Hi, I am currently trying to run CollectGcBiasMetrics on an aligned bam file and keep encountering the same error. I have tried adding read groups to the file and am currently running the newest version of picard so I do not understand what could be causing the problem. The version of java I am using is 1.8.0_05.
The command line I am using is: unset _JAVA_OPTIONS java -Xmx10G -jar /directory/directory/directory/directory/directory/picard-tools-1.134/picard.jar CollectGcBiasMetrics R='/directory/directory/directory/genome.fa' I='/directory/directory/directory/directory/A1.bam' O='/directory/directory/directory/picard_out/A1.GCbias' CHART='/directory/directory/directory/A1.GCbias.pdf' The error I keep receiving is: Exception in thread "main" java.lang.ArrayIndexOutOfBoundsException: 133858600 at picard.analysis.directed.GcBiasMetricsCollector.addRead(GcBiasMetricsCollector.java:270) at picard.analysis.directed.GcBiasMetricsCollector.access$100(GcBiasMetricsCollector.java:25) at picard.analysis.directed.GcBiasMetricsCollector$PerUnitGcBiasMetricsCollector.acceptRecord(GcBiasMetricsCollector.java:123) at picard.analysis.directed.GcBiasMetricsCollector$PerUnitGcBiasMetricsCollector.acceptRecord(GcBiasMetricsCollector.java:64) at picard.metrics.MultiLevelCollector$AllReadsDistributor.acceptRecord(MultiLevelCollector.java:192) at picard.metrics.MultiLevelCollector.acceptRecord(MultiLevelCollector.java:315) at picard.analysis.directed.GcBiasMetricsCollector.acceptRecord(GcBiasMetricsCollector.java:58) at picard.analysis.CollectGcBiasMetrics.acceptRead(CollectGcBiasMetrics.java:149) at picard.analysis.SinglePassSamProgram.makeItSo(SinglePassSamProgram.java:114) at picard.analysis.SinglePassSamProgram.doWork(SinglePassSamProgram.java:53) at picard.cmdline.CommandLineProgram.instanceMain(CommandLineProgram.java:206) at picard.cmdline.PicardCommandLine.instanceMain(PicardCommandLine.java:95) at picard.cmdline.PicardCommandLine.main(PicardCommandLine.java:105) Thank you in advance for any help.
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