I get errors trying to run CollectWgsMetics similar to a previous post (http://gatkforums.broadinstitute.org/dsde/discussion/6692/error-while-using-collectwgsmetrics). It appears to have run, but it won't write the output file?
I ran ValidateSamFile and got "NO ERRORS".
Any help is appreciated.
Thanks,
Jeff
/usr/lib/jvm/jre-1.8.0/bin/java -Xmx4g -jar /home/projects/picard-tools-2.0.1/picard.jar CollectWgsMetrics \
I=/home/projects/Sample.final.bam \
O=/home/projects/Sample1069205.out \
REFERENCE_SEQUENCE= /home/projects/Refs/hs37d5/hs37d5.fa \
java -version
openjdk version "1.8.0_25"
OpenJDK Runtime Environment (build 1.8.0_25-b17)
OpenJDK 64-Bit Server VM (build 25.20-b23, mixed mode)
...
[Mon Aug 08 15:45:08 EDT 2016] picard.analysis.CollectWgsMetrics done. Elapsed time: 166.35 minutes.
Runtime.totalMemory()=1371013120
To get help, see http://broadinstitute.github.io/picard/index.html#GettingHelp
Exception in thread "main" java.lang.ArrayIndexOutOfBoundsException: 4262
at picard.analysis.CollectWgsMetrics.doWork(CollectWgsMetrics.java:175)
at picard.cmdline.CommandLineProgram.instanceMain(CommandLineProgram.java:209)
at picard.cmdline.PicardCommandLine.instanceMain(PicardCommandLine.java:95)
at picard.cmdline.PicardCommandLine.main(PicardCommandLine.java:105)
