Fix test_bgc_pyrodigal config #1597
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failed
Aug 21, 2024 in 0s
1 tests run, 0 passed, 0 skipped, 1 failed.
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Check failure on line 1 in conf/test_taxonomy_pyrodigal.config
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:
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