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help with picard CollectHsMetrics

I tried to run CollectHsMetrics with this command

java -jar /picard.jar CollectHsMetrics \
I=190.sortedDeDup.bam \
O=190_hs_metrics.txt \
R=ucsc.hg19.fasta \
BAIT_INTERVALS=AgilentSSV6_bait_list.interval_list \
TARGET_INTERVALS=V6SureSelect/AgilentSSV6_targets_list.interval_list

it works ok until minute 2, when it stops and display this error:
[Wed Dec 06 19:23:49 CST 2017] picard.analysis.directed.CollectHsMetrics done. Elapsed time: 2.74 minutes.
Runtime.totalMemory()=5752487936
To get help, see http://broadinstitute.github.io/picard/index.html#GettingHelp
Exception in thread "main" java.lang.IllegalStateException: Could not find percentile: 0.2
at htsjdk.samtools.util.Histogram.getPercentile(Histogram.java:327)
at picard.analysis.directed.TargetMetricsCollector$PerUnitTargetMetricCollector.calculateTargetCoverageMetrics(TargetMetricsCollector.java:688)
at picard.analysis.directed.TargetMetricsCollector$PerUnitTargetMetricCollector.finish(TargetMetricsCollector.java:626)
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:153)
at picard.cmdline.CommandLineProgram.instanceMain(CommandLineProgram.java:268)
at picard.cmdline.PicardCommandLine.instanceMain(PicardCommandLine.java:98)
at picard.cmdline.PicardCommandLine.main(PicardCommandLine.java:108)

What am I doing something wrong?

Thank you

Answers

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