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openvax / mhcflurry

Peptide-MHC I binding affinity prediction
http://openvax.github.io/mhcflurry/
Apache License 2.0
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The error of downloing the trained models #116

Closed zhouqiuhu closed 6 years ago

zhouqiuhu commented 7 years ago

Hi, When I download the trained models with the command "mhcflurry-downloads fetch", it didn't work.

Here is the error: IOError: [Errno socket error] EOF occurred in violation of protocol (_ssl.c:661)

P.S: I could donwload those data with browser. Where should I put the files?

timodonnell commented 7 years ago

Looks like a possibly transient error - try it again maybe?

You can also run mhcflurry-downloads info to see where to unpack it to manually. When I run this command I get:

(py3k) [tim@tims-macbook ~]$ mhcflurry-downloads info

... (other output) ...

Configuration
  current release                     = 0.9.2
  downloads dir                       = '/Users/tim/Library/Application Support/mhcflurry/4/0.9.2' [exists]

... (other output) ...

If you unpack the models_class1.tar.bz2 file into the path indicated by "downloads dir" above, it will work. E.g. on my machine:

(py3k) [tim@tims-macbook ~]$ ls '/Users/tim/Library/Application Support/mhcflurry/4/0.9.2/models_class1'
GENERATE.sh          LOG.txt.bz2          hyperparameters.json models
zhouqiuhu commented 6 years ago

Thanks for your help. The mhcflurry work well now. The error is still there though. Maybe there is a problem of my system configuration.

timodonnell commented 6 years ago

It might be this issue, which seems to be related to having a python linked against a really old version of openssl: https://github.com/requests/requests/issues/3006

One suggestion in that thread is to try:

pip install --force-reinstall requests[security]

There's also some other suggestions in that thread. If you figure out a solution please let us know. If you find a way to modify the download code to work for you we'd be interested in that as well.

zhouqiuhu commented 6 years ago

Hi. Sorry for replying late. I tried that code you mentioned but it didn't work neither.

timodonnell commented 6 years ago

Stumped on this one. Closing for now, please reopen if you continue to have an issue downloading data and models.