Tagged with #callvariants
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Created 2014-07-02 20:02:53 | Updated | Tags: unifiedgenotyper fastareference heapsize callvariants

Comments (11)

Hi all,

Do you have a recommendation to estimate how much heap memory (-Xmx) is necessary to cal variants using the Unified Genotyper. I think that with my project I might be facing a situation where I will run out of memory until there is not more left to increase. To give you an idea, I have 185 samples (that together are 8Gb) and the fasta reference that I am using has too many scaffolds (3 Million). I don't have the opportunity to improve the reference I have at the moment. I have been using -Xmx52G and -nt 10 (in GATK 3.1) but it gives an error at the same point.

INFO 14:45:41,790 HelpFormatter - -------------------------------------------------------------------------------- INFO 14:45:42,773 GenomeAnalysisEngine - Strictness is SILENT INFO 14:59:01,106 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 250 INFO 14:59:01,171 SAMDataSource$SAMReaders - Initializing SAMRecords in serial

ERROR ------------------------------------------------------------------------------------------
ERROR A USER ERROR has occurred (version 3.1-1-g07a4bf8):
ERROR This means that one or more arguments or inputs in your command are incorrect.
ERROR The error message below tells you what is the problem.
ERROR If the problem is an invalid argument, please check the online documentation guide
ERROR (or rerun your command with --help) to view allowable command-line arguments for this tool.
ERROR Visit our website and forum for extensive documentation and answers to
ERROR commonly asked questions http://www.broadinstitute.org/gatk
ERROR Please do NOT post this error to the GATK forum unless you have really tried to fix it yourself.
ERROR MESSAGE: There was a failure because you did not provide enough memory to run this program. See the -Xmx JVM argument to adjust the maximum heap size provided to Java
ERROR ------------------------------------------------------------------------------------------

If you have a suggestion/advice of how to make the analysis work it would be very much appreciated. I know that increasing scaffolds length (reducing number of scaffolds) can improve the analysis so I am wondering if I am facing a situation where I can't do any analysis until the fasta reference is improved.

Many thanks,


Created 2013-08-19 08:54:23 | Updated | Tags: best-practices webinar callvariants

Comments (2)

I am not sure where I should ask this question, but the GATK forum seemed the most appropriate place. I am currently viewing the webinars from the BroadE Workshop 2013 July 9-10 and the "Call Variants" streaming doesn't seem to work:


Would you have a work around to view this file? or is the file inaccessible for some reason?