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openvax / mhctools

Python interface to running command-line and web-based MHC binding predictors
Apache License 2.0
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problem with netChop #120

Open weipenegHU opened 7 years ago

weipenegHU commented 7 years ago

Hi, guys, I deployed netchop locally, but it seems don't work. Have you bumped into the similar problems before? '''' paste: 2134/32138/hmm.inp: No such file or directory sh: line 1: /hmm.inp: No such file or directory sh: line 2: 2134/32138/hmm.inp: No such file or directory sh: line 3: /sparse.inp: No such file or directory paste: 2134/32138/hmm.inp: No such file or directory sh: line 1: /hmm.inp: No such file or directory sh: line 2: 2134/32138/hmm.inp: No such file or directory sh: line 3: /bl.inp: No such file or directory Unable to open(r) file 2134/32138/hmm.inp sh: line 1: /bl.inp: No such file or directory sh: line 1: 2134/32138/hmm.inp: No such file or directory sh: line 2: /bl.res: No such file or directory Unable to open(r) file 2134/32138/hmm.inp sh: line 1: /sparse.inp: No such file or directory sh: line 1: 2134/32138/hmm.inp: No such file or directory sh: line 2: /sparse.res: No such file or directory paste: 2134/32138/hmm.inp: No such file or directory sh: line 1: /sparse.res: No such file or directory sh: line 2: /bl.res: No such file or directory ''''''' when I appoint a tmp dir specifically, it interrupts on the test fasta data shipped with the gz file. ''''' 14 K . 0.226844 gi|3333147 15 A . 0.039277 gi|3333147 16 V . 0.087684 gi|3333147 17 R . 0.038433 gi|3333147 18 I . 0.071550 gi|3333147 Error. Wrong format for prediction line 18 I . ''''''

Whylas commented 6 years ago

I have the same problem. I got 0 results. $ ../netchop test.fsa > test.myout paste: /user/pVACtools/netchop-3.1/tmp/22729/22732/hmm.inp: No such file or directory sh: line 1: /hmm.inp: No such file or directory sh: line 2: /user/pVACtools/netchop-3.1/tmp/22729/22732/hmm.inp: No such file or directory sh: line 3: /sparse.inp: No such file or directory paste: /user/pVACtools/netchop-3.1/tmp/22729/22732/hmm.inp: No such file or directory sh: line 1: /hmm.inp: No such file or directory sh: line 2: /user/pVACtools/netchop-3.1/tmp/22729/22732/hmm.inp: No such file or directory sh: line 3: /bl.inp: No such file or directory Unable to open(r) file /wanglishi/pVACtools/netchop-3.1/tmp/22729/22732/hmm.inp sh: line 1: /bl.inp: No such file or directory sh: line 1: /user/pVACtools/netchop-3.1/tmp/22729/22732/hmm.inp: No such file or directory sh: line 2: /bl.res: No such file or directory Unable to open(r) file /user/pVACtools/netchop-3.1/tmp/22729/22732/hmm.inp sh: line 1: /sparse.inp: No such file or directory sh: line 1: /user/pVACtools/netchop-3.1/tmp/22729/22732/hmm.inp: No such file or directory sh: line 2: /sparse.res: No such file or directory paste: /user/pVACtools/netchop-3.1/tmp/22729/22732/hmm.inp: No such file or directory sh: line 1: /sparse.res: No such file or directory sh: line 2: /bl.res: No such file or directory

pos AA C score Ident

Number of cleavage sites 0. Number of amino acids 0. Protein name gi|3333147

I did let the tmp files writable to all users.

lucazammataro commented 6 years ago

I have the same issue witha macos high Sierra 10.13.6 "Number of cleavage sites 0. Number of amino acids 0. Protein name xxxx" Instead with a macOS Sierra 10.12.5 netChop works properly. I have tried different things but without success. :(