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PEPATAC error: ConnectionResetError: [Errno 104] Connection reset by peer

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
• 6,340 views • link
updated by nathan • nathan • written by m.taheri • m.taheri

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.

• 0 views • link
written by karl.stamm karl.stamm

1 answer

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.

• 0 views • link
written by nathan • nathan

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