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java.lang.NullPointerException for Picard SamToFastq OUTPUT_PER_RG=T on bam without read groups

hgiblinghgibling Member
edited March 2016 in Ask the GATK team


When running Picard's SamToFastq with OUTPUT_PER_RG=T on a bam file without read group information, you get the following error:

Exception in thread "main" java.lang.NullPointerException
        at net.sf.picard.sam.SamToFastq.doWork(
        at net.sf.picard.cmdline.CommandLineProgram.instanceMain(
        at net.sf.picard.sam.SamToFastq.main(

Obviously the command shouldn't work if there is no read group information, but it would be nice if there was a more informative error provided, as the NullPointerException makes it seem like an issue with memory allocation.

Issue · Github
by Sheila

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