On Dec 20, 2011, at 12:19 AM, Le-Shin Wu wrote:

Thanks a million, Nate. I was able to submit my PBS job though galaxy. But I got another problem once the PBS job is finished.

I submit a bowtie alignment testing job to our cluster by using PBS runner through galaxy. But I always got an error message showing on the right history panel as below.

An error occurred running this job: # reads processed: 17214026 # reads with at least one reported alignment: 16405756 (95.30%) # reads that failed to align: 808270 (4.70%) Reported 16405756 alignments to 1 output stream(s)

In fact, the message showing here is the output message from bowtie application and I did get the correct alignment result stored on galaxy server machine. Therefore, I tried adding some PBS options, such as "-k eo" or "-j eo -o /dev/null", to the PBS runner in universe_wsgi.ini to remove the standard output message from bowtie. But this time I got the following error message.

Hi Le-Shin, I am not familiar enough with bowtie to know why this error occurred. Perhaps someone else on the list can reply with some information. Please keep replies on the mailing list to ensure this is possible.

An error occurred running this job:Job output not returned by PBS: the output datasets were deleted while the job was running, the job was manually dequeued or there was a cluster error.

It looks like if galaxy PBS runner did not receive the standard output from cluster, it will throw an error. Could you please help us to solve this problem. Thanks a lot.

That's correct, Galaxy controls the location of the stdout/stderr files, changing these will cause such failures. --nate

Le-Shin