[galaxy-user] error on indel analysis

2011-03-15 Thread Evan Schwab 
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
___
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[galaxy-user] Error on Indel Analysis Tool

2011-03-15 Thread Evan Schwab 
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
___
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:

  http://lists.bx.psu.edu/

[galaxy-user] Problems using aaChanges tool

2011-02-14 Thread Evan Schwab 
Hi,

I am trying to use the aaChanges tool.  I have a file of SNPs in the correct
interval format and a UCSC uploaded bed file of genomic intervals.  These
are both for the Zebrafish Zv9 build and are appropriately labeled this way
in their attributes.  But when I try to run the tool it says for both the
SNP interval file and UCSC bed file:  Sequences are not currently available
for the specified build.

Am I doing something wrong with my formatting or does this tool not yet
support Zebrafish Zv9 build?   I tried using it in the Human Genome
Variation section of the main Galaxy site as well as the Evolution section
of the test site and both gave me the same error.

Please let me know what is happening.

Thank you so much

Evan





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

  http://lists.bx.psu.edu/