DFAST CI failures due to connection refused issues #287
Description
Description of the bug
DFAST Failure
The DFAST connection issue is blocking multiple PRs ( #275, #284... )
and is unrelated to the changes in those PRs.
Command used and terminal output
$ Test [32a60ed0] '-profile test_dfast'
ERROR ~ Error executing process > 'NFCORE_BACASS:BACASS:DFAST (ERR064912-unicycler)'
Caused by:
Process `NFCORE_BACASS:BACASS:DFAST (ERR064912-unicycler)` terminated with an error exit status (1)
Command executed:
dfast_file_downloader.py \
\
--protein dfast \
--dbroot .
dfast \
\
--genome ERR064912-unicycler.scaffolds.fa.gz \
--config test_config_dfast.py
mv RESULT_TEST/ ERR064912-unicycler_results/
cat <<-END_VERSIONS > versions.yml
"NFCORE_BACASS:BACASS:DFAST":
dfast: $( dfast --version | sed -e "s/DFAST ver. //g" )
END_VERSIONS
Command exit status:
1
Command output:
(empty)
Command error:
File "/usr/local/lib/python3.12/http/client.py", line 1336, in request
self._send_request(method, url, body, headers, encode_chunked)
File "/usr/local/lib/python3.12/http/client.py", line 1382, in _send_request
self.endheaders(body, encode_chunked=encode_chunked)
File "/usr/local/lib/python3.12/http/client.py", line 1331, in endheaders
self._send_output(message_body, encode_chunked=encode_chunked)
File "/usr/local/lib/python3.12/http/client.py", line 1091, in _send_output
self.send(msg)
File "/usr/local/lib/python3.12/http/client.py", line 1035, in send
self.connect()
File "/usr/local/lib/python3.12/http/client.py", line 1470, in connect
super().connect()
File "/usr/local/lib/python3.12/http/client.py", line 1001, in connect
self.sock = self._create_connection(
^^^^^^^^^^^^^^^^^^^^^^^^
File "/usr/local/lib/python3.12/socket.py", line 865, in create_connection
raise exceptions[0]
File "/usr/local/lib/python3.12/socket.py", line 850, in create_connection
sock.connect(sa)
ConnectionRefusedError: [Errno 111] Connection refused
During handling of the above exception, another exception occurred:
Traceback (most recent call last):
File "/usr/local/bin/dfast_file_downloader.py", line 247, in <module>
retrieved_file = retrieve_dfast_reference(db_name, out_dir)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/usr/local/bin/dfast_file_downloader.py", line 110, in retrieve_dfast_reference
request.urlretrieve(target_url, output_file)
File "/usr/local/lib/python3.12/urllib/request.py", line 240, in urlretrieve
with contextlib.closing(urlopen(url, data)) as fp:
^^^^^^^^^^^^^^^^^^
File "/usr/local/lib/python3.12/urllib/request.py", line 215, in urlopen
return opener.open(url, data, timeout)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/usr/local/lib/python3.12/urllib/request.py", line 515, in open
response = self._open(req, data)
^^^^^^^^^^^^^^^^^^^^^
File "/usr/local/lib/python3.12/urllib/request.py", line 532, in _open
result = self._call_chain(self.handle_open, protocol, protocol +
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/usr/local/lib/python3.12/urllib/request.py", line 492, in _call_chain
result = func(*args)
^^^^^^^^^^^
File "/usr/local/lib/python3.12/urllib/request.py", line 1392, in https_open
return self.do_open(http.client.HTTPSConnection, req,
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/usr/local/lib/python3.12/urllib/request.py", line 1347, in do_open
raise URLError(err)
urllib.error.URLError: <urlopen error [Errno 111] Connection refused>Relevant files
No response
System information
No response