Nextflow stdout:

N E X T F L O W  ~  version 23.04.0
Launching `/home/runner/work/metapep/metapep/main.nf` [irreverent_heisenberg] 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                   : irreverent_heisenberg
  containerEngine           : docker
  launchDir                 : /home/runner/work/metapep/metapep/.nf-test/tests/3569a14223b7f5129f371cabebf105ac
  workDir                   : /home/runner/work/metapep/metapep/.nf-test/tests/3569a14223b7f5129f371cabebf105ac/work
  projectDir                : /home/runner/work/metapep/metapep
  userName                  : runner
  profile                   : test_all,docker
  configFiles               : 

Input/output options
  input                     : https://raw.githubusercontent.com/nf-core/test-datasets/metapep/samplesheets/v1.0/samplesheet.all.csv
  outdir                    : /home/runner/work/metapep/metapep/.nf-test/tests/3569a14223b7f5129f371cabebf105ac/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

!! 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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[9f/875509] Submitted process > NFCORE_METAPEP:METAPEP:PROCESS_INPUT:CHECK_SAMPLESHEET_CREATE_TABLES (samplesheet.all.csv)
[51/4b530e] Submitted process > NFCORE_METAPEP:METAPEP:PROCESS_INPUT:UNIFY_MODEL_LENGTHS (samplesheet.valid.csv)
[16/a91c44] Submitted process > NFCORE_METAPEP:METAPEP:ASSIGN_NUCL_ENTITY_WEIGHTS (2)
[e9/5e89c4] Submitted process > NFCORE_METAPEP:METAPEP:DOWNLOAD_PROTEINS ([0])
[58/b03be8] Submitted process > NFCORE_METAPEP:METAPEP:PRODIGAL (2)
[7c/5aa867] Submitted process > NFCORE_METAPEP:METAPEP:PROCESS_INPUT:UNPACK_BIN_ARCHIVES (1)
[e6/32f6d1] Submitted process > NFCORE_METAPEP:METAPEP:CREATE_PROTEIN_TSV (2)
[e9/5e89c4] NOTE: Process `NFCORE_METAPEP:METAPEP:DOWNLOAD_PROTEINS ([0])` terminated with an error exit status (1) -- Execution is retried (1)
[12/30acfd] Re-submitted process > NFCORE_METAPEP:METAPEP:DOWNLOAD_PROTEINS ([0])
[14/5d3c79] Submitted process > NFCORE_METAPEP:METAPEP:PRODIGAL (1)
[12/30acfd] NOTE: Process `NFCORE_METAPEP:METAPEP:DOWNLOAD_PROTEINS ([0])` terminated with an error exit status (1) -- Execution is retried (2)
[53/ece9be] Submitted process > NFCORE_METAPEP:METAPEP:PRODIGAL (1)
[c9/8b9e46] Re-submitted process > NFCORE_METAPEP:METAPEP:DOWNLOAD_PROTEINS ([0])
[9e/3f0321] Submitted process > NFCORE_METAPEP:METAPEP:CREATE_PROTEIN_TSV (1)
[5d/05b7c6] 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/c9/8b9e46d3bcacc82d1543fc2820e873

Tip: view the complete command output by changing to the process work dir and entering the command `cat .command.out`

 -- 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
-[nf-core/metapep] Pipeline completed with errors-
WARN: Killing running tasks (2)
Nextflow stderr: