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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 conf/test_taxonomy_pyrodigal.config

See this annotation in the file changed.

@github-actions github-actions / JUnit Test Report

test_taxonomy_pyrodigal

Assertion failed: 

16 of 17 assertions failed
Raw output
Nextflow stdout:

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

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


Command executed:

  download-antismash-databases \
      --database-dir antismash_db \
  
  
  cp -r /usr/local/lib/python3.10/site-packages/antismash antismash_dir;
  
  cat <<-END_VERSIONS > versions.yml
  "NFCORE_FUNCSCAN:FUNCSCAN:BGC:ANTISMASH_ANTISMASHLITEDOWNLOADDATABASES":
      antismash-lite: $(antismash --version | sed 's/antiSMASH //')
  END_VERSIONS

Command exit status:
  1

Command output:
  
  Downloading antismash.js: 54.32% downloaded.
  Downloading antismash.js: 100.00% downloaded.
  Downloading PFAM version 35.0

Command error:
    File "/usr/local/lib/python3.10/http/client.py", line 1038, in _send_output
      self.send(msg)
    File "/usr/local/lib/python3.10/http/client.py", line 976, in send
      self.connect()
    File "/usr/local/lib/python3.10/http/client.py", line 1455, in connect
      self.sock = self._context.wrap_socket(self.sock,
    File "/usr/local/lib/python3.10/ssl.py", line 513, in wrap_socket
      return self.sslsocket_class._create(
    File "/usr/local/lib/python3.10/ssl.py", line 1104, in _create
      self.do_handshake()
    File "/usr/local/lib/python3.10/ssl.py", line 1375, 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/python3.10/site-packages/antismash/download_databases.py", line 125, in download_file
      req = request.urlopen(url)  # pylint: disable=consider-using-with
    File "/usr/local/lib/python3.10/urllib/request.py", line 216, in urlopen
      return opener.open(url, data, timeout)
    File "/usr/local/lib/python3.10/urllib/request.py", line 519, in open
      response = self._open(req, data)
    File "/usr/local/lib/python3.10/urllib/request.py", line 536, in _open
      result = self._call_chain(self.handle_open, protocol, protocol +
    File "/usr/local/lib/python3.10/urllib/request.py", line 496, in _call_chain
      result = func(*args)
    File "/usr/local/lib/python3.10/urllib/request.py", line 1391, in https_open
      return self.do_open(http.client.HTTPSConnection, req,
    File "/usr/local/lib/python3.10/urllib/request.py", line 1351, in do_open
      raise URLError(err)
  urllib.error.URLError: <urlopen error [Errno 104] Connection reset by peer>
  
  During handling of the above exception, another exception occurred:
  
  Traceback (most recent call last):
    File "/usr/local/bin/download-antismash-databases", line 10, in <module>
      sys.exit(_main())
    File "/usr/local/lib/python3.10/site-packages/antismash/download_databases.py", line 521, in _main
      if not download(args):
    File "/usr/local/lib/python3.10/site-packages/antismash/download_databases.py", line 474, in download
      download_pfam(
    File "/usr/local/lib/python3.10/site-packages/antismash/download_databases.py", line 254, in download_pfam
      download_if_not_present(url, archive_filename, archive_checksum)
    File "/usr/local/lib/python3.10/site-packages/antismash/download_databases.py", line 226, in download_if_not_present
      download_file(url, filename)
    File "/usr/local/lib/python3.10/site-packages/antismash/download_databases.py", line 127, in download_file
      raise DownloadError("ERROR: File not found on server.\nPlease check your internet connection.")
  antismash.download_databases.DownloadError: ERROR: File not found on server.
  Please check your internet connection.

Work dir:
  /home/runner/work/funcscan/funcscan/.nf-test/tests/237a9cc7d7305da4ae99f8a5873c779a/work/44/0a1ee69139fa8a19f13b0a513b367c

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/funcscan/funcscan/.nf-test/tests/237a9cc7d7305da4ae99f8a5873c779a/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/237a9cc7d7305da4ae99f8a5873c779a/meta/nextflow.log' file for details
Nextflow stderr: