metagenomic-assembly: update metaSPAdes to 4.3.0+galaxy3 by paulzierep · Pull Request #1545 · galaxyproject/iwc

paulzierep · 2026-11-12T19:29:55Z

Updates metaSPAdes from 4.3.0+galaxy2 to 4.3.0+galaxy3 (galaxyproject/tools-iuc#8872). Release 1.2 → 1.3.

The new wrapper puts the read inputs under a file_processing conditional with two modes. This workflow uses the co-assembly mode, which takes the same per-group nested read lists as the previous version, so the workflow logic, the optional long-read handling (including long reads for only some groups) and the tests are unchanged. Only the tool version, the parameter paths and the Tool Shed revision change.

The new individual mode (one job per group, mapped over the paired list) was tried first but not kept: in the MAGs generation workflow (#1454), which embeds this one, a missing long-read type can only be passed on as a collection of skipped placeholder datasets, never as a null input, and metaSPAdes then receives a placeholder as a read file. Keeping co mode lets #1454 embed this release unchanged.

IWC checklist

FOR CONTRIBUTOR:

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

…idual mode

github-actions · 2026-11-12T19:49:26Z

Test Results (powered by Planemo)

Test Summary

Test State	Count
Total	5
Passed	0
Error	5
Failure	0
Skipped	0

Errored Tests

❌ metagenomic-assembly.ga_0

Execution Problem:

Unexpected HTTP status code: 400: {"err_msg":"Workflow was not invoked; the following required tools are not installed: toolshed.g2.bx.psu.edu/repos/nml/metaspades/metaspades/4.3.0+galaxy2 (version 4.3.0+galaxy3)","err_code":0}

❌ metagenomic-assembly.ga_1

Execution Problem:

Unexpected HTTP status code: 400: {"err_msg":"Workflow was not invoked; the following required tools are not installed: toolshed.g2.bx.psu.edu/repos/nml/metaspades/metaspades/4.3.0+galaxy2 (version 4.3.0+galaxy3)","err_code":0}

❌ metagenomic-assembly.ga_2

Execution Problem:

Unexpected HTTP status code: 400: {"err_msg":"Workflow was not invoked; the following required tools are not installed: toolshed.g2.bx.psu.edu/repos/nml/metaspades/metaspades/4.3.0+galaxy2 (version 4.3.0+galaxy3)","err_code":0}

❌ metagenomic-assembly.ga_3

Execution Problem:

Unexpected HTTP status code: 400: {"err_msg":"Workflow was not invoked; the following required tools are not installed: toolshed.g2.bx.psu.edu/repos/nml/metaspades/metaspades/4.3.0+galaxy2 (version 4.3.0+galaxy3)","err_code":0}

❌ metagenomic-assembly.ga_4

Execution Problem:

Unexpected HTTP status code: 400: {"err_msg":"Workflow was not invoked; the following required tools are not installed: toolshed.g2.bx.psu.edu/repos/nml/metaspades/metaspades/4.3.0+galaxy2 (version 4.3.0+galaxy3)","err_code":0}

github-actions · 2026-11-12T20:32:18Z

Test Results (powered by Planemo)

Test Summary

Test State	Count
Total	5
Passed	3
Error	2
Failure	0
Skipped	0

Errored Tests

❌ metagenomic-assembly.ga_3

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 14: 'Cannot match collection types.'

Steps

Step 1: create text file (toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_text_file_with_recurring_lines/9.11+galaxy0):

step_state: scheduled

Jobs

Job 1:

Job state is running

Command Line:

times=1; yes -- '' 2>/dev/null | head -n $times >> '/home/runner/work/_temp/tmpq9hj5k8k/job_working_directory/000/65/outputs/dataset_f4f0560a-e713-4c60-8fc9-980761c3f24d.dat';

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"input"`
__workflow_invocation_uuid__	`"178141c8dec711f180003833c5d96987"`
chromInfo	`"/home/runner/work/_temp/tmpq9hj5k8k/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
dbkey	`"?"`
token_set	`[{"__index__": 0, "line": null, "repeat_select": {"__current_case__": 0, "repeat_select_opts": "user", "times": "1"}}]`

Step 2: Trimmed paired reads from grouped samples:
- step_state: scheduled
Step 3: Trimmed nanopore reads from grouped samples:
- step_state: scheduled
Step 4: Trimmed PacBio reads from grouped samples:
- step_state: scheduled
Step 5: Choose Assembler:
- step_state: scheduled
Step 6: Minimum length of contigs to output:
- step_state: scheduled
Step 7: Custom Assemblies:
- step_state: scheduled

Step 8: Select (Grep1):

step_state: scheduled

Jobs

Job 1:

Job state is new

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"input"`
__workflow_invocation_uuid__	`"178141c8dec711f180003833c5d96987"`
chromInfo	`"/home/runner/work/_temp/tmpq9hj5k8k/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
dbkey	`"?"`
invert	`""`
keep_header	`false`
pattern	`"^chr([0-9A-Za-z])+"`

Step 9: Extract reads element identifiers (toolshed.g2.bx.psu.edu/repos/iuc/collection_element_identifiers/collection_element_identifiers/0.0.3):

step_state: scheduled

Jobs

Job 1:

Job state is new

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"input"`
__workflow_invocation_uuid__	`"178141c8dec711f180003833c5d96987"`
chromInfo	`"/home/runner/work/_temp/tmpq9hj5k8k/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
dbkey	`"?"`
input_collection	`{"values": [{"id": 61, "src": "hdca"}]}`

Step 10: Unzip paired reads (__UNZIP_COLLECTION__):
- step_state: scheduled
- Jobs
  - Job 1:
    - Job state is ok
    Traceback:
    Job Parameters:
    - Job parameter Parameter value
      
      __workflow_invocation_uuid__ "178141c8dec711f180003833c5d96987"
      
      input {"values": [{"id": 67, "src": "dce"}]}
  - Job 2:
    - Job state is ok
    Traceback:
    Job Parameters:
    - Job parameter Parameter value
      
      __workflow_invocation_uuid__ "178141c8dec711f180003833c5d96987"
      
      input {"values": [{"id": 70, "src": "dce"}]}

Step 11: Run metaSPAdes? (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 queued

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"input"`
__workflow_invocation_uuid__	`"178141c8dec711f180003833c5d96987"`
chromInfo	`"/home/runner/work/_temp/tmpq9hj5k8k/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
dbkey	`"?"`
input_param_type	`{"__current_case__": 0, "input_param": "Custom Assembly", "mappings": [{"__index__": 0, "from": "metaSPAdes", "to": "True"}], "type": "text"}`
output_param_type	`"boolean"`
unmapped	`{"__current_case__": 2, "default_value": "False", "on_unmapped": "default"}`

Step 12: Run MEGAHIT? (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 queued

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"input"`
__workflow_invocation_uuid__	`"178141c8dec711f180003833c5d96987"`
chromInfo	`"/home/runner/work/_temp/tmpq9hj5k8k/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
dbkey	`"?"`
input_param_type	`{"__current_case__": 0, "input_param": "Custom Assembly", "mappings": [{"__index__": 0, "from": "MEGAHIT", "to": "True"}], "type": "text"}`
output_param_type	`"boolean"`
unmapped	`{"__current_case__": 2, "default_value": "False", "on_unmapped": "default"}`

Step 13: Count number of samples (wc_gnu):

step_state: scheduled

Jobs

Job 1:

Job state is new

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"txt"`
__workflow_invocation_uuid__	`"178141c8dec711f180003833c5d96987"`
chromInfo	`"/home/runner/work/_temp/tmpq9hj5k8k/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
dbkey	`"?"`
include_header	`false`
options	`["lines"]`

Step 14: metaSPAdes:
- step_state: new

Other invocation details
- error_message
  - Failed to run workflow, invocation ended in [failed] state.
- history_id
  - 8895fae39cde6fb8
- history_state
  - running
- invocation_id
  - 8895fae39cde6fb8
- invocation_state
  - failed
- messages
  - [{'details': 'Cannot match collection types.', 'reason': 'unexpected_failure', 'workflow_step_id': 13, 'workflow_step_index_path': None}]
- workflow_id
  - 6d1c4cf83da0921e

❌ metagenomic-assembly.ga_4

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 14: 'Cannot match collection types.'

Steps

Step 1: create text file (toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_text_file_with_recurring_lines/9.11+galaxy0):

step_state: scheduled

Jobs

Job 1:

Job state is running

Command Line:

times=1; yes -- '' 2>/dev/null | head -n $times >> '/home/runner/work/_temp/tmpq9hj5k8k/job_working_directory/000/78/outputs/dataset_e8d8a390-7367-4d2d-8994-6f006e3950ff.dat';

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"input"`
__workflow_invocation_uuid__	`"355f8a56dec711f180003833c5d96987"`
chromInfo	`"/home/runner/work/_temp/tmpq9hj5k8k/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
dbkey	`"?"`
token_set	`[{"__index__": 0, "line": null, "repeat_select": {"__current_case__": 0, "repeat_select_opts": "user", "times": "1"}}]`

Step 2: Trimmed paired reads from grouped samples:
- step_state: scheduled
Step 3: Trimmed nanopore reads from grouped samples:
- step_state: scheduled
Step 4: Trimmed PacBio reads from grouped samples:
- step_state: scheduled
Step 5: Choose Assembler:
- step_state: scheduled
Step 6: Minimum length of contigs to output:
- step_state: scheduled
Step 7: Custom Assemblies:
- step_state: scheduled

Step 8: Select (Grep1):

step_state: scheduled

Jobs

Job 1:

Job state is new

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"input"`
__workflow_invocation_uuid__	`"355f8a56dec711f180003833c5d96987"`
chromInfo	`"/home/runner/work/_temp/tmpq9hj5k8k/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
dbkey	`"?"`
invert	`""`
keep_header	`false`
pattern	`"^chr([0-9A-Za-z])+"`

Step 9: Extract reads element identifiers (toolshed.g2.bx.psu.edu/repos/iuc/collection_element_identifiers/collection_element_identifiers/0.0.3):

step_state: scheduled

Jobs

Job 1:

Job state is queued

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"input"`
__workflow_invocation_uuid__	`"355f8a56dec711f180003833c5d96987"`
chromInfo	`"/home/runner/work/_temp/tmpq9hj5k8k/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
dbkey	`"?"`
input_collection	`{"values": [{"id": 67, "src": "hdca"}]}`

Step 10: Unzip paired reads (__UNZIP_COLLECTION__):
- step_state: scheduled
- Jobs
  - Job 1:
    - Job state is ok
    Traceback:
    Job Parameters:
    - Job parameter Parameter value
      
      __workflow_invocation_uuid__ "355f8a56dec711f180003833c5d96987"
      
      input {"values": [{"id": 83, "src": "dce"}]}
  - Job 2:
    - Job state is ok
    Traceback:
    Job Parameters:
    - Job parameter Parameter value
      
      __workflow_invocation_uuid__ "355f8a56dec711f180003833c5d96987"
      
      input {"values": [{"id": 86, "src": "dce"}]}

Step 11: Run metaSPAdes? (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 queued

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"input"`
__workflow_invocation_uuid__	`"355f8a56dec711f180003833c5d96987"`
chromInfo	`"/home/runner/work/_temp/tmpq9hj5k8k/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
dbkey	`"?"`
input_param_type	`{"__current_case__": 0, "input_param": "metaSPAdes", "mappings": [{"__index__": 0, "from": "metaSPAdes", "to": "True"}], "type": "text"}`
output_param_type	`"boolean"`
unmapped	`{"__current_case__": 2, "default_value": "False", "on_unmapped": "default"}`

Step 12: Run MEGAHIT? (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 queued

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"input"`
__workflow_invocation_uuid__	`"355f8a56dec711f180003833c5d96987"`
chromInfo	`"/home/runner/work/_temp/tmpq9hj5k8k/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
dbkey	`"?"`
input_param_type	`{"__current_case__": 0, "input_param": "metaSPAdes", "mappings": [{"__index__": 0, "from": "MEGAHIT", "to": "True"}], "type": "text"}`
output_param_type	`"boolean"`
unmapped	`{"__current_case__": 2, "default_value": "False", "on_unmapped": "default"}`

Step 13: Count number of samples (wc_gnu):

step_state: scheduled

Jobs

Job 1:

Job state is new

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"txt"`
__workflow_invocation_uuid__	`"355f8a56dec711f180003833c5d96987"`
chromInfo	`"/home/runner/work/_temp/tmpq9hj5k8k/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
dbkey	`"?"`
include_header	`false`
options	`["lines"]`

Step 14: metaSPAdes:
- step_state: new

Other invocation details
- error_message
  - Failed to run workflow, invocation ended in [failed] state.
- history_id
  - 6d1c4cf83da0921e
- history_state
  - running
- invocation_id
  - 6d1c4cf83da0921e
- invocation_state
  - failed
- messages
  - [{'details': 'Cannot match collection types.', 'reason': 'unexpected_failure', 'workflow_step_id': 13, 'workflow_step_index_path': None}]
- workflow_id
  - 6d1c4cf83da0921e

Passed Tests

✅ metagenomic-assembly.ga_0

Workflow invocation details

Invocation Messages

Steps

Step 1: create text file (toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_text_file_with_recurring_lines/9.11+galaxy0):

step_state: scheduled

Jobs

Job 1:

Job state is ok

Container:

```
quay.io/biocontainers/coreutils:9.11
```

Command Line:

times=1; yes -- '' 2>/dev/null | head -n $times >> '/home/runner/work/_temp/tmpq9hj5k8k/job_working_directory/000/4/outputs/dataset_2409f8de-0c9c-4774-bfaa-7810829d0a58.dat';

Exit Code:

```
0
```

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"input"`
__workflow_invocation_uuid__	`"81ba2396dec411f180003833c5d96987"`
chromInfo	`"/home/runner/work/_temp/tmpq9hj5k8k/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
dbkey	`"?"`
token_set	`[{"__index__": 0, "line": null, "repeat_select": {"__current_case__": 0, "repeat_select_opts": "user", "times": "1"}}]`

Step 2: Trimmed paired reads from grouped samples:
- step_state: scheduled
Step 3: Trimmed nanopore reads from grouped samples:
- step_state: scheduled
Step 4: Trimmed PacBio reads from grouped samples:
- step_state: scheduled
Step 5: Choose Assembler:
- step_state: scheduled
Step 6: Minimum length of contigs to output:
- step_state: scheduled
Step 7: Custom Assemblies:
- step_state: scheduled

Step 8: Select (Grep1):

step_state: scheduled

Jobs

Job 1:

Job state is ok

Container:

quay.io/biocontainers/grep:3.4--hf43ccf4_4

Command Line:

set -eo pipefail; cat '/home/runner/work/_temp/tmpq9hj5k8k/files/2/4/0/dataset_2409f8de-0c9c-4774-bfaa-7810829d0a58.dat' | grep -P -f '/home/runner/work/_temp/tmpq9hj5k8k/job_working_directory/000/5/configs/tmp4b5di5vf'  >> '/home/runner/work/_temp/tmpq9hj5k8k/job_working_directory/000/5/outputs/dataset_83f02498-ecab-499c-b8de-2fa6146ea830.dat'

Exit Code:

```
1
```

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"input"`
__workflow_invocation_uuid__	`"81ba2396dec411f180003833c5d96987"`
chromInfo	`"/home/runner/work/_temp/tmpq9hj5k8k/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
dbkey	`"?"`
invert	`""`
keep_header	`false`
pattern	`"^chr([0-9A-Za-z])+"`

Step 9: Extract reads element identifiers (toolshed.g2.bx.psu.edu/repos/iuc/collection_element_identifiers/collection_element_identifiers/0.0.3):

step_state: scheduled

Jobs

Job 1:

Job state is ok

Command Line:

mv '/home/runner/work/_temp/tmpq9hj5k8k/job_working_directory/000/6/configs/tmpa43o4rpu' '/home/runner/work/_temp/tmpq9hj5k8k/job_working_directory/000/6/outputs/dataset_3fe66145-b3d3-4dd9-b1b7-aedd3f75d2a8.dat'

Exit Code:

```
0
```

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"input"`
__workflow_invocation_uuid__	`"81ba2396dec411f180003833c5d96987"`
chromInfo	`"/home/runner/work/_temp/tmpq9hj5k8k/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
dbkey	`"?"`
input_collection	`{"values": [{"id": 1, "src": "hdca"}]}`

Step 10: Unzip paired reads (__UNZIP_COLLECTION__):
- step_state: scheduled
- Jobs
  - Job 1:
    - Job state is ok
    Traceback:
    Job Parameters:
    - Job parameter Parameter value
      
      __workflow_invocation_uuid__ "81ba2396dec411f180003833c5d96987"
      
      input {"values": [{"id": 1, "src": "dce"}]}

Step 11: Run metaSPAdes? (toolshed.g2.bx.psu.edu/repos/iuc/map_param_value/map_param_value/0.2.0):

step_state: scheduled

Jobs

Job 1:

Job state is ok

Command Line:

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

Exit Code:

```
0
```

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"input"`
__workflow_invocation_uuid__	`"81ba2396dec411f180003833c5d96987"`
chromInfo	`"/home/runner/work/_temp/tmpq9hj5k8k/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
dbkey	`"?"`
input_param_type	`{"__current_case__": 0, "input_param": "MEGAHIT", "mappings": [{"__index__": 0, "from": "metaSPAdes", "to": "True"}], "type": "text"}`
output_param_type	`"boolean"`
unmapped	`{"__current_case__": 2, "default_value": "False", "on_unmapped": "default"}`

Step 12: Run MEGAHIT? (toolshed.g2.bx.psu.edu/repos/iuc/map_param_value/map_param_value/0.2.0):

step_state: scheduled

Jobs

Job 1:

Job state is ok

Command Line:

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

Exit Code:

```
0
```

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"input"`
__workflow_invocation_uuid__	`"81ba2396dec411f180003833c5d96987"`
chromInfo	`"/home/runner/work/_temp/tmpq9hj5k8k/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
dbkey	`"?"`
input_param_type	`{"__current_case__": 0, "input_param": "MEGAHIT", "mappings": [{"__index__": 0, "from": "MEGAHIT", "to": "True"}], "type": "text"}`
output_param_type	`"boolean"`
unmapped	`{"__current_case__": 2, "default_value": "False", "on_unmapped": "default"}`

Step 13: Count number of samples (wc_gnu):

step_state: scheduled

Jobs

Job 1:

Job state is ok

Command Line:

cat '/home/runner/work/_temp/tmpq9hj5k8k/files/3/f/e/dataset_3fe66145-b3d3-4dd9-b1b7-aedd3f75d2a8.dat' | wc -l | awk '{ print $1 }' >> /home/runner/work/_temp/tmpq9hj5k8k/job_working_directory/000/10/outputs/dataset_0bb949eb-30a3-40d1-a18e-3e6ee888967e.dat

Exit Code:

```
0
```

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"txt"`
__workflow_invocation_uuid__	`"81ba2396dec411f180003833c5d96987"`
chromInfo	`"/home/runner/work/_temp/tmpq9hj5k8k/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
dbkey	`"?"`
include_header	`false`
options	`["lines"]`

Step 14: metaSPAdes (toolshed.g2.bx.psu.edu/repos/nml/metaspades/metaspades/4.3.0+galaxy3):

step_state: scheduled

Jobs

Job 1:

Job state is skipped

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"input"`
__workflow_invocation_uuid__	`"81ba2396dec411f180003833c5d96987"`
chromInfo	`"/home/runner/work/_temp/tmpq9hj5k8k/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
dbkey	`"?"`
file_processing	`{"__current_case__": 1, "additional_reads": {"__current_case__": 1, "selector": "false"}, "arf": {"nanopore": {"values": [{"id": 4, "src": "dce"}]}, "pacbio": null}, "is_select": "individual", "library_number": "true", "singlePaired": {"__current_case__": 1, "input": {"values": [{"id": 1, "src": "dce"}]}, "orientation": "fr", "sPaired": "paired_collection", "type_paired": "pe"}}`
kmer_cond	`{"__current_case__": 0, "kmer_sel": "auto"}`
mode_sel	`None`
optional_output	`["ag", "ags", "cn", "sc"]`
phred_offset	`"auto"`

Step 15: MEGAHIT (toolshed.g2.bx.psu.edu/repos/iuc/megahit/megahit/1.2.9+galaxy2):

step_state: scheduled

Jobs

Job 1:

Job state is ok

Container:

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

Command Line:

if [[ -n "$GALAXY_MEMORY_MB" ]]; then MEMORY="-m $((GALAXY_MEMORY_MB * 1024))"; fi;  megahit --num-cpu-threads ${GALAXY_SLOTS:-4}  -1 '/home/runner/work/_temp/tmpq9hj5k8k/files/f/c/0/dataset_fc0415f9-e38b-43ca-9af7-caf082f219c3.dat' -2 '/home/runner/work/_temp/tmpq9hj5k8k/files/f/1/9/dataset_f193f40e-e905-4f92-9942-336fa0e5fd01.dat' --min-count '2' --k-list '21,29,39,59,79,99,119,141'  --bubble-level '2' --merge-level '20,0.95' --prune-level '2' --prune-depth '2' --disconnect-ratio '0.1' --low-local-ratio '0.2' --cleaning-rounds '5'   --min-contig-len '100' $MEMORY

Exit Code:

```
0
```

Standard Error:

2026-11-12 20:13:16 - MEGAHIT v1.2.9
2026-11-12 20:13:16 - Using megahit_core with POPCNT and BMI2 support
2026-11-12 20:13:16 - Convert reads to binary library
2026-11-12 20:13:16 - b'INFO  sequence/io/sequence_lib.cpp  :   75 - Lib 0 (/home/runner/work/_temp/tmpq9hj5k8k/files/f/c/0/dataset_fc0415f9-e38b-43ca-9af7-caf082f219c3.dat,/home/runner/work/_temp/tmpq9hj5k8k/files/f/1/9/dataset_f193f40e-e905-4f92-9942-336fa0e5fd01.dat): pe, 100000 reads, 126 max length'
2026-11-12 20:13:16 - b'INFO  utils/utils.h                 :  152 - Real: 0.1511\tuser: 0.1437\tsys: 0.0080\tmaxrss: 16960'
2026-11-12 20:13:16 - Start assembly. Number of CPU threads 1 
2026-11-12 20:13:16 - k list: 21,29,39,59,79,99,119,141 
2026-11-12 20:13:16 - Memory used: 15082562764
2026-11-12 20:13:16 - Extract solid (k+1)-mers for k = 21 
2026-11-12 20:13:18 - Build graph for k = 21 
2026-11-12 20:13:20 - Assemble contigs from SdBG for k = 21
2026-11-12 20:13:23 - Local assembly for k = 21
2026-11-12 20:13:26 - Extract iterative edges from k = 21 to 29 
2026-11-12 20:13:26 - Build graph for k = 29 
2026-11-12 20:13:27 - Assemble contigs from SdBG for k = 29
2026-11-12 20:13:30 - Local assembly for k = 29
2026-11-12 20:13:33 - Extract iterative edges from k = 29 to 39 
2026-11-12 20:13:34 - Build graph for k = 39 
2026-11-12 20:13:35 - Assemble contigs from SdBG for k = 39
2026-11-12 20:13:38 - Local assembly for k = 39
2026-11-12 20:13:42 - Extract iterative edges from k = 39 to 59 
2026-11-12 20:13:43 - Build graph for k = 59 
2026-11-12 20:13:44 - Assemble contigs from SdBG for k = 59
2026-11-12 20:13:46 - Local assembly for k = 59
2026-11-12 20:13:52 - Extract iterative edges from k = 59 to 79 
2026-11-12 20:13:52 - Build graph for k = 79 
2026-11-12 20:13:53 - Assemble contigs from SdBG for k = 79
2026-11-12 20:13:55 - Local assembly for k = 79
2026-11-12 20:14:02 - Extract iterative edges from k = 79 to 99 
2026-11-12 20:14:02 - Build graph for k = 99 
2026-11-12 20:14:03 - Assemble contigs from SdBG for k = 99
2026-11-12 20:14:05 - Local assembly for k = 99
2026-11-12 20:14:13 - Extract iterative edges from k = 99 to 119 
2026-11-12 20:14:13 - Build graph for k = 119 
2026-11-12 20:14:14 - Assemble contigs from SdBG for k = 119
2026-11-12 20:14:16 - Local assembly for k = 119
2026-11-12 20:14:23 - Extract iterative edges from k = 119 to 141 
2026-11-12 20:14:23 - Build graph for k = 141 
2026-11-12 20:14:24 - Assemble contigs from SdBG for k = 141
2026-11-12 20:14:26 - Merging to output final contigs 
2026-11-12 20:14:26 - 610 contigs, total 1803740 bp, min 145 bp, max 117788 bp, avg 2956 bp, N50 10728 bp
2026-11-12 20:14:26 - ALL DONE. Time elapsed: 70.418094 seconds

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"fastqsanger.gz"`
__workflow_invocation_uuid__	`"81ba2396dec411f180003833c5d96987"`
advanced_section	`{"bubble_level": "2", "cleaning_rounds": "5", "disconnect_ratio": "0.1", "kmin1pass": false, "low_local_ratio": "0.2", "merge_level": "20,0.95", "nolocal": false, "nomercy": false, "prune_depth": "2", "prune_level": "2"}`
basic_section	`{"k_mer": {"__current_case__": 0, "k_list": "21,29,39,59,79,99,119,141", "k_mer_method": "klist_method"}, "min_count": "2"}`
chromInfo	`"/home/runner/work/_temp/tmpq9hj5k8k/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
dbkey	`"?"`
input_option	`{"__current_case__": 3, "batchmode": {"__current_case__": 0, "pair_input": {"values": [{"id": 1, "src": "dce"}]}, "processmode": "individual"}, "choice": "paired_collection"}`
output_section	`{"log_file": false, "min_contig_len": "100", "show_intermediate_contigs": false}`

Step 16: Parse the number of samples (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	`"input"`
__workflow_invocation_uuid__	`"81ba2396dec411f180003833c5d96987"`
chromInfo	`"/home/runner/work/_temp/tmpq9hj5k8k/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
dbkey	`"?"`
param_type	`"integer"`
remove_newlines	`true`

Step 17: Duplicate file to collection (__DUPLICATE_FILE_TO_COLLECTION__):
- step_state: scheduled
- Jobs
  - Job 1:
    - Job state is ok
    Traceback:
    Job Parameters:
    - Job parameter Parameter value
      
      __workflow_invocation_uuid__ "81ba2396dec411f180003833c5d96987"
      
      element_identifier None
      
      number "1"

Step 18: Relabel identifiers (__RELABEL_FROM_FILE__):

step_state: scheduled

Jobs

Job 1:

Job state is ok

Traceback:

Job Parameters:

Job parameter	Parameter value
__workflow_invocation_uuid__	`"81ba2396dec411f180003833c5d96987"`
how	`{"__current_case__": 0, "how_select": "txt", "labels": {"values": [{"id": 6, "src": "hda"}]}, "strict": false}`
input	`{"values": [{"id": 10, "src": "hdca"}]}`

Step 19: Match custom assemblies by group identifier (__HARMONIZELISTS__):
- step_state: scheduled
- Jobs
  - Job 1:
    - Job state is ok
    Traceback:
    Job Parameters:
    - Job parameter Parameter value
      
      __workflow_invocation_uuid__ "81ba2396dec411f180003833c5d96987"
      
      input1 {"values": [{"id": 11, "src": "hdca"}]}
      
      input2 None

Step 20: Pick the chosen assemblies (toolshed.g2.bx.psu.edu/repos/iuc/pick_value/pick_value/0.2.0):

step_state: scheduled

Jobs

Job 1:

Job state is ok

Command Line:

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

Exit Code:

```
0
```

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"input"`
__workflow_invocation_uuid__	`"81ba2396dec411f180003833c5d96987"`
chromInfo	`"/home/runner/work/_temp/tmpq9hj5k8k/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
dbkey	`"?"`
style_cond	`{"__current_case__": 2, "pick_style": "first_or_error", "type_cond": {"__current_case__": 4, "param_type": "data", "pick_from": [{"__index__": 0, "value": {"values": [{"id": 9, "src": "dce"}]}}, {"__index__": 1, "value": {"values": [{"id": 11, "src": "dce"}]}}, {"__index__": 2, "value": {"values": [{"id": 15, "src": "dce"}]}}]}}`

Step 21: Quast (toolshed.g2.bx.psu.edu/repos/iuc/quast/quast/5.3.0+galaxy2):

step_state: scheduled

Jobs

Job 1:

Job state is ok

Container:

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

Command Line:

echo test_minigut &&   ln -s '/home/runner/work/_temp/tmpq9hj5k8k/files/f/c/0/dataset_fc0415f9-e38b-43ca-9af7-caf082f219c3.dat' 'pe1-test_minigut.fastqsanger.gz' && ln -s '/home/runner/work/_temp/tmpq9hj5k8k/files/f/1/9/dataset_f193f40e-e905-4f92-9942-336fa0e5fd01.dat' 'pe2-test_minigut.fastqsanger.gz' &&  metaquast  --pe1 'pe1-test_minigut.fastqsanger.gz' --pe2 'pe2-test_minigut.fastqsanger.gz' --labels 'test_minigut' -o 'outputdir'  --max-ref-num 0  --min-identity 90.0 --min-contig 500        --min-alignment 65 --ambiguity-usage 'one' --ambiguity-score 0.99   --local-mis-size 200   --contig-thresholds '0,1000'  --extensive-mis-size 1000 --scaffold-gap-max-size 1000 --unaligned-part-size 500   --x-for-Nx 90  '/home/runner/work/_temp/tmpq9hj5k8k/files/3/9/f/dataset_39f45fea-63c4-4bed-9fff-def0a3089e80.dat' --threads ${GALAXY_SLOTS:-1}   && if [[ -f "outputdir/report.tsv" ]]; then mkdir -p "outputdir/combined_reference/" && cp "outputdir/report.tsv" "outputdir/combined_reference/report.tsv"; fi && if [[ -f "outputdir/report.html" ]]; then mkdir -p "outputdir/combined_reference/" && cp outputdir/*.html "outputdir/combined_reference/"; fi && mkdir -p '/home/runner/work/_temp/tmpq9hj5k8k/job_working_directory/000/18/outputs/dataset_68c35c4e-f4bf-46a3-a7b1-4b46b30247a9_files' && cp outputdir/combined_reference/*.html '/home/runner/work/_temp/tmpq9hj5k8k/job_working_directory/000/18/outputs/dataset_68c35c4e-f4bf-46a3-a7b1-4b46b30247a9_files' && if [[ -d "outputdir/icarus_viewers" ]]; then cp -R outputdir/icarus_viewers 'outputdir/combined_reference/'; fi && if [[ -d "outputdir/combined_reference/icarus_viewers" ]]; then cp -R outputdir/combined_reference/icarus_viewers '/home/runner/work/_temp/tmpq9hj5k8k/job_working_directory/000/18/outputs/dataset_68c35c4e-f4bf-46a3-a7b1-4b46b30247a9_files'; fi && if [[ -d "outputdir/krona_charts/" ]]; then mkdir -p '/home/runner/work/_temp/tmpq9hj5k8k/job_working_directory/000/18/outputs/dataset_bdc02f31-09f1-40de-8814-b43536215945_files' && cp outputdir/krona_charts/*.html '/home/runner/work/_temp/tmpq9hj5k8k/job_working_directory/000/18/outputs/dataset_bdc02f31-09f1-40de-8814-b43536215945_files'; fi

Exit Code:

```
0
```

Standard Output:

test_minigut
/usr/local/opt/quast-5.3.0/metaquast.py --pe1 pe1-test_minigut.fastqsanger.gz --pe2 pe2-test_minigut.fastqsanger.gz --labels test_minigut -o outputdir --max-ref-num 0 --min-identity 90.0 --min-contig 500 --min-alignment 65 --ambiguity-usage one --ambiguity-score 0.99 --local-mis-size 200 --contig-thresholds 0,1000 --extensive-mis-size 1000 --scaffold-gap-max-size 1000 --unaligned-part-size 500 --x-for-Nx 90 /home/runner/work/_temp/tmpq9hj5k8k/files/3/9/f/dataset_39f45fea-63c4-4bed-9fff-def0a3089e80.dat --threads 1

Version: 5.3.0

System information:
  OS: Linux-7.0.0-1019-azure-x86_64-with-glibc2.36 (linux_64)
  Python version: 3.12.3
  CPUs number: 4

Started: 2026-11-12 20:15:40

Logging to /home/runner/work/_temp/tmpq9hj5k8k/job_working_directory/000/18/working/outputdir/metaquast.log
WARNING: --ambiguity-usage was set to 'all' because not default --ambiguity-score was specified
INFO	generated new fontManager
INFO	generated new fontManager

Contigs:
  Pre-processing...
  /home/runner/work/_temp/tmpq9hj5k8k/files/3/9/f/dataset_39f45fea-63c4-4bed-9fff-def0a3089e80.dat ==> test_minigut

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

NOTICE: No references are provided, starting regular QUAST with MetaGeneMark gene finder
/usr/local/opt/quast-5.3.0/quast.py --pe1 pe1-test_minigut.fastqsanger.gz --pe2 pe2-test_minigut.fastqsanger.gz --min-identity 90.0 --min-contig 500 --min-alignment 65 --ambiguity-usage one --ambiguity-score 0.99 --local-mis-size 200 --contig-thresholds 0,1000 --extensive-mis-size 1000 --scaffold-gap-max-size 1000 --unaligned-part-size 500 --x-for-Nx 90 --threads 1 /home/runner/work/_temp/tmpq9hj5k8k/files/3/9/f/dataset_39f45fea-63c4-4bed-9fff-def0a3089e80.dat -o /home/runner/work/_temp/tmpq9hj5k8k/job_working_directory/000/18/working/outputdir --labels test_minigut

Version: 5.3.0

System information:
  OS: Linux-7.0.0-1019-azure-x86_64-with-glibc2.36 (linux_64)
  Python version: 3.12.3
  CPUs number: 4

Started: 2026-11-12 20:15:40

Logging to /home/runner/work/_temp/tmpq9hj5k8k/job_working_directory/000/18/working/outputdir/quast.log
NOTICE: Output directory already exists and looks like a QUAST output dir. Existing results can be reused (e.g. previously generated alignments)!
WARNING: --ambiguity-usage was set to 'all' because not default --ambiguity-score was specified

CWD: /home/runner/work/_temp/tmpq9hj5k8k/job_working_directory/000/18/working
Main parameters: 
  MODE: meta, threads: 1, min contig length: 500, min alignment length: 65, min alignment IDY: 90.0, \
  ambiguity: all, min local misassembly length: 200, min extensive misassembly length: 1000

Contigs:
  Pre-processing...
  /home/runner/work/_temp/tmpq9hj5k8k/files/3/9/f/dataset_39f45fea-63c4-4bed-9fff-def0a3089e80.dat ==> test_minigut

2026-11-12 20:15:40
Running Reads analyzer...
NOTICE: Permission denied accessing /usr/local/lib/python3.12/site-packages/quast_libs/gridss. GRIDSS will be downloaded to home directory /home/runner/work/_temp/tmpq9hj5k8k/job_working_directory/000/18/home/.quast
Downloading gridss (file: gridss-1.4.1.jar)...
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gridss successfully downloaded!
  Logging to files /home/runner/work/_temp/tmpq9hj5k8k/job_working_directory/000/18/working/outputdir/reads_stats/reads_stats.log and /home/runner/work/_temp/tmpq9hj5k8k/job_working_directory/000/18/working/outputdir/reads_stats/reads_stats.err...
  Pre-processing reads...
  Running BWA...
  Done.
  Sorting SAM-file...
  Analysis is finished.
  Creating total report...
    saved to /home/runner/work/_temp/tmpq9hj5k8k/job_working_directory/000/18/working/outputdir/reads_stats/reads_report.txt, reads_report.tsv, and reads_report.tex
Done.

2026-11-12 20:15:54
Running Basic statistics processor...
  Contig files: 
    test_minigut
  Calculating N50 and L50...
    test_minigut, N50 = 11284, L50 = 36, auN = 25695.9, Total length = 1722460, GC % = 47.32, # N's per 100 kbp =  0.00
  Drawing Nx plot...
    saved to /home/runner/work/_temp/tmpq9hj5k8k/job_working_directory/000/18/working/outputdir/basic_stats/Nx_plot.pdf
  Drawing cumulative plot...
    saved to /home/runner/work/_temp/tmpq9hj5k8k/job_working_directory/000/18/working/outputdir/basic_stats/cumulative_plot.pdf
  Drawing GC content plot...
    saved to /home/runner/work/_temp/tmpq9hj5k8k/job_working_directory/000/18/working/outputdir/basic_stats/GC_content_plot.pdf
  Drawing test_minigut GC content plot...
    saved to /home/runner/work/_temp/tmpq9hj5k8k/job_working_directory/000/18/working/outputdir/basic_stats/test_minigut_GC_content_plot.pdf
Done.

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

2026-11-12 20:15:55
Creating large visual summaries...
This may take a while: press Ctrl-C to skip this step..
  1 of 2: Creating PDF with all tables and plots...
  2 of 2: Creating Icarus viewers...
Done

2026-11-12 20:15:55
RESULTS:
  Text versions of total report are saved to /home/runner/work/_temp/tmpq9hj5k8k/job_working_directory/000/18/working/outputdir/report.txt, report.tsv, and report.tex
  Text versions of transposed total report are saved to /home/runner/work/_temp/tmpq9hj5k8k/job_working_directory/000/18/working/outputdir/transposed_report.txt, transposed_report.tsv, and transposed_report.tex
  HTML version (interactive tables and plots) is saved to /home/runner/work/_temp/tmpq9hj5k8k/job_working_directory/000/18/working/outputdir/report.html
  PDF version (tables and plots) is saved to /home/runner/work/_temp/tmpq9hj5k8k/job_working_directory/000/18/working/outputdir/report.pdf
  Icarus (contig browser) is saved to /home/runner/work/_temp/tmpq9hj5k8k/job_working_directory/000/18/working/outputdir/icarus.html
  Log is saved to /home/runner/work/_temp/tmpq9hj5k8k/job_working_directory/000/18/working/outputdir/quast.log

Finished: 2026-11-12 20:15:55
Elapsed time: 0:00:14.918485
NOTICEs: 3; WARNINGs: 1; non-fatal ERRORs: 0

Thank you for using QUAST!

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"input"`
__workflow_invocation_uuid__	`"81ba2396dec411f180003833c5d96987"`
advanced	`{"contig_thresholds": "0,1000", "extensive_mis_size": "1000", "fragmented_max_indent": null, "report_all_metrics": false, "scaffold_gap_max_size": "1000", "skip_unaligned_mis_contigs": true, "strict_NA": false, "unaligned_part_size": "500", "x_for_Nx": "90"}`
alignments	`{"ambiguity_score": "0.99", "ambiguity_usage": "one", "fragmented": false, "local_mis_size": "200", "min_alignment": "65", "upper_bound_assembly": false, "upper_bound_min_con": null, "use_all_alignments": false}`
assembly	`{"__current_case__": 1, "min_identity": "90.0", "ref": {"__current_case__": 0, "max_ref_num": "0", "origin": "silva"}, "reuse_combined_alignments": false, "type": "metagenome"}`
chromInfo	`"/home/runner/work/_temp/tmpq9hj5k8k/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
dbkey	`"?"`
genes	`{"conserved_genes_finding": false, "gene_finding": {"__current_case__": 0, "tool": "none"}, "rna_finding": false}`
large	`false`
min_contig	`"500"`
mode	`{"__current_case__": 0, "in": {"__current_case__": 1, "custom": "false", "inputs": {"values": [{"id": 16, "src": "dce"}]}}, "mode": "individual", "reads": {"__current_case__": 2, "input_1": {"values": [{"id": 5, "src": "dce"}]}, "input_2": {"values": [{"id": 6, "src": "dce"}]}, "reads_option": "paired"}}`
output_files	`["html", "krona", "summary", "log", "pdf", "tabular"]`
split_scaffolds	`false`

Other invocation details
- history_id
  - 3a6ec3d964d45ee7
- history_state
  - ok
- invocation_id
  - 3a6ec3d964d45ee7
- invocation_state
  - scheduled
- workflow_id
  - 6d1c4cf83da0921e

✅ metagenomic-assembly.ga_1

Workflow invocation details

Invocation Messages

Steps

Step 1: create text file (toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_text_file_with_recurring_lines/9.11+galaxy0):

step_state: scheduled

Jobs

Job 1:

Job state is ok

Container:

```
quay.io/biocontainers/coreutils:9.11
```

Command Line:

times=1; yes -- '' 2>/dev/null | head -n $times >> '/home/runner/work/_temp/tmpq9hj5k8k/job_working_directory/000/22/outputs/dataset_86377306-f083-4e8d-ad21-76e6452165c4.dat';

Exit Code:

```
0
```

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"input"`
__workflow_invocation_uuid__	`"3306124adec511f180003833c5d96987"`
chromInfo	`"/home/runner/work/_temp/tmpq9hj5k8k/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
dbkey	`"?"`
token_set	`[{"__index__": 0, "line": null, "repeat_select": {"__current_case__": 0, "repeat_select_opts": "user", "times": "1"}}]`

Step 2: Trimmed paired reads from grouped samples:
- step_state: scheduled
Step 3: Trimmed nanopore reads from grouped samples:
- step_state: scheduled
Step 4: Trimmed PacBio reads from grouped samples:
- step_state: scheduled
Step 5: Choose Assembler:
- step_state: scheduled
Step 6: Minimum length of contigs to output:
- step_state: scheduled
Step 7: Custom Assemblies:
- step_state: scheduled

Step 8: Select (Grep1):

step_state: scheduled

Jobs

Job 1:

Job state is ok

Container:

quay.io/biocontainers/grep:3.4--hf43ccf4_4

Command Line:

set -eo pipefail; cat '/home/runner/work/_temp/tmpq9hj5k8k/files/8/6/3/dataset_86377306-f083-4e8d-ad21-76e6452165c4.dat' | grep -P -f '/home/runner/work/_temp/tmpq9hj5k8k/job_working_directory/000/23/configs/tmpr6xr0p55'  >> '/home/runner/work/_temp/tmpq9hj5k8k/job_working_directory/000/23/outputs/dataset_c84bebc5-bbd8-44dc-9868-85b6a6c1920b.dat'

Exit Code:

```
1
```

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"input"`
__workflow_invocation_uuid__	`"3306124adec511f180003833c5d96987"`
chromInfo	`"/home/runner/work/_temp/tmpq9hj5k8k/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
dbkey	`"?"`
invert	`""`
keep_header	`false`
pattern	`"^chr([0-9A-Za-z])+"`

Step 9: Extract reads element identifiers (toolshed.g2.bx.psu.edu/repos/iuc/collection_element_identifiers/collection_element_identifiers/0.0.3):

step_state: scheduled

Jobs

Job 1:

Job state is ok

Command Line:

mv '/home/runner/work/_temp/tmpq9hj5k8k/job_working_directory/000/24/configs/tmptedx349c' '/home/runner/work/_temp/tmpq9hj5k8k/job_working_directory/000/24/outputs/dataset_b6104c00-c582-4c91-ad71-dc5b2a5e91e6.dat'

Exit Code:

```
0
```

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"input"`
__workflow_invocation_uuid__	`"3306124adec511f180003833c5d96987"`
chromInfo	`"/home/runner/work/_temp/tmpq9hj5k8k/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
dbkey	`"?"`
input_collection	`{"values": [{"id": 21, "src": "hdca"}]}`

Step 10: Unzip paired reads (__UNZIP_COLLECTION__):
- step_state: scheduled
- Jobs
  - Job 1:
    - Job state is ok
    Traceback:
    Job Parameters:
    - Job parameter Parameter value
      
      __workflow_invocation_uuid__ "3306124adec511f180003833c5d96987"
      
      input {"values": [{"id": 23, "src": "dce"}]}

Step 11: Run metaSPAdes? (toolshed.g2.bx.psu.edu/repos/iuc/map_param_value/map_param_value/0.2.0):

step_state: scheduled

Jobs

Job 1:

Job state is ok

Command Line:

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

Exit Code:

```
0
```

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"input"`
__workflow_invocation_uuid__	`"3306124adec511f180003833c5d96987"`
chromInfo	`"/home/runner/work/_temp/tmpq9hj5k8k/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
dbkey	`"?"`
input_param_type	`{"__current_case__": 0, "input_param": "metaSPAdes", "mappings": [{"__index__": 0, "from": "metaSPAdes", "to": "True"}], "type": "text"}`
output_param_type	`"boolean"`
unmapped	`{"__current_case__": 2, "default_value": "False", "on_unmapped": "default"}`

Step 12: Run MEGAHIT? (toolshed.g2.bx.psu.edu/repos/iuc/map_param_value/map_param_value/0.2.0):

step_state: scheduled

Jobs

Job 1:

Job state is ok

Command Line:

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

Exit Code:

```
0
```

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"input"`
__workflow_invocation_uuid__	`"3306124adec511f180003833c5d96987"`
chromInfo	`"/home/runner/work/_temp/tmpq9hj5k8k/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
dbkey	`"?"`
input_param_type	`{"__current_case__": 0, "input_param": "metaSPAdes", "mappings": [{"__index__": 0, "from": "MEGAHIT", "to": "True"}], "type": "text"}`
output_param_type	`"boolean"`
unmapped	`{"__current_case__": 2, "default_value": "False", "on_unmapped": "default"}`

Step 13: Count number of samples (wc_gnu):

step_state: scheduled

Jobs

Job 1:

Job state is ok

Command Line:

cat '/home/runner/work/_temp/tmpq9hj5k8k/files/b/6/1/dataset_b6104c00-c582-4c91-ad71-dc5b2a5e91e6.dat' | wc -l | awk '{ print $1 }' >> /home/runner/work/_temp/tmpq9hj5k8k/job_working_directory/000/28/outputs/dataset_60e10913-3025-4b27-a3fc-46164b1d30ce.dat

Exit Code:

```
0
```

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"txt"`
__workflow_invocation_uuid__	`"3306124adec511f180003833c5d96987"`
chromInfo	`"/home/runner/work/_temp/tmpq9hj5k8k/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
dbkey	`"?"`
include_header	`false`
options	`["lines"]`

Step 14: metaSPAdes (toolshed.g2.bx.psu.edu/repos/nml/metaspades/metaspades/4.3.0+galaxy3):

step_state: scheduled

Jobs

Job 1:

Job state is ok

Container:

quay.io/biocontainers/spades:4.3.0--hde4eca7_2

Command Line:

mkdir -p paired_reads1 && ln -s '/home/runner/work/_temp/tmpq9hj5k8k/files/9/6/3/dataset_963cab8b-64d1-4bfd-872c-559e71c1d7fd.dat' 'paired_reads1/test_minigut1.fastq.gz' &&  ln -s '/home/runner/work/_temp/tmpq9hj5k8k/files/9/5/e/dataset_95e758b0-fac1-4449-80ed-ee372252baab.dat' 'paired_reads1/test_minigut2.fastq.gz' &&    mkdir -p nanopore_reads && ln -s '/home/runner/work/_temp/tmpq9hj5k8k/files/d/b/1/dataset_db13f771-deeb-481e-9117-d2d522630de7.dat' 'nanopore_reads/file1.fastq.gz' &&     export OMP_THREAD_LIMIT=${GALAXY_SLOTS:-4} &&  metaspades.py -o 'output'  -t ${GALAXY_SLOTS:-4} -m $((${GALAXY_MEMORY_MB:-8192}/1024)) --tmp-dir ${TMPDIR}   --pe-1 1 'paired_reads1/test_minigut1.fastq.gz' --pe-2 1 'paired_reads1/test_minigut2.fastq.gz' --pe-or 1 fr   --nanopore nanopore_reads/file1.fastq.gz

Exit Code:

```
0
```

Standard Output:

Command line: /usr/local/bin/metaspades.py	-o	/home/runner/work/_temp/tmpq9hj5k8k/job_working_directory/000/30/working/output	-t	1	-m	8	--tmp-dir	/home/runner/work/_temp/tmpq9hj5k8k/job_working_directory/000/30/tmp	--pe-1	1	/home/runner/work/_temp/tmpq9hj5k8k/job_working_directory/000/30/working/paired_reads1/test_minigut1.fastq.gz	--pe-2	1	/home/runner/work/_temp/tmpq9hj5k8k/job_working_directory/000/30/working/paired_reads1/test_minigut2.fastq.gz	--pe-or	1	fr	--nanopore	/home/runner/work/_temp/tmpq9hj5k8k/job_working_directory/000/30/working/nanopore_reads/file1.fastq.gz	

System information:
  SPAdes version: 4.3.0
  Python version: 3.14.7
  OS: Linux-7.0.0-1019-azure-x86_64-with-glibc2.36

Output dir: /home/runner/work/_temp/tmpq9hj5k8k/job_working_directory/000/30/working/output
Mode: read error correction and assembling
Debug mode is turned OFF

Dataset parameters:
  Metagenomic mode
  Reads:
    Library number: 1, library type: paired-end
      orientation: fr
      left reads: ['/home/runner/work/_temp/tmpq9hj5k8k/job_working_directory/000/30/working/paired_reads1/test_minigut1.fastq.gz']
      right reads: ['/home/runner/work/_temp/tmpq9hj5k8k/job_working_directory/000/30/working/paired_reads1/test_minigut2.fastq.gz']
      interlaced reads: not specified
      single reads: not specified
      merged reads: not specified
    Library number: 2, library type: nanopore
      left reads: not specified
      right reads: not specified
      interlaced reads: not specified
      single reads: ['/home/runner/work/_temp/tmpq9hj5k8k/job_working_directory/000/30/working/nanopore_reads/file1.fastq.gz']
      merged reads: not specified
Read error correction parameters:
  Iterations: 1
  PHRED offset will be auto-detected
  Corrected reads will be compressed
Assembly parameters:
  k: [21, 33, 55]
  Repeat resolution is enabled
  Mismatch careful mode is turned OFF
  MismatchCorrector will be SKIPPED
  Coverage cutoff is turned OFF
  Assembly graph output will use GFA v1.2 format
Other parameters:
  Dir for temp files: /home/runner/work/_temp/tmpq9hj5k8k/job_working_directory/000/30/tmp
  Threads: 1
  Memory limit (in Gb): 8


======= SPAdes pipeline started. Log can be found here: /home/runner/work/_temp/tmpq9hj5k8k/job_working_directory/000/30/working/output/spades.log

/home/runner/work/_temp/tmpq9hj5k8k/job_working_directory/000/30/working/paired_reads1/test_minigut1.fastq.gz: max reads length: 126
/home/runner/work/_temp/tmpq9hj5k8k/job_working_directory/000/30/working/paired_reads1/test_minigut2.fastq.gz: max reads length: 126

Reads length: 126


===== Before start started. 


===== Read error correction started. 


===== Read error correction started. 


== Running: /usr/local/bin/spades-hammer /home/runner/work/_temp/tmpq9hj5k8k/job_working_directory/000/30/working/output/corrected/configs/config.info

  0:00:00.000     1M / 23M   INFO    General                 (main.cpp                  :  76)   Starting BayesHammer, built from N/A, git revision N/A
  0:00:00.000     1M / 23M   INFO    General                 (main.cpp                  :  77)   Loading config from "/home/runner/work/_temp/tmpq9hj5k8k/job_working_directory/000/30/working/output/corrected/configs/config.info"
  0:00:00.000     1M / 23M   INFO    General                 (main.cpp                  :  79)   Maximum # of threads to use (adjusted due to OMP capabilities): 1
  0:00:00.000     1M / 23M   INFO    General                 (memory_limit.cpp          :  55)   Memory limit set to 8 Gb
  0:00:00.000     1M / 23M   INFO    General                 (main.cpp                  :  87)   Trying to determine PHRED offset
  0:00:00.000     1M / 23M   INFO    General                 (main.cpp                  :  93)   Determined value is 33
  0:00:00.000     1M / 23M   INFO    General                 (hammer_tools.cpp          :  40)   Hamming graph threshold tau=1, k=21, subkmer positions = [ 0 10 ]
  0:00:00.000     1M / 23M   INFO    General                 (main.cpp                  : 114)   Size of aux. kmer data 24 bytes
     === ITERATION 0 begins ===
  0:00:00.000     1M / 23M   INFO   K-mer Counting           (kmer_data.cpp             : 284)   Estimating k-mer count
  0:00:00.008    17M / 23M   INFO   K-mer Counting           (kmer_data.cpp             : 289)   Processing "/home/runner/work/_temp/tmpq9hj5k8k/job_working_directory/000/30/working/paired_reads1/test_minigut1.fastq.gz"
  0:00:00.931    17M / 23M   INFO   K-mer Counting           (kmer_data.cpp             : 298)   Processed 50000 reads
  0:00:00.931    17M / 23M   INFO   K-mer Counting           (kmer_data.cpp             : 289)   Processing "/home/runner/work/_temp/tmpq9hj5k8k/job_working_directory/000/30/working/paired_reads1/test_minigut2.fastq.gz"
  0:00:01.854    17M / 23M   INFO   K-mer Counting           (kmer_data.cpp             : 298)   Processed 100000 reads
  0:00:01.854    17M / 23M   INFO   K-mer Counting           (kmer_data.cpp             : 303)   Total 100000 reads processed
  0:00:01.992    17M / 23M   INFO   K-mer Counting           (kmer_data.cpp             : 306)   Estimated 4749954 distinct kmers
  0:00:01.992     1M / 23M   INFO   K-mer Counting           (kmer_data.cpp             : 310)   Filtering singleton k-mers
  0:00:01.996    22M / 27M   INFO   K-mer Counting           (kmer_data.cpp             : 316)   Processing "/home/runner/work/_temp/tmpq9hj5k8k/job_working_directory/000/30/working/paired_reads1/test_minigut1.fastq.gz"
  0:00:04.351    22M / 27M   INFO   K-mer Counting           (kmer_data.cpp             : 325)   Processed 50000 reads
  0:00:04.351    22M / 27M   INFO   K-mer Counting           (kmer_data.cpp             : 316)   Processing "/home/runner/work/_temp/tmpq9hj5k8k/job_working_directory/000/30/working/paired_reads1/test_minigut2.fastq.gz"
  0:00:06.988    22M / 27M   INFO   K-mer Counting           (kmer_data.cpp             : 325)   Processed 100000 reads
  0:00:06.988    22M / 27M   INFO   K-mer Counting           (kmer_data.cpp             : 330)   Total 100000 reads processed
  0:00:06.988    22M / 27M   INFO    General                 (kmer_index_builder.hpp    : 308)   Splitting kmer instances into 16 files using 1 threads. This might take a while.
  0:00:06.988    22M / 27M   INFO    General                 (file_limit.hpp            :  43)   Open file limit set to 65536
  0:00:06.988    22M / 27M   INFO    General                 (kmer_splitter.hpp         :  96)   Memory available for splitting buffers: 2.65979 Gb
  0:00:06.988    22M / 27M   INFO    General                 (kmer_splitter.hpp         : 104)   Using cell size of 4194304
  0:00:06.989   598M / 598M  INFO   K-mer Splitting          (kmer_data.cpp             :  98)   Processing "/home/runner/work/_temp/tmpq9hj5k8k/job_working_directory/000/30/working/paired_reads1/test_minigut1.fastq.gz"
  0:00:09.005   598M / 598M  INFO   K-mer Splitting          (kmer_data.cpp             : 108)   Processed 50000 reads
  0:00:09.005   598M / 598M  INFO   K-mer Splitting          (kmer_data.cpp             :  98)   Processing "/home/runner/work/_temp/tmpq9hj5k8k/job_working_directory/000/30/working/paired_reads1/test_minigut2.fastq.gz"
  0:00:10.978   598M / 598M  INFO   K-mer Splitting          (kmer_data.cpp             : 108)   Processed 100000 reads
  0:00:10.978   598M / 598M  INFO   K-mer Splitting          (kmer_data.cpp             : 113)   Total 100000 reads processed
  0:00:10.982    22M / 110M  INFO    General                 (kmer_index_builder.hpp    : 314)   Starting k-mer counting.
  0:00:11.022    22M / 110M  INFO    General                 (kmer_index_builder.hpp    : 325)   K-mer counting done. There are 3382402 kmers in total.
  0:00:11.022     1M / 110M  INFO   K-mer Index Building     (kmer_index_builder.hpp    : 460)   Building perfect hash indices
  0:00:11.362     3M / 110M  INFO   K-mer Index Building     (kmer_index_builder.hpp    : 496)   Index built. Total 3382402 kmers, 2454856 bytes occupied (5.80618 bits per kmer).
  0:00:11.362     3M / 110M  INFO   K-mer Counting           (kmer_data.cpp             : 355)   Arranging kmers in hash map order
  0:00:11.536    55M / 110M  INFO    General                 (main.cpp                  : 149)   Clustering Hamming graph.
  0:00:22.820    55M / 110M  INFO    General                 (main.cpp                  : 156)   Extracting clusters:
  0:00:22.820    55M / 110M  INFO    General                 (concurrent_dsu.cpp        :  19)   Connecting to root
  0:00:22.825    55M / 110M  INFO    General                 (concurrent_dsu.cpp        :  35)   Calculating counts
  0:00:23.670   123M / 147M  INFO    General                 (concurrent_dsu.cpp        :  64)   Writing down entries
  0:00:24.758    55M / 198M  INFO    General                 (main.cpp                  : 168)   Clustering done. Total clusters: 3369253
  0:00:24.758    29M / 198M  INFO   K-mer Counting           (kmer_data.cpp             : 372)   Collecting K-mer information, this takes a while.
  0:00:24.798   109M / 198M  INFO   K-mer Counting           (kmer_data.cpp             : 378)   Processing "/home/runner/work/_temp/tmpq9hj5k8k/job_working_directory/000/30/working/paired_reads1/test_minigut1.fastq.gz"
  0:00:29.147   109M / 198M  INFO   K-mer Counting           (kmer_data.cpp             : 378)   Processing "/home/runner/work/_temp/tmpq9hj5k8k/job_working_directory/000/30/working/paired_reads1/test_minigut2.fastq.gz"
  0:00:33.323   109M / 198M  INFO   K-mer Counting           (kmer_data.cpp             : 385)   Collection done, postprocessing.
  0:00:33.337   109M / 198M  INFO   K-mer Counting           (kmer_data.cpp             : 398)   There are 3382402 kmers in total. Among them 950 (0.0280865%) are singletons.
  0:00:33.337   109M / 198M  INFO    General                 (main.cpp                  : 174)   Subclustering Hamming graph
  0:00:33.502   109M / 198M  INFO   Hamming Subclustering    (kmer_cluster.cpp          : 637)   Subclustering done. Total 0 non-read kmers were generated.
  0:00:33.502   109M / 198M  INFO   Hamming Subclustering    (kmer_cluster.cpp          : 638)   Subclustering statistics:
  0:00:33.502   109M / 198M  INFO   Hamming Subclustering    (kmer_cluster.cpp          : 639)     Total singleton hamming clusters: 3359050. Among them 3349000 (99.7008%) are good
  0:00:33.502   109M / 198M  INFO   Hamming Subclustering    (kmer_cluster.cpp          : 640)     Total singleton subclusters: 4780. Among them 4780 (100%) are good
  0:00:33.502   109M / 198M  INFO   Hamming Subclustering    (kmer_cluster.cpp          : 641)     Total non-singleton subcluster centers: 8554. Among them 8145 (95.2186%) are good
  0:00:33.502   109M / 198M  INFO   Hamming Subclustering    (kmer_cluster.cpp          : 642)     Average size of non-trivial subcluster: 2.72995 kmers
  0:00:33.502   109M / 198M  INFO   Hamming Subclustering    (kmer_cluster.cpp          : 643)     Average number of sub-clusters per non-singleton cluster: 1.30687
  0:00:33.502   109M / 198M  INFO   Hamming Subclustering    (kmer_cluster.cpp          : 644)     Total solid k-mers: 3361925
  0:00:33.502   109M / 198M  INFO   Hamming Subclustering    (kmer_cluster.cpp          : 645)     Substitution probabilities: (     0.950126    0.0136492    0.0244347    0.0117896 )
(   0.00967335     0.948376   0.00591257    0.0360376 )
(    0.0337959   0.00509173     0.950521    0.0105916 )
(     0.010362    0.0217882    0.0133119     0.954538 )
  0:00:33.503   109M / 198M  INFO    General                 (main.cpp                  : 179)   Finished clustering.
  0:00:33.503   109M / 198M  INFO    General                 (main.cpp                  : 198)   Starting solid k-mers expansion in 1 threads.
  0:00:35.419   109M / 198M  INFO    General                 (main.cpp                  : 219)   Solid k-mers iteration 0 produced 4743 new k-mers.
  0:00:37.338   109M / 198M  INFO    General                 (main.cpp                  : 219)   Solid k-mers iteration 1 produced 115 new k-mers.
  0:00:39.226   109M / 198M  INFO    General                 (main.cpp                  : 219)   Solid k-mers iteration 2 produced 0 new k-mers.
  0:00:39.227   109M / 198M  INFO    General                 (main.cpp                  : 223)   Solid k-mers finalized
  0:00:39.227   109M / 198M  INFO    General                 (hammer_tools.cpp          : 226)   Starting read correction in 1 threads.
  0:00:39.227   109M / 198M  INFO    General                 (hammer_tools.cpp          : 239)   Correcting pair of reads: "/home/runner/work/_temp/tmpq9hj5k8k/job_working_directory/000/30/working/paired_reads1/test_minigut1.fastq.gz" and "/home/runner/work/_temp/tmpq9hj5k8k/job_working_directory/000/30/working/paired_reads1/test_minigut2.fastq.gz"
  0:00:39.430   159M / 198M  INFO    General                 (hammer_tools.cpp          : 173)   Prepared batch 0 of 50000 reads.
  0:00:42.353   159M / 198M  INFO    General                 (hammer_tools.cpp          : 180)   Processed batch 0
  0:00:42.396   159M / 198M  INFO    General                 (hammer_tools.cpp          : 190)   Written batch 0
  0:00:42.405   109M / 198M  INFO    General                 (hammer_tools.cpp          : 280)   Correction done. Changed 26030 bases in 19067 reads.
  0:00:42.406   109M / 198M  INFO    General                 (hammer_tools.cpp          : 281)   Failed to correct 0 bases out of 12599930.
  0:00:42.409     1M / 198M  INFO    General                 (main.cpp                  : 256)   Saving corrected dataset description to /home/runner/work/_temp/tmpq9hj5k8k/job_working_directory/000/30/working/output/corrected/corrected.yaml
  0:00:42.409     1M / 198M  INFO    General                 (main.cpp                  : 263)   All done. Exiting.

===== Read error correction finished. 


===== corrected reads compression started. 


== Running: /usr/local/bin/python3 /usr/local/share/spades/spades_pipeline/supplemetary/compress_all.py --input_file /home/runner/work/_temp/tmpq9hj5k8k/job_working_directory/000/30/working/output/corrected/corrected.yaml --ext_python_modules_home /usr/local/share/spades --max_threads 1 --output_dir /home/runner/work/_temp/tmpq9hj5k8k/job_working_directory/000/30/working/output/corrected --not_used_yaml_file /home/runner/work/_temp/tmpq9hj5k8k/job_working_directory/000/30/working/output/corrected/dont_correct.yaml --gzip_output

== Compressing corrected reads (with pigz)
== Files to compress: ['/home/runner/work/_temp/tmpq9hj5k8k/job_working_directory/000/30/working/output/corrected/test_minigut1.fastq00.0_0.cor.fastq', '/home/runner/work/_temp/tmpq9hj5k8k/job_working_directory/000/30/working/output/corrected/test_minigut2.fastq00.0_0.cor.fastq', '/home/runner/work/_temp/tmpq9hj5k8k/job_working_directory/000/30/working/output/corrected/test_minigut_unpaired00.0_0.cor.fastq']
== Files compression is finished
== Info about datasets not used in error correction stage is loaded
== Dataset yaml file is updated

===== corrected reads compression finished. 


===== Read error correction finished. 


===== Assembling started. 


===== K21 started. 


== Running: /usr/local/bin/spades-core /home/runner/work/_temp/tmpq9hj5k8k/job_working_directory/000/30/working/output/K21/configs/config.info /home/runner/work/_temp/tmpq9hj5k8k/job_working_directory/000/30/working/output/K21/configs/mda_mode.info /home/runner/work/_temp/tmpq9hj5k8k/job_working_directory/000/30/working/output/K21/configs/meta_mode.info

  0:00:00.000     1M / 23M   INFO    General                 (main.cpp                  :  94)   Loaded config from "/home/runner/work/_temp/tmpq9hj5k8k/job_working_directory/000/30/working/output/K21/configs/config.info"
  0:00:00.000     1M / 23M   INFO    General                 (main.cpp                  :  94)   Loaded config from "/home/runner/work/_temp/tmpq9hj5k8k/job_working_directory/000/30/working/output/K21/configs/mda_mode.info"
  0:00:00.000     1M / 23M   INFO    General                 (main.cpp                  :  94)   Loaded config from "/home/runner/work/_temp/tmpq9hj5k8k/job_working_directory/000/30/working/output/K21/configs/meta_mode.info"
  0:00:00.000     1M / 23M   INFO    General                 (memory_limit.cpp          :  55)   Memory limit set to 8 Gb
  0:00:00.000     1M / 23M   INFO    Gener
..
l                 (distance_estimation.cpp   :  75)   Processing library #0
  0:06:13.901    18M / 157M  INFO    General                 (distance_estimation_utils.:  23)   Estimating distances
  0:06:13.901    18M / 157M  INFO   DistanceEstimator        (distance_estimation.hpp   : 132)   Using SIMPLE distance estimator
  0:06:13.911    18M / 157M  INFO    General                 (distance_estimation_utils.: 137)   Refining clustered pair information
  0:06:13.911    18M / 157M  INFO    General                 (distance_estimation_utils.: 139)   The refining of clustered pair information has been finished
  0:06:13.911    18M / 157M  INFO    General                 (distance_estimation_utils.: 141)   Improving paired information
  0:06:13.919    18M / 157M  INFO   PairInfoImprover         (pair_info_improver.hpp    :  80)   Paired info stats: missing = 224; contradictional = 0
  0:06:13.926    18M / 157M  INFO   PairInfoImprover         (pair_info_improver.hpp    :  80)   Paired info stats: missing = 30; contradictional = 0
  0:06:13.926    18M / 157M  INFO    General                 (distance_estimation_utils.:  81)   Filling scaffolding index
  0:06:13.926    18M / 157M  INFO    General                 (distance_estimation_utils.:  23)   Estimating distances
  0:06:13.926    18M / 157M  INFO   DistanceEstimator        (distance_estimation.hpp   : 132)   Using SMOOTHING distance estimator
  0:06:13.950    18M / 157M  INFO    General                 (distance_estimation.cpp   :  84)   Clearing raw paired index
  0:06:13.950    18M / 157M  INFO   StageManager             (stage.cpp                 : 210)   STAGE == Repeat Resolving (id: repeat_resolving)
  0:06:13.950    18M / 157M  INFO    General                 (repeat_resolving.cpp      :  88)   Using Path-Extend repeat resolving
  0:06:13.950    18M / 157M  INFO    General                 (launcher.cpp              : 636)   ExSPAnder repeat resolving tool started
  0:06:13.950    18M / 157M  INFO    General                 (launcher.cpp              : 193)   Autodetecting unique edge set parameters...
  0:06:13.950    18M / 157M  INFO    General                 (launcher.cpp              : 195)   Minimal unique edge length set to the smallest MP library IS: 2000
  0:06:13.950    18M / 157M  INFO    General                 (coverage_uniformity_analyz:  25)   genomic coverage is 4.4574 calculated of length 1716077
  0:06:13.950    18M / 157M  INFO    General                 (launcher.cpp              : 200)   median coverage for edges longer than 2000 is 4.4574 uniformity 100%
  0:06:13.951    18M / 157M  INFO   ScaffoldingUniqueEdgeAna (scaff_supplementary.cpp   :  76)   With length cutoff: 2000, median long edge coverage: 4.46134, and maximal unique coverage: 0.5
  0:06:13.951    18M / 157M  INFO   ScaffoldingUniqueEdgeAna (scaff_supplementary.cpp   :  79)   Unique edges quantity: 124, unique edges length 3432154, total edges length 3473534
  0:06:13.951    18M / 157M  INFO    General                 (launcher.cpp              : 444)   Creating main extenders, unique edge length = 2000
  0:06:13.951    18M / 157M  INFO    General                 (launcher.cpp              : 362)   filling path container
  0:06:13.951    18M / 157M  INFO    General                 (launcher.cpp              : 362)   filling path container
  0:06:13.951    18M / 157M  INFO    General                 (extenders_logic.cpp       : 352)   Creating extender; library index size: 890
  0:06:13.951    18M / 157M  INFO    General                 (extenders_logic.cpp       : 352)   Creating extender; library index size: 890
  0:06:13.952    18M / 157M  INFO    General                 (extenders_logic.cpp       :  54)   resolvable_repeat_length_bound set to 773417
  0:06:13.952    18M / 157M  INFO    General                 (extenders_logic.cpp       :  54)   resolvable_repeat_length_bound set to 10000
  0:06:13.952    19M / 157M  INFO    General                 (extenders_logic.cpp       : 550)   Using 1 paired-end library
  0:06:13.952    19M / 157M  INFO    General                 (extenders_logic.cpp       : 551)   Using 1 paired-end scaffolding library
  0:06:13.952    19M / 157M  INFO    General                 (extenders_logic.cpp       : 552)   Using 2 single read libraries
  0:06:13.952    19M / 157M  INFO    General                 (launcher.cpp              : 409)   Filling backbone edges for long reads scaffolding...
  0:06:13.952    19M / 157M  INFO    General                 (launcher.cpp              : 411)    with long reads paths
  0:06:13.953    19M / 157M  INFO    General                 (launcher.cpp              : 420)   Removing fake unique with paired-end libs
  0:06:13.954    19M / 157M  INFO    General                 (launcher.cpp              : 431)   124 unique edges
  0:06:13.954    19M / 157M  INFO    General                 (extenders_logic.cpp       : 427)   Creating scaffolding extender for lib 1
  0:06:13.954    19M / 157M  INFO   ExtensionChooser2015     (extension_chooser2015.hpp :  57)   ExtensionChooser2015 created
  0:06:13.954    19M / 157M  INFO    General                 (extenders_logic.cpp       : 453)   Using 1 long reads scaffolding library
  0:06:13.954    19M / 157M  INFO    General                 (extenders_logic.cpp       : 463)   Using additional coordinated coverage extender
  0:06:13.954    19M / 157M  INFO    General                 (launcher.cpp              : 473)   Total number of extenders is 7
  0:06:13.954    19M / 157M  INFO    General                 (path_extenders.cpp        :  36)   Processed 0 paths from 123 (0%)
  0:06:13.960    19M / 157M  INFO    General                 (path_extenders.cpp        :  36)   Processed 13 paths from 123 (10%)
  0:06:13.960    19M / 157M  INFO    General                 (path_extenders.cpp        :  36)   Processed 26 paths from 123 (21%)
  0:06:13.961    19M / 157M  INFO    General                 (path_extenders.cpp        :  36)   Processed 39 paths from 123 (31%)
  0:06:13.961    19M / 157M  INFO    General                 (path_extenders.cpp        :  36)   Processed 52 paths from 123 (42%)
  0:06:13.961    19M / 157M  INFO    General                 (path_extenders.cpp        :  36)   Processed 65 paths from 123 (52%)
  0:06:13.961    19M / 157M  INFO    General                 (path_extenders.cpp        :  36)   Processed 78 paths from 123 (63%)
  0:06:13.962    19M / 157M  INFO    General                 (path_extenders.cpp        :  36)   Processed 91 paths from 123 (73%)
  0:06:13.962    19M / 157M  INFO    General                 (path_extenders.cpp        :  36)   Processed 104 paths from 123 (84%)
  0:06:13.962    19M / 157M  INFO    General                 (path_extenders.cpp        :  36)   Processed 117 paths from 123 (95%)
  0:06:13.962    19M / 157M  INFO    General                 (launcher.cpp              : 264)   Finalizing paths
  0:06:13.962    19M / 157M  INFO    General                 (launcher.cpp              : 266)   Deduplicating paths
  0:06:13.962    19M / 157M  INFO    General                 (launcher.cpp              : 270)   Paths deduplicated
  0:06:13.962    19M / 157M  INFO   PEResolver               (pe_resolver.cpp           :  70)   Removing overlaps
  0:06:13.962    19M / 157M  INFO   PEResolver               (pe_resolver.cpp           :  80)   Marking overlaps
  0:06:13.962    19M / 157M  INFO   OverlapRemover           (overlap_remover.hpp       : 120)   Marking start/end overlaps
  0:06:13.962    19M / 157M  INFO   OverlapRemover           (overlap_remover.hpp       : 123)   Marking remaining overlaps
  0:06:13.962    19M / 157M  INFO   PEResolver               (pe_resolver.cpp           :  83)   Splitting paths
  0:06:13.962    19M / 157M  INFO   PEResolver               (pe_resolver.cpp           :  88)   Deduplicating paths
  0:06:13.962    19M / 157M  INFO   PEResolver               (pe_resolver.cpp           :  90)   Overlaps removed
  0:06:13.962    19M / 157M  INFO    General                 (launcher.cpp              : 287)   Paths finalized
  0:06:13.962    19M / 157M  INFO    General                 (launcher.cpp              : 482)   Closing gaps in paths
  0:06:13.963    19M / 157M  INFO    General                 (launcher.cpp              : 512)   Gap closing completed
  0:06:13.963    18M / 157M  INFO    General                 (launcher.cpp              : 320)   Traversing tandem repeats
  0:06:13.964    18M / 157M  INFO    General                 (launcher.cpp              : 330)   Traversed 1 loops
  0:06:13.964    18M / 157M  INFO    General                 (launcher.cpp              : 264)   Finalizing paths
  0:06:13.964    18M / 157M  INFO    General                 (launcher.cpp              : 266)   Deduplicating paths
  0:06:13.964    18M / 157M  INFO    General                 (launcher.cpp              : 270)   Paths deduplicated
  0:06:13.964    18M / 157M  INFO   PEResolver               (pe_resolver.cpp           :  70)   Removing overlaps
  0:06:13.964    18M / 157M  INFO   PEResolver               (pe_resolver.cpp           :  80)   Marking overlaps
  0:06:13.964    18M / 157M  INFO   OverlapRemover           (overlap_remover.hpp       : 120)   Marking start/end overlaps
  0:06:13.964    18M / 157M  INFO   OverlapRemover           (overlap_remover.hpp       : 123)   Marking remaining overlaps
  0:06:13.964    18M / 157M  INFO   PEResolver               (pe_resolver.cpp           :  83)   Splitting paths
  0:06:13.964    18M / 157M  INFO   PEResolver               (pe_resolver.cpp           :  88)   Deduplicating paths
  0:06:13.964    18M / 157M  INFO   PEResolver               (pe_resolver.cpp           :  90)   Overlaps removed
  0:06:13.964    18M / 157M  INFO    General                 (launcher.cpp              : 287)   Paths finalized
  0:06:13.964    18M / 157M  INFO    General                 (launcher.cpp              : 701)   ExSPAnder repeat resolving tool finished
  0:06:13.964    18M / 157M  INFO   StageManager             (stage.cpp                 : 210)   STAGE == Contig Output (id: contig_output)
  0:06:13.964    18M / 157M  INFO    General                 (contig_output.hpp         :  20)   Outputting contigs to "/home/runner/work/_temp/tmpq9hj5k8k/job_working_directory/000/30/working/output/K55/before_rr.fasta"
  0:06:13.971    18M / 157M  INFO    General                 (contig_output_stage.cpp   : 159)   Writing GFA graph to "/home/runner/work/_temp/tmpq9hj5k8k/job_working_directory/000/30/working/output/K55/assembly_graph_with_scaffolds.gfa"
  0:06:13.976    18M / 157M  INFO    General                 (contig_output_stage.cpp   : 175)   Outputting FastG graph to "/home/runner/work/_temp/tmpq9hj5k8k/job_working_directory/000/30/working/output/K55/assembly_graph.fastg"
  0:06:13.990    18M / 157M  INFO    General                 (contig_output_stage.cpp   : 210)   Breaking scaffolds
  0:06:13.994    20M / 157M  INFO    General                 (contig_output_stage.cpp   : 101)   Outputting contigs to /home/runner/work/_temp/tmpq9hj5k8k/job_working_directory/000/30/working/output/K55/final_contigs.fasta
  0:06:13.998    20M / 157M  INFO    General                 (contig_output_stage.cpp   : 107)   Outputting FastG paths to /home/runner/work/_temp/tmpq9hj5k8k/job_working_directory/000/30/working/output/K55/final_contigs.paths
  0:06:14.001    20M / 157M  INFO    General                 (contig_output_stage.cpp   : 101)   Outputting contigs to /home/runner/work/_temp/tmpq9hj5k8k/job_working_directory/000/30/working/output/K55/scaffolds.fasta
  0:06:14.004    20M / 157M  INFO    General                 (contig_output_stage.cpp   : 107)   Outputting FastG paths to /home/runner/work/_temp/tmpq9hj5k8k/job_working_directory/000/30/working/output/K55/scaffolds.paths
  0:06:14.004    20M / 157M  INFO    General                 (contig_output_stage.cpp   : 114)   Populating GFA with scaffold paths
  0:06:14.005    18M / 157M  INFO    General                 (pipeline.cpp              : 305)   SPAdes finished
  0:06:14.005     1M / 157M  INFO    General                 (main.cpp                  : 131)   Assembling time: 0 hours 6 minutes 14 seconds

===== K55 finished. 


===== Copy files started. 


== Running: /usr/local/bin/python3 /usr/local/share/spades/spades_pipeline/supplemetary/copy_files.py /home/runner/work/_temp/tmpq9hj5k8k/job_working_directory/000/30/working/output/K55/before_rr.fasta /home/runner/work/_temp/tmpq9hj5k8k/job_working_directory/000/30/working/output/before_rr.fasta /home/runner/work/_temp/tmpq9hj5k8k/job_working_directory/000/30/working/output/K55/assembly_graph_after_simplification.gfa /home/runner/work/_temp/tmpq9hj5k8k/job_working_directory/000/30/working/output/assembly_graph_after_simplification.gfa /home/runner/work/_temp/tmpq9hj5k8k/job_working_directory/000/30/working/output/K55/final_contigs.fasta /home/runner/work/_temp/tmpq9hj5k8k/job_working_directory/000/30/working/output/contigs.fasta /home/runner/work/_temp/tmpq9hj5k8k/job_working_directory/000/30/working/output/K55/first_pe_contigs.fasta /home/runner/work/_temp/tmpq9hj5k8k/job_working_directory/000/30/working/output/first_pe_contigs.fasta /home/runner/work/_temp/tmpq9hj5k8k/job_working_directory/000/30/working/output/K55/strain_graph.gfa /home/runner/work/_temp/tmpq9hj5k8k/job_working_directory/000/30/working/output/strain_graph.gfa /home/runner/work/_temp/tmpq9hj5k8k/job_working_directory/000/30/working/output/K55/scaffolds.fasta /home/runner/work/_temp/tmpq9hj5k8k/job_working_directory/000/30/working/output/scaffolds.fasta /home/runner/work/_temp/tmpq9hj5k8k/job_working_directory/000/30/working/output/K55/scaffolds.paths /home/runner/work/_temp/tmpq9hj5k8k/job_working_directory/000/30/working/output/scaffolds.paths /home/runner/work/_temp/tmpq9hj5k8k/job_working_directory/000/30/working/output/K55/assembly_graph_with_scaffolds.gfa /home/runner/work/_temp/tmpq9hj5k8k/job_working_directory/000/30/working/output/assembly_graph_with_scaffolds.gfa /home/runner/work/_temp/tmpq9hj5k8k/job_working_directory/000/30/working/output/K55/assembly_graph.fastg /home/runner/work/_temp/tmpq9hj5k8k/job_working_directory/000/30/working/output/assembly_graph.fastg /home/runner/work/_temp/tmpq9hj5k8k/job_working_directory/000/30/working/output/K55/final_contigs.paths /home/runner/work/_temp/tmpq9hj5k8k/job_working_directory/000/30/working/output/contigs.paths


===== Copy files finished. 


===== Assembling finished. 


===== Breaking scaffolds started. 


== Running: /usr/local/bin/python3 /usr/local/share/spades/spades_pipeline/supplemetary/breaking_scaffolds_script.py --result_scaffolds_filename /home/runner/work/_temp/tmpq9hj5k8k/job_working_directory/000/30/working/output/scaffolds.fasta --misc_dir /home/runner/work/_temp/tmpq9hj5k8k/job_working_directory/000/30/working/output/misc --threshold_for_breaking_scaffolds 3


===== Breaking scaffolds finished. 


===== Terminate started. 


===== Terminate finished. 

 * Corrected reads are in /home/runner/work/_temp/tmpq9hj5k8k/job_working_directory/000/30/working/output/corrected/
 * Assembled contigs are in /home/runner/work/_temp/tmpq9hj5k8k/job_working_directory/000/30/working/output/contigs.fasta
 * Assembled scaffolds are in /home/runner/work/_temp/tmpq9hj5k8k/job_working_directory/000/30/working/output/scaffolds.fasta
 * Paths in the assembly graph corresponding to the contigs are in /home/runner/work/_temp/tmpq9hj5k8k/job_working_directory/000/30/working/output/contigs.paths
 * Paths in the assembly graph corresponding to the scaffolds are in /home/runner/work/_temp/tmpq9hj5k8k/job_working_directory/000/30/working/output/scaffolds.paths
 * Assembly graph is in /home/runner/work/_temp/tmpq9hj5k8k/job_working_directory/000/30/working/output/assembly_graph.fastg
 * Assembly graph in GFA format is in /home/runner/work/_temp/tmpq9hj5k8k/job_working_directory/000/30/working/output/assembly_graph_with_scaffolds.gfa

======= SPAdes pipeline finished.

SPAdes log can be found here: /home/runner/work/_temp/tmpq9hj5k8k/job_working_directory/000/30/working/output/spades.log

Thank you for using metaSPAdes! If you use it in your research, please cite:

  Nurk, S., Meleshko, D., Korobeynikov, A. and Pevzner, P.A., 2017. metaSPAdes: a new versatile metagenomic assembler. Genome research, 27(5), pp.824-834.
  doi.org/10.1101/gr.213959.116

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"input"`
__workflow_invocation_uuid__	`"3306124adec511f180003833c5d96987"`
chromInfo	`"/home/runner/work/_temp/tmpq9hj5k8k/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
dbkey	`"?"`
file_processing	`{"__current_case__": 1, "additional_reads": {"__current_case__": 1, "selector": "false"}, "arf": {"nanopore": {"values": [{"id": 26, "src": "dce"}]}, "pacbio": null}, "is_select": "individual", "library_number": "true", "singlePaired": {"__current_case__": 1, "input": {"values": [{"id": 23, "src": "dce"}]}, "orientation": "fr", "sPaired": "paired_collection", "type_paired": "pe"}}`
kmer_cond	`{"__current_case__": 0, "kmer_sel": "auto"}`
mode_sel	`None`
optional_output	`["ag", "ags", "cn", "sc"]`
phred_offset	`"auto"`

Step 15: MEGAHIT (toolshed.g2.bx.psu.edu/repos/iuc/megahit/megahit/1.2.9+galaxy2):

step_state: scheduled

Jobs

Job 1:

Job state is skipped

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"fastqsanger.gz"`
__workflow_invocation_uuid__	`"3306124adec511f180003833c5d96987"`
advanced_section	`{"bubble_level": "2", "cleaning_rounds": "5", "disconnect_ratio": "0.1", "kmin1pass": false, "low_local_ratio": "0.2", "merge_level": "20,0.95", "nolocal": false, "nomercy": false, "prune_depth": "2", "prune_level": "2"}`
basic_section	`{"k_mer": {"__current_case__": 0, "k_list": "21,29,39,59,79,99,119,141", "k_mer_method": "klist_method"}, "min_count": "2"}`
chromInfo	`"/home/runner/work/_temp/tmpq9hj5k8k/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
dbkey	`"?"`
input_option	`{"__current_case__": 3, "batchmode": {"__current_case__": 0, "pair_input": {"values": [{"id": 23, "src": "dce"}]}, "processmode": "individual"}, "choice": "paired_collection"}`
output_section	`{"log_file": false, "min_contig_len": "100", "show_intermediate_contigs": false}`

Step 16: Parse the number of samples (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	`"input"`
__workflow_invocation_uuid__	`"3306124adec511f180003833c5d96987"`
chromInfo	`"/home/runner/work/_temp/tmpq9hj5k8k/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
dbkey	`"?"`
param_type	`"integer"`
remove_newlines	`true`

Step 17: Duplicate file to collection (__DUPLICATE_FILE_TO_COLLECTION__):
- step_state: scheduled
- Jobs
  - Job 1:
    - Job state is ok
    Traceback:
    Job Parameters:
    - Job parameter Parameter value
      
      __workflow_invocation_uuid__ "3306124adec511f180003833c5d96987"
      
      element_identifier None
      
      number "1"

Step 18: Relabel identifiers (__RELABEL_FROM_FILE__):

step_state: scheduled

Jobs

Job 1:

Job state is ok

Traceback:

Job Parameters:

Job parameter	Parameter value
__workflow_invocation_uuid__	`"3306124adec511f180003833c5d96987"`
how	`{"__current_case__": 0, "how_select": "txt", "labels": {"values": [{"id": 32, "src": "hda"}]}, "strict": false}`
input	`{"values": [{"id": 30, "src": "hdca"}]}`

Step 19: Match custom assemblies by group identifier (__HARMONIZELISTS__):
- step_state: scheduled
- Jobs
  - Job 1:
    - Job state is ok
    Traceback:
    Job Parameters:
    - Job parameter Parameter value
      
      __workflow_invocation_uuid__ "3306124adec511f180003833c5d96987"
      
      input1 {"values": [{"id": 31, "src": "hdca"}]}
      
      input2 None

Step 20: Pick the chosen assemblies (toolshed.g2.bx.psu.edu/repos/iuc/pick_value/pick_value/0.2.0):

step_state: scheduled

Jobs

Job 1:

Job state is ok

Command Line:

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

Exit Code:

```
0
```

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"input"`
__workflow_invocation_uuid__	`"3306124adec511f180003833c5d96987"`
chromInfo	`"/home/runner/work/_temp/tmpq9hj5k8k/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
dbkey	`"?"`
style_cond	`{"__current_case__": 2, "pick_style": "first_or_error", "type_cond": {"__current_case__": 4, "param_type": "data", "pick_from": [{"__index__": 0, "value": {"values": [{"id": 31, "src": "dce"}]}}, {"__index__": 1, "value": {"values": [{"id": 33, "src": "dce"}]}}, {"__index__": 2, "value": {"values": [{"id": 37, "src": "dce"}]}}]}}`

Step 21: Quast (toolshed.g2.bx.psu.edu/repos/iuc/quast/quast/5.3.0+galaxy2):

step_state: scheduled

Jobs

Job 1:

Job state is ok

Container:

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

Command Line:

echo test_minigut &&   ln -s '/home/runner/work/_temp/tmpq9hj5k8k/files/9/6/3/dataset_963cab8b-64d1-4bfd-872c-559e71c1d7fd.dat' 'pe1-test_minigut.fastqsanger.gz' && ln -s '/home/runner/work/_temp/tmpq9hj5k8k/files/9/5/e/dataset_95e758b0-fac1-4449-80ed-ee372252baab.dat' 'pe2-test_minigut.fastqsanger.gz' &&  metaquast  --pe1 'pe1-test_minigut.fastqsanger.gz' --pe2 'pe2-test_minigut.fastqsanger.gz' --labels 'test_minigut' -o 'outputdir'  --max-ref-num 0  --min-identity 90.0 --min-contig 500        --min-alignment 65 --ambiguity-usage 'one' --ambiguity-score 0.99   --local-mis-size 200   --contig-thresholds '0,1000'  --extensive-mis-size 1000 --scaffold-gap-max-size 1000 --unaligned-part-size 500   --x-for-Nx 90  '/home/runner/work/_temp/tmpq9hj5k8k/files/b/b/7/dataset_bb799924-6b78-4836-aaca-60df30fd7953.dat' --threads ${GALAXY_SLOTS:-1}   && if [[ -f "outputdir/report.tsv" ]]; then mkdir -p "outputdir/combined_reference/" && cp "outputdir/report.tsv" "outputdir/combined_reference/report.tsv"; fi && if [[ -f "outputdir/report.html" ]]; then mkdir -p "outputdir/combined_reference/" && cp outputdir/*.html "outputdir/combined_reference/"; fi && mkdir -p '/home/runner/work/_temp/tmpq9hj5k8k/job_working_directory/000/36/outputs/dataset_25f56e31-768e-4e93-94d2-11aaf34d22bc_files' && cp outputdir/combined_reference/*.html '/home/runner/work/_temp/tmpq9hj5k8k/job_working_directory/000/36/outputs/dataset_25f56e31-768e-4e93-94d2-11aaf34d22bc_files' && if [[ -d "outputdir/icarus_viewers" ]]; then cp -R outputdir/icarus_viewers 'outputdir/combined_reference/'; fi && if [[ -d "outputdir/combined_reference/icarus_viewers" ]]; then cp -R outputdir/combined_reference/icarus_viewers '/home/runner/work/_temp/tmpq9hj5k8k/job_working_directory/000/36/outputs/dataset_25f56e31-768e-4e93-94d2-11aaf34d22bc_files'; fi && if [[ -d "outputdir/krona_charts/" ]]; then mkdir -p '/home/runner/work/_temp/tmpq9hj5k8k/job_working_directory/000/36/outputs/dataset_e766899c-ade2-46bb-b6dc-3a506eed23ba_files' && cp outputdir/krona_charts/*.html '/home/runner/work/_temp/tmpq9hj5k8k/job_working_directory/000/36/outputs/dataset_e766899c-ade2-46bb-b6dc-3a506eed23ba_files'; fi

Exit Code:

```
0
```

Standard Output:

test_minigut
/usr/local/opt/quast-5.3.0/metaquast.py --pe1 pe1-test_minigut.fastqsanger.gz --pe2 pe2-test_minigut.fastqsanger.gz --labels test_minigut -o outputdir --max-ref-num 0 --min-identity 90.0 --min-contig 500 --min-alignment 65 --ambiguity-usage one --ambiguity-score 0.99 --local-mis-size 200 --contig-thresholds 0,1000 --extensive-mis-size 1000 --scaffold-gap-max-size 1000 --unaligned-part-size 500 --x-for-Nx 90 /home/runner/work/_temp/tmpq9hj5k8k/files/b/b/7/dataset_bb799924-6b78-4836-aaca-60df30fd7953.dat --threads 1

Version: 5.3.0

System information:
  OS: Linux-7.0.0-1019-azure-x86_64-with-glibc2.36 (linux_64)
  Python version: 3.12.3
  CPUs number: 4

Started: 2026-11-12 20:26:28

Logging to /home/runner/work/_temp/tmpq9hj5k8k/job_working_directory/000/36/working/outputdir/metaquast.log
WARNING: --ambiguity-usage was set to 'all' because not default --ambiguity-score was specified
INFO	generated new fontManager
INFO	generated new fontManager

Contigs:
  Pre-processing...
  /home/runner/work/_temp/tmpq9hj5k8k/files/b/b/7/dataset_bb799924-6b78-4836-aaca-60df30fd7953.dat ==> test_minigut

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

NOTICE: No references are provided, starting regular QUAST with MetaGeneMark gene finder
/usr/local/opt/quast-5.3.0/quast.py --pe1 pe1-test_minigut.fastqsanger.gz --pe2 pe2-test_minigut.fastqsanger.gz --min-identity 90.0 --min-contig 500 --min-alignment 65 --ambiguity-usage one --ambiguity-score 0.99 --local-mis-size 200 --contig-thresholds 0,1000 --extensive-mis-size 1000 --scaffold-gap-max-size 1000 --unaligned-part-size 500 --x-for-Nx 90 --threads 1 /home/runner/work/_temp/tmpq9hj5k8k/files/b/b/7/dataset_bb799924-6b78-4836-aaca-60df30fd7953.dat -o /home/runner/work/_temp/tmpq9hj5k8k/job_working_directory/000/36/working/outputdir --labels test_minigut

Version: 5.3.0

System information:
  OS: Linux-7.0.0-1019-azure-x86_64-with-glibc2.36 (linux_64)
  Python version: 3.12.3
  CPUs number: 4

Started: 2026-11-12 20:26:29

Logging to /home/runner/work/_temp/tmpq9hj5k8k/job_working_directory/000/36/working/outputdir/quast.log
NOTICE: Output directory already exists and looks like a QUAST output dir. Existing results can be reused (e.g. previously generated alignments)!
WARNING: --ambiguity-usage was set to 'all' because not default --ambiguity-score was specified

CWD: /home/runner/work/_temp/tmpq9hj5k8k/job_working_directory/000/36/working
Main parameters: 
  MODE: meta, threads: 1, min contig length: 500, min alignment length: 65, min alignment IDY: 90.0, \
  ambiguity: all, min local misassembly length: 200, min extensive misassembly length: 1000

Contigs:
  Pre-processing...
  /home/runner/work/_temp/tmpq9hj5k8k/files/b/b/7/dataset_bb799924-6b78-4836-aaca-60df30fd7953.dat ==> test_minigut

2026-11-12 20:26:29
Running Reads analyzer...
NOTICE: Permission denied accessing /usr/local/lib/python3.12/site-packages/quast_libs/gridss. GRIDSS will be downloaded to home directory /home/runner/work/_temp/tmpq9hj5k8k/job_working_directory/000/36/home/.quast
Downloading gridss (file: gridss-1.4.1.jar)...
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gridss successfully downloaded!
  Logging to files /home/runner/work/_temp/tmpq9hj5k8k/job_working_directory/000/36/working/outputdir/reads_stats/reads_stats.log and /home/runner/work/_temp/tmpq9hj5k8k/job_working_directory/000/36/working/outputdir/reads_stats/reads_stats.err...
  Pre-processing reads...
  Running BWA...
  Done.
  Sorting SAM-file...
  Analysis is finished.
  Creating total report...
    saved to /home/runner/work/_temp/tmpq9hj5k8k/job_working_directory/000/36/working/outputdir/reads_stats/reads_report.txt, reads_report.tsv, and reads_report.tex
Done.

2026-11-12 20:26:42
Running Basic statistics processor...
  Contig files: 
    test_minigut
  Calculating N50 and L50...
    test_minigut, N50 = 169988, L50 = 2, auN = 350583.0, Total length = 1741556, GC % = 47.38, # N's per 100 kbp =  0.00
  Drawing Nx plot...
    saved to /home/runner/work/_temp/tmpq9hj5k8k/job_working_directory/000/36/working/outputdir/basic_stats/Nx_plot.pdf
  Drawing cumulative plot...
    saved to /home/runner/work/_temp/tmpq9hj5k8k/job_working_directory/000/36/working/outputdir/basic_stats/cumulative_plot.pdf
  Drawing GC content plot...
    saved to /home/runner/work/_temp/tmpq9hj5k8k/job_working_directory/000/36/working/outputdir/basic_stats/GC_content_plot.pdf
  Drawing test_minigut GC content plot...
    saved to /home/runner/work/_temp/tmpq9hj5k8k/job_working_directory/000/36/working/outputdir/basic_stats/test_minigut_GC_content_plot.pdf
  Drawing Coverage histogram (bin size: 1x)...
    saved to /home/runner/work/_temp/tmpq9hj5k8k/job_working_directory/000/36/working/outputdir/basic_stats/coverage_histogram.pdf
  Drawing test_minigut coverage histogram (bin size: 1x)...
    saved to /home/runner/work/_temp/tmpq9hj5k8k/job_working_directory/000/36/working/outputdir/basic_stats/test_minigut_coverage_histogram.pdf
Done.

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

2026-11-12 20:26:43
Creating large visual summaries...
This may take a while: press Ctrl-C to skip this step..
  1 of 2: Creating PDF with all tables and plots...
  2 of 2: Creating Icarus viewers...
Done

2026-11-12 20:26:44
RESULTS:
  Text versions of total report are saved to /home/runner/work/_temp/tmpq9hj5k8k/job_working_directory/000/36/working/outputdir/report.txt, report.tsv, and report.tex
  Text versions of transposed total report are saved to /home/runner/work/_temp/tmpq9hj5k8k/job_working_directory/000/36/working/outputdir/transposed_report.txt, transposed_report.tsv, and transposed_report.tex
  HTML version (interactive tables and plots) is saved to /home/runner/work/_temp/tmpq9hj5k8k/job_working_directory/000/36/working/outputdir/report.html
  PDF version (tables and plots) is saved to /home/runner/work/_temp/tmpq9hj5k8k/job_working_directory/000/36/working/outputdir/report.pdf
  Icarus (contig browser) is saved to /home/runner/work/_temp/tmpq9hj5k8k/job_working_directory/000/36/working/outputdir/icarus.html
  Log is saved to /home/runner/work/_temp/tmpq9hj5k8k/job_working_directory/000/36/working/outputdir/quast.log

Finished: 2026-11-12 20:26:44
Elapsed time: 0:00:15.017027
NOTICEs: 3; WARNINGs: 1; non-fatal ERRORs: 0

Thank you for using QUAST!

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"input"`
__workflow_invocation_uuid__	`"3306124adec511f180003833c5d96987"`
advanced	`{"contig_thresholds": "0,1000", "extensive_mis_size": "1000", "fragmented_max_indent": null, "report_all_metrics": false, "scaffold_gap_max_size": "1000", "skip_unaligned_mis_contigs": true, "strict_NA": false, "unaligned_part_size": "500", "x_for_Nx": "90"}`
alignments	`{"ambiguity_score": "0.99", "ambiguity_usage": "one", "fragmented": false, "local_mis_size": "200", "min_alignment": "65", "upper_bound_assembly": false, "upper_bound_min_con": null, "use_all_alignments": false}`
assembly	`{"__current_case__": 1, "min_identity": "90.0", "ref": {"__current_case__": 0, "max_ref_num": "0", "origin": "silva"}, "reuse_combined_alignments": false, "type": "metagenome"}`
chromInfo	`"/home/runner/work/_temp/tmpq9hj5k8k/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
dbkey	`"?"`
genes	`{"conserved_genes_finding": false, "gene_finding": {"__current_case__": 0, "tool": "none"}, "rna_finding": false}`
large	`false`
min_contig	`"500"`
mode	`{"__current_case__": 0, "in": {"__current_case__": 1, "custom": "false", "inputs": {"values": [{"id": 38, "src": "dce"}]}}, "mode": "individual", "reads": {"__current_case__": 2, "input_1": {"values": [{"id": 27, "src": "dce"}]}, "input_2": {"values": [{"id": 28, "src": "dce"}]}, "reads_option": "paired"}}`
output_files	`["html", "krona", "summary", "log", "pdf", "tabular"]`
split_scaffolds	`false`

Other invocation details
- history_id
  - da83f302725b3a85
- history_state
  - ok
- invocation_id
  - da83f302725b3a85
- invocation_state
  - scheduled
- workflow_id
  - 6d1c4cf83da0921e

✅ metagenomic-assembly.ga_2

Workflow invocation details

Invocation Messages

Steps

Step 1: create text file (toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_text_file_with_recurring_lines/9.11+galaxy0):

step_state: scheduled

Jobs

Job 1:

Job state is ok

Container:

```
quay.io/biocontainers/coreutils:9.11
```

Command Line:

times=1; yes -- '' 2>/dev/null | head -n $times >> '/home/runner/work/_temp/tmpq9hj5k8k/job_working_directory/000/40/outputs/dataset_d099db4b-2915-4fbe-8dcd-e90fdce96440.dat';

Exit Code:

```
0
```

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"input"`
__workflow_invocation_uuid__	`"b5560646dec611f180003833c5d96987"`
chromInfo	`"/home/runner/work/_temp/tmpq9hj5k8k/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
dbkey	`"?"`
token_set	`[{"__index__": 0, "line": null, "repeat_select": {"__current_case__": 0, "repeat_select_opts": "user", "times": "1"}}]`

Step 2: Trimmed paired reads from grouped samples:
- step_state: scheduled
Step 3: Trimmed nanopore reads from grouped samples:
- step_state: scheduled
Step 4: Trimmed PacBio reads from grouped samples:
- step_state: scheduled
Step 5: Choose Assembler:
- step_state: scheduled
Step 6: Minimum length of contigs to output:
- step_state: scheduled
Step 7: Custom Assemblies:
- step_state: scheduled

Step 8: Select (Grep1):

step_state: scheduled

Jobs

Job 1:

Job state is ok

Container:

quay.io/biocontainers/grep:3.4--hf43ccf4_4

Command Line:

set -eo pipefail; cat '/home/runner/work/_temp/tmpq9hj5k8k/files/d/0/9/dataset_d099db4b-2915-4fbe-8dcd-e90fdce96440.dat' | grep -P -f '/home/runner/work/_temp/tmpq9hj5k8k/job_working_directory/000/41/configs/tmpmf6auhh_'  >> '/home/runner/work/_temp/tmpq9hj5k8k/job_working_directory/000/41/outputs/dataset_a9bbf061-df02-4d8b-a4e1-c8cbf9dcedd2.dat'

Exit Code:

```
1
```

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"input"`
__workflow_invocation_uuid__	`"b5560646dec611f180003833c5d96987"`
chromInfo	`"/home/runner/work/_temp/tmpq9hj5k8k/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
dbkey	`"?"`
invert	`""`
keep_header	`false`
pattern	`"^chr([0-9A-Za-z])+"`

Step 9: Extract reads element identifiers (toolshed.g2.bx.psu.edu/repos/iuc/collection_element_identifiers/collection_element_identifiers/0.0.3):

step_state: scheduled

Jobs

Job 1:

Job state is ok

Command Line:

mv '/home/runner/work/_temp/tmpq9hj5k8k/job_working_directory/000/42/configs/tmpa5aguzxn' '/home/runner/work/_temp/tmpq9hj5k8k/job_working_directory/000/42/outputs/dataset_eda5ecdb-59ce-4ef0-9111-e93219944099.dat'

Exit Code:

```
0
```

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"input"`
__workflow_invocation_uuid__	`"b5560646dec611f180003833c5d96987"`
chromInfo	`"/home/runner/work/_temp/tmpq9hj5k8k/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
dbkey	`"?"`
input_collection	`{"values": [{"id": 41, "src": "hdca"}]}`

Step 10: Unzip paired reads (__UNZIP_COLLECTION__):
- step_state: scheduled
- Jobs
  - Job 1:
    - Job state is ok
    Traceback:
    Job Parameters:
    - Job parameter Parameter value
      
      __workflow_invocation_uuid__ "b5560646dec611f180003833c5d96987"
      
      input {"values": [{"id": 45, "src": "dce"}]}

Step 11: Run metaSPAdes? (toolshed.g2.bx.psu.edu/repos/iuc/map_param_value/map_param_value/0.2.0):

step_state: scheduled

Jobs

Job 1:

Job state is ok

Command Line:

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

Exit Code:

```
0
```

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"input"`
__workflow_invocation_uuid__	`"b5560646dec611f180003833c5d96987"`
chromInfo	`"/home/runner/work/_temp/tmpq9hj5k8k/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
dbkey	`"?"`
input_param_type	`{"__current_case__": 0, "input_param": "Custom Assembly", "mappings": [{"__index__": 0, "from": "metaSPAdes", "to": "True"}], "type": "text"}`
output_param_type	`"boolean"`
unmapped	`{"__current_case__": 2, "default_value": "False", "on_unmapped": "default"}`

Step 12: Run MEGAHIT? (toolshed.g2.bx.psu.edu/repos/iuc/map_param_value/map_param_value/0.2.0):

step_state: scheduled

Jobs

Job 1:

Job state is ok

Command Line:

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

Exit Code:

```
0
```

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"input"`
__workflow_invocation_uuid__	`"b5560646dec611f180003833c5d96987"`
chromInfo	`"/home/runner/work/_temp/tmpq9hj5k8k/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
dbkey	`"?"`
input_param_type	`{"__current_case__": 0, "input_param": "Custom Assembly", "mappings": [{"__index__": 0, "from": "MEGAHIT", "to": "True"}], "type": "text"}`
output_param_type	`"boolean"`
unmapped	`{"__current_case__": 2, "default_value": "False", "on_unmapped": "default"}`

Step 13: Count number of samples (wc_gnu):

step_state: scheduled

Jobs

Job 1:

Job state is ok

Command Line:

cat '/home/runner/work/_temp/tmpq9hj5k8k/files/e/d/a/dataset_eda5ecdb-59ce-4ef0-9111-e93219944099.dat' | wc -l | awk '{ print $1 }' >> /home/runner/work/_temp/tmpq9hj5k8k/job_working_directory/000/46/outputs/dataset_d264790b-0b0e-4d54-86b0-7cfe5980c516.dat

Exit Code:

```
0
```

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"txt"`
__workflow_invocation_uuid__	`"b5560646dec611f180003833c5d96987"`
chromInfo	`"/home/runner/work/_temp/tmpq9hj5k8k/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
dbkey	`"?"`
include_header	`false`
options	`["lines"]`

Step 14: metaSPAdes (toolshed.g2.bx.psu.edu/repos/nml/metaspades/metaspades/4.3.0+galaxy3):

step_state: scheduled

Jobs

Job 1:

Job state is skipped

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"input"`
__workflow_invocation_uuid__	`"b5560646dec611f180003833c5d96987"`
chromInfo	`"/home/runner/work/_temp/tmpq9hj5k8k/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
dbkey	`"?"`
file_processing	`{"__current_case__": 1, "additional_reads": {"__current_case__": 1, "selector": "false"}, "arf": {"nanopore": null, "pacbio": null}, "is_select": "individual", "library_number": "true", "singlePaired": {"__current_case__": 1, "input": {"values": [{"id": 45, "src": "dce"}]}, "orientation": "fr", "sPaired": "paired_collection", "type_paired": "pe"}}`
kmer_cond	`{"__current_case__": 0, "kmer_sel": "auto"}`
mode_sel	`None`
optional_output	`["ag", "ags", "cn", "sc"]`
phred_offset	`"auto"`

Step 15: MEGAHIT (toolshed.g2.bx.psu.edu/repos/iuc/megahit/megahit/1.2.9+galaxy2):

step_state: scheduled

Jobs

Job 1:

Job state is skipped

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"fastqsanger"`
__workflow_invocation_uuid__	`"b5560646dec611f180003833c5d96987"`
advanced_section	`{"bubble_level": "2", "cleaning_rounds": "5", "disconnect_ratio": "0.1", "kmin1pass": false, "low_local_ratio": "0.2", "merge_level": "20,0.95", "nolocal": false, "nomercy": false, "prune_depth": "2", "prune_level": "2"}`
basic_section	`{"k_mer": {"__current_case__": 0, "k_list": "21,29,39,59,79,99,119,141", "k_mer_method": "klist_method"}, "min_count": "2"}`
chromInfo	`"/home/runner/work/_temp/tmpq9hj5k8k/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
dbkey	`"?"`
input_option	`{"__current_case__": 3, "batchmode": {"__current_case__": 0, "pair_input": {"values": [{"id": 45, "src": "dce"}]}, "processmode": "individual"}, "choice": "paired_collection"}`
output_section	`{"log_file": false, "min_contig_len": "200", "show_intermediate_contigs": false}`

Step 16: Parse the number of samples (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	`"input"`
__workflow_invocation_uuid__	`"b5560646dec611f180003833c5d96987"`
chromInfo	`"/home/runner/work/_temp/tmpq9hj5k8k/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
dbkey	`"?"`
param_type	`"integer"`
remove_newlines	`true`

Step 17: Duplicate file to collection (__DUPLICATE_FILE_TO_COLLECTION__):
- step_state: scheduled
- Jobs
  - Job 1:
    - Job state is ok
    Traceback:
    Job Parameters:
    - Job parameter Parameter value
      
      __workflow_invocation_uuid__ "b5560646dec611f180003833c5d96987"
      
      element_identifier None
      
      number "1"

Step 18: Relabel identifiers (__RELABEL_FROM_FILE__):

step_state: scheduled

Jobs

Job 1:

Job state is ok

Traceback:

Job Parameters:

Job parameter	Parameter value
__workflow_invocation_uuid__	`"b5560646dec611f180003833c5d96987"`
how	`{"__current_case__": 0, "how_select": "txt", "labels": {"values": [{"id": 58, "src": "hda"}]}, "strict": false}`
input	`{"values": [{"id": 50, "src": "hdca"}]}`

Step 19: Match custom assemblies by group identifier (__HARMONIZELISTS__):

step_state: scheduled

Jobs

Job 1:

Job state is ok

Traceback:

Job Parameters:

Job parameter	Parameter value
__workflow_invocation_uuid__	`"b5560646dec611f180003833c5d96987"`
input1	`{"values": [{"id": 51, "src": "hdca"}]}`
input2	`{"values": [{"id": 42, "src": "hdca"}]}`

Step 20: Pick the chosen assemblies (toolshed.g2.bx.psu.edu/repos/iuc/pick_value/pick_value/0.2.0):

step_state: scheduled

Jobs

Job 1:

Job state is ok

Command Line:

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

Exit Code:

```
0
```

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"input"`
__workflow_invocation_uuid__	`"b5560646dec611f180003833c5d96987"`
chromInfo	`"/home/runner/work/_temp/tmpq9hj5k8k/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
dbkey	`"?"`
style_cond	`{"__current_case__": 2, "pick_style": "first_or_error", "type_cond": {"__current_case__": 4, "param_type": "data", "pick_from": [{"__index__": 0, "value": {"values": [{"id": 53, "src": "dce"}]}}, {"__index__": 1, "value": {"values": [{"id": 55, "src": "dce"}]}}, {"__index__": 2, "value": {"values": [{"id": 59, "src": "dce"}]}}]}}`

Step 21: Quast (toolshed.g2.bx.psu.edu/repos/iuc/quast/quast/5.3.0+galaxy2):

step_state: scheduled

Jobs

Job 1:

Job state is ok

Container:

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

Command Line:

echo marine_pooled &&   ln -s '/home/runner/work/_temp/tmpq9hj5k8k/files/3/c/e/dataset_3cef3e91-b077-4fc3-b422-c0a430856022.dat' 'pe1-marine_pooled.fastqsanger' && ln -s '/home/runner/work/_temp/tmpq9hj5k8k/files/c/5/c/dataset_c5c38b7b-91e7-4b70-9023-726b03277ce8.dat' 'pe2-marine_pooled.fastqsanger' &&  metaquast  --pe1 'pe1-marine_pooled.fastqsanger' --pe2 'pe2-marine_pooled.fastqsanger' --labels 'marine_pooled' -o 'outputdir'  --max-ref-num 0  --min-identity 90.0 --min-contig 500        --min-alignment 65 --ambiguity-usage 'one' --ambiguity-score 0.99   --local-mis-size 200   --contig-thresholds '0,1000'  --extensive-mis-size 1000 --scaffold-gap-max-size 1000 --unaligned-part-size 500   --x-for-Nx 90  '/home/runner/work/_temp/tmpq9hj5k8k/files/4/9/7/dataset_497fbc7c-c2c1-493e-aaba-e0a3d130b0ba.dat' --threads ${GALAXY_SLOTS:-1}   && if [[ -f "outputdir/report.tsv" ]]; then mkdir -p "outputdir/combined_reference/" && cp "outputdir/report.tsv" "outputdir/combined_reference/report.tsv"; fi && if [[ -f "outputdir/report.html" ]]; then mkdir -p "outputdir/combined_reference/" && cp outputdir/*.html "outputdir/combined_reference/"; fi && mkdir -p '/home/runner/work/_temp/tmpq9hj5k8k/job_working_directory/000/54/outputs/dataset_6361e47a-d377-42dc-9517-f5fbf83c3450_files' && cp outputdir/combined_reference/*.html '/home/runner/work/_temp/tmpq9hj5k8k/job_working_directory/000/54/outputs/dataset_6361e47a-d377-42dc-9517-f5fbf83c3450_files' && if [[ -d "outputdir/icarus_viewers" ]]; then cp -R outputdir/icarus_viewers 'outputdir/combined_reference/'; fi && if [[ -d "outputdir/combined_reference/icarus_viewers" ]]; then cp -R outputdir/combined_reference/icarus_viewers '/home/runner/work/_temp/tmpq9hj5k8k/job_working_directory/000/54/outputs/dataset_6361e47a-d377-42dc-9517-f5fbf83c3450_files'; fi && if [[ -d "outputdir/krona_charts/" ]]; then mkdir -p '/home/runner/work/_temp/tmpq9hj5k8k/job_working_directory/000/54/outputs/dataset_d6db058e-0057-45b2-b6e8-78daae747470_files' && cp outputdir/krona_charts/*.html '/home/runner/work/_temp/tmpq9hj5k8k/job_working_directory/000/54/outputs/dataset_d6db058e-0057-45b2-b6e8-78daae747470_files'; fi

Exit Code:

```
0
```

Standard Output:

marine_pooled
/usr/local/opt/quast-5.3.0/metaquast.py --pe1 pe1-marine_pooled.fastqsanger --pe2 pe2-marine_pooled.fastqsanger --labels marine_pooled -o outputdir --max-ref-num 0 --min-identity 90.0 --min-contig 500 --min-alignment 65 --ambiguity-usage one --ambiguity-score 0.99 --local-mis-size 200 --contig-thresholds 0,1000 --extensive-mis-size 1000 --scaffold-gap-max-size 1000 --unaligned-part-size 500 --x-for-Nx 90 /home/runner/work/_temp/tmpq9hj5k8k/files/4/9/7/dataset_497fbc7c-c2c1-493e-aaba-e0a3d130b0ba.dat --threads 1

Version: 5.3.0

System information:
  OS: Linux-7.0.0-1019-azure-x86_64-with-glibc2.36 (linux_64)
  Python version: 3.12.3
  CPUs number: 4

Started: 2026-11-12 20:28:47

Logging to /home/runner/work/_temp/tmpq9hj5k8k/job_working_directory/000/54/working/outputdir/metaquast.log
WARNING: --ambiguity-usage was set to 'all' because not default --ambiguity-score was specified
INFO	generated new fontManager
INFO	generated new fontManager

Contigs:
  Pre-processing...
  /home/runner/work/_temp/tmpq9hj5k8k/files/4/9/7/dataset_497fbc7c-c2c1-493e-aaba-e0a3d130b0ba.dat ==> marine_pooled

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

NOTICE: No references are provided, starting regular QUAST with MetaGeneMark gene finder
/usr/local/opt/quast-5.3.0/quast.py --pe1 pe1-marine_pooled.fastqsanger --pe2 pe2-marine_pooled.fastqsanger --min-identity 90.0 --min-contig 500 --min-alignment 65 --ambiguity-usage one --ambiguity-score 0.99 --local-mis-size 200 --contig-thresholds 0,1000 --extensive-mis-size 1000 --scaffold-gap-max-size 1000 --unaligned-part-size 500 --x-for-Nx 90 --threads 1 /home/runner/work/_temp/tmpq9hj5k8k/files/4/9/7/dataset_497fbc7c-c2c1-493e-aaba-e0a3d130b0ba.dat -o /home/runner/work/_temp/tmpq9hj5k8k/job_working_directory/000/54/working/outputdir --labels marine_pooled

Version: 5.3.0

System information:
  OS: Linux-7.0.0-1019-azure-x86_64-with-glibc2.36 (linux_64)
  Python version: 3.12.3
  CPUs number: 4

Started: 2026-11-12 20:28:48

Logging to /home/runner/work/_temp/tmpq9hj5k8k/job_working_directory/000/54/working/outputdir/quast.log
NOTICE: Output directory already exists and looks like a QUAST output dir. Existing results can be reused (e.g. previously generated alignments)!
WARNING: --ambiguity-usage was set to 'all' because not default --ambiguity-score was specified

CWD: /home/runner/work/_temp/tmpq9hj5k8k/job_working_directory/000/54/working
Main parameters: 
  MODE: meta, threads: 1, min contig length: 500, min alignment length: 65, min alignment IDY: 90.0, \
  ambiguity: all, min local misassembly length: 200, min extensive misassembly length: 1000

Contigs:
  Pre-processing...
  /home/runner/work/_temp/tmpq9hj5k8k/files/4/9/7/dataset_497fbc7c-c2c1-493e-aaba-e0a3d130b0ba.dat ==> marine_pooled

2026-11-12 20:28:48
Running Reads analyzer...
NOTICE: Permission denied accessing /usr/local/lib/python3.12/site-packages/quast_libs/gridss. GRIDSS will be downloaded to home directory /home/runner/work/_temp/tmpq9hj5k8k/job_working_directory/000/54/home/.quast
Downloading gridss (file: gridss-1.4.1.jar)...
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gridss successfully downloaded!
  Logging to files /home/runner/work/_temp/tmpq9hj5k8k/job_working_directory/000/54/working/outputdir/reads_stats/reads_stats.log and /home/runner/work/_temp/tmpq9hj5k8k/job_working_directory/000/54/working/outputdir/reads_stats/reads_stats.err...
  Pre-processing reads...
  Running BWA...
  Done.
  Sorting SAM-file...
  Analysis is finished.
  Creating total report...
    saved to /home/runner/work/_temp/tmpq9hj5k8k/job_working_directory/000/54/working/outputdir/reads_stats/reads_report.txt, reads_report.tsv, and reads_report.tex
Done.

2026-11-12 20:28:58
Running Basic statistics processor...
  Contig files: 
    marine_pooled
  Calculating N50 and L50...
    marine_pooled, N50 = 3061548, L50 = 2, auN = 2822448.5, Total length = 13347801, GC % = 43.16, # N's per 100 kbp =  0.60
  Drawing Nx plot...
    saved to /home/runner/work/_temp/tmpq9hj5k8k/job_working_directory/000/54/working/outputdir/basic_stats/Nx_plot.pdf
  Drawing cumulative plot...
    saved to /home/runner/work/_temp/tmpq9hj5k8k/job_working_directory/000/54/working/outputdir/basic_stats/cumulative_plot.pdf
  Drawing GC content plot...
    saved to /home/runner/work/_temp/tmpq9hj5k8k/job_working_directory/000/54/working/outputdir/basic_stats/GC_content_plot.pdf
  Drawing marine_pooled GC content plot...
    saved to /home/runner/work/_temp/tmpq9hj5k8k/job_working_directory/000/54/working/outputdir/basic_stats/marine_pooled_GC_content_plot.pdf
Done.

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

2026-11-12 20:28:59
Creating large visual summaries...
This may take a while: press Ctrl-C to skip this step..
  1 of 2: Creating PDF with all tables and plots...
  2 of 2: Creating Icarus viewers...
Done

2026-11-12 20:28:59
RESULTS:
  Text versions of total report are saved to /home/runner/work/_temp/tmpq9hj5k8k/job_working_directory/000/54/working/outputdir/report.txt, report.tsv, and report.tex
  Text versions of transposed total report are saved to /home/runner/work/_temp/tmpq9hj5k8k/job_working_directory/000/54/working/outputdir/transposed_report.txt, transposed_report.tsv, and transposed_report.tex
  HTML version (interactive tables and plots) is saved to /home/runner/work/_temp/tmpq9hj5k8k/job_working_directory/000/54/working/outputdir/report.html
  PDF version (tables and plots) is saved to /home/runner/work/_temp/tmpq9hj5k8k/job_working_directory/000/54/working/outputdir/report.pdf
  Icarus (contig browser) is saved to /home/runner/work/_temp/tmpq9hj5k8k/job_working_directory/000/54/working/outputdir/icarus.html
  Log is saved to /home/runner/work/_temp/tmpq9hj5k8k/job_working_directory/000/54/working/outputdir/quast.log

Finished: 2026-11-12 20:28:59
Elapsed time: 0:00:10.837047
NOTICEs: 3; WARNINGs: 1; non-fatal ERRORs: 0

Thank you for using QUAST!

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"input"`
__workflow_invocation_uuid__	`"b5560646dec611f180003833c5d96987"`
advanced	`{"contig_thresholds": "0,1000", "extensive_mis_size": "1000", "fragmented_max_indent": null, "report_all_metrics": false, "scaffold_gap_max_size": "1000", "skip_unaligned_mis_contigs": true, "strict_NA": false, "unaligned_part_size": "500", "x_for_Nx": "90"}`
alignments	`{"ambiguity_score": "0.99", "ambiguity_usage": "one", "fragmented": false, "local_mis_size": "200", "min_alignment": "65", "upper_bound_assembly": false, "upper_bound_min_con": null, "use_all_alignments": false}`
assembly	`{"__current_case__": 1, "min_identity": "90.0", "ref": {"__current_case__": 0, "max_ref_num": "0", "origin": "silva"}, "reuse_combined_alignments": false, "type": "metagenome"}`
chromInfo	`"/home/runner/work/_temp/tmpq9hj5k8k/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
dbkey	`"?"`
genes	`{"conserved_genes_finding": false, "gene_finding": {"__current_case__": 0, "tool": "none"}, "rna_finding": false}`
large	`false`
min_contig	`"500"`
mode	`{"__current_case__": 0, "in": {"__current_case__": 1, "custom": "false", "inputs": {"values": [{"id": 60, "src": "dce"}]}}, "mode": "individual", "reads": {"__current_case__": 2, "input_1": {"values": [{"id": 49, "src": "dce"}]}, "input_2": {"values": [{"id": 50, "src": "dce"}]}, "reads_option": "paired"}}`
output_files	`["html", "krona", "summary", "log", "pdf", "tabular"]`
split_scaffolds	`false`

Other invocation details
- history_id
  - 2f9999c32f71de26
- history_state
  - ok
- invocation_id
  - 2f9999c32f71de26
- invocation_state
  - scheduled
- workflow_id
  - 6d1c4cf83da0921e

….3.0+galaxy3 in co mode

paulzierep added 2 commits November 11, 2026 21:08

metagenomic-assembly: run metaSPAdes 4.3.0+galaxy3 per group in indiv…

4fd41a8

…idual mode

metagenomic-assembly: pin the nml/metaspades repository revision

c446ef6

paulzierep requested a review from SantaMcCloud as a code owner November 12, 2026 19:29

paulzierep mentioned this pull request Nov 12, 2026

Modularize MAG generation with read grouping and selectable binning strategies #1454

Open

4 of 13 tasks

Point content_id at the updated tool versions

a17fd21

paulzierep added 2 commits November 13, 2026 07:20

metagenomic-assembly: give long reads for every group in the tests

484f688

metagenomic-assembly: keep the per-group nesting and run metaSPAdes 4…

df3e787

….3.0+galaxy3 in co mode

paulzierep changed the title ~~metagenomic-assembly: run metaSPAdes 4.3.0 per group in individual mode~~ metagenomic-assembly: update metaSPAdes to 4.3.0+galaxy3 Nov 13, 2026

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metagenomic-assembly: update metaSPAdes to 4.3.0+galaxy3 - #1545

metagenomic-assembly: update metaSPAdes to 4.3.0+galaxy3#1545
paulzierep wants to merge 5 commits into
galaxyproject:mainfrom
paulzierep:metaspades-individual-assembly

paulzierep commented Nov 12, 2026 •

edited

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