Great news & info, thanks Glen for getting back to us!

Take care,


On 3/1/11 2:06 PM, Glen Beane wrote:
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<>  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!


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 
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

Jennifer Jackson

Jennifer Jackson
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