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


___________________________________________________________
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/

To search Galaxy mailing lists use the unified search at:
  http://galaxyproject.org/search/mailinglists/


-- 

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.vandeweyer@ua.ac.be
http://ua.ac.be/cognitivegenetics
http://www.linkedin.com/pub/geert-vandeweyer/26/457/726