Hey Folks,

Is there really nobody that can help Geert and me? Thats quite important to
me right now.
This is obviously not something specific to me, as Geert has the exact same
error.
I meanwhile tried to replace the id with "1" but it still doesnt work.

Best
Moritz

______________________________
Von: galaxy-dev-boun...@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
Prins Boudewijnlaan 43
2650 Edegem
Belgium
Tel: +32 (0)3 275 97 56
E-mail: geert.vandewe...@ua.ac.be<mailto:geert.vandewe...@ua.ac.be>
http://ua.ac.be/cognitivegenetics
http://www.linkedin.com/pub/geert-vandeweyer/26/457/726
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