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UmiAwareMarkDuplicatesWithMateCigar java.lang.NullPointerException error

Hello,

I've annotated a SAM file with UMI information (using fgbio's AnnotateBamWithUmis) and am trying to mark duplicates with the tool "UmiAwareMarkDuplicatesWithMateCigar".

My command is as follows:
java -jar ../Tools/picard.jar UmiAwareMarkDuplicatesWithMateCigar I=aligned_umi.sam O=aligned_umi_dup.sam M=aligned_M.txt UMI_METRICS=aligned_umi_met.txt

The version of Picard is 2.18.12-SNAPSHOT

However I receive the following error:

Exception in thread "main" java.lang.NullPointerException at picard.sam.markduplicates.UmiAwareDuplicateSetIterator.process(UmiAwareDuplicateSetIterator.java:138) at picard.sam.markduplicates.UmiAwareDuplicateSetIterator.next(UmiAwareDuplicateSetIterator.java:117) at picard.sam.markduplicates.UmiAwareDuplicateSetIterator.next(UmiAwareDuplicateSetIterator.java:53) at picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigar.doWork(SimpleMarkDuplicatesWithMateCigar.java:133) at picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigar.doWork(UmiAwareMarkDuplicatesWithMateCigar.java:141) at picard.cmdline.CommandLineProgram.instanceMain(CommandLineProgram.java:277) at picard.cmdline.PicardCommandLine.instanceMain(PicardCommandLine.java:103) at picard.cmdline.PicardCommandLine.main(PicardCommandLine.java:113)

I'm unsure why I'm getting this error. I can do the duplicate marking using the original MarkDuplicates tool without issue:
java -jar ../Tools/picard.jar MarkDuplicates INPUT=aligned_umi.sam OUTPUT=aligned_umi_dup.sam METRICS_FILE=aligned_M.txt BARCODE_TAG=RX

But I really want to be able to use the MAX_EDIT_DISTANCE_TO_JOIN parameter with the UmiAwareMarkDuplicatesWithMateCigar tool, and I'm also interested in the UMI_METICS statistics that this tool should report.

Thanks in advance for your help.
Devin

Answers

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