On Jan 5, 2012, at 2:48 PM, Ryan Golhar wrote:
> On Thu, Jan 5, 2012 at 11:59 AM, Nate Coraor <n...@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?
> 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.
Thread 1180711232, <Thread(Thread-8, started 1180711232)>:
File "/share/apps/Python-2.6.7/lib/python2.6/threading.py", line 504, in
File "/share/apps/Python-2.6.7/lib/python2.6/threading.py", line 532, in
File "/share/apps/Python-2.6.7/lib/python2.6/threading.py", line 484, in run
File "/home/galaxy/galaxy-dist-9/lib/galaxy/jobs/runners/pbs.py", line 190,
self.finish_job( obj )
File "/home/galaxy/galaxy-dist-9/lib/galaxy/jobs/runners/pbs.py", line 514,
pbs_job_state.job_wrapper.finish( stdout, stderr )
File "/home/galaxy/galaxy-dist-9/lib/galaxy/jobs/__init__.py", line 611, in
dataset.set_meta( overwrite = False )
File "/home/galaxy/galaxy-dist-9/lib/galaxy/model/__init__.py", line 886, in
return self.datatype.set_meta( self, **kwd )
File "/home/galaxy/galaxy-dist-9/lib/galaxy/datatypes/binary.py", line 173,
exit_code = proc.wait()
File "/share/apps/Python-2.6.7/lib/python2.6/subprocess.py", line 1182, in
pid, sts = _eintr_retry_call(os.waitpid, self.pid, 0)
File "/share/apps/Python-2.6.7/lib/python2.6/subprocess.py", line 455, in
This indicates that set_meta is running locally, in the runner process. Can
you make sure there's not a typo in your config? The other possibility is that
external metadata setting failed and it's being retried internally (if that was
true, you'd see messages indicated such in the server log).
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