Question: Unable To Debug Pacbio Resource (Gfftovcf.Py) Module Error
0
gravatar for Raymond301
6.9 years ago by
Raymond301140
Rochester, MN
Raymond301140 wrote:

I am just trying to use the gffToVcf.py module. I have already run the cmd to set up the environmental variables. I know that my python_home environment is mapped.

I can successfully run the setup script.

. /data2/labdata/mbcf/pacbio/software/smrtanalysis/etc/setup.sh

But when I try to run:

/data2/labdata/mbcf/pacbio/software/smrtanalysis/analysis/bin/gffToVcf.py --help

- Traceback (most recent call last):
- File "/data2/labdata/mbcf/pacbio/software/smrtanalysis/analysis/bin/gffToVcf.py", line 5, in <module>
    pkg_resources.run_script('pbpy==0.1', 'gffToVcf.py')
- File "/usr/local/biotools/python/2.7/lib/python2.7/site-packages/setuptools-0.6c11-py2.7.egg/pkg_resources.py", line 489, in run_script
    keys.append(dist.key)
- File "/usr/local/biotools/python/2.7/lib/python2.7/site-packages/setuptools-0.6c11-py2.7.egg/pkg_resources.py", line 1207, in run_script
    def __init__(self,module):
- File "/data2/labdata/mbcf/pacbio/software/smrtanalysis-1.3.0/analysis/lib/python2.7/pbpy-0.1-py2.7.egg/EGG-INFO/s                         cripts/gffToVcf.py", line 8, in <module>
    from pbpy.io.GffIO import *
- File "/data2/labdata/mbcf/pacbio/software/smrtanalysis/analysis/lib/python2.7/pbpy-0.1-py2.7.egg/pbpy/io/GffIO.py", line 5, in <module>
    import gzip
- File "/usr/local/biotools/python/2.7/lib/python2.7/gzip.py", line 10, in <module>
    import io
- File "/usr/local/biotools/python/2.7/lib/python2.7/io.py", line 60, in <module>
    import _io
- ImportError: /usr/local/biotools/python/2.7/lib/python2.7/lib-dynload/_io.so: undefined symbol: PyUnicodeUCS2_FromObject

I've been playing with environmental variables, and I can't seem to figure out what it is that I'm missing. I'm hoping that it's something obvious, and I'm just missing it.

error • 2.3k views
ADD COMMENTlink modified 5.5 years ago by Biostar ♦♦ 20 • written 6.9 years ago by Raymond301140
1
gravatar for Istvan Albert
6.9 years ago by
Istvan Albert ♦♦ 79k
University Park, USA
Istvan Albert ♦♦ 79k wrote:

I think your Python installation is damaged in some way. Note that your error traces back to a package that is part of Python and is unrelated to the library that you are using.

ADD COMMENTlink written 6.9 years ago by Istvan Albert ♦♦ 79k

Yes, you are correct! Python 2.5.1 causes FAILURE. Thank you so very much!

ADD REPLYlink written 6.9 years ago by Raymond301140
0
gravatar for Houkto
6.9 years ago by
Houkto210
Houkto210 wrote:

Hi Raymond,

Does the conversion process went well. I am trying to convert gff to vcf.

ADD COMMENTlink written 6.9 years ago by Houkto210

If you have a real gff to begin with then, http://www.smrtcommunity.com/SMRT-Analysis/Tools. The SMRT package is great. But I have a non-standard gff.

ADD REPLYlink written 6.9 years ago by Raymond301140

Thanks for the fast reply raymond, I signed up for an account and clicked on the link, however, it says GFF to VCF is available as part of the SMRT Analysis download. and when I click on this link its direct me to SMRT analysis download page which has link to SMRT Analysis Source Code or VMware image or CentOS Binaries or Ubuntu Binaries all of these over 1Gb which one shall i download to get the tool (to run on linux) ? cheers

ADD REPLYlink written 6.9 years ago by Houkto210
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