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DoaneAS / rseqc

Automatically exported from code.google.com/p/rseqc
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OverflowError: unsigned byte integer is less than minimum #20

Open GoogleCodeExporter opened 9 years ago

GoogleCodeExporter commented 9 years ago 

I am getting this error with more than one RSeQC scripts like bam_stat.py, 
annotation_junction.py etc. No output or a blank file outputs. Please help

What version of the product are you using? On what operating system?
I am using version 2.3.3

Please provide any additional information below.

Detail error for bam_stat.py:

Load BAM file ... Traceback (most recent call last):
  File "/soft/devel/python-2.7/bin/bam_stat.py", line 5, in <module>
    pkg_resources.run_script('RSeQC==2.3.3', 'bam_stat.py')
  File "/soft/devel/python-2.7/lib/python2.7/site-packages/setuptools-0.6c11-py2.7.egg/pkg_resources.py", line 489, in run_script
    if insert:
  File "/soft/devel/python-2.7/lib/python2.7/site-packages/setuptools-0.6c11-py2.7.egg/pkg_resources.py", line 1207, in run_script

  File "/soft/devel/python-2.7/lib/python2.7/site-packages/RSeQC-2.3.3-py2.7-linux-x86_64.egg/EGG-INFO/scripts/bam_stat.py", line 62, in <module>
    main()
  File "/soft/devel/python-2.7/lib/python2.7/site-packages/RSeQC-2.3.3-py2.7-linux-x86_64.egg/EGG-INFO/scripts/bam_stat.py", line 58, in main
    obj.stat()
  File "/soft/devel/python-2.7/lib/python2.7/site-packages/RSeQC-2.3.3-py2.7-linux-x86_64.egg/qcmodule/SAM.py", line 2365, in stat
    if len(aligned_read.tags) > 0:
  File "csamtools.pyx", line 2240, in csamtools.AlignedRead.tags.__get__ (pysam/csamtools.c:19907)
OverflowError: unsigned byte integer is less than minimum

Original issue reported on code.google.com by babitasi...@gmail.com on 27 Mar 2013 at 2:56

GoogleCodeExporter commented 9 years ago 
Do you install the latest pysam module? RSeQC use pysam 0.6, if you install 
newer version like 0.7.3 and this version probably is not compatible with 
RSeQC. After figuring out this, we can update RSeQC to the latest version of 
pysam. Thanks

Liguo

Original comment by wangligu...@gmail.com on 16 Apr 2013 at 2:47

GoogleCodeExporter commented 9 years ago 
This problem should be addressed in v2.3.6

Original comment by wangligu...@gmail.com on 17 Apr 2013 at 8:53