Nextflow stdout:

N E X T F L O W  ~  version 23.04.0
Launching `/home/runner/work/metapep/metapep/main.nf` [clever_edison] 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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  |\ | |__  __ /  ` /  \ |__) |__         }  {
  | \| |       \__, \__/ |  \ |___     \`-._,-`-,
                                        `._,._,'
  nf-core/metapep v1.0.0
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Core Nextflow options
  runName                   : clever_edison
  containerEngine           : docker
  launchDir                 : /home/runner/work/metapep/metapep/.nf-test/tests/6183a1a7db05f8512bca2196d4417b18
  workDir                   : /home/runner/work/metapep/metapep/.nf-test/tests/6183a1a7db05f8512bca2196d4417b18/work
  projectDir                : /home/runner/work/metapep/metapep
  userName                  : runner
  profile                   : test_mouse,docker
  configFiles               : 

Input/output options
  input                     : https://raw.githubusercontent.com/nf-core/test-datasets/metapep/samplesheets/v1.0/samplesheet.mouse.csv
  outdir                    : /home/runner/work/metapep/metapep/.nf-test/tests/6183a1a7db05f8512bca2196d4417b18/output

Institutional config options
  config_profile_name       : Test profile
  config_profile_description: Minimal test dataset to check pipeline function

Max job request options
  max_cpus                  : 2
  max_memory                : 6 GB
  max_time                  : 2d

Pipeline options
  min_pep_len               : 8

!! 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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[5b/556f6e] Submitted process > NFCORE_METAPEP:METAPEP:PROCESS_INPUT:CHECK_SAMPLESHEET_CREATE_TABLES (samplesheet.mouse.csv)
[c9/23d77b] Submitted process > NFCORE_METAPEP:METAPEP:PROCESS_INPUT:UNIFY_MODEL_LENGTHS (samplesheet.valid.csv)
[5a/9174dd] Submitted process > NFCORE_METAPEP:METAPEP:ASSIGN_NUCL_ENTITY_WEIGHTS (1)
[21/cda0b1] Submitted process > NFCORE_METAPEP:METAPEP:DOWNLOAD_PROTEINS ([0])
WARN: There is no SYFPEITHI model available for at least one allele and the peptide lengths are reduced to the common denominator of the alleles.
WARN: For more information about which peptide lengths were used check '/home/runner/work/metapep/metapep/.nf-test/tests/6183a1a7db05f8512bca2196d4417b18/output/logs/WARNING_unify_peptide_lengths.log'
[59/ad5f67] Submitted process > NFCORE_METAPEP:METAPEP:PRODIGAL (1)
[a0/4b04d6] Submitted process > NFCORE_METAPEP:METAPEP:CREATE_PROTEIN_TSV (1)
[21/cda0b1] NOTE: Process `NFCORE_METAPEP:METAPEP:DOWNLOAD_PROTEINS ([0])` terminated with an error exit status (1) -- Execution is retried (1)
[bb/287f33] Re-submitted process > NFCORE_METAPEP:METAPEP:DOWNLOAD_PROTEINS ([0])
[bb/287f33] NOTE: Process `NFCORE_METAPEP:METAPEP:DOWNLOAD_PROTEINS ([0])` terminated with an error exit status (1) -- Execution is retried (2)
[4a/1529f6] Re-submitted process > NFCORE_METAPEP:METAPEP:DOWNLOAD_PROTEINS ([0])
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/6183a1a7db05f8512bca2196d4417b18/work/4a/1529f6134982e0d8bade33678f9fb7

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/6183a1a7db05f8512bca2196d4417b18/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/6183a1a7db05f8512bca2196d4417b18/meta/nextflow.log' file for details
-[nf-core/metapep] Pipeline completed with errors-
Nextflow stderr: