SEQanswers

Go Back   SEQanswers > Bioinformatics > Bioinformatics



Similar Threads
Thread Thread Starter Forum Replies Last Post
CASAVA running on PBS pro westerman Illumina/Solexa 6 05-03-2013 10:30 AM
gatk python script m_elena_bioinfo Bioinformatics 7 11-20-2011 06:40 AM
problem submitting job to queue seq_newbie Bioinformatics 2 07-13-2011 04:47 AM
GATK CountCovariates running very slow indapa Bioinformatics 1 06-30-2011 05:46 AM
GATK Queue and options kasthuri Bioinformatics 2 06-10-2011 07:57 AM

Reply
 
Thread Tools
Old 05-24-2011, 01:31 PM   #1
orionzhou
Member
 
Location: St. Paul

Join Date: Sep 2009
Posts: 14
Unhappy running GATK Queue script under PBS environment?

Hi, I am wondering if any of you have the experience running the GATK Queue scripts (for parallelism) under PBS environment.

It seems the Queue.jar only accepts -bsub command:

http://www.broadinstitute.org/gsa/wi...the_first_time
orionzhou is offline   Reply With Quote
Old 12-09-2012, 04:24 AM   #2
severin
Genome Informatics Facility
 
Location: Iowa @isugif

Join Date: Sep 2009
Posts: 105
Default PBS Torque

Did you ever figure his out? I find the GATK-Queue documentation a little lacking for applying to individual systems. The Best practices document appears to have pieces of code that correspond to each of the steps but not the base script that you put those pieces into.
severin is offline   Reply With Quote
Reply

Thread Tools

Posting Rules
You may not post new threads
You may not post replies
You may not post attachments
You may not edit your posts

BB code is On
Smilies are On
[IMG] code is On
HTML code is Off




All times are GMT -8. The time now is 01:59 AM.


Powered by vBulletin® Version 3.8.9
Copyright ©2000 - 2020, vBulletin Solutions, Inc.
Single Sign On provided by vBSSO