This is not a good candidate for the current pipeline. We might consider rejecting it or we could ask Alex to test his new metagene driven ORF calling? On the Cmd Line? Folker On Nov 27, 2008, at 12:48 AM, Mark D'Souza wrote:

I ran the steps from the command line -- preprocess, sims etc.

I had not looked into 1568 before, it is ~66MB, with 34 contigs.

Any suggestions on how to deal with this.

The sims are churning away, and have eaten up a lot of time on the cluster.

Mark

qstat: 523482 0.57410 ms_1568 mgrastprod r 11/20/2008 15:11:05 compute.q@bio-intel-compute-1. 523482 0.57410 ms_1568 mgrastprod Rr 11/24/2008 10:43:20 compute.q@bio-intel-compute-1. 523482 0.57410 ms_1568 mgrastprod r 11/20/2008 15:13:50 compute.q@bio-intel-compute-10 523482 0.57410 ms_1568 mgrastprod r 11/20/2008 15:14:05 compute.q@bio-intel-compute-13 523482 0.57410 ms_1568 mgrastprod Rr 11/25/2008 12:11:20 compute.q@bio-intel-compute-2. 523482 0.57410 ms_1568 mgrastprod r 11/20/2008 15:15:20 compute.q@bio-intel-compute-2. 523482 0.57410 ms_1568 mgrastprod r 11/20/2008 15:13:50 compute.q@bio-intel-compute-3. 523482 0.57410 ms_1568 mgrastprod r 11/20/2008 15:14:50 compute.q@bio-intel-compute-3. 523482 0.57410 ms_1568 mgrastprod Rr 11/25/2008 12:11:20 compute.q@bio-intel-compute-5. 523482 0.57410 ms_1568 mgrastprod r 11/20/2008 15:15:05 compute.q@bio-intel-compute-6. 523482 0.57410 ms_1568 mgrastprod r 11/20/2008 15:14:20 compute.q@bio-intel-compute-9.

On Wed, 26 Nov 2008, Rob Edwards wrote:

...

What was the fix for this? There are other jobs that are in a seemingly similar state (e.g. 1568).

Rob

On Nov 19, 2008, at 11:26 AM, Ken Dewar, Dr. wrote:

...

Thank you Mark Ken -----Original Message----- From: Mark D'Souza [mailto:[email protected]] Sent: November 19, 2008 1:38 PM To: Ken Dewar, Dr. Cc: [email protected] Subject: Re: [mg-rast] is there any hope for job 1556? Hi Ken, I am looking into what went wrong with your job, it does not seem to be a problem that you can fix. I will get back to you when I have more information. Regards, Mark D'Souza On Wed, 19 Nov 2008, Ken Dewar, Dr. wrote:

...

Is there anything I could do at my end to help? Thanks Ken