Hi everyone,
Thank you in advance for reading this. Has anyone else had the following problem when running CollectHSmetrics:
[Tue Apr 12 12:17:52 EDT 2016] picard.analysis.directed.CollectHsMetrics done. Elapsed time: 14.54 minutes.
Runtime.totalMemory()=920649728
To get help, see http://broadinstitute.github.io/picard/index.html#GettingHelp
Exception in thread "main" java.lang.ArrayIndexOutOfBoundsException: -1
at picard.analysis.directed.TargetMetricsCollector$PerUnitTargetMetricCollector.calculateTargetCoverageMetrics(TargetMetricsCollector.java:637)
at picard.analysis.directed.TargetMetricsCollector$PerUnitTargetMetricCollector.finish(TargetMetricsCollector.java:577)
at picard.metrics.MultiLevelCollector$AllReadsDistributor.finish(MultiLevelCollector.java:208)
at picard.metrics.MultiLevelCollector.finish(MultiLevelCollector.java:324)
at picard.analysis.directed.CollectTargetedMetrics.doWork(CollectTargetedMetrics.java:152)
at picard.cmdline.CommandLineProgram.instanceMain(CommandLineProgram.java:209)
at picard.cmdline.PicardCommandLine.instanceMain(PicardCommandLine.java:95)
at picard.cmdline.PicardCommandLine.main(PicardCommandLine.java:105)
The Bait and Target I used was just the header of my BAM file pulled by Samtools view header.
I saw something in the FAQ saying that, "The BAM index format imposes a limit of 512MB for a single reference sequence. If this limit is exceeded, various errors may occur depending on what steps have been taken."
Any explanation on how to address this? Thank you again!