Hey guys,
I want to use RNA-SeQC for my Rna-seq data. Preparing it like it's done on the website I get the following error:
java.lang.IllegalStateException: Inappropriate call if not paired read
at net.sf.samtools.SAMRecord.requireReadPaired(SAMRecord.java:642)
at net.sf.samtools.SAMRecord.getMateUnmappedFlag(SAMRecord.java:669)
at org.broadinstitute.sting.utils.sam.GATKSAMRecord.getMateUnmappedFlag(GATKSAMRecord.java:307)
at org.broadinstitute.cga.rnaseq.gatk.CountReadMetricsWalker.map(CountReadMetricsWalker.java:188)
at org.broadinstitute.cga.rnaseq.gatk.CountReadMetricsWalker.map(CountReadMetricsWalker.java:37)
at org.broadinstitute.sting.gatk.traversals.TraverseReads.traverse(TraverseReads.java:103)
at org.broadinstitute.sting.gatk.traversals.TraverseReads.traverse(TraverseReads.java:51)
at org.broadinstitute.sting.gatk.executive.LinearMicroScheduler.execute(LinearMicroScheduler.java:69)
at org.broadinstitute.sting.gatk.GenomeAnalysisEngine.execute(GenomeAnalysisEngine.java:225)
at org.broadinstitute.sting.gatk.CommandLineExecutable.execute(CommandLineExecutable.java:104)
at org.broadinstitute.sting.commandline.CommandLineProgram.start(CommandLineProgram.java:227)
at org.broadinstitute.cga.rnaseq.gatk.GATKTools.runIntronReadCount(GATKTools.java:225)
at org.broadinstitute.cga.rnaseq.ReadCountMetrics.runRegionCounting(ReadCountMetrics.java:236)
at org.broadinstitute.cga.rnaseq.ReadCountMetrics.runReadCountMetrics(ReadCountMetrics.java:57)
at org.broadinstitute.cga.rnaseq.RNASeqMetrics.runMetrics(RNASeqMetrics.java:207)
at org.broadinstitute.cga.rnaseq.RNASeqMetrics.execute(RNASeqMetrics.java:158)
at org.broadinstitute.cga.rnaseq.RNASeqMetrics.main(RNASeqMetrics.java:127)
It proposes that the reads are :
Inappropriate call if not paired read
however i call with the '-singelEnd' flag such that it should be fine. Any guesses how to fix it?
Best,
Phil
I want to use RNA-SeQC for my Rna-seq data. Preparing it like it's done on the website I get the following error:
java.lang.IllegalStateException: Inappropriate call if not paired read
at net.sf.samtools.SAMRecord.requireReadPaired(SAMRecord.java:642)
at net.sf.samtools.SAMRecord.getMateUnmappedFlag(SAMRecord.java:669)
at org.broadinstitute.sting.utils.sam.GATKSAMRecord.getMateUnmappedFlag(GATKSAMRecord.java:307)
at org.broadinstitute.cga.rnaseq.gatk.CountReadMetricsWalker.map(CountReadMetricsWalker.java:188)
at org.broadinstitute.cga.rnaseq.gatk.CountReadMetricsWalker.map(CountReadMetricsWalker.java:37)
at org.broadinstitute.sting.gatk.traversals.TraverseReads.traverse(TraverseReads.java:103)
at org.broadinstitute.sting.gatk.traversals.TraverseReads.traverse(TraverseReads.java:51)
at org.broadinstitute.sting.gatk.executive.LinearMicroScheduler.execute(LinearMicroScheduler.java:69)
at org.broadinstitute.sting.gatk.GenomeAnalysisEngine.execute(GenomeAnalysisEngine.java:225)
at org.broadinstitute.sting.gatk.CommandLineExecutable.execute(CommandLineExecutable.java:104)
at org.broadinstitute.sting.commandline.CommandLineProgram.start(CommandLineProgram.java:227)
at org.broadinstitute.cga.rnaseq.gatk.GATKTools.runIntronReadCount(GATKTools.java:225)
at org.broadinstitute.cga.rnaseq.ReadCountMetrics.runRegionCounting(ReadCountMetrics.java:236)
at org.broadinstitute.cga.rnaseq.ReadCountMetrics.runReadCountMetrics(ReadCountMetrics.java:57)
at org.broadinstitute.cga.rnaseq.RNASeqMetrics.runMetrics(RNASeqMetrics.java:207)
at org.broadinstitute.cga.rnaseq.RNASeqMetrics.execute(RNASeqMetrics.java:158)
at org.broadinstitute.cga.rnaseq.RNASeqMetrics.main(RNASeqMetrics.java:127)
It proposes that the reads are :
Inappropriate call if not paired read
however i call with the '-singelEnd' flag such that it should be fine. Any guesses how to fix it?
Best,
Phil
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