On Jan 11, 2012, at 10:56 AM, Ryan Golhar wrote:

> it is also set to True:
> > [galaxy@bic galaxy-dist]$ grep Ryan *.log
> > runner0.log:galaxy.jobs WARNING 2012-01-10 22:17:26,381 Ryan Golhar - 
> > self.set_metadata_externally = True
> >
> > Clearly something else is going on here.  On my last import of BAM file, 
> > even after samtools finished indexing the BAM files, Galaxy never 
> > registered those jobs as completed.  So this problem is still there as well.
> 
> Thanks for checking these.  So, what does your server log for runner0 look 
> like?
> 
>  
> > it is also set to True:
> > [galaxy@bic galaxy-dist]$ grep Ryan *.log
> > runner0.log:galaxy.jobs WARNING 2012-01-10 22:17:26,381 Ryan Golhar - 
> > self.set_metadata_externally = True

Sorry, I should have been more specific.  What are the contents of the log from 
job start to finish?

--nate

>  


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