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
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E-mail: geert.vandewe...@ua.ac.be
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