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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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mhcflurry-downloads fetch failed #104

Closed weipenegHU closed 7 years ago

weipenegHU commented 7 years ago

Hi, guys, I am trying to deploy mhcflurry. When I used “”mhcflutty-downloads fetch" to download the model, it kept prompting connection failed. And I checked this link "http://github.com/hammerlab/mhcflurry/releases/download/0.9.1/“ on my browser, it said the page was not found.

timodonnell commented 7 years ago

Hi @weipenegHU ,

Can you paste the full error you're seeing when you run mhcflurry-downloads fetch? When I go to http://github.com/hammerlab/mhcflurry/releases/download/0.9.1/models_class1.tar.bz2 I am able to download these models so the full error may help see what's up.

Thanks,

Tim

timodonnell commented 7 years ago

Closing for now, please reopen if still an issue

weipenegHU commented 7 years ago

Sorry for the delay. The full error : Using TensorFlow backend. Fetching 1/5 downloads from release 0.9.1 DOWNLOAD NAME ALREADY DOWNLOADED? WILL DOWNLOAD NOW? URL models_class1 YES NO http://github.com/hammerlab/mhcflurry/releases/download/0.9.1/models_class1.tar.bz2 data_curated NO YES https://github.com/hammerlab/mhcflurry/releases/download/0.9.1/data_curated.tar.bz2 data_kim2014 NO NO http://github.com/hammerlab/mhcflurry/releases/download/0.9.1/data_kim2014.tar.bz2 data_iedb NO NO https://github.com/hammerlab/mhcflurry/releases/download/0.9.1/data_iedb.tar.bz2 models_class1_experiments1 NO NO http://github.com/hammerlab/mhcflurry/releases/download/0.9.1/models_class1_experiments1.tar.bz2 Downloading: https://github.com/hammerlab/mhcflurry/releases/download/0.9.1/data_curated.tar.bz2 Traceback (most recent call last): File "/hwfssz1/BIGDATA_COMPUTING/software/tools/anaconda/lib/python3.6/urllib/request.py", line 1318, in do_open encode_chunked=req.has_header('Transfer-encoding')) File "/hwfssz1/BIGDATA_COMPUTING/software/tools/anaconda/lib/python3.6/http/client.py", line 1239, in request self._send_request(method, url, body, headers, encode_chunked) File "/hwfssz1/BIGDATA_COMPUTING/software/tools/anaconda/lib/python3.6/http/client.py", line 1285, in _send_request self.endheaders(body, encode_chunked=encode_chunked) File "/hwfssz1/BIGDATA_COMPUTING/software/tools/anaconda/lib/python3.6/http/client.py", line 1234, in endheaders self._send_output(message_body, encode_chunked=encode_chunked) File "/hwfssz1/BIGDATA_COMPUTING/software/tools/anaconda/lib/python3.6/http/client.py", line 1026, in _send_output self.send(msg) File "/hwfssz1/BIGDATA_COMPUTING/software/tools/anaconda/lib/python3.6/http/client.py", line 964, in send self.connect() File "/hwfssz1/BIGDATA_COMPUTING/software/tools/anaconda/lib/python3.6/http/client.py", line 1392, in connect super().connect() File "/hwfssz1/BIGDATA_COMPUTING/software/tools/anaconda/lib/python3.6/http/client.py", line 936, in connect (self.host,self.port), self.timeout, self.source_address) File "/hwfssz1/BIGDATA_COMPUTING/software/tools/anaconda/lib/python3.6/socket.py", line 722, in create_connection raise err File "/hwfssz1/BIGDATA_COMPUTING/software/tools/anaconda/lib/python3.6/socket.py", line 713, in create_connection sock.connect(sa) TimeoutError: [Errno 110] Connection timed out

and when I open https://github.com/hammerlab/mhcflurry/releases/download/0.9.1/ in the browser, it prompted that the page is not found.

timodonnell commented 7 years ago

This URL, which is what it is trying to download, works for me:

https://github.com/hammerlab/mhcflurry/releases/download/0.9.1/data_curated.tar.bz2

The URL to the parent directory gives me the error you're seeing from github but I don't believe that URL is intended to work and as far as I know nothing should relies on it: https://github.com/hammerlab/ mhcflurry/releases/download/0.9.1/

So my best guess is this is a connectivity issue on your end. Can you try downloading the file manually with a command like:

wget https://github.com/hammerlab/mhcflurry/releases/download/0.9.1/data_curated.tar.bz2

to see if this is a connectivity issue?

On Mon, Oct 16, 2017 at 4:44 AM, huweipeng notifications@github.com wrote:

Sorry for the delay. The full error : Using TensorFlow backend. Fetching 1/5 downloads from release 0.9.1 DOWNLOAD NAME ALREADY DOWNLOADED? WILL DOWNLOAD NOW? URL models_class1 YES NO http://github.com/hammerlab/ mhcflurry/releases/download/0.9.1/models_class1.tar.bz2 https://github.com/hammerlab/mhcflurry/releases/download/0.9.1/models_class1.tar.bz2 data_curated NO YES https://github.com/hammerlab/ mhcflurry/releases/download/0.9.1/data_curated.tar.bz2 data_kim2014 NO NO http://github.com/hammerlab/ mhcflurry/releases/download/0.9.1/data_kim2014.tar.bz2 https://github.com/hammerlab/mhcflurry/releases/download/0.9.1/data_kim2014.tar.bz2 data_iedb NO NO https://github.com/hammerlab/ mhcflurry/releases/download/0.9.1/data_iedb.tar.bz2 models_class1_experiments1 NO NO http://github.com/hammerlab/ mhcflurry/releases/download/0.9.1/models_class1_experiments1.tar.bz2 https://github.com/hammerlab/mhcflurry/releases/download/0.9.1/models_class1_experiments1.tar.bz2 Downloading: https://github.com/hammerlab/mhcflurry/releases/download/0. 9.1/data_curated.tar.bz2 Traceback (most recent call last): File "/hwfssz1/BIGDATA_COMPUTING/software/tools/anaconda/lib/python3.6/urllib/request.py", line 1318, in do_open encode_chunked=req.has_header('Transfer-encoding')) File "/hwfssz1/BIGDATA_COMPUTING/software/tools/anaconda/lib/python3.6/http/client.py", line 1239, in request self._send_request(method, url, body, headers, encode_chunked) File "/hwfssz1/BIGDATA_COMPUTING/software/tools/anaconda/lib/python3.6/http/client.py", line 1285, in _send_request self.endheaders(body, encode_chunked=encode_chunked) File "/hwfssz1/BIGDATA_COMPUTING/software/tools/anaconda/lib/python3.6/http/client.py", line 1234, in endheaders self._send_output(message_body, encode_chunked=encode_chunked) File "/hwfssz1/BIGDATA_COMPUTING/software/tools/anaconda/lib/python3.6/http/client.py", line 1026, in _send_output self.send(msg) File "/hwfssz1/BIGDATA_COMPUTING/software/tools/anaconda/lib/python3.6/http/client.py", line 964, in send self.connect() File "/hwfssz1/BIGDATA_COMPUTING/software/tools/anaconda/lib/python3.6/http/client.py", line 1392, in connect super().connect() File "/hwfssz1/BIGDATA_COMPUTING/software/tools/anaconda/lib/python3.6/http/client.py", line 936, in connect (self.host,self.port), self.timeout, self.source_address) File "/hwfssz1/BIGDATA_COMPUTING/software/tools/anaconda/lib/python3.6/socket.py", line 722, in create_connection raise err File "/hwfssz1/BIGDATA_COMPUTING/software/tools/anaconda/lib/python3.6/socket.py", line 713, in create_connection sock.connect(sa) TimeoutError: [Errno 110] Connection timed out

and when I open https://github.com/hammerlab/ mhcflurry/releases/download/0.9.1/ in the browser, it prompted that the page is not found.

— You are receiving this because you modified the open/close state. Reply to this email directly, view it on GitHub https://github.com/hammerlab/mhcflurry/issues/104#issuecomment-336820217, or mute the thread https://github.com/notifications/unsubscribe-auth/AAcjuB4e_GIi2kb7hsE0NiilJnBSzTvWks5ssxdUgaJpZM4PoJ94 .

weipenegHU commented 7 years ago

Using wget can download the data successfully, however the mhcflurry-fetch command gave me the connection error. Is it OK if I run mhcflurry without downloading the data?

timodonnell commented 7 years ago

hmm that's puzzling. Definitely possible there's something not quite right with how I'm downloading the data, but there's not much I can do at this point without a way to reproduce it on my end.

I see from the output you posted that you have already downloaded the mhcflurry models (models_class1), so, yes, you have everything you need to generate predictions from these models as is.

weipenegHU commented 7 years ago

all right, thanks.