I am receiving the following error when I try to run the Indel Analysis tool
on a sam file.  I kept the Frequency threshold at the default 0.015.

Traceback (most recent call last):
  File "/galaxy/home/g2main/galaxy_main/tools/indels/indel_analysis.py",
line 227, in
    if __name__=="__main__": __main__()
  File "/galaxy/home/g2main/galaxy_main/tools/indels/indel_analysis.py",
line 84, in __main__
    add_to_mis_matches( mis_matches[ chrom ], pos, bases )
  File "/galaxy/home/g2main/galaxy_main/tools/indels/indel_analysis.py",
line 34, in add_to_mis_matches
    mis_matches[ pos + j ] = { base: 1 }

Prior to that I tried with Frequency threshold 0.0 and it ran for days on
end without any results. And I've tried Frequency threshold of 0.10 and it
gave and error that said "Killed" with no explaination.

Is there an error with the tool?



Evan Schwab
Research Associate
Megason Lab
Department of Systems Biology
Harvard Medical School
200 Longwood Ave
Boston, MA 02115
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