Esmecata x eggnog singularity error #15
Description
Hi,
We would like to implement eggnog in the singularity of Esmecata, but we (@lecorguille) met an error:
INFO: underlay of /etc/localtime required more than 50 (82) bind mounts
Traceback (most recent call last):
File "/opt/conda/lib/python3.12/urllib/request.py", line 1344, in do_open
h.request(req.get_method(), req.selector, req.data, headers,
File "/opt/conda/lib/python3.12/http/client.py", line 1331, in request
self._send_request(method, url, body, headers, encode_chunked)
File "/opt/conda/lib/python3.12/http/client.py", line 1377, in _send_request
self.endheaders(body, encode_chunked=encode_chunked)
File "/opt/conda/lib/python3.12/http/client.py", line 1326, in endheaders
self._send_output(message_body, encode_chunked=encode_chunked)
File "/opt/conda/lib/python3.12/http/client.py", line 1085, in _send_output
self.send(msg)
File "/opt/conda/lib/python3.12/http/client.py", line 1029, in send
self.connect()
File "/opt/conda/lib/python3.12/http/client.py", line 1472, in connect
self.sock = self._context.wrap_socket(self.sock,
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/opt/conda/lib/python3.12/ssl.py", line 455, in wrap_socket
return self.sslsocket_class._create(
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/opt/conda/lib/python3.12/ssl.py", line 1042, in _create
self.do_handshake()
File "/opt/conda/lib/python3.12/ssl.py", line 1320, 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 "/opt/conda/bin/esmecata", line 8, in
sys.exit(main())
^^^^^^
File "/opt/conda/lib/python3.12/site-packages/esmecata/main.py", line 433, in main
perform_workflow_eggnog(args.input, args.output, args.eggnog_database, busco_score,
File "/opt/conda/lib/python3.12/site-packages/esmecata/workflow.py", line 203, in perform_workflow_eggnog
retrieve_proteomes(input_file, proteomes_output_folder, busco_percentage_keep,
File "/opt/conda/lib/python3.12/site-packages/esmecata/proteomes.py", line 1409, in retrieve_proteomes
uniprot_releases = get_rest_uniprot_release(options)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/opt/conda/lib/python3.12/site-packages/esmecata/utils.py", line 167, in get_rest_uniprot_release
uniprot_response = urllib_query(uniprot_urllib_request)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/opt/conda/lib/python3.12/site-packages/esmecata/utils.py", line 142, in urllib_query
response = urllib.request.urlopen(request)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/opt/conda/lib/python3.12/urllib/request.py", line 215, in urlopen
return opener.open(url, data, timeout)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/opt/conda/lib/python3.12/urllib/request.py", line 515, in open
response = self._open(req, data)
^^^^^^^^^^^^^^^^^^^^^
File "/opt/conda/lib/python3.12/urllib/request.py", line 532, in _open
result = self._call_chain(self.handle_open, protocol, protocol +
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/opt/conda/lib/python3.12/urllib/request.py", line 492, in _call_chain
result = func(*args)
^^^^^^^^^^^
File "/opt/conda/lib/python3.12/urllib/request.py", line 1392, in https_open
return self.do_open(http.client.HTTPSConnection, req,
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/opt/conda/lib/python3.12/urllib/request.py", line 1347, in do_open
raise URLError(err)
urllib.error.URLError: <urlopen error [Errno 104] Connection reset by peer>
It seems that esmecata in the eggnog workflow attempts to access the Uniprot REST API (uniprot_releases = get_rest_uniprot_release(options).
Could you help us ? :)
Thank you for your help,
Coralie