Question: Extract MAF not working - NameError
0
gravatar for ana16
22 months ago by
ana1620
ana1620 wrote:

Hello all,

I am unable to extract MAF files from a set of genomic intervals. I was previously able to do this (last week) but after the release of the new version I couldn't do this again. I have seen posts on biostars reporting similar problems, but none yet related to MAF tools.

The error I am getting is:

Traceback (most recent call last):
  File "/cvmfs/main.galaxyproject.org/galaxy/tools/maf/interval2maf.py", line 142, in <module>
    __main__()
  File "/cvmfs/main.galaxyproject.org/galaxy/tools/maf/interval2maf.py", line 112, in __main__
    for block in index.get_as_iterator( src, region.start, region.end ):
  File "/cvmfs/main.galaxyproject.org/venv/lib/python2.7/site-packages/bx/interval_index_file.py", line 167, in get_as_iterator
    for block, index, offset in self.get_as_iterator_with_index_and_offset( src, start, end ):
  File "/cvmfs/main.galaxyproject.org/venv/lib/python2.7/site-packages/bx/interval_index_file.py", line 171, in get_as_iterator_with_index_and_offset
    for block, idx, offset in index.get_as_iterator_with_index_and_offset( src, start, end ):
  File "/cvmfs/main.galaxyproject.org/venv/lib/python2.7/site-packages/bx/interval_index_file.py", line 249, in get_as_iterator_with_index_and_offset
    yield self.get_at_offset( val ), self, val
  File "/cvmfs/main.galaxyproject.org/venv/lib/python2.7/site-packages/bx/interval_index_file.py", line 254, in get_at_offset
    return self.read_at_current_offset( self.f, **self.data_kwargs )
  File "/cvmfs/main.galaxyproject.org/venv/lib/python2.7/site-packages/bx/align/maf.py", line 37, in read_at_current_offset
    return read_next_maf( file, **kwargs )
  File "/cvmfs/main.galaxyproject.org/venv/lib/python2.7/site-packages/bx/align/maf.py", line 136, in read_next_maf
    line = readline( file, skip_blank=True )
  File "/cvmfs/main.galaxyproject.org/venv/lib/python2.7/site-packages/bx/align/maf.py", line 201, in readline
    line = file.readline()
  File "/cvmfs/main.galaxyproject.org/venv/lib/python2.7/site-packages/bx/misc/seeklzop.py", line 117, in readline
    self.fix_dirty()
  File "/cvmfs/main.galaxyproject.org/venv/lib/python2.7/site-packages/bx/misc/seeklzop.py", line 77, in fix_dirty
    self.current_block = StringIO( self.load_block( chunk ) )
  File "/cvmfs/main.galaxyproject.org/venv/lib/python2.7/site-packages/bx/misc/seeklzop.py", line 69, in load_block
    value = lzo.decompress( data )

NameError: global name 'lzo' is not defined

Thanks in advance!

galaxy maf • 466 views
ADD COMMENTlink modified 22 months ago by Jennifer Hillman Jackson24k • written 22 months ago by ana1620

We are testing, thanks for reporting the problem. This is at http://usegalaxy.org, correct?

ADD REPLYlink written 22 months ago by Jennifer Hillman Jackson24k
1
gravatar for Jennifer Hillman Jackson
22 months ago by
United States
Jennifer Hillman Jackson24k wrote:

Hi Ana,

I was able to confirm this with an independent test. A ticket has been opened to track the correction. You can track that and testing after deployment to http://usegalaxy.org here:

MAF specific issue: https://github.com/galaxyproject/galaxy/issues/2187 Known issues: https://github.com/jennaj/support-known-issues/wiki

Thanks for reporting the problem! Jen, Galaxy team

ADD COMMENTlink written 22 months ago by Jennifer Hillman Jackson24k
Please log in to add an answer.

Help
Access

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 16.09
Traffic: 65 users visited in the last hour