Hi Moritz,

do you installed bwa through the toolshed or manually?

Cheers,
Bjoern

> 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
> 
> 
> 
> 
> 
> ___________________________________________________________
> Please keep all replies on the list by using "reply all"
> in your mail client.  To manage your subscriptions to this
> and other Galaxy lists, please use the interface at:
>   http://lists.bx.psu.edu/
> 
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