PEPATAC error: ConnectionResetError: [Errno 104] Connection reset by peer
1
0
Entering edit mode
6 months ago
m.taheri ▴ 50

To install and run PEPATC I followed this guide: https://pepatac.databio.org/en/latest/install/. I think I did every step right. But when I run the following command:

cd pepatac
looper run -d examples/test_project/test_config.yaml

I receive this error:

Looper version: 1.3.0
Command: run
ProjectContext pipeline_interfaces: '['/home/ptaklifi/pepatac/sample_pipeline_interface.yaml']'
Traceback (most recent call last):
  File "/home/ptaklifi/.local/bin/looper", line 8, in <module>
    sys.exit(main())
  File "/home/ptaklifi/.local/lib/python3.6/site-packages/looper/looper.py", line 743, in main
    run(args, rerun=(args.command == "rerun"), **compute_kwargs)
  File "/home/ptaklifi/.local/lib/python3.6/site-packages/looper/looper.py", line 308, in __call__
    for schema_file in self.prj.get_schemas(self.prj.pipeline_interfaces)]
  File "/home/ptaklifi/.local/lib/python3.6/site-packages/looper/looper.py", line 308, in <listcomp>
    for schema_file in self.prj.get_schemas(self.prj.pipeline_interfaces)]
  File "/home/ptaklifi/.local/lib/python3.6/site-packages/eido/eido.py", line 209, in validate_config
    schema_dicts = read_schema(schema=schema)
  File "/home/ptaklifi/.local/lib/python3.6/site-packages/eido/eido.py", line 139, in read_schema
    return _recursively_read_schemas(_load_yaml(schema), schema_list)
  File "/home/ptaklifi/.local/lib/python3.6/site-packages/eido/eido.py", line 130, in _recursively_read_schemas
    lst.extend(read_schema(sch))
  File "/home/ptaklifi/.local/lib/python3.6/site-packages/eido/eido.py", line 139, in read_schema
    return _recursively_read_schemas(_load_yaml(schema), schema_list)
  File "/home/ptaklifi/.local/lib/python3.6/site-packages/yacman/yacman.py", line 291, in load_yaml
    response = urlopen(filepath)
  File "/usr/lib/python3.6/urllib/request.py", line 223, in urlopen
    return opener.open(url, data, timeout)
  File "/usr/lib/python3.6/urllib/request.py", line 526, in open
    response = self._open(req, data)
  File "/usr/lib/python3.6/urllib/request.py", line 544, in _open
    '_open', req)
  File "/usr/lib/python3.6/urllib/request.py", line 504, in _call_chain
    result = func(*args)
  File "/usr/lib/python3.6/urllib/request.py", line 1353, in http_open
    return self.do_open(http.client.HTTPConnection, req)
  File "/usr/lib/python3.6/urllib/request.py", line 1328, in do_open
    r = h.getresponse()
  File "/usr/lib/python3.6/http/client.py", line 1373, in getresponse
    response.begin()
  File "/usr/lib/python3.6/http/client.py", line 311, in begin
    version, status, reason = self._read_status()
  File "/usr/lib/python3.6/http/client.py", line 272, in _read_status
    line = str(self.fp.readline(_MAXLINE + 1), "iso-8859-1")
  File "/usr/lib/python3.6/socket.py", line 586, in readinto
    return self._sock.recv_into(b)
ConnectionResetError: [Errno 104] Connection reset by peer

I searched a lot but could not find out what is the solution. May anyone please help me in this issue?

ATAC-seq PEPATAC refgenie • 533 views
ADD COMMENT
0
Entering edit mode

That's a network connection problem. Talk to your computer administrators or network engineers. Sometimes network connection problems are intermittent: they will be fixed tomorrow. Sometimes it's a real mis-configuration or the server cannot talk to yours. May be due to your network location.

ADD REPLY
0
Entering edit mode
5 months ago
nathan • 0

This issue was reposted and has been solved here: https://github.com/databio/pepatac/issues/165

The issue is that the server was not able to handle http traffic. switching to https solved it.

ADD COMMENT

Login before adding your answer.

Traffic: 1170 users visited in the last hour
Help About
FAQ
Access RSS
API
Stats

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.

Powered by the version 2.3.6