Tagged with #buffer
0 documentation articles | 0 announcements | 2 forum discussions


No posts found with the requested search criteria.
No posts found with the requested search criteria.

Created 2014-12-04 16:29:54 | Updated | Tags: buffer
Comments (0)

Hello, I'm running GATK over a parallel file system. This system runs optimally when IO requests use 4Mb blocks. Since GATK uses htsjdk to parse BAMs and various other inputs I thought that setting '-Dsamjdk.buffer_size=4194304' as I do for picard and other htsjdk apps would fix this, but it does nothing.

Looking at the source code, I don't know why -Dsamjdk.buffer_size=4194304 doesn't work (it doesn't seem to be overridden in SAMDataSource), BUT I do see multiple parts of code that hardcodes buffer sizes or just doesn't set them (oracle jdk default being 8k)

Are there any plans to add a configurable way to set buffers? read_buffer is not the same thing, and doesn't serve the same purpose.

Thanks


Created 2013-08-26 12:52:23 | Updated | Tags: baserecalibrator error buffer
Comments (7)

Hi, I have an error in the step BaseRecalibrator and even increasing the memory allocated to the job, I still have the same error and nothing found on previous published posts :

ERROR ------------------------------------------------------------------------------------------
ERROR stack trace

org.broadinstitute.sting.utils.exceptions.ReviewedStingException: Insufficient buffer size for Xs overhanging genome -- expand BUFFER at org.broadinstitute.sting.gatk.datasources.providers.ReferenceView.getReferenceBases(ReferenceView.java:121) at org.broadinstitute.sting.gatk.datasources.providers.ReadReferenceView$Provider.getBases(ReadReferenceView.java:87) at org.broadinstitute.sting.gatk.contexts.ReferenceContext.fetchBasesFromProvider(ReferenceContext.java:145) at org.broadinstitute.sting.gatk.contexts.ReferenceContext.getBases(ReferenceContext.java:189) at org.broadinstitute.sting.gatk.walkers.bqsr.BaseRecalibrator.calculateIsSNP(BaseRecalibrator.java:335) at org.broadinstitute.sting.gatk.walkers.bqsr.BaseRecalibrator.map(BaseRecalibrator.java:253) at org.broadinstitute.sting.gatk.walkers.bqsr.BaseRecalibrator.map(BaseRecalibrator.java:132) at org.broadinstitute.sting.gatk.traversals.TraverseReadsNano$TraverseReadsMap.apply(TraverseReadsNano.java:228) at org.broadinstitute.sting.gatk.traversals.TraverseReadsNano$TraverseReadsMap.apply(TraverseReadsNano.java:216) at org.broadinstitute.sting.utils.nanoScheduler.NanoScheduler.executeSingleThreaded(NanoScheduler.java:274) at org.broadinstitute.sting.utils.nanoScheduler.NanoScheduler.execute(NanoScheduler.java:245) at org.broadinstitute.sting.gatk.traversals.TraverseReadsNano.traverse(TraverseReadsNano.java:102) at org.broadinstitute.sting.gatk.traversals.TraverseReadsNano.traverse(TraverseReadsNano.java:56) at org.broadinstitute.sting.gatk.executive.LinearMicroScheduler.execute(LinearMicroScheduler.java:108) at org.broadinstitute.sting.gatk.GenomeAnalysisEngine.execute(GenomeAnalysisEngine.java:311) at org.broadinstitute.sting.gatk.CommandLineExecutable.execute(CommandLineExecutable.java:113) at org.broadinstitute.sting.commandline.CommandLineProgram.start(CommandLineProgram.java:245) at org.broadinstitute.sting.commandline.CommandLineProgram.start(CommandLineProgram.java:152) at org.broadinstitute.sting.gatk.CommandLineGATK.main(CommandLineGATK.java:91)

ERROR ------------------------------------------------------------------------------------------
ERROR A GATK RUNTIME ERROR has occurred (version 2.6-5-gba531bd):
ERROR
ERROR Please check the documentation guide to see if this is a known problem
ERROR If not, please post the error, with stack trace, to the GATK forum
ERROR Visit our website and forum for extensive documentation and answers to
ERROR commonly asked questions http://www.broadinstitute.org/gatk
ERROR
ERROR MESSAGE: Insufficient buffer size for Xs overhanging genome -- expand BUFFER
ERROR ------------------------------------------------------------------------------------------

Thank you in advance