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!
> 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
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