Question: Picard CollectHsMetrics malfunctioning
0
gravatar for erarroji
3 days ago by
erarroji0
erarroji0 wrote:

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

ADD COMMENTlink modified 3 days ago by Pierre Lindenbaum102k • written 3 days ago by erarroji0

check this please: https://github.com/broadinstitute/picard/issues/1003

ADD REPLYlink written 3 days ago by Pierre Lindenbaum102k

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

ADD REPLYlink written 3 days ago by erarroji0

What kind of "metrics" do you need ? you should add your problem to the issues of picard. https://github.com/broadinstitute/picard/issues

ADD REPLYlink written 3 days ago by Pierre Lindenbaum102k

Already did. Coverage depth, mean coverage and off target.

ADD REPLYlink written 3 days ago by erarroji0

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

ADD REPLYlink written 3 days ago by Pierre Lindenbaum102k

I really thank you it has been really useful

ADD REPLYlink written 3 days ago by erarroji0
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