Error during picard.analysis.QualityScoreDistribution #404
Description
Hi, I am running GRIDSS on a bwa-mem aligned tumour/normal pair and the execution is failing during this step:
[Tue Sep 22 17:51:12 AEST 2020] gridss.analysis.CollectGridssMetrics done. Elapsed time: 0.25 minutes.
Runtime.totalMemory()=1095761920
Exception in thread "main" java.lang.RuntimeException: java.lang.RuntimeException: Exception when running picard.analysis.QualityScoreDistribution
at picard.analysis.SinglePassSamProgram.makeItSo(SinglePassSamProgram.java:238)
at picard.analysis.SinglePassSamProgram.makeItSo(SinglePassSamProgram.java:125)
at picard.analysis.CollectMultipleMetrics.doWork(CollectMultipleMetrics.java:598)
at gridss.analysis.CollectGridssMetrics.doWork(CollectGridssMetrics.java:67)
at picard.cmdline.CommandLineProgram.instanceMain(CommandLineProgram.java:305)
at picard.cmdline.CommandLineProgram.instanceMainWithExit(CommandLineProgram.java:196)
at gridss.analysis.CollectGridssMetrics.main(CollectGridssMetrics.java:51)
Caused by: java.lang.RuntimeException: Exception when running picard.analysis.QualityScoreDistribution
at picard.analysis.SinglePassSamProgram.raiseAsyncException(SinglePassSamProgram.java:267)
at picard.analysis.SinglePassSamProgram.asyncAcceptRead(SinglePassSamProgram.java:258)
at picard.analysis.SinglePassSamProgram.asyncAcceptReads(SinglePassSamProgram.java:248)
at picard.analysis.SinglePassSamProgram.makeItSo(SinglePassSamProgram.java:205)
... 6 more
Caused by: java.lang.ArrayIndexOutOfBoundsException: Index -4 out of bounds for length 128
at picard.analysis.QualityScoreDistribution.acceptRead(QualityScoreDistribution.java:130)
at picard.analysis.SinglePassSamProgram$SinglePassSamProgramRunner.run(SinglePassSamProgram.java:305)
at java.base/java.lang.Thread.run(Thread.java:834)
I have tracked it down to a single entry in the gridss.assembly.bam (see attached image/txt). I'm not sure if this is a bug in GRIDSS or a problem with my fastq/bam files that is carrying over. Removing this line seems to allow the tool to continue running normally.
CorruptBAMline.txt
gridss_minimal_reproduction_data_for_error_1.zip
gridss_minimal_reproduction_data_for_error_2.zip
Thanks for your help!
Aidan