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 test_bgc_pyrodigal_profile
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
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