From 154f65e0dec1e75fc318b501014e65b2f833a73c Mon Sep 17 00:00:00 2001 From: Eric Banks Date: Mon, 20 Aug 2012 12:43:17 -0400 Subject: [PATCH] Temporarily disabling multi-threaded usage of BaseRecalibrator for performance reasons. --- .../sting/gatk/walkers/bqsr/BQSRIntegrationTest.java | 9 +++++---- .../sting/gatk/walkers/bqsr/BaseRecalibrator.java | 4 ++++ 2 files changed, 9 insertions(+), 4 deletions(-) diff --git a/protected/java/test/org/broadinstitute/sting/gatk/walkers/bqsr/BQSRIntegrationTest.java b/protected/java/test/org/broadinstitute/sting/gatk/walkers/bqsr/BQSRIntegrationTest.java index bd75806dd..580667ee2 100644 --- a/protected/java/test/org/broadinstitute/sting/gatk/walkers/bqsr/BQSRIntegrationTest.java +++ b/protected/java/test/org/broadinstitute/sting/gatk/walkers/bqsr/BQSRIntegrationTest.java @@ -75,10 +75,11 @@ public class BQSRIntegrationTest extends WalkerTest { Arrays.asList(params.md5)); executeTest("testBQSR-"+params.args, spec).getFirst(); - WalkerTestSpec specNT2 = new WalkerTestSpec( - params.getCommandLine() + " -nt 2", - Arrays.asList(params.md5)); - executeTest("testBQSR-nt2-"+params.args, specNT2).getFirst(); + // TODO -- re-enable once parallelization is fixed in BaseRecalibrator + //WalkerTestSpec specNT2 = new WalkerTestSpec( + // params.getCommandLine() + " -nt 2", + // Arrays.asList(params.md5)); + //executeTest("testBQSR-nt2-"+params.args, specNT2).getFirst(); } @Test diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/bqsr/BaseRecalibrator.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/bqsr/BaseRecalibrator.java index e45cad971..91d982f20 100755 --- a/public/java/src/org/broadinstitute/sting/gatk/walkers/bqsr/BaseRecalibrator.java +++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/bqsr/BaseRecalibrator.java @@ -136,6 +136,10 @@ public class BaseRecalibrator extends LocusWalker implements TreeRed */ public void initialize() { + // TODO -- remove me after the 2.1 release + if ( getToolkit().getArguments().numberOfThreads > 1 ) + throw new UserException("We have temporarily disabled the ability to run BaseRecalibrator multi-threaded for performance reasons. We hope to have this fixed for the next GATK release (2.2) and apologize for the inconvenience."); + // check for unsupported access if (getToolkit().isGATKLite() && !getToolkit().getArguments().disableIndelQuals) throw new UserException.NotSupportedInGATKLite("base insertion/deletion recalibration is not supported, please use the --disable_indel_quals argument");