On Thu, Jan 5, 2012 at 11:59 AM, Nate Coraor <nate@bx.psu.edu> wrote:

On Jan 5, 2012, at 11:41 AM, Ryan Golhar wrote:

> I set it to run on the cluster:
>
> [galaxy@bic galaxy-dist]$ grep upload1 universe_wsgi.runner.ini
> #upload1 = local:///

Could you set use_heartbeat = True in the runner's config file and then check the resulting heartbeat log files created in the root directory to get a stack trace to the call of samtools?

Thanks,
--nate

Hi Nate,

I just tried importing another BAM file. I see the upload working on a compute node, but the indexing happens on the head node. 'samtools index' is never submitted to the cluster. Attached is a copy of the heartbeat log. Its 990K, hopefully it will go through.

Ryan