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luispedro / waldo

Waldo Project
MIT License
2 stars 3 forks source link

Failed to run install.sh #71

Closed icaoberg closed 10 years ago

icaoberg commented 10 years ago

I made a virtual machine running Ubuntu 14.04.1 and I followed the instructions in README.rst but I get this error

screen shot 08-05-14 at 04 38 pm

It installs the package, downloads all the databases but fails at the last step.

Database refseq has been updated
GO has changed, reindexing all libraries
GO will be reindexed. This triggers whole-database reindexing.
Indexing go...
Indexing mgi...
Indexing uniprot...
Traceback (most recent call last):
  File "./bin/update-waldo", line 194, in <module>
    main(argv)
  File "./bin/update-waldo", line 190, in main
    mod.load(datadir=options.datadir)
  File "/usr/local/lib/python2.7/dist-packages/waldo-0.1-py2.7.egg/waldo/uniprot/load.py", line 83, in load
    loaded += _load_idmapping(datadir, session, organism_set)
  File "/usr/local/lib/python2.7/dist-packages/waldo-0.1-py2.7.egg/waldo/uniprot/load.py", line 210, in _load_idmapping
    Additional_PubMed = line[:-1].split('\t')
ValueError: need more than 22 values to unpack

gzip: stdout: Broken pipe
luispedro commented 10 years ago

Hi, I can now reproduce this on my side. Probably some format change in uniprot.