nf-test failing for pharokka
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Description
Have you checked the docs?
Description of the bug
Phakorra failed the nf-test using conda, raising a fail check for https://github.com/nf-core/modules/pull/7978
Below is the error message.
`Test Process PHAROKKA_PHAROKKA
Test [f4ff6f3f] 'sarscov2 - genome - fasta'
> Nextflow 24.10.5 is available - Please consider updating your version to it
> N E X T F L O W ~ version 24.10.2
> Launching /home/runner/_work/modules/modules/.nf-test-f4ff6f3ff2c31cdd0ae0bfea1540e4f4.nf [hopeful_hilbert] DSL2 - revision: e51904f677
> Creating env using conda: /home/runner/_work/modules/modules/modules/nf-core/pharokka/pharokka/tests/../../installdatabases/environment.yml [cache /home/runner/_work/modules/modules/.nf-test/tests/f4ff6f3ff2c31cdd0ae0bfea1540e4f4/work/conda/env-8796bb19d0606be9-38590c47211f7272b7570db0336b1682]
> [79/da17d2] Submitted process > PHAROKKA_INSTALLDATABASES
> Creating env using conda: /home/runner/_work/modules/modules/modules/nf-core/pharokka/pharokka/tests/../environment.yml [cache /home/runner/_work/modules/modules/.nf-test/tests/f4ff6f3ff2c31cdd0ae0bfea1540e4f4/work/conda/env-59d3ccaaf552043f-38590c47211f7272b7570db0336b1682]
> [6d/ac833f] Submitted process > PHAROKKA_PHAROKKA (test)
> ERROR ~ Error executing process > 'PHAROKKA_PHAROKKA (test)'
>
> Caused by:
> Process PHAROKKA_PHAROKKA (test) terminated with an error exit status (1)
>
>
> Command executed:
>
> pharokka.py
> --infile genome.fasta
> --outdir test_pharokka
> --database pharokka_db
> --threads 2
> --prefix test
> --fast --skip_extra_annotations --skip_mash
>
> cat <<-END_VERSIONS > versions.yml
> "PHAROKKA_PHAROKKA":
> pharokka: $(pharokka.py --version)
> END_VERSIONS
>
> Command exit status:
> 1
>
> Command output:
> (empty)
>
> Command error:
> 2025-03-24 19:14:10.680 | INFO | input_commands:check_dependencies:493 - MinCED version is ok.
> 2025-03-24 19:14:10.689 | INFO | input_commands:check_dependencies:519 - ARAGORN version found is v1.2.41
> 2025-03-24 19:14:10.689 | INFO | input_commands:check_dependencies:530 - ARAGORN version is ok.
> 2025-03-24 19:14:11.034 | INFO | input_commands:check_dependencies:573 - Dnaapler version found is v1.2.0
> 2025-03-24 19:14:11.035 | INFO | input_commands:check_dependencies:580 - Dnaapler version is ok.
> 2025-03-24 19:14:11.035 | INFO | input_commands:check_dependencies:592 - Pyrodigal version is v3.6.3
> 2025-03-24 19:14:11.035 | INFO | input_commands:check_dependencies:593 - Pyrodigal version is ok.
> 2025-03-24 19:14:11.035 | INFO | input_commands:check_dependencies:605 - Pyrodigal_gv version is v0.3.2
> 2025-03-24 19:14:11.035 | INFO | input_commands:check_dependencies:606 - Pyrodigal_gv version is ok.
> 2025-03-24 19:14:11.039 | INFO | input_commands:validate_fasta:230 - Checking input genome.fasta.
> 2025-03-24 19:14:11.040 | INFO | input_commands:validate_fasta:232 - Input genome.fasta is in FASTA format.
> 2025-03-24 19:14:11.040 | INFO | input_commands:validate_fasta:237 - Checking input genome.fasta for duplicate FASTA headers.
> 2025-03-24 19:14:11.040 | INFO | input_commands:validate_fasta:239 - All headers in genome.fasta are unique.
> 2025-03-24 19:14:11.040 | INFO | input_commands:validate_gene_predictor:268 - Phanotate will be used for gene prediction.
> 2025-03-24 19:14:11.040 | INFO | main:main:255 - You have specified --fast or --hmm_only. MMseqs2 will not be run.
> 2025-03-24 19:14:11.040 | INFO |
> 2025-03-24 19:14:10.496 | INFO | input_commands:check_dependencies:414 - MMseqs2 version found is v13.45111
> 2025-03-24 19:14:10.496 | INFO | input_commands:check_dependencies:423 - MMseqs2 version is ok.
> 2025-03-24 19:14:10.621 | INFO | input_commands:check_dependencies:447 - tRNAscan-SE version found is v2.0.12
> 2025-03-24 19:14:10.621 | INFO | input_commands:check_dependencies:458 - tRNAscan-SE version is ok.
> 2025-03-24 19:14:10.679 | INFO | input_commands:check_dependencies:482 - MinCED version found is v0.4.2
> 2025-03-24 19:14:10.680 | INFO | input_commands:check_dependencies:493 - MinCED version is ok.
> 2025-03-24 19:14:10.689 | INFO | input_commands:check_dependencies:519 - ARAGORN version found is v1.2.41
> 2025-03-24 19:14:10.689 | INFO | input_commands:check_dependencies:530 - ARAGORN version is ok.
> 2025-03-24 19:14:11.034 | INFO | input_commands:check_dependencies:573 - Dnaapler version found is v1.2.0
> 2025-03-24 19:14:11.035 | INFO | input_commands:check_dependencies:580 - Dnaapler version is ok.
> 2025-03-24 19:14:11.035 | INFO | input_commands:check_dependencies:592 - Pyrodigal version is v3.6.3
> 2025-03-24 19:14:11.035 | INFO | input_commands:check_dependencies:593 - Pyrodigal version is ok.
> 2025-03-24 19:14:11.035 | INFO | input_commands:check_dependencies:605 - Pyrodigal_gv version is v0.3.2
> 2025-03-24 19:14:11.035 | INFO | input_commands:check_dependencies:606 - Pyrodigal_gv version is ok.
> 2025-03-24 19:14:11.039 | INFO | input_commands:validate_fasta:230 - Checking input genome.fasta.
> 2025-03-24 19:14:11.040 | INFO | input_commands:validate_fasta:232 - Input genome.fasta is in FASTA format.
> 2025-03-24 19:14:11.040 | INFO | input_commands:validate_fasta:237 - Checking input genome.fasta for duplicate FASTA headers.
> 2025-03-24 19:14:11.040 | INFO | input_commands:validate_fasta:239 - All headers in genome.fasta are unique.
> 2025-03-24 19:14:11.040 | INFO | input_commands:validate_gene_predictor:268 - Phanotate will be used for gene prediction.
> 2025-03-24 19:14:11.040 | INFO | main:main:255 - You have specified --fast or --hmm_only. MMseqs2 will not be run.
> 2025-03-24 19:14:11.040 | INFO | main:main:280 - Running Phanotate.
> 2025-03-24 19:14:11.041 | INFO | external_tools:run:50 - Started running phanotate.py -f fasta -o test_pharokka/phanotate_out_tmp.fasta genome.fasta ...
> 2025-03-24 19:14:21.724 | INFO | external_tools:run:52 - Done running phanotate.py -f fasta -o test_pharokka/phanotate_out_tmp.fasta genome.fasta
> 2025-03-24 19:14:21.725 | INFO | external_tools:run:50 - Started running phanotate.py -f tabular -o test_pharokka/phanotate_out.txt genome.fasta ...
> 2025-03-24 19:14:32.367 | INFO | external_tools:run:52 - Done running phanotate.py -f tabular -o test_pharokka/phanotate_out.txt genome.fasta
> 2025-03-24 19:14:32.377 | INFO | main:main:348 - Running PyHMMER on PHROGs.
> Traceback (most recent call last):
> File "/home/runner/_work/modules/modules/.nf-test/tests/f4ff6f3ff2c31cdd0ae0bfea1540e4f4/work/conda/env-59d3ccaaf552043f-38590c47211f7272b7570db0336b1682/bin/pharokka.py", line 489, in
> main()
> File "/home/runner/_work/modules/modules/.nf-test/tests/f4ff6f3ff2c31cdd0ae0bfea1540e4f4/work/conda/env-59d3ccaaf552043f-38590c47211f7272b7570db0336b1682/bin/pharokka.py", line 349, in main
> best_results_pyhmmer = run_pyhmmer(
> File "/home/runner/_work/modules/modules/.nf-test/tests/f4ff6f3ff2c31cdd0ae0bfea1540e4f4/work/conda/env-59d3ccaaf552043f-38590c47211f7272b7570db0336b1682/bin/hmm.py", line 40, in run_pyhmmer
> protein = hits.query_name.decode() # get protein from the hit
> AttributeError: 'pyhmmer.plan7.TopHits' object has no attribute 'query_name'
>
> Work dir:
> /home/runner/_work/modules/modules/.nf-test/tests/f4ff6f3ff2c31cdd0ae0bfea1540e4f4/work/6d/ac833ff7a6dab833a1f049c80dd7a6
>
> Tip: view the complete command output by changing to the process work dir and entering the command cat .command.out
>
> -- Check '/home/runner/_work/modules/modules/.nf-test/tests/f4ff6f3ff2c31cdd0ae0bfea1540e4f4/meta/nextflow.log' file for details
Assertion failed:
assert process.success
| |
| false
PHAROKKA_PHAROKKA
java.lang.RuntimeException: Different Snapshot:
[ [
[ [
[ |
{ <
"id": "test" <
}, <
"test_cds_functions.tsv:md5,ba4bd022017c08732cc0d4605c6d3239" <
] <
], ],
[ [
[ |
{ <
"id": "test" <
}, <
"test_length_gc_cds_density.tsv:md5,de7140ac240f436b5a8d12e31f60a8d7" <
] <
], ],
[ [
"versions.yml:md5,244cd911d1c071dc1f6ec9effc6fdd3d" |
] ]
] ]
java.lang.NullPointerException: Cannot invoke method getAt() on null object
FAILED (83.515s)`
Command used and terminal output
Relevant files
No response
System information
No response
Contributor guide
First steps
- Read the whole issue, then the project's contributing guide.
- Comment on the issue to say you are picking it up — it saves two people doing the same work.
- Fork the repository and make your change on a branch.
- Open a pull request that references the issue number.
Research direction
Start with the PHAROKKA module test under modules/nf-core/pharokka/pharokka/tests and its environment.yml, then reproduce the conda nf-test failure. Use the reported hmm.py/pyhmmer traceback and snapshot mismatch as checks; done when PHAROKKA_PHAROKKA succeeds and its expected snapshot passes.
Written by the indexing model from the issue text.
Assessment
- Tech stack
- python
- Domain
- testing-qa
- Issue type
- Bug
- Difficulty
- 4/5
- Estimated time
- 3-5 days
- Activity status
- Stale
- Clarity
- Needs clarification
- Newbie friendliness
- 35/100