Updating workflows/VGP-assembly-v2/Assembly-decontamination-VGP9 from 0.3 to 0.4 by gxydevbot · Pull Request #572 · galaxyproject/iwc

gxydevbot · 2024-10-14T04:23:22Z

Hello! This is an automated update of the following workflow: workflows/VGP-assembly-v2/Assembly-decontamination-VGP9. I created this PR because I think one or more of the component tools are out of date, i.e. there is a newer version available on the ToolShed.

By comparing with the latest versions available on the ToolShed, it seems the following tools are outdated:

toolshed.g2.bx.psu.edu/repos/bgruening/gfastats/gfastats/1.3.6+galaxy0 should be updated to toolshed.g2.bx.psu.edu/repos/bgruening/gfastats/gfastats/1.3.8+galaxy0

The workflow release number has been updated from 0.3 to 0.4.

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

github-actions · 2024-10-14T04:36:28Z

Test Results (powered by Planemo)

Test Summary

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

Passed Tests

✅ Assembly-decontamination-VGP9.ga_0

Workflow invocation details

Invocation Messages

Steps

Step 1: Scaffolded assembly (fasta):
- step_state: scheduled
Step 2: Database for Kraken2:
- step_state: scheduled

Step 11: concatenate scaffold lists:

step_state: scheduled

Jobs

Job 1:

Job state is ok

Command Line:

cat '/tmp/tmpm36tshk2/files/5/3/f/dataset_53fc7098-302b-4a89-aada-ef86a607b6bb.dat' >> '/tmp/tmpm36tshk2/job_working_directory/000/10/outputs/dataset_be97d550-6f41-40d0-9248-7afd6365b97a.dat' && cat '/tmp/tmpm36tshk2/files/d/7/a/dataset_d7a043b6-b8fa-4c30-ac0c-985a70c450df.dat' >> '/tmp/tmpm36tshk2/job_working_directory/000/10/outputs/dataset_be97d550-6f41-40d0-9248-7afd6365b97a.dat' && exit 0

Exit Code:

```
0
```

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"input"`
__workflow_invocation_uuid__	`"edfc915689e411efb621000d3a38214b"`
chromInfo	`"/tmp/tmpm36tshk2/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
dbkey	`"?"`
queries	`[]`

**Step 12: removing scaffolds **:

step_state: scheduled

Jobs

Job 1:

Job state is ok

Command Line:

gfastats '/tmp/tmpm36tshk2/files/c/8/0/dataset_c8036db4-7b6a-4d7d-a325-488b34e5bfce.dat'  --exclude-bed /tmp/tmpm36tshk2/files/b/e/9/dataset_be97d550-6f41-40d0-9248-7afd6365b97a.dat   -o dataset.fasta.gz --threads ${GALAXY_SLOTS:-8} && mv dataset* output_dataset

Exit Code:

```
0
```

Standard Output:

+++Assembly summary+++: 
# scaffolds: 0
Total scaffold length: 0
Average scaffold length: nan
Scaffold N50: 0
Scaffold auN: 0.00
Scaffold L50: 0
Largest scaffold: 0
Smallest scaffold: 0
# contigs: 0
Total contig length: 0
Average contig length: nan
Contig N50: 0
Contig auN: 0.00
Contig L50: 0
Largest contig: 0
Smallest contig: 0
# gaps in scaffolds: 0
Total gap length in scaffolds: 0
Average gap length in scaffolds: 0.00
Gap N50 in scaffolds: 0
Gap auN in scaffolds: 0.00
Gap L50 in scaffolds: 0
Largest gap in scaffolds: 0
Smallest gap in scaffolds: 0
Base composition (A:C:G:T): 0:0:0:0
GC content %: 0.00
# soft-masked bases: 0
# segments: 0
Total segment length: 0
Average segment length: nan
# gaps: 0
# paths: 0

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"input"`
__workflow_invocation_uuid__	`"edfc915689e411efb621000d3a38214b"`
chromInfo	`"/tmp/tmpm36tshk2/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
dbkey	`"?"`
mode_condition	`{"__current_case__": 0, "discover_paths": false, "homopolymer_compress": null, "output_condition": {"__current_case__": 1, "line_length": null, "out_format": "fasta.gz"}, "remove_terminal_gaps": false, "selector": "manipulation", "sort": "", "swiss_army_knife": null}`
target_condition	`{"__current_case__": 1, "exclude_bed": {"values": [{"id": 13, "src": "hda"}]}, "include_bed": null, "target_option": "true", "target_sequence": ""}`

**Step 3: soft-masking **:

step_state: scheduled

Jobs

Job 1:

Job state is ok

Command Line:

dustmasker -in '/tmp/tmpm36tshk2/files/c/8/0/dataset_c8036db4-7b6a-4d7d-a325-488b34e5bfce.dat' -infmt fasta -out '/tmp/tmpm36tshk2/job_working_directory/000/2/outputs/dataset_a29418e9-2758-40cc-bc87-3cf000ceee83.dat' -window 64 -level 40 -linker 1 -outfmt fasta

Exit Code:

```
0
```

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"fasta"`
__workflow_invocation_uuid__	`"edfc915689e411efb621000d3a38214b"`
chromInfo	`"/tmp/tmpm36tshk2/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
db_opts	`{"__current_case__": 2, "database": "", "db_opts_selector": "file", "histdb": "", "subject": {"values": [{"id": 1, "src": "hda"}]}}`
dbkey	`"?"`
level	`"40"`
linker	`"1"`
outformat	`"fasta"`
window	`"64"`

Step 4: hard-masking:

step_state: scheduled

Jobs

Job 1:

Job state is ok

Command Line:

sed --sandbox -r -f '/tmp/tmpm36tshk2/job_working_directory/000/3/configs/tmp5bp40fsu' '/tmp/tmpm36tshk2/files/a/2/9/dataset_a29418e9-2758-40cc-bc87-3cf000ceee83.dat' > '/tmp/tmpm36tshk2/job_working_directory/000/3/outputs/dataset_c4d0e10f-93d3-46a9-99bb-b8b608bfc949.dat'

Exit Code:

```
0
```

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"input"`
__workflow_invocation_uuid__	`"edfc915689e411efb621000d3a38214b"`
adv_opts	`{"__current_case__": 0, "adv_opts_selector": "basic"}`
chromInfo	`"/tmp/tmpm36tshk2/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
code	`"/^>/!y/atcgn/NNNNN/"`
dbkey	`"?"`

Step 5: ID non-target contaminants:

step_state: scheduled

Jobs

Job 1:

Job state is ok

Command Line:

kraken2 --threads ${GALAXY_SLOTS:-1} --db '/cvmfs/data.galaxyproject.org/managed/kraken2_databases/kraken2_viral_db'    '/tmp/tmpm36tshk2/files/c/4/d/dataset_c4d0e10f-93d3-46a9-99bb-b8b608bfc949.dat'  --classified-out '/tmp/tmpm36tshk2/job_working_directory/000/4/outputs/dataset_d03399c1-1e39-415e-9060-1365536aa84a.dat' --unclassified-out '/tmp/tmpm36tshk2/job_working_directory/000/4/outputs/dataset_78aea8b4-47a9-44bd-bba8-1305dfa384b9.dat'  --confidence '0.3' --minimum-base-quality '0' --minimum-hit-groups '2'  --use-names   > '/tmp/tmpm36tshk2/job_working_directory/000/4/outputs/dataset_4c65beec-8f49-40b8-8de9-533a944f9811.dat'

Exit Code:

```
0
```

Standard Error:

Loading database information... done.
9 sequences (2.57 Mbp) processed in 0.171s (3.2 Kseq/m, 902.82 Mbp/m).
  1 sequences classified (11.11%)
  8 sequences unclassified (88.89%)

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"fasta"`
__workflow_invocation_uuid__	`"edfc915689e411efb621000d3a38214b"`
chromInfo	`"/tmp/tmpm36tshk2/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
confidence	`"0.3"`
dbkey	`"?"`
kraken2_database	`"viral2019-03"`
min_base_quality	`"0"`
minimum_hit_groups	`"2"`
quick	`false`
report	`{"create_report": false, "report_minimizer_data": false, "report_zero_counts": false, "use_mpa_style": false}`
single_paired	`{"__current_case__": 2, "input_sequences": {"values": [{"id": 3, "src": "hda"}]}, "single_paired_selector": "no"}`
split_reads	`true`
use_names	`true`

Step 6: blast mitochondria DB:

step_state: scheduled

Jobs

Job 1:

Job state is ok

Command Line:

blastn  -query '/tmp/tmpm36tshk2/files/c/4/d/dataset_c4d0e10f-93d3-46a9-99bb-b8b608bfc949.dat'   -db '"/cvmfs/data.galaxyproject.org/byhand/refseq/mitochondrion/genomic/2022-03-10/mitochondrion"'  -task 'blastn' -evalue '0.001' -out '/tmp/tmpm36tshk2/job_working_directory/000/5/outputs/dataset_34eb4cef-ecaf-4ff3-bfcf-846f10b2cb57.dat' -outfmt '6 qseqid sseqid length qstart qend evalue qlen qcovs qcovhsp'  -num_threads "${GALAXY_SLOTS:-8}"

Exit Code:

```
0
```

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"fasta"`
__workflow_invocation_uuid__	`"edfc915689e411efb621000d3a38214b"`
adv_opts	`{"__current_case__": 0, "adv_opts_selector": "basic"}`
blast_type	`"blastn"`
chromInfo	`"/tmp/tmpm36tshk2/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
db_opts	`{"__current_case__": 0, "database": ["refseq_mitochondrion"], "db_opts_selector": "db", "histdb": "", "subject": ""}`
dbkey	`"?"`
evalue_cutoff	`"0.001"`
output	`{"__current_case__": 2, "ext_cols": ["qlen"], "ids_cols": null, "misc_cols": ["qcovs", "qcovhsp"], "out_format": "cols", "std_cols": ["qseqid", "sseqid", "length", "qstart", "qend", "evalue"], "tax_cols": null}`

Step 7: Cut1:

step_state: scheduled

Jobs

Job 1:

Job state is ok

Command Line:

perl '/tmp/tmpm36tshk2/galaxy-dev/tools/filters/cutWrapper.pl' '/tmp/tmpm36tshk2/files/4/c/6/dataset_4c65beec-8f49-40b8-8de9-533a944f9811.dat' 'c1,c2,c3' T '/tmp/tmpm36tshk2/job_working_directory/000/6/outputs/dataset_36bfae06-bc86-42f1-94ed-8a8aff06f646.dat'

Exit Code:

```
0
```

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"tabular"`
__workflow_invocation_uuid__	`"edfc915689e411efb621000d3a38214b"`
chromInfo	`"/tmp/tmpm36tshk2/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
columnList	`"c1,c2,c3"`
dbkey	`"?"`
delimiter	`"T"`

Step 8: parsing blast output:

step_state: scheduled

Jobs

Job 1:

Job state is ok

Command Line:

parse_mito_blast.py --blastout '/tmp/tmpm36tshk2/files/3/4/e/dataset_34eb4cef-ecaf-4ff3-bfcf-846f10b2cb57.dat'

Exit Code:

```
0
```

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"input"`
__workflow_invocation_uuid__	`"edfc915689e411efb621000d3a38214b"`
chromInfo	`"/tmp/tmpm36tshk2/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
dbkey	`"?"`

Step 9: Filter1:

step_state: scheduled

Jobs

Job 1:

Job state is ok

Command Line:

python '/tmp/tmpm36tshk2/galaxy-dev/tools/stats/filtering.py' '/tmp/tmpm36tshk2/files/3/6/b/dataset_36bfae06-bc86-42f1-94ed-8a8aff06f646.dat' '/tmp/tmpm36tshk2/job_working_directory/000/8/outputs/dataset_29e6f4ba-2a6b-4167-ba63-088b436c4d04.dat' '/tmp/tmpm36tshk2/job_working_directory/000/8/configs/tmpa659kidl' 3 "str,str,str" 0

Exit Code:

```
0
```

Standard Output:

Filtering with c1!='U', 
kept 11.11% of 9 valid lines (9 total lines).

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"tabular"`
__workflow_invocation_uuid__	`"edfc915689e411efb621000d3a38214b"`
chromInfo	`"/tmp/tmpm36tshk2/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
cond	`"c1!='U'"`
dbkey	`"?"`
header_lines	`"0"`

Step 10: Cut1:

step_state: scheduled

Jobs

Job 1:

Job state is ok

Command Line:

perl '/tmp/tmpm36tshk2/galaxy-dev/tools/filters/cutWrapper.pl' '/tmp/tmpm36tshk2/files/2/9/e/dataset_29e6f4ba-2a6b-4167-ba63-088b436c4d04.dat' 'c2' T '/tmp/tmpm36tshk2/job_working_directory/000/9/outputs/dataset_d7a043b6-b8fa-4c30-ac0c-985a70c450df.dat'

Exit Code:

```
0
```

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"tabular"`
__workflow_invocation_uuid__	`"edfc915689e411efb621000d3a38214b"`
chromInfo	`"/tmp/tmpm36tshk2/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
columnList	`"c2"`
dbkey	`"?"`
delimiter	`"T"`

Other invocation details
- history_id
  - ed4d2e2de0cf11c0
- history_state
  - ok
- invocation_id
  - ed4d2e2de0cf11c0
- invocation_state
  - scheduled
- workflow_id
  - ed4d2e2de0cf11c0

gxydevbot · 2024-11-11T04:24:25Z

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

github-actions · 2024-11-11T04:35:09Z

Test Results (powered by Planemo)

Test Summary

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

Passed Tests

✅ Assembly-decontamination-VGP9.ga_0

Workflow invocation details

Invocation Messages

Steps

Step 1: Scaffolded assembly (fasta):
- step_state: scheduled
Step 2: Database for Kraken2:
- step_state: scheduled

Step 11: concatenate scaffold lists:

step_state: scheduled

Jobs

Job 1:

Job state is ok

Command Line:

cat '/tmp/tmp6tz70b9f/files/2/2/c/dataset_22c68043-868d-4b25-920a-3ee2d9a48493.dat' >> '/tmp/tmp6tz70b9f/job_working_directory/000/10/outputs/dataset_1c67b6bd-9b9c-4bf8-84ab-8964a2c2344a.dat' && cat '/tmp/tmp6tz70b9f/files/8/a/8/dataset_8a81d4d2-5edb-4a4b-b151-fa69608b7df0.dat' >> '/tmp/tmp6tz70b9f/job_working_directory/000/10/outputs/dataset_1c67b6bd-9b9c-4bf8-84ab-8964a2c2344a.dat' && exit 0

Exit Code:

```
0
```

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"input"`
__workflow_invocation_uuid__	`"a930cc2e9fe511ef922ea14234ecf3ca"`
chromInfo	`"/tmp/tmp6tz70b9f/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
dbkey	`"?"`
queries	`[]`

**Step 12: removing scaffolds **:

step_state: scheduled

Jobs

Job 1:

Job state is ok

Command Line:

gfastats '/tmp/tmp6tz70b9f/files/3/b/3/dataset_3b34d0c6-7570-4491-bed0-09baf5af5d3d.dat'  --exclude-bed /tmp/tmp6tz70b9f/files/1/c/6/dataset_1c67b6bd-9b9c-4bf8-84ab-8964a2c2344a.dat   -o dataset.fasta.gz --threads ${GALAXY_SLOTS:-8} && mv dataset* output_dataset

Exit Code:

```
0
```

Standard Output:

+++Assembly summary+++: 
# scaffolds: 0
Total scaffold length: 0
Average scaffold length: nan
Scaffold N50: 0
Scaffold auN: 0.00
Scaffold L50: 0
Largest scaffold: 0
Smallest scaffold: 0
# contigs: 0
Total contig length: 0
Average contig length: nan
Contig N50: 0
Contig auN: 0.00
Contig L50: 0
Largest contig: 0
Smallest contig: 0
# gaps in scaffolds: 0
Total gap length in scaffolds: 0
Average gap length in scaffolds: 0.00
Gap N50 in scaffolds: 0
Gap auN in scaffolds: 0.00
Gap L50 in scaffolds: 0
Largest gap in scaffolds: 0
Smallest gap in scaffolds: 0
Base composition (A:C:G:T): 0:0:0:0
GC content %: 0.00
# soft-masked bases: 0
# segments: 0
Total segment length: 0
Average segment length: nan
# gaps: 0
# paths: 0

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"input"`
__workflow_invocation_uuid__	`"a930cc2e9fe511ef922ea14234ecf3ca"`
chromInfo	`"/tmp/tmp6tz70b9f/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
dbkey	`"?"`
mode_condition	`{"__current_case__": 0, "discover_paths": false, "homopolymer_compress": null, "output_condition": {"__current_case__": 1, "line_length": null, "out_format": "fasta.gz"}, "remove_terminal_gaps": false, "selector": "manipulation", "sort": "", "swiss_army_knife": null}`
target_condition	`{"__current_case__": 1, "exclude_bed": {"values": [{"id": 13, "src": "hda"}]}, "include_bed": null, "target_option": "true", "target_sequence": ""}`

**Step 3: soft-masking **:

step_state: scheduled

Jobs

Job 1:

Job state is ok

Command Line:

dustmasker -in '/tmp/tmp6tz70b9f/files/3/b/3/dataset_3b34d0c6-7570-4491-bed0-09baf5af5d3d.dat' -infmt fasta -out '/tmp/tmp6tz70b9f/job_working_directory/000/2/outputs/dataset_0fc2c64b-7b3b-40fb-aba1-22bbbb32179f.dat' -window 64 -level 40 -linker 1 -outfmt fasta

Exit Code:

```
0
```

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"fasta"`
__workflow_invocation_uuid__	`"a930cc2e9fe511ef922ea14234ecf3ca"`
chromInfo	`"/tmp/tmp6tz70b9f/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
db_opts	`{"__current_case__": 2, "database": "", "db_opts_selector": "file", "histdb": "", "subject": {"values": [{"id": 1, "src": "hda"}]}}`
dbkey	`"?"`
level	`"40"`
linker	`"1"`
outformat	`"fasta"`
window	`"64"`

Step 4: hard-masking:

step_state: scheduled

Jobs

Job 1:

Job state is ok

Command Line:

sed --sandbox -r -f '/tmp/tmp6tz70b9f/job_working_directory/000/3/configs/tmp3pip5qw2' '/tmp/tmp6tz70b9f/files/0/f/c/dataset_0fc2c64b-7b3b-40fb-aba1-22bbbb32179f.dat' > '/tmp/tmp6tz70b9f/job_working_directory/000/3/outputs/dataset_9ca9b338-1b63-4809-b95e-5a8ecf00dda2.dat'

Exit Code:

```
0
```

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"input"`
__workflow_invocation_uuid__	`"a930cc2e9fe511ef922ea14234ecf3ca"`
adv_opts	`{"__current_case__": 0, "adv_opts_selector": "basic"}`
chromInfo	`"/tmp/tmp6tz70b9f/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
code	`"/^>/!y/atcgn/NNNNN/"`
dbkey	`"?"`

Step 5: ID non-target contaminants:

step_state: scheduled

Jobs

Job 1:

Job state is ok

Command Line:

kraken2 --threads ${GALAXY_SLOTS:-1} --db '/cvmfs/data.galaxyproject.org/managed/kraken2_databases/kraken2_viral_db'    '/tmp/tmp6tz70b9f/files/9/c/a/dataset_9ca9b338-1b63-4809-b95e-5a8ecf00dda2.dat'  --classified-out '/tmp/tmp6tz70b9f/job_working_directory/000/4/outputs/dataset_e313e52c-48db-4201-b1eb-cf8776855e27.dat' --unclassified-out '/tmp/tmp6tz70b9f/job_working_directory/000/4/outputs/dataset_3975fec8-980e-4822-88dc-fba4754abed1.dat'  --confidence '0.3' --minimum-base-quality '0' --minimum-hit-groups '2'  --use-names   > '/tmp/tmp6tz70b9f/job_working_directory/000/4/outputs/dataset_934919fa-066f-49b8-96ab-884d3ffb62b6.dat'

Exit Code:

```
0
```

Standard Error:

Loading database information... done.
9 sequences (2.57 Mbp) processed in 0.181s (3.0 Kseq/m, 854.46 Mbp/m).
  1 sequences classified (11.11%)
  8 sequences unclassified (88.89%)

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"fasta"`
__workflow_invocation_uuid__	`"a930cc2e9fe511ef922ea14234ecf3ca"`
chromInfo	`"/tmp/tmp6tz70b9f/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
confidence	`"0.3"`
dbkey	`"?"`
kraken2_database	`"viral2019-03"`
min_base_quality	`"0"`
minimum_hit_groups	`"2"`
quick	`false`
report	`{"create_report": false, "report_minimizer_data": false, "report_zero_counts": false, "use_mpa_style": false}`
single_paired	`{"__current_case__": 2, "input_sequences": {"values": [{"id": 3, "src": "hda"}]}, "single_paired_selector": "no"}`
split_reads	`true`
use_names	`true`

Step 6: blast mitochondria DB:

step_state: scheduled

Jobs

Job 1:

Job state is ok

Command Line:

blastn  -query '/tmp/tmp6tz70b9f/files/9/c/a/dataset_9ca9b338-1b63-4809-b95e-5a8ecf00dda2.dat'   -db '"/cvmfs/data.galaxyproject.org/byhand/refseq/mitochondrion/genomic/2022-03-10/mitochondrion"'  -task 'blastn' -evalue '0.001' -out '/tmp/tmp6tz70b9f/job_working_directory/000/5/outputs/dataset_82f9bbff-96b1-4c8e-a5f6-6987879951d9.dat' -outfmt '6 qseqid sseqid length qstart qend evalue qlen qcovs qcovhsp'  -num_threads "${GALAXY_SLOTS:-8}"

Exit Code:

```
0
```

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"fasta"`
__workflow_invocation_uuid__	`"a930cc2e9fe511ef922ea14234ecf3ca"`
adv_opts	`{"__current_case__": 0, "adv_opts_selector": "basic"}`
blast_type	`"blastn"`
chromInfo	`"/tmp/tmp6tz70b9f/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
db_opts	`{"__current_case__": 0, "database": ["refseq_mitochondrion"], "db_opts_selector": "db", "histdb": "", "subject": ""}`
dbkey	`"?"`
evalue_cutoff	`"0.001"`
output	`{"__current_case__": 2, "ext_cols": ["qlen"], "ids_cols": null, "misc_cols": ["qcovs", "qcovhsp"], "out_format": "cols", "std_cols": ["qseqid", "sseqid", "length", "qstart", "qend", "evalue"], "tax_cols": null}`

Step 7: Cut1:

step_state: scheduled

Jobs

Job 1:

Job state is ok

Command Line:

perl '/tmp/tmp6tz70b9f/galaxy-dev/tools/filters/cutWrapper.pl' '/tmp/tmp6tz70b9f/files/9/3/4/dataset_934919fa-066f-49b8-96ab-884d3ffb62b6.dat' 'c1,c2,c3' T '/tmp/tmp6tz70b9f/job_working_directory/000/6/outputs/dataset_02c219e4-4807-4423-b3a9-4da64461861d.dat'

Exit Code:

```
0
```

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"tabular"`
__workflow_invocation_uuid__	`"a930cc2e9fe511ef922ea14234ecf3ca"`
chromInfo	`"/tmp/tmp6tz70b9f/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
columnList	`"c1,c2,c3"`
dbkey	`"?"`
delimiter	`"T"`

Step 8: parsing blast output:

step_state: scheduled

Jobs

Job 1:

Job state is ok

Command Line:

parse_mito_blast.py --blastout '/tmp/tmp6tz70b9f/files/8/2/f/dataset_82f9bbff-96b1-4c8e-a5f6-6987879951d9.dat'

Exit Code:

```
0
```

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"input"`
__workflow_invocation_uuid__	`"a930cc2e9fe511ef922ea14234ecf3ca"`
chromInfo	`"/tmp/tmp6tz70b9f/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
dbkey	`"?"`

Step 9: Filter1:

step_state: scheduled

Jobs

Job 1:

Job state is ok

Command Line:

python '/tmp/tmp6tz70b9f/galaxy-dev/tools/stats/filtering.py' '/tmp/tmp6tz70b9f/files/0/2/c/dataset_02c219e4-4807-4423-b3a9-4da64461861d.dat' '/tmp/tmp6tz70b9f/job_working_directory/000/8/outputs/dataset_53a2ac47-170c-4f8d-b8a3-6c0b42abc18f.dat' '/tmp/tmp6tz70b9f/job_working_directory/000/8/configs/tmpp1eq6s_n' 3 "str,str,str" 0

Exit Code:

```
0
```

Standard Output:

Filtering with c1!='U', 
kept 11.11% of 9 valid lines (9 total lines).

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"tabular"`
__workflow_invocation_uuid__	`"a930cc2e9fe511ef922ea14234ecf3ca"`
chromInfo	`"/tmp/tmp6tz70b9f/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
cond	`"c1!='U'"`
dbkey	`"?"`
header_lines	`"0"`

Step 10: Cut1:

step_state: scheduled

Jobs

Job 1:

Job state is ok

Command Line:

perl '/tmp/tmp6tz70b9f/galaxy-dev/tools/filters/cutWrapper.pl' '/tmp/tmp6tz70b9f/files/5/3/a/dataset_53a2ac47-170c-4f8d-b8a3-6c0b42abc18f.dat' 'c2' T '/tmp/tmp6tz70b9f/job_working_directory/000/9/outputs/dataset_8a81d4d2-5edb-4a4b-b151-fa69608b7df0.dat'

Exit Code:

```
0
```

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"tabular"`
__workflow_invocation_uuid__	`"a930cc2e9fe511ef922ea14234ecf3ca"`
chromInfo	`"/tmp/tmp6tz70b9f/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
columnList	`"c2"`
dbkey	`"?"`
delimiter	`"T"`

Other invocation details
- history_id
  - de0b17c6ea5f428c
- history_state
  - ok
- invocation_id
  - de0b17c6ea5f428c
- invocation_state
  - scheduled
- workflow_id
  - de0b17c6ea5f428c

gxydevbot · 2024-12-16T04:38:33Z

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

github-actions · 2024-12-16T04:56:34Z

Test Results (powered by Planemo)

Test Summary

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

Passed Tests

✅ Assembly-decontamination-VGP9.ga_0

Workflow invocation details

Invocation Messages

Steps

Step 1: Scaffolded assembly (fasta):
- step_state: scheduled
Step 2: Database for Kraken2:
- step_state: scheduled

Step 11: concatenate scaffold lists:

step_state: scheduled

Jobs

Job 1:

Job state is ok

Command Line:

cat '/tmp/tmp9qu9u6_p/files/4/b/7/dataset_4b7e7247-dc5d-411c-96ba-59e9576ccd9c.dat' >> '/tmp/tmp9qu9u6_p/job_working_directory/000/10/outputs/dataset_c05c8e03-b65c-47fd-8c5c-63bb308e2518.dat' && cat '/tmp/tmp9qu9u6_p/files/1/7/2/dataset_172dd922-b2ea-4e3c-9d54-fa067f51ffa7.dat' >> '/tmp/tmp9qu9u6_p/job_working_directory/000/10/outputs/dataset_c05c8e03-b65c-47fd-8c5c-63bb308e2518.dat' && exit 0

Exit Code:

```
0
```

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"input"`
__workflow_invocation_uuid__	`"520cbc74bb6911ef899e000d3a5c80c6"`
chromInfo	`"/tmp/tmp9qu9u6_p/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
dbkey	`"?"`
queries	`[]`

**Step 12: removing scaffolds **:

step_state: scheduled

Jobs

Job 1:

Job state is ok

Command Line:

gfastats '/tmp/tmp9qu9u6_p/files/c/b/1/dataset_cb10d7a2-b21c-4346-b6ba-29f39e1b5a71.dat'  --exclude-bed /tmp/tmp9qu9u6_p/files/c/0/5/dataset_c05c8e03-b65c-47fd-8c5c-63bb308e2518.dat   -o dataset.fasta.gz --threads ${GALAXY_SLOTS:-8} && mv dataset* output_dataset

Exit Code:

```
0
```

Standard Output:

+++Assembly summary+++: 
# scaffolds: 0
Total scaffold length: 0
Average scaffold length: nan
Scaffold N50: 0
Scaffold auN: 0.00
Scaffold L50: 0
Largest scaffold: 0
Smallest scaffold: 0
# contigs: 0
Total contig length: 0
Average contig length: nan
Contig N50: 0
Contig auN: 0.00
Contig L50: 0
Largest contig: 0
Smallest contig: 0
# gaps in scaffolds: 0
Total gap length in scaffolds: 0
Average gap length in scaffolds: 0.00
Gap N50 in scaffolds: 0
Gap auN in scaffolds: 0.00
Gap L50 in scaffolds: 0
Largest gap in scaffolds: 0
Smallest gap in scaffolds: 0
Base composition (A:C:G:T): 0:0:0:0
GC content %: 0.00
# soft-masked bases: 0
# segments: 0
Total segment length: 0
Average segment length: nan
# gaps: 0
# paths: 0

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"input"`
__workflow_invocation_uuid__	`"520cbc74bb6911ef899e000d3a5c80c6"`
chromInfo	`"/tmp/tmp9qu9u6_p/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
dbkey	`"?"`
mode_condition	`{"__current_case__": 0, "discover_paths": false, "homopolymer_compress": null, "output_condition": {"__current_case__": 1, "line_length": null, "out_format": "fasta.gz"}, "remove_terminal_gaps": false, "selector": "manipulation", "sort": "", "swiss_army_knife": null}`
target_condition	`{"__current_case__": 1, "exclude_bed": {"values": [{"id": 13, "src": "hda"}]}, "include_bed": null, "target_option": "true", "target_sequence": ""}`

**Step 3: soft-masking **:

step_state: scheduled

Jobs

Job 1:

Job state is ok

Command Line:

dustmasker -in '/tmp/tmp9qu9u6_p/files/c/b/1/dataset_cb10d7a2-b21c-4346-b6ba-29f39e1b5a71.dat' -infmt fasta -out '/tmp/tmp9qu9u6_p/job_working_directory/000/2/outputs/dataset_3e434d62-e151-44fa-8ffa-5927c4917606.dat' -window 64 -level 40 -linker 1 -outfmt fasta

Exit Code:

```
0
```

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"fasta"`
__workflow_invocation_uuid__	`"520cbc74bb6911ef899e000d3a5c80c6"`
chromInfo	`"/tmp/tmp9qu9u6_p/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
db_opts	`{"__current_case__": 2, "database": "", "db_opts_selector": "file", "histdb": "", "subject": {"values": [{"id": 1, "src": "hda"}]}}`
dbkey	`"?"`
level	`"40"`
linker	`"1"`
outformat	`"fasta"`
window	`"64"`

Step 4: hard-masking:

step_state: scheduled

Jobs

Job 1:

Job state is ok

Command Line:

sed --sandbox -r -f '/tmp/tmp9qu9u6_p/job_working_directory/000/3/configs/tmp6bn5mcyx' '/tmp/tmp9qu9u6_p/files/3/e/4/dataset_3e434d62-e151-44fa-8ffa-5927c4917606.dat' > '/tmp/tmp9qu9u6_p/job_working_directory/000/3/outputs/dataset_d63c9e82-369f-43b5-9807-fad802e60a87.dat'

Exit Code:

```
0
```

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"input"`
__workflow_invocation_uuid__	`"520cbc74bb6911ef899e000d3a5c80c6"`
adv_opts	`{"__current_case__": 0, "adv_opts_selector": "basic"}`
chromInfo	`"/tmp/tmp9qu9u6_p/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
code	`"/^>/!y/atcgn/NNNNN/"`
dbkey	`"?"`

Step 5: ID non-target contaminants:

step_state: scheduled

Jobs

Job 1:

Job state is ok

Command Line:

kraken2 --threads ${GALAXY_SLOTS:-1} --db '/cvmfs/data.galaxyproject.org/managed/kraken2_databases/kraken2_viral_db'    '/tmp/tmp9qu9u6_p/files/d/6/3/dataset_d63c9e82-369f-43b5-9807-fad802e60a87.dat'  --classified-out '/tmp/tmp9qu9u6_p/job_working_directory/000/4/outputs/dataset_901a77a5-c464-4dbd-b040-8f567193c521.dat' --unclassified-out '/tmp/tmp9qu9u6_p/job_working_directory/000/4/outputs/dataset_eda37914-7d69-45db-931b-80ed5eaefa34.dat'  --confidence '0.3' --minimum-base-quality '0' --minimum-hit-groups '2'  --use-names   > '/tmp/tmp9qu9u6_p/job_working_directory/000/4/outputs/dataset_1bbbd418-d4b9-4430-9c33-2cd3e6beff3c.dat'

Exit Code:

```
0
```

Standard Error:

Loading database information... done.
9 sequences (2.57 Mbp) processed in 0.178s (3.0 Kseq/m, 867.88 Mbp/m).
  1 sequences classified (11.11%)
  8 sequences unclassified (88.89%)

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"fasta"`
__workflow_invocation_uuid__	`"520cbc74bb6911ef899e000d3a5c80c6"`
chromInfo	`"/tmp/tmp9qu9u6_p/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
confidence	`"0.3"`
dbkey	`"?"`
kraken2_database	`"viral2019-03"`
min_base_quality	`"0"`
minimum_hit_groups	`"2"`
quick	`false`
report	`{"create_report": false, "report_minimizer_data": false, "report_zero_counts": false, "use_mpa_style": false}`
single_paired	`{"__current_case__": 2, "input_sequences": {"values": [{"id": 3, "src": "hda"}]}, "single_paired_selector": "no"}`
split_reads	`true`
use_names	`true`

Step 6: blast mitochondria DB:

step_state: scheduled

Jobs

Job 1:

Job state is ok

Command Line:

blastn  -query '/tmp/tmp9qu9u6_p/files/d/6/3/dataset_d63c9e82-369f-43b5-9807-fad802e60a87.dat'   -db '"/cvmfs/data.galaxyproject.org/byhand/refseq/mitochondrion/genomic/2022-03-10/mitochondrion"'  -task 'blastn' -evalue '0.001' -out '/tmp/tmp9qu9u6_p/job_working_directory/000/5/outputs/dataset_48af96d3-ef37-4e06-a96f-02be23b58ba7.dat' -outfmt '6 qseqid sseqid length qstart qend evalue qlen qcovs qcovhsp'  -num_threads "${GALAXY_SLOTS:-8}"

Exit Code:

```
0
```

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"fasta"`
__workflow_invocation_uuid__	`"520cbc74bb6911ef899e000d3a5c80c6"`
adv_opts	`{"__current_case__": 0, "adv_opts_selector": "basic"}`
blast_type	`"blastn"`
chromInfo	`"/tmp/tmp9qu9u6_p/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
db_opts	`{"__current_case__": 0, "database": ["refseq_mitochondrion"], "db_opts_selector": "db", "histdb": "", "subject": ""}`
dbkey	`"?"`
evalue_cutoff	`"0.001"`
output	`{"__current_case__": 2, "ext_cols": ["qlen"], "ids_cols": null, "misc_cols": ["qcovs", "qcovhsp"], "out_format": "cols", "std_cols": ["qseqid", "sseqid", "length", "qstart", "qend", "evalue"], "tax_cols": null}`

Step 7: Cut1:

step_state: scheduled

Jobs

Job 1:

Job state is ok

Command Line:

perl '/tmp/tmp9qu9u6_p/galaxy-dev/tools/filters/cutWrapper.pl' '/tmp/tmp9qu9u6_p/files/1/b/b/dataset_1bbbd418-d4b9-4430-9c33-2cd3e6beff3c.dat' 'c1,c2,c3' T '/tmp/tmp9qu9u6_p/job_working_directory/000/6/outputs/dataset_a755fd8b-c93e-4fdd-9bfe-f6d7a5d07dd9.dat'

Exit Code:

```
0
```

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"tabular"`
__workflow_invocation_uuid__	`"520cbc74bb6911ef899e000d3a5c80c6"`
chromInfo	`"/tmp/tmp9qu9u6_p/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
columnList	`"c1,c2,c3"`
dbkey	`"?"`
delimiter	`"T"`

Step 8: parsing blast output:

step_state: scheduled

Jobs

Job 1:

Job state is ok

Command Line:

parse_mito_blast.py --blastout '/tmp/tmp9qu9u6_p/files/4/8/a/dataset_48af96d3-ef37-4e06-a96f-02be23b58ba7.dat'

Exit Code:

```
0
```

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"input"`
__workflow_invocation_uuid__	`"520cbc74bb6911ef899e000d3a5c80c6"`
chromInfo	`"/tmp/tmp9qu9u6_p/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
dbkey	`"?"`

Step 9: Filter1:

step_state: scheduled

Jobs

Job 1:

Job state is ok

Command Line:

python '/tmp/tmp9qu9u6_p/galaxy-dev/tools/stats/filtering.py' '/tmp/tmp9qu9u6_p/files/a/7/5/dataset_a755fd8b-c93e-4fdd-9bfe-f6d7a5d07dd9.dat' '/tmp/tmp9qu9u6_p/job_working_directory/000/8/outputs/dataset_7531039c-96c8-4dfb-ab9d-e398068d1038.dat' '/tmp/tmp9qu9u6_p/job_working_directory/000/8/configs/tmpwe3ysytj' 3 "str,str,str" 0

Exit Code:

```
0
```

Standard Output:

Filtering with c1!='U', 
kept 11.11% of 9 valid lines (9 total lines).

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"tabular"`
__workflow_invocation_uuid__	`"520cbc74bb6911ef899e000d3a5c80c6"`
chromInfo	`"/tmp/tmp9qu9u6_p/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
cond	`"c1!='U'"`
dbkey	`"?"`
header_lines	`"0"`

Step 10: Cut1:

step_state: scheduled

Jobs

Job 1:

Job state is ok

Command Line:

perl '/tmp/tmp9qu9u6_p/galaxy-dev/tools/filters/cutWrapper.pl' '/tmp/tmp9qu9u6_p/files/7/5/3/dataset_7531039c-96c8-4dfb-ab9d-e398068d1038.dat' 'c2' T '/tmp/tmp9qu9u6_p/job_working_directory/000/9/outputs/dataset_172dd922-b2ea-4e3c-9d54-fa067f51ffa7.dat'

Exit Code:

```
0
```

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"tabular"`
__workflow_invocation_uuid__	`"520cbc74bb6911ef899e000d3a5c80c6"`
chromInfo	`"/tmp/tmp9qu9u6_p/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
columnList	`"c2"`
dbkey	`"?"`
delimiter	`"T"`

Other invocation details
- history_id
  - a779903344e781c6
- history_state
  - ok
- invocation_id
  - a779903344e781c6
- invocation_state
  - scheduled
- workflow_id
  - a779903344e781c6

gxydevbot · 2025-02-10T04:23:48Z

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

github-actions · 2025-02-10T04:40:15Z

Test Results (powered by Planemo)

Test Summary

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

Passed Tests

✅ Assembly-decontamination-VGP9.ga_0

Workflow invocation details

Invocation Messages

Steps

Step 1: Scaffolded assembly (fasta):
- step_state: scheduled
Step 2: Database for Kraken2:
- step_state: scheduled

Step 11: concatenate scaffold lists:

step_state: scheduled

Jobs

Job 1:

Job state is ok

Command Line:

cat '/tmp/tmpc4n7bxwf/files/f/2/a/dataset_f2af2de7-91b7-4cca-9a1c-ae1e09c07408.dat' >> '/tmp/tmpc4n7bxwf/job_working_directory/000/10/outputs/dataset_635e9e87-3682-4600-96e0-7755856c858b.dat' && cat '/tmp/tmpc4n7bxwf/files/f/f/e/dataset_ffe4a193-f2df-44b6-92b8-6a0d69336039.dat' >> '/tmp/tmpc4n7bxwf/job_working_directory/000/10/outputs/dataset_635e9e87-3682-4600-96e0-7755856c858b.dat' && exit 0

Exit Code:

```
0
```

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"input"`
__workflow_invocation_uuid__	`"660f93a6e76811efb46f6045bdb94df4"`
chromInfo	`"/tmp/tmpc4n7bxwf/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
dbkey	`"?"`
queries	`[]`

**Step 12: removing scaffolds **:

step_state: scheduled

Jobs

Job 1:

Job state is ok

Command Line:

gfastats '/tmp/tmpc4n7bxwf/files/9/f/5/dataset_9f5213f2-9ee9-4a14-baf9-222a4da9bcd2.dat'  --exclude-bed /tmp/tmpc4n7bxwf/files/6/3/5/dataset_635e9e87-3682-4600-96e0-7755856c858b.dat   -o dataset.fasta.gz --threads ${GALAXY_SLOTS:-8} && mv dataset* output_dataset

Exit Code:

```
0
```

Standard Output:

+++Assembly summary+++: 
# scaffolds: 0
Total scaffold length: 0
Average scaffold length: nan
Scaffold N50: 0
Scaffold auN: 0.00
Scaffold L50: 0
Largest scaffold: 0
Smallest scaffold: 0
# contigs: 0
Total contig length: 0
Average contig length: nan
Contig N50: 0
Contig auN: 0.00
Contig L50: 0
Largest contig: 0
Smallest contig: 0
# gaps in scaffolds: 0
Total gap length in scaffolds: 0
Average gap length in scaffolds: 0.00
Gap N50 in scaffolds: 0
Gap auN in scaffolds: 0.00
Gap L50 in scaffolds: 0
Largest gap in scaffolds: 0
Smallest gap in scaffolds: 0
Base composition (A:C:G:T): 0:0:0:0
GC content %: 0.00
# soft-masked bases: 0
# segments: 0
Total segment length: 0
Average segment length: nan
# gaps: 0
# paths: 0

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"input"`
__workflow_invocation_uuid__	`"660f93a6e76811efb46f6045bdb94df4"`
chromInfo	`"/tmp/tmpc4n7bxwf/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
dbkey	`"?"`
mode_condition	`{"__current_case__": 0, "discover_paths": false, "homopolymer_compress": null, "output_condition": {"__current_case__": 1, "line_length": null, "out_format": "fasta.gz"}, "remove_terminal_gaps": false, "selector": "manipulation", "sort": "", "swiss_army_knife": null}`
target_condition	`{"__current_case__": 1, "exclude_bed": {"values": [{"id": 13, "src": "hda"}]}, "include_bed": null, "target_option": "true", "target_sequence": ""}`

**Step 3: soft-masking **:

step_state: scheduled

Jobs

Job 1:

Job state is ok

Command Line:

dustmasker -in '/tmp/tmpc4n7bxwf/files/9/f/5/dataset_9f5213f2-9ee9-4a14-baf9-222a4da9bcd2.dat' -infmt fasta -out '/tmp/tmpc4n7bxwf/job_working_directory/000/2/outputs/dataset_5a939278-4bdc-4c11-92f0-3a0a338dce30.dat' -window 64 -level 40 -linker 1 -outfmt fasta

Exit Code:

```
0
```

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"fasta"`
__workflow_invocation_uuid__	`"660f93a6e76811efb46f6045bdb94df4"`
chromInfo	`"/tmp/tmpc4n7bxwf/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
db_opts	`{"__current_case__": 2, "database": "", "db_opts_selector": "file", "histdb": "", "subject": {"values": [{"id": 1, "src": "hda"}]}}`
dbkey	`"?"`
level	`"40"`
linker	`"1"`
outformat	`"fasta"`
window	`"64"`

Step 4: hard-masking:

step_state: scheduled

Jobs

Job 1:

Job state is ok

Command Line:

sed --sandbox -r -f '/tmp/tmpc4n7bxwf/job_working_directory/000/3/configs/tmpngeqzqp6' '/tmp/tmpc4n7bxwf/files/5/a/9/dataset_5a939278-4bdc-4c11-92f0-3a0a338dce30.dat' > '/tmp/tmpc4n7bxwf/job_working_directory/000/3/outputs/dataset_69545757-64eb-4581-9ba7-bfafc8aa2827.dat'

Exit Code:

```
0
```

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"input"`
__workflow_invocation_uuid__	`"660f93a6e76811efb46f6045bdb94df4"`
adv_opts	`{"__current_case__": 0, "adv_opts_selector": "basic"}`
chromInfo	`"/tmp/tmpc4n7bxwf/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
code	`"/^>/!y/atcgn/NNNNN/"`
dbkey	`"?"`

Step 5: ID non-target contaminants:

step_state: scheduled

Jobs

Job 1:

Job state is ok

Command Line:

kraken2 --threads ${GALAXY_SLOTS:-1} --db '/cvmfs/data.galaxyproject.org/managed/kraken2_databases/kraken2_viral_db'    '/tmp/tmpc4n7bxwf/files/6/9/5/dataset_69545757-64eb-4581-9ba7-bfafc8aa2827.dat'  --classified-out '/tmp/tmpc4n7bxwf/job_working_directory/000/4/outputs/dataset_191ba2fc-dfa6-4fda-a8b8-1b5fe1b8695b.dat' --unclassified-out '/tmp/tmpc4n7bxwf/job_working_directory/000/4/outputs/dataset_52aea1b9-bbf6-4b2f-a1a0-cda1470341e2.dat'  --confidence '0.3' --minimum-base-quality '0' --minimum-hit-groups '2'  --use-names   > '/tmp/tmpc4n7bxwf/job_working_directory/000/4/outputs/dataset_87a53f3c-8500-4dc4-a6b7-dbacfb1a7ca3.dat'

Exit Code:

```
0
```

Standard Error:

Loading database information... done.
9 sequences (2.57 Mbp) processed in 0.174s (3.1 Kseq/m, 886.32 Mbp/m).
  1 sequences classified (11.11%)
  8 sequences unclassified (88.89%)

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"fasta"`
__workflow_invocation_uuid__	`"660f93a6e76811efb46f6045bdb94df4"`
chromInfo	`"/tmp/tmpc4n7bxwf/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
confidence	`"0.3"`
dbkey	`"?"`
kraken2_database	`"viral2019-03"`
min_base_quality	`"0"`
minimum_hit_groups	`"2"`
quick	`false`
report	`{"create_report": false, "report_minimizer_data": false, "report_zero_counts": false, "use_mpa_style": false}`
single_paired	`{"__current_case__": 2, "input_sequences": {"values": [{"id": 3, "src": "hda"}]}, "single_paired_selector": "no"}`
split_reads	`true`
use_names	`true`

Step 6: blast mitochondria DB:

step_state: scheduled

Jobs

Job 1:

Job state is ok

Command Line:

blastn  -query '/tmp/tmpc4n7bxwf/files/6/9/5/dataset_69545757-64eb-4581-9ba7-bfafc8aa2827.dat'   -db '"/cvmfs/data.galaxyproject.org/byhand/refseq/mitochondrion/genomic/2022-03-10/mitochondrion"'  -task 'blastn' -evalue '0.001' -out '/tmp/tmpc4n7bxwf/job_working_directory/000/5/outputs/dataset_609c68ab-0397-47b8-af58-2ccf54a2bfdf.dat' -outfmt '6 qseqid sseqid length qstart qend evalue qlen qcovs qcovhsp'  -num_threads "${GALAXY_SLOTS:-8}"

Exit Code:

```
0
```

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"fasta"`
__workflow_invocation_uuid__	`"660f93a6e76811efb46f6045bdb94df4"`
adv_opts	`{"__current_case__": 0, "adv_opts_selector": "basic"}`
blast_type	`"blastn"`
chromInfo	`"/tmp/tmpc4n7bxwf/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
db_opts	`{"__current_case__": 0, "database": ["refseq_mitochondrion"], "db_opts_selector": "db", "histdb": "", "subject": ""}`
dbkey	`"?"`
evalue_cutoff	`"0.001"`
output	`{"__current_case__": 2, "ext_cols": ["qlen"], "ids_cols": null, "misc_cols": ["qcovs", "qcovhsp"], "out_format": "cols", "std_cols": ["qseqid", "sseqid", "length", "qstart", "qend", "evalue"], "tax_cols": null}`

Step 7: Cut1:

step_state: scheduled

Jobs

Job 1:

Job state is ok

Command Line:

perl '/tmp/tmpc4n7bxwf/galaxy-dev/tools/filters/cutWrapper.pl' '/tmp/tmpc4n7bxwf/files/8/7/a/dataset_87a53f3c-8500-4dc4-a6b7-dbacfb1a7ca3.dat' 'c1,c2,c3' T '/tmp/tmpc4n7bxwf/job_working_directory/000/6/outputs/dataset_3dbf20d6-8044-47a5-bd71-bc4262530020.dat'

Exit Code:

```
0
```

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"tabular"`
__workflow_invocation_uuid__	`"660f93a6e76811efb46f6045bdb94df4"`
chromInfo	`"/tmp/tmpc4n7bxwf/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
columnList	`"c1,c2,c3"`
dbkey	`"?"`
delimiter	`"T"`

Step 8: parsing blast output:

step_state: scheduled

Jobs

Job 1:

Job state is ok

Command Line:

parse_mito_blast.py --blastout '/tmp/tmpc4n7bxwf/files/6/0/9/dataset_609c68ab-0397-47b8-af58-2ccf54a2bfdf.dat'

Exit Code:

```
0
```

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"input"`
__workflow_invocation_uuid__	`"660f93a6e76811efb46f6045bdb94df4"`
chromInfo	`"/tmp/tmpc4n7bxwf/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
dbkey	`"?"`

Step 9: Filter1:

step_state: scheduled

Jobs

Job 1:

Job state is ok

Command Line:

python '/tmp/tmpc4n7bxwf/galaxy-dev/tools/stats/filtering.py' '/tmp/tmpc4n7bxwf/files/3/d/b/dataset_3dbf20d6-8044-47a5-bd71-bc4262530020.dat' '/tmp/tmpc4n7bxwf/job_working_directory/000/8/outputs/dataset_60b7099f-c0f8-47c2-b91c-3eb8e7dd28f1.dat' '/tmp/tmpc4n7bxwf/job_working_directory/000/8/configs/tmpto45zzwz' 3 "str,str,str" 0

Exit Code:

```
0
```

Standard Output:

Filtering with c1!='U', 
kept 11.11% of 9 valid lines (9 total lines).

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"tabular"`
__workflow_invocation_uuid__	`"660f93a6e76811efb46f6045bdb94df4"`
chromInfo	`"/tmp/tmpc4n7bxwf/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
cond	`"c1!='U'"`
dbkey	`"?"`
header_lines	`"0"`

Step 10: Cut1:

step_state: scheduled

Jobs

Job 1:

Job state is ok

Command Line:

perl '/tmp/tmpc4n7bxwf/galaxy-dev/tools/filters/cutWrapper.pl' '/tmp/tmpc4n7bxwf/files/6/0/b/dataset_60b7099f-c0f8-47c2-b91c-3eb8e7dd28f1.dat' 'c2' T '/tmp/tmpc4n7bxwf/job_working_directory/000/9/outputs/dataset_ffe4a193-f2df-44b6-92b8-6a0d69336039.dat'

Exit Code:

```
0
```

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"tabular"`
__workflow_invocation_uuid__	`"660f93a6e76811efb46f6045bdb94df4"`
chromInfo	`"/tmp/tmpc4n7bxwf/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
columnList	`"c2"`
dbkey	`"?"`
delimiter	`"T"`

Other invocation details
- history_id
  - 610c30a7bff99df5
- history_state
  - ok
- invocation_id
  - 610c30a7bff99df5
- invocation_state
  - scheduled
- workflow_id
  - 610c30a7bff99df5

gxydevbot · 2025-03-10T04:19:34Z

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

github-actions · 2025-03-10T04:36:54Z

Test Results (powered by Planemo)

Test Summary

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

Passed Tests

✅ Assembly-decontamination-VGP9.ga_0

Workflow invocation details

Invocation Messages

Steps

Step 1: Scaffolded assembly (fasta):
- step_state: scheduled
Step 2: Database for Kraken2:
- step_state: scheduled

Step 11: concatenate scaffold lists:

step_state: scheduled

Jobs

Job 1:

Job state is ok

Command Line:

cat '/tmp/tmpq2u22p80/files/9/0/1/dataset_901e5a0e-d4b3-4191-8687-a0ea8a506f40.dat' >> '/tmp/tmpq2u22p80/job_working_directory/000/10/outputs/dataset_0b39238c-81c0-487a-abf4-8e35241dc561.dat' && cat '/tmp/tmpq2u22p80/files/4/f/6/dataset_4f6feef1-c2d1-4be8-be86-f187e21e0cb6.dat' >> '/tmp/tmpq2u22p80/job_working_directory/000/10/outputs/dataset_0b39238c-81c0-487a-abf4-8e35241dc561.dat' && exit 0

Exit Code:

```
0
```

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"input"`
__workflow_invocation_uuid__	`"655985f0fd6811efbdfa7c1e5224f7da"`
chromInfo	`"/tmp/tmpq2u22p80/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
dbkey	`"?"`
queries	`[]`

**Step 12: removing scaffolds **:

step_state: scheduled

Jobs

Job 1:

Job state is ok

Command Line:

gfastats '/tmp/tmpq2u22p80/files/e/6/c/dataset_e6ce60de-556f-4c17-91d7-bea80d041f3b.dat'  --exclude-bed /tmp/tmpq2u22p80/files/0/b/3/dataset_0b39238c-81c0-487a-abf4-8e35241dc561.dat   -o dataset.fasta.gz --threads ${GALAXY_SLOTS:-8} && mv dataset* output_dataset

Exit Code:

```
0
```

Standard Output:

+++Assembly summary+++: 
# scaffolds: 0
Total scaffold length: 0
Average scaffold length: nan
Scaffold N50: 0
Scaffold auN: 0.00
Scaffold L50: 0
Largest scaffold: 0
Smallest scaffold: 0
# contigs: 0
Total contig length: 0
Average contig length: nan
Contig N50: 0
Contig auN: 0.00
Contig L50: 0
Largest contig: 0
Smallest contig: 0
# gaps in scaffolds: 0
Total gap length in scaffolds: 0
Average gap length in scaffolds: 0.00
Gap N50 in scaffolds: 0
Gap auN in scaffolds: 0.00
Gap L50 in scaffolds: 0
Largest gap in scaffolds: 0
Smallest gap in scaffolds: 0
Base composition (A:C:G:T): 0:0:0:0
GC content %: 0.00
# soft-masked bases: 0
# segments: 0
Total segment length: 0
Average segment length: nan
# gaps: 0
# paths: 0

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"input"`
__workflow_invocation_uuid__	`"655985f0fd6811efbdfa7c1e5224f7da"`
chromInfo	`"/tmp/tmpq2u22p80/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
dbkey	`"?"`
mode_condition	`{"__current_case__": 0, "discover_paths": false, "homopolymer_compress": null, "output_condition": {"__current_case__": 1, "line_length": null, "out_format": "fasta.gz"}, "remove_terminal_gaps": false, "selector": "manipulation", "sort": "", "swiss_army_knife": null}`
target_condition	`{"__current_case__": 1, "exclude_bed": {"values": [{"id": 13, "src": "hda"}]}, "include_bed": null, "target_option": "true", "target_sequence": ""}`

**Step 3: soft-masking **:

step_state: scheduled

Jobs

Job 1:

Job state is ok

Command Line:

dustmasker -in '/tmp/tmpq2u22p80/files/e/6/c/dataset_e6ce60de-556f-4c17-91d7-bea80d041f3b.dat' -infmt fasta -out '/tmp/tmpq2u22p80/job_working_directory/000/2/outputs/dataset_53bdb0a7-404d-4531-a50d-ed8d3bb977da.dat' -window 64 -level 40 -linker 1 -outfmt fasta

Exit Code:

```
0
```

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"fasta"`
__workflow_invocation_uuid__	`"655985f0fd6811efbdfa7c1e5224f7da"`
chromInfo	`"/tmp/tmpq2u22p80/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
db_opts	`{"__current_case__": 2, "database": "", "db_opts_selector": "file", "histdb": "", "subject": {"values": [{"id": 1, "src": "hda"}]}}`
dbkey	`"?"`
level	`"40"`
linker	`"1"`
outformat	`"fasta"`
window	`"64"`

Step 4: hard-masking:

step_state: scheduled

Jobs

Job 1:

Job state is ok

Command Line:

sed --sandbox -r -f '/tmp/tmpq2u22p80/job_working_directory/000/3/configs/tmpugksapji' '/tmp/tmpq2u22p80/files/5/3/b/dataset_53bdb0a7-404d-4531-a50d-ed8d3bb977da.dat' > '/tmp/tmpq2u22p80/job_working_directory/000/3/outputs/dataset_e4dc4f6d-5201-4568-af1f-27a776189e8a.dat'

Exit Code:

```
0
```

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"input"`
__workflow_invocation_uuid__	`"655985f0fd6811efbdfa7c1e5224f7da"`
adv_opts	`{"__current_case__": 0, "adv_opts_selector": "basic"}`
chromInfo	`"/tmp/tmpq2u22p80/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
code	`"/^>/!y/atcgn/NNNNN/"`
dbkey	`"?"`

Step 5: ID non-target contaminants:

step_state: scheduled

Jobs

Job 1:

Job state is ok

Command Line:

kraken2 --threads ${GALAXY_SLOTS:-1} --db '/cvmfs/data.galaxyproject.org/managed/kraken2_databases/kraken2_viral_db'    '/tmp/tmpq2u22p80/files/e/4/d/dataset_e4dc4f6d-5201-4568-af1f-27a776189e8a.dat'  --classified-out '/tmp/tmpq2u22p80/job_working_directory/000/4/outputs/dataset_468ca171-beef-40b2-9823-c9de64f67085.dat' --unclassified-out '/tmp/tmpq2u22p80/job_working_directory/000/4/outputs/dataset_ab80b2ab-a561-4419-b8d0-681a9fd72e1a.dat'  --confidence '0.3' --minimum-base-quality '0' --minimum-hit-groups '2'  --use-names   > '/tmp/tmpq2u22p80/job_working_directory/000/4/outputs/dataset_ce2aa200-2a84-47ed-8c40-579aa6bbdbb1.dat'

Exit Code:

```
0
```

Standard Error:

Loading database information... done.
9 sequences (2.57 Mbp) processed in 0.179s (3.0 Kseq/m, 864.68 Mbp/m).
  1 sequences classified (11.11%)
  8 sequences unclassified (88.89%)

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"fasta"`
__workflow_invocation_uuid__	`"655985f0fd6811efbdfa7c1e5224f7da"`
chromInfo	`"/tmp/tmpq2u22p80/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
confidence	`"0.3"`
dbkey	`"?"`
kraken2_database	`"viral2019-03"`
min_base_quality	`"0"`
minimum_hit_groups	`"2"`
quick	`false`
report	`{"create_report": false, "report_minimizer_data": false, "report_zero_counts": false, "use_mpa_style": false}`
single_paired	`{"__current_case__": 2, "input_sequences": {"values": [{"id": 3, "src": "hda"}]}, "single_paired_selector": "no"}`
split_reads	`true`
use_names	`true`

Step 6: blast mitochondria DB:

step_state: scheduled

Jobs

Job 1:

Job state is ok

Command Line:

blastn  -query '/tmp/tmpq2u22p80/files/e/4/d/dataset_e4dc4f6d-5201-4568-af1f-27a776189e8a.dat'   -db '"/cvmfs/data.galaxyproject.org/byhand/refseq/mitochondrion/genomic/2022-03-10/mitochondrion"'  -task 'blastn' -evalue '0.001' -out '/tmp/tmpq2u22p80/job_working_directory/000/5/outputs/dataset_05c8cb2d-d39e-40cc-b990-661b4ab5fc3b.dat' -outfmt '6 qseqid sseqid length qstart qend evalue qlen qcovs qcovhsp'  -num_threads "${GALAXY_SLOTS:-8}"

Exit Code:

```
0
```

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"fasta"`
__workflow_invocation_uuid__	`"655985f0fd6811efbdfa7c1e5224f7da"`
adv_opts	`{"__current_case__": 0, "adv_opts_selector": "basic"}`
blast_type	`"blastn"`
chromInfo	`"/tmp/tmpq2u22p80/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
db_opts	`{"__current_case__": 0, "database": ["refseq_mitochondrion"], "db_opts_selector": "db", "histdb": "", "subject": ""}`
dbkey	`"?"`
evalue_cutoff	`"0.001"`
output	`{"__current_case__": 2, "ext_cols": ["qlen"], "ids_cols": null, "misc_cols": ["qcovs", "qcovhsp"], "out_format": "cols", "std_cols": ["qseqid", "sseqid", "length", "qstart", "qend", "evalue"], "tax_cols": null}`

Step 7: Cut1:

step_state: scheduled

Jobs

Job 1:

Job state is ok

Command Line:

perl '/tmp/tmpq2u22p80/galaxy-dev/tools/filters/cutWrapper.pl' '/tmp/tmpq2u22p80/files/c/e/2/dataset_ce2aa200-2a84-47ed-8c40-579aa6bbdbb1.dat' 'c1,c2,c3' T '/tmp/tmpq2u22p80/job_working_directory/000/6/outputs/dataset_042a93b4-7384-42b4-b7d8-2f4e9d70e39e.dat'

Exit Code:

```
0
```

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"tabular"`
__workflow_invocation_uuid__	`"655985f0fd6811efbdfa7c1e5224f7da"`
chromInfo	`"/tmp/tmpq2u22p80/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
columnList	`"c1,c2,c3"`
dbkey	`"?"`
delimiter	`"T"`

Step 8: parsing blast output:

step_state: scheduled

Jobs

Job 1:

Job state is ok

Command Line:

parse_mito_blast.py --blastout '/tmp/tmpq2u22p80/files/0/5/c/dataset_05c8cb2d-d39e-40cc-b990-661b4ab5fc3b.dat'

Exit Code:

```
0
```

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"input"`
__workflow_invocation_uuid__	`"655985f0fd6811efbdfa7c1e5224f7da"`
chromInfo	`"/tmp/tmpq2u22p80/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
dbkey	`"?"`

Step 9: Filter1:

step_state: scheduled

Jobs

Job 1:

Job state is ok

Command Line:

python '/tmp/tmpq2u22p80/galaxy-dev/tools/stats/filtering.py' '/tmp/tmpq2u22p80/files/0/4/2/dataset_042a93b4-7384-42b4-b7d8-2f4e9d70e39e.dat' '/tmp/tmpq2u22p80/job_working_directory/000/8/outputs/dataset_5b572abd-27c7-489d-94cd-515894ef2419.dat' '/tmp/tmpq2u22p80/job_working_directory/000/8/configs/tmpbe5w9nzf' 3 "str,str,str" 0

Exit Code:

```
0
```

Standard Output:

Filtering with c1!='U', 
kept 11.11% of 9 valid lines (9 total lines).

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"tabular"`
__workflow_invocation_uuid__	`"655985f0fd6811efbdfa7c1e5224f7da"`
chromInfo	`"/tmp/tmpq2u22p80/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
cond	`"c1!='U'"`
dbkey	`"?"`
header_lines	`"0"`

Step 10: Cut1:

step_state: scheduled

Jobs

Job 1:

Job state is ok

Command Line:

perl '/tmp/tmpq2u22p80/galaxy-dev/tools/filters/cutWrapper.pl' '/tmp/tmpq2u22p80/files/5/b/5/dataset_5b572abd-27c7-489d-94cd-515894ef2419.dat' 'c2' T '/tmp/tmpq2u22p80/job_working_directory/000/9/outputs/dataset_4f6feef1-c2d1-4be8-be86-f187e21e0cb6.dat'

Exit Code:

```
0
```

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"tabular"`
__workflow_invocation_uuid__	`"655985f0fd6811efbdfa7c1e5224f7da"`
chromInfo	`"/tmp/tmpq2u22p80/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
columnList	`"c2"`
dbkey	`"?"`
delimiter	`"T"`

Other invocation details
- history_id
  - 77f72952993306b8
- history_state
  - ok
- invocation_id
  - 77f72952993306b8
- invocation_state
  - scheduled
- workflow_id
  - 77f72952993306b8

… 0.3 to 0.4

gxydevbot · 2025-03-17T04:21:55Z

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

github-actions · 2025-03-17T04:37:21Z

Test Results (powered by Planemo)

Test Summary

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

Passed Tests

✅ Assembly-decontamination-VGP9.ga_0

Workflow invocation details

Invocation Messages

Steps

Step 1: Scaffolded assembly (fasta):
- step_state: scheduled
Step 2: Database for Kraken2:
- step_state: scheduled

Step 11: concatenate scaffold lists:

step_state: scheduled

Jobs

Job 1:

Job state is ok

Command Line:

cat '/tmp/tmp1b6r_ugk/files/a/a/b/dataset_aabfd163-2143-4265-9b57-16c9a6e1be30.dat' >> '/tmp/tmp1b6r_ugk/job_working_directory/000/10/outputs/dataset_db8b8146-ff4c-4594-9be7-9cb6137f90d7.dat' && cat '/tmp/tmp1b6r_ugk/files/d/d/9/dataset_dd901dd1-b641-4a9c-a85f-1ea38ee23ccc.dat' >> '/tmp/tmp1b6r_ugk/job_working_directory/000/10/outputs/dataset_db8b8146-ff4c-4594-9be7-9cb6137f90d7.dat' && exit 0

Exit Code:

```
0
```

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"input"`
__workflow_invocation_uuid__	`"c2c91de202e811f08d456045bd4cd061"`
chromInfo	`"/tmp/tmp1b6r_ugk/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
dbkey	`"?"`
queries	`[]`

**Step 12: removing scaffolds **:

step_state: scheduled

Jobs

Job 1:

Job state is ok

Command Line:

gfastats '/tmp/tmp1b6r_ugk/files/9/a/b/dataset_9ab4b5ef-a209-4269-812a-7221cb9a80a5.dat'  --exclude-bed /tmp/tmp1b6r_ugk/files/d/b/8/dataset_db8b8146-ff4c-4594-9be7-9cb6137f90d7.dat   -o dataset.fasta.gz --threads ${GALAXY_SLOTS:-8} && mv dataset* output_dataset

Exit Code:

```
0
```

Standard Output:

+++Assembly summary+++: 
# scaffolds: 7
Total scaffold length: 2460516
Average scaffold length: 351502.29
Scaffold N50: 1472940
Scaffold auN: 953989.69
Scaffold L50: 1
Largest scaffold: 1472940
Smallest scaffold: 52080
# contigs: 7
Total contig length: 2460516
Average contig length: 351502.29
Contig N50: 1472940
Contig auN: 953989.69
Contig L50: 1
Largest contig: 1472940
Smallest contig: 52080
# gaps in scaffolds: 0
Total gap length in scaffolds: 0
Average gap length in scaffolds: 0.00
Gap N50 in scaffolds: 0
Gap auN in scaffolds: 0.00
Gap L50 in scaffolds: 0
Largest gap in scaffolds: 0
Smallest gap in scaffolds: 0
Base composition (A:C:G:T): 569747:632853:681993:575923
GC content %: 53.44
# soft-masked bases: 0
# segments: 7
Total segment length: 2460516
Average segment length: 351502.29
# gaps: 0
# paths: 7

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"input"`
__workflow_invocation_uuid__	`"c2c91de202e811f08d456045bd4cd061"`
chromInfo	`"/tmp/tmp1b6r_ugk/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
dbkey	`"?"`
mode_condition	`{"__current_case__": 0, "discover_paths": false, "homopolymer_compress": null, "output_condition": {"__current_case__": 1, "line_length": null, "out_format": "fasta.gz"}, "remove_terminal_gaps": false, "selector": "manipulation", "sort": "", "swiss_army_knife": null}`
target_condition	`{"__current_case__": 1, "exclude_bed": {"values": [{"id": 13, "src": "hda"}]}, "include_bed": null, "target_option": "true", "target_sequence": ""}`

**Step 3: soft-masking **:

step_state: scheduled

Jobs

Job 1:

Job state is ok

Command Line:

dustmasker -in '/tmp/tmp1b6r_ugk/files/9/a/b/dataset_9ab4b5ef-a209-4269-812a-7221cb9a80a5.dat' -infmt fasta -out '/tmp/tmp1b6r_ugk/job_working_directory/000/2/outputs/dataset_90feef1a-9dbf-464c-8e20-9a515bc7497a.dat' -window 64 -level 40 -linker 1 -outfmt fasta

Exit Code:

```
0
```

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"fasta"`
__workflow_invocation_uuid__	`"c2c91de202e811f08d456045bd4cd061"`
chromInfo	`"/tmp/tmp1b6r_ugk/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
db_opts	`{"__current_case__": 2, "database": "", "db_opts_selector": "file", "histdb": "", "subject": {"values": [{"id": 1, "src": "hda"}]}}`
dbkey	`"?"`
level	`"40"`
linker	`"1"`
outformat	`"fasta"`
window	`"64"`

Step 4: hard-masking:

step_state: scheduled

Jobs

Job 1:

Job state is ok

Command Line:

sed --sandbox -r -f '/tmp/tmp1b6r_ugk/job_working_directory/000/3/configs/tmprljkmt9n' '/tmp/tmp1b6r_ugk/files/9/0/f/dataset_90feef1a-9dbf-464c-8e20-9a515bc7497a.dat' > '/tmp/tmp1b6r_ugk/job_working_directory/000/3/outputs/dataset_52407c91-8752-4204-8928-ac10e7a6821e.dat'

Exit Code:

```
0
```

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"input"`
__workflow_invocation_uuid__	`"c2c91de202e811f08d456045bd4cd061"`
adv_opts	`{"__current_case__": 0, "adv_opts_selector": "basic"}`
chromInfo	`"/tmp/tmp1b6r_ugk/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
code	`"/^>/!y/atcgn/NNNNN/"`
dbkey	`"?"`

Step 5: ID non-target contaminants:

step_state: scheduled

Jobs

Job 1:

Job state is ok

Command Line:

kraken2 --threads ${GALAXY_SLOTS:-1} --db '/cvmfs/data.galaxyproject.org/managed/kraken2_databases/kraken2_viral_db'    '/tmp/tmp1b6r_ugk/files/5/2/4/dataset_52407c91-8752-4204-8928-ac10e7a6821e.dat'  --classified-out '/tmp/tmp1b6r_ugk/job_working_directory/000/4/outputs/dataset_248ea540-4433-4a01-98a4-09c2d99fe376.dat' --unclassified-out '/tmp/tmp1b6r_ugk/job_working_directory/000/4/outputs/dataset_01d9019e-541e-47aa-937c-1bfc9d48babb.dat'  --confidence '0.3' --minimum-base-quality '0' --minimum-hit-groups '2'  --use-names   > '/tmp/tmp1b6r_ugk/job_working_directory/000/4/outputs/dataset_8a202689-7550-4f1d-9d89-f95d8922db1c.dat'

Exit Code:

```
0
```

Standard Error:

Loading database information... done.
9 sequences (2.57 Mbp) processed in 0.173s (3.1 Kseq/m, 890.97 Mbp/m).
  1 sequences classified (11.11%)
  8 sequences unclassified (88.89%)

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"fasta"`
__workflow_invocation_uuid__	`"c2c91de202e811f08d456045bd4cd061"`
chromInfo	`"/tmp/tmp1b6r_ugk/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
confidence	`"0.3"`
dbkey	`"?"`
kraken2_database	`"viral2019-03"`
min_base_quality	`"0"`
minimum_hit_groups	`"2"`
quick	`false`
report	`{"create_report": false, "report_minimizer_data": false, "report_zero_counts": false, "use_mpa_style": false}`
single_paired	`{"__current_case__": 2, "input_sequences": {"values": [{"id": 3, "src": "hda"}]}, "single_paired_selector": "no"}`
split_reads	`true`
use_names	`true`

Step 6: blast mitochondria DB:

step_state: scheduled

Jobs

Job 1:

Job state is ok

Command Line:

blastn  -query '/tmp/tmp1b6r_ugk/files/5/2/4/dataset_52407c91-8752-4204-8928-ac10e7a6821e.dat'   -db '"/cvmfs/data.galaxyproject.org/byhand/refseq/mitochondrion/genomic/2022-03-10/mitochondrion"'  -task 'blastn' -evalue '0.001' -out '/tmp/tmp1b6r_ugk/job_working_directory/000/5/outputs/dataset_e24c7caa-92f0-4078-82a9-1608da2ad791.dat' -outfmt '6 qseqid sseqid length qstart qend evalue qlen qcovs qcovhsp'  -num_threads "${GALAXY_SLOTS:-8}"

Exit Code:

```
0
```

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"fasta"`
__workflow_invocation_uuid__	`"c2c91de202e811f08d456045bd4cd061"`
adv_opts	`{"__current_case__": 0, "adv_opts_selector": "basic"}`
blast_type	`"blastn"`
chromInfo	`"/tmp/tmp1b6r_ugk/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
db_opts	`{"__current_case__": 0, "database": ["refseq_mitochondrion"], "db_opts_selector": "db", "histdb": "", "subject": ""}`
dbkey	`"?"`
evalue_cutoff	`"0.001"`
output	`{"__current_case__": 2, "ext_cols": ["qlen"], "ids_cols": null, "misc_cols": ["qcovs", "qcovhsp"], "out_format": "cols", "std_cols": ["qseqid", "sseqid", "length", "qstart", "qend", "evalue"], "tax_cols": null}`

Step 7: Cut1:

step_state: scheduled

Jobs

Job 1:

Job state is ok

Command Line:

perl '/tmp/tmp1b6r_ugk/galaxy-dev/tools/filters/cutWrapper.pl' '/tmp/tmp1b6r_ugk/files/8/a/2/dataset_8a202689-7550-4f1d-9d89-f95d8922db1c.dat' 'c1,c2,c3' T '/tmp/tmp1b6r_ugk/job_working_directory/000/6/outputs/dataset_0bee731b-4db7-4e77-b4bb-ee52efaffbd0.dat'

Exit Code:

```
0
```

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"tabular"`
__workflow_invocation_uuid__	`"c2c91de202e811f08d456045bd4cd061"`
chromInfo	`"/tmp/tmp1b6r_ugk/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
columnList	`"c1,c2,c3"`
dbkey	`"?"`
delimiter	`"T"`

Step 8: parsing blast output:

step_state: scheduled

Jobs

Job 1:

Job state is ok

Command Line:

parse_mito_blast.py --blastout '/tmp/tmp1b6r_ugk/files/e/2/4/dataset_e24c7caa-92f0-4078-82a9-1608da2ad791.dat'

Exit Code:

```
0
```

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"input"`
__workflow_invocation_uuid__	`"c2c91de202e811f08d456045bd4cd061"`
chromInfo	`"/tmp/tmp1b6r_ugk/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
dbkey	`"?"`

Step 9: Filter1:

step_state: scheduled

Jobs

Job 1:

Job state is ok

Command Line:

python '/tmp/tmp1b6r_ugk/galaxy-dev/tools/stats/filtering.py' '/tmp/tmp1b6r_ugk/files/0/b/e/dataset_0bee731b-4db7-4e77-b4bb-ee52efaffbd0.dat' '/tmp/tmp1b6r_ugk/job_working_directory/000/8/outputs/dataset_ed8bc3e4-df92-44d8-907b-5da21aaa08da.dat' '/tmp/tmp1b6r_ugk/job_working_directory/000/8/configs/tmpp1qib6xy' 3 "str,str,str" 0

Exit Code:

```
0
```

Standard Output:

Filtering with c1!='U', 
kept 11.11% of 9 valid lines (9 total lines).

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"tabular"`
__workflow_invocation_uuid__	`"c2c91de202e811f08d456045bd4cd061"`
chromInfo	`"/tmp/tmp1b6r_ugk/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
cond	`"c1!='U'"`
dbkey	`"?"`
header_lines	`"0"`

Step 10: Cut1:

step_state: scheduled

Jobs

Job 1:

Job state is ok

Command Line:

perl '/tmp/tmp1b6r_ugk/galaxy-dev/tools/filters/cutWrapper.pl' '/tmp/tmp1b6r_ugk/files/e/d/8/dataset_ed8bc3e4-df92-44d8-907b-5da21aaa08da.dat' 'c2' T '/tmp/tmp1b6r_ugk/job_working_directory/000/9/outputs/dataset_dd901dd1-b641-4a9c-a85f-1ea38ee23ccc.dat'

Exit Code:

```
0
```

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"tabular"`
__workflow_invocation_uuid__	`"c2c91de202e811f08d456045bd4cd061"`
chromInfo	`"/tmp/tmp1b6r_ugk/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
columnList	`"c2"`
dbkey	`"?"`
delimiter	`"T"`

Other invocation details
- history_id
  - ec0c744c40071cc2
- history_state
  - ok
- invocation_id
  - ec0c744c40071cc2
- invocation_state
  - scheduled
- workflow_id
  - ec0c744c40071cc2

gxydevbot changed the title ~~Updating workflows/VGP-assembly-v2/Assembly-decontamination-VGP9 from 0.3 to 0.4~~ Updating workflows/VGP-assembly-v2/Assembly-decontamination-VGP9 from 0.3 to 0.4 Nov 11, 2024

gxydevbot force-pushed the workflows/VGP-assembly-v2/Assembly-decontamination-VGP9 branch from 2e270bc to 8c96aaf Compare November 11, 2024 04:24

gxydevbot force-pushed the workflows/VGP-assembly-v2/Assembly-decontamination-VGP9 branch from 8c96aaf to 5d3ed92 Compare December 16, 2024 04:38

gxydevbot force-pushed the workflows/VGP-assembly-v2/Assembly-decontamination-VGP9 branch from 5d3ed92 to 21f4eb8 Compare February 10, 2025 04:23

gxydevbot force-pushed the workflows/VGP-assembly-v2/Assembly-decontamination-VGP9 branch from 21f4eb8 to 543dc95 Compare March 10, 2025 04:19

Updating workflows/VGP-assembly-v2/Assembly-decontamination-VGP9 from…

0dfe1bb

… 0.3 to 0.4

gxydevbot force-pushed the workflows/VGP-assembly-v2/Assembly-decontamination-VGP9 branch from 543dc95 to 0dfe1bb Compare March 17, 2025 04:21

Delphine-L added 2 commits March 18, 2025 12:11

Create README.md

bf19f9d

remove runtime parameters

d54dddd

Delphine-L approved these changes Mar 18, 2025

View reviewed changes

Delphine-L enabled auto-merge March 18, 2025 21:36

Delphine-L merged commit 1140080 into galaxyproject:main Mar 18, 2025
7 checks passed

gxydevbot deleted the workflows/VGP-assembly-v2/Assembly-decontamination-VGP9 branch March 31, 2025 04:35

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