From 0b30588d67ad72177b5d1ecb9d0553b0c9832b17 Mon Sep 17 00:00:00 2001 From: Eric Banks Date: Mon, 30 Jul 2012 11:59:56 -0400 Subject: [PATCH] Catch yet another class of User Errors --- .../src/org/broadinstitute/sting/gatk/CommandLineGATK.java | 6 ++++++ 1 file changed, 6 insertions(+) diff --git a/public/java/src/org/broadinstitute/sting/gatk/CommandLineGATK.java b/public/java/src/org/broadinstitute/sting/gatk/CommandLineGATK.java index b1ad19e69..306ebdd0e 100755 --- a/public/java/src/org/broadinstitute/sting/gatk/CommandLineGATK.java +++ b/public/java/src/org/broadinstitute/sting/gatk/CommandLineGATK.java @@ -131,6 +131,12 @@ public class CommandLineGATK extends CommandLineExecutable { // can't close tribble index when writing if ( message.indexOf("Unable to close index for") != -1 ) exitSystemWithUserError(new UserException(t.getCause().getMessage())); + + // disk is full + if ( message.indexOf("No space left on device") != -1 ) + exitSystemWithUserError(new UserException(t.getMessage())); + if ( t.getCause().getMessage().indexOf("No space left on device") != -1 ) + exitSystemWithUserError(new UserException(t.getCause().getMessage())); } /**