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nf-test failing for pharokka

Open scorreard opened this issue 9 months ago • 0 comments

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

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System information

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scorreard avatar Mar 25 '25 11:03 scorreard