When I try to run CollectMultipleMetrics with PROGRAM=RnaSeqMetrics and I= R= O= set to something I get :
Exception in thread "main" java.lang.NullPointerException
at htsjdk.samtools.util.IOUtil.openFileForReading(IOUtil.java:502)
at picard.util.BasicInputParser.filesToInputStreams(BasicInputParser.java:172)
at picard.util.BasicInputParser.(BasicInputParser.java:78)
at picard.util.TabbedInputParser.(TabbedInputParser.java:51)
at picard.util.TabbedTextFileWithHeaderParser.(TabbedTextFileWithHeaderParser.java:125)
at picard.annotation.RefFlatReader.load(RefFlatReader.java:73)
at picard.annotation.RefFlatReader.load(RefFlatReader.java:66)
at picard.annotation.GeneAnnotationReader.loadRefFlat(GeneAnnotationReader.java:37)
at picard.analysis.CollectRnaSeqMetrics.setup(CollectRnaSeqMetrics.java:141)
at picard.analysis.SinglePassSamProgram.makeItSo(SinglePassSamProgram.java:122)
at picard.analysis.CollectMultipleMetrics.doWork(CollectMultipleMetrics.java:407)
at picard.cmdline.CommandLineProgram.instanceMain(CommandLineProgram.java:208)
at picard.cmdline.PicardCommandLine.instanceMain(PicardCommandLine.java:95)
at picard.cmdline.PicardCommandLine.main(PicardCommandLine.java:105)
Why does the module RnaSeqMetrics not work while all the others do ? I did notice that the program CollectRnaSeqMetrics uses a flat file with annotations rather then a genome fastA file (as the other programs corresponding to modules do). Has that something to do with it ?
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problem with RnaSeqMetrics in Picard CollectMultipleMetrics
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