Re: [galaxy-dev] requested number of bytes is more than a Python string can hold

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<jen(a)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(a)lists.bx.psu.edu >> http://lists.bx.psu.edu/listinfo/galaxy-dev > > -- > Jennifer Jackson > http://usegalaxy.org > http://galaxyproject.org