 0 finished: dataset_7a8425b7-a209-4210-8bb2-d58c3044d20e.dat with 18924 reads and 8473 readsWellMapped (44.7738%)
Creating depth matrix file: /tmp/tmpbo76svqj/job_working_directory/000/17/outputs/dataset_3baebf7c-d0ea-4486-a616-e20b7ce0cefb.dat
Closing last bam file
Finished

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"input"`
__workflow_invocation_uuid__	`"639edb8a148211f0aeac6045bda70f2c"`
advanced	`{"includeEdgeBases": false, "maxEdgeBases": "75", "minMapQual": "0", "noIntraDepthVariance": false, "output_paired_contigs": false, "percentIdentity": "97", "showDepth": false, "weightMapQual": "0.0"}`
bam_indiv_input	__identifier__
chromInfo	`"/tmp/tmpbo76svqj/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
dbkey	`"?"`
mode	`{"__current_case__": 0, "bam_indiv_input": {"values": [{"id": 20, "src": "dce"}]}, "type": "individual", "use_reference_cond": {"__current_case__": 0, "use_reference": "no"}}`
shredding	`{"minContigDepth": "0.0", "minContigLength": "1", "shredDepth": "5", "shredLength": "16000"}`

Step 33: toolshed.g2.bx.psu.edu/repos/iuc/fasta_to_contig2bin/Fasta_to_Contig2Bin/1.1.7+galaxy1:

step_state: scheduled

Jobs

Job 1:

Job state is ok

Command Line:

mkdir "inputs" && ln -s '/tmp/tmpbo76svqj/files/0/a/5/dataset_0a5a242d-bdb8-4341-91e1-ce4b559b8e4c.dat' 'inputs/SemiBin_0.fasta' && Fasta_to_Contig2Bin.sh --extension fasta --input_folder 'inputs' > '/tmp/tmpbo76svqj/job_working_directory/000/25/outputs/dataset_8908e207-800e-45aa-9429-b8e285786422.dat'

Exit Code:

```
0
```

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"input"`
__workflow_invocation_uuid__	`"639edb8a148211f0aeac6045bda70f2c"`
chromInfo	`"/tmp/tmpbo76svqj/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
dbkey	`"?"`
inputs	`{"values": [{"id": 21, "src": "dce"}]}`

Step 34: toolshed.g2.bx.psu.edu/repos/iuc/concoct/concoct/1.1.0+galaxy2:

step_state: scheduled

Jobs

Job 1:

Job state is ok

Command Line:

ln -s '/tmp/tmpbo76svqj/files/9/7/9/dataset_979c6b30-d621-4027-b77a-e875cc7da112.dat' 'composition_file.fa' &&  mkdir outdir && concoct --coverage_file '/tmp/tmpbo76svqj/files/2/d/d/dataset_2dd8d97a-0d51-4828-a323-c51ea729610b.dat' --composition_file 'composition_file.fa' --clusters 400 --kmer_length 4 --threads ${GALAXY_SLOTS:-4} --length_threshold 1000 --read_length 100 --total_percentage_pca 90 --basename 'outdir/' --seed 1 --iterations 500   --no_original_data

Exit Code:

```
0
```

Standard Error:

WARNING:root:CONCOCT is running in single threaded mode. Please, consider adjusting the --threads parameter.
Up and running. Check /tmp/tmpbo76svqj/job_working_directory/000/18/working/outdir/log.txt for progress
Setting 1 OMP threads
Generate input data
0,-32769.159419,695.861881
1,-23702.908064,9066.251354
2,-10301.271601,13401.636463
3,-9099.561931,1201.709670
4,-8491.920398,607.641533
5,-8491.793887,0.126512
6,-8491.793444,0.000443
7,-8491.793370,0.000074

Standard Output:

```
59 2 1
```

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"input"`
__workflow_invocation_uuid__	`"639edb8a148211f0aeac6045bda70f2c"`
advanced	`{"clusters": "400", "iterations": "500", "kmer_length": "4", "length_threshold": "1000", "no_cov_normalization": false, "read_length": "100", "seed": "1", "total_percentage_pca": "90"}`
chromInfo	`"/tmp/tmpbo76svqj/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
dbkey	`"?"`
output	`{"converge_out": false, "log": false, "no_total_coverage": false}`

Step 35: toolshed.g2.bx.psu.edu/repos/mbernt/maxbin2/maxbin2/2.2.7+galaxy6:

step_state: scheduled

Jobs

Job 1:

Job state is ok

Command Line:

echo '/tmp/tmpbo76svqj/files/3/b/a/dataset_3baebf7c-d0ea-4486-a616-e20b7ce0cefb.dat' >> abund_list &&   run_MaxBin.pl -contig '/tmp/tmpbo76svqj/files/1/8/b/dataset_18b41470-af6e-41fc-8ca4-51e94f07d355.dat' -out out -abund_list abund_list -min_contig_length 1000 -max_iteration 50 -prob_threshold 0.5 -plotmarker -markerset 107 -thread ${GALAXY_SLOTS:-1}  && gzip -cd out.marker_of_each_bin.tar.gz | tar -xf -

Exit Code:

```
0
```

Standard Error:

Attaching package: ‘gplots’

The following object is masked from ‘package:stats’:

    lowess

Standard Output:

MaxBin 2.2.7
Input contig: /tmp/tmpbo76svqj/files/1/8/b/dataset_18b41470-af6e-41fc-8ca4-51e94f07d355.dat
out header: out
Min contig length: 1000
Max iteration: 50
Probability threshold: 0.5
Thread: 1
Located abundance file [/tmp/tmpbo76svqj/files/3/b/a/dataset_3baebf7c-d0ea-4486-a616-e20b7ce0cefb.dat]
Searching against 107 marker genes to find starting seed contigs for [/tmp/tmpbo76svqj/files/1/8/b/dataset_18b41470-af6e-41fc-8ca4-51e94f07d355.dat]...
Running FragGeneScan....
Running HMMER hmmsearch....
Try harder to dig out marker genes from contigs.
Done data collection. Running MaxBin...
Command: /usr/local/opt/MaxBin-2.2.7/src/MaxBin -fasta out.contig.tmp  -abund out.contig.tmp.abund1 -seed out.seed -out out -min_contig_length 1000 -max_run 50 -prob_threshold 0.5 
Minimum contig length set to 1000.
Reading seed list...
Looking for seeds in sequences.
	k141_52 [11001.000000]
	k141_59 [9465.000000]
Get 2 seeds.

Start EM process.
Iteration 1
Iteration 2
Iteration 3
Iteration 4
Iteration 5
Iteration 6
Iteration 7
Iteration 8
Iteration 9
Iteration 10
Iteration 11
Iteration 12
Iteration 13

EM finishes successfully.

Classifying sequences based on the EM result.
Minimum probability for binning: 0.50
Ignoring 0 bins without any sequences.
Number of unclassified sequences: 0 (0.00%)
Elapsed time:  0 days 00:00:00

Rscript /usr/local/opt/MaxBin-2.2.7/heatmap.r out.marker out.marker.pdf
null device 
          1 
out.001.marker.fasta
out.002.marker.fasta
Deleting intermediate files.


========== Job finished ==========
Yielded 2 bins for contig (scaffold) file /tmp/tmpbo76svqj/files/1/8/b/dataset_18b41470-af6e-41fc-8ca4-51e94f07d355.dat

Here are the output files for this run.
Please refer to the README file for further details.

Summary file: out.summary
Marker counts: out.marker
Marker genes for each bin: out.marker_of_each_gene.tar.gz
Bin files: out.001.fasta - out.002.fasta
Unbinned sequences: out.noclass
Marker plot: out.marker.pdf


========== Elapsed Time ==========
0 hours 0 minutes and 2 seconds.

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"expression.json"`
__workflow_invocation_uuid__	`"639edb8a148211f0aeac6045bda70f2c"`
adv	`{"max_iteration": "50", "min_contig_length": "1000", "prob_threshold": "0.5"}`
assembly	`{"__current_case__": 0, "inputs": {"__current_case__": 1, "abund": {"values": [{"id": 27, "src": "dce"}]}, "type": "abund"}, "type": "individual"}`
chromInfo	`"/tmp/tmpbo76svqj/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
dbkey	`"?"`
output	`{"log": true, "marker": true, "markers": true, "markerset": "107", "plotmarker": true}`

Step 36: toolshed.g2.bx.psu.edu/repos/iuc/metabat2/metabat2/2.17+galaxy0:

step_state: scheduled

Jobs

Job 1:

Job state is ok

Command Line:

mkdir bins && metabat2 --inFile '/tmp/tmpbo76svqj/files/1/8/b/dataset_18b41470-af6e-41fc-8ca4-51e94f07d355.dat' --outFile 'bins/bin' --abdFile '/tmp/tmpbo76svqj/files/3/b/a/dataset_3baebf7c-d0ea-4486-a616-e20b7ce0cefb.dat' --minContig 1500 --maxP 95 --minS 60 --maxEdges 200 --pTNF 0  --minCV 1.0 --minCVSum 1.0 --seed 0 --minClsSize 200000 --numThreads ${GALAXY_SLOTS:-4}  --unbinned > process_log.txt && mv process_log.txt '/tmp/tmpbo76svqj/job_working_directory/000/20/outputs/dataset_c21a993b-6caf-4739-8f13-162efbf15d43.dat'

Exit Code:

```
0
```

Standard Error:

[Warning!] Negative coverage depth is not allowed for the contig k141_0, column 1: -4.30218e+08
[Warning!] Negative coverage depth is not allowed for the contig k141_52, column 1: -2.7651e+08

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"input"`
__workflow_invocation_uuid__	`"639edb8a148211f0aeac6045bda70f2c"`
advanced	`{"base_coverage_depth_cond": {"__current_case__": 1, "abdFile": {"values": [{"id": 27, "src": "dce"}]}, "base_coverage_depth": "yes", "cvExt": null}, "maxEdges": "200", "maxP": "95", "minCV": "1.0", "minCVSum": "1.0", "minContig": "1500", "minS": "60", "noAdd": false, "pTNF": "0", "seed": "0"}`
advanced	abdFile
chromInfo	`"/tmp/tmpbo76svqj/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
dbkey	`"?"`
inFile	__identifier__
out	`{"extra_outputs": ["lowDepth", "tooShort", "unbinned", "log"], "minClsSize": "200000", "onlyLabel": false, "saveCls": false}`

Step 37: toolshed.g2.bx.psu.edu/repos/iuc/concoct_merge_cut_up_clustering/concoct_merge_cut_up_clustering/1.1.0+galaxy2:

step_state: scheduled

Jobs

Job 1:

Job state is ok

Command Line:

merge_cutup_clustering.py '/tmp/tmpbo76svqj/files/3/7/0/dataset_37014003-9e06-4c4c-bbb2-c319f632d067.dat' > '/tmp/tmpbo76svqj/job_working_directory/000/21/outputs/dataset_32a65316-5433-41d8-8529-5ad6070b9cf6.dat'

Exit Code:

```
0
```

Standard Error:

/usr/local/bin/merge_cutup_clustering.py:17: SyntaxWarning: invalid escape sequence '\.'
  CONTIG_PART_EXPR = re.compile("(.*)\.concoct_part_([0-9]*)")

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"input"`
__workflow_invocation_uuid__	`"639edb8a148211f0aeac6045bda70f2c"`
chromInfo	`"/tmp/tmpbo76svqj/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
cutup_clustering_result	__identifier__
dbkey	`"?"`

Step 38: toolshed.g2.bx.psu.edu/repos/iuc/fasta_to_contig2bin/Fasta_to_Contig2Bin/1.1.7+galaxy1:

step_state: scheduled

Jobs

Job 1:

Job state is ok

Command Line:

mkdir "inputs" && ln -s '/tmp/tmpbo76svqj/files/2/c/b/dataset_2cb70f16-77f8-4346-94de-ff620500e606.dat' 'inputs/001.fasta' && ln -s '/tmp/tmpbo76svqj/files/6/4/1/dataset_641e8ede-7647-4ced-a70a-e79a93714e7c.dat' 'inputs/002.fasta' && Fasta_to_Contig2Bin.sh --extension fasta --input_folder 'inputs' > '/tmp/tmpbo76svqj/job_working_directory/000/26/outputs/dataset_cdf66de2-f37b-4ba4-bc38-e4ad7e7282f4.dat'

Exit Code:

```
0
```

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"input"`
__workflow_invocation_uuid__	`"639edb8a148211f0aeac6045bda70f2c"`
chromInfo	`"/tmp/tmpbo76svqj/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
dbkey	`"?"`
inputs	`{"values": [{"id": 31, "src": "dce"}]}`

Step 39: toolshed.g2.bx.psu.edu/repos/iuc/fasta_to_contig2bin/Fasta_to_Contig2Bin/1.1.7+galaxy1:

step_state: scheduled

Jobs

Job 1:

Job state is ok

Command Line:

mkdir "inputs" && ln -s '/tmp/tmpbo76svqj/files/6/e/7/dataset_6e7933bb-f1d2-4ae2-a497-da6acfc701c2.dat' 'inputs/1.fasta' && Fasta_to_Contig2Bin.sh --extension fasta --input_folder 'inputs' > '/tmp/tmpbo76svqj/job_working_directory/000/23/outputs/dataset_89b52c48-d763-47ea-a97b-c7c864e8b314.dat'

Exit Code:

```
0
```

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"input"`
__workflow_invocation_uuid__	`"639edb8a148211f0aeac6045bda70f2c"`
chromInfo	`"/tmp/tmpbo76svqj/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
dbkey	`"?"`
inputs	`{"values": [{"id": 39, "src": "dce"}]}`

Step 40: toolshed.g2.bx.psu.edu/repos/iuc/concoct_extract_fasta_bins/concoct_extract_fasta_bins/1.1.0+galaxy2:

step_state: scheduled

Jobs

Job 1:

Job state is ok

Command Line:

ln -s '/tmp/tmpbo76svqj/files/1/8/b/dataset_18b41470-af6e-41fc-8ca4-51e94f07d355.dat' 'contigs.fa' &&  mkdir outdir && extract_fasta_bins.py 'contigs.fa' '/tmp/tmpbo76svqj/files/3/2/a/dataset_32a65316-5433-41d8-8529-5ad6070b9cf6.dat' --output_path 'outdir'

Exit Code:

```
0
```

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"input"`
__workflow_invocation_uuid__	`"639edb8a148211f0aeac6045bda70f2c"`
chromInfo	`"/tmp/tmpbo76svqj/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
cluster_file	__identifier__
dbkey	`"?"`
fasta_file	__identifier__

Step 5: Environment for the built-in model (SemiBin):
- step_state: scheduled

Step 41: toolshed.g2.bx.psu.edu/repos/iuc/fasta_to_contig2bin/Fasta_to_Contig2Bin/1.1.7+galaxy1:

step_state: scheduled

Jobs

Job 1:

Job state is ok

Command Line:

mkdir "inputs" && ln -s '/tmp/tmpbo76svqj/files/8/f/6/dataset_8f6a7fb0-d2bd-4118-ad48-6b35386b1f70.dat' 'inputs/0.fasta' && ln -s '/tmp/tmpbo76svqj/files/8/b/2/dataset_8b22b944-4cc7-4eb3-a189-dd9fa1a45b55.dat' 'inputs/1.fasta' && ln -s '/tmp/tmpbo76svqj/files/3/7/8/dataset_378a00a2-628e-4f8e-8442-caa4ce82c2c1.dat' 'inputs/10.fasta' && ln -s '/tmp/tmpbo76svqj/files/a/9/d/dataset_a9dd4c2e-fa32-4d19-99ec-3c52594cf2aa.dat' 'inputs/11.fasta' && ln -s '/tmp/tmpbo76svqj/files/e/8/2/dataset_e82c4453-829e-4325-a891-55795f5af147.dat' 'inputs/2.fasta' && ln -s '/tmp/tmpbo76svqj/files/5/9/e/dataset_59e89dc2-14d5-4040-9baa-de0cbf4cb4eb.dat' 'inputs/3.fasta' && ln -s '/tmp/tmpbo76svqj/files/5/b/b/dataset_5bb85b3a-15e5-4fbb-b799-8d67fc97afb2.dat' 'inputs/4.fasta' && ln -s '/tmp/tmpbo76svqj/files/6/a/c/dataset_6acaaa55-a18b-40d6-80b4-0eaa570d0ec5.dat' 'inputs/5.fasta' && ln -s '/tmp/tmpbo76svqj/files/1/5/3/dataset_1539f41f-3b55-4f77-9662-c513f66713cd.dat' 'inputs/6.fasta' && ln -s '/tmp/tmpbo76svqj/files/3/0/7/dataset_30717f78-30ec-4649-b604-a0e7b8b8060f.dat' 'inputs/7.fasta' && ln -s '/tmp/tmpbo76svqj/files/f/5/9/dataset_f59a1415-436a-4755-b760-2681aa006850.dat' 'inputs/8.fasta' && ln -s '/tmp/tmpbo76svqj/files/5/9/e/dataset_59ecc137-a237-45a6-bef7-5f1b5b5836fc.dat' 'inputs/9.fasta' && Fasta_to_Contig2Bin.sh --extension fasta --input_folder 'inputs' > '/tmp/tmpbo76svqj/job_working_directory/000/24/outputs/dataset_7c8742dd-7601-4127-9fc0-13da4a0cc8a1.dat'

Exit Code:

```
0
```

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"input"`
__workflow_invocation_uuid__	`"639edb8a148211f0aeac6045bda70f2c"`
chromInfo	`"/tmp/tmpbo76svqj/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
dbkey	`"?"`
inputs	`{"values": [{"id": 45, "src": "dce"}]}`

Step 42: __BUILD_LIST__:

step_state: scheduled

Jobs

Job 1:

Job state is ok

Traceback:

Job Parameters:

Job parameter	Parameter value
__workflow_invocation_uuid__	`"639edb8a148211f0aeac6045bda70f2c"`
datasets	`[{"__index__": 0, "id_cond": {"__current_case__": 0, "id_select": "idx"}, "input": {"values": [{"id": 57, "src": "hda"}]}}, {"__index__": 1, "id_cond": {"__current_case__": 0, "id_select": "idx"}, "input": {"values": [{"id": 44, "src": "hda"}]}}, {"__index__": 2, "id_cond": {"__current_case__": 0, "id_select": "idx"}, "input": {"values": [{"id": 64, "src": "hda"}]}}, {"__index__": 3, "id_cond": {"__current_case__": 0, "id_select": "idx"}, "input": {"values": [{"id": 59, "src": "hda"}]}}]`

Step 43: toolshed.g2.bx.psu.edu/repos/iuc/binette/binette/1.0.5+galaxy1:

step_state: scheduled

Jobs

Job 1:

Job state is ok

Command Line:

mkdir -p 'input' 'output' &&  ln -s '/tmp/tmpbo76svqj/files/7/c/8/dataset_7c8742dd-7601-4127-9fc0-13da4a0cc8a1.dat' 'input/bin_table_0.tsv' && ln -s '/tmp/tmpbo76svqj/files/8/9/b/dataset_89b52c48-d763-47ea-a97b-c7c864e8b314.dat' 'input/bin_table_1.tsv' && ln -s '/tmp/tmpbo76svqj/files/c/d/f/dataset_cdf66de2-f37b-4ba4-bc38-e4ad7e7282f4.dat' 'input/bin_table_2.tsv' && ln -s '/tmp/tmpbo76svqj/files/8/9/0/dataset_8908e207-800e-45aa-9429-b8e285786422.dat' 'input/bin_table_3.tsv' &&  ln -s '/tmp/tmpbo76svqj/files/1/8/b/dataset_18b41470-af6e-41fc-8ca4-51e94f07d355.dat' 'input_contigs.fasta' &&   binette -b input/*.tsv -c 'input_contigs.fasta' -m 1 -t "${GALAXY_SLOTS:-1}" -o 'output/' -w 2 --checkm2_db '/cvmfs/data.galaxyproject.org/byhand/checkm2/1.0.2/uniref100.KO.1.dmnd'

Exit Code:

```
0
```

Standard Error:

  0%|          | 0/59 [00:00<?, ?it/s]
100%|██████████| 59/59 [00:00<00:00, 4888.47it/s]

  0%|          | 0/59 [00:00<?, ?contig/s]
100%|██████████| 59/59 [00:00<00:00, 409708.50contig/s]

  0%|          | 0/59 [00:00<?, ?contig/s]
100%|██████████| 59/59 [00:00<00:00, 672456.35contig/s]

  0%|          | 0/16 [00:00<?, ?bin/s]
100%|██████████| 16/16 [00:05<00:00,  2.85bin/s]
100%|██████████| 16/16 [00:05<00:00,  2.85bin/s]

  0%|          | 0/17 [00:00<?, ?bin/s]
100%|██████████| 17/17 [00:05<00:00,  3.36bin/s]
100%|██████████| 17/17 [00:05<00:00,  3.36bin/s]

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"input"`
__workflow_invocation_uuid__	`"639edb8a148211f0aeac6045bda70f2c"`
chromInfo	`"/tmp/tmpbo76svqj/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
contamination_weight	`"2"`
database_type	`{"__current_case__": 1, "datamanager": "1.0.2", "is_select": "cached"}`
dbkey	`"?"`
min_completeness	`"1"`
proteins	`None`

Step 44: Pool Bins from all samples:
- step_state: scheduled
- Jobs
  - Job 1:
    - Job state is ok
    Traceback:
    Job Parameters:
    - Job parameter Parameter value
      
      __workflow_invocation_uuid__ "639edb8a148211f0aeac6045bda70f2c"
      
      input {"values": [{"id": 47, "src": "hdca"}]}
      
      join_identifier "_"

Step 45: toolshed.g2.bx.psu.edu/repos/iuc/checkm2/checkm2/1.0.2+galaxy0:

step_state: scheduled

Jobs

Job 1:

Job state is ok

Command Line:

mkdir input_dir && ln -s '/tmp/tmpbo76svqj/files/7/1/1/dataset_711ad373-2a0f-4824-b1f6-8b836d8b0ac6.dat' 'input_dir/50contig_reads_bin_1.dat' && ln -s '/tmp/tmpbo76svqj/files/7/c/0/dataset_7c09ebaa-2fde-4b3e-ad76-72b4c7650533.dat' 'input_dir/50contig_reads_bin_11.dat' && ln -s '/tmp/tmpbo76svqj/files/1/d/2/dataset_1d21d281-6b34-4bf0-9e49-9f773092df80.dat' 'input_dir/50contig_reads_bin_6.dat' && ln -s '/tmp/tmpbo76svqj/files/1/8/3/dataset_1834363a-74a8-4b8d-b14c-a03efeb1450e.dat' 'input_dir/50contig_reads_bin_60.dat' && checkm2 predict --input input_dir   -x .dat --threads "${GALAXY_SLOTS:-1}" --database_path '/cvmfs/data.galaxyproject.org/byhand/checkm2/1.0.2/uniref100.KO.1.dmnd' --output-directory output

Exit Code:

```
0
```

Standard Error:

[04/08/2025 02:56:58 PM] INFO: Running CheckM2 version 1.0.2
[04/08/2025 02:56:58 PM] INFO: Custom database path provided for predict run. Checking database at /cvmfs/data.galaxyproject.org/byhand/checkm2/1.0.2/uniref100.KO.1.dmnd...
[04/08/2025 02:57:04 PM] INFO: Running quality prediction workflow with 1 threads.
[04/08/2025 02:57:05 PM] INFO: Calling genes in 4 bins with 1 threads:
[04/08/2025 02:57:07 PM] INFO: Calculating metadata for 4 bins with 1 threads:
[04/08/2025 02:57:07 PM] INFO: Annotating input genomes with DIAMOND using 1 threads
[04/08/2025 02:59:54 PM] INFO: Processing DIAMOND output
[04/08/2025 02:59:54 PM] INFO: Predicting completeness and contamination using ML models.
[04/08/2025 02:59:59 PM] INFO: Parsing all results and constructing final output table.
[04/08/2025 02:59:59 PM] INFO: CheckM2 finished successfully.

Standard Output:

    Finished processing 1 of 4 (25.00%) bins.
    Finished processing 2 of 4 (50.00%) bins.
    Finished processing 3 of 4 (75.00%) bins.
    Finished processing 4 of 4 (100.00%) bins.

    Finished processing 1 of 4 (25.00%) bin metadata.
    Finished processing 2 of 4 (50.00%) bin metadata.
    Finished processing 3 of 4 (75.00%) bin metadata.
    Finished processing 4 of 4 (100.00%) bin metadata.

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"input"`
__workflow_invocation_uuid__	`"639edb8a148211f0aeac6045bda70f2c"`
chromInfo	`"/tmp/tmpbo76svqj/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
database	`"1.0.2"`
dbkey	`"?"`
genes	`false`
model	`""`
ttable	`None`

Step 46: toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_awk_tool/9.5+galaxy0:

step_state: scheduled

Jobs

Job 1:

Job state is ok

Command Line:

env -i $(which awk) --sandbox -v FS='	' -v OFS='	' --re-interval -f '/tmp/tmpbo76svqj/job_working_directory/000/31/configs/tmp_4g2jo17' '/tmp/tmpbo76svqj/files/9/0/1/dataset_901f4efc-723b-4081-b4fc-f6974072f359.dat' > '/tmp/tmpbo76svqj/job_working_directory/000/31/outputs/dataset_2426e53f-7267-40ed-8e27-b7c149bb51d9.dat'

Exit Code:

```
0
```

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"input"`
__workflow_invocation_uuid__	`"639edb8a148211f0aeac6045bda70f2c"`
chromInfo	`"/tmp/tmpbo76svqj/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
code	`"BEGIN {OFS=\"\\t\"; print \"genome\\tcompleteness\\tcontamination\"} \nNR > 1 {\n if ($1 !~ /\\.fasta$/) \n $1 = $1 \".fasta\"\n print $1, $2, $3\n}"`
dbkey	`"?"`

Step 47: toolshed.g2.bx.psu.edu/repos/iuc/drep_dereplicate/drep_dereplicate/3.5.0+galaxy1:

step_state: scheduled

Jobs

Job 1:

Job state is ok

Command Line:

ln -s '/tmp/tmpbo76svqj/files/7/1/1/dataset_711ad373-2a0f-4824-b1f6-8b836d8b0ac6.dat' '50contig_reads_bin_1.fasta' &&  ln -s '/tmp/tmpbo76svqj/files/7/c/0/dataset_7c09ebaa-2fde-4b3e-ad76-72b4c7650533.dat' '50contig_reads_bin_11.fasta' &&  ln -s '/tmp/tmpbo76svqj/files/1/d/2/dataset_1d21d281-6b34-4bf0-9e49-9f773092df80.dat' '50contig_reads_bin_6.fasta' &&  ln -s '/tmp/tmpbo76svqj/files/1/8/3/dataset_1834363a-74a8-4b8d-b14c-a03efeb1450e.dat' '50contig_reads_bin_60.fasta' &&   dRep dereplicate outdir  -g '50contig_reads_bin_1.fasta' '50contig_reads_bin_11.fasta' '50contig_reads_bin_6.fasta' '50contig_reads_bin_60.fasta'   --length 100 --completeness 1 --contamination 25   --genomeInfo '/tmp/tmpbo76svqj/files/8/1/0/dataset_8109dd45-b2d2-4dcc-8b4a-abf7a892c6fb.dat'    --MASH_sketch '1000' --P_ani 0.9  --primary_chunksize 5000   --S_algorithm 'ANImf'  --n_PRESET 'normal'   --coverage_method 'larger'  --S_ani 0.95 --cov_thresh 0.1  --clusterAlg 'average'    --completeness_weight 1.0 --contamination_weight 5.0 --strain_heterogeneity_weight 1.0 --N50_weight 0.5 --size_weight 0.0 --centrality_weight 1.0    --warn_dist 0.25 --warn_sim 0.98 --warn_aln 0.25  --debug || (rc=$?; ls -ltr `find outdir -type f`; cat outdir/data/checkM/checkM_outdir/checkm.log; cat outdir/log/logger.log; exit $rc)

Exit Code:

```
0
```

Standard Error:

***************************************************
    ..:: dRep dereplicate Step 1. Filter ::..
***************************************************
    
Will filter the genome list
4 genomes were input to dRep
Calculating genome info of genomes
100.00% of genomes passed length filtering
100.00% of genomes passed checkM filtering
***************************************************
    ..:: dRep dereplicate Step 2. Cluster ::..
***************************************************
    
Running primary clustering
Running pair-wise MASH clustering
4 primary clusters made
Running secondary clustering
Running 4 ANImf comparisons- should take ~ 0.3 min
Step 4. Return output
***************************************************
    ..:: dRep dereplicate Step 3. Choose ::..
***************************************************
    
Loading work directory
***************************************************
    ..:: dRep dereplicate Step 4. Evaluate ::..
***************************************************
    
will produce Widb (winner information db)
Winner database saved to /tmp/tmpbo76svqj/job_working_directory/000/33/working/outdirdata_tables/Widb.csv
***************************************************
    ..:: dRep dereplicate Step 5. Analyze ::..
***************************************************
    
making plots 1, 2, 3, 4, 5, 6
Plotting primary dendrogram
Plotting secondary dendrograms
Plotting MDS plot
Plotting scatterplots
Plotting bin scorring plot
Plotting winning genomes plot...

$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$

    ..:: dRep dereplicate finished ::..

Dereplicated genomes................. /tmp/tmpbo76svqj/job_working_directory/000/33/working/outdir/dereplicated_genomes/
Dereplicated genomes information..... /tmp/tmpbo76svqj/job_working_directory/000/33/working/outdir/data_tables/Widb.csv
Figures.............................. /tmp/tmpbo76svqj/job_working_directory/000/33/working/outdir/figures/
Warnings............................. /tmp/tmpbo76svqj/job_working_directory/000/33/working/outdir/log/warnings.txt

$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"input"`
__workflow_invocation_uuid__	`"639edb8a148211f0aeac6045bda70f2c"`
chromInfo	`"/tmp/tmpbo76svqj/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
comp_clust	`{"clusterAlg": "average", "run_tertiary_clustering": false, "steps": {"MASH_sketch": "1000", "P_ani": "0.9", "S_ani": "0.95", "__current_case__": 0, "clustering": {"S_algorithm": "ANImf", "__current_case__": 1, "coverage_method": "larger", "n_PRESET": "normal"}, "cov_thresh": "0.1", "multiround_primary_clustering": false, "primary_chunksize": "5000", "select": "default"}}`
dbkey	`"?"`
filter	`{"completeness": "1", "contamination": "25", "length": "100"}`
quality	`{"__current_case__": 1, "genomeInfo": {"values": [{"id": 84, "src": "hda"}]}, "source": "genomeInfo"}`
scoring	`{"N50_weight": "0.5", "centrality_weight": "1.0", "completeness_weight": "1.0", "contamination_weight": "5.0", "extra_weight_table": null, "size_weight": "0.0", "strain_heterogeneity_weight": "1.0"}`
select_outputs	`["log", "warnings", "Primary_clustering_dendrogram", "Clustering_scatterplots", "Widb", "Chdb"]`
warning	`{"warn_aln": "0.25", "warn_dist": "0.25", "warn_sim": "0.98"}`

Step 48: toolshed.g2.bx.psu.edu/repos/iuc/gtdbtk_classify_wf/gtdbtk_classify_wf/2.4.0+galaxy0:

step_state: scheduled

Jobs

Job 1:

Job state is error

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"input"`
__workflow_invocation_uuid__	`"639edb8a148211f0aeac6045bda70f2c"`
advanced	`{"force": false, "min_af": "0.65", "min_perc_aa": "10", "output_process_log": false}`
chromInfo	`"/tmp/tmpbo76svqj/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
dbkey	`"?"`
gtdbtk_db	`"full_database_release_220_downloaded_2024-10-28"`

Step 49: toolshed.g2.bx.psu.edu/repos/iuc/checkm2/checkm2/1.0.2+galaxy0:

step_state: scheduled

Jobs

Job 1:

Job state is running

Command Line:

mkdir input_dir && ln -s '/tmp/tmpbo76svqj/files/6/3/2/dataset_63279e7d-d10f-4461-95a5-ea0dbb452657.dat' 'input_dir/50contig_reads_bin_1.fasta.dat' && ln -s '/tmp/tmpbo76svqj/files/c/7/6/dataset_c7676744-cf64-46e2-821f-54435af89a67.dat' 'input_dir/50contig_reads_bin_11.fasta.dat' && ln -s '/tmp/tmpbo76svqj/files/2/6/7/dataset_267984a9-fce0-408b-a392-19d53e11442a.dat' 'input_dir/50contig_reads_bin_6.fasta.dat' && ln -s '/tmp/tmpbo76svqj/files/d/9/c/dataset_d9c21b93-428b-4b57-9a9f-35d636ac3c4e.dat' 'input_dir/50contig_reads_bin_60.fasta.dat' && checkm2 predict --input input_dir   -x .dat --threads "${GALAXY_SLOTS:-1}" --database_path '/cvmfs/data.galaxyproject.org/byhand/checkm2/1.0.2/uniref100.KO.1.dmnd' --output-directory output

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"input"`
__workflow_invocation_uuid__	`"639edb8a148211f0aeac6045bda70f2c"`
chromInfo	`"/tmp/tmpbo76svqj/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
database	`"1.0.2"`
dbkey	`"?"`
genes	`false`
model	`""`
ttable	`None`

Step 50: toolshed.g2.bx.psu.edu/repos/iuc/checkm_lineage_wf/checkm_lineage_wf/1.2.3+galaxy0:

step_state: scheduled

Jobs

Job 1:

Job state is queued

Command Line:

mkdir 'bins' && ln -s '/tmp/tmpbo76svqj/files/6/3/2/dataset_63279e7d-d10f-4461-95a5-ea0dbb452657.dat' 'bins/50contig_reads_bin_1.fasta.fasta' && ln -s '/tmp/tmpbo76svqj/files/c/7/6/dataset_c7676744-cf64-46e2-821f-54435af89a67.dat' 'bins/50contig_reads_bin_11.fasta.fasta' && ln -s '/tmp/tmpbo76svqj/files/2/6/7/dataset_267984a9-fce0-408b-a392-19d53e11442a.dat' 'bins/50contig_reads_bin_6.fasta.fasta' && ln -s '/tmp/tmpbo76svqj/files/d/9/c/dataset_d9c21b93-428b-4b57-9a9f-35d636ac3c4e.dat' 'bins/50contig_reads_bin_60.fasta.fasta' &&   checkm lineage_wf 'bins' 'output'     --unique '10' --multi '10'      --aai_strain 0.9  --e_value 1e-10 --length 0.7 --file '/tmp/tmpbo76svqj/job_working_directory/000/36/outputs/dataset_02370dc3-42c6-43f1-abc9-c2303db37641.dat' --tab_table --extension 'fasta' --threads ${GALAXY_SLOTS:-1} --pplacer_threads ${GALAXY_SLOTS:-1}

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"input"`
__workflow_invocation_uuid__	`"639edb8a148211f0aeac6045bda70f2c"`
bins	`{"__current_case__": 0, "bins_coll": {"values": [{"id": 53, "src": "hdca"}]}, "select": "collection"}`
chromInfo	`"/tmp/tmpbo76svqj/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
dbkey	`"?"`
extra_outputs	`None`
lineage_set	`{"force_domain": false, "multi": "10", "no_refinement": false, "unique": "10"}`
qa	`{"aai_strain": "0.9", "e_value": "1e-10", "ignore_thresholds": false, "individual_markers": false, "length": "0.7", "skip_adj_correction": false, "skip_pseudogene_correction": false}`
tree_analyze	`{"ali": false, "genes": false, "nt": false, "reduced_tree": false}`

Step 6: Trimmed grouped paired reads:
- step_state: scheduled

Step 51: toolshed.g2.bx.psu.edu/repos/iuc/coverm_genome/coverm_genome/0.7.0+galaxy0:

step_state: scheduled

Jobs

Job 1:

Job state is queued

Command Line:

mkdir 'single/' && mkdir 'fw/' && mkdir 'rv/' && mkdir 'interl/' && mkdir 'ref/' && mkdir 'bam/' &&   ln -s '/tmp/tmpbo76svqj/files/1/5/0/dataset_150653ab-6cb3-42fd-92b7-e56e727f1f0b.dat' 'fw/50contig_reads' && ln -s '/tmp/tmpbo76svqj/files/7/a/0/dataset_7a0b5be5-a56f-4607-a22a-57074fac905d.dat' 'rv/50contig_reads' &&   echo "GENOME_FOR_READS mapped.mode.genome.genomic.source=history" && echo "GENOME_FOR_READS mapped.mode.genome.genomic.genome_fasta_files=/tmp/tmpbo76svqj/files/6/3/2/dataset_63279e7d-d10f-4461-95a5-ea0dbb452657.dat,/tmp/tmpbo76svqj/files/c/7/6/dataset_c7676744-cf64-46e2-821f-54435af89a67.dat,/tmp/tmpbo76svqj/files/2/6/7/dataset_267984a9-fce0-408b-a392-19d53e11442a.dat,/tmp/tmpbo76svqj/files/d/9/c/dataset_d9c21b93-428b-4b57-9a9f-35d636ac3c4e.dat" && ln -s '/tmp/tmpbo76svqj/files/6/3/2/dataset_63279e7d-d10f-4461-95a5-ea0dbb452657.dat' '50contig_reads_bin_1.fasta' && ln -s '/tmp/tmpbo76svqj/files/c/7/6/dataset_c7676744-cf64-46e2-821f-54435af89a67.dat' '50contig_reads_bin_11.fasta' && ln -s '/tmp/tmpbo76svqj/files/2/6/7/dataset_267984a9-fce0-408b-a392-19d53e11442a.dat' '50contig_reads_bin_6.fasta' && ln -s '/tmp/tmpbo76svqj/files/d/9/c/dataset_d9c21b93-428b-4b57-9a9f-35d636ac3c4e.dat' '50contig_reads_bin_60.fasta' &&   mkdir 'representative-fasta/' && coverm genome -1 'fw/50contig_reads' -2 'rv/50contig_reads'  --mapper 'minimap2-sr' --genome-fasta-files '50contig_reads_bin_1.fasta' '50contig_reads_bin_11.fasta' '50contig_reads_bin_6.fasta' '50contig_reads_bin_60.fasta'   --min-read-aligned-length 0 --min-read-percent-identity 0.0 --min-read-aligned-percent 0.0   --methods 'relative_abundance' --min-covered-fraction 10 --contig-end-exclusion 75 --trim-min 5 --trim-max 95    --output-format 'dense' --output-file '/tmp/tmpbo76svqj/job_working_directory/000/37/outputs/dataset_48dde814-4d2f-44b6-9954-33a452dc47cd.dat'  --threads ${GALAXY_SLOTS:-1}

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"input"`
__workflow_invocation_uuid__	`"639edb8a148211f0aeac6045bda70f2c"`
alignment	`{"exclude_supplementary": false, "min_read_aligned_length": "0", "min_read_aligned_percent": "0.0", "min_read_percent_identity": "0.0", "proper_pairs_only": {"__current_case__": 1, "proper_pairs_only": ""}}`
chromInfo	`"/tmp/tmpbo76svqj/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
cov	`{"contig_end_exclusion": "75", "methods": ["relative_abundance"], "min_covered_fraction": "10", "trim_max": "95", "trim_min": "5"}`
dbkey	`"?"`
derep	`{"checkm_tab_table": null, "dereplicate": {"__current_case__": 1, "dereplicate": ""}, "genome_info": null, "max_contamination": null, "min_completeness": null}`
exclude_genomes_from_deshard	`false`
mapped	`{"__current_case__": 1, "mapped": "not-mapped", "mapper": "minimap2-sr", "mode": {"__current_case__": 0, "genome": {"__current_case__": 1, "genomic": {"__current_case__": 0, "genome_fasta_files": {"values": [{"id": 53, "src": "hdca"}]}, "source": "history"}, "ref_or_genome": "genomic"}, "mode": "individual", "read_type": {"__current_case__": 2, "paired_reads": {"values": [{"id": 4, "src": "dce"}]}, "type": "paired_collection"}}}`
out	`{"dereplication_output_cluster_definition": false, "dereplication_output_representative_fasta_directory_copy": false, "no_zeros": false, "output_format": "dense"}`

Step 52: toolshed.g2.bx.psu.edu/repos/iuc/quast/quast/5.3.0+galaxy0:

step_state: scheduled

Jobs

Job 1:

Job state is running

Command Line:

echo 50contig_reads_bin_1_fasta &&    metaquast  --labels '50contig_reads_bin_1_fasta' -o 'outputdir'  --max-ref-num 0  --min-identity 90.0 --min-contig 500        --min-alignment 65 --ambiguity-usage 'one' --ambiguity-score 0.99   --local-mis-size 200   --contig-thresholds '0,1000'  --extensive-mis-size 1000 --scaffold-gap-max-size 1000 --unaligned-part-size 500   --x-for-Nx 90  '/tmp/tmpbo76svqj/files/6/3/2/dataset_63279e7d-d10f-4461-95a5-ea0dbb452657.dat' --threads ${GALAXY_SLOTS:-1}  && 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/tmpbo76svqj/job_working_directory/000/38/outputs/dataset_455f6b7c-0828-47ec-8721-e241bb99c410_files' && cp outputdir/combined_reference/*.html '/tmp/tmpbo76svqj/job_working_directory/000/38/outputs/dataset_455f6b7c-0828-47ec-8721-e241bb99c410_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/tmpbo76svqj/job_working_directory/000/38/outputs/dataset_455f6b7c-0828-47ec-8721-e241bb99c410_files'; fi && if [[ -d "outputdir/krona_charts/" ]]; then mkdir -p 'None' && cp outputdir/krona_charts/*.html 'None'; fi

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"input"`
__workflow_invocation_uuid__	`"639edb8a148211f0aeac6045bda70f2c"`
advanced	`{"contig_thresholds": "0,1000", "extensive_mis_size": "1000", "fragmented_max_indent": null, "report_all_metrics": false, "scaffold_gap_max_size": "1000", "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": "90.0", "ref": {"__current_case__": 0, "max_ref_num": "0", "origin": "silva"}, "reuse_combined_alignments": false, "type": "metagenome"}`
chromInfo	`"/tmp/tmpbo76svqj/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	`"500"`
mode	`{"__current_case__": 0, "in": {"__current_case__": 1, "custom": "false", "inputs": {"values": [{"id": 93, "src": "dce"}]}}, "mode": "individual", "reads": {"__current_case__": 0, "reads_option": "disabled"}}`
output_files	`["html", "tabular", "summary", "krona"]`
split_scaffolds	`false`

Job 2:

Job state is queued

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"input"`
__workflow_invocation_uuid__	`"639edb8a148211f0aeac6045bda70f2c"`
advanced	`{"contig_thresholds": "0,1000", "extensive_mis_size": "1000", "fragmented_max_indent": null, "report_all_metrics": false, "scaffold_gap_max_size": "1000", "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": "90.0", "ref": {"__current_case__": 0, "max_ref_num": "0", "origin": "silva"}, "reuse_combined_alignments": false, "type": "metagenome"}`
chromInfo	`"/tmp/tmpbo76svqj/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	`"500"`
mode	`{"__current_case__": 0, "in": {"__current_case__": 1, "custom": "false", "inputs": {"values": [{"id": 94, "src": "dce"}]}}, "mode": "individual", "reads": {"__current_case__": 0, "reads_option": "disabled"}}`
output_files	`["html", "tabular", "summary", "krona"]`
split_scaffolds	`false`

Job 3:

Job state is queued

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"input"`
__workflow_invocation_uuid__	`"639edb8a148211f0aeac6045bda70f2c"`
advanced	`{"contig_thresholds": "0,1000", "extensive_mis_size": "1000", "fragmented_max_indent": null, "report_all_metrics": false, "scaffold_gap_max_size": "1000", "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": "90.0", "ref": {"__current_case__": 0, "max_ref_num": "0", "origin": "silva"}, "reuse_combined_alignments": false, "type": "metagenome"}`
chromInfo	`"/tmp/tmpbo76svqj/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	`"500"`
mode	`{"__current_case__": 0, "in": {"__current_case__": 1, "custom": "false", "inputs": {"values": [{"id": 95, "src": "dce"}]}}, "mode": "individual", "reads": {"__current_case__": 0, "reads_option": "disabled"}}`
output_files	`["html", "tabular", "summary", "krona"]`
split_scaffolds	`false`

Job 4:

Job state is queued

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"input"`
__workflow_invocation_uuid__	`"639edb8a148211f0aeac6045bda70f2c"`
advanced	`{"contig_thresholds": "0,1000", "extensive_mis_size": "1000", "fragmented_max_indent": null, "report_all_metrics": false, "scaffold_gap_max_size": "1000", "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": "90.0", "ref": {"__current_case__": 0, "max_ref_num": "0", "origin": "silva"}, "reuse_combined_alignments": false, "type": "metagenome"}`
chromInfo	`"/tmp/tmpbo76svqj/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	`"500"`
mode	`{"__current_case__": 0, "in": {"__current_case__": 1, "custom": "false", "inputs": {"values": [{"id": 96, "src": "dce"}]}}, "mode": "individual", "reads": {"__current_case__": 0, "reads_option": "disabled"}}`
output_files	`["html", "tabular", "summary", "krona"]`
split_scaffolds	`false`

Step 53: toolshed.g2.bx.psu.edu/repos/iuc/bakta/bakta/1.9.4+galaxy0:

step_state: scheduled

Jobs

Job 1:

Job state is queued

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"input"`
__workflow_invocation_uuid__	`"639edb8a148211f0aeac6045bda70f2c"`
annotation	`{"complete": false, "compliant": false, "keep_contig_headers": false, "meta": false, "prodigal": null, "proteins": null, "regions": null, "replicons": null, "translation_table": "11"}`
chromInfo	`"/tmp/tmpbo76svqj/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
dbkey	`"?"`
input_option	`{"amrfinder_db_select": "amrfinderplus_V3.12_2024-05-02.2", "bakta_db_select": "V5.1_2024-01-19", "input_file": {"values": [{"id": 93, "src": "dce"}]}, "min_contig_length": null}`
organism	`{"genus": null, "plasmid": null, "species": null, "strain": null}`
output_files	`{"output_selection": ["file_tsv", "file_gff3", "file_ffn", "file_plot", "sum_txt"]}`
workflow	`{"skip_analysis": null}`

Job 2:

Job state is queued

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"input"`
__workflow_invocation_uuid__	`"639edb8a148211f0aeac6045bda70f2c"`
annotation	`{"complete": false, "compliant": false, "keep_contig_headers": false, "meta": false, "prodigal": null, "proteins": null, "regions": null, "replicons": null, "translation_table": "11"}`
chromInfo	`"/tmp/tmpbo76svqj/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
dbkey	`"?"`
input_option	`{"amrfinder_db_select": "amrfinderplus_V3.12_2024-05-02.2", "bakta_db_select": "V5.1_2024-01-19", "input_file": {"values": [{"id": 94, "src": "dce"}]}, "min_contig_length": null}`
organism	`{"genus": null, "plasmid": null, "species": null, "strain": null}`
output_files	`{"output_selection": ["file_tsv", "file_gff3", "file_ffn", "file_plot", "sum_txt"]}`
workflow	`{"skip_analysis": null}`

Job 3:

Job state is queued

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"input"`
__workflow_invocation_uuid__	`"639edb8a148211f0aeac6045bda70f2c"`
annotation	`{"complete": false, "compliant": false, "keep_contig_headers": false, "meta": false, "prodigal": null, "proteins": null, "regions": null, "replicons": null, "translation_table": "11"}`
chromInfo	`"/tmp/tmpbo76svqj/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
dbkey	`"?"`
input_option	`{"amrfinder_db_select": "amrfinderplus_V3.12_2024-05-02.2", "bakta_db_select": "V5.1_2024-01-19", "input_file": {"values": [{"id": 95, "src": "dce"}]}, "min_contig_length": null}`
organism	`{"genus": null, "plasmid": null, "species": null, "strain": null}`
output_files	`{"output_selection": ["file_tsv", "file_gff3", "file_ffn", "file_plot", "sum_txt"]}`
workflow	`{"skip_analysis": null}`

Job 4:

Job state is queued

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"input"`
__workflow_invocation_uuid__	`"639edb8a148211f0aeac6045bda70f2c"`
annotation	`{"complete": false, "compliant": false, "keep_contig_headers": false, "meta": false, "prodigal": null, "proteins": null, "regions": null, "replicons": null, "translation_table": "11"}`
chromInfo	`"/tmp/tmpbo76svqj/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
dbkey	`"?"`
input_option	`{"amrfinder_db_select": "amrfinderplus_V3.12_2024-05-02.2", "bakta_db_select": "V5.1_2024-01-19", "input_file": {"values": [{"id": 96, "src": "dce"}]}, "min_contig_length": null}`
organism	`{"genus": null, "plasmid": null, "species": null, "strain": null}`
output_files	`{"output_selection": ["file_tsv", "file_gff3", "file_ffn", "file_plot", "sum_txt"]}`
workflow	`{"skip_analysis": null}`

Step 54: toolshed.g2.bx.psu.edu/repos/iuc/collection_column_join/collection_column_join/0.0.3:

step_state: scheduled

Jobs

Job 1:

Job state is new

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"tabular"`
__workflow_invocation_uuid__	`"639edb8a148211f0aeac6045bda70f2c"`
chromInfo	`"/tmp/tmpbo76svqj/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
dbkey	`"?"`
fill_char	`"."`
has_header	`"1"`
identifier_column	`"1"`
include_outputs	`None`
old_col_in_header	`true`

Step 55: Unlabelled step:
- step_state: new
Step 7: Trimmed sample paired reads:
- step_state: scheduled
Step 8: Contamination weight (Binette):
- step_state: scheduled
Step 9: CheckM2 Database for Binette:
- step_state: scheduled
Step 10: Minimum MAG completeness percentage:
- step_state: scheduled

Other invocation details
- error_message
  - Final state of invocation 1ed2e242fb805563 is [failed]. Failed to run workflow, at least one job is in [error] state.
- history_id
  - 1ed2e242fb805563
- history_state
  - error
- invocation_id
  - 1ed2e242fb805563
- invocation_state
  - failed
- messages
  - [{'dependent_workflow_step_id': 47, 'hdca_id': 'f2b79f2e7fefe971', 'reason': 'collection_failed', 'workflow_step_id': 54}]
- workflow_id
  - 1ed2e242fb805563

github-actions · 2025-04-10T09:18:23Z

Test Results (powered by Planemo)

Test Summary

Test State	Count
Total	1
Passed	0
Error	0
Failure	1
Skipped	0

Failed Tests

❌ MAGs-generation.ga_0

Problems:

Output with path /tmp/tmpfh4xfkb2/Quast on data 12, data 11, and data 20 HTML report for combined reference genome__a81ec982-15db-4182-89f1-1c9dd6c0dfdd different than expected
Expected file size of 363000+-5000 found 372079

Workflow invocation details

Invocation Messages

Steps

Step 1: Choose Assembler:
- step_state: scheduled
Step 2: Custom Assemblies:
- step_state: scheduled
Step 11: Maximum MAG contamination percentage:
- step_state: scheduled
Step 12: Minimum MAG length:
- step_state: scheduled
Step 13: CheckM2 Database (dRep step):
- step_state: scheduled
Step 14: ANI threshold for dereplication:
- step_state: scheduled
Step 15: CheckM2 Database (Bin step):
- step_state: scheduled
Step 16: GTDB-tk Database:
- step_state: scheduled
Step 17: Run GTDB-Tk on MAGs:
- step_state: scheduled
Step 18: Bakta Database:
- step_state: scheduled
Step 19: AMRFinderPlus Database for Bakta:
- step_state: scheduled
Step 20: Run Bakta on MAGs:
- step_state: scheduled
Step 3: Minimum length of contigs to output:
- step_state: scheduled

Step 21: toolshed.g2.bx.psu.edu/repos/iuc/map_param_value/map_param_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__	`"85d8fbb215e611f0aeac6045bd812dcf"`
chromInfo	`"/tmp/tmprt3848zx/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
dbkey	`"?"`
input_param_type	`{"__current_case__": 0, "input_param": "MEGAHIT", "mappings": [{"__index__": 0, "from": "MEGAHIT", "to": "True"}], "type": "text"}`
output_param_type	`"boolean"`
unmapped	`{"__current_case__": 2, "default_value": "False", "on_unmapped": "default"}`

Step 22: toolshed.g2.bx.psu.edu/repos/iuc/map_param_value/map_param_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__	`"85d8fbb215e611f0aeac6045bd812dcf"`
chromInfo	`"/tmp/tmprt3848zx/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
dbkey	`"?"`
input_param_type	`{"__current_case__": 0, "input_param": "MEGAHIT", "mappings": [{"__index__": 0, "from": "metaSPAdes", "to": "True"}], "type": "text"}`
output_param_type	`"boolean"`
unmapped	`{"__current_case__": 2, "default_value": "False", "on_unmapped": "default"}`

Step 23: __UNZIP_COLLECTION__:
- step_state: scheduled
- Jobs
  - Job 1:
    - Job state is ok
    Traceback:
    Job Parameters:
    - Job parameter Parameter value
      
      __workflow_invocation_uuid__ "85d8fbb215e611f0aeac6045bd812dcf"
      
      input {"values": [{"id": 1, "src": "dce"}]}

Step 24: toolshed.g2.bx.psu.edu/repos/iuc/megahit/megahit/1.2.9+galaxy2:

step_state: scheduled

Jobs

Job 1:

Job state is ok

Command Line:

if [[ -n "$GALAXY_MEMORY_MB" ]]; then MEMORY="-m $((GALAXY_MEMORY_MB * 1024))"; fi;  megahit --num-cpu-threads ${GALAXY_SLOTS:-4}  -1 '/tmp/tmprt3848zx/files/2/8/2/dataset_28228683-09f8-4a16-a632-dc47b6787386.dat' -2 '/tmp/tmprt3848zx/files/3/a/1/dataset_3a16e83b-8f5d-4f72-9525-9611cef44b4e.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:

2025-04-10 08:34:46 - MEGAHIT v1.2.9
2025-04-10 08:34:46 - Using megahit_core with POPCNT and BMI2 support
2025-04-10 08:34:46 - Convert reads to binary library
2025-04-10 08:34:46 - b'INFO  sequence/io/sequence_lib.cpp  :   75 - Lib 0 (/tmp/tmprt3848zx/files/2/8/2/dataset_28228683-09f8-4a16-a632-dc47b6787386.dat,/tmp/tmprt3848zx/files/3/a/1/dataset_3a16e83b-8f5d-4f72-9525-9611cef44b4e.dat): pe, 18924 reads, 150 max length'
2025-04-10 08:34:46 - b'INFO  utils/utils.h                 :  152 - Real: 0.0554\tuser: 0.0492\tsys: 0.0069\tmaxrss: 20844'
2025-04-10 08:34:46 - Start assembly. Number of CPU threads 1 
2025-04-10 08:34:46 - k list: 21,29,39,59,79,99,119,141 
2025-04-10 08:34:46 - Memory used: 15090090393
2025-04-10 08:34:46 - Extract solid (k+1)-mers for k = 21 
2025-04-10 08:34:47 - Build graph for k = 21 
2025-04-10 08:34:47 - Assemble contigs from SdBG for k = 21
2025-04-10 08:34:47 - Local assembly for k = 21
2025-04-10 08:34:48 - Extract iterative edges from k = 21 to 29 
2025-04-10 08:34:48 - Build graph for k = 29 
2025-04-10 08:34:49 - Assemble contigs from SdBG for k = 29
2025-04-10 08:34:49 - Local assembly for k = 29
2025-04-10 08:34:50 - Extract iterative edges from k = 29 to 39 
2025-04-10 08:34:50 - Build graph for k = 39 
2025-04-10 08:34:50 - Assemble contigs from SdBG for k = 39
2025-04-10 08:34:51 - Local assembly for k = 39
2025-04-10 08:34:51 - Extract iterative edges from k = 39 to 59 
2025-04-10 08:34:51 - Build graph for k = 59 
2025-04-10 08:34:52 - Assemble contigs from SdBG for k = 59
2025-04-10 08:34:52 - Local assembly for k = 59
2025-04-10 08:34:52 - Extract iterative edges from k = 59 to 79 
2025-04-10 08:34:52 - Build graph for k = 79 
2025-04-10 08:34:53 - Assemble contigs from SdBG for k = 79
2025-04-10 08:34:53 - Local assembly for k = 79
2025-04-10 08:34:53 - Extract iterative edges from k = 79 to 99 
2025-04-10 08:34:53 - Build graph for k = 99 
2025-04-10 08:34:54 - Assemble contigs from SdBG for k = 99
2025-04-10 08:34:54 - Local assembly for k = 99
2025-04-10 08:34:54 - Extract iterative edges from k = 99 to 119 
2025-04-10 08:34:54 - Build graph for k = 119 
2025-04-10 08:34:54 - Assemble contigs from SdBG for k = 119
2025-04-10 08:34:55 - Local assembly for k = 119
2025-04-10 08:34:55 - Extract iterative edges from k = 119 to 141 
2025-04-10 08:34:55 - Build graph for k = 141 
2025-04-10 08:34:55 - Assemble contigs from SdBG for k = 141
2025-04-10 08:34:55 - Merging to output final contigs 
2025-04-10 08:34:55 - 63 contigs, total 266124 bp, min 354 bp, max 11001 bp, avg 4224 bp, N50 4877 bp
2025-04-10 08:34:55 - ALL DONE. Time elapsed: 9.692088 seconds

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"fastqsanger.gz"`
__workflow_invocation_uuid__	`"85d8fbb215e611f0aeac6045bd812dcf"`
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/tmprt3848zx/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": false, "min_contig_len": "200", "show_intermediate_contigs": false}`

Step 25: toolshed.g2.bx.psu.edu/repos/nml/metaspades/metaspades/4.1.0+galaxy0:

step_state: scheduled

Jobs

Job 1:

Job state is skipped

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"input"`
__workflow_invocation_uuid__	`"85d8fbb215e611f0aeac6045bd812dcf"`
additional_reads	`{"__current_case__": 1, "selector": "false"}`
arf	`{"nanopore": null, "pacbio": null}`
chromInfo	`"/tmp/tmprt3848zx/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
dbkey	`"?"`
kmer_cond	`{"__current_case__": 0, "kmer_sel": "auto"}`
library_number	`"true"`
mode_sel	`None`
optional_output	`["ag", "ags", "cn", "cs"]`
phred_offset	`"auto"`
singlePaired	`{"__current_case__": 1, "input": {"values": [{"id": 1, "src": "hdca"}]}, "orientation": "fr", "sPaired": "paired_collection", "type_paired": "pe"}`

Step 26: 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__	`"85d8fbb215e611f0aeac6045bd812dcf"`
chromInfo	`"/tmp/tmprt3848zx/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
dbkey	`"?"`
style_cond	`{"__current_case__": 0, "pick_style": "first", "type_cond": {"__current_case__": 4, "param_type": "data", "pick_from": [{"__index__": 0, "value": {"values": [{"id": 12, "src": "hda"}]}}, {"__index__": 1, "value": {"values": [{"id": 9, "src": "dce"}]}}, {"__index__": 2, "value": null}]}}`

Step 27: toolshed.g2.bx.psu.edu/repos/iuc/quast/quast/5.3.0+galaxy0:

step_state: scheduled

Jobs

Job 1:

Job state is ok

Command Line:

echo 50contig_reads &&   ln -s '/tmp/tmprt3848zx/files/2/8/2/dataset_28228683-09f8-4a16-a632-dc47b6787386.dat' 'pe1-50contig_reads.fastqsanger.gz' && ln -s '/tmp/tmprt3848zx/files/3/a/1/dataset_3a16e83b-8f5d-4f72-9525-9611cef44b4e.dat' 'pe2-50contig_reads.fastqsanger.gz' &&  metaquast  --pe1 'pe1-50contig_reads.fastqsanger.gz' --pe2 'pe2-50contig_reads.fastqsanger.gz' --labels '50contig_reads' -o 'outputdir'  --max-ref-num 0  --min-identity 90.0 --min-contig 500        --min-alignment 65 --ambiguity-usage 'one' --ambiguity-score 0.99   --local-mis-size 200   --contig-thresholds '0,1000'  --extensive-mis-size 1000 --scaffold-gap-max-size 1000 --unaligned-part-size 500   --x-for-Nx 90  '/tmp/tmprt3848zx/files/f/5/6/dataset_f56caa53-2f68-4615-b2bf-37274711c329.dat' --threads ${GALAXY_SLOTS:-1}  && 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/tmprt3848zx/job_working_directory/000/11/outputs/dataset_a81ec982-15db-4182-89f1-1c9dd6c0dfdd_files' && cp outputdir/combined_reference/*.html '/tmp/tmprt3848zx/job_working_directory/000/11/outputs/dataset_a81ec982-15db-4182-89f1-1c9dd6c0dfdd_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/tmprt3848zx/job_working_directory/000/11/outputs/dataset_a81ec982-15db-4182-89f1-1c9dd6c0dfdd_files'; fi && if [[ -d "outputdir/krona_charts/" ]]; then mkdir -p 'None' && cp outputdir/krona_charts/*.html 'None'; fi

Exit Code:

```
0
```

Standard Output:

50contig_reads
/usr/local/opt/quast-5.3.0/metaquast.py --pe1 pe1-50contig_reads.fastqsanger.gz --pe2 pe2-50contig_reads.fastqsanger.gz --labels 50contig_reads -o outputdir --max-ref-num 0 --min-identity 90.0 --min-contig 500 --min-alignment 65 --ambiguity-usage one --ambiguity-score 0.99 --local-mis-size 200 --contig-thresholds 0,1000 --extensive-mis-size 1000 --scaffold-gap-max-size 1000 --unaligned-part-size 500 --x-for-Nx 90 /tmp/tmprt3848zx/files/f/5/6/dataset_f56caa53-2f68-4615-b2bf-37274711c329.dat --threads 1

Version: 5.3.0

System information:
  OS: Linux-6.8.0-1021-azure-x86_64-with-glibc2.36 (linux_64)
  Python version: 3.12.3
  CPUs number: 4

Started: 2025-04-10 08:35:59

Logging to /tmp/tmprt3848zx/job_working_directory/000/11/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/tmprt3848zx/files/f/5/6/dataset_f56caa53-2f68-4615-b2bf-37274711c329.dat ==> 50contig_reads

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 pe1-50contig_reads.fastqsanger.gz --pe2 pe2-50contig_reads.fastqsanger.gz --min-identity 90.0 --min-contig 500 --min-alignment 65 --ambiguity-usage one --ambiguity-score 0.99 --local-mis-size 200 --contig-thresholds 0,1000 --extensive-mis-size 1000 --scaffold-gap-max-size 1000 --unaligned-part-size 500 --x-for-Nx 90 --threads 1 /tmp/tmprt3848zx/files/f/5/6/dataset_f56caa53-2f68-4615-b2bf-37274711c329.dat -o /tmp/tmprt3848zx/job_working_directory/000/11/working/outputdir --labels 50contig_reads

Version: 5.3.0

System information:
  OS: Linux-6.8.0-1021-azure-x86_64-with-glibc2.36 (linux_64)
  Python version: 3.12.3
  CPUs number: 4

Started: 2025-04-10 08:36:00

Logging to /tmp/tmprt3848zx/job_working_directory/000/11/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/tmprt3848zx/job_working_directory/000/11/working
Main parameters: 
  MODE: meta, threads: 1, min contig length: 500, min alignment length: 65, min alignment IDY: 90.0, \
  ambiguity: all, min local misassembly length: 200, min extensive misassembly length: 1000

Contigs:
  Pre-processing...
  /tmp/tmprt3848zx/files/f/5/6/dataset_f56caa53-2f68-4615-b2bf-37274711c329.dat ==> 50contig_reads

2025-04-10 08:36:00
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/tmprt3848zx/job_working_directory/000/11/home/.quast
Downloading gridss (file: gridss-1.4.1.jar)...
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gridss successfully downloaded!
  Logging to files /tmp/tmprt3848zx/job_working_directory/000/11/working/outputdir/reads_stats/reads_stats.log and /tmp/tmprt3848zx/job_working_directory/000/11/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/tmprt3848zx/job_working_directory/000/11/working/outputdir/reads_stats/reads_report.txt, reads_report.tsv, and reads_report.tex
Done.

2025-04-10 08:36:05
Running Basic statistics processor...
  Contig files: 
    50contig_reads
  Calculating N50 and L50...
    50contig_reads, N50 = 4877, L50 = 22, auN = 5187.8, Total length = 265405, GC % = 36.45, # N's per 100 kbp =  0.00
  Drawing Nx plot...
    saved to /tmp/tmprt3848zx/job_working_directory/000/11/working/outputdir/basic_stats/Nx_plot.pdf
  Drawing cumulative plot...
    saved to /tmp/tmprt3848zx/job_working_directory/000/11/working/outputdir/basic_stats/cumulative_plot.pdf
  Drawing GC content plot...
    saved to /tmp/tmprt3848zx/job_working_directory/000/11/working/outputdir/basic_stats/GC_content_plot.pdf
  Drawing 50contig_reads GC content plot...
    saved to /tmp/tmprt3848zx/job_working_directory/000/11/working/outputdir/basic_stats/50contig_reads_GC_content_plot.pdf
Done.

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

2025-04-10 08:36:06
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

2025-04-10 08:36:07
RESULTS:
  Text versions of total report are saved to /tmp/tmprt3848zx/job_working_directory/000/11/working/outputdir/report.txt, report.tsv, and report.tex
  Text versions of transposed total report are saved to /tmp/tmprt3848zx/job_working_directory/000/11/working/outputdir/transposed_report.txt, transposed_report.tsv, and transposed_report.tex
  HTML version (interactive tables and plots) is saved to /tmp/tmprt3848zx/job_working_directory/000/11/working/outputdir/report.html
  PDF version (tables and plots) is saved to /tmp/tmprt3848zx/job_working_directory/000/11/working/outputdir/report.pdf
  Icarus (contig browser) is saved to /tmp/tmprt3848zx/job_working_directory/000/11/working/outputdir/icarus.html
  Log is saved to /tmp/tmprt3848zx/job_working_directory/000/11/working/outputdir/quast.log

Finished: 2025-04-10 08:36:07
Elapsed time: 0:00:06.967949
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__	`"85d8fbb215e611f0aeac6045bd812dcf"`
advanced	`{"contig_thresholds": "0,1000", "extensive_mis_size": "1000", "fragmented_max_indent": null, "report_all_metrics": false, "scaffold_gap_max_size": "1000", "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": "90.0", "ref": {"__current_case__": 0, "max_ref_num": "0", "origin": "silva"}, "reuse_combined_alignments": false, "type": "metagenome"}`
chromInfo	`"/tmp/tmprt3848zx/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	`"500"`
mode	`{"__current_case__": 0, "in": {"__current_case__": 1, "custom": "false", "inputs": {"values": [{"id": 10, "src": "dce"}]}}, "mode": "individual", "reads": {"__current_case__": 2, "input_1": {"values": [{"id": 7, "src": "dce"}]}, "input_2": {"values": [{"id": 8, "src": "dce"}]}, "reads_option": "paired"}}`
output_files	`["html", "pdf", "tabular", "log", "summary", "krona"]`
split_scaffolds	`false`

Step 28: toolshed.g2.bx.psu.edu/repos/devteam/bowtie2/bowtie2/2.5.3+galaxy1:

step_state: scheduled

Jobs

Job 1:

Job state is ok

Command Line:

set -o | grep -q pipefail && set -o pipefail; bowtie2-build --threads ${GALAXY_SLOTS:-4} '/tmp/tmprt3848zx/files/f/5/6/dataset_f56caa53-2f68-4615-b2bf-37274711c329.dat' genome && ln -s -f '/tmp/tmprt3848zx/files/f/5/6/dataset_f56caa53-2f68-4615-b2bf-37274711c329.dat' genome.fa &&   ln -f -s '/tmp/tmprt3848zx/files/2/8/2/dataset_28228683-09f8-4a16-a632-dc47b6787386.dat' input_f.fastq.gz &&  ln -f -s '/tmp/tmprt3848zx/files/3/a/1/dataset_3a16e83b-8f5d-4f72-9525-9611cef44b4e.dat' input_r.fastq.gz &&    THREADS=${GALAXY_SLOTS:-4} && if [ "$THREADS" -gt 1 ]; then (( THREADS-- )); fi &&   bowtie2  -p "$THREADS"  -x 'genome'   -1 'input_f.fastq.gz' -2 'input_r.fastq.gz'                2> >(tee '/tmp/tmprt3848zx/job_working_directory/000/12/outputs/dataset_5c850e40-c06a-42aa-91a7-ceb370e774f3.dat' >&2)  | samtools sort -l 0 -T "${TMPDIR:-.}" -O bam | samtools view --no-PG -O bam -@ ${GALAXY_SLOTS:-1} -o '/tmp/tmprt3848zx/job_working_directory/000/12/outputs/dataset_c93f3612-c51c-408f-84c5-2d80d96ace49.dat'

Exit Code:

```
0
```

Standard Error:

Building a SMALL index
Renaming genome.3.bt2.tmp to genome.3.bt2
Renaming genome.4.bt2.tmp to genome.4.bt2
Renaming genome.1.bt2.tmp to genome.1.bt2
Renaming genome.2.bt2.tmp to genome.2.bt2
Renaming genome.rev.1.bt2.tmp to genome.rev.1.bt2
Renaming genome.rev.2.bt2.tmp to genome.rev.2.bt2
9462 reads; of these:
  9462 (100.00%) were paired; of these:
    90 (0.95%) aligned concordantly 0 times
    9300 (98.29%) aligned concordantly exactly 1 time
    72 (0.76%) aligned concordantly >1 times
    ----
    90 pairs aligned concordantly 0 times; of these:
      8 (8.89%) aligned discordantly 1 time
    ----
    82 pairs aligned 0 times concordantly or discordantly; of these:
      164 mates make up the pairs; of these:
        93 (56.71%) aligned 0 times
        70 (42.68%) aligned exactly 1 time
        1 (0.61%) aligned >1 times
99.51% overall alignment rate

Standard Output:

Settings:
  Output files: "genome.*.bt2"
  Line rate: 6 (line is 64 bytes)
  Lines per side: 1 (side is 64 bytes)
  Offset rate: 4 (one in 16)
  FTable chars: 10
  Strings: unpacked
  Max bucket size: default
  Max bucket size, sqrt multiplier: default
  Max bucket size, len divisor: 4
  Difference-cover sample period: 1024
  Endianness: little
  Actual local endianness: little
  Sanity checking: disabled
  Assertions: disabled
  Random seed: 0
  Sizeofs: void*:8, int:4, long:8, size_t:8
Input files DNA, FASTA:
  /tmp/tmprt3848zx/files/f/5/6/dataset_f56caa53-2f68-4615-b2bf-37274711c329.dat
Reading reference sizes
  Time reading reference sizes: 00:00:00
Calculating joined length
Writing header
Reserving space for joined string
Joining reference sequences
  Time to join reference sequences: 00:00:00
bmax according to bmaxDivN setting: 66531
Using parameters --bmax 49899 --dcv 1024
  Doing ahead-of-time memory usage test
  Passed!  Constructing with these parameters: --bmax 49899 --dcv 1024
Constructing suffix-array element generator
Building DifferenceCoverSample
  Building sPrime
  Building sPrimeOrder
  V-Sorting samples
  V-Sorting samples time: 00:00:00
  Allocating rank array
  Ranking v-sort output
  Ranking v-sort output time: 00:00:00
  Invoking Larsson-Sadakane on ranks
  Invoking Larsson-Sadakane on ranks time: 00:00:00
  Sanity-checking and returning
Building samples
Reserving space for 12 sample suffixes
Generating random suffixes
QSorting 12 sample offsets, eliminating duplicates
QSorting sample offsets, eliminating duplicates time: 00:00:00
Multikey QSorting 12 samples
  (Using difference cover)
  Multikey QSorting samples time: 00:00:00
Calculating bucket sizes
Splitting and merging
  Splitting and merging time: 00:00:00
Split 1, merged 6; iterating...
Splitting and merging
  Splitting and merging time: 00:00:00
Avg bucket size: 38016.9 (target: 49898)
Converting suffix-array elements to index image
Allocating ftab, absorbFtab
Entering Ebwt loop
Getting block 1 of 7
  Reserving size (49899) for bucket 1
  Calculating Z arrays for bucket 1
  Entering block accumulator loop for bucket 1:
  bucket 1: 10%
  bucket 1: 20%
  bucket 1: 30%
  bucket 1: 40%
  bucket 1: 50%
  bucket 1: 60%
  bucket 1: 70%
  bucket 1: 80%
  bucket 1: 90%
  bucket 1: 100%
  Sorting block of length 18323 for bucket 1
  (Using difference cover)
  Sorting block time: 00:00:00
Returning block of 18324 for bucket 1
Getting block 2 of 7
  Reserving size (49899) for bucket 2
  Calculating Z arrays for bucket 2
  Entering block accumulator loop for bucket 2:
  bucket 2: 10%
  bucket 2: 20%
  bucket 2: 30%
  bucket 2: 40%
  bucket 2: 50%
  bucket 2: 60%
  bucket 2: 70%
  bucket 2: 80%
  bucket 2: 90%
  bucket 2: 100%
  Sorting block of length 49606 for bucket 2
  (Using difference cover)
  Sorting block time: 00:00:00
Returning block of 49607 for bucket 2
Getting block 3 of 7
  Reserving size (49899) for bucket 3
  Calculating Z arrays for bucket 3
  Entering block accumulator loop for bucket 3:
  bucket 3: 10%
  bucket 3: 20%
  bucket 3: 30%
  bucket 3: 40%
  bucket 3: 50%
  bucket 3: 60%
  bucket 3: 70%
  bucket 3: 80%
  bucket 3: 90%
  bucket 3: 100%
  Sorting block of length 45151 for bucket 3
  (Using difference cover)
  Sorting block time: 00:00:00
Returning block of 45152 for bucket 3
Getting block 4 of 7
  Reserving size (49899) for bucket 4
  Calculating Z arrays for bucket 4
  Entering block accumulator loop for bucket 4:
  bucket 4: 10%
  bucket 4: 20%
  bucket 4: 30%
  bucket 4: 40%
  bucket 4: 50%
  bucket 4: 60%
  bucket 4: 70%
  bucket 4: 80%
  bucket 4: 90%
  bucket 4: 100%
  Sorting block of length 49787 for bucket 4
  (Using difference cover)
  Sorting block time: 00:00:00
Returning block of 49788 for bucket 4
Getting block 5 of 7
  Reserving size (49899) for bucket 5
  Calculating Z arrays for bucket 5
  Entering block accumulator loop for bucket 5:
  bucket 5: 10%
  bucket 5: 20%
  bucket 5: 30%
  bucket 5: 40%
  bucket 5: 50%
  bucket 5: 60%
  bucket 5: 70%
  bucket 5: 80%
  bucket 5: 90%
  bucket 5: 100%
  Sorting block of length 28638 for bucket 5
  (Using difference cover)
  Sorting block time: 00:00:00
Returning block of 28639 for bucket 5
Getting block 6 of 7
  Reserving size (49899) for bucket 6
  Calculating Z arrays for bucket 6
  Entering block accumulator loop for bucket 6:
  bucket 6: 10%
  bucket 6: 20%
  bucket 6: 30%
  bucket 6: 40%
  bucket 6: 50%
  bucket 6: 60%
  bucket 6: 70%
  bucket 6: 80%
  bucket 6: 90%
  bucket 6: 100%
  Sorting block of length 43194 for bucket 6
  (Using difference cover)
  Sorting block time: 00:00:00
Returning block of 43195 for bucket 6
Getting block 7 of 7
  Reserving size (49899) for bucket 7
  Calculating Z arrays for bucket 7
  Entering block accumulator loop for bucket 7:
  bucket 7: 10%
  bucket 7: 20%
  bucket 7: 30%
  bucket 7: 40%
  bucket 7: 50%
  bucket 7: 60%
  bucket 7: 70%
  bucket 7: 80%
  bucket 7: 90%
  bucket 7: 100%
  Sorting block of length 31419 for bucket 7
  (Using difference cover)
  Sorting block time: 00:00:00
Returning block of 31420 for bucket 7
Exited Ebwt loop
fchr[A]: 0
fchr[C]: 84325
fchr[G]: 133305
fchr[T]: 181307
fchr[$]: 266124
Exiting Ebwt::buildToDisk()
Returning from initFromVector
Wrote 4286544 bytes to primary EBWT file: genome.1.bt2.tmp
Wrote 66536 bytes to secondary EBWT file: genome.2.bt2.tmp
Re-opening _in1 and _in2 as input streams
Returning from Ebwt constructor
Headers:
    len: 266124
    bwtLen: 266125
    sz: 66531
    bwtSz: 66532
    lineRate: 6
    offRate: 4
    offMask: 0xfffffff0
    ftabChars: 10
    eftabLen: 20
    eftabSz: 80
    ftabLen: 1048577
    ftabSz: 4194308
    offsLen: 16633
    offsSz: 66532
    lineSz: 64
    sideSz: 64
    sideBwtSz: 48
    sideBwtLen: 192
    numSides: 1387
    numLines: 1387
    ebwtTotLen: 88768
    ebwtTotSz: 88768
    color: 0
    reverse: 0
Total time for call to driver() for forward index: 00:00:00
Reading reference sizes
  Time reading reference sizes: 00:00:00
Calculating joined length
Writing header
Reserving space for joined string
Joining reference sequences
  Time to join reference sequences: 00:00:00
  Time to reverse reference sequence: 00:00:00
bmax according to bmaxDivN setting: 66531
Using parameters --bmax 49899 --dcv 1024
  Doing ahead-of-time memory usage test
  Passed!  Constructing with these parameters: --bmax 49899 --dcv 1024
Constructing suffix-array element generator
Building DifferenceCoverSample
  Building sPrime
  Building sPrimeOrder
  V-Sorting samples
  V-Sorting samples time: 00:00:00
  Allocating rank array
  Ranking v-sort output
  Ranking v-sort output time: 00:00:00
  Invoking Larsson-Sadakane on ranks
  Invoking Larsson-Sadakane on ranks time: 00:00:00
  Sanity-checking and returning
Building samples
Reserving space for 12 sample suffixes
Generating random suffixes
QSorting 12 sample offsets, eliminating duplicates
QSorting sample offsets, eliminating duplicates time: 00:00:00
Multikey QSorting 12 samples
  (Using difference cover)
  Multikey QSorting samples time: 00:00:00
Calculating bucket sizes
Splitting and merging
  Splitting and merging time: 00:00:00
Split 1, merged 7; iterating...
Splitting and merging
  Splitting and merging time: 00:00:00
Avg bucket size: 44353.2 (target: 49898)
Converting suffix-array elements to index image
Allocating ftab, absorbFtab
Entering Ebwt loop
Getting block 1 of 6
  Reserving size (49899) for bucket 1
  Calculating Z arrays for bucket 1
  Entering block accumulator loop for bucket 1:
  bucket 1: 10%
  bucket 1: 20%
  bucket 1: 30%
  bucket 1: 40%
  bucket 1: 50%
  bucket 1: 60%
  bucket 1: 70%
  bucket 1: 80%
  bucket 1: 90%
  bucket 1: 100%
  Sorting block of length 47687 for bucket 1
  (Using difference cover)
  Sorting block time: 00:00:00
Returning block of 47688 for bucket 1
Getting block 2 of 6
  Reserving size (49899) for bucket 2
  Calculating Z arrays for bucket 2
  Entering block accumulator loop for bucket 2:
  bucket 2: 10%
  bucket 2: 20%
  bucket 2: 30%
  bucket 2: 40%
  bucket 2: 50%
  bucket 2: 60%
  bucket 2: 70%
  bucket 2: 80%
  bucket 2: 90%
  bucket 2: 100%
  Sorting block of length 36636 for bucket 2
  (Using difference cover)
  Sorting block time: 00:00:00
Returning block of 36637 for bucket 2
Getting block 3 of 6
  Reserving size (49899) for bucket 3
  Calculating Z arrays for bucket 3
  Entering block accumulator loop for bucket 3:
  bucket 3: 10%
  bucket 3: 20%
  bucket 3: 30%
  bucket 3: 40%
  bucket 3: 50%
  bucket 3: 60%
  bucket 3: 70%
  bucket 3: 80%
  bucket 3: 90%
  bucket 3: 100%
  Sorting block of length 49027 for bucket 3
  (Using difference cover)
  Sorting block time: 00:00:00
Returning block of 49028 for bucket 3
Getting block 4 of 6
  Reserving size (49899) for bucket 4
  Calculating Z arrays for bucket 4
  Entering block accumulator loop for bucket 4:
  bucket 4: 10%
  bucket 4: 20%
  bucket 4: 30%
  bucket 4: 40%
  bucket 4: 50%
  bucket 4: 60%
  bucket 4: 70%
  bucket 4: 80%
  bucket 4: 90%
  bucket 4: 100%
  Sorting block of length 37449 for bucket 4
  (Using difference cover)
  Sorting block time: 00:00:00
Returning block of 37450 for bucket 4
Getting block 5 of 6
  Reserving size (49899) for bucket 5
  Calculating Z arrays for bucket 5
  Entering block accumulator loop for bucket 5:
  bucket 5: 10%
  bucket 5: 20%
  bucket 5: 30%
  bucket 5: 40%
  bucket 5: 50%
  bucket 5: 60%
  bucket 5: 70%
  bucket 5: 80%
  bucket 5: 90%
  bucket 5: 100%
  Sorting block of length 47142 for bucket 5
  (Using difference cover)
  Sorting block time: 00:00:00
Returning block of 47143 for bucket 5
Getting block 6 of 6
  Reserving size (49899) for bucket 6
  Calculating Z arrays for bucket 6
  Entering block accumulator loop for bucket 6:
  bucket 6: 10%
  bucket 6: 20%
  bucket 6: 30%
  bucket 6: 40%
  bucket 6: 50%
  bucket 6: 60%
  bucket 6: 70%
  bucket 6: 80%
  bucket 6: 90%
  bucket 6: 100%
  Sorting block of length 48178 for bucket 6
  (Using difference cover)
  Sorting block time: 00:00:00
Returning block of 48179 for bucket 6
Exited Ebwt loop
fchr[A]: 0
fchr[C]: 84325
fchr[G]: 133305
fchr[T]: 181307
fchr[$]: 266124
Exiting Ebwt::buildToDisk()
Returning from initFromVector
Wrote 4286544 bytes to primary EBWT file: genome.rev.1.bt2.tmp
Wrote 66536 bytes to secondary EBWT file: genome.rev.2.bt2.tmp
Re-opening _in1 and _in2 as input streams
Returning from Ebwt constructor
Headers:
    len: 266124
    bwtLen: 266125
    sz: 66531
    bwtSz: 66532
    lineRate: 6
    offRate: 4
    offMask: 0xfffffff0
    ftabChars: 10
    eftabLen: 20
    eftabSz: 80
    ftabLen: 1048577
    ftabSz: 4194308
    offsLen: 16633
    offsSz: 66532
    lineSz: 64
    sideSz: 64
    sideBwtSz: 48
    sideBwtLen: 192
    numSides: 1387
    numLines: 1387
    ebwtTotLen: 88768
    ebwtTotSz: 88768
    color: 0
    reverse: 1
Total time for backward call to driver() for mirror index: 00:00:00

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"input"`
__workflow_invocation_uuid__	`"85d8fbb215e611f0aeac6045bd812dcf"`
analysis_type	`{"__current_case__": 0, "analysis_type_selector": "simple", "presets": "no_presets"}`
chromInfo	`"/tmp/tmprt3848zx/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
dbkey	`"?"`
library	`{"__current_case__": 2, "aligned_file": false, "input_1": {"values": [{"id": 1, "src": "dce"}]}, "paired_options": {"__current_case__": 1, "paired_options_selector": "no"}, "type": "paired_collection", "unaligned_file": false}`
own_file	__identifier__
reference_genome	`{"__current_case__": 1, "own_file": {"values": [{"id": 10, "src": "dce"}]}, "source": "history"}`
rg	`{"__current_case__": 3, "rg_selector": "do_not_set"}`
sam_options	`{"__current_case__": 1, "sam_options_selector": "no"}`
save_mapping_stats	`true`

Step 29: toolshed.g2.bx.psu.edu/repos/iuc/concoct_cut_up_fasta/concoct_cut_up_fasta/1.1.0+galaxy2:

step_state: scheduled

Jobs

Job 1:

Job state is ok

Command Line:

ln -s '/tmp/tmprt3848zx/files/f/5/6/dataset_f56caa53-2f68-4615-b2bf-37274711c329.dat' 'input.fa' &&  cut_up_fasta.py 'input.fa' --chunk_size 10000 --overlap_size 0 --merge_last --bedfile '/tmp/tmprt3848zx/job_working_directory/000/13/outputs/dataset_37f8de3e-f68b-444a-9f04-f8aac7ff4955.dat' > '/tmp/tmprt3848zx/job_working_directory/000/13/outputs/dataset_427437bc-34ba-411c-8993-eeae950b0e46.dat'

Exit Code:

```
0
```

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"input"`
__workflow_invocation_uuid__	`"85d8fbb215e611f0aeac6045bd812dcf"`
bedfile	`true`
chromInfo	`"/tmp/tmprt3848zx/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
chunk_size	`"10000"`
dbkey	`"?"`
input_fasta	__identifier__
merge_last	`true`
overlap_size	`"0"`

Step 30: toolshed.g2.bx.psu.edu/repos/devteam/samtools_sort/samtools_sort/2.0.5:

step_state: scheduled

Jobs

Job 1:

Job state is ok

Command Line:

addthreads=${GALAXY_SLOTS:-1} && (( addthreads-- )) &&   addmemory=${GALAXY_MEMORY_MB_PER_SLOT:-768} && ((addmemory=addmemory*75/100)) &&  samtools sort -@ $addthreads -m $addmemory"M"   -O bam -T "${TMPDIR:-.}" '/tmp/tmprt3848zx/files/c/9/3/dataset_c93f3612-c51c-408f-84c5-2d80d96ace49.dat' > '/tmp/tmprt3848zx/job_working_directory/000/14/outputs/dataset_1fae1fad-6c83-48b9-aa58-8d63340b3f94.dat'

Exit Code:

```
0
```

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"input"`
__workflow_invocation_uuid__	`"85d8fbb215e611f0aeac6045bd812dcf"`
chromInfo	`"/tmp/tmprt3848zx/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
dbkey	`"?"`
input1	__identifier__
minhash	`false`
prim_key_cond	`{"__current_case__": 0, "prim_key_select": ""}`

Step 4: Read length (CONCOCT):
- step_state: scheduled

Step 31: toolshed.g2.bx.psu.edu/repos/iuc/semibin/semibin/2.0.2+galaxy1:

step_state: scheduled

Jobs

Job 1:

Job state is ok

Command Line:

ln -s '/tmp/tmprt3848zx/files/1/f/a/dataset_1fae1fad-6c83-48b9-aa58-8d63340b3f94.dat' '50contig_reads.bam' &&   ln -s '/tmp/tmprt3848zx/files/f/5/6/dataset_f56caa53-2f68-4615-b2bf-37274711c329.dat' 'contigs.fasta' &&  SemiBin2 single_easy_bin --environment 'global' --input-fasta 'contigs.fasta' --input-bam *.bam --output 'output' --cannot-name 'cannot'   --orf-finder 'fast-naive' --random-seed 0  --epoches 20 --batch-size 2048 --max-node 1.0 --max-edges 200 --minfasta-kbs 200 --compression none --threads ${GALAXY_SLOTS:-1} --processes ${GALAXY_SLOTS:-1} && echo "output" && ls output

Exit Code:

```
0
```

Standard Error:

2025-04-10 08:36:39 dd5582054a32 SemiBin[9] INFO Binning for short_read
2025-04-10 08:36:44 dd5582054a32 SemiBin[9] INFO Did not detect GPU, using CPU.
2025-04-10 08:36:44 dd5582054a32 SemiBin[9] INFO Generating training data...
2025-04-10 08:36:45 dd5582054a32 SemiBin[9] INFO Calculating coverage for every sample.
2025-04-10 08:36:45 dd5582054a32 SemiBin[9] INFO Processed: 50contig_reads.bam
2025-04-10 08:36:45 dd5582054a32 SemiBin[9] INFO Start binning.
2025-04-10 08:36:47 dd5582054a32 SemiBin[9] INFO Number of bins prior to reclustering: 1
2025-04-10 08:36:47 dd5582054a32 SemiBin[9] INFO Running naive ORF finder
2025-04-10 08:36:48 dd5582054a32 SemiBin[9] INFO Number of bins after reclustering: 1
2025-04-10 08:36:48 dd5582054a32 SemiBin[9] INFO Binning finished

Standard Output:

If you find SemiBin useful, please cite:
        Pan, S.; Zhu, C.; Zhao, XM.; Coelho, LP. A deep siamese neural network improves metagenome-assembled genomes in microbiome datasets across different environments. Nat Commun 13, 2326 (2022). https://doi.org/10.1038/s41467-022-29843-y

        Pan, S.; Zhao, XM; Coelho, LP. SemiBin2: self-supervised contrastive learning leads to better MAGs for short- and long-read sequencing. Bioinformatics Volume 39, Issue Supplement_1, June 2023, Pages i21–i29. https://doi.org/10.1093/bioinformatics/btad209


output
50contig_reads.bam_0_data_cov.csv
SemiBinRun.log
contig_bins.tsv
data.csv
data_split.csv
output_bins
recluster_bins_info.tsv

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"input"`
__workflow_invocation_uuid__	`"85d8fbb215e611f0aeac6045bd812dcf"`
annot	`{"ml_threshold": null}`
bin	`{"max_edges": "200", "max_node": "1.0", "minfasta_kbs": "200"}`
chromInfo	`"/tmp/tmprt3848zx/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
dbkey	`"?"`
extra_output	`["data", "coverage"]`
min_len	`{"__current_case__": 0, "method": "automatic"}`
mode	`{"__current_case__": 0, "environment": "global", "input_bam": {"values": [{"id": 20, "src": "dce"}]}, "input_fasta": {"values": [{"id": 10, "src": "dce"}]}, "ref": {"__current_case__": 2, "select": "ml"}, "select": "single"}`
orf_finder	`"fast-naive"`
random_seed	`"0"`
training	`{"batch_size": "2048", "epoches": "20"}`

Step 32: toolshed.g2.bx.psu.edu/repos/iuc/concoct_coverage_table/concoct_coverage_table/1.1.0+galaxy2:

step_state: scheduled

Jobs

Job 1:

Job state is ok

Command Line:

mkdir 'mapping' && ln -s '/tmp/tmprt3848zx/files/1/f/a/dataset_1fae1fad-6c83-48b9-aa58-8d63340b3f94.dat' 'mapping/_tmp_tmprt3848zx_files_1_f_a_dataset_1fae1fad-6c83-48b9-aa58-8d63340b3f94.dat.sorted.bam' && samtools index 'mapping/_tmp_tmprt3848zx_files_1_f_a_dataset_1fae1fad-6c83-48b9-aa58-8d63340b3f94.dat.sorted.bam' 'mapping/_tmp_tmprt3848zx_files_1_f_a_dataset_1fae1fad-6c83-48b9-aa58-8d63340b3f94.dat.bam.bai' && mv 'mapping/_tmp_tmprt3848zx_files_1_f_a_dataset_1fae1fad-6c83-48b9-aa58-8d63340b3f94.dat.sorted.bam' 'mapping/_tmp_tmprt3848zx_files_1_f_a_dataset_1fae1fad-6c83-48b9-aa58-8d63340b3f94.dat.bam' && concoct_coverage_table.py '/tmp/tmprt3848zx/files/3/7/f/dataset_37f8de3e-f68b-444a-9f04-f8aac7ff4955.dat' mapping/*.bam > '/tmp/tmprt3848zx/job_working_directory/000/16/outputs/dataset_f877af85-c3a7-4d9c-88d4-79864a47077b.dat'

Exit Code:

```
0
```

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"input"`
__workflow_invocation_uuid__	`"85d8fbb215e611f0aeac6045bd812dcf"`
bedfile	__identifier__
chromInfo	`"/tmp/tmprt3848zx/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
dbkey	`"?"`
mode	`{"__current_case__": 0, "bamfile": {"values": [{"id": 20, "src": "dce"}]}, "type": "individual"}`
mode	bamfile

Step 33: toolshed.g2.bx.psu.edu/repos/iuc/metabat2_jgi_summarize_bam_contig_depths/metabat2_jgi_summarize_bam_contig_depths/2.17+galaxy0:

step_state: scheduled

Jobs

Job 1:

Job state is ok

Command Line:

jgi_summarize_bam_contig_depths --outputDepth '/tmp/tmprt3848zx/job_working_directory/000/17/outputs/dataset_3198f2d6-2daa-413f-bf6a-3a1554beb9b3.dat' --percentIdentity 97   --minMapQual 0 --weightMapQual 0.0  --maxEdgeBases 75 --shredLength 16000 --shredDepth 5 --minContigLength 1 --minContigDepth 0.0 '/tmp/tmprt3848zx/files/1/f/a/dataset_1fae1fad-6c83-48b9-aa58-8d63340b3f94.dat'

Exit Code:

```
0
```

Standard Error:

Output depth matrix to /tmp/tmprt3848zx/job_working_directory/000/17/outputs/dataset_3198f2d6-2daa-413f-bf6a-3a1554beb9b3.dat
Minimum percent identity for a mapped read: 0.97
minMapQual: 0
weightMapQual: 0
Edge bases will be included up to 75 bases
shredLength: 16000
shredDepth: 5
minContigLength: 1
minContigDepth: 0
jgi_summarize_bam_contig_depths 2.17 (Bioconda) 2024-12-15T06:34:17
Running with 4 threads to save memory you can reduce the number of threads with the OMP_NUM_THREADS variable
Output matrix to /tmp/tmprt3848zx/job_working_directory/000/17/outputs/dataset_3198f2d6-2daa-413f-bf6a-3a1554beb9b3.dat
Opening all bam files and validating headers
Processing bam files with largest_contig=0
Thread 0 opening and reading the header for file: /tmp/tmprt3848zx/files/1/f/a/dataset_1fae1fad-6c83-48b9-aa58-8d63340b3f94.dat
Thread 0 opened the file: /tmp/tmprt3848zx/files/1/f/a/dataset_1fae1fad-6c83-48b9-aa58-8d63340b3f94.dat
Thread 0 processing bam 0: dataset_1fae1fad-6c83-48b9-aa58-8d63340b3f94.dat
Thread 0 finished reading bam 0: dataset_1fae1fad-6c83-48b9-aa58-8d63340b3f94.dat
Thread 0 finished: dataset_1fae1fad-6c83-48b9-aa58-8d63340b3f94.dat with 18924 reads and 8473 readsWellMapped (44.7738%)
Creating depth matrix file: /tmp/tmprt3848zx/job_working_directory/000/17/outputs/dataset_3198f2d6-2daa-413f-bf6a-3a1554beb9b3.dat
Closing last bam file
Finished

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"input"`
__workflow_invocation_uuid__	`"85d8fbb215e611f0aeac6045bd812dcf"`
advanced	`{"includeEdgeBases": false, "maxEdgeBases": "75", "minMapQual": "0", "noIntraDepthVariance": false, "output_paired_contigs": false, "percentIdentity": "97", "showDepth": false, "weightMapQual": "0.0"}`
bam_indiv_input	__identifier__
chromInfo	`"/tmp/tmprt3848zx/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
dbkey	`"?"`
mode	`{"__current_case__": 0, "bam_indiv_input": {"values": [{"id": 20, "src": "dce"}]}, "type": "individual", "use_reference_cond": {"__current_case__": 0, "use_reference": "no"}}`
shredding	`{"minContigDepth": "0.0", "minContigLength": "1", "shredDepth": "5", "shredLength": "16000"}`

Step 34: toolshed.g2.bx.psu.edu/repos/iuc/fasta_to_contig2bin/Fasta_to_Contig2Bin/1.1.7+galaxy1:

step_state: scheduled

Jobs

Job 1:

Job state is ok

Command Line:

mkdir "inputs" && ln -s '/tmp/tmprt3848zx/files/2/4/a/dataset_24ae73b9-a6e2-4215-ba32-22c1d46c6a5c.dat' 'inputs/SemiBin_0.fasta' && Fasta_to_Contig2Bin.sh --extension fasta --input_folder 'inputs' > '/tmp/tmprt3848zx/job_working_directory/000/25/outputs/dataset_33341154-822d-4123-8d83-f89e1bf8fb3a.dat'

Exit Code:

```
0
```

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"input"`
__workflow_invocation_uuid__	`"85d8fbb215e611f0aeac6045bd812dcf"`
chromInfo	`"/tmp/tmprt3848zx/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
dbkey	`"?"`
inputs	`{"values": [{"id": 21, "src": "dce"}]}`

Step 35: toolshed.g2.bx.psu.edu/repos/iuc/concoct/concoct/1.1.0+galaxy2:

step_state: scheduled

Jobs

Job 1:

Job state is ok

Command Line:

ln -s '/tmp/tmprt3848zx/files/4/2/7/dataset_427437bc-34ba-411c-8993-eeae950b0e46.dat' 'composition_file.fa' &&  mkdir outdir && concoct --coverage_file '/tmp/tmprt3848zx/files/f/8/7/dataset_f877af85-c3a7-4d9c-88d4-79864a47077b.dat' --composition_file 'composition_file.fa' --clusters 400 --kmer_length 4 --threads ${GALAXY_SLOTS:-4} --length_threshold 1000 --read_length 100 --total_percentage_pca 90 --basename 'outdir/' --seed 1 --iterations 500   --no_original_data

Exit Code:

```
0
```

Standard Error:

WARNING:root:CONCOCT is running in single threaded mode. Please, consider adjusting the --threads parameter.
Up and running. Check /tmp/tmprt3848zx/job_working_directory/000/18/working/outdir/log.txt for progress
Setting 1 OMP threads
Generate input data
0,-32769.159419,695.861881
1,-23702.908064,9066.251354
2,-10301.271601,13401.636463
3,-9099.561931,1201.709670
4,-8491.920398,607.641533
5,-8491.793887,0.126512
6,-8491.793444,0.000443
7,-8491.793370,0.000074

Standard Output:

```
59 2 1
```

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"input"`
__workflow_invocation_uuid__	`"85d8fbb215e611f0aeac6045bd812dcf"`
advanced	`{"clusters": "400", "iterations": "500", "kmer_length": "4", "length_threshold": "1000", "no_cov_normalization": false, "read_length": "100", "seed": "1", "total_percentage_pca": "90"}`
chromInfo	`"/tmp/tmprt3848zx/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
dbkey	`"?"`
output	`{"converge_out": false, "log": false, "no_total_coverage": false}`

Step 36: toolshed.g2.bx.psu.edu/repos/mbernt/maxbin2/maxbin2/2.2.7+galaxy6:

step_state: scheduled

Jobs

Job 1:

Job state is ok

Command Line:

echo '/tmp/tmprt3848zx/files/3/1/9/dataset_3198f2d6-2daa-413f-bf6a-3a1554beb9b3.dat' >> abund_list &&   run_MaxBin.pl -contig '/tmp/tmprt3848zx/files/f/5/6/dataset_f56caa53-2f68-4615-b2bf-37274711c329.dat' -out out -abund_list abund_list -min_contig_length 1000 -max_iteration 50 -prob_threshold 0.5 -plotmarker -markerset 107 -thread ${GALAXY_SLOTS:-1}  && gzip -cd out.marker_of_each_bin.tar.gz | tar -xf -

Exit Code:

```
0
```

Standard Error:

Attaching package: ‘gplots’

The following object is masked from ‘package:stats’:

    lowess

Standard Output:

MaxBin 2.2.7
Input contig: /tmp/tmprt3848zx/files/f/5/6/dataset_f56caa53-2f68-4615-b2bf-37274711c329.dat
out header: out
Min contig length: 1000
Max iteration: 50
Probability threshold: 0.5
Thread: 1
Located abundance file [/tmp/tmprt3848zx/files/3/1/9/dataset_3198f2d6-2daa-413f-bf6a-3a1554beb9b3.dat]
Searching against 107 marker genes to find starting seed contigs for [/tmp/tmprt3848zx/files/f/5/6/dataset_f56caa53-2f68-4615-b2bf-37274711c329.dat]...
Running FragGeneScan....
Running HMMER hmmsearch....
Try harder to dig out marker genes from contigs.
Done data collection. Running MaxBin...
Command: /usr/local/opt/MaxBin-2.2.7/src/MaxBin -fasta out.contig.tmp  -abund out.contig.tmp.abund1 -seed out.seed -out out -min_contig_length 1000 -max_run 50 -prob_threshold 0.5 
Minimum contig length set to 1000.
Reading seed list...
Looking for seeds in sequences.
	k141_52 [11001.000000]
	k141_59 [9465.000000]
Get 2 seeds.

Start EM process.
Iteration 1
Iteration 2
Iteration 3
Iteration 4
Iteration 5
Iteration 6
Iteration 7
Iteration 8
Iteration 9
Iteration 10
Iteration 11
Iteration 12
Iteration 13

EM finishes successfully.

Classifying sequences based on the EM result.
Minimum probability for binning: 0.50
Ignoring 0 bins without any sequences.
Number of unclassified sequences: 0 (0.00%)
Elapsed time:  0 days 00:00:00

Rscript /usr/local/opt/MaxBin-2.2.7/heatmap.r out.marker out.marker.pdf
null device 
          1 
out.001.marker.fasta
out.002.marker.fasta
Deleting intermediate files.


========== Job finished ==========
Yielded 2 bins for contig (scaffold) file /tmp/tmprt3848zx/files/f/5/6/dataset_f56caa53-2f68-4615-b2bf-37274711c329.dat

Here are the output files for this run.
Please refer to the README file for further details.

Summary file: out.summary
Marker counts: out.marker
Marker genes for each bin: out.marker_of_each_gene.tar.gz
Bin files: out.001.fasta - out.002.fasta
Unbinned sequences: out.noclass
Marker plot: out.marker.pdf


========== Elapsed Time ==========
0 hours 0 minutes and 2 seconds.

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"expression.json"`
__workflow_invocation_uuid__	`"85d8fbb215e611f0aeac6045bd812dcf"`
adv	`{"max_iteration": "50", "min_contig_length": "1000", "prob_threshold": "0.5"}`
assembly	`{"__current_case__": 0, "inputs": {"__current_case__": 1, "abund": {"values": [{"id": 27, "src": "dce"}]}, "type": "abund"}, "type": "individual"}`
chromInfo	`"/tmp/tmprt3848zx/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
dbkey	`"?"`
output	`{"log": true, "marker": true, "markers": true, "markerset": "107", "plotmarker": true}`

Step 37: toolshed.g2.bx.psu.edu/repos/iuc/metabat2/metabat2/2.17+galaxy0:

step_state: scheduled

Jobs

Job 1:

Job state is ok

Command Line:

mkdir bins && metabat2 --inFile '/tmp/tmprt3848zx/files/f/5/6/dataset_f56caa53-2f68-4615-b2bf-37274711c329.dat' --outFile 'bins/bin' --abdFile '/tmp/tmprt3848zx/files/3/1/9/dataset_3198f2d6-2daa-413f-bf6a-3a1554beb9b3.dat' --minContig 1500 --maxP 95 --minS 60 --maxEdges 200 --pTNF 0  --minCV 1.0 --minCVSum 1.0 --seed 0 --minClsSize 200000 --numThreads ${GALAXY_SLOTS:-4}  --unbinned > process_log.txt && mv process_log.txt '/tmp/tmprt3848zx/job_working_directory/000/20/outputs/dataset_ede1a3a6-a682-4d2c-a77a-07e30a56298a.dat'

Exit Code:

```
0
```

Standard Error:

[Warning!] Negative coverage depth is not allowed for the contig k141_0, column 1: -4.29775e+08
[Warning!] Negative coverage depth is not allowed for the contig k141_52, column 1: -2.76243e+08

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"input"`
__workflow_invocation_uuid__	`"85d8fbb215e611f0aeac6045bd812dcf"`
advanced	`{"base_coverage_depth_cond": {"__current_case__": 1, "abdFile": {"values": [{"id": 27, "src": "dce"}]}, "base_coverage_depth": "yes", "cvExt": null}, "maxEdges": "200", "maxP": "95", "minCV": "1.0", "minCVSum": "1.0", "minContig": "1500", "minS": "60", "noAdd": false, "pTNF": "0", "seed": "0"}`
advanced	abdFile
chromInfo	`"/tmp/tmprt3848zx/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
dbkey	`"?"`
inFile	__identifier__
out	`{"extra_outputs": ["lowDepth", "tooShort", "unbinned", "log"], "minClsSize": "200000", "onlyLabel": false, "saveCls": false}`

Step 38: toolshed.g2.bx.psu.edu/repos/iuc/concoct_merge_cut_up_clustering/concoct_merge_cut_up_clustering/1.1.0+galaxy2:

step_state: scheduled

Jobs

Job 1:

Job state is ok

Command Line:

merge_cutup_clustering.py '/tmp/tmprt3848zx/files/1/b/7/dataset_1b7ea032-d4d3-4b32-a09c-a9aa6ebe12b6.dat' > '/tmp/tmprt3848zx/job_working_directory/000/21/outputs/dataset_677e6137-b807-4266-8f7b-2aa00c797357.dat'

Exit Code:

```
0
```

Standard Error:

/usr/local/bin/merge_cutup_clustering.py:17: SyntaxWarning: invalid escape sequence '\.'
  CONTIG_PART_EXPR = re.compile("(.*)\.concoct_part_([0-9]*)")

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"input"`
__workflow_invocation_uuid__	`"85d8fbb215e611f0aeac6045bd812dcf"`
chromInfo	`"/tmp/tmprt3848zx/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
cutup_clustering_result	__identifier__
dbkey	`"?"`

Step 39: toolshed.g2.bx.psu.edu/repos/iuc/fasta_to_contig2bin/Fasta_to_Contig2Bin/1.1.7+galaxy1:

step_state: scheduled

Jobs

Job 1:

Job state is ok

Command Line:

mkdir "inputs" && ln -s '/tmp/tmprt3848zx/files/1/6/4/dataset_164be511-eaa9-4351-b89f-feb62eacc7f5.dat' 'inputs/001.fasta' && ln -s '/tmp/tmprt3848zx/files/f/5/4/dataset_f543dbfc-9c42-4276-9405-72ced6811ba8.dat' 'inputs/002.fasta' && Fasta_to_Contig2Bin.sh --extension fasta --input_folder 'inputs' > '/tmp/tmprt3848zx/job_working_directory/000/26/outputs/dataset_5da7aadc-0962-455f-bfb4-5908a4e8a0f0.dat'

Exit Code:

```
0
```

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"input"`
__workflow_invocation_uuid__	`"85d8fbb215e611f0aeac6045bd812dcf"`
chromInfo	`"/tmp/tmprt3848zx/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
dbkey	`"?"`
inputs	`{"values": [{"id": 31, "src": "dce"}]}`

Step 40: toolshed.g2.bx.psu.edu/repos/iuc/fasta_to_contig2bin/Fasta_to_Contig2Bin/1.1.7+galaxy1:

step_state: scheduled

Jobs

Job 1:

Job state is ok

Command Line:

mkdir "inputs" && ln -s '/tmp/tmprt3848zx/files/f/8/6/dataset_f86d9845-cf35-4942-ae22-95a6f068a815.dat' 'inputs/1.fasta' && Fasta_to_Contig2Bin.sh --extension fasta --input_folder 'inputs' > '/tmp/tmprt3848zx/job_working_directory/000/23/outputs/dataset_302b8401-c545-40d3-aceb-1262496fd528.dat'

Exit Code:

```
0
```

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"input"`
__workflow_invocation_uuid__	`"85d8fbb215e611f0aeac6045bd812dcf"`
chromInfo	`"/tmp/tmprt3848zx/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
dbkey	`"?"`
inputs	`{"values": [{"id": 39, "src": "dce"}]}`

Step 5: Environment for the built-in model (SemiBin):
- step_state: scheduled

Step 41: toolshed.g2.bx.psu.edu/repos/iuc/concoct_extract_fasta_bins/concoct_extract_fasta_bins/1.1.0+galaxy2:

step_state: scheduled

Jobs

Job 1:

Job state is ok

Command Line:

ln -s '/tmp/tmprt3848zx/files/f/5/6/dataset_f56caa53-2f68-4615-b2bf-37274711c329.dat' 'contigs.fa' &&  mkdir outdir && extract_fasta_bins.py 'contigs.fa' '/tmp/tmprt3848zx/files/6/7/7/dataset_677e6137-b807-4266-8f7b-2aa00c797357.dat' --output_path 'outdir'

Exit Code:

```
0
```

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"input"`
__workflow_invocation_uuid__	`"85d8fbb215e611f0aeac6045bd812dcf"`
chromInfo	`"/tmp/tmprt3848zx/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
cluster_file	__identifier__
dbkey	`"?"`
fasta_file	__identifier__

Step 42: toolshed.g2.bx.psu.edu/repos/iuc/fasta_to_contig2bin/Fasta_to_Contig2Bin/1.1.7+galaxy1:

step_state: scheduled

Jobs

Job 1:

Job state is ok

Command Line:

mkdir "inputs" && ln -s '/tmp/tmprt3848zx/files/3/1/4/dataset_314bdaf1-b95e-40d0-8ff7-d09cc1ab0793.dat' 'inputs/0.fasta' && ln -s '/tmp/tmprt3848zx/files/2/1/d/dataset_21df73a8-fc29-40e2-8ff4-da12c5d13ea4.dat' 'inputs/1.fasta' && ln -s '/tmp/tmprt3848zx/files/4/c/a/dataset_4caf8293-abf4-4dea-826e-3456cd193f14.dat' 'inputs/10.fasta' && ln -s '/tmp/tmprt3848zx/files/4/9/a/dataset_49a3d93e-a661-4853-ac27-158e5def016b.dat' 'inputs/11.fasta' && ln -s '/tmp/tmprt3848zx/files/c/4/4/dataset_c448867b-4378-414d-a567-c3bc9ce92ec8.dat' 'inputs/2.fasta' && ln -s '/tmp/tmprt3848zx/files/4/4/8/dataset_448f29ba-fac2-4c91-8b77-b0fa7f667fe8.dat' 'inputs/3.fasta' && ln -s '/tmp/tmprt3848zx/files/b/d/e/dataset_bdea65e3-9a7f-41a2-8e67-76c08002b02b.dat' 'inputs/4.fasta' && ln -s '/tmp/tmprt3848zx/files/e/6/c/dataset_e6c2a8f5-e49e-4819-b87a-637d5f3b6601.dat' 'inputs/5.fasta' && ln -s '/tmp/tmprt3848zx/files/b/6/9/dataset_b69606cf-206b-4ca3-999d-d83684ea9167.dat' 'inputs/6.fasta' && ln -s '/tmp/tmprt3848zx/files/f/6/a/dataset_f6aa9197-ba99-469e-997c-e37c974070af.dat' 'inputs/7.fasta' && ln -s '/tmp/tmprt3848zx/files/2/c/e/dataset_2cebedbf-9505-4fc3-83eb-48c44d1d1ad8.dat' 'inputs/8.fasta' && ln -s '/tmp/tmprt3848zx/files/8/5/8/dataset_8582530d-fef6-4058-9948-b1e6dfb59a59.dat' 'inputs/9.fasta' && Fasta_to_Contig2Bin.sh --extension fasta --input_folder 'inputs' > '/tmp/tmprt3848zx/job_working_directory/000/24/outputs/dataset_1a7ce1c7-d94e-4625-a07e-f7b220055362.dat'

Exit Code:

```
0
```

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"input"`
__workflow_invocation_uuid__	`"85d8fbb215e611f0aeac6045bd812dcf"`
chromInfo	`"/tmp/tmprt3848zx/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
dbkey	`"?"`
inputs	`{"values": [{"id": 45, "src": "dce"}]}`

Step 43: __BUILD_LIST__:

step_state: scheduled

Jobs

Job 1:

Job state is ok

Traceback:

Job Parameters:

Job parameter	Parameter value
__workflow_invocation_uuid__	`"85d8fbb215e611f0aeac6045bd812dcf"`
datasets	`[{"__index__": 0, "id_cond": {"__current_case__": 0, "id_select": "idx"}, "input": {"values": [{"id": 57, "src": "hda"}]}}, {"__index__": 1, "id_cond": {"__current_case__": 0, "id_select": "idx"}, "input": {"values": [{"id": 44, "src": "hda"}]}}, {"__index__": 2, "id_cond": {"__current_case__": 0, "id_select": "idx"}, "input": {"values": [{"id": 64, "src": "hda"}]}}, {"__index__": 3, "id_cond": {"__current_case__": 0, "id_select": "idx"}, "input": {"values": [{"id": 59, "src": "hda"}]}}]`

Step 44: toolshed.g2.bx.psu.edu/repos/iuc/binette/binette/1.0.5+galaxy1:

step_state: scheduled

Jobs

Job 1:

Job state is ok

Command Line:

mkdir -p 'input' 'output' &&  ln -s '/tmp/tmprt3848zx/files/1/a/7/dataset_1a7ce1c7-d94e-4625-a07e-f7b220055362.dat' 'input/bin_table_0.tsv' && ln -s '/tmp/tmprt3848zx/files/3/0/2/dataset_302b8401-c545-40d3-aceb-1262496fd528.dat' 'input/bin_table_1.tsv' && ln -s '/tmp/tmprt3848zx/files/5/d/a/dataset_5da7aadc-0962-455f-bfb4-5908a4e8a0f0.dat' 'input/bin_table_2.tsv' && ln -s '/tmp/tmprt3848zx/files/3/3/3/dataset_33341154-822d-4123-8d83-f89e1bf8fb3a.dat' 'input/bin_table_3.tsv' &&  ln -s '/tmp/tmprt3848zx/files/f/5/6/dataset_f56caa53-2f68-4615-b2bf-37274711c329.dat' 'input_contigs.fasta' &&   binette -b input/*.tsv -c 'input_contigs.fasta' -m 1 -t "${GALAXY_SLOTS:-1}" -o 'output/' -w 2 --checkm2_db '/cvmfs/data.galaxyproject.org/byhand/checkm2/1.0.2/uniref100.KO.1.dmnd'

Exit Code:

```
0
```

Standard Error:

  0%|          | 0/59 [00:00<?, ?it/s]
100%|██████████| 59/59 [00:00<00:00, 6901.41it/s]

  0%|          | 0/59 [00:00<?, ?contig/s]
100%|██████████| 59/59 [00:00<00:00, 480512.50contig/s]

  0%|          | 0/59 [00:00<?, ?contig/s]
100%|██████████| 59/59 [00:00<00:00, 642763.47contig/s]

  0%|          | 0/16 [00:00<?, ?bin/s]
100%|██████████| 16/16 [00:05<00:00,  2.86bin/s]
100%|██████████| 16/16 [00:05<00:00,  2.86bin/s]

  0%|          | 0/17 [00:00<?, ?bin/s]
100%|██████████| 17/17 [00:05<00:00,  3.32bin/s]
100%|██████████| 17/17 [00:05<00:00,  3.32bin/s]

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"input"`
__workflow_invocation_uuid__	`"85d8fbb215e611f0aeac6045bd812dcf"`
chromInfo	`"/tmp/tmprt3848zx/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
contamination_weight	`"2"`
database_type	`{"__current_case__": 1, "datamanager": "1.0.2", "is_select": "cached"}`
dbkey	`"?"`
min_completeness	`"1"`
proteins	`None`

Step 45: Pool Bins from all samples:
- step_state: scheduled
- Jobs
  - Job 1:
    - Job state is ok
    Traceback:
    Job Parameters:
    - Job parameter Parameter value
      
      __workflow_invocation_uuid__ "85d8fbb215e611f0aeac6045bd812dcf"
      
      input {"values": [{"id": 47, "src": "hdca"}]}
      
      join_identifier "_"

Step 46: toolshed.g2.bx.psu.edu/repos/iuc/checkm2/checkm2/1.0.2+galaxy0:

step_state: scheduled

Jobs

Job 1:

Job state is ok

Command Line:

mkdir input_dir && ln -s '/tmp/tmprt3848zx/files/4/c/f/dataset_4cfbc079-cb1c-45ca-a7ab-897e176ae1b8.dat' 'input_dir/50contig_reads_bin_1.dat' && ln -s '/tmp/tmprt3848zx/files/6/5/b/dataset_65b0aee2-328e-4732-9548-cf1b70171ccd.dat' 'input_dir/50contig_reads_bin_11.dat' && ln -s '/tmp/tmprt3848zx/files/a/e/d/dataset_aed6f725-4bfb-4b47-b195-8508696a7273.dat' 'input_dir/50contig_reads_bin_55.dat' && ln -s '/tmp/tmprt3848zx/files/3/a/a/dataset_3aa28516-c26d-4559-a20e-4d3fe42881b2.dat' 'input_dir/50contig_reads_bin_6.dat' && checkm2 predict --input input_dir   -x .dat --threads "${GALAXY_SLOTS:-1}" --database_path '/cvmfs/data.galaxyproject.org/byhand/checkm2/1.0.2/uniref100.KO.1.dmnd' --output-directory output

Exit Code:

```
0
```

Standard Error:

[04/10/2025 09:08:48 AM] INFO: Running CheckM2 version 1.0.2
[04/10/2025 09:08:48 AM] INFO: Custom database path provided for predict run. Checking database at /cvmfs/data.galaxyproject.org/byhand/checkm2/1.0.2/uniref100.KO.1.dmnd...
[04/10/2025 09:08:51 AM] INFO: Running quality prediction workflow with 1 threads.
[04/10/2025 09:08:52 AM] INFO: Calling genes in 4 bins with 1 threads:
[04/10/2025 09:08:53 AM] INFO: Calculating metadata for 4 bins with 1 threads:
[04/10/2025 09:08:54 AM] INFO: Annotating input genomes with DIAMOND using 1 threads
[04/10/2025 09:11:41 AM] INFO: Processing DIAMOND output
[04/10/2025 09:11:41 AM] INFO: Predicting completeness and contamination using ML models.
[04/10/2025 09:11:46 AM] INFO: Parsing all results and constructing final output table.
[04/10/2025 09:11:46 AM] INFO: CheckM2 finished successfully.

Standard Output:

    Finished processing 1 of 4 (25.00%) bins.
    Finished processing 2 of 4 (50.00%) bins.
    Finished processing 3 of 4 (75.00%) bins.
    Finished processing 4 of 4 (100.00%) bins.

    Finished processing 1 of 4 (25.00%) bin metadata.
    Finished processing 2 of 4 (50.00%) bin metadata.
    Finished processing 3 of 4 (75.00%) bin metadata.
    Finished processing 4 of 4 (100.00%) bin metadata.

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"input"`
__workflow_invocation_uuid__	`"85d8fbb215e611f0aeac6045bd812dcf"`
chromInfo	`"/tmp/tmprt3848zx/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
database	`"1.0.2"`
dbkey	`"?"`
genes	`false`
model	`""`
ttable	`None`

Step 47: toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_awk_tool/9.5+galaxy0:

step_state: scheduled

Jobs

Job 1:

Job state is ok

Command Line:

env -i $(which awk) --sandbox -v FS='	' -v OFS='	' --re-interval -f '/tmp/tmprt3848zx/job_working_directory/000/31/configs/tmpnuov_1au' '/tmp/tmprt3848zx/files/a/b/5/dataset_ab51551c-8980-4f68-ab5a-4bcc2c784137.dat' > '/tmp/tmprt3848zx/job_working_directory/000/31/outputs/dataset_1a3ce119-f7e9-43e9-bc99-3ba438a89007.dat'

Exit Code:

```
0
```

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"input"`
__workflow_invocation_uuid__	`"85d8fbb215e611f0aeac6045bd812dcf"`
chromInfo	`"/tmp/tmprt3848zx/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
code	`"BEGIN {OFS=\"\\t\"; print \"genome\\tcompleteness\\tcontamination\"} \nNR > 1 {\n if ($1 !~ /\\.fasta$/) \n $1 = $1 \".fasta\"\n print $1, $2, $3\n}"`
dbkey	`"?"`

Step 48: toolshed.g2.bx.psu.edu/repos/iuc/drep_dereplicate/drep_dereplicate/3.5.0+galaxy1:

step_state: scheduled

Jobs

Job 1:

Job state is ok

Command Line:

ln -s '/tmp/tmprt3848zx/files/4/c/f/dataset_4cfbc079-cb1c-45ca-a7ab-897e176ae1b8.dat' '50contig_reads_bin_1.fasta' &&  ln -s '/tmp/tmprt3848zx/files/6/5/b/dataset_65b0aee2-328e-4732-9548-cf1b70171ccd.dat' '50contig_reads_bin_11.fasta' &&  ln -s '/tmp/tmprt3848zx/files/a/e/d/dataset_aed6f725-4bfb-4b47-b195-8508696a7273.dat' '50contig_reads_bin_55.fasta' &&  ln -s '/tmp/tmprt3848zx/files/3/a/a/dataset_3aa28516-c26d-4559-a20e-4d3fe42881b2.dat' '50contig_reads_bin_6.fasta' &&   dRep dereplicate outdir  -g '50contig_reads_bin_1.fasta' '50contig_reads_bin_11.fasta' '50contig_reads_bin_55.fasta' '50contig_reads_bin_6.fasta'   --length 100 --completeness 1 --contamination 25   --genomeInfo '/tmp/tmprt3848zx/files/0/1/b/dataset_01b21884-f9f9-4dcf-a383-bd609688ef98.dat'    --MASH_sketch '1000' --P_ani 0.9  --primary_chunksize 5000   --S_algorithm 'ANImf'  --n_PRESET 'normal'   --coverage_method 'larger'  --S_ani 0.95 --cov_thresh 0.1  --clusterAlg 'average'    --completeness_weight 1.0 --contamination_weight 5.0 --strain_heterogeneity_weight 1.0 --N50_weight 0.5 --size_weight 0.0 --centrality_weight 1.0    --warn_dist 0.25 --warn_sim 0.98 --warn_aln 0.25  --debug || (rc=$?; ls -ltr `find outdir -type f`; cat outdir/data/checkM/checkM_outdir/checkm.log; cat outdir/log/logger.log; exit $rc)

Exit Code:

```
0
```

Standard Error:

***************************************************
    ..:: dRep dereplicate Step 1. Filter ::..
***************************************************
    
Will filter the genome list
4 genomes were input to dRep
Calculating genome info of genomes
100.00% of genomes passed length filtering
100.00% of genomes passed checkM filtering
***************************************************
    ..:: dRep dereplicate Step 2. Cluster ::..
***************************************************
    
Running primary clustering
Running pair-wise MASH clustering
4 primary clusters made
Running secondary clustering
Running 4 ANImf comparisons- should take ~ 0.3 min
Step 4. Return output
***************************************************
    ..:: dRep dereplicate Step 3. Choose ::..
***************************************************
    
Loading work directory
***************************************************
    ..:: dRep dereplicate Step 4. Evaluate ::..
***************************************************
    
will produce Widb (winner information db)
Winner database saved to /tmp/tmprt3848zx/job_working_directory/000/33/working/outdirdata_tables/Widb.csv
***************************************************
    ..:: dRep dereplicate Step 5. Analyze ::..
***************************************************
    
making plots 1, 2, 3, 4, 5, 6
Plotting primary dendrogram
Plotting secondary dendrograms
Plotting MDS plot
Plotting scatterplots
Plotting bin scorring plot
Plotting winning genomes plot...

$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$

    ..:: dRep dereplicate finished ::..

Dereplicated genomes................. /tmp/tmprt3848zx/job_working_directory/000/33/working/outdir/dereplicated_genomes/
Dereplicated genomes information..... /tmp/tmprt3848zx/job_working_directory/000/33/working/outdir/data_tables/Widb.csv
Figures.............................. /tmp/tmprt3848zx/job_working_directory/000/33/working/outdir/figures/
Warnings............................. /tmp/tmprt3848zx/job_working_directory/000/33/working/outdir/log/warnings.txt

$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"input"`
__workflow_invocation_uuid__	`"85d8fbb215e611f0aeac6045bd812dcf"`
chromInfo	`"/tmp/tmprt3848zx/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
comp_clust	`{"clusterAlg": "average", "run_tertiary_clustering": false, "steps": {"MASH_sketch": "1000", "P_ani": "0.9", "S_ani": "0.95", "__current_case__": 0, "clustering": {"S_algorithm": "ANImf", "__current_case__": 1, "coverage_method": "larger", "n_PRESET": "normal"}, "cov_thresh": "0.1", "multiround_primary_clustering": false, "primary_chunksize": "5000", "select": "default"}}`
dbkey	`"?"`
filter	`{"completeness": "1", "contamination": "25", "length": "100"}`
quality	`{"__current_case__": 1, "genomeInfo": {"values": [{"id": 84, "src": "hda"}]}, "source": "genomeInfo"}`
scoring	`{"N50_weight": "0.5", "centrality_weight": "1.0", "completeness_weight": "1.0", "contamination_weight": "5.0", "extra_weight_table": null, "size_weight": "0.0", "strain_heterogeneity_weight": "1.0"}`
select_outputs	`["log", "warnings", "Primary_clustering_dendrogram", "Clustering_scatterplots", "Widb", "Chdb"]`
warning	`{"warn_aln": "0.25", "warn_dist": "0.25", "warn_sim": "0.98"}`

Step 49: toolshed.g2.bx.psu.edu/repos/iuc/gtdbtk_classify_wf/gtdbtk_classify_wf/2.4.0+galaxy0:

step_state: scheduled

Jobs

Job 1:

Job state is skipped

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"input"`
__workflow_invocation_uuid__	`"85d8fbb215e611f0aeac6045bd812dcf"`
advanced	`{"force": false, "min_af": "0.65", "min_perc_aa": "10", "output_process_log": false}`
chromInfo	`"/tmp/tmprt3848zx/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
dbkey	`"?"`
gtdbtk_db	`"full_database_release_220_downloaded_2024-10-19"`

Step 50: toolshed.g2.bx.psu.edu/repos/iuc/checkm2/checkm2/1.0.2+galaxy0:

step_state: scheduled

Jobs

Job 1:

Job state is ok

Command Line:

mkdir input_dir && ln -s '/tmp/tmprt3848zx/files/5/b/7/dataset_5b725d9e-0214-472e-ac90-3302b11af51c.dat' 'input_dir/50contig_reads_bin_1.fasta.dat' && ln -s '/tmp/tmprt3848zx/files/8/0/9/dataset_809ece5c-f028-4d72-913f-60ccd0f9b71a.dat' 'input_dir/50contig_reads_bin_11.fasta.dat' && ln -s '/tmp/tmprt3848zx/files/f/0/c/dataset_f0c33f60-365a-44bf-b5ad-f1584230167d.dat' 'input_dir/50contig_reads_bin_55.fasta.dat' && ln -s '/tmp/tmprt3848zx/files/f/b/e/dataset_fbe5c0d6-af8a-4e6d-b0ca-46c3391bda82.dat' 'input_dir/50contig_reads_bin_6.fasta.dat' && checkm2 predict --input input_dir   -x .dat --threads "${GALAXY_SLOTS:-1}" --database_path '/cvmfs/data.galaxyproject.org/byhand/checkm2/1.0.2/uniref100.KO.1.dmnd' --output-directory output

Exit Code:

```
0
```

Standard Error:

[04/10/2025 09:13:19 AM] INFO: Running CheckM2 version 1.0.2
[04/10/2025 09:13:19 AM] INFO: Custom database path provided for predict run. Checking database at /cvmfs/data.galaxyproject.org/byhand/checkm2/1.0.2/uniref100.KO.1.dmnd...
[04/10/2025 09:13:25 AM] INFO: Running quality prediction workflow with 1 threads.
[04/10/2025 09:13:26 AM] INFO: Calling genes in 4 bins with 1 threads:
[04/10/2025 09:13:28 AM] INFO: Calculating metadata for 4 bins with 1 threads:
[04/10/2025 09:13:28 AM] INFO: Annotating input genomes with DIAMOND using 1 threads
[04/10/2025 09:16:14 AM] INFO: Processing DIAMOND output
[04/10/2025 09:16:14 AM] INFO: Predicting completeness and contamination using ML models.
[04/10/2025 09:16:19 AM] INFO: Parsing all results and constructing final output table.
[04/10/2025 09:16:19 AM] INFO: CheckM2 finished successfully.

Standard Output:

    Finished processing 1 of 4 (25.00%) bins.
    Finished processing 2 of 4 (50.00%) bins.
    Finished processing 3 of 4 (75.00%) bins.
    Finished processing 4 of 4 (100.00%) bins.

    Finished processing 1 of 4 (25.00%) bin metadata.
    Finished processing 2 of 4 (50.00%) bin metadata.
    Finished processing 3 of 4 (75.00%) bin metadata.
    Finished processing 4 of 4 (100.00%) bin metadata.

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"input"`
__workflow_invocation_uuid__	`"85d8fbb215e611f0aeac6045bd812dcf"`
chromInfo	`"/tmp/tmprt3848zx/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
database	`"1.0.2"`
dbkey	`"?"`
genes	`false`
model	`""`
ttable	`None`

Step 6: Trimmed grouped paired reads:
- step_state: scheduled

Step 51: toolshed.g2.bx.psu.edu/repos/iuc/checkm_lineage_wf/checkm_lineage_wf/1.2.3+galaxy0:

step_state: scheduled

Jobs

Job 1:

Job state is ok

Command Line:

mkdir 'bins' && ln -s '/tmp/tmprt3848zx/files/5/b/7/dataset_5b725d9e-0214-472e-ac90-3302b11af51c.dat' 'bins/50contig_reads_bin_1.fasta.fasta' && ln -s '/tmp/tmprt3848zx/files/8/0/9/dataset_809ece5c-f028-4d72-913f-60ccd0f9b71a.dat' 'bins/50contig_reads_bin_11.fasta.fasta' && ln -s '/tmp/tmprt3848zx/files/f/0/c/dataset_f0c33f60-365a-44bf-b5ad-f1584230167d.dat' 'bins/50contig_reads_bin_55.fasta.fasta' && ln -s '/tmp/tmprt3848zx/files/f/b/e/dataset_fbe5c0d6-af8a-4e6d-b0ca-46c3391bda82.dat' 'bins/50contig_reads_bin_6.fasta.fasta' &&   checkm lineage_wf 'bins' 'output'     --unique '10' --multi '10'      --aai_strain 0.9  --e_value 1e-10 --length 0.7 --file '/tmp/tmprt3848zx/job_working_directory/000/36/outputs/dataset_182937f4-c241-4988-bec9-8fb0fcac2d91.dat' --tab_table --extension 'fasta' --threads ${GALAXY_SLOTS:-1} --pplacer_threads ${GALAXY_SLOTS:-1}

Exit Code:

```
0
```

Standard Error:

    Finished processing 0 of 4 (0.00%) bins.
    Finished processing 1 of 4 (25.00%) bins.
    Finished processing 2 of 4 (50.00%) bins.
    Finished processing 3 of 4 (75.00%) bins.
    Finished processing 4 of 4 (100.00%) bins.
    Finished processing 0 of 4 (0.00%) bins.
    Finished processing 1 of 4 (25.00%) bins.
    Finished processing 2 of 4 (50.00%) bins.
    Finished processing 3 of 4 (75.00%) bins.
    Finished processing 4 of 4 (100.00%) bins.
    Finished parsing hits for 1 of 4 (25.00%) bins.
    Finished parsing hits for 2 of 4 (50.00%) bins.
    Finished parsing hits for 3 of 4 (75.00%) bins.
    Finished parsing hits for 4 of 4 (100.00%) bins.
    Finished extracting 0 of 43 (0.00%) HMMs.
    Finished extracting 1 of 43 (2.33%) HMMs.
    Finished extracting 2 of 43 (4.65%) HMMs.
    Finished extracting 3 of 43 (6.98%) HMMs.
    Finished extracting 4 of 43 (9.30%) HMMs.
    Finished extracting 5 of 43 (11.63%) HMMs.
    Finished extracting 6 of 43 (13.95%) HMMs.
    Finished extracting 7 of 43 (16.28%) HMMs.
    Finished extracting 8 of 43 (18.60%) HMMs.
    Finished extracting 9 of 43 (20.93%) HMMs.
    Finished extracting 10 of 43 (23.26%) HMMs.
    Finished extracting 11 of 43 (25.58%) HMMs.
    Finished extracting 12 of 43 (27.91%) HMMs.
    Finished extracting 13 of 43 (30.23%) HMMs.
    Finished extracting 14 of 43 (32.56%) HMMs.
    Finished extracting 15 of 43 (34.88%) HMMs.
    Finished extracting 16 of 43 (37.21%) HMMs.
    Finished extracting 17 of 43 (39.53%) HMMs.
    Finished extracting 18 of 43 (41.86%) HMMs.
    Finished extracting 19 of 43 (44.19%) HMMs.
    Finished extracting 20 of 43 (46.51%) HMMs.
    Finished extracting 21 of 43 (48.84%) HMMs.
    Finished extracting 22 of 43 (51.16%) HMMs.
    Finished extracting 23 of 43 (53.49%) HMMs.
    Finished extracting 24 of 43 (55.81%) HMMs.
    Finished extracting 25 of 43 (58.14%) HMMs.
    Finished extracting 26 of 43 (60.47%) HMMs.
    Finished extracting 27 of 43 (62.79%) HMMs.
    Finished extracting 28 of 43 (65.12%) HMMs.
    Finished extracting 29 of 43 (67.44%) HMMs.
    Finished extracting 30 of 43 (69.77%) HMMs.
    Finished extracting 31 of 43 (72.09%) HMMs.
    Finished extracting 32 of 43 (74.42%) HMMs.
    Finished extracting 33 of 43 (76.74%) HMMs.
    Finished extracting 34 of 43 (79.07%) HMMs.
    Finished extracting 35 of 43 (81.40%) HMMs.
    Finished extracting 36 of 43 (83.72%) HMMs.
    Finished extracting 37 of 43 (86.05%) HMMs.
    Finished extracting 38 of 43 (88.37%) HMMs.
    Finished extracting 39 of 43 (90.70%) HMMs.
    Finished extracting 40 of 43 (93.02%) HMMs.
    Finished extracting 41 of 43 (95.35%) HMMs.
    Finished extracting 42 of 43 (97.67%) HMMs.
    Finished extracting 43 of 43 (100.00%) HMMs.
    Finished aligning 0 of 43 (0.00%) marker genes.
    Finished aligning 1 of 43 (2.33%) marker genes.
    Finished aligning 2 of 43 (4.65%) marker genes.
    Finished aligning 3 of 43 (6.98%) marker genes.
    Finished aligning 4 of 43 (9.30%) marker genes.
    Finished aligning 5 of 43 (11.63%) marker genes.
    Finished aligning 6 of 43 (13.95%) marker genes.
    Finished aligning 7 of 43 (16.28%) marker genes.
    Finished aligning 8 of 43 (18.60%) marker genes.
    Finished aligning 9 of 43 (20.93%) marker genes.
    Finished aligning 10 of 43 (23.26%) marker genes.
    Finished aligning 11 of 43 (25.58%) marker genes.
    Finished aligning 12 of 43 (27.91%) marker genes.
    Finished aligning 13 of 43 (30.23%) marker genes.
    Finished aligning 14 of 43 (32.56%) marker genes.
    Finished aligning 15 of 43 (34.88%) marker genes.
    Finished aligning 16 of 43 (37.21%) marker genes.
    Finished aligning 17 of 43 (39.53%) marker genes.
    Finished aligning 18 of 43 (41.86%) marker genes.
    Finished aligning 19 of 43 (44.19%) marker genes.
    Finished aligning 20 of 43 (46.51%) marker genes.
    Finished aligning 21 of 43 (48.84%) marker genes.
    Finished aligning 22 of 43 (51.16%) marker genes.
    Finished aligning 23 of 43 (53.49%) marker genes.
    Finished aligning 24 of 43 (55.81%) marker genes.
    Finished aligning 25 of 43 (58.14%) marker genes.
    Finished aligning 26 of 43 (60.47%) marker genes.
    Finished aligning 27 of 43 (62.79%) marker genes.
    Finished aligning 28 of 43 (65.12%) marker genes.
    Finished aligning 29 of 43 (67.44%) marker genes.
    Finished aligning 30 of 43 (69.77%) marker genes.
    Finished aligning 31 of 43 (72.09%) marker genes.
    Finished aligning 32 of 43 (74.42%) marker genes.
    Finished aligning 33 of 43 (76.74%) marker genes.
    Finished aligning 34 of 43 (79.07%) marker genes.
    Finished aligning 35 of 43 (81.40%) marker genes.
    Finished aligning 36 of 43 (83.72%) marker genes.
    Finished aligning 37 of 43 (86.05%) marker genes.
    Finished aligning 38 of 43 (88.37%) marker genes.
    Finished aligning 39 of 43 (90.70%) marker genes.
    Finished aligning 40 of 43 (93.02%) marker genes.
    Finished aligning 41 of 43 (95.35%) marker genes.
    Finished aligning 42 of 43 (97.67%) marker genes.
    Finished aligning 43 of 43 (100.00%) marker genes.
    Finished parsing hits for 1 of 4 (25.00%) bins.
    Finished parsing hits for 2 of 4 (50.00%) bins.
    Finished parsing hits for 3 of 4 (75.00%) bins.
    Finished parsing hits for 4 of 4 (100.00%) bins.

    Finished processing 1 of 4 (25.00%) bins (current: 50contig_reads_bin_55.fasta).
                                                                                    
    Finished processing 2 of 4 (50.00%) bins (current: 50contig_reads_bin_6.fasta).
                                                                                   
    Finished processing 3 of 4 (75.00%) bins (current: 50contig_reads_bin_11.fasta).
                                                                                    
    Finished processing 4 of 4 (100.00%) bins (current: 50contig_reads_bin_1.fasta).
    Finished processing 0 of 4 (0.00%) bins.
    Finished processing 1 of 4 (25.00%) bins.
    Finished processing 2 of 4 (50.00%) bins.
    Finished processing 3 of 4 (75.00%) bins.
    Finished processing 4 of 4 (100.00%) bins.
    Finished parsing hits for 1 of 4 (25.00%) bins.
    Finished parsing hits for 2 of 4 (50.00%) bins.
    Finished parsing hits for 3 of 4 (75.00%) bins.
    Finished parsing hits for 4 of 4 (100.00%) bins.
    Finished processing 0 of 4 (0.00%) bins.
    Finished processing 1 of 4 (25.00%) bins.
    Finished processing 2 of 4 (50.00%) bins.
    Finished processing 3 of 4 (75.00%) bins.
    Finished processing 4 of 4 (100.00%) bins.
    Finished processing 0 of 4 (0.00%) bins.
    Finished processing 1 of 4 (25.00%) bins.
    Finished processing 2 of 4 (50.00%) bins.
    Finished processing 3 of 4 (75.00%) bins.
    Finished processing 4 of 4 (100.00%) bins.
    Finished parsing hits for 1 of 4 (25.00%) bins.
    Finished parsing hits for 2 of 4 (50.00%) bins.
    Finished parsing hits for 3 of 4 (75.00%) bins.
    Finished parsing hits for 4 of 4 (100.00%) bins.

Standard Output:

[2025-04-10 09:13:48] INFO: CheckM v1.2.3
[2025-04-10 09:13:48] INFO: checkm lineage_wf bins output --unique 10 --multi 10 --aai_strain 0.9 --e_value 1e-10 --length 0.7 --file /tmp/tmprt3848zx/job_working_directory/000/36/outputs/dataset_182937f4-c241-4988-bec9-8fb0fcac2d91.dat --tab_table --extension fasta --threads 1 --pplacer_threads 1
[2025-04-10 09:13:48] INFO: CheckM data: /usr/local/checkm_data
[2025-04-10 09:13:48] INFO: [CheckM - tree] Placing bins in reference genome tree.
[2025-04-10 09:13:48] INFO: Identifying marker genes in 4 bins with 1 threads:
[2025-04-10 09:13:50] INFO: Saving HMM info to file.
[2025-04-10 09:13:50] INFO: Calculating genome statistics for 4 bins with 1 threads:
[2025-04-10 09:13:50] INFO: Extracting marker genes to align.
[2025-04-10 09:13:50] INFO: Parsing HMM hits to marker genes:
[2025-04-10 09:13:50] INFO: Extracting 43 HMMs with 1 threads:
[2025-04-10 09:13:51] INFO: Aligning 43 marker genes with 1 threads:
[2025-04-10 09:13:51] INFO: Reading marker alignment files.
[2025-04-10 09:13:51] INFO: Concatenating alignments.
[2025-04-10 09:13:51] INFO: Placing 4 bins into the genome tree with pplacer (be patient).
[2025-04-10 09:14:28] INFO: { Current stage: 0:00:40.240 || Total: 0:00:40.240 }
[2025-04-10 09:14:28] INFO: [CheckM - lineage_set] Inferring lineage-specific marker sets.
[2025-04-10 09:14:28] INFO: Reading HMM info from file.
[2025-04-10 09:14:28] INFO: Parsing HMM hits to marker genes:
[2025-04-10 09:14:29] INFO: Determining marker sets for each genome bin.
[2025-04-10 09:14:29] INFO: Marker set written to: output/lineage.ms
[2025-04-10 09:14:29] INFO: { Current stage: 0:00:00.827 || Total: 0:00:41.067 }
[2025-04-10 09:14:29] INFO: [CheckM - analyze] Identifying marker genes in bins.
[2025-04-10 09:14:29] INFO: Identifying marker genes in 4 bins with 1 threads:
[2025-04-10 09:14:37] INFO: Saving HMM info to file.
[2025-04-10 09:14:37] INFO: { Current stage: 0:00:07.859 || Total: 0:00:48.927 }
[2025-04-10 09:14:37] INFO: Parsing HMM hits to marker genes:
[2025-04-10 09:14:37] INFO: Aligning marker genes with multiple hits in a single bin:
[2025-04-10 09:14:37] INFO: { Current stage: 0:00:00.127 || Total: 0:00:49.055 }
[2025-04-10 09:14:37] INFO: Calculating genome statistics for 4 bins with 1 threads:
[2025-04-10 09:14:37] INFO: { Current stage: 0:00:00.027 || Total: 0:00:49.082 }
[2025-04-10 09:14:37] INFO: [CheckM - qa] Tabulating genome statistics.
[2025-04-10 09:14:37] INFO: Calculating AAI between multi-copy marker genes.
[2025-04-10 09:14:37] INFO: Reading HMM info from file.
[2025-04-10 09:14:37] INFO: Parsing HMM hits to marker genes:
[2025-04-10 09:14:37] INFO: QA information written to: /tmp/tmprt3848zx/job_working_directory/000/36/outputs/dataset_182937f4-c241-4988-bec9-8fb0fcac2d91.dat
[2025-04-10 09:14:37] INFO: { Current stage: 0:00:00.110 || Total: 0:00:49.193 }

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"input"`
__workflow_invocation_uuid__	`"85d8fbb215e611f0aeac6045bd812dcf"`
bins	`{"__current_case__": 0, "bins_coll": {"values": [{"id": 53, "src": "hdca"}]}, "select": "collection"}`
chromInfo	`"/tmp/tmprt3848zx/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
dbkey	`"?"`
extra_outputs	`None`
lineage_set	`{"force_domain": false, "multi": "10", "no_refinement": false, "unique": "10"}`
qa	`{"aai_strain": "0.9", "e_value": "1e-10", "ignore_thresholds": false, "individual_markers": false, "length": "0.7", "skip_adj_correction": false, "skip_pseudogene_correction": false}`
tree_analyze	`{"ali": false, "genes": false, "nt": false, "reduced_tree": false}`

Step 52: toolshed.g2.bx.psu.edu/repos/iuc/coverm_genome/coverm_genome/0.7.0+galaxy0:

step_state: scheduled

Jobs

Job 1:

Job state is ok

Command Line:

mkdir 'single/' && mkdir 'fw/' && mkdir 'rv/' && mkdir 'interl/' && mkdir 'ref/' && mkdir 'bam/' &&   ln -s '/tmp/tmprt3848zx/files/7/9/a/dataset_79a7ee8f-7135-4f1f-8b89-90780f1339fe.dat' 'fw/50contig_reads' && ln -s '/tmp/tmprt3848zx/files/a/b/6/dataset_ab64de63-9e95-40b1-b42e-88ebf6636371.dat' 'rv/50contig_reads' &&   echo "GENOME_FOR_READS mapped.mode.genome.genomic.source=history" && echo "GENOME_FOR_READS mapped.mode.genome.genomic.genome_fasta_files=/tmp/tmprt3848zx/files/5/b/7/dataset_5b725d9e-0214-472e-ac90-3302b11af51c.dat,/tmp/tmprt3848zx/files/8/0/9/dataset_809ece5c-f028-4d72-913f-60ccd0f9b71a.dat,/tmp/tmprt3848zx/files/f/0/c/dataset_f0c33f60-365a-44bf-b5ad-f1584230167d.dat,/tmp/tmprt3848zx/files/f/b/e/dataset_fbe5c0d6-af8a-4e6d-b0ca-46c3391bda82.dat" && ln -s '/tmp/tmprt3848zx/files/5/b/7/dataset_5b725d9e-0214-472e-ac90-3302b11af51c.dat' '50contig_reads_bin_1.fasta' && ln -s '/tmp/tmprt3848zx/files/8/0/9/dataset_809ece5c-f028-4d72-913f-60ccd0f9b71a.dat' '50contig_reads_bin_11.fasta' && ln -s '/tmp/tmprt3848zx/files/f/0/c/dataset_f0c33f60-365a-44bf-b5ad-f1584230167d.dat' '50contig_reads_bin_55.fasta' && ln -s '/tmp/tmprt3848zx/files/f/b/e/dataset_fbe5c0d6-af8a-4e6d-b0ca-46c3391bda82.dat' '50contig_reads_bin_6.fasta' &&   mkdir 'representative-fasta/' && coverm genome -1 'fw/50contig_reads' -2 'rv/50contig_reads'  --mapper 'minimap2-sr' --genome-fasta-files '50contig_reads_bin_1.fasta' '50contig_reads_bin_11.fasta' '50contig_reads_bin_55.fasta' '50contig_reads_bin_6.fasta'   --min-read-aligned-length 0 --min-read-percent-identity 0.0 --min-read-aligned-percent 0.0   --methods 'relative_abundance' --min-covered-fraction 10 --contig-end-exclusion 75 --trim-min 5 --trim-max 95    --output-format 'dense' --output-file '/tmp/tmprt3848zx/job_working_directory/000/37/outputs/dataset_4b61af85-2fd5-4880-b3da-c60367d51d8c.dat'  --threads ${GALAXY_SLOTS:-1}

Exit Code:

```
0
```

Standard Error:

[2025-04-10T09:13:31Z INFO  bird_tool_utils::clap_utils] CoverM version 0.7.0
[2025-04-10T09:13:31Z INFO  coverm] Writing output to file: /tmp/tmprt3848zx/job_working_directory/000/37/outputs/dataset_4b61af85-2fd5-4880-b3da-c60367d51d8c.dat
[2025-04-10T09:13:31Z INFO  coverm] Using min-covered-fraction 10%
[2025-04-10T09:13:31Z INFO  coverm] Using min-read-percent-identity 0%
[2025-04-10T09:13:31Z INFO  coverm] Using min-read-aligned-percent 0%
[2025-04-10T09:13:31Z INFO  bird_tool_utils::external_command_checker] Found minimap2 version 2.28-r1209 
[2025-04-10T09:13:31Z INFO  bird_tool_utils::external_command_checker] Found samtools version 1.21 
[2025-04-10T09:13:31Z INFO  coverm] Profiling 4 genomes
[2025-04-10T09:13:31Z INFO  coverm] Generating concatenated reference FASTA file of 4 genomes ..
[2025-04-10T09:13:31Z INFO  coverm] Not pre-generating minimap2 index
[2025-04-10T09:13:31Z INFO  coverm] Using min-read-percent-identity 0%
[2025-04-10T09:13:31Z INFO  coverm] Using min-read-aligned-percent 0%
[2025-04-10T09:13:32Z INFO  coverm::genome] In sample '50contig_reads', found 18791 reads mapped out of 18924 total (99.30%)

Standard Output:

GENOME_FOR_READS mapped.mode.genome.genomic.source=history
GENOME_FOR_READS mapped.mode.genome.genomic.genome_fasta_files=/tmp/tmprt3848zx/files/5/b/7/dataset_5b725d9e-0214-472e-ac90-3302b11af51c.dat,/tmp/tmprt3848zx/files/8/0/9/dataset_809ece5c-f028-4d72-913f-60ccd0f9b71a.dat,/tmp/tmprt3848zx/files/f/0/c/dataset_f0c33f60-365a-44bf-b5ad-f1584230167d.dat,/tmp/tmprt3848zx/files/f/b/e/dataset_fbe5c0d6-af8a-4e6d-b0ca-46c3391bda82.dat

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"input"`
__workflow_invocation_uuid__	`"85d8fbb215e611f0aeac6045bd812dcf"`
alignment	`{"exclude_supplementary": false, "min_read_aligned_length": "0", "min_read_aligned_percent": "0.0", "min_read_percent_identity": "0.0", "proper_pairs_only": {"__current_case__": 1, "proper_pairs_only": ""}}`
chromInfo	`"/tmp/tmprt3848zx/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
cov	`{"contig_end_exclusion": "75", "methods": ["relative_abundance"], "min_covered_fraction": "10", "trim_max": "95", "trim_min": "5"}`
dbkey	`"?"`
derep	`{"checkm_tab_table": null, "dereplicate": {"__current_case__": 1, "dereplicate": ""}, "genome_info": null, "max_contamination": null, "min_completeness": null}`
exclude_genomes_from_deshard	`false`
mapped	`{"__current_case__": 1, "mapped": "not-mapped", "mapper": "minimap2-sr", "mode": {"__current_case__": 0, "genome": {"__current_case__": 1, "genomic": {"__current_case__": 0, "genome_fasta_files": {"values": [{"id": 53, "src": "hdca"}]}, "source": "history"}, "ref_or_genome": "genomic"}, "mode": "individual", "read_type": {"__current_case__": 2, "paired_reads": {"values": [{"id": 4, "src": "dce"}]}, "type": "paired_collection"}}}`
out	`{"dereplication_output_cluster_definition": false, "dereplication_output_representative_fasta_directory_copy": false, "no_zeros": false, "output_format": "dense"}`

Step 53: toolshed.g2.bx.psu.edu/repos/iuc/quast/quast/5.3.0+galaxy0:

step_state: scheduled

Jobs

Job 1:

Job state is ok

Command Line:

echo 50contig_reads_bin_1_fasta &&    metaquast  --labels '50contig_reads_bin_1_fasta' -o 'outputdir'  --max-ref-num 0  --min-identity 90.0 --min-contig 500        --min-alignment 65 --ambiguity-usage 'one' --ambiguity-score 0.99   --local-mis-size 200   --contig-thresholds '0,1000'  --extensive-mis-size 1000 --scaffold-gap-max-size 1000 --unaligned-part-size 500   --x-for-Nx 90  '/tmp/tmprt3848zx/files/5/b/7/dataset_5b725d9e-0214-472e-ac90-3302b11af51c.dat' --threads ${GALAXY_SLOTS:-1}  && 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/tmprt3848zx/job_working_directory/000/38/outputs/dataset_57758adf-d8de-476a-88f0-16563ce1b032_files' && cp outputdir/combined_reference/*.html '/tmp/tmprt3848zx/job_working_directory/000/38/outputs/dataset_57758adf-d8de-476a-88f0-16563ce1b032_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/tmprt3848zx/job_working_directory/000/38/outputs/dataset_57758adf-d8de-476a-88f0-16563ce1b032_files'; fi && if [[ -d "outputdir/krona_charts/" ]]; then mkdir -p 'None' && cp outputdir/krona_charts/*.html 'None'; fi

Exit Code:

```
0
```

Standard Output:

50contig_reads_bin_1_fasta
/usr/local/opt/quast-5.3.0/metaquast.py --labels 50contig_reads_bin_1_fasta -o outputdir --max-ref-num 0 --min-identity 90.0 --min-contig 500 --min-alignment 65 --ambiguity-usage one --ambiguity-score 0.99 --local-mis-size 200 --contig-thresholds 0,1000 --extensive-mis-size 1000 --scaffold-gap-max-size 1000 --unaligned-part-size 500 --x-for-Nx 90 /tmp/tmprt3848zx/files/5/b/7/dataset_5b725d9e-0214-472e-ac90-3302b11af51c.dat --threads 1

Version: 5.3.0

System information:
  OS: Linux-6.8.0-1021-azure-x86_64-with-glibc2.36 (linux_64)
  Python version: 3.12.3
  CPUs number: 4

Started: 2025-04-10 09:13:04

Logging to /tmp/tmprt3848zx/job_working_directory/000/38/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/tmprt3848zx/files/5/b/7/dataset_5b725d9e-0214-472e-ac90-3302b11af51c.dat ==> 50contig_reads_bin_1_fasta

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 --min-identity 90.0 --min-contig 500 --min-alignment 65 --ambiguity-usage one --ambiguity-score 0.99 --local-mis-size 200 --contig-thresholds 0,1000 --extensive-mis-size 1000 --scaffold-gap-max-size 1000 --unaligned-part-size 500 --x-for-Nx 90 --threads 1 /tmp/tmprt3848zx/files/5/b/7/dataset_5b725d9e-0214-472e-ac90-3302b11af51c.dat -o /tmp/tmprt3848zx/job_working_directory/000/38/working/outputdir --labels 50contig_reads_bin_1_fasta

Version: 5.3.0

System information:
  OS: Linux-6.8.0-1021-azure-x86_64-with-glibc2.36 (linux_64)
  Python version: 3.12.3
  CPUs number: 4

Started: 2025-04-10 09:13:05

Logging to /tmp/tmprt3848zx/job_working_directory/000/38/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/tmprt3848zx/job_working_directory/000/38/working
Main parameters: 
  MODE: meta, threads: 1, min contig length: 500, min alignment length: 65, min alignment IDY: 90.0, \
  ambiguity: all, min local misassembly length: 200, min extensive misassembly length: 1000

Contigs:
  Pre-processing...
  /tmp/tmprt3848zx/files/5/b/7/dataset_5b725d9e-0214-472e-ac90-3302b11af51c.dat ==> 50contig_reads_bin_1_fasta

2025-04-10 09:13:05
Running Basic statistics processor...
  Contig files: 
    50contig_reads_bin_1_fasta
  Calculating N50 and L50...
    50contig_reads_bin_1_fasta, N50 = 1357, L50 = 1, auN = 1357.0, Total length = 1357, GC % = 38.76, # N's per 100 kbp =  0.00
  Drawing Nx plot...
    saved to /tmp/tmprt3848zx/job_working_directory/000/38/working/outputdir/basic_stats/Nx_plot.pdf
  Drawing cumulative plot...
    saved to /tmp/tmprt3848zx/job_working_directory/000/38/working/outputdir/basic_stats/cumulative_plot.pdf
  Drawing GC content plot...
    saved to /tmp/tmprt3848zx/job_working_directory/000/38/working/outputdir/basic_stats/GC_content_plot.pdf
  Drawing 50contig_reads_bin_1_fasta GC content plot...
    saved to /tmp/tmprt3848zx/job_working_directory/000/38/working/outputdir/basic_stats/50contig_reads_bin_1_fasta_GC_content_plot.pdf
Done.

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

2025-04-10 09:13:06
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

2025-04-10 09:13:06
RESULTS:
  Text versions of total report are saved to /tmp/tmprt3848zx/job_working_directory/000/38/working/outputdir/report.txt, report.tsv, and report.tex
  Text versions of transposed total report are saved to /tmp/tmprt3848zx/job_working_directory/000/38/working/outputdir/transposed_report.txt, transposed_report.tsv, and transposed_report.tex
  HTML version (interactive tables and plots) is saved to /tmp/tmprt3848zx/job_working_directory/000/38/working/outputdir/report.html
  PDF version (tables and plots) is saved to /tmp/tmprt3848zx/job_working_directory/000/38/working/outputdir/report.pdf
  Icarus (contig browser) is saved to /tmp/tmprt3848zx/job_working_directory/000/38/working/outputdir/icarus.html
  Log is saved to /tmp/tmprt3848zx/job_working_directory/000/38/working/outputdir/quast.log

Finished: 2025-04-10 09:13:06
Elapsed time: 0:00:01.437248
NOTICEs: 2; WARNINGs: 1; non-fatal ERRORs: 0

Thank you for using QUAST!

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"input"`
__workflow_invocation_uuid__	`"85d8fbb215e611f0aeac6045bd812dcf"`
advanced	`{"contig_thresholds": "0,1000", "extensive_mis_size": "1000", "fragmented_max_indent": null, "report_all_metrics": false, "scaffold_gap_max_size": "1000", "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": "90.0", "ref": {"__current_case__": 0, "max_ref_num": "0", "origin": "silva"}, "reuse_combined_alignments": false, "type": "metagenome"}`
chromInfo	`"/tmp/tmprt3848zx/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	`"500"`
mode	`{"__current_case__": 0, "in": {"__current_case__": 1, "custom": "false", "inputs": {"values": [{"id": 93, "src": "dce"}]}}, "mode": "individual", "reads": {"__current_case__": 0, "reads_option": "disabled"}}`
output_files	`["html", "tabular", "summary", "krona"]`
split_scaffolds	`false`

Job 2:

Job state is ok

Command Line:

echo 50contig_reads_bin_11_fasta &&    metaquast  --labels '50contig_reads_bin_11_fasta' -o 'outputdir'  --max-ref-num 0  --min-identity 90.0 --min-contig 500        --min-alignment 65 --ambiguity-usage 'one' --ambiguity-score 0.99   --local-mis-size 200   --contig-thresholds '0,1000'  --extensive-mis-size 1000 --scaffold-gap-max-size 1000 --unaligned-part-size 500   --x-for-Nx 90  '/tmp/tmprt3848zx/files/8/0/9/dataset_809ece5c-f028-4d72-913f-60ccd0f9b71a.dat' --threads ${GALAXY_SLOTS:-1}  && 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/tmprt3848zx/job_working_directory/000/39/outputs/dataset_f92d3a11-d39b-4e6e-8753-d594a0290718_files' && cp outputdir/combined_reference/*.html '/tmp/tmprt3848zx/job_working_directory/000/39/outputs/dataset_f92d3a11-d39b-4e6e-8753-d594a0290718_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/tmprt3848zx/job_working_directory/000/39/outputs/dataset_f92d3a11-d39b-4e6e-8753-d594a0290718_files'; fi && if [[ -d "outputdir/krona_charts/" ]]; then mkdir -p 'None' && cp outputdir/krona_charts/*.html 'None'; fi

Exit Code:

```
0
```

Standard Output:

50contig_reads_bin_11_fasta
/usr/local/opt/quast-5.3.0/metaquast.py --labels 50contig_reads_bin_11_fasta -o outputdir --max-ref-num 0 --min-identity 90.0 --min-contig 500 --min-alignment 65 --ambiguity-usage one --ambiguity-score 0.99 --local-mis-size 200 --contig-thresholds 0,1000 --extensive-mis-size 1000 --scaffold-gap-max-size 1000 --unaligned-part-size 500 --x-for-Nx 90 /tmp/tmprt3848zx/files/8/0/9/dataset_809ece5c-f028-4d72-913f-60ccd0f9b71a.dat --threads 1

Version: 5.3.0

System information:
  OS: Linux-6.8.0-1021-azure-x86_64-with-glibc2.36 (linux_64)
  Python version: 3.12.3
  CPUs number: 4

Started: 2025-04-10 09:13:04

Logging to /tmp/tmprt3848zx/job_working_directory/000/39/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/tmprt3848zx/files/8/0/9/dataset_809ece5c-f028-4d72-913f-60ccd0f9b71a.dat ==> 50contig_reads_bin_11_fasta

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 --min-identity 90.0 --min-contig 500 --min-alignment 65 --ambiguity-usage one --ambiguity-score 0.99 --local-mis-size 200 --contig-thresholds 0,1000 --extensive-mis-size 1000 --scaffold-gap-max-size 1000 --unaligned-part-size 500 --x-for-Nx 90 --threads 1 /tmp/tmprt3848zx/files/8/0/9/dataset_809ece5c-f028-4d72-913f-60ccd0f9b71a.dat -o /tmp/tmprt3848zx/job_working_directory/000/39/working/outputdir --labels 50contig_reads_bin_11_fasta

Version: 5.3.0

System information:
  OS: Linux-6.8.0-1021-azure-x86_64-with-glibc2.36 (linux_64)
  Python version: 3.12.3
  CPUs number: 4

Started: 2025-04-10 09:13:05

Logging to /tmp/tmprt3848zx/job_working_directory/000/39/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/tmprt3848zx/job_working_directory/000/39/working
Main parameters: 
  MODE: meta, threads: 1, min contig length: 500, min alignment length: 65, min alignment IDY: 90.0, \
  ambiguity: all, min local misassembly length: 200, min extensive misassembly length: 1000

Contigs:
  Pre-processing...
  /tmp/tmprt3848zx/files/8/0/9/dataset_809ece5c-f028-4d72-913f-60ccd0f9b71a.dat ==> 50contig_reads_bin_11_fasta

2025-04-10 09:13:05
Running Basic statistics processor...
  Contig files: 
    50contig_reads_bin_11_fasta
  Calculating N50 and L50...
    50contig_reads_bin_11_fasta, N50 = 2275, L50 = 1, auN = 2275.0, Total length = 2275, GC % = 38.42, # N's per 100 kbp =  0.00
  Drawing Nx plot...
    saved to /tmp/tmprt3848zx/job_working_directory/000/39/working/outputdir/basic_stats/Nx_plot.pdf
  Drawing cumulative plot...
    saved to /tmp/tmprt3848zx/job_working_directory/000/39/working/outputdir/basic_stats/cumulative_plot.pdf
  Drawing GC content plot...
    saved to /tmp/tmprt3848zx/job_working_directory/000/39/working/outputdir/basic_stats/GC_content_plot.pdf
  Drawing 50contig_reads_bin_11_fasta GC content plot...
    saved to /tmp/tmprt3848zx/job_working_directory/000/39/working/outputdir/basic_stats/50contig_reads_bin_11_fasta_GC_content_plot.pdf
Done.

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

2025-04-10 09:13:06
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

2025-04-10 09:13:06
RESULTS:
  Text versions of total report are saved to /tmp/tmprt3848zx/job_working_directory/000/39/working/outputdir/report.txt, report.tsv, and report.tex
  Text versions of transposed total report are saved to /tmp/tmprt3848zx/job_working_directory/000/39/working/outputdir/transposed_report.txt, transposed_report.tsv, and transposed_report.tex
  HTML version (interactive tables and plots) is saved to /tmp/tmprt3848zx/job_working_directory/000/39/working/outputdir/report.html
  PDF version (tables and plots) is saved to /tmp/tmprt3848zx/job_working_directory/000/39/working/outputdir/report.pdf
  Icarus (contig browser) is saved to /tmp/tmprt3848zx/job_working_directory/000/39/working/outputdir/icarus.html
  Log is saved to /tmp/tmprt3848zx/job_working_directory/000/39/working/outputdir/quast.log

Finished: 2025-04-10 09:13:06
Elapsed time: 0:00:01.454717
NOTICEs: 2; WARNINGs: 1; non-fatal ERRORs: 0

Thank you for using QUAST!

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"input"`
__workflow_invocation_uuid__	`"85d8fbb215e611f0aeac6045bd812dcf"`
advanced	`{"contig_thresholds": "0,1000", "extensive_mis_size": "1000", "fragmented_max_indent": null, "report_all_metrics": false, "scaffold_gap_max_size": "1000", "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": "90.0", "ref": {"__current_case__": 0, "max_ref_num": "0", "origin": "silva"}, "reuse_combined_alignments": false, "type": "metagenome"}`
chromInfo	`"/tmp/tmprt3848zx/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	`"500"`
mode	`{"__current_case__": 0, "in": {"__current_case__": 1, "custom": "false", "inputs": {"values": [{"id": 94, "src": "dce"}]}}, "mode": "individual", "reads": {"__current_case__": 0, "reads_option": "disabled"}}`
output_files	`["html", "tabular", "summary", "krona"]`
split_scaffolds	`false`

Job 3:

Job state is ok

Command Line:

echo 50contig_reads_bin_55_fasta &&    metaquast  --labels '50contig_reads_bin_55_fasta' -o 'outputdir'  --max-ref-num 0  --min-identity 90.0 --min-contig 500        --min-alignment 65 --ambiguity-usage 'one' --ambiguity-score 0.99   --local-mis-size 200   --contig-thresholds '0,1000'  --extensive-mis-size 1000 --scaffold-gap-max-size 1000 --unaligned-part-size 500   --x-for-Nx 90  '/tmp/tmprt3848zx/files/f/0/c/dataset_f0c33f60-365a-44bf-b5ad-f1584230167d.dat' --threads ${GALAXY_SLOTS:-1}  && 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/tmprt3848zx/job_working_directory/000/40/outputs/dataset_ed59b0db-0841-4df9-8461-61a1bad95807_files' && cp outputdir/combined_reference/*.html '/tmp/tmprt3848zx/job_working_directory/000/40/outputs/dataset_ed59b0db-0841-4df9-8461-61a1bad95807_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/tmprt3848zx/job_working_directory/000/40/outputs/dataset_ed59b0db-0841-4df9-8461-61a1bad95807_files'; fi && if [[ -d "outputdir/krona_charts/" ]]; then mkdir -p 'None' && cp outputdir/krona_charts/*.html 'None'; fi

Exit Code:

```
0
```

Standard Output:

50contig_reads_bin_55_fasta
/usr/local/opt/quast-5.3.0/metaquast.py --labels 50contig_reads_bin_55_fasta -o outputdir --max-ref-num 0 --min-identity 90.0 --min-contig 500 --min-alignment 65 --ambiguity-usage one --ambiguity-score 0.99 --local-mis-size 200 --contig-thresholds 0,1000 --extensive-mis-size 1000 --scaffold-gap-max-size 1000 --unaligned-part-size 500 --x-for-Nx 90 /tmp/tmprt3848zx/files/f/0/c/dataset_f0c33f60-365a-44bf-b5ad-f1584230167d.dat --threads 1

Version: 5.3.0

System information:
  OS: Linux-6.8.0-1021-azure-x86_64-with-glibc2.36 (linux_64)
  Python version: 3.12.3
  CPUs number: 4

Started: 2025-04-10 09:13:04

Logging to /tmp/tmprt3848zx/job_working_directory/000/40/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/tmprt3848zx/files/f/0/c/dataset_f0c33f60-365a-44bf-b5ad-f1584230167d.dat ==> 50contig_reads_bin_55_fasta

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 --min-identity 90.0 --min-contig 500 --min-alignment 65 --ambiguity-usage one --ambiguity-score 0.99 --local-mis-size 200 --contig-thresholds 0,1000 --extensive-mis-size 1000 --scaffold-gap-max-size 1000 --unaligned-part-size 500 --x-for-Nx 90 --threads 1 /tmp/tmprt3848zx/files/f/0/c/dataset_f0c33f60-365a-44bf-b5ad-f1584230167d.dat -o /tmp/tmprt3848zx/job_working_directory/000/40/working/outputdir --labels 50contig_reads_bin_55_fasta

Version: 5.3.0

System information:
  OS: Linux-6.8.0-1021-azure-x86_64-with-glibc2.36 (linux_64)
  Python version: 3.12.3
  CPUs number: 4

Started: 2025-04-10 09:13:05

Logging to /tmp/tmprt3848zx/job_working_directory/000/40/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/tmprt3848zx/job_working_directory/000/40/working
Main parameters: 
  MODE: meta, threads: 1, min contig length: 500, min alignment length: 65, min alignment IDY: 90.0, \
  ambiguity: all, min local misassembly length: 200, min extensive misassembly length: 1000

Contigs:
  Pre-processing...
  /tmp/tmprt3848zx/files/f/0/c/dataset_f0c33f60-365a-44bf-b5ad-f1584230167d.dat ==> 50contig_reads_bin_55_fasta

2025-04-10 09:13:05
Running Basic statistics processor...
  Contig files: 
    50contig_reads_bin_55_fasta
  Calculating N50 and L50...
    50contig_reads_bin_55_fasta, N50 = 5014, L50 = 21, auN = 5279.4, Total length = 258860, GC % = 36.41, # N's per 100 kbp =  0.00
  Drawing Nx plot...
    saved to /tmp/tmprt3848zx/job_working_directory/000/40/working/outputdir/basic_stats/Nx_plot.pdf
  Drawing cumulative plot...
    saved to /tmp/tmprt3848zx/job_working_directory/000/40/working/outputdir/basic_stats/cumulative_plot.pdf
  Drawing GC content plot...
    saved to /tmp/tmprt3848zx/job_working_directory/000/40/working/outputdir/basic_stats/GC_content_plot.pdf
  Drawing 50contig_reads_bin_55_fasta GC content plot...
    saved to /tmp/tmprt3848zx/job_working_directory/000/40/working/outputdir/basic_stats/50contig_reads_bin_55_fasta_GC_content_plot.pdf
Done.

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

2025-04-10 09:13:06
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

2025-04-10 09:13:06
RESULTS:
  Text versions of total report are saved to /tmp/tmprt3848zx/job_working_directory/000/40/working/outputdir/report.txt, report.tsv, and report.tex
  Text versions of transposed total report are saved to /tmp/tmprt3848zx/job_working_directory/000/40/working/outputdir/transposed_report.txt, transposed_report.tsv, and transposed_report.tex
  HTML version (interactive tables and plots) is saved to /tmp/tmprt3848zx/job_working_directory/000/40/working/outputdir/report.html
  PDF version (tables and plots) is saved to /tmp/tmprt3848zx/job_working_directory/000/40/working/outputdir/report.pdf
  Icarus (contig browser) is saved to /tmp/tmprt3848zx/job_working_directory/000/40/working/outputdir/icarus.html
  Log is saved to /tmp/tmprt3848zx/job_working_directory/000/40/working/outputdir/quast.log

Finished: 2025-04-10 09:13:06
Elapsed time: 0:00:01.462968
NOTICEs: 2; WARNINGs: 1; non-fatal ERRORs: 0

Thank you for using QUAST!

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"input"`
__workflow_invocation_uuid__	`"85d8fbb215e611f0aeac6045bd812dcf"`
advanced	`{"contig_thresholds": "0,1000", "extensive_mis_size": "1000", "fragmented_max_indent": null, "report_all_metrics": false, "scaffold_gap_max_size": "1000", "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": "90.0", "ref": {"__current_case__": 0, "max_ref_num": "0", "origin": "silva"}, "reuse_combined_alignments": false, "type": "metagenome"}`
chromInfo	`"/tmp/tmprt3848zx/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	`"500"`
mode	`{"__current_case__": 0, "in": {"__current_case__": 1, "custom": "false", "inputs": {"values": [{"id": 95, "src": "dce"}]}}, "mode": "individual", "reads": {"__current_case__": 0, "reads_option": "disabled"}}`
output_files	`["html", "tabular", "summary", "krona"]`
split_scaffolds	`false`

Job 4:

Job state is ok

Command Line:

echo 50contig_reads_bin_6_fasta &&    metaquast  --labels '50contig_reads_bin_6_fasta' -o 'outputdir'  --max-ref-num 0  --min-identity 90.0 --min-contig 500        --min-alignment 65 --ambiguity-usage 'one' --ambiguity-score 0.99   --local-mis-size 200   --contig-thresholds '0,1000'  --extensive-mis-size 1000 --scaffold-gap-max-size 1000 --unaligned-part-size 500   --x-for-Nx 90  '/tmp/tmprt3848zx/files/f/b/e/dataset_fbe5c0d6-af8a-4e6d-b0ca-46c3391bda82.dat' --threads ${GALAXY_SLOTS:-1}  && 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/tmprt3848zx/job_working_directory/000/41/outputs/dataset_5e8042cf-3f2b-42bf-b28e-786730d1814f_files' && cp outputdir/combined_reference/*.html '/tmp/tmprt3848zx/job_working_directory/000/41/outputs/dataset_5e8042cf-3f2b-42bf-b28e-786730d1814f_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/tmprt3848zx/job_working_directory/000/41/outputs/dataset_5e8042cf-3f2b-42bf-b28e-786730d1814f_files'; fi && if [[ -d "outputdir/krona_charts/" ]]; then mkdir -p 'None' && cp outputdir/krona_charts/*.html 'None'; fi

Exit Code:

```
0
```

Standard Output:

50contig_reads_bin_6_fasta
/usr/local/opt/quast-5.3.0/metaquast.py --labels 50contig_reads_bin_6_fasta -o outputdir --max-ref-num 0 --min-identity 90.0 --min-contig 500 --min-alignment 65 --ambiguity-usage one --ambiguity-score 0.99 --local-mis-size 200 --contig-thresholds 0,1000 --extensive-mis-size 1000 --scaffold-gap-max-size 1000 --unaligned-part-size 500 --x-for-Nx 90 /tmp/tmprt3848zx/files/f/b/e/dataset_fbe5c0d6-af8a-4e6d-b0ca-46c3391bda82.dat --threads 1

Version: 5.3.0

System information:
  OS: Linux-6.8.0-1021-azure-x86_64-with-glibc2.36 (linux_64)
  Python version: 3.12.3
  CPUs number: 4

Started: 2025-04-10 09:13:04

Logging to /tmp/tmprt3848zx/job_working_directory/000/41/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/tmprt3848zx/files/f/b/e/dataset_fbe5c0d6-af8a-4e6d-b0ca-46c3391bda82.dat ==> 50contig_reads_bin_6_fasta

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 --min-identity 90.0 --min-contig 500 --min-alignment 65 --ambiguity-usage one --ambiguity-score 0.99 --local-mis-size 200 --contig-thresholds 0,1000 --extensive-mis-size 1000 --scaffold-gap-max-size 1000 --unaligned-part-size 500 --x-for-Nx 90 --threads 1 /tmp/tmprt3848zx/files/f/b/e/dataset_fbe5c0d6-af8a-4e6d-b0ca-46c3391bda82.dat -o /tmp/tmprt3848zx/job_working_directory/000/41/working/outputdir --labels 50contig_reads_bin_6_fasta

Version: 5.3.0

System information:
  OS: Linux-6.8.0-1021-azure-x86_64-with-glibc2.36 (linux_64)
  Python version: 3.12.3
  CPUs number: 4

Started: 2025-04-10 09:13:05

Logging to /tmp/tmprt3848zx/job_working_directory/000/41/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/tmprt3848zx/job_working_directory/000/41/working
Main parameters: 
  MODE: meta, threads: 1, min contig length: 500, min alignment length: 65, min alignment IDY: 90.0, \
  ambiguity: all, min local misassembly length: 200, min extensive misassembly length: 1000

Contigs:
  Pre-processing...
  /tmp/tmprt3848zx/files/f/b/e/dataset_fbe5c0d6-af8a-4e6d-b0ca-46c3391bda82.dat ==> 50contig_reads_bin_6_fasta

2025-04-10 09:13:05
Running Basic statistics processor...
  Contig files: 
    50contig_reads_bin_6_fasta
  Calculating N50 and L50...
    50contig_reads_bin_6_fasta, N50 = 1469, L50 = 1, auN = 1469.0, Total length = 1469, GC % = 38.67, # N's per 100 kbp =  0.00
  Drawing Nx plot...
    saved to /tmp/tmprt3848zx/job_working_directory/000/41/working/outputdir/basic_stats/Nx_plot.pdf
  Drawing cumulative plot...
    saved to /tmp/tmprt3848zx/job_working_directory/000/41/working/outputdir/basic_stats/cumulative_plot.pdf
  Drawing GC content plot...
    saved to /tmp/tmprt3848zx/job_working_directory/000/41/working/outputdir/basic_stats/GC_content_plot.pdf
  Drawing 50contig_reads_bin_6_fasta GC content plot...
    saved to /tmp/tmprt3848zx/job_working_directory/000/41/working/outputdir/basic_stats/50contig_reads_bin_6_fasta_GC_content_plot.pdf
Done.

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

2025-04-10 09:13:06
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

2025-04-10 09:13:06
RESULTS:
  Text versions of total report are saved to /tmp/tmprt3848zx/job_working_directory/000/41/working/outputdir/report.txt, report.tsv, and report.tex
  Text versions of transposed total report are saved to /tmp/tmprt3848zx/job_working_directory/000/41/working/outputdir/transposed_report.txt, transposed_report.tsv, and transposed_report.tex
  HTML version (interactive tables and plots) is saved to /tmp/tmprt3848zx/job_working_directory/000/41/working/outputdir/report.html
  PDF version (tables and plots) is saved to /tmp/tmprt3848zx/job_working_directory/000/41/working/outputdir/report.pdf
  Icarus (contig browser) is saved to /tmp/tmprt3848zx/job_working_directory/000/41/working/outputdir/icarus.html
  Log is saved to /tmp/tmprt3848zx/job_working_directory/000/41/working/outputdir/quast.log

Finished: 2025-04-10 09:13:06
Elapsed time: 0:00:01.445620
NOTICEs: 2; WARNINGs: 1; non-fatal ERRORs: 0

Thank you for using QUAST!

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"input"`
__workflow_invocation_uuid__	`"85d8fbb215e611f0aeac6045bd812dcf"`
advanced	`{"contig_thresholds": "0,1000", "extensive_mis_size": "1000", "fragmented_max_indent": null, "report_all_metrics": false, "scaffold_gap_max_size": "1000", "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": "90.0", "ref": {"__current_case__": 0, "max_ref_num": "0", "origin": "silva"}, "reuse_combined_alignments": false, "type": "metagenome"}`
chromInfo	`"/tmp/tmprt3848zx/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	`"500"`
mode	`{"__current_case__": 0, "in": {"__current_case__": 1, "custom": "false", "inputs": {"values": [{"id": 96, "src": "dce"}]}}, "mode": "individual", "reads": {"__current_case__": 0, "reads_option": "disabled"}}`
output_files	`["html", "tabular", "summary", "krona"]`
split_scaffolds	`false`

Step 54: toolshed.g2.bx.psu.edu/repos/iuc/bakta/bakta/1.9.4+galaxy0:

step_state: scheduled

Jobs

Job 1:

Job state is skipped

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"input"`
__workflow_invocation_uuid__	`"85d8fbb215e611f0aeac6045bd812dcf"`
annotation	`{"complete": false, "compliant": false, "keep_contig_headers": false, "meta": false, "prodigal": null, "proteins": null, "regions": null, "replicons": null, "translation_table": "11"}`
chromInfo	`"/tmp/tmprt3848zx/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
dbkey	`"?"`
input_option	`{"amrfinder_db_select": "amrfinderplus_V3.12_2024-05-02.2", "bakta_db_select": "V5.1_2024-01-19", "input_file": {"values": [{"id": 93, "src": "dce"}]}, "min_contig_length": null}`
organism	`{"genus": null, "plasmid": null, "species": null, "strain": null}`
output_files	`{"output_selection": ["file_tsv", "file_gff3", "file_ffn", "file_plot", "sum_txt"]}`
workflow	`{"skip_analysis": null}`

Job 2:

Job state is skipped

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"input"`
__workflow_invocation_uuid__	`"85d8fbb215e611f0aeac6045bd812dcf"`
annotation	`{"complete": false, "compliant": false, "keep_contig_headers": false, "meta": false, "prodigal": null, "proteins": null, "regions": null, "replicons": null, "translation_table": "11"}`
chromInfo	`"/tmp/tmprt3848zx/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
dbkey	`"?"`
input_option	`{"amrfinder_db_select": "amrfinderplus_V3.12_2024-05-02.2", "bakta_db_select": "V5.1_2024-01-19", "input_file": {"values": [{"id": 94, "src": "dce"}]}, "min_contig_length": null}`
organism	`{"genus": null, "plasmid": null, "species": null, "strain": null}`
output_files	`{"output_selection": ["file_tsv", "file_gff3", "file_ffn", "file_plot", "sum_txt"]}`
workflow	`{"skip_analysis": null}`

Job 3:

Job state is skipped

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"input"`
__workflow_invocation_uuid__	`"85d8fbb215e611f0aeac6045bd812dcf"`
annotation	`{"complete": false, "compliant": false, "keep_contig_headers": false, "meta": false, "prodigal": null, "proteins": null, "regions": null, "replicons": null, "translation_table": "11"}`
chromInfo	`"/tmp/tmprt3848zx/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
dbkey	`"?"`
input_option	`{"amrfinder_db_select": "amrfinderplus_V3.12_2024-05-02.2", "bakta_db_select": "V5.1_2024-01-19", "input_file": {"values": [{"id": 95, "src": "dce"}]}, "min_contig_length": null}`
organism	`{"genus": null, "plasmid": null, "species": null, "strain": null}`
output_files	`{"output_selection": ["file_tsv", "file_gff3", "file_ffn", "file_plot", "sum_txt"]}`
workflow	`{"skip_analysis": null}`

Job 4:

Job state is skipped

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"input"`
__workflow_invocation_uuid__	`"85d8fbb215e611f0aeac6045bd812dcf"`
annotation	`{"complete": false, "compliant": false, "keep_contig_headers": false, "meta": false, "prodigal": null, "proteins": null, "regions": null, "replicons": null, "translation_table": "11"}`
chromInfo	`"/tmp/tmprt3848zx/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
dbkey	`"?"`
input_option	`{"amrfinder_db_select": "amrfinderplus_V3.12_2024-05-02.2", "bakta_db_select": "V5.1_2024-01-19", "input_file": {"values": [{"id": 96, "src": "dce"}]}, "min_contig_length": null}`
organism	`{"genus": null, "plasmid": null, "species": null, "strain": null}`
output_files	`{"output_selection": ["file_tsv", "file_gff3", "file_ffn", "file_plot", "sum_txt"]}`
workflow	`{"skip_analysis": null}`

Step 55: toolshed.g2.bx.psu.edu/repos/iuc/collection_column_join/collection_column_join/0.0.3:

step_state: scheduled

Jobs

Job 1:

Job state is ok

Command Line:

sh '/tmp/tmprt3848zx/job_working_directory/000/46/configs/tmp3xw2lolz'

Exit Code:

```
0
```

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"tabular"`
__workflow_invocation_uuid__	`"85d8fbb215e611f0aeac6045bd812dcf"`
chromInfo	`"/tmp/tmprt3848zx/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
dbkey	`"?"`
fill_char	`"."`
has_header	`"1"`
identifier_column	`"1"`
include_outputs	`None`
old_col_in_header	`true`

Step 56: toolshed.g2.bx.psu.edu/repos/iuc/multiqc/multiqc/1.27+galaxy3:

step_state: scheduled

Jobs

Job 1:

Job state is ok

Command Line:

die() { echo "$@" 1>&2 ; exit 1; } &&  mkdir multiqc_WDir &&   mkdir multiqc_WDir/quast_0 && mkdir 'multiqc_WDir/quast_0/file_0' && ln -s '/tmp/tmprt3848zx/files/4/2/1/dataset_421e33f0-0f17-4c03-a10d-dd617c655623.dat' 'multiqc_WDir/quast_0/file_0/report.tsv' && mkdir 'multiqc_WDir/quast_0/file_1' && ln -s '/tmp/tmprt3848zx/files/b/f/8/dataset_bf84ecbb-8a5b-4c33-a996-a18aa9038b44.dat' 'multiqc_WDir/quast_0/file_1/report.tsv' && mkdir 'multiqc_WDir/quast_0/file_2' && ln -s '/tmp/tmprt3848zx/files/e/d/7/dataset_ed77817e-f289-4fae-bf42-c966814ecc21.dat' 'multiqc_WDir/quast_0/file_2/report.tsv' && mkdir 'multiqc_WDir/quast_0/file_3' && ln -s '/tmp/tmprt3848zx/files/e/6/8/dataset_e686e8aa-f208-4426-a853-338b3f87c309.dat' 'multiqc_WDir/quast_0/file_3/report.tsv' && mkdir multiqc_WDir/custom_content_1 && ln -s '/tmp/tmprt3848zx/files/a/6/e/dataset_a6eecb3b-b66d-45d3-9f7b-846b6e33a77a.dat' 'multiqc_WDir/custom_content_1/file_1_0' && more /tmp/tmprt3848zx/files/a/6/e/dataset_a6eecb3b-b66d-45d3-9f7b-846b6e33a77a.dat && mkdir multiqc_WDir/custom_content_2 && ln -s '/tmp/tmprt3848zx/files/1/c/8/dataset_1c8d4f04-8d75-4fa8-af8a-2245a2445c57.dat' 'multiqc_WDir/custom_content_2/file_2_0' && more /tmp/tmprt3848zx/files/1/c/8/dataset_1c8d4f04-8d75-4fa8-af8a-2245a2445c57.dat && mkdir multiqc_WDir/custom_content_3 && mkdir multiqc_WDir/bakta_4 &&     ln -s '/tmp/tmprt3848zx/files/3/5/3/dataset_3532e158-fd03-4e9d-9abb-f4b98fd32c84.dat' 'multiqc_WDir/bakta_4/50contig_reads_bin_1_fasta.txt' &&    ln -s '/tmp/tmprt3848zx/files/4/9/2/dataset_4926ecaa-5c5d-4384-ac34-acb9e189eb6c.dat' 'multiqc_WDir/bakta_4/50contig_reads_bin_11_fasta.txt' &&    ln -s '/tmp/tmprt3848zx/files/a/9/b/dataset_a9bb8a73-2816-4b1a-b75c-36bbda065fb1.dat' 'multiqc_WDir/bakta_4/50contig_reads_bin_55_fasta.txt' &&    ln -s '/tmp/tmprt3848zx/files/3/d/2/dataset_3d28f2c5-dfd4-435c-9685-cc74f02499d2.dat' 'multiqc_WDir/bakta_4/50contig_reads_bin_6_fasta.txt' &&  mkdir multiqc_WDir/custom_content_5 && ln -s '/tmp/tmprt3848zx/files/1/8/2/dataset_182937f4-c241-4988-bec9-8fb0fcac2d91.dat' 'multiqc_WDir/custom_content_5/file_5_0' && more /tmp/tmprt3848zx/files/1/8/2/dataset_182937f4-c241-4988-bec9-8fb0fcac2d91.dat &&   multiqc multiqc_WDir --filename 'report'      --config '/tmp/tmprt3848zx/job_working_directory/000/47/configs/tmpu72v_u3o'  && mkdir -p ./plots && ls -l ./report_data/ && cp ./report_data/*plot*.txt ./plots/ | true

Exit Code:

```
0
```

Standard Error:

/// MultiQC 🔍 v1.27

            config | Loading config settings from: /tmp/tmprt3848zx/job_working_directory/000/47/configs/tmpu72v_u3o
     version_check | MultiQC Version v1.28 now available!
       file_search | Search path: /tmp/tmprt3848zx/job_working_directory/000/47/working/multiqc_WDir

    custom_content | section_1: Found 4 samples (PlotType.TABLE)
    custom_content | section_2: Found 5 samples (PlotType.TABLE)
    custom_content | section_5: Found 4 samples (PlotType.TABLE)
             quast | Found 4 reports

     write_results | Data        : report_data
     write_results | Report      : report.html
           multiqc | MultiQC complete
cp: cannot stat './report_data/*plot*.txt': No such file or directory

Standard Output:

::::::::::::::
/tmp/tmprt3848zx/files/a/6/e/dataset_a6eecb3b-b66d-45d3-9f7b-846b6e33a77a.dat
::::::::::::::
Name	Completeness	Contamination	Completeness_Model_Used	Translation_Table_Used	Coding_Density	Contig_N50	Average_Gene_Length	Genome_Size	GC_Content	Total_Coding_Sequences	Total_Contigs	Max_Contig_Length	Additional_Notes
50contig_reads_bin_1.fasta	6.65	0.0	Gradient Boost (General Model)	11	0.693	1357	157.0	1357	0.39	2	1	1357	None
50contig_reads_bin_11.fasta	5.68	0.0	Gradient Boost (General Model)	11	0.941	2275	357.0	2275	0.38	2	1	2275	None
50contig_reads_bin_55.fasta	16.77	0.02	Neural Network (Specific Model)	11	0.916	5014	281.8505338078292	258860	0.36	281	56	11001	None
50contig_reads_bin_6.fasta	6.41	0.0	Gradient Boost (General Model)	11	0.908	1469	222.5	1469	0.39	2	1	1469	None
::::::::::::::
/tmp/tmprt3848zx/files/1/c/8/dataset_1c8d4f04-8d75-4fa8-af8a-2245a2445c57.dat
::::::::::::::
Genome	50contig_reads_50contig_reads Relative Abundance (%)
50contig_reads_bin_1	24.097418
50contig_reads_bin_11	26.34404
50contig_reads_bin_55	25.653187
50contig_reads_bin_6	23.202549
unmapped	0.7028103
::::::::::::::
/tmp/tmprt3848zx/files/1/8/2/dataset_182937f4-c241-4988-bec9-8fb0fcac2d91.dat
::::::::::::::
Bin Id	Marker lineage	# genomes	# markers	# marker sets	0	1	2	3	4	5+	Completeness	Contamination	Strain heterogeneity
50contig_reads_bin_1.fasta	root (UID1)	5656	56	24	56	0	0	0	0	0	0.00	0.00	0.00
50contig_reads_bin_11.fasta	root (UID1)	5656	56	24	56	0	0	0	0	0	0.00	0.00	0.00
50contig_reads_bin_55.fasta	k__Bacteria (UID203)	5449	103	58	88	15	0	0	0	0	17.40	0.00	0.00
50contig_reads_bin_6.fasta	root (UID1)	5656	56	24	56	0	0	0	0	0	0.00	0.00	0.00
total 300
-rw-r--r-- 1 1001 118    977 Apr 10 09:16 multiqc.log
-rw-r--r-- 1 1001 118    121 Apr 10 09:16 multiqc_citations.txt
-rw-r--r-- 1 1001 118 263513 Apr 10 09:16 multiqc_data.json
-rw-r--r-- 1 1001 118    205 Apr 10 09:16 multiqc_general_stats.txt
-rw-r--r-- 1 1001 118    620 Apr 10 09:16 multiqc_quast.txt
-rw-r--r-- 1 1001 118    689 Apr 10 09:16 multiqc_section_1_table.txt
-rw-r--r-- 1 1001 118    204 Apr 10 09:16 multiqc_section_2_table.txt
-rw-r--r-- 1 1001 118    431 Apr 10 09:16 multiqc_section_5_table.txt
-rw-r--r-- 1 1001 118    592 Apr 10 09:16 multiqc_sources.txt
-rw-r--r-- 1 1001 118    145 Apr 10 09:16 quast_num_contigs.txt
-rw-r--r-- 1 1001 118    277 Apr 10 09:16 quast_table.txt

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"input"`
__workflow_invocation_uuid__	`"85d8fbb215e611f0aeac6045bd812dcf"`
chromInfo	`"/tmp/tmprt3848zx/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
comment	`""`
dbkey	`"?"`
export	`false`
flat	`false`
image_content_input	`None`
results	[{"__index__": 0, "software_cond": {"__current_case__": 21, "input": {"values": [{"id": 63, "src": "hdca"}]}, "software": "quast"}}, {"__index__": 1, "software_cond": {"__current_case__": 46, "description": null, "input": {"values": [{"id": 100, "src": "hda"}]}, "plot_type": "table", "section_name": "CheckM2 Bin quality", "software": "custom_content", "title": null, "xlab": null, "ylab": null}}, {"__index__": 2, "software_cond": {"__current_case__": 46, "description": null, "input": {"values": [{"id": 131, "src": "hda"}]}, "plot_type": "table", "section_name": "CoverM Bin coverage", "software": "custom_content", "title": null, "xlab": null, "ylab": null}}, {"__index__": 3, "software_cond": {"__current_case__": 46, "description": null, "input": {"values": [{"id": 57, "src": "hdca"}]}, "plot_type": "table", "section_name": "GTDB-Tk taxonomy", "software": "custom_content", "title": null, "xlab": null, "ylab": null}}, {"__index__": 4, "software_cond": {"__current_case__": 34, "input": {"values": [{"id": 68, "src": "hdca"}]}, "software": "bakta"}}, {"__index__": 5, "software_cond": {"__current_case__": 46, "description": null, "input": {"values": [{"id": 101, "src": "hda"}]}, "plot_type": "table", "section_name": " CheckM Bin quality", "software": "custom_content", "title": null, "xlab": null, "ylab": null}}]
title	`""`

Step 7: Trimmed sample paired reads:
- step_state: scheduled
Step 8: Contamination weight (Binette):
- step_state: scheduled
Step 9: CheckM2 Database for Binette:
- step_state: scheduled
Step 10: Minimum MAG completeness percentage:
- step_state: scheduled

Other invocation details
- history_id
  - 3aa8f39cd3274f86
- history_state
  - ok
- invocation_id
  - 3aa8f39cd3274f86
- invocation_state
  - scheduled
- workflow_id
  - 3aa8f39cd3274f86

workflows/microbiome/mags-building/MAGs-generation.ga

workflows/microbiome/mags-building/MAGs-generation-tests.yml

workflows/microbiome/mags-building/MAGs-generation.ga

workflows/microbiome/mags-building/README.md

Co-authored-by: Marius van den Beek <m.vandenbeek@gmail.com>

…o MAGs-workflow

github-actions · 2025-04-10T14:09:28Z

Test Results (powered by Planemo)

Test Summary

Test State	Count
Total	1
Passed	0
Error	1
Failure	0
Skipped	0

Errored Tests

❌ MAGs-generation.ga_0

Execution Problem:

Unexpected HTTP status code: 400: {"err_msg":"Workflow cannot be run because input step '41' (CheckM2 Database) is not optional and no input provided.","err_code":0}

paulzierep · 2025-04-22T09:42:16Z

Hi @mvdbeek, it seems the latest test was successful: https://github.com/galaxyproject/iwc/actions/runs/14382300139?pr=769
Was the explanation for Trimmed reads / Grouped trimmed reads OK ? Can we do anything else to get this further ?

mvdbeek

Awesome, thank you!

workflows/microbiome/mags-building/MAGs-generation.ga

workflows/microbiome/mags-building/README.md

paulzierep · 2025-04-29T08:29:53Z

what needs to be done to finish: Check workflow success Expected — Waiting for status to be reported -sorry for the rush, it would be great to have this merged for project reporting

paulzierep · 2025-04-29T11:39:01Z

Ready for merge ?

paulzierep added 6 commits March 25, 2025 13:59

init MAGs workflow

0f1f197

trimmed tests

2075602

remove unwanted test files

545a4ca

meta, readme, dockstore

0537915

add test from zenodo, readme

e9496d0

lint

a946930

paulzierep mentioned this pull request Mar 27, 2025

Check IWC requirements usegalaxy-eu/FAIRyMAGs#25

Open

6 tasks

paulzierep added 3 commits April 8, 2025 15:45

update workflow

2fd5841

update dockstore

64425b9

dockstore yml

6521027

fix test

9551746

update GTDB-tk DB

5ca1796

paulzierep mentioned this pull request Apr 9, 2025

How to create a small test DB ? Ecogenomics/GTDBTk#629

Open

paulzierep added 3 commits April 9, 2025 15:45

Update readme

11a8fc6

update test, skip gtdb

438b897

skip bakta as well

3e8385e

fix test

64b0dcd