Error while downloading resources - PathwayCommons11.All.hgnc.sif.gz

Hi there,

I was trying to get genewalk going on my data, however when running genewalk like this

genewalk --project test --genes ./input.csv --id_type hgnc_symbol --nproc 4

I’m presented with the following error message(s):

INFO: [2019-10-31 12:37:46] genewalk.cli - Creating project folder at /users/lule/genewalk/test
INFO: [2019-10-31 12:37:46] genewalk.resources - Using /users/lule/genewalk/resources as resource folder.
INFO: [2019-10-31 12:37:46] genewalk.resources - Downloading http://www.pathwaycommons.org/archives/PC2/v11/PathwayCommons11.All.hgnc.sif.gz and extracting into /users/lule/genewalk/resources/PathwayCommons11.All.hgnc.sif
Traceback (most recent call last):
  File "/software/2020/software/python/3.6.6-foss-2018b/lib/python3.6/urllib/request.py", line 1318, in do_open
    encode_chunked=req.has_header('Transfer-encoding'))
  File "/software/2020/software/python/3.6.6-foss-2018b/lib/python3.6/http/client.py", line 1239, in request
    self._send_request(method, url, body, headers, encode_chunked)
  File "/software/2020/software/python/3.6.6-foss-2018b/lib/python3.6/http/client.py", line 1285, in _send_request
    self.endheaders(body, encode_chunked=encode_chunked)
  File "/software/2020/software/python/3.6.6-foss-2018b/lib/python3.6/http/client.py", line 1234, in endheaders
    self._send_output(message_body, encode_chunked=encode_chunked)
  File "/software/2020/software/python/3.6.6-foss-2018b/lib/python3.6/http/client.py", line 1026, in _send_output
    self.send(msg)
  File "/software/2020/software/python/3.6.6-foss-2018b/lib/python3.6/http/client.py", line 964, in send
    self.connect()
  File "/software/2020/software/python/3.6.6-foss-2018b/lib/python3.6/http/client.py", line 936, in connect
    (self.host,self.port), self.timeout, self.source_address)
  File "/software/2020/software/python/3.6.6-foss-2018b/lib/python3.6/socket.py", line 724, in create_connection
    raise err
  File "/software/2020/software/python/3.6.6-foss-2018b/lib/python3.6/socket.py", line 713, in create_connection
    sock.connect(sa)
OSError: [Errno 113] No route to host

During handling of the above exception, another exception occurred:

Traceback (most recent call last):
  File "/users/lule/.local/bin/genewalk", line 11, in <module>
    sys.exit(main())
  File "/users/lule/.local/lib/python3.6/site-packages/genewalk/cli.py", line 145, in main
    rm.download_all()
  File "/users/lule/.local/lib/python3.6/site-packages/genewalk/resources.py", line 53, in download_all
    self.get_pc()
  File "/users/lule/.local/lib/python3.6/site-packages/genewalk/resources.py", line 37, in get_pc
    download_gz(fname, url_pc)
  File "/users/lule/.local/lib/python3.6/site-packages/genewalk/resources.py", line 65, in download_gz
    urllib.request.urlretrieve(url, gz_file)
  File "/software/2020/software/python/3.6.6-foss-2018b/lib/python3.6/urllib/request.py", line 248, in urlretrieve
    with contextlib.closing(urlopen(url, data)) as fp:
  File "/software/2020/software/python/3.6.6-foss-2018b/lib/python3.6/urllib/request.py", line 223, in urlopen
    return opener.open(url, data, timeout)
  File "/software/2020/software/python/3.6.6-foss-2018b/lib/python3.6/urllib/request.py", line 526, in open
    response = self._open(req, data)
  File "/software/2020/software/python/3.6.6-foss-2018b/lib/python3.6/urllib/request.py", line 544, in _open
    '_open', req)
  File "/software/2020/software/python/3.6.6-foss-2018b/lib/python3.6/urllib/request.py", line 504, in _call_chain
    result = func(*args)
  File "/software/2020/software/python/3.6.6-foss-2018b/lib/python3.6/urllib/request.py", line 1346, in http_open
    return self.do_open(http.client.HTTPConnection, req)
  File "/software/2020/software/python/3.6.6-foss-2018b/lib/python3.6/urllib/request.py", line 1320, in do_open
    raise URLError(err)
urllib.error.URLError: <urlopen error [Errno 113] No route to host>

Is the PathwayCommons11.All.hgnc.sif.gz file no longer available under the URL?

Thanks, Lukas

[andrewbcaldwell]

Thanks for the response and clarification regarding INDRA. After waiting for the PathwayCommons website to come back online, I was able to proceed with the analysis. I think I just happened to try to run the program for the first time when the PC site was down, and I didn’t realize that INDRA required an additional parameter.

[bgyori]

Hi @andrewbcaldwell, I just checked and the PathwayCommons resource download worked for me so it’s possible that this was a temporary network issue. You can also manually download http://www.pathwaycommons.org/archives/PC2/v12/PathwayCommons12.All.hgnc.sif.gz and decompress it into ~/genewalk/resources/PathwayCommons12.All.hgnc.sif. GeneWalk will then not try to re-download it.

As for the --network_source indra option, that requires and additional parameter --network_file [statements.pkl] pointing to a pickle file containing INDRA Statements that were collected independent of GeneWalk (see https://indra.readthedocs.io/). In principle, the PathwayCommons resource file should not be accessed if --network_source is something other than pc, we can look into whether that happens inadvertently.