Skip to content
New issue

Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.

Sign up for GitHub

By clicking “Sign up for GitHub”, you agree to our terms of service and privacy statement. We’ll occasionally send you account related emails.

Already on GitHub? Sign in to your account

Jump to bottom

Update citations #422

Open
wants to merge 1 commit into
base: dev
Choose a base branch
from

Update antismash, argnorm, rgi citations

2f48508
Select commit
Loading
Failed to load commit list.
Refresh
Sign in for the full log view
Open

Update citations #422

Update antismash, argnorm, rgi citations
2f48508
Select commit
Loading
Failed to load commit list.
GitHub Actions / JUnit Test Report failed Oct 11, 2024 in 0s

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

Annotations

Check failure on line 1 in test_prokka_profile

See this annotation in the file changed.

@github-actions github-actions / JUnit Test Report

test_prokka_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
  32ac20ce48fd: Waiting
  bd9ddc54bea9: Download complete
  ca7680d1025d: 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/d99a60cee47c5be7a5168986c5ae96ee/work/ca/c970217d1a883dd9a917078bc2b31e

Container:
  quay.io/biocontainers/ampcombi:0.2.2--pyhdfd78af_0

Tip: you can replicate the issue by changing to the process work dir and entering the command `bash .command.run`

 -- Check '/home/runner/work/funcscan/funcscan/.nf-test/tests/d99a60cee47c5be7a5168986c5ae96ee/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/d99a60cee47c5be7a5168986c5ae96ee/meta/nextflow.log' file for details
Nextflow stderr:
View more details on GitHub Actions