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via broadinstitute.org by Unknown author, 1 year ago
via broadinstitute.org by Unknown author, 1 year ago
Array length mismatch detected. Malformed read?
org.broadinstitute.sting.utils.exceptions.ReviewedStingException: Array length mismatch detected. Malformed read?	at org.broadinstitute.sting.gatk.walkers.bqsr.BaseRecalibrator.calculateFractionalErrorArray(BaseRecalibrator.java:371)	at org.broadinstitute.sting.gatk.walkers.bqsr.BaseRecalibrator.map(BaseRecalibrator.java:246)	at org.broadinstitute.sting.gatk.walkers.bqsr.BaseRecalibrator.map(BaseRecalibrator.java:112)	at org.broadinstitute.sting.gatk.traversals.TraverseReadsNano$TraverseReadsMap.apply(TraverseReadsNano.java:203)	at org.broadinstitute.sting.gatk.traversals.TraverseReadsNano$TraverseReadsMap.apply(TraverseReadsNano.java:191)	at org.broadinstitute.sting.utils.nanoScheduler.NanoScheduler.executeSingleThreaded(NanoScheduler.java:287)	at org.broadinstitute.sting.utils.nanoScheduler.NanoScheduler.execute(NanoScheduler.java:252)	at org.broadinstitute.sting.gatk.traversals.TraverseReadsNano.traverse(TraverseReadsNano.java:91)	at org.broadinstitute.sting.gatk.traversals.TraverseReadsNano.traverse(TraverseReadsNano.java:55)	at org.broadinstitute.sting.gatk.executive.LinearMicroScheduler.execute(LinearMicroScheduler.java:83)	at org.broadinstitute.sting.gatk.GenomeAnalysisEngine.execute(GenomeAnalysisEngine.java:281)	at org.broadinstitute.sting.gatk.CommandLineExecutable.execute(CommandLineExecutable.java:113)	at org.broadinstitute.sting.commandline.CommandLineProgram.start(CommandLineProgram.java:236)	at org.broadinstitute.sting.commandline.CommandLineProgram.start(CommandLineProgram.java:146)	at org.broadinstitute.sting.gatk.CommandLineGATK.main(CommandLineGATK.java:93)