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Important! Template update for nf-core/tools v3.0.2 #1377

Important! Template update for nf-core/tools v3.0.2

Important! Template update for nf-core/tools v3.0.2 #1377

GitHub Actions / JUnit Test Report failed Oct 23, 2024 in 0s

1 tests run, 0 passed, 0 skipped, 1 failed.

Annotations

Check failure on line 1 in Test pipeline: NFCORE_FUNCSCAN

See this annotation in the file changed.

@github-actions github-actions / JUnit Test Report

Test pipeline: NFCORE_FUNCSCAN.test_profile

Assertion failed: 

19 of 22 assertions failed
Raw output
Nextflow stdout:

ERROR ~ Error executing process > 'NFCORE_FUNCSCAN:FUNCSCAN:AMP:DRAMP_DOWNLOAD'

Caused by:
  Process `NFCORE_FUNCSCAN:FUNCSCAN:AMP:DRAMP_DOWNLOAD` terminated with an error exit status (1)


Command executed:

  mkdir amp_ref_database/
  ampcombi_download.py
  
  cat <<-END_VERSIONS > versions.yml
  "NFCORE_FUNCSCAN:FUNCSCAN:AMP:DRAMP_DOWNLOAD":
      ampcombi: $(ampcombi --version | sed 's/ampcombi //')
  END_VERSIONS

Command exit status:
  1

Command output:
  (empty)

Command error:
  Unable to find image 'quay.io/biocontainers/ampcombi:0.2.2--pyhdfd78af_0' locally
  0.2.2--pyhdfd78af_0: Pulling from biocontainers/ampcombi
  ca7680d1025d: Pulling fs layer
  bd9ddc54bea9: Pulling fs layer
  32ac20ce48fd: Pulling fs layer
  ca7680d1025d: Verifying Checksum
  ca7680d1025d: Download complete
  bd9ddc54bea9: Download complete
  ca7680d1025d: Pull complete
  bd9ddc54bea9: Pull complete
  32ac20ce48fd: Verifying Checksum
  32ac20ce48fd: Download complete
  32ac20ce48fd: Pull complete
  Digest: sha256:e146a1e61af09d923f2dc7bd63ea8fa43b1c1aca18e139edeaf0f2da0720647f
  Status: Downloaded newer image for quay.io/biocontainers/ampcombi:0.2.2--pyhdfd78af_0
  Traceback (most recent call last):
    File "/home/runner/work/funcscan/funcscan/bin/ampcombi_download.py", line 78, in <module>
      download_DRAMP("amp_ref_database")
    File "/home/runner/work/funcscan/funcscan/bin/ampcombi_download.py", line 49, in download_DRAMP
      for record in seq_record:
    File "/usr/local/lib/python3.11/site-packages/Bio/SeqIO/Interfaces.py", line 72, in __next__
      return next(self.records)
             ^^^^^^^^^^^^^^^^^^
    File "/usr/local/lib/python3.11/site-packages/Bio/SeqIO/FastaIO.py", line 246, in iterate
      Seq(sequence), id=first_word, name=first_word, description=title
      ^^^^^^^^^^^^^
    File "/usr/local/lib/python3.11/site-packages/Bio/Seq.py", line 2034, in __init__
      self._data = bytes(data, encoding="ASCII")
                   ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  UnicodeEncodeError: 'ascii' codec can't encode character '\u5de5' in position 20: ordinal not in range(128)

Work dir:
  /home/runner/work/funcscan/funcscan/.nf-test/tests/b21ace592902b8c74614205f24730282/work/85/37f28e2dd2b1a7acd9f67e52f39e8a

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

 -- Check '/home/runner/work/funcscan/funcscan/.nf-test/tests/b21ace592902b8c74614205f24730282/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/funcscan/funcscan/.nf-test/tests/b21ace592902b8c74614205f24730282/meta/nextflow.log' file for details
Nextflow stderr:

Nextflow 24.04.4 is available - Please consider updating your version to it