From e2bf899a8f213115e9cf2edb413dacd7d82bf6c5 Mon Sep 17 00:00:00 2001 From: Louis Bergelson Date: Tue, 1 Aug 2017 17:56:52 -0400 Subject: [PATCH 1/2] removing the explicit System.exit(0) from Main this fixes the yarn early termination bug reported in #2666 and #3166 --- src/main/java/org/broadinstitute/hellbender/Main.java | 1 - 1 file changed, 1 deletion(-) diff --git a/src/main/java/org/broadinstitute/hellbender/Main.java b/src/main/java/org/broadinstitute/hellbender/Main.java index 94755d56ff2..d737b2bde98 100644 --- a/src/main/java/org/broadinstitute/hellbender/Main.java +++ b/src/main/java/org/broadinstitute/hellbender/Main.java @@ -151,7 +151,6 @@ protected final void mainEntry(final String[] args) { try { final Object result = runCommandLineProgram(program, args); handleResult(result); - System.exit(0); } catch (final CommandLineException e){ System.err.println(program.getUsage()); handleUserException(e); From c54bb7f40bbec0e1407fefa8af2dbb32f7642f2d Mon Sep 17 00:00:00 2001 From: Louis Bergelson Date: Wed, 2 Aug 2017 13:28:11 -0400 Subject: [PATCH 2/2] adding comment --- src/main/java/org/broadinstitute/hellbender/Main.java | 1 + 1 file changed, 1 insertion(+) diff --git a/src/main/java/org/broadinstitute/hellbender/Main.java b/src/main/java/org/broadinstitute/hellbender/Main.java index d737b2bde98..bc6e7b8c477 100644 --- a/src/main/java/org/broadinstitute/hellbender/Main.java +++ b/src/main/java/org/broadinstitute/hellbender/Main.java @@ -151,6 +151,7 @@ protected final void mainEntry(final String[] args) { try { final Object result = runCommandLineProgram(program, args); handleResult(result); + //no explicit System.exit(0) since that causes issues when running in Yarn containers } catch (final CommandLineException e){ System.err.println(program.getUsage()); handleUserException(e);