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
The Galaxy User list should be used for the discussion of Galaxy analysis and other features on the public server at usegalaxy.org. Please keep all replies on the list by using "reply all" in your mail client. For discussion of local Galaxy instances and the Galaxy source code, please use the Galaxy Development list:
http://lists.bx.psu.edu/listinfo/galaxy-dev
To manage your subscriptions to this and other Galaxy lists, please use the interface at: