to add on this :
we have similar issues (sam-to-bam conversion fails with similar
errors). it seems to be related to the BWA output getting messed up,
with (part of) columns missing or duplicated on some lines.
I have not found a systematic pattern in the errors, they seem to happen
rather random.
On 08/08/2013 05:06 PM, Moritz Juchler wrote:
Dear Galaxy Community,
I have a local instance and installed 0.5.9-r16 BWA and the toolshed
wrapper. The mapping is successful. I then use the Filter Sam Tool on
the sam file from the alignment, but it spits out this error:
*Dataset 26: Filter SAM on data 24*
Tool execution generated the following error message:
Traceback (most recent call last):
File "/home/trr/galaxy-dist/tools/samtools/sam_bitwise_flag_filter.py", line 148,
in <module>
if __name__ == "__main__": main()
File "/home/trr/galaxy-dist/tools/samtools/sam_bitwise_flag_filter.py", line
137, in main
flags = int( fields[flag_col] )
ValueError: invalid literal for int() with base 10: 'RG:Z:lane712s006433'
I have the same workflow online and did the exact same steps on the
same fastq files.
Is there anything I am missing? Is there any information I can provide
to answer this question?
Best
Moritz
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--
Geert Vandeweyer, Ph.D.
Department of Medical Genetics
University of Antwerp
Prins Boudewijnlaan 43
2650 Edegem
Belgium
Tel: +32 (0)3 275 97 56
E-mail: geert.vandewe...@ua.ac.be
http://ua.ac.be/cognitivegenetics
http://www.linkedin.com/pub/geert-vandeweyer/26/457/726
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