Metagenomic raw reads analysis workflow without assembly #1014

hugolefeuvre · 2025-11-03T14:36:12Z

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.

FOR REVIEWERS:

.dockstore.yml: file is present and aligned with creator metadata in workflow. ORCID identifiers are strongly encouraged in creator metadata. The .dockstore.yml file is required to run tests
Workflow is sufficiently generic to be used with lab data and does not hardcode sample names, reference data and can be run without reading an accompanying tutorial.
In workflow: annotation field contains short description of what the workflow does. Should start with This workflow does/runs/performs … xyz … to generate/analyze/etc …
In workflow: workflow inputs and outputs have human readable names (spaces are fine, no underscore, dash only where spelling dictates it), no abbreviation unless it is generally understood. Altering input or output labels requires adjusting these labels in the the workflow-tests.yml file as well
In workflow: name field should be human readable (spaces are fine, no underscore, dash only where spelling dictates it), no abbreviation unless generally understood
Workflow folder: prefer dash (-) over underscore (_), prefer all lowercase. Folder becomes repository in iwc-workflows organization and is included in TRS id
Readme explains what workflow does, what are valid inputs and what outputs users can expect. If a tutorial or other resources exist they can be linked. If a similar workflow exists in IWC readme should explain differences with existing workflow and when one might prefer one workflow over another
Changelog contains appropriate entries
Large files (> 100 KB) are uploaded to zenodo and location urls are used in test file

hugolefeuvre · 2025-11-03T14:44:07Z

They are missing DBs on cvmfs (Sylph, Groot and DeepARG) so tests will fail but I ask IDC to added DBs : galaxyproject/idc#77

github-actions · 2025-11-03T14:46:45Z

Test Results (powered by Planemo)

Test Summary

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

Errored Tests

❌ metagenomic-raw-reads-analysis.ga_0

Execution Problem:

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

Workflow invocation details

Invocation Messages
- Invocation scheduling failed because step 16 requires a dataset collection created by step 13, but dataset collection entered a failed state.

Steps

Step 1: Metagenomics Trimmed reads:
- step_state: scheduled
Step 2: Select a DeepARG database:
- step_state: scheduled

Step 11: 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 running

Command Line:

```
cd ../; python _evaluate_expression_.py
```

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"input"`
__workflow_invocation_uuid__	`"be6195f4b8c311f082707ced8d0a0a79"`
chromInfo	`"/tmp/tmpozvmlccj/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
dbkey	`"?"`
input_param_type	{"__current_case__": 0, "input_param": "arg-annot.90-1.1.2-09122024", "mappings": [{"__index__": 0, "from": "arg-annot.90-1.1.2-09122024", "to": "groot-argannot"}, {"__index__": 1, "from": "card (90 percent identity)", "to": "groot-card"}, {"__index__": 2, "from": "groot-core-db (90 percent identity)", "to": "groot-core-db"}, {"__index__": 3, "from": "resfinder (90 percent identity)", "to": "groot-resfinder"}, {"__index__": 4, "from": "groot-db (90 percent identity)", "to": "groot-db"}], "type": "text"}
output_param_type	`"text"`
unmapped	`{"__current_case__": 1, "on_unmapped": "fail"}`

Step 12: toolshed.g2.bx.psu.edu/repos/iuc/deeparg_short_reads/deeparg_short_reads/1.0.4+galaxy1:

step_state: scheduled

Jobs

Job 1:

Job state is error

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"input"`
__workflow_invocation_uuid__	`"be6195f4b8c311f082707ced8d0a0a79"`
bowtie_16s_identity	`"0.8"`
chromInfo	`"/tmp/tmpozvmlccj/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
dbkey	`"?"`
deeparg_db	`"deeparg_1.0.4-03072025"`
deeparg_evalue	`"1e-10"`
deeparg_identity	`"80"`
deeparg_probability	`"0.8"`
gene_coverage	`"95"`
hide_db_build	`""`
input_option	`{"__current_case__": 1, "choice": "paired_collection", "pair_input": {"values": [{"id": 1, "src": "dce"}]}}`
output_files	`{"output_selection": ["file_ARG_tsv", "file_ARG_subtype_tsv", "file_ARG_type_tsv", "file_merged_ARG_tsv", "file_potential_ARG_tsv", "file_all_hits_tsv"]}`

Step 13: toolshed.g2.bx.psu.edu/repos/bgruening/sylph_profile/sylph_profile/0.8.1+galaxy0:

step_state: scheduled

Jobs

Job 1:

Job state is error

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"input"`
__workflow_invocation_uuid__	`"be6195f4b8c311f082707ced8d0a0a79"`
chromInfo	`"/tmp/tmpozvmlccj/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
database_select	`{"__current_case__": 0, "column": "relative_abundance", "select": "cached", "sylph_database": "sylph_downloaded_21072025_gtdb-r220-c200-dbv1.syldb", "sylph_tax_metadata": "sylph_tax_downloaded_21072025"}`
dbkey	`"?"`
estimate_unknown	`false`
min_num_kmers	`"50"`
sketch_reads	`{"__current_case__": 3, "input": {"values": [{"id": 1, "src": "dce"}]}, "type_reads": "paired_group"}`

**Step 14: Combines files R1 and R2 **:

step_state: scheduled

Jobs

Job 1:

Job state is queued

Command Line:

gx-fastq-paired-end-interlacer '/tmp/tmpozvmlccj/files/6/8/5/dataset_6857f6bd-be7a-40a6-be93-5230ab2606bc.dat' sanger.gz '/tmp/tmpozvmlccj/files/d/2/6/dataset_d2602e61-033b-4dd3-bd1d-535391126046.dat' sanger.gz '/tmp/tmpozvmlccj/job_working_directory/000/8/outputs/dataset_6c55de04-ceca-4944-942f-4bb19b321b89.dat' '/tmp/tmpozvmlccj/job_working_directory/000/8/outputs/dataset_e37bb5ff-a365-4247-9657-9ff9242f6e60.dat'

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"fastqsanger.gz"`
__workflow_invocation_uuid__	`"be6195f4b8c311f082707ced8d0a0a79"`
chromInfo	`"/tmp/tmpozvmlccj/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
dbkey	`"?"`
reads	`{"__current_case__": 0, "input1_file": {"values": [{"id": 4, "src": "dce"}]}, "input2_file": {"values": [{"id": 5, "src": "dce"}]}, "reads_selector": "paired"}`

Step 15: argNorm Deeparg:

step_state: scheduled

Jobs

Job 1:

Job state is paused

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"input"`
__workflow_invocation_uuid__	`"be6195f4b8c311f082707ced8d0a0a79"`
choose_tool	`{"__current_case__": 0, "tool": "deeparg"}`
chromInfo	`"/tmp/tmpozvmlccj/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
dbkey	`"?"`

Step 16: Unlabelled step:
- step_state: new

Step 17: toolshed.g2.bx.psu.edu/repos/iuc/groot/groot/1.1.2+galaxy2:

step_state: scheduled

Jobs

Job 1:

Job state is new

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"input"`
__workflow_invocation_uuid__	`"be6195f4b8c311f082707ced8d0a0a79"`
align	`{"contThresh": "0.97", "minKmerCov": "1", "noAlign": true}`
chromInfo	`"/tmp/tmpozvmlccj/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
dbkey	`"?"`
index	`{"groot_db_select": "arg-annot.90-1.1.2-09122024", "kmerSize": "31", "maxK": "4", "maxSketchSpan": "30", "numPart": "8", "sketchSize": "21", "windowSize": "100"}`
report	`{"coverage": {"__current_case__": 0, "covCutoff": "0.6", "mode": "cutoff"}}`

Step 18: addValue:

step_state: scheduled

Jobs

Job 1:

Job state is paused

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"input"`
__workflow_invocation_uuid__	`"be6195f4b8c311f082707ced8d0a0a79"`
chromInfo	`"/tmp/tmpozvmlccj/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
dbkey	`"?"`
exp	`"DeepARG"`
iterate	`"no"`

Step 19: Unlabelled step:
- step_state: new
Step 20: Unlabelled step:
- step_state: new
Step 3: Select a Groot database:
- step_state: scheduled
Step 21: Unlabelled step:
- step_state: new
Step 22: Unlabelled step:
- step_state: new
Step 23: Unlabelled step:
- step_state: new
Step 24: Unlabelled step:
- step_state: new
Step 4: Deeparg minimum probability for considering a reads as ARG-like:
- step_state: scheduled
Step 5: Select a Sylph database:
- step_state: scheduled
Step 6: Select a Sylph tax database:
- step_state: scheduled
Step 7: Groot average base pair length of reads:
- step_state: scheduled
Step 8: Groot coverage cutoff for reporting ARGs:
- step_state: scheduled

Step 9: toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_text_file_with_recurring_lines/9.5+galaxy2:

step_state: scheduled

Jobs

Job 1:

Job state is queued

Command Line:

times=1; yes -- 'no_results' 2>/dev/null | head -n $times >> '/tmp/tmpozvmlccj/job_working_directory/000/3/outputs/dataset_301ac29e-616d-48da-800e-ecf01bf67b21.dat'; times=1; yes -- 'no_results' 2>/dev/null | head -n $times >> '/tmp/tmpozvmlccj/job_working_directory/000/3/outputs/dataset_301ac29e-616d-48da-800e-ecf01bf67b21.dat';

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"input"`
__workflow_invocation_uuid__	`"be6195f4b8c311f082707ced8d0a0a79"`
chromInfo	`"/tmp/tmpozvmlccj/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
dbkey	`"?"`
token_set	`[{"__index__": 0, "line": "no_results", "repeat_select": {"__current_case__": 0, "repeat_select_opts": "user", "times": "1"}}, {"__index__": 1, "line": "no_results", "repeat_select": {"__current_case__": 0, "repeat_select_opts": "user", "times": "1"}}]`

Step 10: __UNZIP_COLLECTION__:
- step_state: scheduled
- Jobs
  - Job 1:
    - Job state is ok
    Traceback:
    Job Parameters:
    - Job parameter Parameter value
      
      __workflow_invocation_uuid__ "be6195f4b8c311f082707ced8d0a0a79"
      
      input {"values": [{"id": 1, "src": "dce"}]}

Other invocation details
- error_message
  - Failed to run workflow, invocation ended in [failed] state.
- history_id
  - f8affb27b52afdab
- history_state
  - new
- invocation_id
  - f8affb27b52afdab
- invocation_state
  - failed
- messages
  - [{'dependent_workflow_step_id': 12, 'hdca_id': 'f9b1b179fbb2dfa1', 'reason': 'collection_failed', 'workflow_step_id': 15}]
- workflow_id
  - f8affb27b52afdab

github-actions · 2025-11-11T12:20:53Z

Test Results (powered by Planemo)

Test Summary

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

Errored Tests

❌ metagenomic-raw-reads-analysis.ga_0

Execution Problem:

Upload job [590e8452f07b35d7] produced output [1: PSM6XBT3_500k_R1.fastq.gz] in state [error]

github-actions · 2025-11-12T13:01:34Z

Test Results (powered by Planemo)

Test Summary

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

Errored Tests

❌ metagenomic-raw-reads-analysis.ga_0

Execution Problem:

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

Workflow invocation details

Invocation Messages
- Invocation scheduling failed because an unexpected failure occurred at step 23: 'Cannot match collection types.'

Steps

Step 1: Metagenomics Trimmed reads:
- step_state: scheduled
Step 2: Select a DeepARG database:
- step_state: scheduled
Step 11: __UNZIP_COLLECTION__:
- step_state: scheduled
- Jobs
  - Job 1:
    - Job state is ok
    Traceback:
    Job Parameters:
    - Job parameter Parameter value
      
      __workflow_invocation_uuid__ "83c5d47cbfbd11f0bb736045bd8384a1"
      
      input {"values": [{"id": 1, "src": "dce"}]}

Step 12: toolshed.g2.bx.psu.edu/repos/iuc/deeparg_short_reads/deeparg_short_reads/1.0.4+galaxy1:

step_state: scheduled

Jobs

Job 1:

Job state is ok

Command Line:

mkdir -p deeparg_short_reads_output && ln -s -f '/tmp/tmp0xmsn2s3/files/7/c/6/dataset_7c642f47-35fd-4214-a3a7-e084b84017a7.dat' 'input_forward.fastqsanger.gz' && ln -s -f '/tmp/tmp0xmsn2s3/files/4/b/d/dataset_4bdf702a-9578-497b-b8ec-f5b805daf349.dat' 'input_reverse.fastqsanger.gz' && deeparg short_reads_pipeline --forward_pe_file 'input_forward.fastqsanger.gz' --reverse_pe_file 'input_reverse.fastqsanger.gz' --output_file 'deeparg_short_reads_output/SR' -d '/cvmfs/data.galaxyproject.org/byhand/deeparg/deeparg_1.0.4' --deeparg_identity 80 --deeparg_probability 0.8 --deeparg_evalue 1e-10 --gene_coverage 95 --bowtie_16s_identity 0.8

Exit Code:

```
0
```

Standard Error:

WARNING (theano.configdefaults): g++ not detected ! Theano will be unable to execute optimized C-implementations (for both CPU and GPU) and will default to Python implementations. Performance will be severely degraded. To remove this warning, set Theano flags cxx to an empty string.
/usr/local/lib/python2.7/site-packages/theano/tensor/signal/downsample.py:6: UserWarning: downsample module has been moved to the theano.tensor.signal.pool module.
  "downsample module has been moved to the theano.tensor.signal.pool module.")
/usr/local/lib/python2.7/site-packages/sklearn/cross_validation.py:41: DeprecationWarning: This module was deprecated in version 0.18 in favor of the model_selection module into which all the refactored classes and functions are moved. Also note that the interface of the new CV iterators are different from that of this module. This module will be removed in 0.20.
  "This module will be removed in 0.20.", DeprecationWarning)
TrimmomaticPE: Started with arguments:
 -phred33 input_forward.fastqsanger.gz input_reverse.fastqsanger.gz input_forward.fastqsanger.gz.paired input_forward.fastqsanger.gz.unpaired input_reverse.fastqsanger.gz.paired input_reverse.fastqsanger.gz.unpaired LEADING:3 TRAILING:3 SLIDINGWINDOW:4:15 MINLEN:36
Multiple cores found: Using 4 threads
Input Read Pairs: 125000 Both Surviving: 125000 (100.00%) Forward Only Surviving: 0 (0.00%) Reverse Only Surviving: 0 (0.00%) Dropped: 0 (0.00%)
TrimmomaticPE: Completed successfully
vsearch v2.27.1_linux_x86_64, 15.6GB RAM, 4 cores
https://github.com/torognes/vsearch

Merging reads 100%
    125000  Pairs
     69309  Merged (55.4%)
     55691  Not merged (44.6%)

Pairs that failed merging due to various reasons:
     39021  too few kmers found on same diagonal
       265  multiple potential alignments
     12101  alignment score too low, or score drop too high
       295  overlap too short
      4009  staggered read pairs

Statistics of all reads:
     92.44  Mean read length

Statistics of merged reads:
    109.97  Mean fragment length
     40.60  Standard deviation of fragment length
      0.07  Mean expected error in forward sequences
      0.06  Mean expected error in reverse sequences
      0.04  Mean expected error in merged sequences
      0.01  Mean observed errors in merged region of forward sequences
      0.00  Mean observed errors in merged region of reverse sequences
      0.01  Mean observed errors in merged region
WARNING (theano.configdefaults): g++ not detected ! Theano will be unable to execute optimized C-implementations (for both CPU and GPU) and will default to Python implementations. Performance will be severely degraded. To remove this warning, set Theano flags cxx to an empty string.
/usr/local/lib/python2.7/site-packages/theano/tensor/signal/downsample.py:6: UserWarning: downsample module has been moved to the theano.tensor.signal.pool module.
  "downsample module has been moved to the theano.tensor.signal.pool module.")
/usr/local/lib/python2.7/site-packages/sklearn/cross_validation.py:41: DeprecationWarning: This module was deprecated in version 0.18 in favor of the model_selection module into which all the refactored classes and functions are moved. Also note that the interface of the new CV iterators are different from that of this module. This module will be removed in 0.20.
  "This module will be removed in 0.20.", DeprecationWarning)
INFO:root:DIAMOND blastx alignment
INFO:root:Running: diamond  blastx -q deeparg_short_reads_output/SR.clean -d /cvmfs/data.galaxyproject.org/byhand/deeparg/deeparg_1.0.4/database/v2/features -k 1000 --id 80.0 --sensitive -e 1e-10 -a deeparg_short_reads_output/SR.clean.deeparg.align
INFO:root:Input:deeparg_short_reads_output/SR.clean output:deeparg_short_reads_output/SR.clean.deeparg model: deepARG_SS, Input type: blastx
INFO:root:parsing output file diamond view -a deeparg_short_reads_output/SR.clean.deeparg.align.daa -o deeparg_short_reads_output/SR.clean.deeparg.align.daa.tsv
diamond v2.1.10.164 (C) Max Planck Society for the Advancement of Science, Benjamin Buchfink, University of Tuebingen
Documentation, support and updates available at http://www.diamondsearch.org
Please cite: http://dx.doi.org/10.1038/s41592-021-01101-x Nature Methods (2021)

#CPU threads: 4
Loading subject IDs...  [0s]
Scoring parameters: (Matrix=blosum62 Lambda=0.267 K=0.041 Penalties=11/1)
DB sequences = 12279
DB sequences used = 642
DB letters = 5088898
#Target sequences to report alignments for: 25
Generating output...  [0.001s]
INFO:root:Loading deep learning model ...
INFO:root:loading gene lengths
INFO:root:Loading sample to analyze

0reads [00:00, ?reads/s]
1237reads [00:00, 244169.33reads/s]
INFO:root:Predicting ARG-like reads: Running deepARG_SS model version v2
INFO:root:input dataset is splitted into chunks of 10000 reads

0chunks [00:00, ?chunks/s]
1chunks [00:07,  7.44s/chunks]
1chunks [00:07,  7.44s/chunks]
INFO:root:Predicting ARGs

  0%|          | 0/136 [00:00<?, ?it/s]
100%|██████████| 136/136 [00:00<00:00, 41731.31it/s]
180691 reads; of these:
  180691 (100.00%) were unpaired; of these:
    180399 (99.84%) aligned 0 times
    0 (0.00%) aligned exactly 1 time
    292 (0.16%) aligned >1 times
0.16% overall alignment rate

Standard Output:

Step 1: Trimming and QC using Trimmomatic
['/usr/local/bin', '/usr/local/lib/python27.zip', '/usr/local/lib/python2.7', '/usr/local/lib/python2.7/plat-linux2', '/usr/local/lib/python2.7/lib-tk', '/usr/local/lib/python2.7/lib-old', '/usr/local/lib/python2.7/lib-dynload', '/usr/local/lib/python2.7/site-packages']



Step 2: Merging paired end reads using Vsearch
['/usr/local/bin', '/usr/local/lib/python27.zip', '/usr/local/lib/python2.7', '/usr/local/lib/python2.7/plat-linux2', '/usr/local/lib/python2.7/lib-tk', '/usr/local/lib/python2.7/lib-old', '/usr/local/lib/python2.7/lib-dynload', '/usr/local/lib/python2.7/site-packages']



Step 3: Run DeepARG-SS to identify ARG-like reads
deeparg predict --type nucl --model SS -d /cvmfs/data.galaxyproject.org/byhand/deeparg/deeparg_1.0.4 -i deeparg_short_reads_output/SR.clean -o deeparg_short_reads_output/SR.clean.deeparg --arg-alignment-identity 80.0 --min-prob 0.8 --arg-alignment-evalue 1e-10



Step 4: Quantification of ARG-like counts
sort -k1,1 -k2,2n deeparg_short_reads_output/SR.clean.deeparg.mapping.ARG  | bedtools merge -c 12,5 -o sum,distinct >deeparg_short_reads_output/SR.clean.deeparg.mapping.ARG.merged



Step 5: Normalize to 16S rRNAs - this may take a while ...
Total number of 16S Reads in the sample: 178

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"input"`
__workflow_invocation_uuid__	`"83c5d47cbfbd11f0bb736045bd8384a1"`
bowtie_16s_identity	`"0.8"`
chromInfo	`"/tmp/tmp0xmsn2s3/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
dbkey	`"?"`
deeparg_db	`"deeparg_1.0.4-07112025"`
deeparg_evalue	`"1e-10"`
deeparg_identity	`"80"`
deeparg_probability	`"0.8"`
gene_coverage	`"95"`
hide_db_build	`""`
input_option	`{"__current_case__": 1, "choice": "paired_collection", "pair_input": {"values": [{"id": 1, "src": "dce"}]}}`
output_files	`{"output_selection": ["file_ARG_tsv", "file_ARG_subtype_tsv", "file_ARG_type_tsv", "file_merged_ARG_tsv", "file_potential_ARG_tsv", "file_all_hits_tsv"]}`

Step 13: toolshed.g2.bx.psu.edu/repos/bgruening/sylph_profile/sylph_profile/0.8.1+galaxy0:

step_state: scheduled

Jobs

Job 1:

Job state is error

Command Line:

ln -s '/cvmfs/data.galaxyproject.org/byhand/sylph/gtdb-r220-c200-dbv1.syldb' '0_sylph_database.syldb' &&       ln -s '/tmp/tmp0xmsn2s3/files/7/c/6/dataset_7c642f47-35fd-4214-a3a7-e084b84017a7.dat' 'raw_reads_metag_test.fastq.gz' && ln -s '/tmp/tmp0xmsn2s3/files/4/b/d/dataset_4bdf702a-9578-497b-b8ec-f5b805daf349.dat' 'raw_reads_metag_test_r2.fastq.gz' &&  sylph sketch -1 raw_reads_metag_test.fastq.gz -2 raw_reads_metag_test_r2.fastq.gz -t ${GALAXY_SLOTS:-4} -d sylph_sketches &&   sylph profile *.syldb sylph_sketches/*.sylsp --min-number-kmers 50 -t ${GALAXY_SLOTS:-4} -o '/tmp/tmp0xmsn2s3/job_working_directory/000/6/outputs/dataset_2acf163a-57a6-448d-9f05-105ac2f9cb8d.dat'  && cp '/tmp/tmp0xmsn2s3/job_working_directory/000/6/configs/tmpmsrpgsbe' config.json && export SYLPH_TAXONOMY_CONFIG=config.json && mkdir -p sylph_taxprof_out && sylph-tax taxprof '/tmp/tmp0xmsn2s3/job_working_directory/000/6/outputs/dataset_2acf163a-57a6-448d-9f05-105ac2f9cb8d.dat' -o sylph_taxprof_out/'sylph_tax_out-' --taxonomy-metadata GTDB_r220 && sylph-tax merge sylph_taxprof_out/*.sylphmpa --column relative_abundance -o output_tax_merge.tsv

Exit Code:

```
137
```

Standard Error:

2025-11-12T11:49:06.567Z INFO  [sylph::sketch] Sketching paired sequences...
2025-11-12T11:49:06.768Z INFO  [sylph::sketch] Sketching sylph_sketches/raw_reads_metag_test.fastq.gz.paired.sylsp complete.
2025-11-12T11:49:06.768Z INFO  [sylph::sketch] Finished.
2025-11-12T11:49:06.771Z INFO  [sylph::contain] Obtaining sketches...
/tmp/tmp0xmsn2s3/job_working_directory/000/6/tool_script.sh: line 23:    12 Killed                  sylph profile *.syldb sylph_sketches/*.sylsp --min-number-kmers 50 -t ${GALAXY_SLOTS:-4} -o '/tmp/tmp0xmsn2s3/job_working_directory/000/6/outputs/dataset_2acf163a-57a6-448d-9f05-105ac2f9cb8d.dat'

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"input"`
__workflow_invocation_uuid__	`"83c5d47cbfbd11f0bb736045bd8384a1"`
chromInfo	`"/tmp/tmp0xmsn2s3/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
database_select	`{"__current_case__": 0, "column": "relative_abundance", "select": "cached", "sylph_database": "sylph_downloaded_07112025_gtdb-r220-c200-dbv1.syldb", "sylph_tax_metadata": "sylph_tax_downloaded_08112025"}`
dbkey	`"?"`
estimate_unknown	`false`
min_num_kmers	`"50"`
sketch_reads	`{"__current_case__": 3, "input": {"values": [{"id": 1, "src": "dce"}]}, "type_reads": "paired_group"}`

**Step 14: Combines files R1 and R2 **:

step_state: scheduled

Jobs

Job 1:

Job state is ok

Command Line:

gx-fastq-paired-end-interlacer '/tmp/tmp0xmsn2s3/files/7/c/6/dataset_7c642f47-35fd-4214-a3a7-e084b84017a7.dat' sanger.gz '/tmp/tmp0xmsn2s3/files/4/b/d/dataset_4bdf702a-9578-497b-b8ec-f5b805daf349.dat' sanger.gz '/tmp/tmp0xmsn2s3/job_working_directory/000/7/outputs/dataset_a453d95c-839d-494e-bb94-f0843a8b98e7.dat' '/tmp/tmp0xmsn2s3/job_working_directory/000/7/outputs/dataset_615e273f-3da9-4c8c-9869-2db69e725879.dat'

Exit Code:

```
0
```

Standard Output:

There were 0 single reads.
Interlaced 125000 pairs of sequences.

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"fastqsanger.gz"`
__workflow_invocation_uuid__	`"83c5d47cbfbd11f0bb736045bd8384a1"`
chromInfo	`"/tmp/tmp0xmsn2s3/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
dbkey	`"?"`
reads	`{"__current_case__": 0, "input1_file": {"values": [{"id": 4, "src": "dce"}]}, "input2_file": {"values": [{"id": 5, "src": "dce"}]}, "reads_selector": "paired"}`

Step 15: argNorm Deeparg:

step_state: scheduled

Jobs

Job 1:

Job state is ok

Command Line:

argnorm 'deeparg' -i '/tmp/tmp0xmsn2s3/files/6/c/3/dataset_6c33f76d-ab25-4bdd-85c6-1e53e1ee4dfb.dat' -o '/tmp/tmp0xmsn2s3/job_working_directory/000/8/outputs/dataset_bb7e74db-579b-4f15-ab6b-39b92cf5deda.dat'

Exit Code:

```
0
```

Standard Output:

/tmp/tmp0xmsn2s3/job_working_directory/000/8/outputs/dataset_bb7e74db-579b-4f15-ab6b-39b92cf5deda.dat: 100.0% ARGs mapped.

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"input"`
__workflow_invocation_uuid__	`"83c5d47cbfbd11f0bb736045bd8384a1"`
choose_tool	`{"__current_case__": 0, "tool": "deeparg"}`
chromInfo	`"/tmp/tmp0xmsn2s3/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
dbkey	`"?"`

Step 16: Unlabelled step:
- step_state: scheduled

Step 17: toolshed.g2.bx.psu.edu/repos/iuc/groot/groot/1.1.2+galaxy2:

step_state: scheduled

Jobs

Job 1:

Job state is ok

Command Line:

set -x pipefail; ln -s -f '/tmp/tmp0xmsn2s3/files/a/4/5/dataset_a453d95c-839d-494e-bb94-f0843a8b98e7.dat' 'input.fastq.gz' && groot index --msaDir '/cvmfs/data.galaxyproject.org/byhand/groot_database/arg-annot.90' --indexDir 'grootIndex' --windowSize 100 --kmerSize 31 --maxK 4 --maxSketchSpan 30 --numPart 8 --sketchSize 21 &&  groot align --fastq 'input.fastq.gz' --indexDir 'grootIndex' --contThresh 0.97 --minKmerCov 1  --processors "${GALAXY_SLOTS:-1}"  | groot report --covCutoff '0.6' > '/tmp/tmp0xmsn2s3/job_working_directory/000/9/outputs/dataset_afc6aebe-aa71-45b3-b777-794d601d6a8b.dat'

Exit Code:

```
0
```

Standard Error:

+ ln -s -f /tmp/tmp0xmsn2s3/files/a/4/5/dataset_a453d95c-839d-494e-bb94-f0843a8b98e7.dat input.fastq.gz
+ groot index --msaDir /cvmfs/data.galaxyproject.org/byhand/groot_database/arg-annot.90 --indexDir grootIndex --windowSize 100 --kmerSize 31 --maxK 4 --maxSketchSpan 30 --numPart 8 --sketchSize 21
+ groot align --fastq input.fastq.gz --indexDir grootIndex --contThresh 0.97 --minKmerCov 1 --processors 1
+ groot report --covCutoff 0.6

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"input"`
__workflow_invocation_uuid__	`"83c5d47cbfbd11f0bb736045bd8384a1"`
align	`{"contThresh": "0.97", "minKmerCov": "1", "noAlign": true}`
chromInfo	`"/tmp/tmp0xmsn2s3/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
dbkey	`"?"`
index	`{"groot_db_select": "arg-annot.90-1.1.2-08112025", "kmerSize": "31", "maxK": "4", "maxSketchSpan": "30", "numPart": "8", "sketchSize": "21", "windowSize": "100"}`
report	`{"coverage": {"__current_case__": 0, "covCutoff": "0.6", "mode": "cutoff"}}`

Step 18: addValue:

step_state: scheduled

Jobs

Job 1:

Job state is ok

Command Line:

perl '/tmp/tmp0xmsn2s3/galaxy-dev/tools/filters/fixedValueColumn.pl' '/tmp/tmp0xmsn2s3/files/b/b/7/dataset_bb7e74db-579b-4f15-ab6b-39b92cf5deda.dat' '/tmp/tmp0xmsn2s3/job_working_directory/000/10/outputs/dataset_3fa7d410-8b10-47ca-953a-dabf67ec2a0f.dat' 'DeepARG' no

Exit Code:

```
0
```

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"input"`
__workflow_invocation_uuid__	`"83c5d47cbfbd11f0bb736045bd8384a1"`
chromInfo	`"/tmp/tmp0xmsn2s3/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
dbkey	`"?"`
exp	`"DeepARG"`
iterate	`"no"`

Step 19: __FLATTEN__:
- step_state: scheduled
- Jobs
  - Job 1:
    - Job state is ok
    Traceback:
    Job Parameters:
    - Job parameter Parameter value
      
      __workflow_invocation_uuid__ "83c5d47cbfbd11f0bb736045bd8384a1"
      
      input {"values": [{"id": 21, "src": "hdca"}]}
      
      join_identifier "_"

Step 20: toolshed.g2.bx.psu.edu/repos/iuc/argnorm/argnorm/1.0.0+galaxy0:

step_state: scheduled

Jobs

Job 1:

Job state is ok

Command Line:

argnorm 'groot' --db 'groot-argannot' -i '/tmp/tmp0xmsn2s3/files/a/f/c/dataset_afc6aebe-aa71-45b3-b777-794d601d6a8b.dat' -o '/tmp/tmp0xmsn2s3/job_working_directory/000/11/outputs/dataset_57feef54-eb18-49df-9da6-c31ac5c4c94f.dat'

Exit Code:

```
0
```

Standard Output:

/tmp/tmp0xmsn2s3/job_working_directory/000/11/outputs/dataset_57feef54-eb18-49df-9da6-c31ac5c4c94f.dat: 100.0% ARGs mapped.

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"input"`
__workflow_invocation_uuid__	`"83c5d47cbfbd11f0bb736045bd8384a1"`
choose_tool	`{"__current_case__": 5, "db": "groot-argannot", "tool": "groot"}`
chromInfo	`"/tmp/tmp0xmsn2s3/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
dbkey	`"?"`

Step 3: Select a Groot database:
- step_state: scheduled
Step 21: __FILTER_FAILED_DATASETS__:
- step_state: scheduled
- Jobs
  - Job 1:
    - Job state is ok
    Traceback:
    Job Parameters:
    - Job parameter Parameter value
      
      __workflow_invocation_uuid__ "83c5d47cbfbd11f0bb736045bd8384a1"
      
      input {"values": [{"id": 18, "src": "hdca"}]}

Step 22: addValue:

step_state: scheduled

Jobs

Job 1:

Job state is ok

Command Line:

perl '/tmp/tmp0xmsn2s3/galaxy-dev/tools/filters/fixedValueColumn.pl' '/tmp/tmp0xmsn2s3/files/5/7/f/dataset_57feef54-eb18-49df-9da6-c31ac5c4c94f.dat' '/tmp/tmp0xmsn2s3/job_working_directory/000/13/outputs/dataset_8b2ec3ba-c23b-41b5-bc60-1dececb0ec88.dat' 'Groot' no

Exit Code:

```
0
```

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"input"`
__workflow_invocation_uuid__	`"83c5d47cbfbd11f0bb736045bd8384a1"`
chromInfo	`"/tmp/tmp0xmsn2s3/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
dbkey	`"?"`
exp	`"Groot"`
iterate	`"no"`

Step 23: Unlabelled step:
- step_state: new
Step 24: Unlabelled step:
- step_state: new
Step 4: Select a Groot database for ARGnorm:
- step_state: scheduled
Step 5: Deeparg minimum probability for considering a reads as ARG-like:
- step_state: scheduled
Step 6: Select a Sylph database:
- step_state: scheduled
Step 7: Select a Sylph tax database:
- step_state: scheduled
Step 8: Groot average base pair length of reads:
- step_state: scheduled
Step 9: Groot coverage cutoff for reporting ARGs:
- step_state: scheduled

Step 10: toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_text_file_with_recurring_lines/9.5+galaxy2:

step_state: scheduled

Jobs

Job 1:

Job state is ok

Command Line:

times=1; yes -- 'no_results' 2>/dev/null | head -n $times >> '/tmp/tmp0xmsn2s3/job_working_directory/000/3/outputs/dataset_b803da1d-79a0-4da6-9daf-2ea54fb48497.dat'; times=1; yes -- 'no_results' 2>/dev/null | head -n $times >> '/tmp/tmp0xmsn2s3/job_working_directory/000/3/outputs/dataset_b803da1d-79a0-4da6-9daf-2ea54fb48497.dat';

Exit Code:

```
0
```

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"input"`
__workflow_invocation_uuid__	`"83c5d47cbfbd11f0bb736045bd8384a1"`
chromInfo	`"/tmp/tmp0xmsn2s3/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
dbkey	`"?"`
token_set	`[{"__index__": 0, "line": "no_results", "repeat_select": {"__current_case__": 0, "repeat_select_opts": "user", "times": "1"}}, {"__index__": 1, "line": "no_results", "repeat_select": {"__current_case__": 0, "repeat_select_opts": "user", "times": "1"}}]`

Other invocation details
- error_message
  - Failed to run workflow, invocation ended in [failed] state.
- history_id
  - ed2addef42524e29
- history_state
  - error
- invocation_id
  - ed2addef42524e29
- invocation_state
  - failed
- messages
  - [{'details': 'Cannot match collection types.', 'reason': 'unexpected_failure', 'workflow_step_id': 22}]
- workflow_id
  - ed2addef42524e29

hugolefeuvre · 2025-11-12T13:46:24Z

Hi, it seems that the tests fail for sylph job due to memory issue, do you know how to handle this ?

❌ Failed job f08065326a26f9cc:
Tool ID:
toolshed.g2.bx.psu.edu/repos/bgruening/sylph_profile/sylph_profile/0.8.1+galaxy0
Exit code: 137

github-actions · 2025-11-14T11:57:04Z

Test Results (powered by Planemo)

Test Summary

Test State	Count
Total	2
Passed	0
Error	2
Failure	0
Skipped	0

Errored Tests

❌ metagenomic-raw-reads-amr-analysis.ga_0

Execution Problem:

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

Workflow invocation details

Invocation Messages
- Invocation scheduling failed because an unexpected failure occurred at step 23: 'Cannot match collection types.'

Steps

Step 1: Metagenomics Trimmed reads:
- step_state: scheduled
Step 2: Select a DeepARG database:
- step_state: scheduled
Step 11: __UNZIP_COLLECTION__:
- step_state: scheduled
- Jobs
  - Job 1:
    - Job state is ok
    Traceback:
    Job Parameters:
    - Job parameter Parameter value
      
      __workflow_invocation_uuid__ "cc2b60fec14a11f0a059000d3a047ab5"
      
      input {"values": [{"id": 1, "src": "dce"}]}

Step 12: toolshed.g2.bx.psu.edu/repos/iuc/deeparg_short_reads/deeparg_short_reads/1.0.4+galaxy1:

step_state: scheduled

Jobs

Job 1:

Job state is ok

Command Line:

mkdir -p deeparg_short_reads_output && ln -s -f '/tmp/tmp9yfvh3ca/files/9/d/d/dataset_9ddb3a13-517f-4f52-9e9f-ebb128586c72.dat' 'input_forward.fastqsanger.gz' && ln -s -f '/tmp/tmp9yfvh3ca/files/b/b/f/dataset_bbf1e905-17ae-4d59-803c-c30b96c6bb09.dat' 'input_reverse.fastqsanger.gz' && deeparg short_reads_pipeline --forward_pe_file 'input_forward.fastqsanger.gz' --reverse_pe_file 'input_reverse.fastqsanger.gz' --output_file 'deeparg_short_reads_output/SR' -d '/cvmfs/data.galaxyproject.org/byhand/deeparg/deeparg_1.0.4' --deeparg_identity 80 --deeparg_probability 0.8 --deeparg_evalue 1e-10 --gene_coverage 95 --bowtie_16s_identity 0.8

Exit Code:

```
0
```

Standard Error:

WARNING (theano.configdefaults): g++ not detected ! Theano will be unable to execute optimized C-implementations (for both CPU and GPU) and will default to Python implementations. Performance will be severely degraded. To remove this warning, set Theano flags cxx to an empty string.
/usr/local/lib/python2.7/site-packages/theano/tensor/signal/downsample.py:6: UserWarning: downsample module has been moved to the theano.tensor.signal.pool module.
  "downsample module has been moved to the theano.tensor.signal.pool module.")
/usr/local/lib/python2.7/site-packages/sklearn/cross_validation.py:41: DeprecationWarning: This module was deprecated in version 0.18 in favor of the model_selection module into which all the refactored classes and functions are moved. Also note that the interface of the new CV iterators are different from that of this module. This module will be removed in 0.20.
  "This module will be removed in 0.20.", DeprecationWarning)
TrimmomaticPE: Started with arguments:
 -phred33 input_forward.fastqsanger.gz input_reverse.fastqsanger.gz input_forward.fastqsanger.gz.paired input_forward.fastqsanger.gz.unpaired input_reverse.fastqsanger.gz.paired input_reverse.fastqsanger.gz.unpaired LEADING:3 TRAILING:3 SLIDINGWINDOW:4:15 MINLEN:36
Multiple cores found: Using 4 threads
Input Read Pairs: 125000 Both Surviving: 125000 (100.00%) Forward Only Surviving: 0 (0.00%) Reverse Only Surviving: 0 (0.00%) Dropped: 0 (0.00%)
TrimmomaticPE: Completed successfully
vsearch v2.27.1_linux_x86_64, 15.6GB RAM, 4 cores
https://github.com/torognes/vsearch

Merging reads 100%
    125000  Pairs
     69309  Merged (55.4%)
     55691  Not merged (44.6%)

Pairs that failed merging due to various reasons:
     39021  too few kmers found on same diagonal
       265  multiple potential alignments
     12101  alignment score too low, or score drop too high
       295  overlap too short
      4009  staggered read pairs

Statistics of all reads:
     92.44  Mean read length

Statistics of merged reads:
    109.97  Mean fragment length
     40.60  Standard deviation of fragment length
      0.07  Mean expected error in forward sequences
      0.06  Mean expected error in reverse sequences
      0.04  Mean expected error in merged sequences
      0.01  Mean observed errors in merged region of forward sequences
      0.00  Mean observed errors in merged region of reverse sequences
      0.01  Mean observed errors in merged region
WARNING (theano.configdefaults): g++ not detected ! Theano will be unable to execute optimized C-implementations (for both CPU and GPU) and will default to Python implementations. Performance will be severely degraded. To remove this warning, set Theano flags cxx to an empty string.
/usr/local/lib/python2.7/site-packages/theano/tensor/signal/downsample.py:6: UserWarning: downsample module has been moved to the theano.tensor.signal.pool module.
  "downsample module has been moved to the theano.tensor.signal.pool module.")
/usr/local/lib/python2.7/site-packages/sklearn/cross_validation.py:41: DeprecationWarning: This module was deprecated in version 0.18 in favor of the model_selection module into which all the refactored classes and functions are moved. Also note that the interface of the new CV iterators are different from that of this module. This module will be removed in 0.20.
  "This module will be removed in 0.20.", DeprecationWarning)
INFO:root:DIAMOND blastx alignment
INFO:root:Running: diamond  blastx -q deeparg_short_reads_output/SR.clean -d /cvmfs/data.galaxyproject.org/byhand/deeparg/deeparg_1.0.4/database/v2/features -k 1000 --id 80.0 --sensitive -e 1e-10 -a deeparg_short_reads_output/SR.clean.deeparg.align
INFO:root:Input:deeparg_short_reads_output/SR.clean output:deeparg_short_reads_output/SR.clean.deeparg model: deepARG_SS, Input type: blastx
INFO:root:parsing output file diamond view -a deeparg_short_reads_output/SR.clean.deeparg.align.daa -o deeparg_short_reads_output/SR.clean.deeparg.align.daa.tsv
diamond v2.1.10.164 (C) Max Planck Society for the Advancement of Science, Benjamin Buchfink, University of Tuebingen
Documentation, support and updates available at http://www.diamondsearch.org
Please cite: http://dx.doi.org/10.1038/s41592-021-01101-x Nature Methods (2021)

#CPU threads: 4
Loading subject IDs...  [0s]
Scoring parameters: (Matrix=blosum62 Lambda=0.267 K=0.041 Penalties=11/1)
DB sequences = 12279
DB sequences used = 642
DB letters = 5088898
#Target sequences to report alignments for: 25
Generating output...  [0.001s]
INFO:root:Loading deep learning model ...
INFO:root:loading gene lengths
INFO:root:Loading sample to analyze

0reads [00:00, ?reads/s]
1237reads [00:00, 256164.41reads/s]
INFO:root:Predicting ARG-like reads: Running deepARG_SS model version v2
INFO:root:input dataset is splitted into chunks of 10000 reads

0chunks [00:00, ?chunks/s]
1chunks [00:07,  7.95s/chunks]
1chunks [00:07,  7.95s/chunks]
INFO:root:Predicting ARGs

  0%|          | 0/136 [00:00<?, ?it/s]
100%|██████████| 136/136 [00:00<00:00, 40366.95it/s]
180691 reads; of these:
  180691 (100.00%) were unpaired; of these:
    180399 (99.84%) aligned 0 times
    0 (0.00%) aligned exactly 1 time
    292 (0.16%) aligned >1 times
0.16% overall alignment rate

Standard Output:

Step 1: Trimming and QC using Trimmomatic
['/usr/local/bin', '/usr/local/lib/python27.zip', '/usr/local/lib/python2.7', '/usr/local/lib/python2.7/plat-linux2', '/usr/local/lib/python2.7/lib-tk', '/usr/local/lib/python2.7/lib-old', '/usr/local/lib/python2.7/lib-dynload', '/usr/local/lib/python2.7/site-packages']



Step 2: Merging paired end reads using Vsearch
['/usr/local/bin', '/usr/local/lib/python27.zip', '/usr/local/lib/python2.7', '/usr/local/lib/python2.7/plat-linux2', '/usr/local/lib/python2.7/lib-tk', '/usr/local/lib/python2.7/lib-old', '/usr/local/lib/python2.7/lib-dynload', '/usr/local/lib/python2.7/site-packages']



Step 3: Run DeepARG-SS to identify ARG-like reads
deeparg predict --type nucl --model SS -d /cvmfs/data.galaxyproject.org/byhand/deeparg/deeparg_1.0.4 -i deeparg_short_reads_output/SR.clean -o deeparg_short_reads_output/SR.clean.deeparg --arg-alignment-identity 80.0 --min-prob 0.8 --arg-alignment-evalue 1e-10



Step 4: Quantification of ARG-like counts
sort -k1,1 -k2,2n deeparg_short_reads_output/SR.clean.deeparg.mapping.ARG  | bedtools merge -c 12,5 -o sum,distinct >deeparg_short_reads_output/SR.clean.deeparg.mapping.ARG.merged



Step 5: Normalize to 16S rRNAs - this may take a while ...
Total number of 16S Reads in the sample: 178

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"input"`
__workflow_invocation_uuid__	`"cc2b60fec14a11f0a059000d3a047ab5"`
bowtie_16s_identity	`"0.8"`
chromInfo	`"/tmp/tmp9yfvh3ca/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
dbkey	`"?"`
deeparg_db	`"deeparg_1.0.4-07112025"`
deeparg_evalue	`"1e-10"`
deeparg_identity	`"80"`
deeparg_probability	`"0.8"`
gene_coverage	`"95"`
hide_db_build	`""`
input_option	`{"__current_case__": 1, "choice": "paired_collection", "pair_input": {"values": [{"id": 1, "src": "dce"}]}}`
output_files	`{"output_selection": ["file_ARG_tsv", "file_ARG_subtype_tsv", "file_ARG_type_tsv", "file_merged_ARG_tsv", "file_potential_ARG_tsv", "file_all_hits_tsv"]}`

Step 13: toolshed.g2.bx.psu.edu/repos/bgruening/sylph_profile/sylph_profile/0.8.1+galaxy0:

step_state: scheduled

Jobs

Job 1:

Job state is error

Command Line:

ln -s '/cvmfs/data.galaxyproject.org/byhand/sylph/gtdb-r220-c200-dbv1.syldb' '0_sylph_database.syldb' &&       ln -s '/tmp/tmp9yfvh3ca/files/9/d/d/dataset_9ddb3a13-517f-4f52-9e9f-ebb128586c72.dat' 'raw_reads_metag_test.fastq.gz' && ln -s '/tmp/tmp9yfvh3ca/files/b/b/f/dataset_bbf1e905-17ae-4d59-803c-c30b96c6bb09.dat' 'raw_reads_metag_test_r2.fastq.gz' &&  sylph sketch -1 raw_reads_metag_test.fastq.gz -2 raw_reads_metag_test_r2.fastq.gz -t ${GALAXY_SLOTS:-4} -d sylph_sketches &&   sylph profile *.syldb sylph_sketches/*.sylsp --min-number-kmers 50 -t ${GALAXY_SLOTS:-4} -o '/tmp/tmp9yfvh3ca/job_working_directory/000/6/outputs/dataset_84f682e3-66cc-4a3d-a9a2-494762ae71cd.dat'  && cp '/tmp/tmp9yfvh3ca/job_working_directory/000/6/configs/tmpx61m__8i' config.json && export SYLPH_TAXONOMY_CONFIG=config.json && mkdir -p sylph_taxprof_out && sylph-tax taxprof '/tmp/tmp9yfvh3ca/job_working_directory/000/6/outputs/dataset_84f682e3-66cc-4a3d-a9a2-494762ae71cd.dat' -o sylph_taxprof_out/'sylph_tax_out-' --taxonomy-metadata GTDB_r220 && sylph-tax merge sylph_taxprof_out/*.sylphmpa --column relative_abundance -o output_tax_merge.tsv

Exit Code:

```
137
```

Standard Error:

2025-11-14T11:12:57.423Z INFO  [sylph::sketch] Sketching paired sequences...
2025-11-14T11:12:57.671Z INFO  [sylph::sketch] Sketching sylph_sketches/raw_reads_metag_test.fastq.gz.paired.sylsp complete.
2025-11-14T11:12:57.671Z INFO  [sylph::sketch] Finished.
2025-11-14T11:12:57.674Z INFO  [sylph::contain] Obtaining sketches...
/tmp/tmp9yfvh3ca/job_working_directory/000/6/tool_script.sh: line 23:    12 Killed                  sylph profile *.syldb sylph_sketches/*.sylsp --min-number-kmers 50 -t ${GALAXY_SLOTS:-4} -o '/tmp/tmp9yfvh3ca/job_working_directory/000/6/outputs/dataset_84f682e3-66cc-4a3d-a9a2-494762ae71cd.dat'

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"input"`
__workflow_invocation_uuid__	`"cc2b60fec14a11f0a059000d3a047ab5"`
chromInfo	`"/tmp/tmp9yfvh3ca/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
database_select	`{"__current_case__": 0, "column": "relative_abundance", "select": "cached", "sylph_database": "sylph_downloaded_07112025_gtdb-r220-c200-dbv1.syldb", "sylph_tax_metadata": "sylph_tax_downloaded_08112025"}`
dbkey	`"?"`
estimate_unknown	`false`
min_num_kmers	`"50"`
sketch_reads	`{"__current_case__": 3, "input": {"values": [{"id": 1, "src": "dce"}]}, "type_reads": "paired_group"}`

**Step 14: Combines files R1 and R2 **:

step_state: scheduled

Jobs

Job 1:

Job state is ok

Command Line:

gx-fastq-paired-end-interlacer '/tmp/tmp9yfvh3ca/files/9/d/d/dataset_9ddb3a13-517f-4f52-9e9f-ebb128586c72.dat' sanger.gz '/tmp/tmp9yfvh3ca/files/b/b/f/dataset_bbf1e905-17ae-4d59-803c-c30b96c6bb09.dat' sanger.gz '/tmp/tmp9yfvh3ca/job_working_directory/000/7/outputs/dataset_1eba606f-714f-46d8-9950-ea159ac4921e.dat' '/tmp/tmp9yfvh3ca/job_working_directory/000/7/outputs/dataset_50fadc42-800e-434b-b1e5-09451cdb5c8f.dat'

Exit Code:

```
0
```

Standard Output:

There were 0 single reads.
Interlaced 125000 pairs of sequences.

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"fastqsanger.gz"`
__workflow_invocation_uuid__	`"cc2b60fec14a11f0a059000d3a047ab5"`
chromInfo	`"/tmp/tmp9yfvh3ca/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
dbkey	`"?"`
reads	`{"__current_case__": 0, "input1_file": {"values": [{"id": 4, "src": "dce"}]}, "input2_file": {"values": [{"id": 5, "src": "dce"}]}, "reads_selector": "paired"}`

Step 15: argNorm Deeparg:

step_state: scheduled

Jobs

Job 1:

Job state is ok

Command Line:

argnorm 'deeparg' -i '/tmp/tmp9yfvh3ca/files/6/f/8/dataset_6f898eb6-8bd6-4c34-bdbf-e3a5b8ecfc5f.dat' -o '/tmp/tmp9yfvh3ca/job_working_directory/000/8/outputs/dataset_a511072b-5819-47eb-b7a6-12a8bc150d55.dat'

Exit Code:

```
0
```

Standard Output:

/tmp/tmp9yfvh3ca/job_working_directory/000/8/outputs/dataset_a511072b-5819-47eb-b7a6-12a8bc150d55.dat: 100.0% ARGs mapped.

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"input"`
__workflow_invocation_uuid__	`"cc2b60fec14a11f0a059000d3a047ab5"`
choose_tool	`{"__current_case__": 0, "tool": "deeparg"}`
chromInfo	`"/tmp/tmp9yfvh3ca/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
dbkey	`"?"`

Step 16: Unlabelled step:
- step_state: scheduled

Step 17: toolshed.g2.bx.psu.edu/repos/iuc/groot/groot/1.1.2+galaxy2:

step_state: scheduled

Jobs

Job 1:

Job state is ok

Command Line:

set -x pipefail; ln -s -f '/tmp/tmp9yfvh3ca/files/1/e/b/dataset_1eba606f-714f-46d8-9950-ea159ac4921e.dat' 'input.fastq.gz' && groot index --msaDir '/cvmfs/data.galaxyproject.org/byhand/groot_database/arg-annot.90' --indexDir 'grootIndex' --windowSize 100 --kmerSize 31 --maxK 4 --maxSketchSpan 30 --numPart 8 --sketchSize 21 &&  groot align --fastq 'input.fastq.gz' --indexDir 'grootIndex' --contThresh 0.97 --minKmerCov 1  --processors "${GALAXY_SLOTS:-1}"  | groot report --covCutoff '0.6' > '/tmp/tmp9yfvh3ca/job_working_directory/000/9/outputs/dataset_21aaf928-50e7-46a0-ada4-7cdc0552aa46.dat'

Exit Code:

```
0
```

Standard Error:

+ ln -s -f /tmp/tmp9yfvh3ca/files/1/e/b/dataset_1eba606f-714f-46d8-9950-ea159ac4921e.dat input.fastq.gz
+ groot index --msaDir /cvmfs/data.galaxyproject.org/byhand/groot_database/arg-annot.90 --indexDir grootIndex --windowSize 100 --kmerSize 31 --maxK 4 --maxSketchSpan 30 --numPart 8 --sketchSize 21
+ groot report --covCutoff 0.6
+ groot align --fastq input.fastq.gz --indexDir grootIndex --contThresh 0.97 --minKmerCov 1 --processors 1

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"input"`
__workflow_invocation_uuid__	`"cc2b60fec14a11f0a059000d3a047ab5"`
align	`{"contThresh": "0.97", "minKmerCov": "1", "noAlign": true}`
chromInfo	`"/tmp/tmp9yfvh3ca/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
dbkey	`"?"`
index	`{"groot_db_select": "arg-annot.90-1.1.2-08112025", "kmerSize": "31", "maxK": "4", "maxSketchSpan": "30", "numPart": "8", "sketchSize": "21", "windowSize": "100"}`
report	`{"coverage": {"__current_case__": 0, "covCutoff": "0.6", "mode": "cutoff"}}`

Step 18: addValue:

step_state: scheduled

Jobs

Job 1:

Job state is ok

Command Line:

perl '/tmp/tmp9yfvh3ca/galaxy-dev/tools/filters/fixedValueColumn.pl' '/tmp/tmp9yfvh3ca/files/a/5/1/dataset_a511072b-5819-47eb-b7a6-12a8bc150d55.dat' '/tmp/tmp9yfvh3ca/job_working_directory/000/10/outputs/dataset_a4864616-c481-4a50-aa7f-b245f835df8d.dat' 'DeepARG' no

Exit Code:

```
0
```

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"input"`
__workflow_invocation_uuid__	`"cc2b60fec14a11f0a059000d3a047ab5"`
chromInfo	`"/tmp/tmp9yfvh3ca/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
dbkey	`"?"`
exp	`"DeepARG"`
iterate	`"no"`

Step 19: __FLATTEN__:
- step_state: scheduled
- Jobs
  - Job 1:
    - Job state is ok
    Traceback:
    Job Parameters:
    - Job parameter Parameter value
      
      __workflow_invocation_uuid__ "cc2b60fec14a11f0a059000d3a047ab5"
      
      input {"values": [{"id": 21, "src": "hdca"}]}
      
      join_identifier "_"

Step 20: toolshed.g2.bx.psu.edu/repos/iuc/argnorm/argnorm/1.0.0+galaxy0:

step_state: scheduled

Jobs

Job 1:

Job state is ok

Command Line:

argnorm 'groot' --db 'groot-argannot' -i '/tmp/tmp9yfvh3ca/files/2/1/a/dataset_21aaf928-50e7-46a0-ada4-7cdc0552aa46.dat' -o '/tmp/tmp9yfvh3ca/job_working_directory/000/11/outputs/dataset_57d1adf9-2f20-4a57-9f3d-91dc646f0c20.dat'

Exit Code:

```
0
```

Standard Output:

/tmp/tmp9yfvh3ca/job_working_directory/000/11/outputs/dataset_57d1adf9-2f20-4a57-9f3d-91dc646f0c20.dat: 100.0% ARGs mapped.

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"input"`
__workflow_invocation_uuid__	`"cc2b60fec14a11f0a059000d3a047ab5"`
choose_tool	`{"__current_case__": 5, "db": "groot-argannot", "tool": "groot"}`
chromInfo	`"/tmp/tmp9yfvh3ca/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
dbkey	`"?"`

Step 3: Select a Groot database:
- step_state: scheduled
Step 21: __FILTER_FAILED_DATASETS__:
- step_state: scheduled
- Jobs
  - Job 1:
    - Job state is ok
    Traceback:
    Job Parameters:
    - Job parameter Parameter value
      
      __workflow_invocation_uuid__ "cc2b60fec14a11f0a059000d3a047ab5"
      
      input {"values": [{"id": 18, "src": "hdca"}]}

Step 22: addValue:

step_state: scheduled

Jobs

Job 1:

Job state is ok

Command Line:

perl '/tmp/tmp9yfvh3ca/galaxy-dev/tools/filters/fixedValueColumn.pl' '/tmp/tmp9yfvh3ca/files/5/7/d/dataset_57d1adf9-2f20-4a57-9f3d-91dc646f0c20.dat' '/tmp/tmp9yfvh3ca/job_working_directory/000/13/outputs/dataset_ce579c47-318c-471b-a9cb-5e4f1ccfcc33.dat' 'Groot' no

Exit Code:

```
0
```

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"input"`
__workflow_invocation_uuid__	`"cc2b60fec14a11f0a059000d3a047ab5"`
chromInfo	`"/tmp/tmp9yfvh3ca/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
dbkey	`"?"`
exp	`"Groot"`
iterate	`"no"`

Step 23: Unlabelled step:
- step_state: new
Step 24: Unlabelled step:
- step_state: new
Step 4: Select a Groot database for ARGnorm:
- step_state: scheduled
Step 5: Deeparg minimum probability for considering a reads as ARG-like:
- step_state: scheduled
Step 6: Select a Sylph database:
- step_state: scheduled
Step 7: Select a Sylph tax database:
- step_state: scheduled
Step 8: Groot average base pair length of reads:
- step_state: scheduled
Step 9: Groot coverage cutoff for reporting ARGs:
- step_state: scheduled

Step 10: toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_text_file_with_recurring_lines/9.5+galaxy2:

step_state: scheduled

Jobs

Job 1:

Job state is ok

Command Line:

times=1; yes -- 'no_results' 2>/dev/null | head -n $times >> '/tmp/tmp9yfvh3ca/job_working_directory/000/3/outputs/dataset_46005000-7bc0-41ee-84a3-6ff899fc552d.dat'; times=1; yes -- 'no_results' 2>/dev/null | head -n $times >> '/tmp/tmp9yfvh3ca/job_working_directory/000/3/outputs/dataset_46005000-7bc0-41ee-84a3-6ff899fc552d.dat';

Exit Code:

```
0
```

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"input"`
__workflow_invocation_uuid__	`"cc2b60fec14a11f0a059000d3a047ab5"`
chromInfo	`"/tmp/tmp9yfvh3ca/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
dbkey	`"?"`
token_set	`[{"__index__": 0, "line": "no_results", "repeat_select": {"__current_case__": 0, "repeat_select_opts": "user", "times": "1"}}, {"__index__": 1, "line": "no_results", "repeat_select": {"__current_case__": 0, "repeat_select_opts": "user", "times": "1"}}]`

Other invocation details
- error_message
  - Failed to run workflow, invocation ended in [failed] state.
- history_id
  - d9e28052d9b695ad
- history_state
  - error
- invocation_id
  - d9e28052d9b695ad
- invocation_state
  - failed
- messages
  - [{'details': 'Cannot match collection types.', 'reason': 'unexpected_failure', 'workflow_step_id': 22}]
- workflow_id
  - d9e28052d9b695ad

❌ metagenomic-raw-reads-analysis.ga_0

Execution Problem:

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

Workflow invocation details

Invocation Messages
- Invocation scheduling failed because an unexpected failure occurred at step 23: 'Cannot match collection types.'

Steps

Step 1: Metagenomics Trimmed reads:
- step_state: scheduled
Step 2: Select a DeepARG database:
- step_state: scheduled
Step 11: __UNZIP_COLLECTION__:
- step_state: scheduled
- Jobs
  - Job 1:
    - Job state is ok
    Traceback:
    Job Parameters:
    - Job parameter Parameter value
      
      __workflow_invocation_uuid__ "4f3069aac14a11f0bb73000d3a9b19b5"
      
      input {"values": [{"id": 1, "src": "dce"}]}

Step 12: toolshed.g2.bx.psu.edu/repos/iuc/deeparg_short_reads/deeparg_short_reads/1.0.4+galaxy1:

step_state: scheduled

Jobs

Job 1:

Job state is ok

Command Line:

mkdir -p deeparg_short_reads_output && ln -s -f '/tmp/tmpbt8i0a4x/files/a/f/3/dataset_af3b10e7-f9b4-42ad-abb0-ec2d9bb64b5c.dat' 'input_forward.fastqsanger.gz' && ln -s -f '/tmp/tmpbt8i0a4x/files/9/1/6/dataset_916217bb-fb2b-4778-bbe0-d35f775d614d.dat' 'input_reverse.fastqsanger.gz' && deeparg short_reads_pipeline --forward_pe_file 'input_forward.fastqsanger.gz' --reverse_pe_file 'input_reverse.fastqsanger.gz' --output_file 'deeparg_short_reads_output/SR' -d '/cvmfs/data.galaxyproject.org/byhand/deeparg/deeparg_1.0.4' --deeparg_identity 80 --deeparg_probability 0.8 --deeparg_evalue 1e-10 --gene_coverage 95 --bowtie_16s_identity 0.8

Exit Code:

```
0
```

Standard Error:

WARNING (theano.configdefaults): g++ not detected ! Theano will be unable to execute optimized C-implementations (for both CPU and GPU) and will default to Python implementations. Performance will be severely degraded. To remove this warning, set Theano flags cxx to an empty string.
/usr/local/lib/python2.7/site-packages/theano/tensor/signal/downsample.py:6: UserWarning: downsample module has been moved to the theano.tensor.signal.pool module.
  "downsample module has been moved to the theano.tensor.signal.pool module.")
/usr/local/lib/python2.7/site-packages/sklearn/cross_validation.py:41: DeprecationWarning: This module was deprecated in version 0.18 in favor of the model_selection module into which all the refactored classes and functions are moved. Also note that the interface of the new CV iterators are different from that of this module. This module will be removed in 0.20.
  "This module will be removed in 0.20.", DeprecationWarning)
TrimmomaticPE: Started with arguments:
 -phred33 input_forward.fastqsanger.gz input_reverse.fastqsanger.gz input_forward.fastqsanger.gz.paired input_forward.fastqsanger.gz.unpaired input_reverse.fastqsanger.gz.paired input_reverse.fastqsanger.gz.unpaired LEADING:3 TRAILING:3 SLIDINGWINDOW:4:15 MINLEN:36
Multiple cores found: Using 4 threads
Input Read Pairs: 125000 Both Surviving: 125000 (100.00%) Forward Only Surviving: 0 (0.00%) Reverse Only Surviving: 0 (0.00%) Dropped: 0 (0.00%)
TrimmomaticPE: Completed successfully
vsearch v2.27.1_linux_x86_64, 15.6GB RAM, 4 cores
https://github.com/torognes/vsearch

Merging reads 100%
    125000  Pairs
     69309  Merged (55.4%)
     55691  Not merged (44.6%)

Pairs that failed merging due to various reasons:
     39021  too few kmers found on same diagonal
       265  multiple potential alignments
     12101  alignment score too low, or score drop too high
       295  overlap too short
      4009  staggered read pairs

Statistics of all reads:
     92.44  Mean read length

Statistics of merged reads:
    109.97  Mean fragment length
     40.60  Standard deviation of fragment length
      0.07  Mean expected error in forward sequences
      0.06  Mean expected error in reverse sequences
      0.04  Mean expected error in merged sequences
      0.01  Mean observed errors in merged region of forward sequences
      0.00  Mean observed errors in merged region of reverse sequences
      0.01  Mean observed errors in merged region
WARNING (theano.configdefaults): g++ not detected ! Theano will be unable to execute optimized C-implementations (for both CPU and GPU) and will default to Python implementations. Performance will be severely degraded. To remove this warning, set Theano flags cxx to an empty string.
/usr/local/lib/python2.7/site-packages/theano/tensor/signal/downsample.py:6: UserWarning: downsample module has been moved to the theano.tensor.signal.pool module.
  "downsample module has been moved to the theano.tensor.signal.pool module.")
/usr/local/lib/python2.7/site-packages/sklearn/cross_validation.py:41: DeprecationWarning: This module was deprecated in version 0.18 in favor of the model_selection module into which all the refactored classes and functions are moved. Also note that the interface of the new CV iterators are different from that of this module. This module will be removed in 0.20.
  "This module will be removed in 0.20.", DeprecationWarning)
INFO:root:DIAMOND blastx alignment
INFO:root:Running: diamond  blastx -q deeparg_short_reads_output/SR.clean -d /cvmfs/data.galaxyproject.org/byhand/deeparg/deeparg_1.0.4/database/v2/features -k 1000 --id 80.0 --sensitive -e 1e-10 -a deeparg_short_reads_output/SR.clean.deeparg.align
INFO:root:Input:deeparg_short_reads_output/SR.clean output:deeparg_short_reads_output/SR.clean.deeparg model: deepARG_SS, Input type: blastx
INFO:root:parsing output file diamond view -a deeparg_short_reads_output/SR.clean.deeparg.align.daa -o deeparg_short_reads_output/SR.clean.deeparg.align.daa.tsv
diamond v2.1.10.164 (C) Max Planck Society for the Advancement of Science, Benjamin Buchfink, University of Tuebingen
Documentation, support and updates available at http://www.diamondsearch.org
Please cite: http://dx.doi.org/10.1038/s41592-021-01101-x Nature Methods (2021)

#CPU threads: 4
Loading subject IDs...  [0s]
Scoring parameters: (Matrix=blosum62 Lambda=0.267 K=0.041 Penalties=11/1)
DB sequences = 12279
DB sequences used = 642
DB letters = 5088898
#Target sequences to report alignments for: 25
Generating output...  [0.001s]
INFO:root:Loading deep learning model ...
INFO:root:loading gene lengths
INFO:root:Loading sample to analyze

0reads [00:00, ?reads/s]
1237reads [00:00, 191721.01reads/s]
INFO:root:Predicting ARG-like reads: Running deepARG_SS model version v2
INFO:root:input dataset is splitted into chunks of 10000 reads

0chunks [00:00, ?chunks/s]
1chunks [00:06,  6.69s/chunks]
1chunks [00:06,  6.69s/chunks]
INFO:root:Predicting ARGs

  0%|          | 0/136 [00:00<?, ?it/s]
100%|██████████| 136/136 [00:00<00:00, 40937.66it/s]
180691 reads; of these:
  180691 (100.00%) were unpaired; of these:
    180399 (99.84%) aligned 0 times
    0 (0.00%) aligned exactly 1 time
    292 (0.16%) aligned >1 times
0.16% overall alignment rate

Standard Output:

Step 1: Trimming and QC using Trimmomatic
['/usr/local/bin', '/usr/local/lib/python27.zip', '/usr/local/lib/python2.7', '/usr/local/lib/python2.7/plat-linux2', '/usr/local/lib/python2.7/lib-tk', '/usr/local/lib/python2.7/lib-old', '/usr/local/lib/python2.7/lib-dynload', '/usr/local/lib/python2.7/site-packages']



Step 2: Merging paired end reads using Vsearch
['/usr/local/bin', '/usr/local/lib/python27.zip', '/usr/local/lib/python2.7', '/usr/local/lib/python2.7/plat-linux2', '/usr/local/lib/python2.7/lib-tk', '/usr/local/lib/python2.7/lib-old', '/usr/local/lib/python2.7/lib-dynload', '/usr/local/lib/python2.7/site-packages']



Step 3: Run DeepARG-SS to identify ARG-like reads
deeparg predict --type nucl --model SS -d /cvmfs/data.galaxyproject.org/byhand/deeparg/deeparg_1.0.4 -i deeparg_short_reads_output/SR.clean -o deeparg_short_reads_output/SR.clean.deeparg --arg-alignment-identity 80.0 --min-prob 0.8 --arg-alignment-evalue 1e-10



Step 4: Quantification of ARG-like counts
sort -k1,1 -k2,2n deeparg_short_reads_output/SR.clean.deeparg.mapping.ARG  | bedtools merge -c 12,5 -o sum,distinct >deeparg_short_reads_output/SR.clean.deeparg.mapping.ARG.merged



Step 5: Normalize to 16S rRNAs - this may take a while ...
Total number of 16S Reads in the sample: 178

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"input"`
__workflow_invocation_uuid__	`"4f3069aac14a11f0bb73000d3a9b19b5"`
bowtie_16s_identity	`"0.8"`
chromInfo	`"/tmp/tmpbt8i0a4x/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
dbkey	`"?"`
deeparg_db	`"deeparg_1.0.4-07112025"`
deeparg_evalue	`"1e-10"`
deeparg_identity	`"80"`
deeparg_probability	`"0.8"`
gene_coverage	`"95"`
hide_db_build	`""`
input_option	`{"__current_case__": 1, "choice": "paired_collection", "pair_input": {"values": [{"id": 1, "src": "dce"}]}}`
output_files	`{"output_selection": ["file_ARG_tsv", "file_ARG_subtype_tsv", "file_ARG_type_tsv", "file_merged_ARG_tsv", "file_potential_ARG_tsv", "file_all_hits_tsv"]}`

Step 13: toolshed.g2.bx.psu.edu/repos/bgruening/sylph_profile/sylph_profile/0.8.1+galaxy0:

step_state: scheduled

Jobs

Job 1:

Job state is error

Command Line:

ln -s '/cvmfs/data.galaxyproject.org/byhand/sylph/gtdb-r220-c200-dbv1.syldb' '0_sylph_database.syldb' &&       ln -s '/tmp/tmpbt8i0a4x/files/a/f/3/dataset_af3b10e7-f9b4-42ad-abb0-ec2d9bb64b5c.dat' 'raw_reads_metag_test.fastq.gz' && ln -s '/tmp/tmpbt8i0a4x/files/9/1/6/dataset_916217bb-fb2b-4778-bbe0-d35f775d614d.dat' 'raw_reads_metag_test_r2.fastq.gz' &&  sylph sketch -1 raw_reads_metag_test.fastq.gz -2 raw_reads_metag_test_r2.fastq.gz -t ${GALAXY_SLOTS:-4} -d sylph_sketches &&   sylph profile *.syldb sylph_sketches/*.sylsp --min-number-kmers 50 -t ${GALAXY_SLOTS:-4} -o '/tmp/tmpbt8i0a4x/job_working_directory/000/6/outputs/dataset_47fec8bf-206a-4189-a470-68df96ff36fb.dat'  && cp '/tmp/tmpbt8i0a4x/job_working_directory/000/6/configs/tmp8oktn8q_' config.json && export SYLPH_TAXONOMY_CONFIG=config.json && mkdir -p sylph_taxprof_out && sylph-tax taxprof '/tmp/tmpbt8i0a4x/job_working_directory/000/6/outputs/dataset_47fec8bf-206a-4189-a470-68df96ff36fb.dat' -o sylph_taxprof_out/'sylph_tax_out-' --taxonomy-metadata GTDB_r220 && sylph-tax merge sylph_taxprof_out/*.sylphmpa --column relative_abundance -o output_tax_merge.tsv

Exit Code:

```
137
```

Standard Error:

2025-11-14T11:09:25.902Z INFO  [sylph::sketch] Sketching paired sequences...
2025-11-14T11:09:26.111Z INFO  [sylph::sketch] Sketching sylph_sketches/raw_reads_metag_test.fastq.gz.paired.sylsp complete.
2025-11-14T11:09:26.111Z INFO  [sylph::sketch] Finished.
2025-11-14T11:09:26.115Z INFO  [sylph::contain] Obtaining sketches...
/tmp/tmpbt8i0a4x/job_working_directory/000/6/tool_script.sh: line 23:    12 Killed                  sylph profile *.syldb sylph_sketches/*.sylsp --min-number-kmers 50 -t ${GALAXY_SLOTS:-4} -o '/tmp/tmpbt8i0a4x/job_working_directory/000/6/outputs/dataset_47fec8bf-206a-4189-a470-68df96ff36fb.dat'

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"input"`
__workflow_invocation_uuid__	`"4f3069aac14a11f0bb73000d3a9b19b5"`
chromInfo	`"/tmp/tmpbt8i0a4x/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
database_select	`{"__current_case__": 0, "column": "relative_abundance", "select": "cached", "sylph_database": "sylph_downloaded_07112025_gtdb-r220-c200-dbv1.syldb", "sylph_tax_metadata": "sylph_tax_downloaded_08112025"}`
dbkey	`"?"`
estimate_unknown	`false`
min_num_kmers	`"50"`
sketch_reads	`{"__current_case__": 3, "input": {"values": [{"id": 1, "src": "dce"}]}, "type_reads": "paired_group"}`

**Step 14: Combines files R1 and R2 **:

step_state: scheduled

Jobs

Job 1:

Job state is ok

Command Line:

gx-fastq-paired-end-interlacer '/tmp/tmpbt8i0a4x/files/a/f/3/dataset_af3b10e7-f9b4-42ad-abb0-ec2d9bb64b5c.dat' sanger.gz '/tmp/tmpbt8i0a4x/files/9/1/6/dataset_916217bb-fb2b-4778-bbe0-d35f775d614d.dat' sanger.gz '/tmp/tmpbt8i0a4x/job_working_directory/000/7/outputs/dataset_ea71a63e-735f-4cbc-9ea5-2151f141740c.dat' '/tmp/tmpbt8i0a4x/job_working_directory/000/7/outputs/dataset_bd1d60b5-4e07-49b5-a6ed-650b2a4aa2bc.dat'

Exit Code:

```
0
```

Standard Output:

There were 0 single reads.
Interlaced 125000 pairs of sequences.

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"fastqsanger.gz"`
__workflow_invocation_uuid__	`"4f3069aac14a11f0bb73000d3a9b19b5"`
chromInfo	`"/tmp/tmpbt8i0a4x/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
dbkey	`"?"`
reads	`{"__current_case__": 0, "input1_file": {"values": [{"id": 4, "src": "dce"}]}, "input2_file": {"values": [{"id": 5, "src": "dce"}]}, "reads_selector": "paired"}`

Step 15: argNorm Deeparg:

step_state: scheduled

Jobs

Job 1:

Job state is ok

Command Line:

argnorm 'deeparg' -i '/tmp/tmpbt8i0a4x/files/7/f/0/dataset_7f0d1552-6100-4768-8965-530e5a7c4cc4.dat' -o '/tmp/tmpbt8i0a4x/job_working_directory/000/8/outputs/dataset_aefe2f72-d6bd-43c7-a350-883ed4ece463.dat'

Exit Code:

```
0
```

Standard Output:

/tmp/tmpbt8i0a4x/job_working_directory/000/8/outputs/dataset_aefe2f72-d6bd-43c7-a350-883ed4ece463.dat: 100.0% ARGs mapped.

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"input"`
__workflow_invocation_uuid__	`"4f3069aac14a11f0bb73000d3a9b19b5"`
choose_tool	`{"__current_case__": 0, "tool": "deeparg"}`
chromInfo	`"/tmp/tmpbt8i0a4x/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
dbkey	`"?"`

Step 16: Unlabelled step:
- step_state: scheduled

Step 17: toolshed.g2.bx.psu.edu/repos/iuc/groot/groot/1.1.2+galaxy2:

step_state: scheduled

Jobs

Job 1:

Job state is ok

Command Line:

set -x pipefail; ln -s -f '/tmp/tmpbt8i0a4x/files/e/a/7/dataset_ea71a63e-735f-4cbc-9ea5-2151f141740c.dat' 'input.fastq.gz' && groot index --msaDir '/cvmfs/data.galaxyproject.org/byhand/groot_database/arg-annot.90' --indexDir 'grootIndex' --windowSize 100 --kmerSize 31 --maxK 4 --maxSketchSpan 30 --numPart 8 --sketchSize 21 &&  groot align --fastq 'input.fastq.gz' --indexDir 'grootIndex' --contThresh 0.97 --minKmerCov 1  --processors "${GALAXY_SLOTS:-1}"  | groot report --covCutoff '0.6' > '/tmp/tmpbt8i0a4x/job_working_directory/000/9/outputs/dataset_ab951005-147e-4904-9a42-f0f68c819394.dat'

Exit Code:

```
0
```

Standard Error:

+ ln -s -f /tmp/tmpbt8i0a4x/files/e/a/7/dataset_ea71a63e-735f-4cbc-9ea5-2151f141740c.dat input.fastq.gz
+ groot index --msaDir /cvmfs/data.galaxyproject.org/byhand/groot_database/arg-annot.90 --indexDir grootIndex --windowSize 100 --kmerSize 31 --maxK 4 --maxSketchSpan 30 --numPart 8 --sketchSize 21
+ groot align --fastq input.fastq.gz --indexDir grootIndex --contThresh 0.97 --minKmerCov 1 --processors 1
+ groot report --covCutoff 0.6

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"input"`
__workflow_invocation_uuid__	`"4f3069aac14a11f0bb73000d3a9b19b5"`
align	`{"contThresh": "0.97", "minKmerCov": "1", "noAlign": true}`
chromInfo	`"/tmp/tmpbt8i0a4x/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
dbkey	`"?"`
index	`{"groot_db_select": "arg-annot.90-1.1.2-08112025", "kmerSize": "31", "maxK": "4", "maxSketchSpan": "30", "numPart": "8", "sketchSize": "21", "windowSize": "100"}`
report	`{"coverage": {"__current_case__": 0, "covCutoff": "0.6", "mode": "cutoff"}}`

Step 18: addValue:

step_state: scheduled

Jobs

Job 1:

Job state is ok

Command Line:

perl '/tmp/tmpbt8i0a4x/galaxy-dev/tools/filters/fixedValueColumn.pl' '/tmp/tmpbt8i0a4x/files/a/e/f/dataset_aefe2f72-d6bd-43c7-a350-883ed4ece463.dat' '/tmp/tmpbt8i0a4x/job_working_directory/000/10/outputs/dataset_d9c5bfb7-689f-4eba-a7fe-b74670413f20.dat' 'DeepARG' no

Exit Code:

```
0
```

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"input"`
__workflow_invocation_uuid__	`"4f3069aac14a11f0bb73000d3a9b19b5"`
chromInfo	`"/tmp/tmpbt8i0a4x/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
dbkey	`"?"`
exp	`"DeepARG"`
iterate	`"no"`

Step 19: __FLATTEN__:
- step_state: scheduled
- Jobs
  - Job 1:
    - Job state is ok
    Traceback:
    Job Parameters:
    - Job parameter Parameter value
      
      __workflow_invocation_uuid__ "4f3069aac14a11f0bb73000d3a9b19b5"
      
      input {"values": [{"id": 21, "src": "hdca"}]}
      
      join_identifier "_"

Step 20: toolshed.g2.bx.psu.edu/repos/iuc/argnorm/argnorm/1.0.0+galaxy0:

step_state: scheduled

Jobs

Job 1:

Job state is ok

Command Line:

argnorm 'groot' --db 'groot-argannot' -i '/tmp/tmpbt8i0a4x/files/a/b/9/dataset_ab951005-147e-4904-9a42-f0f68c819394.dat' -o '/tmp/tmpbt8i0a4x/job_working_directory/000/11/outputs/dataset_28b60f79-163a-402d-965a-d788a082b941.dat'

Exit Code:

```
0
```

Standard Output:

/tmp/tmpbt8i0a4x/job_working_directory/000/11/outputs/dataset_28b60f79-163a-402d-965a-d788a082b941.dat: 100.0% ARGs mapped.

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"input"`
__workflow_invocation_uuid__	`"4f3069aac14a11f0bb73000d3a9b19b5"`
choose_tool	`{"__current_case__": 5, "db": "groot-argannot", "tool": "groot"}`
chromInfo	`"/tmp/tmpbt8i0a4x/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
dbkey	`"?"`

Step 3: Select a Groot database:
- step_state: scheduled
Step 21: __FILTER_FAILED_DATASETS__:
- step_state: scheduled
- Jobs
  - Job 1:
    - Job state is ok
    Traceback:
    Job Parameters:
    - Job parameter Parameter value
      
      __workflow_invocation_uuid__ "4f3069aac14a11f0bb73000d3a9b19b5"
      
      input {"values": [{"id": 18, "src": "hdca"}]}

Step 22: addValue:

step_state: scheduled

Jobs

Job 1:

Job state is ok

Command Line:

perl '/tmp/tmpbt8i0a4x/galaxy-dev/tools/filters/fixedValueColumn.pl' '/tmp/tmpbt8i0a4x/files/2/8/b/dataset_28b60f79-163a-402d-965a-d788a082b941.dat' '/tmp/tmpbt8i0a4x/job_working_directory/000/13/outputs/dataset_10057fc4-0aed-4086-b1f2-709016bb89c0.dat' 'Groot' no

Exit Code:

```
0
```

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"input"`
__workflow_invocation_uuid__	`"4f3069aac14a11f0bb73000d3a9b19b5"`
chromInfo	`"/tmp/tmpbt8i0a4x/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
dbkey	`"?"`
exp	`"Groot"`
iterate	`"no"`

Step 23: Unlabelled step:
- step_state: new
Step 24: Unlabelled step:
- step_state: new
Step 4: Select a Groot database for ARGnorm:
- step_state: scheduled
Step 5: Deeparg minimum probability for considering a reads as ARG-like:
- step_state: scheduled
Step 6: Select a Sylph database:
- step_state: scheduled
Step 7: Select a Sylph tax database:
- step_state: scheduled
Step 8: Groot average base pair length of reads:
- step_state: scheduled
Step 9: Groot coverage cutoff for reporting ARGs:
- step_state: scheduled

Step 10: toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_text_file_with_recurring_lines/9.5+galaxy2:

step_state: scheduled

Jobs

Job 1:

Job state is ok

Command Line:

times=1; yes -- 'no_results' 2>/dev/null | head -n $times >> '/tmp/tmpbt8i0a4x/job_working_directory/000/3/outputs/dataset_222b2830-867b-4047-aaa4-e55eda319933.dat'; times=1; yes -- 'no_results' 2>/dev/null | head -n $times >> '/tmp/tmpbt8i0a4x/job_working_directory/000/3/outputs/dataset_222b2830-867b-4047-aaa4-e55eda319933.dat';

Exit Code:

```
0
```

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"input"`
__workflow_invocation_uuid__	`"4f3069aac14a11f0bb73000d3a9b19b5"`
chromInfo	`"/tmp/tmpbt8i0a4x/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
dbkey	`"?"`
token_set	`[{"__index__": 0, "line": "no_results", "repeat_select": {"__current_case__": 0, "repeat_select_opts": "user", "times": "1"}}, {"__index__": 1, "line": "no_results", "repeat_select": {"__current_case__": 0, "repeat_select_opts": "user", "times": "1"}}]`

Other invocation details
- error_message
  - Failed to run workflow, invocation ended in [failed] state.
- history_id
  - 03876b3b6663412d
- history_state
  - error
- invocation_id
  - 03876b3b6663412d
- invocation_state
  - failed
- messages
  - [{'details': 'Cannot match collection types.', 'reason': 'unexpected_failure', 'workflow_step_id': 22}]
- workflow_id
  - 03876b3b6663412d

github-actions · 2025-11-14T14:29:31Z

Test Results (powered by Planemo)

Test Summary

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

Errored Tests

❌ metagenomic-raw-reads-amr-analysis.ga_0

Execution Problem:

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

Workflow invocation details

Invocation Messages
- Invocation scheduling failed because an unexpected failure occurred at step 23: 'Cannot match collection types.'

Steps

Step 1: Metagenomics Trimmed reads:
- step_state: scheduled
Step 2: Select a DeepARG database:
- step_state: scheduled
Step 11: __UNZIP_COLLECTION__:
- step_state: scheduled
- Jobs
  - Job 1:
    - Job state is ok
    Traceback:
    Job Parameters:
    - Job parameter Parameter value
      
      __workflow_invocation_uuid__ "475bce76c15f11f0bb736045bdd8cbdf"
      
      input {"values": [{"id": 1, "src": "dce"}]}

Step 12: toolshed.g2.bx.psu.edu/repos/iuc/deeparg_short_reads/deeparg_short_reads/1.0.4+galaxy1:

step_state: scheduled

Jobs

Job 1:

Job state is ok

Command Line:

mkdir -p deeparg_short_reads_output && ln -s -f '/tmp/tmp8rkid8xk/files/7/3/7/dataset_7370928e-a924-44a8-82c8-67dadcd36e0e.dat' 'input_forward.fastqsanger.gz' && ln -s -f '/tmp/tmp8rkid8xk/files/4/2/e/dataset_42e496a6-dcf2-4266-bd7a-b84fa28a4aa5.dat' 'input_reverse.fastqsanger.gz' && deeparg short_reads_pipeline --forward_pe_file 'input_forward.fastqsanger.gz' --reverse_pe_file 'input_reverse.fastqsanger.gz' --output_file 'deeparg_short_reads_output/SR' -d '/cvmfs/data.galaxyproject.org/byhand/deeparg/deeparg_1.0.4' --deeparg_identity 80 --deeparg_probability 0.8 --deeparg_evalue 1e-10 --gene_coverage 95 --bowtie_16s_identity 0.8

Exit Code:

```
0
```

Standard Error:

WARNING (theano.configdefaults): g++ not detected ! Theano will be unable to execute optimized C-implementations (for both CPU and GPU) and will default to Python implementations. Performance will be severely degraded. To remove this warning, set Theano flags cxx to an empty string.
/usr/local/lib/python2.7/site-packages/theano/tensor/signal/downsample.py:6: UserWarning: downsample module has been moved to the theano.tensor.signal.pool module.
  "downsample module has been moved to the theano.tensor.signal.pool module.")
/usr/local/lib/python2.7/site-packages/sklearn/cross_validation.py:41: DeprecationWarning: This module was deprecated in version 0.18 in favor of the model_selection module into which all the refactored classes and functions are moved. Also note that the interface of the new CV iterators are different from that of this module. This module will be removed in 0.20.
  "This module will be removed in 0.20.", DeprecationWarning)
TrimmomaticPE: Started with arguments:
 -phred33 input_forward.fastqsanger.gz input_reverse.fastqsanger.gz input_forward.fastqsanger.gz.paired input_forward.fastqsanger.gz.unpaired input_reverse.fastqsanger.gz.paired input_reverse.fastqsanger.gz.unpaired LEADING:3 TRAILING:3 SLIDINGWINDOW:4:15 MINLEN:36
Multiple cores found: Using 4 threads
Input Read Pairs: 125000 Both Surviving: 125000 (100.00%) Forward Only Surviving: 0 (0.00%) Reverse Only Surviving: 0 (0.00%) Dropped: 0 (0.00%)
TrimmomaticPE: Completed successfully
vsearch v2.27.1_linux_x86_64, 15.6GB RAM, 4 cores
https://github.com/torognes/vsearch

Merging reads 100%
    125000  Pairs
     69309  Merged (55.4%)
     55691  Not merged (44.6%)

Pairs that failed merging due to various reasons:
     39021  too few kmers found on same diagonal
       265  multiple potential alignments
     12101  alignment score too low, or score drop too high
       295  overlap too short
      4009  staggered read pairs

Statistics of all reads:
     92.44  Mean read length

Statistics of merged reads:
    109.97  Mean fragment length
     40.60  Standard deviation of fragment length
      0.07  Mean expected error in forward sequences
      0.06  Mean expected error in reverse sequences
      0.04  Mean expected error in merged sequences
      0.01  Mean observed errors in merged region of forward sequences
      0.00  Mean observed errors in merged region of reverse sequences
      0.01  Mean observed errors in merged region
WARNING (theano.configdefaults): g++ not detected ! Theano will be unable to execute optimized C-implementations (for both CPU and GPU) and will default to Python implementations. Performance will be severely degraded. To remove this warning, set Theano flags cxx to an empty string.
/usr/local/lib/python2.7/site-packages/theano/tensor/signal/downsample.py:6: UserWarning: downsample module has been moved to the theano.tensor.signal.pool module.
  "downsample module has been moved to the theano.tensor.signal.pool module.")
/usr/local/lib/python2.7/site-packages/sklearn/cross_validation.py:41: DeprecationWarning: This module was deprecated in version 0.18 in favor of the model_selection module into which all the refactored classes and functions are moved. Also note that the interface of the new CV iterators are different from that of this module. This module will be removed in 0.20.
  "This module will be removed in 0.20.", DeprecationWarning)
INFO:root:DIAMOND blastx alignment
INFO:root:Running: diamond  blastx -q deeparg_short_reads_output/SR.clean -d /cvmfs/data.galaxyproject.org/byhand/deeparg/deeparg_1.0.4/database/v2/features -k 1000 --id 80.0 --sensitive -e 1e-10 -a deeparg_short_reads_output/SR.clean.deeparg.align
INFO:root:Input:deeparg_short_reads_output/SR.clean output:deeparg_short_reads_output/SR.clean.deeparg model: deepARG_SS, Input type: blastx
INFO:root:parsing output file diamond view -a deeparg_short_reads_output/SR.clean.deeparg.align.daa -o deeparg_short_reads_output/SR.clean.deeparg.align.daa.tsv
diamond v2.1.10.164 (C) Max Planck Society for the Advancement of Science, Benjamin Buchfink, University of Tuebingen
Documentation, support and updates available at http://www.diamondsearch.org
Please cite: http://dx.doi.org/10.1038/s41592-021-01101-x Nature Methods (2021)

#CPU threads: 4
Loading subject IDs...  [0s]
Scoring parameters: (Matrix=blosum62 Lambda=0.267 K=0.041 Penalties=11/1)
DB sequences = 12279
DB sequences used = 642
DB letters = 5088898
#Target sequences to report alignments for: 25
Generating output...  [0.002s]
INFO:root:Loading deep learning model ...
INFO:root:loading gene lengths
INFO:root:Loading sample to analyze

0reads [00:00, ?reads/s]
1237reads [00:00, 150833.01reads/s]
INFO:root:Predicting ARG-like reads: Running deepARG_SS model version v2
INFO:root:input dataset is splitted into chunks of 10000 reads

0chunks [00:00, ?chunks/s]
1chunks [00:07,  7.03s/chunks]
1chunks [00:07,  7.03s/chunks]
INFO:root:Predicting ARGs

  0%|          | 0/136 [00:00<?, ?it/s]
100%|██████████| 136/136 [00:00<00:00, 39418.52it/s]
180691 reads; of these:
  180691 (100.00%) were unpaired; of these:
    180399 (99.84%) aligned 0 times
    0 (0.00%) aligned exactly 1 time
    292 (0.16%) aligned >1 times
0.16% overall alignment rate

Standard Output:

Step 1: Trimming and QC using Trimmomatic
['/usr/local/bin', '/usr/local/lib/python27.zip', '/usr/local/lib/python2.7', '/usr/local/lib/python2.7/plat-linux2', '/usr/local/lib/python2.7/lib-tk', '/usr/local/lib/python2.7/lib-old', '/usr/local/lib/python2.7/lib-dynload', '/usr/local/lib/python2.7/site-packages']



Step 2: Merging paired end reads using Vsearch
['/usr/local/bin', '/usr/local/lib/python27.zip', '/usr/local/lib/python2.7', '/usr/local/lib/python2.7/plat-linux2', '/usr/local/lib/python2.7/lib-tk', '/usr/local/lib/python2.7/lib-old', '/usr/local/lib/python2.7/lib-dynload', '/usr/local/lib/python2.7/site-packages']



Step 3: Run DeepARG-SS to identify ARG-like reads
deeparg predict --type nucl --model SS -d /cvmfs/data.galaxyproject.org/byhand/deeparg/deeparg_1.0.4 -i deeparg_short_reads_output/SR.clean -o deeparg_short_reads_output/SR.clean.deeparg --arg-alignment-identity 80.0 --min-prob 0.8 --arg-alignment-evalue 1e-10



Step 4: Quantification of ARG-like counts
sort -k1,1 -k2,2n deeparg_short_reads_output/SR.clean.deeparg.mapping.ARG  | bedtools merge -c 12,5 -o sum,distinct >deeparg_short_reads_output/SR.clean.deeparg.mapping.ARG.merged



Step 5: Normalize to 16S rRNAs - this may take a while ...
Total number of 16S Reads in the sample: 178

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"input"`
__workflow_invocation_uuid__	`"475bce76c15f11f0bb736045bdd8cbdf"`
bowtie_16s_identity	`"0.8"`
chromInfo	`"/tmp/tmp8rkid8xk/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
dbkey	`"?"`
deeparg_db	`"deeparg_1.0.4-07112025"`
deeparg_evalue	`"1e-10"`
deeparg_identity	`"80"`
deeparg_probability	`"0.8"`
gene_coverage	`"95"`
hide_db_build	`""`
input_option	`{"__current_case__": 1, "choice": "paired_collection", "pair_input": {"values": [{"id": 1, "src": "dce"}]}}`
output_files	`{"output_selection": ["file_ARG_tsv", "file_ARG_subtype_tsv", "file_ARG_type_tsv", "file_merged_ARG_tsv", "file_potential_ARG_tsv", "file_all_hits_tsv"]}`

Step 13: toolshed.g2.bx.psu.edu/repos/bgruening/sylph_profile/sylph_profile/0.8.1+galaxy0:

step_state: scheduled

Jobs

Job 1:

Job state is error

Command Line:

ln -s '/cvmfs/data.galaxyproject.org/byhand/sylph/gtdb-r220-c200-dbv1.syldb' '0_sylph_database.syldb' &&       ln -s '/tmp/tmp8rkid8xk/files/7/3/7/dataset_7370928e-a924-44a8-82c8-67dadcd36e0e.dat' 'raw_reads_metag_test.fastq.gz' && ln -s '/tmp/tmp8rkid8xk/files/4/2/e/dataset_42e496a6-dcf2-4266-bd7a-b84fa28a4aa5.dat' 'raw_reads_metag_test_r2.fastq.gz' &&  sylph sketch -1 raw_reads_metag_test.fastq.gz -2 raw_reads_metag_test_r2.fastq.gz -t ${GALAXY_SLOTS:-4} -d sylph_sketches &&   sylph profile *.syldb sylph_sketches/*.sylsp --min-number-kmers 50 -t ${GALAXY_SLOTS:-4} -o '/tmp/tmp8rkid8xk/job_working_directory/000/6/outputs/dataset_1edbdb09-b3c2-42a8-b231-ded47e6a73e8.dat'  && cp '/tmp/tmp8rkid8xk/job_working_directory/000/6/configs/tmpao47u0nb' config.json && export SYLPH_TAXONOMY_CONFIG=config.json && mkdir -p sylph_taxprof_out && sylph-tax taxprof '/tmp/tmp8rkid8xk/job_working_directory/000/6/outputs/dataset_1edbdb09-b3c2-42a8-b231-ded47e6a73e8.dat' -o sylph_taxprof_out/'sylph_tax_out-' --taxonomy-metadata GTDB_r220 && sylph-tax merge sylph_taxprof_out/*.sylphmpa --column relative_abundance -o output_tax_merge.tsv

Exit Code:

```
137
```

Standard Error:

2025-11-14T13:39:28.114Z INFO  [sylph::sketch] Sketching paired sequences...
2025-11-14T13:39:28.372Z INFO  [sylph::sketch] Sketching sylph_sketches/raw_reads_metag_test.fastq.gz.paired.sylsp complete.
2025-11-14T13:39:28.373Z INFO  [sylph::sketch] Finished.
2025-11-14T13:39:28.376Z INFO  [sylph::contain] Obtaining sketches...
/tmp/tmp8rkid8xk/job_working_directory/000/6/tool_script.sh: line 23:    12 Killed                  sylph profile *.syldb sylph_sketches/*.sylsp --min-number-kmers 50 -t ${GALAXY_SLOTS:-4} -o '/tmp/tmp8rkid8xk/job_working_directory/000/6/outputs/dataset_1edbdb09-b3c2-42a8-b231-ded47e6a73e8.dat'

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"input"`
__workflow_invocation_uuid__	`"475bce76c15f11f0bb736045bdd8cbdf"`
chromInfo	`"/tmp/tmp8rkid8xk/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
database_select	`{"__current_case__": 0, "column": "relative_abundance", "select": "cached", "sylph_database": "sylph_downloaded_07112025_gtdb-r220-c200-dbv1.syldb", "sylph_tax_metadata": "sylph_tax_downloaded_08112025"}`
dbkey	`"?"`
estimate_unknown	`false`
min_num_kmers	`"50"`
sketch_reads	`{"__current_case__": 3, "input": {"values": [{"id": 1, "src": "dce"}]}, "type_reads": "paired_group"}`

**Step 14: Combines files R1 and R2 **:

step_state: scheduled

Jobs

Job 1:

Job state is ok

Command Line:

gx-fastq-paired-end-interlacer '/tmp/tmp8rkid8xk/files/7/3/7/dataset_7370928e-a924-44a8-82c8-67dadcd36e0e.dat' sanger.gz '/tmp/tmp8rkid8xk/files/4/2/e/dataset_42e496a6-dcf2-4266-bd7a-b84fa28a4aa5.dat' sanger.gz '/tmp/tmp8rkid8xk/job_working_directory/000/7/outputs/dataset_3e04cf60-cc89-4c00-b2f1-2da00f285000.dat' '/tmp/tmp8rkid8xk/job_working_directory/000/7/outputs/dataset_0c9191e9-a25a-4b4d-aa7a-088b4a18e486.dat'

Exit Code:

```
0
```

Standard Output:

There were 0 single reads.
Interlaced 125000 pairs of sequences.

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"fastqsanger.gz"`
__workflow_invocation_uuid__	`"475bce76c15f11f0bb736045bdd8cbdf"`
chromInfo	`"/tmp/tmp8rkid8xk/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
dbkey	`"?"`
reads	`{"__current_case__": 0, "input1_file": {"values": [{"id": 4, "src": "dce"}]}, "input2_file": {"values": [{"id": 5, "src": "dce"}]}, "reads_selector": "paired"}`

Step 15: argNorm Deeparg:

step_state: scheduled

Jobs

Job 1:

Job state is ok

Command Line:

argnorm 'deeparg' -i '/tmp/tmp8rkid8xk/files/c/0/e/dataset_c0ec7c2b-15b6-48af-b46c-338d13e0ad0c.dat' -o '/tmp/tmp8rkid8xk/job_working_directory/000/8/outputs/dataset_e7e6f307-15f5-4140-9477-0d08b8ad21ff.dat'

Exit Code:

```
0
```

Standard Output:

/tmp/tmp8rkid8xk/job_working_directory/000/8/outputs/dataset_e7e6f307-15f5-4140-9477-0d08b8ad21ff.dat: 100.0% ARGs mapped.

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"input"`
__workflow_invocation_uuid__	`"475bce76c15f11f0bb736045bdd8cbdf"`
choose_tool	`{"__current_case__": 0, "tool": "deeparg"}`
chromInfo	`"/tmp/tmp8rkid8xk/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
dbkey	`"?"`

Step 16: Unlabelled step:
- step_state: scheduled

Step 17: toolshed.g2.bx.psu.edu/repos/iuc/groot/groot/1.1.2+galaxy2:

step_state: scheduled

Jobs

Job 1:

Job state is ok

Command Line:

set -x pipefail; ln -s -f '/tmp/tmp8rkid8xk/files/3/e/0/dataset_3e04cf60-cc89-4c00-b2f1-2da00f285000.dat' 'input.fastq.gz' && groot index --msaDir '/cvmfs/data.galaxyproject.org/byhand/groot_database/arg-annot.90' --indexDir 'grootIndex' --windowSize 100 --kmerSize 31 --maxK 4 --maxSketchSpan 30 --numPart 8 --sketchSize 21 &&  groot align --fastq 'input.fastq.gz' --indexDir 'grootIndex' --contThresh 0.97 --minKmerCov 1  --processors "${GALAXY_SLOTS:-1}"  | groot report --covCutoff '0.6' > '/tmp/tmp8rkid8xk/job_working_directory/000/9/outputs/dataset_54ec7632-5d12-4a18-ad8b-003741dfa87f.dat'

Exit Code:

```
0
```

Standard Error:

+ ln -s -f /tmp/tmp8rkid8xk/files/3/e/0/dataset_3e04cf60-cc89-4c00-b2f1-2da00f285000.dat input.fastq.gz
+ groot index --msaDir /cvmfs/data.galaxyproject.org/byhand/groot_database/arg-annot.90 --indexDir grootIndex --windowSize 100 --kmerSize 31 --maxK 4 --maxSketchSpan 30 --numPart 8 --sketchSize 21
+ groot align --fastq input.fastq.gz --indexDir grootIndex --contThresh 0.97 --minKmerCov 1 --processors 1
+ groot report --covCutoff 0.6

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"input"`
__workflow_invocation_uuid__	`"475bce76c15f11f0bb736045bdd8cbdf"`
align	`{"contThresh": "0.97", "minKmerCov": "1", "noAlign": true}`
chromInfo	`"/tmp/tmp8rkid8xk/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
dbkey	`"?"`
index	`{"groot_db_select": "arg-annot.90-1.1.2-08112025", "kmerSize": "31", "maxK": "4", "maxSketchSpan": "30", "numPart": "8", "sketchSize": "21", "windowSize": "100"}`
report	`{"coverage": {"__current_case__": 0, "covCutoff": "0.6", "mode": "cutoff"}}`

Step 18: addValue:

step_state: scheduled

Jobs

Job 1:

Job state is ok

Command Line:

perl '/tmp/tmp8rkid8xk/galaxy-dev/tools/filters/fixedValueColumn.pl' '/tmp/tmp8rkid8xk/files/e/7/e/dataset_e7e6f307-15f5-4140-9477-0d08b8ad21ff.dat' '/tmp/tmp8rkid8xk/job_working_directory/000/10/outputs/dataset_38c1b188-a607-4fcb-b187-91436870eaa9.dat' 'DeepARG' no

Exit Code:

```
0
```

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"input"`
__workflow_invocation_uuid__	`"475bce76c15f11f0bb736045bdd8cbdf"`
chromInfo	`"/tmp/tmp8rkid8xk/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
dbkey	`"?"`
exp	`"DeepARG"`
iterate	`"no"`

Step 19: __FLATTEN__:
- step_state: scheduled
- Jobs
  - Job 1:
    - Job state is ok
    Traceback:
    Job Parameters:
    - Job parameter Parameter value
      
      __workflow_invocation_uuid__ "475bce76c15f11f0bb736045bdd8cbdf"
      
      input {"values": [{"id": 21, "src": "hdca"}]}
      
      join_identifier "_"

Step 20: toolshed.g2.bx.psu.edu/repos/iuc/argnorm/argnorm/1.0.0+galaxy0:

step_state: scheduled

Jobs

Job 1:

Job state is ok

Command Line:

argnorm 'groot' --db 'groot-argannot' -i '/tmp/tmp8rkid8xk/files/5/4/e/dataset_54ec7632-5d12-4a18-ad8b-003741dfa87f.dat' -o '/tmp/tmp8rkid8xk/job_working_directory/000/11/outputs/dataset_dd7ba87e-de6b-4cbd-bf59-8199800ff672.dat'

Exit Code:

```
0
```

Standard Output:

/tmp/tmp8rkid8xk/job_working_directory/000/11/outputs/dataset_dd7ba87e-de6b-4cbd-bf59-8199800ff672.dat: 100.0% ARGs mapped.

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"input"`
__workflow_invocation_uuid__	`"475bce76c15f11f0bb736045bdd8cbdf"`
choose_tool	`{"__current_case__": 5, "db": "groot-argannot", "tool": "groot"}`
chromInfo	`"/tmp/tmp8rkid8xk/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
dbkey	`"?"`

Step 3: Select a Groot database:
- step_state: scheduled
Step 21: __FILTER_FAILED_DATASETS__:
- step_state: scheduled
- Jobs
  - Job 1:
    - Job state is ok
    Traceback:
    Job Parameters:
    - Job parameter Parameter value
      
      __workflow_invocation_uuid__ "475bce76c15f11f0bb736045bdd8cbdf"
      
      input {"values": [{"id": 18, "src": "hdca"}]}

Step 22: addValue:

step_state: scheduled

Jobs

Job 1:

Job state is ok

Command Line:

perl '/tmp/tmp8rkid8xk/galaxy-dev/tools/filters/fixedValueColumn.pl' '/tmp/tmp8rkid8xk/files/d/d/7/dataset_dd7ba87e-de6b-4cbd-bf59-8199800ff672.dat' '/tmp/tmp8rkid8xk/job_working_directory/000/13/outputs/dataset_07b8bf66-b5fa-4c4a-aaed-5d63119dc497.dat' 'Groot' no

Exit Code:

```
0
```

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"input"`
__workflow_invocation_uuid__	`"475bce76c15f11f0bb736045bdd8cbdf"`
chromInfo	`"/tmp/tmp8rkid8xk/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
dbkey	`"?"`
exp	`"Groot"`
iterate	`"no"`

Step 23: Unlabelled step:
- step_state: new
Step 24: Unlabelled step:
- step_state: new
Step 4: Select a Groot database for ARGnorm:
- step_state: scheduled
Step 5: Deeparg minimum probability for considering a reads as ARG-like:
- step_state: scheduled
Step 6: Select a Sylph database:
- step_state: scheduled
Step 7: Select a Sylph tax database:
- step_state: scheduled
Step 8: Groot average base pair length of reads:
- step_state: scheduled
Step 9: Groot coverage cutoff for reporting ARGs:
- step_state: scheduled

Step 10: toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_text_file_with_recurring_lines/9.5+galaxy2:

step_state: scheduled

Jobs

Job 1:

Job state is ok

Command Line:

times=1; yes -- 'no_results' 2>/dev/null | head -n $times >> '/tmp/tmp8rkid8xk/job_working_directory/000/3/outputs/dataset_d5ef1f59-618d-4237-ae51-58f3ae3418ed.dat'; times=1; yes -- 'no_results' 2>/dev/null | head -n $times >> '/tmp/tmp8rkid8xk/job_working_directory/000/3/outputs/dataset_d5ef1f59-618d-4237-ae51-58f3ae3418ed.dat';

Exit Code:

```
0
```

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"input"`
__workflow_invocation_uuid__	`"475bce76c15f11f0bb736045bdd8cbdf"`
chromInfo	`"/tmp/tmp8rkid8xk/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
dbkey	`"?"`
token_set	`[{"__index__": 0, "line": "no_results", "repeat_select": {"__current_case__": 0, "repeat_select_opts": "user", "times": "1"}}, {"__index__": 1, "line": "no_results", "repeat_select": {"__current_case__": 0, "repeat_select_opts": "user", "times": "1"}}]`

Other invocation details
- error_message
  - Failed to run workflow, invocation ended in [failed] state.
- history_id
  - 5c0d57b126876b4e
- history_state
  - error
- invocation_id
  - 5c0d57b126876b4e
- invocation_state
  - failed
- messages
  - [{'details': 'Cannot match collection types.', 'reason': 'unexpected_failure', 'workflow_step_id': 22}]
- workflow_id
  - 5c0d57b126876b4e

github-actions · 2025-11-20T10:41:03Z

Test Results (powered by Planemo)

Test Summary

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

Errored Tests

❌ metagenomic-raw-reads-amr-analysis.ga_0

Execution Problem:

Unexpected HTTP status code: 400: {"err_msg":"Workflow cannot be run because input step '14' (DeepARG database) is not optional and no input provided.","err_code":0}

github-actions · 2025-11-20T10:41:07Z

Test Results (powered by Planemo)

Test Summary

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

Errored Tests

❌ metagenomic-raw-reads-amr-analysis.ga_0

Execution Problem:

Unexpected HTTP status code: 400: {"err_msg":"Workflow cannot be run because input step '14' (DeepARG database) is not optional and no input provided.","err_code":0}

github-actions · 2025-11-20T10:59:50Z

Test Results (powered by Planemo)

Test Summary

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

Errored Tests

❌ metagenomic-raw-reads-amr-analysis.ga_0

Execution Problem:

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

Workflow invocation details

Invocation Messages
- Invocation scheduling failed because an unexpected failure occurred at step 23: 'Cannot match collection types.'

Steps

Step 1: Metagenomics Trimmed reads:
- step_state: scheduled
Step 2: DeepARG database:
- step_state: scheduled
Step 11: __UNZIP_COLLECTION__:
- step_state: scheduled
- Jobs
  - Job 1:
    - Job state is ok
    Traceback:
    Job Parameters:
    - Job parameter Parameter value
      
      __workflow_invocation_uuid__ "42526208c5fd11f0a0597c1e52d6ad2f"
      
      input {"values": [{"id": 1, "src": "dce"}]}

Step 12: toolshed.g2.bx.psu.edu/repos/iuc/deeparg_short_reads/deeparg_short_reads/1.0.4+galaxy1:

step_state: scheduled

Jobs

Job 1:

Job state is ok

Command Line:

mkdir -p deeparg_short_reads_output && ln -s -f '/tmp/tmplsda32zq/files/f/e/a/dataset_fea4ac36-2d86-44c2-83f9-004ca2267419.dat' 'input_forward.fastqsanger.gz' && ln -s -f '/tmp/tmplsda32zq/files/d/2/9/dataset_d29baef3-acb8-4dc1-b394-179226d33977.dat' 'input_reverse.fastqsanger.gz' && deeparg short_reads_pipeline --forward_pe_file 'input_forward.fastqsanger.gz' --reverse_pe_file 'input_reverse.fastqsanger.gz' --output_file 'deeparg_short_reads_output/SR' -d '/cvmfs/data.galaxyproject.org/byhand/deeparg/deeparg_1.0.4' --deeparg_identity 80 --deeparg_probability 0.8 --deeparg_evalue 1e-10 --gene_coverage 95 --bowtie_16s_identity 0.8

Exit Code:

```
0
```

Standard Error:

WARNING (theano.configdefaults): g++ not detected ! Theano will be unable to execute optimized C-implementations (for both CPU and GPU) and will default to Python implementations. Performance will be severely degraded. To remove this warning, set Theano flags cxx to an empty string.
/usr/local/lib/python2.7/site-packages/theano/tensor/signal/downsample.py:6: UserWarning: downsample module has been moved to the theano.tensor.signal.pool module.
  "downsample module has been moved to the theano.tensor.signal.pool module.")
/usr/local/lib/python2.7/site-packages/sklearn/cross_validation.py:41: DeprecationWarning: This module was deprecated in version 0.18 in favor of the model_selection module into which all the refactored classes and functions are moved. Also note that the interface of the new CV iterators are different from that of this module. This module will be removed in 0.20.
  "This module will be removed in 0.20.", DeprecationWarning)
TrimmomaticPE: Started with arguments:
 -phred33 input_forward.fastqsanger.gz input_reverse.fastqsanger.gz input_forward.fastqsanger.gz.paired input_forward.fastqsanger.gz.unpaired input_reverse.fastqsanger.gz.paired input_reverse.fastqsanger.gz.unpaired LEADING:3 TRAILING:3 SLIDINGWINDOW:4:15 MINLEN:36
Multiple cores found: Using 4 threads
Input Read Pairs: 125000 Both Surviving: 125000 (100.00%) Forward Only Surviving: 0 (0.00%) Reverse Only Surviving: 0 (0.00%) Dropped: 0 (0.00%)
TrimmomaticPE: Completed successfully
vsearch v2.27.1_linux_x86_64, 15.6GB RAM, 4 cores
https://github.com/torognes/vsearch

Merging reads 100%
    125000  Pairs
     69309  Merged (55.4%)
     55691  Not merged (44.6%)

Pairs that failed merging due to various reasons:
     39021  too few kmers found on same diagonal
       265  multiple potential alignments
     12101  alignment score too low, or score drop too high
       295  overlap too short
      4009  staggered read pairs

Statistics of all reads:
     92.44  Mean read length

Statistics of merged reads:
    109.97  Mean fragment length
     40.60  Standard deviation of fragment length
      0.07  Mean expected error in forward sequences
      0.06  Mean expected error in reverse sequences
      0.04  Mean expected error in merged sequences
      0.01  Mean observed errors in merged region of forward sequences
      0.00  Mean observed errors in merged region of reverse sequences
      0.01  Mean observed errors in merged region
WARNING (theano.configdefaults): g++ not detected ! Theano will be unable to execute optimized C-implementations (for both CPU and GPU) and will default to Python implementations. Performance will be severely degraded. To remove this warning, set Theano flags cxx to an empty string.
/usr/local/lib/python2.7/site-packages/theano/tensor/signal/downsample.py:6: UserWarning: downsample module has been moved to the theano.tensor.signal.pool module.
  "downsample module has been moved to the theano.tensor.signal.pool module.")
/usr/local/lib/python2.7/site-packages/sklearn/cross_validation.py:41: DeprecationWarning: This module was deprecated in version 0.18 in favor of the model_selection module into which all the refactored classes and functions are moved. Also note that the interface of the new CV iterators are different from that of this module. This module will be removed in 0.20.
  "This module will be removed in 0.20.", DeprecationWarning)
INFO:root:DIAMOND blastx alignment
INFO:root:Running: diamond  blastx -q deeparg_short_reads_output/SR.clean -d /cvmfs/data.galaxyproject.org/byhand/deeparg/deeparg_1.0.4/database/v2/features -k 1000 --id 80.0 --sensitive -e 1e-10 -a deeparg_short_reads_output/SR.clean.deeparg.align
INFO:root:Input:deeparg_short_reads_output/SR.clean output:deeparg_short_reads_output/SR.clean.deeparg model: deepARG_SS, Input type: blastx
INFO:root:parsing output file diamond view -a deeparg_short_reads_output/SR.clean.deeparg.align.daa -o deeparg_short_reads_output/SR.clean.deeparg.align.daa.tsv
diamond v2.1.10.164 (C) Max Planck Society for the Advancement of Science, Benjamin Buchfink, University of Tuebingen
Documentation, support and updates available at http://www.diamondsearch.org
Please cite: http://dx.doi.org/10.1038/s41592-021-01101-x Nature Methods (2021)

#CPU threads: 4
Loading subject IDs...  [0s]
Scoring parameters: (Matrix=blosum62 Lambda=0.267 K=0.041 Penalties=11/1)
DB sequences = 12279
DB sequences used = 642
DB letters = 5088898
#Target sequences to report alignments for: 25
Generating output...  [0.001s]
INFO:root:Loading deep learning model ...
INFO:root:loading gene lengths
INFO:root:Loading sample to analyze

0reads [00:00, ?reads/s]
1237reads [00:00, 215168.33reads/s]
INFO:root:Predicting ARG-like reads: Running deepARG_SS model version v2
INFO:root:input dataset is splitted into chunks of 10000 reads

0chunks [00:00, ?chunks/s]
1chunks [00:07,  7.25s/chunks]
1chunks [00:07,  7.25s/chunks]
INFO:root:Predicting ARGs

  0%|          | 0/136 [00:00<?, ?it/s]
100%|██████████| 136/136 [00:00<00:00, 34214.57it/s]
180691 reads; of these:
  180691 (100.00%) were unpaired; of these:
    180399 (99.84%) aligned 0 times
    0 (0.00%) aligned exactly 1 time
    292 (0.16%) aligned >1 times
0.16% overall alignment rate

Standard Output:

Step 1: Trimming and QC using Trimmomatic
['/usr/local/bin', '/usr/local/lib/python27.zip', '/usr/local/lib/python2.7', '/usr/local/lib/python2.7/plat-linux2', '/usr/local/lib/python2.7/lib-tk', '/usr/local/lib/python2.7/lib-old', '/usr/local/lib/python2.7/lib-dynload', '/usr/local/lib/python2.7/site-packages']



Step 2: Merging paired end reads using Vsearch
['/usr/local/bin', '/usr/local/lib/python27.zip', '/usr/local/lib/python2.7', '/usr/local/lib/python2.7/plat-linux2', '/usr/local/lib/python2.7/lib-tk', '/usr/local/lib/python2.7/lib-old', '/usr/local/lib/python2.7/lib-dynload', '/usr/local/lib/python2.7/site-packages']



Step 3: Run DeepARG-SS to identify ARG-like reads
deeparg predict --type nucl --model SS -d /cvmfs/data.galaxyproject.org/byhand/deeparg/deeparg_1.0.4 -i deeparg_short_reads_output/SR.clean -o deeparg_short_reads_output/SR.clean.deeparg --arg-alignment-identity 80.0 --min-prob 0.8 --arg-alignment-evalue 1e-10



Step 4: Quantification of ARG-like counts
sort -k1,1 -k2,2n deeparg_short_reads_output/SR.clean.deeparg.mapping.ARG  | bedtools merge -c 12,5 -o sum,distinct >deeparg_short_reads_output/SR.clean.deeparg.mapping.ARG.merged



Step 5: Normalize to 16S rRNAs - this may take a while ...
Total number of 16S Reads in the sample: 178

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"input"`
__workflow_invocation_uuid__	`"42526208c5fd11f0a0597c1e52d6ad2f"`
bowtie_16s_identity	`"0.8"`
chromInfo	`"/tmp/tmplsda32zq/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
dbkey	`"?"`
deeparg_db	`"deeparg_1.0.4-07112025"`
deeparg_evalue	`"1e-10"`
deeparg_identity	`"80"`
deeparg_probability	`"0.8"`
gene_coverage	`"95"`
hide_db_build	`""`
input_option	`{"__current_case__": 1, "choice": "paired_collection", "pair_input": {"values": [{"id": 1, "src": "dce"}]}}`
output_files	`{"output_selection": ["file_ARG_tsv", "file_ARG_subtype_tsv", "file_ARG_type_tsv", "file_merged_ARG_tsv", "file_potential_ARG_tsv", "file_all_hits_tsv"]}`

Step 13: toolshed.g2.bx.psu.edu/repos/bgruening/sylph_profile/sylph_profile/0.8.1+galaxy0:

step_state: scheduled

Jobs

Job 1:

Job state is error

Command Line:

ln -s '/cvmfs/data.galaxyproject.org/byhand/sylph/gtdb-r220-c200-dbv1.syldb' '0_sylph_database.syldb' &&       ln -s '/tmp/tmplsda32zq/files/f/e/a/dataset_fea4ac36-2d86-44c2-83f9-004ca2267419.dat' 'raw_reads_metag_test.fastq.gz' && ln -s '/tmp/tmplsda32zq/files/d/2/9/dataset_d29baef3-acb8-4dc1-b394-179226d33977.dat' 'raw_reads_metag_test_r2.fastq.gz' &&  sylph sketch -1 raw_reads_metag_test.fastq.gz -2 raw_reads_metag_test_r2.fastq.gz -t ${GALAXY_SLOTS:-4} -d sylph_sketches &&   sylph profile *.syldb sylph_sketches/*.sylsp --min-number-kmers 50 -t ${GALAXY_SLOTS:-4} -o '/tmp/tmplsda32zq/job_working_directory/000/6/outputs/dataset_5b3f4272-1593-4997-8036-a9ebc7531e6a.dat'  && cp '/tmp/tmplsda32zq/job_working_directory/000/6/configs/tmp55m8tqk5' config.json && export SYLPH_TAXONOMY_CONFIG=config.json && mkdir -p sylph_taxprof_out && sylph-tax taxprof '/tmp/tmplsda32zq/job_working_directory/000/6/outputs/dataset_5b3f4272-1593-4997-8036-a9ebc7531e6a.dat' -o sylph_taxprof_out/'sylph_tax_out-' --taxonomy-metadata GTDB_r220 && sylph-tax merge sylph_taxprof_out/*.sylphmpa --column relative_abundance -o output_tax_merge.tsv

Exit Code:

```
137
```

Standard Error:

2025-11-20T10:40:35.319Z INFO  [sylph::sketch] Sketching paired sequences...
2025-11-20T10:40:35.570Z INFO  [sylph::sketch] Sketching sylph_sketches/raw_reads_metag_test.fastq.gz.paired.sylsp complete.
2025-11-20T10:40:35.570Z INFO  [sylph::sketch] Finished.
2025-11-20T10:40:35.574Z INFO  [sylph::contain] Obtaining sketches...
/tmp/tmplsda32zq/job_working_directory/000/6/tool_script.sh: line 23:    11 Killed                  sylph profile *.syldb sylph_sketches/*.sylsp --min-number-kmers 50 -t ${GALAXY_SLOTS:-4} -o '/tmp/tmplsda32zq/job_working_directory/000/6/outputs/dataset_5b3f4272-1593-4997-8036-a9ebc7531e6a.dat'

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"input"`
__workflow_invocation_uuid__	`"42526208c5fd11f0a0597c1e52d6ad2f"`
chromInfo	`"/tmp/tmplsda32zq/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
database_select	`{"__current_case__": 0, "column": "relative_abundance", "select": "cached", "sylph_database": "sylph_downloaded_07112025_gtdb-r220-c200-dbv1.syldb", "sylph_tax_metadata": "sylph_tax_downloaded_08112025"}`
dbkey	`"?"`
estimate_unknown	`false`
min_num_kmers	`"50"`
sketch_reads	`{"__current_case__": 3, "input": {"values": [{"id": 1, "src": "dce"}]}, "type_reads": "paired_group"}`

**Step 14: Combines files R1 and R2 **:

step_state: scheduled

Jobs

Job 1:

Job state is ok

Command Line:

gx-fastq-paired-end-interlacer '/tmp/tmplsda32zq/files/f/e/a/dataset_fea4ac36-2d86-44c2-83f9-004ca2267419.dat' sanger.gz '/tmp/tmplsda32zq/files/d/2/9/dataset_d29baef3-acb8-4dc1-b394-179226d33977.dat' sanger.gz '/tmp/tmplsda32zq/job_working_directory/000/7/outputs/dataset_36dff02b-724c-4f74-9098-69d14f9ae0bd.dat' '/tmp/tmplsda32zq/job_working_directory/000/7/outputs/dataset_7d9553c7-f839-41d2-94d8-4e193d170c3f.dat'

Exit Code:

```
0
```

Standard Output:

There were 0 single reads.
Interlaced 125000 pairs of sequences.

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"fastqsanger.gz"`
__workflow_invocation_uuid__	`"42526208c5fd11f0a0597c1e52d6ad2f"`
chromInfo	`"/tmp/tmplsda32zq/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
dbkey	`"?"`
reads	`{"__current_case__": 0, "input1_file": {"values": [{"id": 4, "src": "dce"}]}, "input2_file": {"values": [{"id": 5, "src": "dce"}]}, "reads_selector": "paired"}`

Step 15: argNorm DeepARG:

step_state: scheduled

Jobs

Job 1:

Job state is ok

Command Line:

argnorm 'deeparg' -i '/tmp/tmplsda32zq/files/0/0/b/dataset_00b65ad5-1c6b-436b-9465-76c9ddf2fe97.dat' -o '/tmp/tmplsda32zq/job_working_directory/000/8/outputs/dataset_6e32be25-e54c-4484-97c6-cf7ac7eef485.dat'

Exit Code:

```
0
```

Standard Output:

/tmp/tmplsda32zq/job_working_directory/000/8/outputs/dataset_6e32be25-e54c-4484-97c6-cf7ac7eef485.dat: 100.0% ARGs mapped.

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"input"`
__workflow_invocation_uuid__	`"42526208c5fd11f0a0597c1e52d6ad2f"`
choose_tool	`{"__current_case__": 0, "tool": "deeparg"}`
chromInfo	`"/tmp/tmplsda32zq/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
dbkey	`"?"`

Step 16: Unlabelled step:
- step_state: scheduled

Step 17: toolshed.g2.bx.psu.edu/repos/iuc/groot/groot/1.1.2+galaxy2:

step_state: scheduled

Jobs

Job 1:

Job state is ok

Command Line:

set -x pipefail; ln -s -f '/tmp/tmplsda32zq/files/3/6/d/dataset_36dff02b-724c-4f74-9098-69d14f9ae0bd.dat' 'input.fastq.gz' && groot index --msaDir '/cvmfs/data.galaxyproject.org/byhand/groot_database/arg-annot.90' --indexDir 'grootIndex' --windowSize 100 --kmerSize 31 --maxK 4 --maxSketchSpan 30 --numPart 8 --sketchSize 21 &&  groot align --fastq 'input.fastq.gz' --indexDir 'grootIndex' --contThresh 0.97 --minKmerCov 1  --processors "${GALAXY_SLOTS:-1}"  | groot report --covCutoff '0.6' > '/tmp/tmplsda32zq/job_working_directory/000/9/outputs/dataset_5a6abb09-d7ba-4b1a-8717-150289de2cda.dat'

Exit Code:

```
0
```

Standard Error:

+ ln -s -f /tmp/tmplsda32zq/files/3/6/d/dataset_36dff02b-724c-4f74-9098-69d14f9ae0bd.dat input.fastq.gz
+ groot index --msaDir /cvmfs/data.galaxyproject.org/byhand/groot_database/arg-annot.90 --indexDir grootIndex --windowSize 100 --kmerSize 31 --maxK 4 --maxSketchSpan 30 --numPart 8 --sketchSize 21
+ groot align --fastq input.fastq.gz --indexDir grootIndex --contThresh 0.97 --minKmerCov 1 --processors 1
+ groot report --covCutoff 0.6

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"input"`
__workflow_invocation_uuid__	`"42526208c5fd11f0a0597c1e52d6ad2f"`
align	`{"contThresh": "0.97", "minKmerCov": "1", "noAlign": true}`
chromInfo	`"/tmp/tmplsda32zq/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
dbkey	`"?"`
index	`{"groot_db_select": "arg-annot.90-1.1.2-08112025", "kmerSize": "31", "maxK": "4", "maxSketchSpan": "30", "numPart": "8", "sketchSize": "21", "windowSize": "100"}`
report	`{"coverage": {"__current_case__": 0, "covCutoff": "0.6", "mode": "cutoff"}}`

Step 18: addValue:

step_state: scheduled

Jobs

Job 1:

Job state is ok

Command Line:

perl '/tmp/tmplsda32zq/galaxy-dev/tools/filters/fixedValueColumn.pl' '/tmp/tmplsda32zq/files/6/e/3/dataset_6e32be25-e54c-4484-97c6-cf7ac7eef485.dat' '/tmp/tmplsda32zq/job_working_directory/000/10/outputs/dataset_364885ba-3456-40fb-b612-58fe1d3eea13.dat' 'DeepARG' no

Exit Code:

```
0
```

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"input"`
__workflow_invocation_uuid__	`"42526208c5fd11f0a0597c1e52d6ad2f"`
chromInfo	`"/tmp/tmplsda32zq/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
dbkey	`"?"`
exp	`"DeepARG"`
iterate	`"no"`

Step 19: __FLATTEN__:
- step_state: scheduled
- Jobs
  - Job 1:
    - Job state is ok
    Traceback:
    Job Parameters:
    - Job parameter Parameter value
      
      __workflow_invocation_uuid__ "42526208c5fd11f0a0597c1e52d6ad2f"
      
      input {"values": [{"id": 21, "src": "hdca"}]}
      
      join_identifier "_"

Step 20: argNorm Groot:

step_state: scheduled

Jobs

Job 1:

Job state is ok

Command Line:

argnorm 'groot' --db 'groot-argannot' -i '/tmp/tmplsda32zq/files/5/a/6/dataset_5a6abb09-d7ba-4b1a-8717-150289de2cda.dat' -o '/tmp/tmplsda32zq/job_working_directory/000/11/outputs/dataset_6d5fefa3-0dbd-431d-a931-eb4079ec007e.dat'

Exit Code:

```
0
```

Standard Output:

/tmp/tmplsda32zq/job_working_directory/000/11/outputs/dataset_6d5fefa3-0dbd-431d-a931-eb4079ec007e.dat: 100.0% ARGs mapped.

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"input"`
__workflow_invocation_uuid__	`"42526208c5fd11f0a0597c1e52d6ad2f"`
choose_tool	`{"__current_case__": 5, "db": "groot-argannot", "tool": "groot"}`
chromInfo	`"/tmp/tmplsda32zq/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
dbkey	`"?"`

Step 3: Groot database:
- step_state: scheduled
Step 21: __FILTER_FAILED_DATASETS__:
- step_state: scheduled
- Jobs
  - Job 1:
    - Job state is ok
    Traceback:
    Job Parameters:
    - Job parameter Parameter value
      
      __workflow_invocation_uuid__ "42526208c5fd11f0a0597c1e52d6ad2f"
      
      input {"values": [{"id": 18, "src": "hdca"}]}

Step 22: addValue:

step_state: scheduled

Jobs

Job 1:

Job state is ok

Command Line:

perl '/tmp/tmplsda32zq/galaxy-dev/tools/filters/fixedValueColumn.pl' '/tmp/tmplsda32zq/files/6/d/5/dataset_6d5fefa3-0dbd-431d-a931-eb4079ec007e.dat' '/tmp/tmplsda32zq/job_working_directory/000/13/outputs/dataset_fc5f978c-6203-4947-92ea-e3082066d070.dat' 'Groot' no

Exit Code:

```
0
```

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"input"`
__workflow_invocation_uuid__	`"42526208c5fd11f0a0597c1e52d6ad2f"`
chromInfo	`"/tmp/tmplsda32zq/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
dbkey	`"?"`
exp	`"Groot"`
iterate	`"no"`

Step 23: Unlabelled step:
- step_state: new
Step 24: Unlabelled step:
- step_state: new
Step 4: Groot database for ARGnorm:
- step_state: scheduled
Step 5: Deeparg minimum probability for considering a reads as ARG-like:
- step_state: scheduled
Step 6: Sylph database:
- step_state: scheduled
Step 7: Sylph tax database:
- step_state: scheduled
Step 8: Groot average base pair length of reads:
- step_state: scheduled
Step 9: Groot coverage cutoff for reporting ARGs:
- step_state: scheduled

Step 10: toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_text_file_with_recurring_lines/9.5+galaxy2:

step_state: scheduled

Jobs

Job 1:

Job state is ok

Command Line:

times=1; yes -- 'no_results' 2>/dev/null | head -n $times >> '/tmp/tmplsda32zq/job_working_directory/000/3/outputs/dataset_2029e14a-2a14-4963-9c93-c4c183c03665.dat'; times=1; yes -- 'no_results' 2>/dev/null | head -n $times >> '/tmp/tmplsda32zq/job_working_directory/000/3/outputs/dataset_2029e14a-2a14-4963-9c93-c4c183c03665.dat';

Exit Code:

```
0
```

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"input"`
__workflow_invocation_uuid__	`"42526208c5fd11f0a0597c1e52d6ad2f"`
chromInfo	`"/tmp/tmplsda32zq/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
dbkey	`"?"`
token_set	`[{"__index__": 0, "line": "no_results", "repeat_select": {"__current_case__": 0, "repeat_select_opts": "user", "times": "1"}}, {"__index__": 1, "line": "no_results", "repeat_select": {"__current_case__": 0, "repeat_select_opts": "user", "times": "1"}}]`

Other invocation details
- error_message
  - Failed to run workflow, invocation ended in [failed] state.
- history_id
  - 42f676f6b5b014ad
- history_state
  - error
- invocation_id
  - 42f676f6b5b014ad
- invocation_state
  - failed
- messages
  - [{'details': 'Cannot match collection types.', 'reason': 'unexpected_failure', 'workflow_step_id': 22}]
- workflow_id
  - 42f676f6b5b014ad

github-actions · 2025-11-20T11:31:26Z

Test Results (powered by Planemo)

Test Summary

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

Errored Tests

❌ metagenomic-raw-reads-amr-analysis.ga_0

Execution Problem:

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

Workflow invocation details

Invocation Messages
- Invocation scheduling failed because an unexpected failure occurred at step 23: 'Cannot match collection types.'

Steps

Step 1: Metagenomics Trimmed reads:
- step_state: scheduled
Step 2: DeepARG database:
- step_state: scheduled
Step 11: __UNZIP_COLLECTION__:
- step_state: scheduled
- Jobs
  - Job 1:
    - Job state is ok
    Traceback:
    Job Parameters:
    - Job parameter Parameter value
      
      __workflow_invocation_uuid__ "12631b72c5fe11f0a059000d3ad90467"
      
      input {"values": [{"id": 1, "src": "dce"}]}

Step 12: toolshed.g2.bx.psu.edu/repos/iuc/deeparg_short_reads/deeparg_short_reads/1.0.4+galaxy1:

step_state: scheduled

Jobs

Job 1:

Job state is ok

Command Line:

mkdir -p deeparg_short_reads_output && ln -s -f '/tmp/tmpyfijlz_q/files/0/d/5/dataset_0d5ba683-5616-4337-bd55-868bdbc80712.dat' 'input_forward.fastqsanger.gz' && ln -s -f '/tmp/tmpyfijlz_q/files/a/e/a/dataset_aeacef9a-5046-4c09-a81c-25b0a7f2b29f.dat' 'input_reverse.fastqsanger.gz' && deeparg short_reads_pipeline --forward_pe_file 'input_forward.fastqsanger.gz' --reverse_pe_file 'input_reverse.fastqsanger.gz' --output_file 'deeparg_short_reads_output/SR' -d '/cvmfs/data.galaxyproject.org/byhand/deeparg/deeparg_1.0.4' --deeparg_identity 80 --deeparg_probability 0.8 --deeparg_evalue 1e-10 --gene_coverage 95 --bowtie_16s_identity 0.8

Exit Code:

```
0
```

Standard Error:

WARNING (theano.configdefaults): g++ not detected ! Theano will be unable to execute optimized C-implementations (for both CPU and GPU) and will default to Python implementations. Performance will be severely degraded. To remove this warning, set Theano flags cxx to an empty string.
/usr/local/lib/python2.7/site-packages/theano/tensor/signal/downsample.py:6: UserWarning: downsample module has been moved to the theano.tensor.signal.pool module.
  "downsample module has been moved to the theano.tensor.signal.pool module.")
/usr/local/lib/python2.7/site-packages/sklearn/cross_validation.py:41: DeprecationWarning: This module was deprecated in version 0.18 in favor of the model_selection module into which all the refactored classes and functions are moved. Also note that the interface of the new CV iterators are different from that of this module. This module will be removed in 0.20.
  "This module will be removed in 0.20.", DeprecationWarning)
TrimmomaticPE: Started with arguments:
 -phred33 input_forward.fastqsanger.gz input_reverse.fastqsanger.gz input_forward.fastqsanger.gz.paired input_forward.fastqsanger.gz.unpaired input_reverse.fastqsanger.gz.paired input_reverse.fastqsanger.gz.unpaired LEADING:3 TRAILING:3 SLIDINGWINDOW:4:15 MINLEN:36
Multiple cores found: Using 4 threads
Input Read Pairs: 125000 Both Surviving: 125000 (100.00%) Forward Only Surviving: 0 (0.00%) Reverse Only Surviving: 0 (0.00%) Dropped: 0 (0.00%)
TrimmomaticPE: Completed successfully
vsearch v2.27.1_linux_x86_64, 15.6GB RAM, 4 cores
https://github.com/torognes/vsearch

Merging reads 100%
    125000  Pairs
     69309  Merged (55.4%)
     55691  Not merged (44.6%)

Pairs that failed merging due to various reasons:
     39021  too few kmers found on same diagonal
       265  multiple potential alignments
     12101  alignment score too low, or score drop too high
       295  overlap too short
      4009  staggered read pairs

Statistics of all reads:
     92.44  Mean read length

Statistics of merged reads:
    109.97  Mean fragment length
     40.60  Standard deviation of fragment length
      0.07  Mean expected error in forward sequences
      0.06  Mean expected error in reverse sequences
      0.04  Mean expected error in merged sequences
      0.01  Mean observed errors in merged region of forward sequences
      0.00  Mean observed errors in merged region of reverse sequences
      0.01  Mean observed errors in merged region
WARNING (theano.configdefaults): g++ not detected ! Theano will be unable to execute optimized C-implementations (for both CPU and GPU) and will default to Python implementations. Performance will be severely degraded. To remove this warning, set Theano flags cxx to an empty string.
/usr/local/lib/python2.7/site-packages/theano/tensor/signal/downsample.py:6: UserWarning: downsample module has been moved to the theano.tensor.signal.pool module.
  "downsample module has been moved to the theano.tensor.signal.pool module.")
/usr/local/lib/python2.7/site-packages/sklearn/cross_validation.py:41: DeprecationWarning: This module was deprecated in version 0.18 in favor of the model_selection module into which all the refactored classes and functions are moved. Also note that the interface of the new CV iterators are different from that of this module. This module will be removed in 0.20.
  "This module will be removed in 0.20.", DeprecationWarning)
INFO:root:DIAMOND blastx alignment
INFO:root:Running: diamond  blastx -q deeparg_short_reads_output/SR.clean -d /cvmfs/data.galaxyproject.org/byhand/deeparg/deeparg_1.0.4/database/v2/features -k 1000 --id 80.0 --sensitive -e 1e-10 -a deeparg_short_reads_output/SR.clean.deeparg.align
INFO:root:Input:deeparg_short_reads_output/SR.clean output:deeparg_short_reads_output/SR.clean.deeparg model: deepARG_SS, Input type: blastx
INFO:root:parsing output file diamond view -a deeparg_short_reads_output/SR.clean.deeparg.align.daa -o deeparg_short_reads_output/SR.clean.deeparg.align.daa.tsv
diamond v2.1.10.164 (C) Max Planck Society for the Advancement of Science, Benjamin Buchfink, University of Tuebingen
Documentation, support and updates available at http://www.diamondsearch.org
Please cite: http://dx.doi.org/10.1038/s41592-021-01101-x Nature Methods (2021)

#CPU threads: 4
Loading subject IDs...  [0s]
Scoring parameters: (Matrix=blosum62 Lambda=0.267 K=0.041 Penalties=11/1)
DB sequences = 12279
DB sequences used = 642
DB letters = 5088898
#Target sequences to report alignments for: 25
Generating output...  [0.002s]
INFO:root:Loading deep learning model ...
INFO:root:loading gene lengths
INFO:root:Loading sample to analyze

0reads [00:00, ?reads/s]
1237reads [00:00, 280375.79reads/s]
INFO:root:Predicting ARG-like reads: Running deepARG_SS model version v2
INFO:root:input dataset is splitted into chunks of 10000 reads

0chunks [00:00, ?chunks/s]
1chunks [00:07,  7.17s/chunks]
1chunks [00:07,  7.17s/chunks]
INFO:root:Predicting ARGs

  0%|          | 0/136 [00:00<?, ?it/s]
100%|██████████| 136/136 [00:00<00:00, 35676.11it/s]
180691 reads; of these:
  180691 (100.00%) were unpaired; of these:
    180399 (99.84%) aligned 0 times
    0 (0.00%) aligned exactly 1 time
    292 (0.16%) aligned >1 times
0.16% overall alignment rate

Standard Output:

Step 1: Trimming and QC using Trimmomatic
['/usr/local/bin', '/usr/local/lib/python27.zip', '/usr/local/lib/python2.7', '/usr/local/lib/python2.7/plat-linux2', '/usr/local/lib/python2.7/lib-tk', '/usr/local/lib/python2.7/lib-old', '/usr/local/lib/python2.7/lib-dynload', '/usr/local/lib/python2.7/site-packages']



Step 2: Merging paired end reads using Vsearch
['/usr/local/bin', '/usr/local/lib/python27.zip', '/usr/local/lib/python2.7', '/usr/local/lib/python2.7/plat-linux2', '/usr/local/lib/python2.7/lib-tk', '/usr/local/lib/python2.7/lib-old', '/usr/local/lib/python2.7/lib-dynload', '/usr/local/lib/python2.7/site-packages']



Step 3: Run DeepARG-SS to identify ARG-like reads
deeparg predict --type nucl --model SS -d /cvmfs/data.galaxyproject.org/byhand/deeparg/deeparg_1.0.4 -i deeparg_short_reads_output/SR.clean -o deeparg_short_reads_output/SR.clean.deeparg --arg-alignment-identity 80.0 --min-prob 0.8 --arg-alignment-evalue 1e-10



Step 4: Quantification of ARG-like counts
sort -k1,1 -k2,2n deeparg_short_reads_output/SR.clean.deeparg.mapping.ARG  | bedtools merge -c 12,5 -o sum,distinct >deeparg_short_reads_output/SR.clean.deeparg.mapping.ARG.merged



Step 5: Normalize to 16S rRNAs - this may take a while ...
Total number of 16S Reads in the sample: 178

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"input"`
__workflow_invocation_uuid__	`"12631b72c5fe11f0a059000d3ad90467"`
bowtie_16s_identity	`"0.8"`
chromInfo	`"/tmp/tmpyfijlz_q/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
dbkey	`"?"`
deeparg_db	`"deeparg_1.0.4-07112025"`
deeparg_evalue	`"1e-10"`
deeparg_identity	`"80"`
deeparg_probability	`"0.8"`
gene_coverage	`"95"`
hide_db_build	`""`
input_option	`{"__current_case__": 1, "choice": "paired_collection", "pair_input": {"values": [{"id": 1, "src": "dce"}]}}`
output_files	`{"output_selection": ["file_ARG_tsv", "file_ARG_subtype_tsv", "file_ARG_type_tsv", "file_merged_ARG_tsv", "file_potential_ARG_tsv", "file_all_hits_tsv"]}`

Step 13: toolshed.g2.bx.psu.edu/repos/bgruening/sylph_profile/sylph_profile/0.8.1+galaxy0:

step_state: scheduled

Jobs

Job 1:

Job state is error

Command Line:

ln -s '/cvmfs/data.galaxyproject.org/byhand/sylph/gtdb-r220-c200-dbv1.syldb' '0_sylph_database.syldb' &&       ln -s '/tmp/tmpyfijlz_q/files/0/d/5/dataset_0d5ba683-5616-4337-bd55-868bdbc80712.dat' 'raw_reads_metag_test.fastq.gz' && ln -s '/tmp/tmpyfijlz_q/files/a/e/a/dataset_aeacef9a-5046-4c09-a81c-25b0a7f2b29f.dat' 'raw_reads_metag_test_r2.fastq.gz' &&  sylph sketch -1 raw_reads_metag_test.fastq.gz -2 raw_reads_metag_test_r2.fastq.gz -t ${GALAXY_SLOTS:-4} -d sylph_sketches &&   sylph profile *.syldb sylph_sketches/*.sylsp --min-number-kmers 50 -t ${GALAXY_SLOTS:-4} -o '/tmp/tmpyfijlz_q/job_working_directory/000/6/outputs/dataset_c7f4aa00-6af2-422e-b00d-1e63b59dedca.dat'  && cp '/tmp/tmpyfijlz_q/job_working_directory/000/6/configs/tmp6_a5o3lt' config.json && export SYLPH_TAXONOMY_CONFIG=config.json && mkdir -p sylph_taxprof_out && sylph-tax taxprof '/tmp/tmpyfijlz_q/job_working_directory/000/6/outputs/dataset_c7f4aa00-6af2-422e-b00d-1e63b59dedca.dat' -o sylph_taxprof_out/'sylph_tax_out-' --taxonomy-metadata GTDB_r220 && sylph-tax merge sylph_taxprof_out/*.sylphmpa --column relative_abundance -o output_tax_merge.tsv

Exit Code:

```
137
```

Standard Error:

2025-11-20T10:46:40.540Z INFO  [sylph::sketch] Sketching paired sequences...
2025-11-20T10:46:40.739Z INFO  [sylph::sketch] Sketching sylph_sketches/raw_reads_metag_test.fastq.gz.paired.sylsp complete.
2025-11-20T10:46:40.740Z INFO  [sylph::sketch] Finished.
2025-11-20T10:46:40.741Z INFO  [sylph::contain] Obtaining sketches...
/tmp/tmpyfijlz_q/job_working_directory/000/6/tool_script.sh: line 23:    12 Killed                  sylph profile *.syldb sylph_sketches/*.sylsp --min-number-kmers 50 -t ${GALAXY_SLOTS:-4} -o '/tmp/tmpyfijlz_q/job_working_directory/000/6/outputs/dataset_c7f4aa00-6af2-422e-b00d-1e63b59dedca.dat'

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"input"`
__workflow_invocation_uuid__	`"12631b72c5fe11f0a059000d3ad90467"`
chromInfo	`"/tmp/tmpyfijlz_q/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
database_select	`{"__current_case__": 0, "column": "relative_abundance", "select": "cached", "sylph_database": "sylph_downloaded_07112025_gtdb-r220-c200-dbv1.syldb", "sylph_tax_metadata": "sylph_tax_downloaded_08112025"}`
dbkey	`"?"`
estimate_unknown	`false`
min_num_kmers	`"50"`
sketch_reads	`{"__current_case__": 3, "input": {"values": [{"id": 1, "src": "dce"}]}, "type_reads": "paired_group"}`

**Step 14: Combines files R1 and R2 **:

step_state: scheduled

Jobs

Job 1:

Job state is ok

Command Line:

gx-fastq-paired-end-interlacer '/tmp/tmpyfijlz_q/files/0/d/5/dataset_0d5ba683-5616-4337-bd55-868bdbc80712.dat' sanger.gz '/tmp/tmpyfijlz_q/files/a/e/a/dataset_aeacef9a-5046-4c09-a81c-25b0a7f2b29f.dat' sanger.gz '/tmp/tmpyfijlz_q/job_working_directory/000/7/outputs/dataset_6ea745cb-9ac0-4b8e-a89f-084f24f8509d.dat' '/tmp/tmpyfijlz_q/job_working_directory/000/7/outputs/dataset_c8e95a59-61e0-4d6c-a30e-e412d800a27d.dat'

Exit Code:

```
0
```

Standard Output:

There were 0 single reads.
Interlaced 125000 pairs of sequences.

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"fastqsanger.gz"`
__workflow_invocation_uuid__	`"12631b72c5fe11f0a059000d3ad90467"`
chromInfo	`"/tmp/tmpyfijlz_q/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
dbkey	`"?"`
reads	`{"__current_case__": 0, "input1_file": {"values": [{"id": 4, "src": "dce"}]}, "input2_file": {"values": [{"id": 5, "src": "dce"}]}, "reads_selector": "paired"}`

Step 15: argNorm DeepARG:

step_state: scheduled

Jobs

Job 1:

Job state is ok

Command Line:

argnorm 'deeparg' -i '/tmp/tmpyfijlz_q/files/2/9/7/dataset_2979c4df-fb11-4212-8f0f-526e203170fd.dat' -o '/tmp/tmpyfijlz_q/job_working_directory/000/8/outputs/dataset_25c34d51-4768-41ba-ab95-2979ec877b6d.dat'

Exit Code:

```
0
```

Standard Output:

/tmp/tmpyfijlz_q/job_working_directory/000/8/outputs/dataset_25c34d51-4768-41ba-ab95-2979ec877b6d.dat: 100.0% ARGs mapped.

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"input"`
__workflow_invocation_uuid__	`"12631b72c5fe11f0a059000d3ad90467"`
choose_tool	`{"__current_case__": 0, "tool": "deeparg"}`
chromInfo	`"/tmp/tmpyfijlz_q/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
dbkey	`"?"`

Step 16: Unlabelled step:
- step_state: scheduled

Step 17: toolshed.g2.bx.psu.edu/repos/iuc/groot/groot/1.1.2+galaxy2:

step_state: scheduled

Jobs

Job 1:

Job state is ok

Command Line:

set -x pipefail; ln -s -f '/tmp/tmpyfijlz_q/files/6/e/a/dataset_6ea745cb-9ac0-4b8e-a89f-084f24f8509d.dat' 'input.fastq.gz' && groot index --msaDir '/cvmfs/data.galaxyproject.org/byhand/groot_database/arg-annot.90' --indexDir 'grootIndex' --windowSize 100 --kmerSize 31 --maxK 4 --maxSketchSpan 30 --numPart 8 --sketchSize 21 &&  groot align --fastq 'input.fastq.gz' --indexDir 'grootIndex' --contThresh 0.97 --minKmerCov 1  --processors "${GALAXY_SLOTS:-1}"  | groot report --covCutoff '0.6' > '/tmp/tmpyfijlz_q/job_working_directory/000/9/outputs/dataset_a4285cd1-a027-4ec7-a1df-ce270e5879d5.dat'

Exit Code:

```
0
```

Standard Error:

+ ln -s -f /tmp/tmpyfijlz_q/files/6/e/a/dataset_6ea745cb-9ac0-4b8e-a89f-084f24f8509d.dat input.fastq.gz
+ groot index --msaDir /cvmfs/data.galaxyproject.org/byhand/groot_database/arg-annot.90 --indexDir grootIndex --windowSize 100 --kmerSize 31 --maxK 4 --maxSketchSpan 30 --numPart 8 --sketchSize 21
+ groot align --fastq input.fastq.gz --indexDir grootIndex --contThresh 0.97 --minKmerCov 1 --processors 1
+ groot report --covCutoff 0.6

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"input"`
__workflow_invocation_uuid__	`"12631b72c5fe11f0a059000d3ad90467"`
align	`{"contThresh": "0.97", "minKmerCov": "1", "noAlign": true}`
chromInfo	`"/tmp/tmpyfijlz_q/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
dbkey	`"?"`
index	`{"groot_db_select": "arg-annot.90-1.1.2-08112025", "kmerSize": "31", "maxK": "4", "maxSketchSpan": "30", "numPart": "8", "sketchSize": "21", "windowSize": "100"}`
report	`{"coverage": {"__current_case__": 0, "covCutoff": "0.6", "mode": "cutoff"}}`

Step 18: addValue:

step_state: scheduled

Jobs

Job 1:

Job state is ok

Command Line:

perl '/tmp/tmpyfijlz_q/galaxy-dev/tools/filters/fixedValueColumn.pl' '/tmp/tmpyfijlz_q/files/2/5/c/dataset_25c34d51-4768-41ba-ab95-2979ec877b6d.dat' '/tmp/tmpyfijlz_q/job_working_directory/000/10/outputs/dataset_ae1e1605-0926-431f-a8c2-e67a4364e376.dat' 'DeepARG' no

Exit Code:

```
0
```

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"input"`
__workflow_invocation_uuid__	`"12631b72c5fe11f0a059000d3ad90467"`
chromInfo	`"/tmp/tmpyfijlz_q/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
dbkey	`"?"`
exp	`"DeepARG"`
iterate	`"no"`

Step 19: __FLATTEN__:
- step_state: scheduled
- Jobs
  - Job 1:
    - Job state is ok
    Traceback:
    Job Parameters:
    - Job parameter Parameter value
      
      __workflow_invocation_uuid__ "12631b72c5fe11f0a059000d3ad90467"
      
      input {"values": [{"id": 21, "src": "hdca"}]}
      
      join_identifier "_"

Step 20: argNorm Groot:

step_state: scheduled

Jobs

Job 1:

Job state is ok

Command Line:

argnorm 'groot' --db 'groot-argannot' -i '/tmp/tmpyfijlz_q/files/a/4/2/dataset_a4285cd1-a027-4ec7-a1df-ce270e5879d5.dat' -o '/tmp/tmpyfijlz_q/job_working_directory/000/11/outputs/dataset_5989dcdc-1ebf-479d-8f0a-41e47d76cb27.dat'

Exit Code:

```
0
```

Standard Output:

/tmp/tmpyfijlz_q/job_working_directory/000/11/outputs/dataset_5989dcdc-1ebf-479d-8f0a-41e47d76cb27.dat: 100.0% ARGs mapped.

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"input"`
__workflow_invocation_uuid__	`"12631b72c5fe11f0a059000d3ad90467"`
choose_tool	`{"__current_case__": 5, "db": "groot-argannot", "tool": "groot"}`
chromInfo	`"/tmp/tmpyfijlz_q/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
dbkey	`"?"`

Step 3: Groot database:
- step_state: scheduled
Step 21: __FILTER_FAILED_DATASETS__:
- step_state: scheduled
- Jobs
  - Job 1:
    - Job state is ok
    Traceback:
    Job Parameters:
    - Job parameter Parameter value
      
      __workflow_invocation_uuid__ "12631b72c5fe11f0a059000d3ad90467"
      
      input {"values": [{"id": 18, "src": "hdca"}]}

Step 22: addValue:

step_state: scheduled

Jobs

Job 1:

Job state is ok

Command Line:

perl '/tmp/tmpyfijlz_q/galaxy-dev/tools/filters/fixedValueColumn.pl' '/tmp/tmpyfijlz_q/files/5/9/8/dataset_5989dcdc-1ebf-479d-8f0a-41e47d76cb27.dat' '/tmp/tmpyfijlz_q/job_working_directory/000/13/outputs/dataset_c4e8be53-821f-47d4-adf4-5f636971a90f.dat' 'Groot' no

Exit Code:

```
0
```

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"input"`
__workflow_invocation_uuid__	`"12631b72c5fe11f0a059000d3ad90467"`
chromInfo	`"/tmp/tmpyfijlz_q/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
dbkey	`"?"`
exp	`"Groot"`
iterate	`"no"`

Step 23: Unlabelled step:
- step_state: new
Step 24: Unlabelled step:
- step_state: new
Step 4: Groot database for ARGnorm:
- step_state: scheduled
Step 5: Deeparg minimum probability for considering a reads as ARG-like:
- step_state: scheduled
Step 6: Sylph database:
- step_state: scheduled
Step 7: Sylph tax database:
- step_state: scheduled
Step 8: Groot average base pair length of reads:
- step_state: scheduled
Step 9: Groot coverage cutoff for reporting ARGs:
- step_state: scheduled

Step 10: toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_text_file_with_recurring_lines/9.5+galaxy2:

step_state: scheduled

Jobs

Job 1:

Job state is ok

Command Line:

times=1; yes -- 'no_results' 2>/dev/null | head -n $times >> '/tmp/tmpyfijlz_q/job_working_directory/000/3/outputs/dataset_b1d9e435-57fa-40c8-9bfb-b1e557027a48.dat'; times=1; yes -- 'no_results' 2>/dev/null | head -n $times >> '/tmp/tmpyfijlz_q/job_working_directory/000/3/outputs/dataset_b1d9e435-57fa-40c8-9bfb-b1e557027a48.dat';

Exit Code:

```
0
```

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"input"`
__workflow_invocation_uuid__	`"12631b72c5fe11f0a059000d3ad90467"`
chromInfo	`"/tmp/tmpyfijlz_q/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
dbkey	`"?"`
token_set	`[{"__index__": 0, "line": "no_results", "repeat_select": {"__current_case__": 0, "repeat_select_opts": "user", "times": "1"}}, {"__index__": 1, "line": "no_results", "repeat_select": {"__current_case__": 0, "repeat_select_opts": "user", "times": "1"}}]`

Other invocation details
- error_message
  - Failed to run workflow, invocation ended in [failed] state.
- history_id
  - b2bc19486b170c0c
- history_state
  - error
- invocation_id
  - b2bc19486b170c0c
- invocation_state
  - failed
- messages
  - [{'details': 'Cannot match collection types.', 'reason': 'unexpected_failure', 'workflow_step_id': 22}]
- workflow_id
  - b2bc19486b170c0c

hugolefeuvre and others added 4 commits October 14, 2025 18:14

init raw reads analysis metag data wf

3b5bd25

workflow modifications

556057d

update tooldistillator version to 1.0.3

d41a0fd

Merge branch 'galaxyproject:main' into raw_reads_metaG

c0a60e6

add cvmfs DBs identifier

1dc8266

add argnorm groot DB input and update tooldistillator

85fc598

rename wf with amr information

d1cf861

delete old repo name

56d60d1

hugolefeuvre added 4 commits November 20, 2025 11:16

modify output name and label, remove select from input

06a562e

miss version

1fd2998

modify inout name in test file

9919690

modify deeparg input in test file

daf6bbc

Metagenomic raw reads analysis workflow without assembly #1014

Are you sure you want to change the base?

Metagenomic raw reads analysis workflow without assembly #1014

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