We've upgraded python and galaxy and I don't recall seeing this error recently. 
I think using our own python (2.6) rather than the Centos syst python (2.4) 
took care of it. 



On Mar 1, 2011, at 5:03 PM, Jennifer Jackson <j...@bx.psu.edu> wrote:

> Hi Glen,
> 
> This is just a quick email to let you know that we are still working on 
> your question. The development team will be getting back to you as soon 
> as possible, but if you have discovered the solution yourself (perhaps 
> using the most recent galaxy-dist?), both the other galaxy-dev list 
> members and we would be glad to learn about how you solved the issue.
> 
> Thank you for your patience!
> 
> Best,
> 
> Jen
> Galaxy team
> 
> On 12/27/10 6:22 AM, Glen Beane wrote:
>> 
>> On Dec 22, 2010, at 3:26 PM, Glen Beane wrote:
>> 
>>> one of our users is experiencing this error from the SAM-to-BAM tool:
>>> 
>>> Error extracting alignments from 
>>> (/hpcdata/galaxy-setup/galaxy-dist/database/files/000/dataset_85.dat), 
>>> requested number of bytes is more than a Python string can hold
>>> 
>>> The SAM file has 58 million lines of mapped paired end reads.
>>> 
>>> 
>>> Any suggestions?
>>> 
>>> 
>>> 
>>> The galaxy jobs running on our cluster are currently using the version of 
>>> Python installed with CentOS 5 (python 2.4.3, 64-bit).   We have been 
>>> considering setting up a new python virtualenv for the galaxy user on the 
>>> cluster that uses a newer version of Python (probably 2.6 so it matches the 
>>> version on the server running the galaxy web app)
>>> 
>> 
>> 
>> Has anyone else experienced this? I don't think we are doing anything 
>> unusual.  Would it help to setup the galaxy user on the cluster to use a 
>> more recent version of Python?
>> 
>> 
>> _______________________________________________
>> galaxy-dev mailing list
>> galaxy-dev@lists.bx.psu.edu
>> http://lists.bx.psu.edu/listinfo/galaxy-dev
> 
> -- 
> Jennifer Jackson
> http://usegalaxy.org
> http://galaxyproject.org

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