Hi,
Thank you for your reply. Then I tested it on a server with 128GB RAM and it improved a lot.
Still, the conda process remains all the time. Output is following.
(64/66) Installing repository create_tool_recommendation_model from bgruening to section "Machine Learning" at revision afec8c595124 (TRT: 0:17:22.295197)
Timeout during install of create_tool_recommendation_model, extending wait to 1h
repository create_tool_recommendation_model installed successfully (in 0:03:40.381343) at revision afec8c595124
(65/66) Installing repository crosscontamination_barcode_filter from iuc to section "RNA-seq" at revision 5ade5cf200da (TRT: 0:21:02.677362)
Timeout during install of crosscontamination_barcode_filter, extending wait to 1h
Traceback (most recent call last):
File "/root/yy/galaxy/.venv/lib/python3.6/site-packages/urllib3/connectionpool.py", line 706, in urlopen
chunked=chunked,
File "/root/yy/galaxy/.venv/lib/python3.6/site-packages/urllib3/connectionpool.py", line 445, in _make_request
six.raise_from(e, None)
File "<string>", line 3, in raise_from
File "/root/yy/galaxy/.venv/lib/python3.6/site-packages/urllib3/connectionpool.py", line 440, in _make_request
httplib_response = conn.getresponse()
File "/root/yy/galaxy-tools/miniconda3/envs/_galaxy_/lib/python3.6/http/client.py", line 1383, in getresponse
response.begin()
File "/root/yy/galaxy-tools/miniconda3/envs/_galaxy_/lib/python3.6/http/client.py", line 320, in begin
version, status, reason = self._read_status()
File "/root/yy/galaxy-tools/miniconda3/envs/_galaxy_/lib/python3.6/http/client.py", line 289, in _read_status
raise RemoteDisconnected("Remote end closed connection without"
http.client.RemoteDisconnected: Remote end closed connection without response
During handling of the above exception, another exception occurred:
Traceback (most recent call last):
File "/root/yy/galaxy/.venv/lib/python3.6/site-packages/requests/adapters.py", line 449, in send
timeout=timeout
File "/root/yy/galaxy/.venv/lib/python3.6/site-packages/urllib3/connectionpool.py", line 756, in urlopen
method, url, error=e, _pool=self, _stacktrace=sys.exc_info()[2]
File "/root/yy/galaxy/.venv/lib/python3.6/site-packages/urllib3/util/retry.py", line 532, in increment
raise six.reraise(type(error), error, _stacktrace)
File "/root/yy/galaxy/.venv/lib/python3.6/site-packages/urllib3/packages/six.py", line 734, in reraise
raise value.with_traceback(tb)
File "/root/yy/galaxy/.venv/lib/python3.6/site-packages/urllib3/connectionpool.py", line 706, in urlopen
chunked=chunked,
File "/root/yy/galaxy/.venv/lib/python3.6/site-packages/urllib3/connectionpool.py", line 445, in _make_request
six.raise_from(e, None)
File "<string>", line 3, in raise_from
File "/root/yy/galaxy/.venv/lib/python3.6/site-packages/urllib3/connectionpool.py", line 440, in _make_request
httplib_response = conn.getresponse()
File "/root/yy/galaxy-tools/miniconda3/envs/_galaxy_/lib/python3.6/http/client.py", line 1383, in getresponse
response.begin()
File "/root/yy/galaxy-tools/miniconda3/envs/_galaxy_/lib/python3.6/http/client.py", line 320, in begin
version, status, reason = self._read_status()
File "/root/yy/galaxy-tools/miniconda3/envs/_galaxy_/lib/python3.6/http/client.py", line 289, in _read_status
raise RemoteDisconnected("Remote end closed connection without"
urllib3.exceptions.ProtocolError: ('Connection aborted.', RemoteDisconnected('Remote end closed connection without response',))
During handling of the above exception, another exception occurred:
Traceback (most recent call last):
File "/root/yy/galaxy/.venv/lib/python3.6/site-packages/ephemeris/shed_tools.py", line 410, in install_repository_revision
response = self.tool_shed_client.install_repository_revision(**repository)
File "/root/yy/galaxy/.venv/lib/python3.6/site-packages/bioblend/galaxy/toolshed/__init__.py", line 144, in install_repository_revision
return self._post(url=url, payload=payload)
File "/root/yy/galaxy/.venv/lib/python3.6/site-packages/bioblend/galaxy/client.py", line 173, in _post
files_attached=files_attached)
File "/root/yy/galaxy/.venv/lib/python3.6/site-packages/bioblend/galaxyclient.py", line 123, in make_post_request
timeout=self.timeout, allow_redirects=False)
File "/root/yy/galaxy/.venv/lib/python3.6/site-packages/requests/api.py", line 119, in post
return request('post', url, data=data, json=json, **kwargs)
File "/root/yy/galaxy/.venv/lib/python3.6/site-packages/requests/api.py", line 61, in request
return session.request(method=method, url=url, **kwargs)
File "/root/yy/galaxy/.venv/lib/python3.6/site-packages/requests/sessions.py", line 542, in request
resp = self.send(prep, **send_kwargs)
File "/root/yy/galaxy/.venv/lib/python3.6/site-packages/requests/sessions.py", line 655, in send
r = adapter.send(request, **kwargs)
File "/root/yy/galaxy/.venv/lib/python3.6/site-packages/requests/adapters.py", line 498, in send
raise ConnectionError(err, request=request)
requests.exceptions.ConnectionError: ('Connection aborted.', RemoteDisconnected('Remote end closed connection without response',))
During handling of the above exception, another exception occurred:
Traceback (most recent call last):
File "/root/yy/galaxy/.venv/bin/shed-tools", line 8, in <module>
sys.exit(main())
File "/root/yy/galaxy/.venv/lib/python3.6/site-packages/ephemeris/shed_tools.py", line 629, in main
**kwargs)
File "/root/yy/galaxy/.venv/lib/python3.6/site-packages/ephemeris/shed_tools.py", line 176, in install_repositories
result = self.install_repository_revision(repository, log)
File "/root/yy/galaxy/.venv/lib/python3.6/site-packages/ephemeris/shed_tools.py", line 448, in install_repository_revision
start=start, msg=e.body,
AttributeError: 'ConnectionError' object has no attribute 'body'
The galaxy.log doesn’t seem to be giving any errors.
Thanks,
Yukie