Timeout Issues with Starting higlass-manage

[arielpourmorady]

Hi there,

I am trying to using higlass-manage to view contact maps of my cooler files. I keep getting the following Timeout errors and I'm not entirely sure what to do to fix it. Any help would be really appreciated, thank you.

ariel@aphrodite:/$ higlass-manage start
Stopping previously running container
Pulling latest image... 
done
Data directory: /home/ariel/hg-data
Temp directory: ()
Starting... default 8989
Docker started: higlass-manage-container-default
sending request 1
Traceback (most recent call last):
  File "/home/ariel/.local/lib/python3.6/site-packages/urllib3/connectionpool.py", line 426, in _make_request
    six.raise_from(e, None)
  File "<string>", line 3, in raise_from
  File "/home/ariel/.local/lib/python3.6/site-packages/urllib3/connectionpool.py", line 421, in _make_request
    httplib_response = conn.getresponse()
  File "/usr/lib/python3.6/http/client.py", line 1356, in getresponse
    response.begin()
  File "/usr/lib/python3.6/http/client.py", line 307, in begin
    version, status, reason = self._read_status()
  File "/usr/lib/python3.6/http/client.py", line 268, 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)
socket.timeout: timed out

During handling of the above exception, another exception occurred:

Traceback (most recent call last):
  File "/home/ariel/.local/lib/python3.6/site-packages/requests/adapters.py", line 449, in send
    timeout=timeout
  File "/home/ariel/.local/lib/python3.6/site-packages/urllib3/connectionpool.py", line 727, in urlopen
    method, url, error=e, _pool=self, _stacktrace=sys.exc_info()[2]
  File "/home/ariel/.local/lib/python3.6/site-packages/urllib3/util/retry.py", line 403, in increment
    raise six.reraise(type(error), error, _stacktrace)
  File "/home/ariel/.local/lib/python3.6/site-packages/urllib3/packages/six.py", line 735, in reraise
    raise value
  File "/home/ariel/.local/lib/python3.6/site-packages/urllib3/connectionpool.py", line 677, in urlopen
    chunked=chunked,
  File "/home/ariel/.local/lib/python3.6/site-packages/urllib3/connectionpool.py", line 428, in _make_request
    self._raise_timeout(err=e, url=url, timeout_value=read_timeout)
  File "/home/ariel/.local/lib/python3.6/site-packages/urllib3/connectionpool.py", line 336, in _raise_timeout
    self, url, "Read timed out. (read timeout=%s)" % timeout_value
urllib3.exceptions.ReadTimeoutError: HTTPConnectionPool(host='gw-srv-01.rc.zi.columbia.edu', port=3128): Read timed out. (read timeout=5)

During handling of the above exception, another exception occurred:

Traceback (most recent call last):
  File "/home/ariel/.local/lib/python3.6/site-packages/higlass_manage/start.py", line 368, in _start
    timeout=5,
  File "/home/ariel/.local/lib/python3.6/site-packages/requests/api.py", line 76, in get
    return request('get', url, params=params, **kwargs)
  File "/home/ariel/.local/lib/python3.6/site-packages/requests/api.py", line 61, in request
    return session.request(method=method, url=url, **kwargs)
  File "/home/ariel/.local/lib/python3.6/site-packages/requests/sessions.py", line 530, in request
    resp = self.send(prep, **send_kwargs)
  File "/home/ariel/.local/lib/python3.6/site-packages/requests/sessions.py", line 643, in send
    r = adapter.send(request, **kwargs)
  File "/home/ariel/.local/lib/python3.6/site-packages/requests/adapters.py", line 529, in send
    raise ReadTimeout(e, request=request)
requests.exceptions.ReadTimeout: HTTPConnectionPool(host='gw-srv-01.rc.zi.columbia.edu', port=3128): Read timed out. (read timeout=5)

During handling of the above exception, another exception occurred:

Traceback (most recent call last):
  File "/home/ariel/.local/bin/higlass-manage", line 11, in <module>
    sys.exit(cli())
  File "/home/ariel/.local/lib/python3.6/site-packages/click/core.py", line 829, in __call__
    return self.main(*args, **kwargs)
  File "/home/ariel/.local/lib/python3.6/site-packages/click/core.py", line 782, in main
    rv = self.invoke(ctx)
  File "/home/ariel/.local/lib/python3.6/site-packages/click/core.py", line 1259, in invoke
    return _process_result(sub_ctx.command.invoke(sub_ctx))
  File "/home/ariel/.local/lib/python3.6/site-packages/click/core.py", line 1066, in invoke
    return ctx.invoke(self.callback, **ctx.params)
  File "/home/ariel/.local/lib/python3.6/site-packages/click/core.py", line 610, in invoke
    return callback(*args, **kwargs)
  File "/home/ariel/.local/lib/python3.6/site-packages/higlass_manage/start.py", line 150, in start
    redis_port,
  File "/home/ariel/.local/lib/python3.6/site-packages/higlass_manage/start.py", line 384, in _start
    except requests.exceptions.ReadTimout:
AttributeError: module 'requests.exceptions' has no attribute 'ReadTimout'

[pkerpedjiev]

Hey! So the timeout occurs because higlass-manage starts a docker container and then determines when it's ready by repeatedly sending queries until they succeed.

I'm not entirely sure why it's not succeeding but it looks like you're not running it on "localhost". Have you tried using the --site-url parameter to specify the name of the host that you're running it on?

[arielpourmorady]

I tried

higlass-manage start --site-url higlass.io
which I saw on the "Manage Higlass Instances" page and it produced the same errors. I am also somewhat new to coding, and this might have to do with the configuration of the server! I'm not entirely sure. Sorry for the trouble, and thanks for your help.

[pkerpedjiev]

You need to use the url of the server that you're running it on. Based on the log message maybe try this:

higlass-manage start --site-url gw-srv-01.rc.zi.columbia.edu