On Jan 30, 2013, at 2:51 PM, Anthonius deBoer wrote:

> Hi,
> 
> I continue to see this error in the logs, every time a jobs finishes:
> 
> galaxy.objectstore CRITICAL 2013-01-30 11:42:14,161 
> /mnt/ngs/analysis/svcgalaxy/DATA/job_working_directory/000/327 delete
> error [Errno 39] Directory not empty: 
> '/mnt/ngs/analysis/svcgalaxy/DATA/job_working_directory/000/327'
> 
> When I check the directory, it is of course empty:
> 
> $ls -la /mnt/ngs/analysis/svcgalaxy/DATA/job_working_directory/000/327
> total 68
> drwxrwsr-x   2 svcgalaxy Domain Linux Users    0 Jan 30 11:42 .
> drwxrwsr-x 283 svcgalaxy Domain Linux Users 5793 Jan 30 11:45 .. 
> 
> Any ideas why this keeps happening?
> I end up with thousands of directories in the working directories which I 
> need to clean out manually now...

Hi Thon,

You'll probably need to add a debug statement to the code that outputs the 
contents of that directory at the time of attempted deletion.   The call to 
delete() is in the cleanup() method in lib/galaxy/jobs/__init__.py.

--nate

> 
> Thanks
> 
> Thon
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