From 5440dd13dfd0bc9fae31bf99f9e21dddd2d75b8a Mon Sep 17 00:00:00 2001 From: hanna Date: Thu, 11 Jun 2009 18:39:33 +0000 Subject: [PATCH] Preparation for point release of read calibrator: no artificial heap size limit, no duplicate dbsnp records. git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@986 348d0f76-0448-11de-a6fe-93d51630548a --- doc/ReadQualityRecalibrator/README | 11 +++++++++++ python/RecalQual.py | 2 +- 2 files changed, 12 insertions(+), 1 deletion(-) diff --git a/doc/ReadQualityRecalibrator/README b/doc/ReadQualityRecalibrator/README index a786df1a5..cbc1605d6 100644 --- a/doc/ReadQualityRecalibrator/README +++ b/doc/ReadQualityRecalibrator/README @@ -97,6 +97,17 @@ Known Issues graphs. If running on a machine via ssh, be certain to enable X tunnelling. +Troubleshooting +--------------- +- The memory requirements of the recalibrator will + vary based on the type of JVM running the application + and the number of read groups in the input bam file. + If the application reports 'java.lang.OutOfMemoryError: + Java heap space', increase the max heap size provided + to the JVM by adding ' -Xmx????m' to the jvm_args + variable in RecalQual.py, where '????' is the maximum + available memory on the processing computer. + Support ------- For support, please email gsadevelopers@broad.mit.edu. diff --git a/python/RecalQual.py b/python/RecalQual.py index 85cfc4be8..a8bbace27 100755 --- a/python/RecalQual.py +++ b/python/RecalQual.py @@ -6,7 +6,7 @@ java_exe='/broad/tools/Linux/x86_64/pkgs/jdk_1.6.0_12/bin/java' R_exe="/broad/tools/apps/R-2.6.0/bin/Rscript" # Any special site-specific arguments to pass the JVM. -jvm_args='-ea -Xmx4096m' +jvm_args='-ea' # Which platforms should the calibration tool be run over? platforms=['illumina']