I'm trying to merge two bam files that I got going through the Drop-seq pipeline. I've check both inputs using ValidateSamFiles and have no errors from either. But when I run MergeBamAlignment, I keep getting the same error when it's running:
WARNING 2018-06-20 11:33:53 SamAlignmentMerger Exception merging bam alignment - attempting to sort aligned reads and try again: Inappropriate call if not paired read
And this one after it finishes reading in all the records from the alignment SAM/BAM:
Exception in thread "main" java.lang.IllegalStateException: Inappropriate call if not paired read at htsjdk.samtools.SAMRecord.requireReadPaired(SAMRecord.java:866) at htsjdk.samtools.SAMRecord.getProperPairFlag(SAMRecord.java:874) at picard.sam.AbstractAlignmentMerger.setValuesFromAlignment(AbstractAlignmentMerger.java:655) at picard.sam.AbstractAlignmentMerger.transferAlignmentInfoToFragment(AbstractAlignmentMerger.java:548) at picard.sam.AbstractAlignmentMerger.transferAlignmentInfoToPairedRead(AbstractAlignmentMerger.java:578) at picard.sam.AbstractAlignmentMerger.mergeAlignment(AbstractAlignmentMerger.java:390) at picard.sam.SamAlignmentMerger.mergeAlignment(SamAlignmentMerger.java:157) at picard.sam.MergeBamAlignment.doWork(MergeBamAlignment.java:266) at picard.cmdline.CommandLineProgram.instanceMain(CommandLineProgram.java:209) at picard.cmdline.PicardCommandLine.instanceMain(PicardCommandLine.java:95) at picard.cmdline.PicardCommandLine.main(PicardCommandLine.java:105)
I'm not sure what the issue is. I've been successful using the same code on previous Drop-seq files but this newest batch is causing these issues. As far as I can tell, they are the same as older runs that worked. Any ideas would be greatly appreciated!