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)
-- Glen L. Beane Software Engineer The Jackson Laboratory Phone (207) 288-6153
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?
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
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@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
Great news & info, thanks Glen for getting back to us!
Take care,
Jen
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 Jacksonjen@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
galaxy-dev@lists.galaxyproject.org
-
Glen Beane -
Jennifer Jackson