Von: galaxy-dev-bounces@lists.bx.psu.eduIm Auftrag vonGeert Vandeweyer
Gesendet: Donnerstag, 8. August 2013 17:18:59 (UTC+01:00) Amsterdam, Berlin, Bern, Rom, Stockholm, Wien
An:
galaxy-dev@lists.bx.psu.edu
Betreff: Re: [galaxy-dev] Map with BWA results in correpted SAM file
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
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