Re: [galaxy-dev] Still seeing this CRITICAL message in the logs when its trying to delete the working directories

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 ___________________________________________________________ Please keep all replies on the list by using "reply all" in your mail client. To manage your subscriptions to this and other Galaxy lists, please use the interface at:

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