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I got this when I ran the IndelRealigner. The output bam is empty.
INFO 15:19:35,568 TraversalEngine - Total runtime 0.00 secs, 0.00 min, 0.00 hours INFO 15:19:36,910 GATKRunReport - Uploaded run statistics report to AWS S3
It didn't initialize. The sample is aligned to specific region of the genome and I did use -L option. For whole genome alignment of the same sample, I don't have any problems. Do you know why?