Initial Release v1.0.0 #132
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Oct 18, 2024 in 0s
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nf.test all input path including protein downloads
Assertion failed:
16 of 18 assertions failed
Raw output
Nextflow stdout:
N E X T F L O W ~ version 24.09.2-edge
Launching `/home/runner/work/metapep/metapep/main.nf` [sharp_pauling] DSL2 - revision: 7fa7aa2a4e
Downloading plugin [email protected]
WARN: Access to undefined parameter `monochromeLogs` -- Initialise it to a default value eg. `params.monochromeLogs = some_value`
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[0;32m,--.[0;30m/[0;32m,-.[0m
[0;34m ___ __ __ __ ___ [0;32m/,-._.--~'[0m
[0;34m |\ | |__ __ / ` / \ |__) |__ [0;33m} {[0m
[0;34m | \| | \__, \__/ | \ |___ [0;32m\`-._,-`-,[0m
[0;32m`._,._,'[0m
[0;35m nf-core/metapep v1.0.0[0m
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[1mCore Nextflow options[0m
[0;34mrunName : [0;32msharp_pauling[0m
[0;34mcontainerEngine : [0;32mdocker[0m
[0;34mlaunchDir : [0;32m/home/runner/work/metapep/metapep/.nf-test/tests/3569a14223b7f5129f371cabebf105ac[0m
[0;34mworkDir : [0;32m/home/runner/work/metapep/metapep/.nf-test/tests/3569a14223b7f5129f371cabebf105ac/work[0m
[0;34mprojectDir : [0;32m/home/runner/work/metapep/metapep[0m
[0;34muserName : [0;32mrunner[0m
[0;34mprofile : [0;32mtest_all,docker[0m
[0;34mconfigFiles : [0;32m[0m
[1mInput/output options[0m
[0;34minput : [0;32mhttps://raw.githubusercontent.com/nf-core/test-datasets/metapep/samplesheets/v1.0/samplesheet.all.csv[0m
[0;34moutdir : [0;32m/home/runner/work/metapep/metapep/.nf-test/tests/3569a14223b7f5129f371cabebf105ac/output[0m
[1mInstitutional config options[0m
[0;34mconfig_profile_name : [0;32mTest profile[0m
[0;34mconfig_profile_description: [0;32mMinimal test dataset to check pipeline function[0m
[1mMax job request options[0m
[0;34mmax_cpus : [0;32m2[0m
[0;34mmax_memory : [0;32m6 GB[0m
[0;34mmax_time : [0;32m2d[0m
!! Only displaying parameters that differ from the pipeline defaults !!
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If you use nf-core/metapep for your analysis please cite:
* The pipeline
* The nf-core framework
https://doi.org/10.1038/s41587-020-0439-x
* Software dependencies
https:/nf-core/metapep/blob/master/CITATIONS.md
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[7a/8cdca5] Submitted process > NFCORE_METAPEP:METAPEP:PROCESS_INPUT:CHECK_SAMPLESHEET_CREATE_TABLES (samplesheet.all.csv)
[c1/a2cbe0] Submitted process > NFCORE_METAPEP:METAPEP:PROCESS_INPUT:UNIFY_MODEL_LENGTHS (samplesheet.valid.csv)
[51/70e072] Submitted process > NFCORE_METAPEP:METAPEP:ASSIGN_NUCL_ENTITY_WEIGHTS (2)
[28/ffd986] Submitted process > NFCORE_METAPEP:METAPEP:DOWNLOAD_PROTEINS ([0])
[e7/00df63] Submitted process > NFCORE_METAPEP:METAPEP:PRODIGAL (2)
[3e/e7864a] Submitted process > NFCORE_METAPEP:METAPEP:PROCESS_INPUT:UNPACK_BIN_ARCHIVES (1)
[c0/574a1f] Submitted process > NFCORE_METAPEP:METAPEP:CREATE_PROTEIN_TSV (2)
[28/ffd986] NOTE: Process `NFCORE_METAPEP:METAPEP:DOWNLOAD_PROTEINS ([0])` terminated with an error exit status (1) -- Execution is retried (1)
[72/dced32] Re-submitted process > NFCORE_METAPEP:METAPEP:DOWNLOAD_PROTEINS ([0])
[33/a9fc9a] Submitted process > NFCORE_METAPEP:METAPEP:PRODIGAL (1)
[72/dced32] NOTE: Process `NFCORE_METAPEP:METAPEP:DOWNLOAD_PROTEINS ([0])` terminated with an error exit status (1) -- Execution is retried (2)
[b6/9a329e] Submitted process > NFCORE_METAPEP:METAPEP:PRODIGAL (1)
[c0/ffc62b] Re-submitted process > NFCORE_METAPEP:METAPEP:DOWNLOAD_PROTEINS ([0])
[0c/c85d82] Submitted process > NFCORE_METAPEP:METAPEP:CREATE_PROTEIN_TSV (1)
ERROR ~ Error executing process > 'NFCORE_METAPEP:METAPEP:DOWNLOAD_PROTEINS ([0])'
Caused by:
Process `NFCORE_METAPEP:METAPEP:DOWNLOAD_PROTEINS ([0])` terminated with an error exit status (1)
Command executed:
# provide new home dir to avoid permission errors with Docker and other artefacts
export HOME="${PWD}/HOME"
download_proteins_entrez.py --email $NCBI_EMAIL \
--key $NCBI_KEY \
-t taxids.tsv \
-m 0 \
-p proteins.entrez.tsv.gz \
-ta taxa_assemblies.tsv \
-ep entities_proteins.entrez.tsv \
-me microbiomes_entities.entrez.tsv \
2>&1 | tee download_proteins.log
cat <<-END_VERSIONS > versions.yml
"NFCORE_METAPEP:METAPEP:DOWNLOAD_PROTEINS":
python: $(python --version | sed 's/Python //g')
biopython: $(python -c "import Bio; print(Bio.__version__)")
END_VERSIONS
Command exit status:
1
Command output:
Processing the following taxonomy IDs:
['243273', '662945']
Check if taxonomy IDs are on strain rank:
Taxids succeeded strain level check.
# taxa: 2
# taxa without assemblyId: 2
for each taxon without assemblyID retrieve assembly IDs ...
get assembly lengths and select largest assembly for each taxon ...
# selected assemblies: 0
for each assembly get nucloetide sequence IDs...
# nucleotide sequences (unique): 0
for each nucleotide sequence get proteins ...
# proteins (unique): 0
download proteins ...
Generated 1 chunks and start processing:
Process chunk with 0 protein_ids:
Traceback (most recent call last):
File "/home/runner/work/metapep/metapep/bin/download_proteins_entrez.py", line 408, in <module>
sys.exit(main())
File "/home/runner/work/metapep/metapep/bin/download_proteins_entrez.py", line 343, in main
protein_summaries.extend(Entrez.read(entrez_handle))
File "/usr/local/lib/python3.9/site-packages/Bio/Entrez/__init__.py", line 508, in read
record = handler.read(handle)
File "/usr/local/lib/python3.9/site-packages/Bio/Entrez/Parser.py", line 304, in read
self.parser.ParseFile(handle)
File "/home/conda/feedstock_root/build_artifacts/python-split_1611624120657/work/Modules/pyexpat.c", line 459, in EndElement
File "/usr/local/lib/python3.9/site-packages/Bio/Entrez/Parser.py", line 666, in endErrorElementHandler
raise RuntimeError(value)
RuntimeError: Empty id list - nothing todo
Command error:
Processing the following taxonomy IDs:
['243273', '662945']
Check if taxonomy IDs are on strain rank:
Taxids succeeded strain level check.
# taxa: 2
# taxa without assemblyId: 2
for each taxon without assemblyID retrieve assembly IDs ...
get assembly lengths and select largest assembly for each taxon ...
# selected assemblies: 0
for each assembly get nucloetide sequence IDs...
# nucleotide sequences (unique): 0
for each nucleotide sequence get proteins ...
# proteins (unique): 0
download proteins ...
Generated 1 chunks and start processing:
Process chunk with 0 protein_ids:
Traceback (most recent call last):
File "/home/runner/work/metapep/metapep/bin/download_proteins_entrez.py", line 408, in <module>
sys.exit(main())
File "/home/runner/work/metapep/metapep/bin/download_proteins_entrez.py", line 343, in main
protein_summaries.extend(Entrez.read(entrez_handle))
File "/usr/local/lib/python3.9/site-packages/Bio/Entrez/__init__.py", line 508, in read
record = handler.read(handle)
File "/usr/local/lib/python3.9/site-packages/Bio/Entrez/Parser.py", line 304, in read
self.parser.ParseFile(handle)
File "/home/conda/feedstock_root/build_artifacts/python-split_1611624120657/work/Modules/pyexpat.c", line 459, in EndElement
File "/usr/local/lib/python3.9/site-packages/Bio/Entrez/Parser.py", line 666, in endErrorElementHandler
raise RuntimeError(value)
RuntimeError: Empty id list - nothing todo
Work dir:
/home/runner/work/metapep/metapep/.nf-test/tests/3569a14223b7f5129f371cabebf105ac/work/c0/ffc62b516fc0a1868eb77118e6411b
Container:
quay.io/biocontainers/biopython:1.78
Tip: when you have fixed the problem you can continue the execution adding the option `-resume` to the run command line
-- Check '/home/runner/work/metapep/metapep/.nf-test/tests/3569a14223b7f5129f371cabebf105ac/meta/nextflow.log' file for details
ERROR ~ Pipeline failed. Please refer to troubleshooting docs: https://nf-co.re/docs/usage/troubleshooting
-- Check '/home/runner/work/metapep/metapep/.nf-test/tests/3569a14223b7f5129f371cabebf105ac/meta/nextflow.log' file for details
-[0;35m[nf-core/metapep][0;31m Pipeline completed with errors[0m-
WARN: Killing running tasks (2)
Nextflow stderr:
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