urllib.error.HTTPError: HTTP Error 404: Not Found

[frankligy]

Hello,

Thanks a lot for providing such a wonderful tool, while building the docker image, I encountered an issue that seems to be buried deep in the source code, so any hints would be deeply appreciated!

The building step in Makefile is successful, see below:

Sending build context to Docker daemon  114.5MB
Step 1/9 : FROM tensorflow/tensorflow:1.10.1-gpu-py3
 ---> 6243acd2b19f
Step 2/9 : RUN pip install keras==2.2.1 h5py tables flask pyteomics lxml
 ---> Using cache
 ---> fbce63c709a1
Step 3/9 : ENV KERAS_BACKEND=tensorflow
 ---> Using cache
 ---> 2ed535403ba1
Step 4/9 : ENV TF_CPP_MIN_LOG_LEVEL=3
 ---> Using cache
 ---> 1db459877d9d
Step 5/9 : ENV LC_ALL=C.UTF-8
 ---> Using cache
 ---> 20370865db4d
Step 6/9 : ENV LANG=C.UTF-8
 ---> Using cache
 ---> e64812162333
Step 7/9 : ADD prosit/ /root/prosit
 ---> 98cd35a56f95
Step 8/9 : RUN cd /root/
 ---> Running in 5e991ffc696b
Removing intermediate container 5e991ffc696b
 ---> 4774e95f0741
Step 9/9 : WORKDIR /root/
 ---> Running in f55d688e105d
Removing intermediate container f55d688e105d
 ---> 8a76ceb1b35c
Successfully built 8a76ceb1b35c

But when running the docker image in the next step of make file:

nvidia-docker run -it \
    -v "/scratch/ligk2e/prosit/prosit/prosit_non_tryptic_fragmentation/hla_cid":/root/model_spectra/ \
    -v "/scratch/ligk2e/prosit/prosit/model_irt_prediction":/root/model_irt/ \
    -e CUDA_VISIBLE_DEVICES=0 \
    -p 5000:5000 \
    prosit python3 -m prosit.server
Using TensorFlow backend.
Traceback (most recent call last):
  File "/usr/lib/python3.5/runpy.py", line 174, in _run_module_as_main
    mod_name, mod_spec, code = _get_module_details(mod_name, _Error)
  File "/usr/lib/python3.5/runpy.py", line 109, in _get_module_details
    __import__(pkg_name)
  File "/root/prosit/__init__.py", line 7, in <module>
    from . import server
  File "/root/prosit/server.py", line 15, in <module>
    from . import converters
  File "/root/prosit/converters/__init__.py", line 3, in <module>
    from . import msp
  File "/root/prosit/converters/msp.py", line 25, in <module>
    aa_comp = generate_aa_comp()
  File "/root/prosit/converters/msp.py", line 16, in generate_aa_comp
    db = pyteomics.mass.Unimod()
  File "/usr/local/lib/python3.5/dist-packages/pyteomics/mass/mass.py", line 1087, in __init__
    self._tree = etree.parse(urlopen(source))
  File "/usr/lib/python3.5/urllib/request.py", line 163, in urlopen
    return opener.open(url, data, timeout)
  File "/usr/lib/python3.5/urllib/request.py", line 472, in open
    response = meth(req, response)
  File "/usr/lib/python3.5/urllib/request.py", line 582, in http_response
    'http', request, response, code, msg, hdrs)
  File "/usr/lib/python3.5/urllib/request.py", line 510, in error
    return self._call_chain(*args)
  File "/usr/lib/python3.5/urllib/request.py", line 444, in _call_chain
    result = func(*args)
  File "/usr/lib/python3.5/urllib/request.py", line 590, in http_error_default
    raise HTTPError(req.full_url, code, msg, hdrs, fp)
urllib.error.HTTPError: HTTP Error 404: Not Found
make: *** [Makefile:17: server] Error 1

It seems that pyteomics package is trying to grab the content from a URL that either doesn't exit or the way it is grabbing the content needs to be modified. Am I interpreting the error correctly and would you mind offering some suggestions on how I can get it to work on our server?

Let me know if I can clarify anything for you and many thanks in advance!

Best,
Frank