Hello Evan,

This may have been a temporary memory problem. Have you been able to run the tool again with the default parameters successfully?


If not, please share a history link ("Options -> Share or Publish) in an email directly to me to keep your data private.

Hopefully this is resolved, but if not we can take a look at the issue,

Best,

Jen
Galaxy team

On 3/15/11 7:31 AM, Evan Schwab wrote:
Hi,

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 }
MemoryError


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?

Thanks

Evan
--
Evan Schwab
Research Associate
Megason Lab
Department of Systems Biology
Harvard Medical School
200 Longwood Ave
Boston, MA 02115
908-938-3779 <tel:908-938-3779>



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