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Fix test_bgc_pyrodigal config #1597

Fix test_bgc_pyrodigal config

Fix test_bgc_pyrodigal config #1597

GitHub Actions / JUnit Test Report failed Aug 21, 2024 in 0s

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

Annotations

Check failure on line 1 in test_bgc_pyrodigal_profile

See this annotation in the file changed.

@github-actions github-actions / JUnit Test Report

test_bgc_pyrodigal_profile

Assertion failed: 

12 of 14 assertions failed
Raw output
Nextflow stdout:

ERROR ~ Error executing process > 'NFCORE_FUNCSCAN:FUNCSCAN:BGC:DEEPBGC_DOWNLOAD'

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

Command executed:

  export DEEPBGC_DOWNLOADS_DIR='./deepbgc_db'
  
  deepbgc \
      download
  
  cat <<-END_VERSIONS > versions.yml
  "NFCORE_FUNCSCAN:FUNCSCAN:BGC:DEEPBGC_DOWNLOAD":
      deepbgc: $(echo $(deepbgc info 2>&1 /dev/null/ | grep 'version' | cut -d " " -f3) )
  END_VERSIONS

Command exit status:
  1

Command output:
  (empty)

Command error:
      self._send_request(method, url, body, headers, encode_chunked)
    File "/usr/local/lib/python3.7/http/client.py", line 1327, in _send_request
      self.endheaders(body, encode_chunked=encode_chunked)
    File "/usr/local/lib/python3.7/http/client.py", line 1276, in endheaders
      self._send_output(message_body, encode_chunked=encode_chunked)
    File "/usr/local/lib/python3.7/http/client.py", line 1036, in _send_output
      self.send(msg)
    File "/usr/local/lib/python3.7/http/client.py", line 976, in send
      self.connect()
    File "/usr/local/lib/python3.7/http/client.py", line 1451, in connect
      server_hostname=server_hostname)
    File "/usr/local/lib/python3.7/ssl.py", line 423, in wrap_socket
      session=session
    File "/usr/local/lib/python3.7/ssl.py", line 870, in _create
      self.do_handshake()
    File "/usr/local/lib/python3.7/ssl.py", line 1139, in do_handshake
      self._sslobj.do_handshake()
  ConnectionResetError: [Errno 104] Connection reset by peer
  
  During handling of the above exception, another exception occurred:
  
  Traceback (most recent call last):
    File "/usr/local/lib/python3.7/site-packages/deepbgc/main.py", line 113, in main
      run(argv)
    File "/usr/local/lib/python3.7/site-packages/deepbgc/main.py", line 102, in run
      args.func.run(**args_dict)
    File "/usr/local/lib/python3.7/site-packages/deepbgc/command/download.py", line 25, in run
      util.download_files(DOWNLOADS)
    File "/usr/local/lib/python3.7/site-packages/deepbgc/util.py", line 403, in download_files
      download_file(url=url, target_path=target_path, checksum=checksum, gzipped=gzipped)
    File "/usr/local/lib/python3.7/site-packages/deepbgc/util.py", line 425, in download_file
      urlretrieve(url, download_path)
    File "/usr/local/lib/python3.7/urllib/request.py", line 247, in urlretrieve
      with contextlib.closing(urlopen(url, data)) as fp:
    File "/usr/local/lib/python3.7/urllib/request.py", line 222, in urlopen
      return opener.open(url, data, timeout)
    File "/usr/local/lib/python3.7/urllib/request.py", line 525, in open
      response = self._open(req, data)
    File "/usr/local/lib/python3.7/urllib/request.py", line 543, in _open
      '_open', req)
    File "/usr/local/lib/python3.7/urllib/request.py", line 503, in _call_chain
      result = func(*args)
    File "/usr/local/lib/python3.7/urllib/request.py", line 1393, in https_open
      context=self._context, check_hostname=self._check_hostname)
    File "/usr/local/lib/python3.7/urllib/request.py", line 1352, in do_open
      raise URLError(err)
  urllib.error.URLError: <urlopen error [Errno 104] Connection reset by peer>
  ERROR   21/08 15:24:31   ================================================================================
  ERROR   21/08 15:24:31   DeepBGC failed with URLError: [Errno 104] Connection reset by peer
  ERROR   21/08 15:24:31   ================================================================================

Work dir:
  /home/runner/work/funcscan/funcscan/.nf-test/tests/2477b7bee34e2ea73b7b824b229ab27d/work/08/3653e236efe4533f74957098bdf0d2

Tip: you can try to figure out what's wrong by changing to the process work dir and showing the script file named `.command.sh`

 -- Check '/home/runner/work/funcscan/funcscan/.nf-test/tests/2477b7bee34e2ea73b7b824b229ab27d/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/2477b7bee34e2ea73b7b824b229ab27d/meta/nextflow.log' file for details
Nextflow stderr:

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