[maker-devel] Maker jobs hanging

[Daniel Ence]

Hi Greg, 

Since this is probably going to be a more complicated situation, would you upload your data and control file at this URL so that we can try to replicate the error on our machines?
http://weatherby.genetics.utah.edu/cgi-bin/mwas/bug.cgi?guest_id=166

Also, which version of MPI are you using? And you might want to try updating MAKER. I think version 2.31 was just updated a few weeks ago. 

Thanks,
Daniel


Daniel Ence
Graduate Student
Eccles Institute of Human Genetics
University of Utah
15 North 2030 East, Room 2100
Salt Lake City, UT 84112-5330
________________________________________
From: maker-devel [maker-devel-bounces at yandell-lab.org] on behalf of Greg Taylor [gtaylor at bcgsc.ca]
Sent: Friday, February 21, 2014 11:48 AM
To: maker-devel at yandell-lab.org
Subject: [maker-devel] Maker jobs hanging

Hello,
 I'm having a problem with Maker_2.28 jobs hanging. I am annotating a 3Gb genome with predictors SNAP and Genemark, and using ABySS assembled RNA-seq data. To do this I am using 480 processors on our local cluster. Once a run begins, 479 contigs are started, as noted in the *_master_datastore_index.log file, the standard error log for the whole job looks normal, as do the run.log and run.log.child.0 for the daughter processes. This seems to be sequence dependent, as re-running contigs that hang doesn't help, the same contigs will always hang. I'm still looking into this myself, but it seems most if not all the jobs are stuck at the Blastx stage. If you have any suggestions, your help would be greatly appreciated.

sincerely,
Greg Taylor
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