Add FAIRyMAGs Binning Evaluation Workflow #924

SantaMcCloud · 2025-07-31T17:58:12Z

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

mvdbeek · 2025-08-04T08:37:38Z

How is this different from #923 ?

SantaMcCloud · 2025-08-04T09:49:51Z

How is this different from #923 ?

The difference is that there is no taxonomic classifcation only the binning and the evaluation.

github-actions · 2025-08-05T02:59:32Z

Test Results (powered by Planemo)

Test Summary

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

Errored Tests

❌ FAIRyMAGs-binning-evaluation.ga_0

Workflow invocation details

Invocation Messages

Steps

Step 1: Reads:
- step_state: scheduled
Step 2: Biobox File(s):
- step_state: scheduled

Step 11: toolshed.g2.bx.psu.edu/repos/iuc/semibin/semibin/2.0.2+galaxy0:

step_state: scheduled

Jobs

Job 1:

Job state is paused

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"input"`
__workflow_invocation_uuid__	`"301f995c718e11f0a03a7ced8d7042ad"`
annot	`{"ml_threshold": null}`
bin	`{"max_edges": "200", "max_node": "1.0", "minfasta_kbs": "200"}`
chromInfo	`"/tmp/tmp2x7w0yy_/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
dbkey	`"?"`
extra_output	`["data", "coverage"]`
min_len	`{"__current_case__": 0, "method": "automatic"}`
mode	`{"__current_case__": 0, "environment": "", "input_bam": {"values": [{"id": 11, "src": "dce"}]}, "input_fasta": {"values": [{"id": 2, "src": "dce"}]}, "ref": {"__current_case__": 0, "cached_db": "17102022", "select": "cached"}, "select": "single"}`
orf_finder	`"fast-naive"`
random_seed	`"0"`
training	`{"batch_size": "2048", "epoches": "20"}`

Step 12: toolshed.g2.bx.psu.edu/repos/iuc/concoct_coverage_table/concoct_coverage_table/1.1.0+galaxy2:

step_state: scheduled

Jobs

Job 1:

Job state is paused

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"input"`
__workflow_invocation_uuid__	`"301f995c718e11f0a03a7ced8d7042ad"`
bedfile	__identifier__
chromInfo	`"/tmp/tmp2x7w0yy_/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
dbkey	`"?"`
mode	`{"__current_case__": 0, "bamfile": {"values": [{"id": 11, "src": "dce"}]}, "type": "individual"}`
mode	bamfile

Step 13: toolshed.g2.bx.psu.edu/repos/iuc/metabat2_jgi_summarize_bam_contig_depths/metabat2_jgi_summarize_bam_contig_depths/2.17+galaxy0:

step_state: scheduled

Jobs

Job 1:

Job state is paused

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"input"`
__workflow_invocation_uuid__	`"301f995c718e11f0a03a7ced8d7042ad"`
advanced	`{"includeEdgeBases": false, "maxEdgeBases": "75", "minMapQual": "0", "noIntraDepthVariance": false, "output_paired_contigs": false, "percentIdentity": "97", "showDepth": false, "weightMapQual": "0.0"}`
bam_indiv_input	__identifier__
chromInfo	`"/tmp/tmp2x7w0yy_/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
dbkey	`"?"`
mode	`{"__current_case__": 0, "bam_indiv_input": {"values": [{"id": 11, "src": "dce"}]}, "type": "individual", "use_reference_cond": {"__current_case__": 0, "use_reference": "no"}}`
shredding	`{"minContigDepth": "0.0", "minContigLength": "1", "shredDepth": "5", "shredLength": "16000"}`

Step 14: toolshed.g2.bx.psu.edu/repos/iuc/collection_element_identifiers/collection_element_identifiers/0.0.2:

step_state: scheduled

Jobs

Job 1:

Job state is ok

Command Line:

mv '/tmp/tmp2x7w0yy_/job_working_directory/000/20/configs/tmpou1ny79_' '/tmp/tmp2x7w0yy_/job_working_directory/000/20/outputs/dataset_a3de71b3-f459-42e4-a819-12b7e5c27dcd.dat'

Exit Code:

```
0
```

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"tabular"`
__workflow_invocation_uuid__	`"301f995c718e11f0a03a7ced8d7042ad"`
chromInfo	`"/tmp/tmp2x7w0yy_/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
dbkey	`"?"`
input_collection	`{"values": [{"id": 31, "src": "hdca"}]}`

Step 15: Unlabelled step:
- step_state: new
Step 16: Unlabelled step:
- step_state: new

Step 17: toolshed.g2.bx.psu.edu/repos/iuc/concoct/concoct/1.1.0+galaxy2:

step_state: scheduled

Jobs

Job 1:

Job state is paused

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"input"`
__workflow_invocation_uuid__	`"301f995c718e11f0a03a7ced8d7042ad"`
advanced	`{"clusters": "400", "iterations": "500", "kmer_length": "4", "length_threshold": "1000", "no_cov_normalization": false, "read_length": "100", "seed": "1", "total_percentage_pca": "90"}`
chromInfo	`"/tmp/tmp2x7w0yy_/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
composition_file	__identifier__
coverage_file	__identifier__
dbkey	`"?"`
output	`{"converge_out": false, "log": false, "no_total_coverage": false}`

Step 18: toolshed.g2.bx.psu.edu/repos/iuc/metabat2/metabat2/2.17+galaxy0:

step_state: scheduled

Jobs

Job 1:

Job state is paused

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"input"`
__workflow_invocation_uuid__	`"301f995c718e11f0a03a7ced8d7042ad"`
advanced	`{"base_coverage_depth_cond": {"__current_case__": 1, "abdFile": {"values": [{"id": 18, "src": "dce"}]}, "base_coverage_depth": "yes", "cvExt": null}, "maxEdges": "200", "maxP": "95", "minCV": "1.0", "minCVSum": "1.0", "minContig": "1500", "minS": "60", "noAdd": false, "pTNF": "0", "seed": "0"}`
advanced	abdFile
chromInfo	`"/tmp/tmp2x7w0yy_/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
dbkey	`"?"`
inFile	__identifier__
out	`{"extra_outputs": ["lowDepth", "tooShort", "unbinned", "log"], "minClsSize": "200000", "onlyLabel": false, "saveCls": false}`

Step 19: toolshed.g2.bx.psu.edu/repos/mbernt/maxbin2/maxbin2/2.2.7+galaxy6:

step_state: scheduled

Jobs

Job 1:

Job state is paused

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"fasta"`
__workflow_invocation_uuid__	`"301f995c718e11f0a03a7ced8d7042ad"`
adv	`{"max_iteration": "50", "min_contig_length": "1000", "prob_threshold": "0.5"}`
assembly	`{"__current_case__": 0, "inputs": {"__current_case__": 1, "abund": {"values": [{"id": 18, "src": "dce"}]}, "type": "abund"}, "type": "individual"}`
chromInfo	`"/tmp/tmp2x7w0yy_/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
dbkey	`"?"`
output	`{"log": false, "marker": false, "markers": false, "markerset": "107", "plotmarker": false}`

Step 20: toolshed.g2.bx.psu.edu/repos/bgruening/split_file_to_collection/split_file_to_collection/0.5.2:

step_state: scheduled

Jobs

Job 1:

Job state is ok

Command Line:

mkdir ./out && python '/tmp/shed_dir/toolshed.g2.bx.psu.edu/repos/bgruening/split_file_to_collection/2dae863c8f42/split_file_to_collection/split_file_to_collection.py' --out ./out --in '/tmp/tmp2x7w0yy_/files/a/3/d/dataset_a3de71b3-f459-42e4-a819-12b7e5c27dcd.dat' --ftype 'txt' --chunksize 1 --file_names 'split_file' --file_ext 'txt'

Exit Code:

```
0
```

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"txt"`
__workflow_invocation_uuid__	`"301f995c718e11f0a03a7ced8d7042ad"`
chromInfo	`"/tmp/tmp2x7w0yy_/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
dbkey	`"?"`
split_parms	`{"__current_case__": 5, "input": {"values": [{"id": 31, "src": "hda"}]}, "newfilenames": "split_file", "select_allocate": {"__current_case__": 2, "allocate": "byrow"}, "select_ftype": "txt", "select_mode": {"__current_case__": 0, "chunksize": "1", "mode": "chunk"}}`

Step 3: Assemblies:
- step_state: scheduled

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

step_state: scheduled

Jobs

Job 1:

Job state is paused

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"input"`
__workflow_invocation_uuid__	`"301f995c718e11f0a03a7ced8d7042ad"`
chromInfo	`"/tmp/tmp2x7w0yy_/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
cutup_clustering_result	__identifier__
dbkey	`"?"`

Step 22: Unlabelled step:
- step_state: new
Step 23: Unlabelled step:
- step_state: new
Step 24: Unlabelled step:
- step_state: new
Step 25: Unlabelled step:
- step_state: new

Step 26: param_value_from_file:

step_state: scheduled

Jobs

Job 1:

Job state is ok

Command Line:

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

Exit Code:

```
0
```

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"txt"`
__workflow_invocation_uuid__	`"301f995c718e11f0a03a7ced8d7042ad"`
chromInfo	`"/tmp/tmp2x7w0yy_/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
dbkey	`"?"`
param_type	`"text"`
remove_newlines	`true`

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

step_state: scheduled

Jobs

Job 1:

Job state is paused

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"input"`
__workflow_invocation_uuid__	`"301f995c718e11f0a03a7ced8d7042ad"`
chromInfo	`"/tmp/tmp2x7w0yy_/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
cluster_file	__identifier__
dbkey	`"?"`
fasta_file	__identifier__

Step 28: toolshed.g2.bx.psu.edu/repos/iuc/compose_text_param/compose_text_param/0.1.1:

step_state: scheduled

Jobs

Job 1:

Job state is ok

Command Line:

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

Exit Code:

```
0
```

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"input"`
__workflow_invocation_uuid__	`"301f995c718e11f0a03a7ced8d7042ad"`
chromInfo	`"/tmp/tmp2x7w0yy_/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
components	`[{"__index__": 0, "param_type": {"__current_case__": 0, "component_value": "@SampleID:", "select_param_type": "text"}}, {"__index__": 1, "param_type": {"__current_case__": 0, "component_value": "sample_0", "select_param_type": "text"}}]`
dbkey	`"?"`

Step 29: Unlabelled step:
- step_state: new
Step 30: Unlabelled step:
- step_state: new

Step 4: toolshed.g2.bx.psu.edu/repos/iuc/collection_element_identifiers/collection_element_identifiers/0.0.2:

step_state: scheduled

Jobs

Job 1:

Job state is ok

Command Line:

mv '/tmp/tmp2x7w0yy_/job_working_directory/000/5/configs/tmphh5imykx' '/tmp/tmp2x7w0yy_/job_working_directory/000/5/outputs/dataset_701169d3-302b-411f-aa08-c33a04e4c462.dat'

Exit Code:

```
0
```

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"tabular"`
__workflow_invocation_uuid__	`"301f995c718e11f0a03a7ced8d7042ad"`
chromInfo	`"/tmp/tmp2x7w0yy_/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
dbkey	`"?"`
input_collection	`{"values": [{"id": 1, "src": "hdca"}]}`

Step 31: toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_replace_in_column/9.3+galaxy1:

step_state: scheduled

Jobs

Job 1:

Job state is ok

Command Line:

awk -v OFS="\t" -v FS="\t" --re-interval --sandbox '{ $1 = gensub( /@SampleID[^ ]*/, "@SampleID:sample_0", "g", $1 ) ; print $0 ; }' '/tmp/tmp2x7w0yy_/files/0/1/4/dataset_01406860-8b7f-4293-8c4d-c2378f9f118e.dat' > '/tmp/tmp2x7w0yy_/job_working_directory/000/24/outputs/dataset_c5634ecb-20ab-4e5b-a35f-190a11b5110b.dat'

Exit Code:

```
0
```

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"input"`
__workflow_invocation_uuid__	`"301f995c718e11f0a03a7ced8d7042ad"`
chromInfo	`"/tmp/tmp2x7w0yy_/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
dbkey	`"?"`
replacements	`[{"__index__": 0, "column": "1", "find_pattern": "@SampleID[^ ]*", "replace_pattern": "@SampleID:sample_0"}]`

Step 32: Unlabelled step:
- step_state: new
Step 33: Unlabelled step:
- step_state: new
Step 34: Unlabelled step:
- step_state: new
Step 35: Unlabelled step:
- step_state: new
Step 36: Unlabelled step:
- step_state: new
Step 37: Unlabelled step:
- step_state: new

Step 38: toolshed.g2.bx.psu.edu/repos/artbio/concatenate_multiple_datasets/cat_multi_datasets/1.4.3:

step_state: scheduled

Jobs

Job 1:

Job state is ok

Command Line:

printf "Concatenating files:\n" && printf "marine_pooled_gsa_trimmed..." && cat '/tmp/tmp2x7w0yy_/files/c/5/6/dataset_c5634ecb-20ab-4e5b-a35f-190a11b5110b.dat' >> '/tmp/tmp2x7w0yy_/job_working_directory/000/25/outputs/dataset_a56b1029-a7e5-4e5a-9974-1bb40c58a27c.dat' && printf "Done\n" && sleep 1

Exit Code:

```
0
```

Standard Output:

Concatenating files:
marine_pooled_gsa_trimmed...Done

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"tabular"`
__workflow_invocation_uuid__	`"301f995c718e11f0a03a7ced8d7042ad"`
chromInfo	`"/tmp/tmp2x7w0yy_/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
dataset_names	`false`
dbkey	`"?"`
global_condition	`{"__current_case__": 0, "input_type": "singles", "inputs": {"values": [{"id": 35, "src": "hdca"}]}}`
headers	`"0"`

Step 39: Unlabelled step:
- step_state: new
Step 40: Unlabelled step:
- step_state: new

Step 5: toolshed.g2.bx.psu.edu/repos/iuc/concoct_cut_up_fasta/concoct_cut_up_fasta/1.1.0+galaxy2:

step_state: scheduled

Jobs

Job 1:

Job state is ok

Command Line:

ln -s '/tmp/tmp2x7w0yy_/files/a/7/8/dataset_a78ce864-cb39-45bb-8333-7598bdc391cd.dat' 'input.fa' &&  cut_up_fasta.py 'input.fa' --chunk_size 10000 --overlap_size 0 --merge_last --bedfile '/tmp/tmp2x7w0yy_/job_working_directory/000/6/outputs/dataset_7b245253-9b6a-4745-a637-1fd349ebd1ce.dat' > '/tmp/tmp2x7w0yy_/job_working_directory/000/6/outputs/dataset_fada775e-8b21-4ffe-9804-318b7767765d.dat'

Exit Code:

```
0
```

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"input"`
__workflow_invocation_uuid__	`"301f995c718e11f0a03a7ced8d7042ad"`
bedfile	`true`
chromInfo	`"/tmp/tmp2x7w0yy_/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
chunk_size	`"10000"`
dbkey	`"?"`
input_fasta	__identifier__
merge_last	`true`
overlap_size	`"0"`

Step 41: Unlabelled step:
- step_state: new
Step 42: Unlabelled step:
- step_state: new
Step 43: Unlabelled step:
- step_state: new
Step 44: Unlabelled step:
- step_state: new
Step 45: Unlabelled step:
- step_state: new
Step 46: Unlabelled step:
- step_state: new
Step 47: Unlabelled step:
- step_state: new
Step 48: Unlabelled step:
- step_state: new
Step 49: Unlabelled step:
- step_state: new
Step 50: Unlabelled step:
- step_state: new

Step 6: toolshed.g2.bx.psu.edu/repos/devteam/bowtie2/bowtie2/2.5.3+galaxy1:

step_state: scheduled

Jobs

Job 1:

Job state is ok

Command Line:

set -o | grep -q pipefail && set -o pipefail; bowtie2-build --threads ${GALAXY_SLOTS:-4} '/tmp/tmp2x7w0yy_/files/a/7/8/dataset_a78ce864-cb39-45bb-8333-7598bdc391cd.dat' genome && ln -s -f '/tmp/tmp2x7w0yy_/files/a/7/8/dataset_a78ce864-cb39-45bb-8333-7598bdc391cd.dat' genome.fa &&   ln -f -s '/tmp/tmp2x7w0yy_/files/b/5/e/dataset_b5ebe2a3-fa62-49c2-af16-ffb2b78c9d5d.dat' input_f.fastq &&  ln -f -s '/tmp/tmp2x7w0yy_/files/4/6/9/dataset_4692d1a6-e279-49cd-b64a-8836486b3a14.dat' input_r.fastq &&    THREADS=${GALAXY_SLOTS:-4} && if [ "$THREADS" -gt 1 ]; then (( THREADS-- )); fi &&   bowtie2  -p "$THREADS"  -x 'genome'   -1 'input_f.fastq' -2 'input_r.fastq'                2> >(tee '/tmp/tmp2x7w0yy_/job_working_directory/000/7/outputs/dataset_8acef0a5-5d85-4c26-8b82-5a2ce19a48cb.dat' >&2)  | samtools sort -l 0 -T "${TMPDIR:-.}" -O bam | samtools view --no-PG -O bam -@ ${GALAXY_SLOTS:-1} -o '/tmp/tmp2x7w0yy_/job_working_directory/000/7/outputs/dataset_30cfe3f8-0a8e-4de9-a75d-5241a62cbee0.dat'

Exit Code:

```
0
```

Standard Error:

Building a SMALL index
Renaming genome.3.bt2.tmp to genome.3.bt2
Renaming genome.4.bt2.tmp to genome.4.bt2
Renaming genome.1.bt2.tmp to genome.1.bt2
Renaming genome.2.bt2.tmp to genome.2.bt2
Renaming genome.rev.1.bt2.tmp to genome.rev.1.bt2
Renaming genome.rev.2.bt2.tmp to genome.rev.2.bt2
10000010 reads; of these:
  10000010 (100.00%) were paired; of these:
    2353230 (23.53%) aligned concordantly 0 times
    4683487 (46.83%) aligned concordantly exactly 1 time
    2963293 (29.63%) aligned concordantly >1 times
    ----
    2353230 pairs aligned concordantly 0 times; of these:
      7036 (0.30%) aligned discordantly 1 time
    ----
    2346194 pairs aligned 0 times concordantly or discordantly; of these:
      4692388 mates make up the pairs; of these:
        4581166 (97.63%) aligned 0 times
        83684 (1.78%) aligned exactly 1 time
        27538 (0.59%) aligned >1 times
77.09% overall alignment rate
[bam_sort_core] merging from 9 files and 1 in-memory blocks...

Standard Output:

Settings:
  Output files: "genome.*.bt2"
  Line rate: 6 (line is 64 bytes)
  Lines per side: 1 (side is 64 bytes)
  Offset rate: 4 (one in 16)
  FTable chars: 10
  Strings: unpacked
  Max bucket size: default
  Max bucket size, sqrt multiplier: default
  Max bucket size, len divisor: 4
  Difference-cover sample period: 1024
  Endianness: little
  Actual local endianness: little
  Sanity checking: disabled
  Assertions: disabled
  Random seed: 0
  Sizeofs: void*:8, int:4, long:8, size_t:8
Input files DNA, FASTA:
  /tmp/tmp2x7w0yy_/files/a/7/8/dataset_a78ce864-cb39-45bb-8333-7598bdc391cd.dat
Reading reference sizes
  Time reading reference sizes: 00:00:17
Calculating joined length
Writing header
Reserving space for joined string
Joining reference sequences
  Time to join reference sequences: 00:00:13
bmax according to bmaxDivN setting: 408958943
Using parameters --bmax 306719208 --dcv 1024
  Doing ahead-of-time memory usage test
  Passed!  Constructing with these parameters: --bmax 306719208 --dcv 1024
Constructing suffix-array element generator
Building DifferenceCoverSample
  Building sPrime
  Building sPrimeOrder
  V-Sorting samples
  V-Sorting samples time: 00:00:39
  Allocating rank array
  Ranking v-sort output
  Ranking v-sort output time: 00:00:09
  Invoking Larsson-Sadakane on ranks
  Invoking Larsson-Sadakane on ranks time: 00:00:15
  Sanity-checking and returning
Building samples
Reserving space for 12 sample suffixes
Generating random suffixes
QSorting 12 sample offsets, eliminating duplicates
QSorting sample offsets, eliminating duplicates time: 00:00:00
Multikey QSorting 12 samples
  (Using difference cover)
  Multikey QSorting samples time: 00:00:00
Calculating bucket sizes
Splitting and merging
  Splitting and merging time: 00:00:00
Split 1, merged 7; iterating...
Splitting and merging
  Splitting and merging time: 00:00:00
Split 2, merged 0; iterating...
Splitting and merging
  Splitting and merging time: 00:00:00
Split 1, merged 2; iterating...
Splitting and merging
  Splitting and merging time: 00:00:00
Avg bucket size: 2.04479e+08 (target: 306719207)
Converting suffix-array elements to index image
Allocating ftab, absorbFtab
Entering Ebwt loop
Getting block 1 of 8
  Reserving size (306719208) for bucket 1
  Calculating Z arrays for bucket 1
  Entering block accumulator loop for bucket 1:
  bucket 1: 10%
  bucket 1: 20%
  bucket 1: 30%
  bucket 1: 40%
  bucket 1: 50%
  bucket 1: 60%
  bucket 1: 70%
  bucket 1: 80%
  bucket 1: 90%
  bucket 1: 100%
  Sorting block of length 127045839 for bucket 1
  (Using difference cover)
  Sorting block time: 00:00:58
Returning block of 127045840 for bucket 1
Getting block 2 of 8
  Reserving size (306719208) for bucket 2
  Calculating Z arrays for bucket 2
  Entering block accumulator loop for bucket 2:
  bucket 2: 10%
  bucket 2: 20%
  bucket 2: 30%
  bucket 2: 40%
  bucket 2: 50%
  bucket 2: 60%
  bucket 2: 70%
  bucket 2: 80%
  bucket 2: 90%
  bucket 2: 100%
  Sorting block of length 302867108 for bucket 2
  (Using difference cover)
  Sorting block time: 00:02:15
Returning block of 302867109 for bucket 2
Getting block 3 of 8
  Reserving size (306719208) for bucket 3
  Calculating Z arrays for bucket 3
  Entering block accumulator loop for bucket 3:
  bucket 3: 10%
  bucket 3: 20%
  bucket 3: 30%
  bucket 3: 40%
  bucket 3: 50%
  bucket 3: 60%
  bucket 3: 70%
  bucket 3: 80%
  bucket 3: 90%
  bucket 3: 100%
  Sorting block of length 54967539 for bucket 3
  (Using difference cover)
  Sorting block time: 00:00:24
Returning block of 54967540 for bucket 3
Getting block 4 of 8
  Reserving size (306719208) for bucket 4
  Calculating Z arrays for bucket 4
  Entering block accumulator loop for bucket 4:
  bucket 4: 10%
  bucket 4: 20%
  bucket 4: 30%
  bucket 4: 40%
  bucket 4: 50%
  bucket 4: 60%
  bucket 4: 70%
  bucket 4: 80%
  bucket 4: 90%
  bucket 4: 100%
  Sorting block of length 252680552 for bucket 4
  (Using difference cover)
  Sorting block time: 00:01:40
Returning block of 252680553 for bucket 4
Getting block 5 of 8
  Reserving size (306719208) for bucket 5
  Calculating Z arrays for bucket 5
  Entering block accumulator loop for bucket 5:
  bucket 5: 10%
  bucket 5: 20%
  bucket 5: 30%
  bucket 5: 40%
  bucket 5: 50%
  bucket 5: 60%
  bucket 5: 70%
  bucket 5: 80%
  bucket 5: 90%
  bucket 5: 100%
  Sorting block of length 269322435 for bucket 5
  (Using difference cover)
  Sorting block time: 00:01:51
Returning block of 269322436 for bucket 5
Getting block 6 of 8
  Reserving size (306719208) for bucket 6
  Calculating Z arrays for bucket 6
  Entering block accumulator loop for bucket 6:
  bucket 6: 10%
  bucket 6: 20%
  bucket 6: 30%
  bucket 6: 40%
  bucket 6: 50%
  bucket 6: 60%
  bucket 6: 70%
  bucket 6: 80%
  bucket 6: 90%
  bucket 6: 100%
  Sorting block of length 248115557 for bucket 6
  (Using difference cover)
  Sorting block time: 00:01:44
Returning block of 248115558 for bucket 6
Getting block 7 of 8
  Reserving size (306719208) for bucket 7
  Calculating Z arrays for bucket 7
  Entering block accumulator loop for bucket 7:
  bucket 7: 10%
  bucket 7: 20%
  bucket 7: 30%
  bucket 7: 40%
  bucket 7: 50%
  bucket 7: 60%
  bucket 7: 70%
  bucket 7: 80%
  bucket 7: 90%
  bucket 7: 100%
  Sorting block of length 270511178 for bucket 7
  (Using difference cover)
  Sorting block time: 00:01:58
Returning block of 270511179 for bucket 7
Getting block 8 of 8
  Reserving size (306719208) for bucket 8
  Calculating Z arrays for bucket 8
  Entering block accumulator loop for bucket 8:
  bucket 8: 10%
  bucket 8: 20%
  bucket 8: 30%
  bucket 8: 40%
  bucket 8: 50%
  bucket 8: 60%
  bucket 8: 70%
  bucket 8: 80%
  bucket 8: 90%
  bucket 8: 100%
  Sorting block of length 110325558 for bucket 8
  (Using difference cover)
  Sorting block time: 00:00:49
Returning block of 110325559 for bucket 8
Exited Ebwt loop
fchr[A]: 0
fchr[C]: 426524502
fchr[G]: 817883105
fchr[T]: 1209183621
fchr[$]: 1635835773
Exiting Ebwt::buildToDisk()
Returning from initFromVector
Wrote 574367765 bytes to primary EBWT file: genome.1.bt2.tmp
Wrote 408958948 bytes to secondary EBWT file: genome.2.bt2.tmp
Re-opening _in1 and _in2 as input streams
Returning from Ebwt constructor
Headers:
    len: 1635835773
    bwtLen: 1635835774
    sz: 408958944
    bwtSz: 408958944
    lineRate: 6
    offRate: 4
    offMask: 0xfffffff0
    ftabChars: 10
    eftabLen: 20
    eftabSz: 80
    ftabLen: 1048577
    ftabSz: 4194308
    offsLen: 102239736
    offsSz: 408958944
    lineSz: 64
    sideSz: 64
    sideBwtSz: 48
    sideBwtLen: 192
    numSides: 8519978
    numLines: 8519978
    ebwtTotLen: 545278592
    ebwtTotSz: 545278592
    color: 0
    reverse: 0
Total time for call to driver() for forward index: 00:21:39
Reading reference sizes
  Time reading reference sizes: 00:00:11
Calculating joined length
Writing header
Reserving space for joined string
Joining reference sequences
  Time to join reference sequences: 00:00:06
  Time to reverse reference sequence: 00:00:02
bmax according to bmaxDivN setting: 408958943
Using parameters --bmax 306719208 --dcv 1024
  Doing ahead-of-time memory usage test
  Passed!  Constructing with these parameters: --bmax 306719208 --dcv 1024
Constructing suffix-array element generator
Building DifferenceCoverSample
  Building sPrime
  Building sPrimeOrder
  V-Sorting samples
  V-Sorting samples time: 00:00:26
  Allocating rank array
  Ranking v-sort output
  Ranking v-sort output time: 00:00:06
  Invoking Larsson-Sadakane on ranks
  Invoking Larsson-Sadakane on ranks time: 00:00:14
  Sanity-checking and returning
Building samples
Reserving space for 12 sample suffixes
Generating random suffixes
QSorting 12 sample offsets, eliminating duplicates
QSorting sample offsets, eliminating duplicates time: 00:00:00
Multikey QSorting 12 samples
  (Using difference cover)
  Multikey QSorting samples time: 00:00:00
Calculating bucket sizes
Splitting and merging
  Splitting and merging time: 00:00:00
Split 1, merged 6; iterating...
Splitting and merging
  Splitting and merging time: 00:00:00
Avg bucket size: 2.33691e+08 (target: 306719207)
Converting suffix-array elements to index image
Allocating ftab, absorbFtab
Entering Ebwt loop
Getting block 1 of 7
  Reserving size (306719208) for bucket 1
  Calculating Z arrays for bucket 1
  Entering block accumulator loop for bucket 1:
  bucket 1: 10%
  bucket 1: 20%
  bucket 1: 30%
  bucket 1: 40%
  bucket 1: 50%
  bucket 1: 60%
  bucket 1: 70%
  bucket 1: 80%
  bucket 1: 90%
  bucket 1: 100%
  Sorting block of length 181991256 for bucket 1
  (Using difference cover)
  Sorting block time: 00:01:16
Returning block of 181991257 for bucket 1
Getting block 2 of 7
  Reserving size (306719208) for bucket 2
  Calculating Z arrays for bucket 2
  Entering block accumulator loop for bucket 2:
  bucket 2: 10%
  bucket 2: 20%
  bucket 2: 30%
  bucket 2: 40%
  bucket 2: 50%
  bucket 2: 60%
  bucket 2: 70%
  bucket 2: 80%
  bucket 2: 90%
  bucket 2: 100%
  Sorting block of length 163456318 for bucket 2
  (Using difference cover)
  Sorting block time: 00:01:04
Returning block of 163456319 for bucket 2
Getting block 3 of 7
  Reserving size (306719208) for bucket 3
  Calculating Z arrays for bucket 3
  Entering block accumulator loop for bucket 3:
  bucket 3: 10%
  bucket 3: 20%
  bucket 3: 30%
  bucket 3: 40%
  bucket 3: 50%
  bucket 3: 60%
  bucket 3: 70%
  bucket 3: 80%
  bucket 3: 90%
  bucket 3: 100%
  Sorting block of length 300365053 for bucket 3
  (Using difference cover)
  Sorting block time: 00:01:59
Returning block of 300365054 for bucket 3
Getting block 4 of 7
  Reserving size (306719208) for bucket 4
  Calculating Z arrays for bucket 4
  Entering block accumulator loop for bucket 4:
  bucket 4: 10%
  bucket 4: 20%
  bucket 4: 30%
  bucket 4: 40%
  bucket 4: 50%
  bucket 4: 60%
  bucket 4: 70%
  bucket 4: 80%
  bucket 4: 90%
  bucket 4: 100%
  Sorting block of length 252666651 for bucket 4
  (Using difference cover)
  Sorting block time: 00:01:36
Returning block of 252666652 for bucket 4
Getting block 5 of 7
  Reserving size (306719208) for bucket 5
  Calculating Z arrays for bucket 5
  Entering block accumulator loop for bucket 5:
  bucket 5: 10%
  bucket 5: 20%
  bucket 5: 30%
  bucket 5: 40%
  bucket 5: 50%
  bucket 5: 60%
  bucket 5: 70%
  bucket 5: 80%
  bucket 5: 90%
  bucket 5: 100%
  Sorting block of length 280318282 for bucket 5
  (Using difference cover)
  Sorting block time: 00:01:43
Returning block of 280318283 for bucket 5
Getting block 6 of 7
  Reserving size (306719208) for bucket 6
  Calculating Z arrays for bucket 6
  Entering block accumulator loop for bucket 6:
  bucket 6: 10%
  bucket 6: 20%
  bucket 6: 30%
  bucket 6: 40%
  bucket 6: 50%
  bucket 6: 60%
  bucket 6: 70%
  bucket 6: 80%
  bucket 6: 90%
  bucket 6: 100%
  Sorting block of length 214333332 for bucket 6
  (Using difference cover)
  Sorting block time: 00:01:30
Returning block of 214333333 for bucket 6
Getting block 7 of 7
  Reserving size (306719208) for bucket 7
  Calculating Z arrays for bucket 7
  Entering block accumulator loop for bucket 7:
  bucket 7: 10%
  bucket 7: 20%
  bucket 7: 30%
  bucket 7: 40%
  bucket 7: 50%
  bucket 7: 60%
  bucket 7: 70%
  bucket 7: 80%
  bucket 7: 90%
  bucket 7: 100%
  Sorting block of length 242704875 for bucket 7
  (Using difference cover)
  Sorting block time: 00:01:42
Returning block of 242704876 for bucket 7
Exited Ebwt loop
fchr[A]: 0
fchr[C]: 426524502
fchr[G]: 817883105
fchr[T]: 1209183621
fchr[$]: 1635835773
Exiting Ebwt::buildToDisk()
Returning from initFromVector
Wrote 574367765 bytes to primary EBWT file: genome.rev.1.bt2.tmp
Wrote 408958948 bytes to secondary EBWT file: genome.rev.2.bt2.tmp
Re-opening _in1 and _in2 as input streams
Returning from Ebwt constructor
Headers:
    len: 1635835773
    bwtLen: 1635835774
    sz: 408958944
    bwtSz: 408958944
    lineRate: 6
    offRate: 4
    offMask: 0xfffffff0
    ftabChars: 10
    eftabLen: 20
    eftabSz: 80
    ftabLen: 1048577
    ftabSz: 4194308
    offsLen: 102239736
    offsSz: 408958944
    lineSz: 64
    sideSz: 64
    sideBwtSz: 48
    sideBwtLen: 192
    numSides: 8519978
    numLines: 8519978
    ebwtTotLen: 545278592
    ebwtTotSz: 545278592
    color: 0
    reverse: 1
Total time for backward call to driver() for mirror index: 00:18:16

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"input"`
__workflow_invocation_uuid__	`"301f995c718e11f0a03a7ced8d7042ad"`
analysis_type	`{"__current_case__": 0, "analysis_type_selector": "simple", "presets": "no_presets"}`
chromInfo	`"/tmp/tmp2x7w0yy_/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
dbkey	`"?"`
library	`{"__current_case__": 2, "aligned_file": false, "input_1": {"values": [{"id": 3, "src": "dce"}]}, "paired_options": {"__current_case__": 1, "paired_options_selector": "no"}, "type": "paired_collection", "unaligned_file": false}`
own_file	__identifier__
reference_genome	`{"__current_case__": 1, "own_file": {"values": [{"id": 2, "src": "dce"}]}, "source": "history"}`
rg	`{"__current_case__": 3, "rg_selector": "do_not_set"}`
sam_options	`{"__current_case__": 1, "sam_options_selector": "no"}`
save_mapping_stats	`true`

Step 7: toolshed.g2.bx.psu.edu/repos/iuc/cami_amber_add/cami_amber_add/2.0.7+galaxy0:

step_state: scheduled

Jobs

Job 1:

Job state is ok

Command Line:

ln -s '/tmp/tmp2x7w0yy_/files/f/a/4/dataset_fa49c4c9-e0dd-499c-adb9-9a0eb6551815.dat' 'marine_pooled_gsb_trimmed' && ln -s '/tmp/tmp2x7w0yy_/files/a/7/8/dataset_a78ce864-cb39-45bb-8333-7598bdc391cd.dat' 'marine_pooled_gsa_trimmed' &&  add_length_column.py -g 'marine_pooled_gsb_trimmed' -f 'marine_pooled_gsa_trimmed' > gold_standard_file.tsv

Exit Code:

```
0
```

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"input"`
__workflow_invocation_uuid__	`"301f995c718e11f0a03a7ced8d7042ad"`
chromInfo	`"/tmp/tmp2x7w0yy_/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
dbkey	`"?"`

Step 8: toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_awk_tool/9.3+galaxy1:

step_state: scheduled

Jobs

Job 1:

Job state is ok

Command Line:

env -i $(which awk) --sandbox -v FS='	' -v OFS='	' --re-interval -f '/tmp/tmp2x7w0yy_/job_working_directory/000/9/configs/tmpimpsyy1u' '/tmp/tmp2x7w0yy_/files/7/0/1/dataset_701169d3-302b-411f-aa08-c33a04e4c462.dat' > '/tmp/tmp2x7w0yy_/job_working_directory/000/9/outputs/dataset_cfad8382-7eb2-4cdc-ab44-19a67970139a.dat'

Exit Code:

```
0
```

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"input"`
__workflow_invocation_uuid__	`"301f995c718e11f0a03a7ced8d7042ad"`
chromInfo	`"/tmp/tmp2x7w0yy_/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
code	`"{gsub( $0 ,\"sample_\" (NR-1)); print}"`
dbkey	`"?"`

Step 9: toolshed.g2.bx.psu.edu/repos/devteam/samtools_sort/samtools_sort/2.0.5:

step_state: scheduled

Jobs

Job 1:

Job state is error

Command Line:

addthreads=${GALAXY_SLOTS:-1} && (( addthreads-- )) &&   addmemory=${GALAXY_MEMORY_MB_PER_SLOT:-768} && ((addmemory=addmemory*75/100)) &&  samtools sort -@ $addthreads -m $addmemory"M"   -O bam -T "${TMPDIR:-.}" '/tmp/tmp2x7w0yy_/files/3/0/c/dataset_30cfe3f8-0a8e-4de9-a75d-5241a62cbee0.dat' > '/tmp/tmp2x7w0yy_/job_working_directory/000/10/outputs/dataset_ee8a9a78-10f5-47b9-8323-a9169157fb39.dat'

Exit Code:

```
1
```

Standard Error:

[bam_sort_core] merging from 12 files and 1 in-memory blocks...
[E::bgzf_flush] File write failed (wrong size)
samtools sort: failed writing to "-": No space left on device
[E::bgzf_close] File write failed

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"input"`
__workflow_invocation_uuid__	`"301f995c718e11f0a03a7ced8d7042ad"`
chromInfo	`"/tmp/tmp2x7w0yy_/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
dbkey	`"?"`
input1	__identifier__
minhash	`false`
prim_key_cond	`{"__current_case__": 0, "prim_key_select": ""}`

Step 10: __RELABEL_FROM_FILE__:

step_state: scheduled

Jobs

Job 1:

Job state is ok

Traceback:

Job Parameters:

Job parameter	Parameter value
__workflow_invocation_uuid__	`"301f995c718e11f0a03a7ced8d7042ad"`
how	`{"__current_case__": 0, "how_select": "txt", "labels": {"values": [{"id": 11, "src": "hda"}]}, "strict": false}`
input	`{"values": [{"id": 1, "src": "hdca"}]}`

Other invocation details
- history_id
  - 14e0d202dd346f1d
- history_state
  - error
- invocation_id
  - 14e0d202dd346f1d
- invocation_state
  - ready
- workflow_id
  - 14e0d202dd346f1d

…into add_binning_eva

SantaMcCloud · 2025-08-28T02:32:01Z

@mvdbeek should i either downgrade this tool or should i wait till it is updated because of this error msg?

Unexpected HTTP status code: 400: {"err_msg":"Workflow was not invoked; the following required tools are not installed: toolshed.g2.bx.psu.edu/repos/devteam/samtools_sort/samtools_sort/2.0.5 (version 2.0.5)","err_code":0}

…into add_binning_eva

Add tools for galaxyproject/iwc#924

SantaMcCloud · 2025-09-01T15:59:54Z

[2025-09-01 00:54:30] ERROR - An error occurred while running DIAMOND. Check log file: output/temporary_files/diamond_result.log

I would make sure your workflow runs on usegalaxy.org as a first step, we use the same reference data via cvmfs. If that doesn't give you a better idea I'm afraid you'll have to modify the binette tool to print the log file to stderr if it fails.

Thank for the information! I did run Binette on .org with the test data generated in .eu and i know the problem now. The memory allocated to Binette has to be increased and after it should run. Also thank you or adding the Tools needed for the Wf to .org.

SantaMcCloud · 2025-09-01T16:12:43Z

I have send a bug report since Binette got allocated ~4 GB but is should have way more because in the tvp it says 32 GB is max for Binette https://github.com/galaxyproject/tpv-shared-database/blob/main/tools.yml#L1172

here is the test history just to be sure: https://usegalaxy.org/u/santinof/h/unnamed-history

mvdbeek · 2025-09-01T16:41:58Z

we use a pinned tpv version, i've updated the allocation now, you can retry

SantaMcCloud · 2025-09-01T17:09:44Z

we use a pinned tpv version, i've updated the allocation now, you can retry

did rerun it and now there was no error in this case.

Should i still wait till the test on .orgwas without error after the tool did isntalled or you want to restart the test in here in GitHub?

mvdbeek · 2025-09-01T17:12:28Z

Can you run the whole workflow against usegalaxy.org ? I see the peak memory was at 15.4GB, which is very tight.

SantaMcCloud · 2025-09-01T17:18:03Z

yes i will run it against org on this case

SantaMcCloud · 2025-09-01T23:58:08Z

I did run the WF in .org and there was no error in this case. I will restart the test to see if there is any other problem now. If there is to much data produce or so i can try to cut the test data even more but im not sure how far i can cut it down.

mvdbeek · 2025-09-04T14:14:12Z

Can you share the invocation please ?

SantaMcCloud · 2025-09-04T14:24:47Z

Can you share the invocation please ?

https://usegalaxy.org/workflows/invocations/e370c44912ff7cbb

here it is

mvdbeek · 2025-09-05T09:12:28Z

I think you'll need to get the memory for binette down a little, reducing the input data might do the trick.

You can see an overview under metrics for your invocation:

SantaMcCloud · 2025-09-05T09:42:31Z

I think you'll need to get the memory for binette down a little, reducing the input data might do the trick.
You can see an overview under metrics for your invocation:

i did see it thank you! but how what is the Limit so i can have a look at it to be under it for All tools

mvdbeek · 2025-09-05T10:51:38Z

16GB https://docs.github.com/en/actions/reference/runners/github-hosted-runners#standard-github-hosted-runners-for-public-repositories

SantaMcCloud · 2025-09-05T14:10:04Z

16GB https://docs.github.com/en/actions/reference/runners/github-hosted-runners#standard-github-hosted-runners-for-public-repositories

Thanks i will keep this in mind and try to be under this Limit!

SantaMcCloud · 2025-09-09T16:41:17Z

@mvdbeek now it should be fine! If there is anything which i shoudl change just let me know it!

SantaMcCloud added 5 commits July 31, 2025 19:57

Add FAIRyMAGs Binning Evaluation Workflow

8289722

typo

54adffe

fix linting

6efcb13

linting

71272a1

typo

c78b392

SantaMcCloud and others added 6 commits August 4, 2025 23:30

Update .dockstore.yml

685ca6a

Update FAIRyMAGs-binning-evaluation-tests.yml

6c86d61

review changes

8f11e09

Update FAIRyMAGs-binning-evaluation.ga

cff7421

change zanodo data

4af7318

Update FAIRyMAGs-binning-evaluation.ga

303305d

SantaMcCloud and others added 8 commits August 7, 2025 22:27

little change

b1aa766

Merge branch 'add_binning_eva' of https://github.com/SantaMcCloud/iwc …

597b2d4

…into add_binning_eva

restart test

4efeaf3

Update WF for more User control

d6b98c0

Merge branch 'add_binning_eva' of https://github.com/SantaMcCloud/iwc …

6379ade

…into add_binning_eva

bump version

28691ee

revert

87c805b

Restart test

0279025

SantaMcCloud and others added 7 commits August 28, 2025 13:42

Update samsort

9301802

typo

0f09e44

fix some links

250a690

Restart test

bb9ed97

Change some test output asserts

b72d10e

Merge branch 'add_binning_eva' of https://github.com/SantaMcCloud/iwc …

d7543c9

…into add_binning_eva

Update FAIRyMAGs-binning-evaluation-tests.yml

2b3aa98

mvdbeek added a commit to mvdbeek/usegalaxy-tools that referenced this pull request Sep 1, 2025

Add tools for galaxyproject/iwc#924

d9c2ec9

mvdbeek added a commit to galaxyproject/usegalaxy-tools that referenced this pull request Sep 1, 2025

Merge pull request #1083 from mvdbeek/iwc_tools_metagenomic

b7225e1

Add tools for galaxyproject/iwc#924

Restart test

56001c2

galaxyproject deleted a comment from github-actions bot Sep 5, 2025

Change input data

652ddd7

change input to a more smaller sice

51cc9f6

Add FAIRyMAGs Binning Evaluation Workflow #924

Are you sure you want to change the base?

Add FAIRyMAGs Binning Evaluation Workflow #924

Conversation

SantaMcCloud commented Jul 31, 2025

Uh oh!

mvdbeek commented Aug 4, 2025

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SantaMcCloud commented Aug 4, 2025

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github-actions bot commented Aug 5, 2025

Test Results (powered by Planemo)

Test Summary

Workflow invocation details

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