Picard CollectHsMetrics malfunctioning
I tried to run CollectHsMetrics, this is my 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
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Pierre Lindenbaum
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erarroji •
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erarroji •
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picard tools installation problems
written by aroso491 •
check this please: https://github.com/broadinstitute/picard/issues/1003
Thank you Pierre, i've been struggling with this all week. It is exactly the same mistake, but my input files are ok. Could you suggest me another software for calculate the metrics? Thank you
What kind of "metrics" do you need ? you should add your problem to the issues of picard. https://github.com/broadinstitute/picard/issues
Already did. Coverage depth, mean coverage and off target.
Coverage depth, mean coverage : gatk DepthOfCoverage https://software.broadinstitute.org/gatk/documentation/tooldocs/current/org_broadinstitute_gatk_tools_walkers_coverage_DepthOfCoverage.php with option -L
off target : gatk DepthOfCoverage with option -XL
I really thank you it has been really useful