Re: [galaxy-dev] Map with BWA results in correpted SAM file

2013-08-08 Thread Geert Vandeweyer 

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 
 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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[galaxy-dev] Map with BWA results in correpted SAM file

2013-08-08 Thread Moritz Juchler 
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 
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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