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
_______________________________________________
To manage your subscriptions to this and other Galaxy lists, please use the 
interface at:

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

Reply via email to