htseq-qa error message

[potato84]

Hi all,

I try to use htseq-qa to check the quality of the run. I used TopHat for the alignment, then transfer the accepted.bam file to sam file with samtools.

I used htseq-qa as follows:

htseq-qa -t sam -o NML.pdf -r 50 NML.sam

I get an error message from htseq-qa, saying:

Traceback (most recent call last):
File "/usr/local/bin/htseq-qa", line 5, in <module>
pkg_resources.run_script('HTSeq==0.5.4p3', 'htseq-qa')
File "build/bdist.linux-x86_64/egg/pkg_resources.py", line 487, in run_script
if name is None:
File "build/bdist.linux-x86_64/egg/pkg_resources.py", line 1337, in run_script

File "/usr/local/lib/python2.7/dist-packages/HTSeq-0.5.4p3-py2.7-linux-x86_64.egg/EGG-INFO/scripts/htseq-qa", line 5, in <module>
HTSeq.scripts.qa.main()
File "/usr/local/lib/python2.7/dist-packages/HTSeq-0.5.4p3-py2.7-linux-x86_64.egg/HTSeq/scripts/qa.py", line 131, in main
r.add_qual_to_count_array( qual_arr_A )
File "_HTSeq.pyx", line 876, in HTSeq._HTSeq.SequenceWithQualities.add_qual_to_count_array (src/_HTSeq.c:15859)
File "_HTSeq.pyx", line 895, in HTSeq._HTSeq.SequenceWithQualities.add_qual_to_count_array (src/_HTSeq.c:15773)
ValueError: Too large quality value encountered.

Dose anyone can give me some suggestions to solve the problem? Thanks