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Using GATK tool on my coordinate sorted bam file, UmiAwareMarkDuplicatesWithMateCigar gives error

Using the tool on my coordinate sorted bam file and i keep getting an error
INFO 2019-12-16 10:46:24 MarkDuplicatesWithMateCigar Read 1,000,000 records. Elapsed time: 00:00:12s. Time for last 1,000,000: 12s. Last read position: */*
INFO 2019-12-16 10:46:39 MarkDuplicatesWithMateCigar Read 2,000,000 records. Elapsed time: 00:00:27s. Time for last 1,000,000: 14s. Last read position: */*
INFO 2019-12-16 10:46:54 MarkDuplicatesWithMateCigar Read 3,000,000 records. Elapsed time: 00:00:42s. Time for last 1,000,000: 15s. Last read position: */*
INFO 2019-12-16 10:47:10 MarkDuplicatesWithMateCigar Read 4,000,000 records. Elapsed time: 00:00:58s. Time for last 1,000,000: 16s. Last read position: */*
INFO 2019-12-16 10:47:27 MarkDuplicatesWithMateCigar Read 5,000,000 records. Elapsed time: 00:01:14s. Time for last 1,000,000: 16s. Last read position: */*
INFO 2019-12-16 10:47:43 MarkDuplicatesWithMateCigar Read 6,000,000 records. Elapsed time: 00:01:30s. Time for last 1,000,000: 15s. Last read position: */*
INFO 2019-12-16 10:47:59 MarkDuplicatesWithMateCigar Read 7,000,000 records. Elapsed time: 00:01:47s. Time for last 1,000,000: 16s. Last read position: */*
INFO 2019-12-16 10:48:17 MarkDuplicatesWithMateCigar Read 8,000,000 records. Elapsed time: 00:02:05s. Time for last 1,000,000: 18s. Last read position: */*
INFO 2019-12-16 10:48:36 MarkDuplicatesWithMateCigar Read 9,000,000 records. Elapsed time: 00:02:23s. Time for last 1,000,000: 18s. Last read position: */*
INFO 2019-12-16 10:48:53 MarkDuplicatesWithMateCigar Read 10,000,000 records. Elapsed time: 00:02:41s. Time for last 1,000,000: 17s. Last read position: */*
INFO 2019-12-16 10:49:11 MarkDuplicatesWithMateCigar Read 11,000,000 records. Elapsed time: 00:02:59s. Time for last 1,000,000: 17s. Last read position: */*
INFO 2019-12-16 10:53:28 MarkDuplicatesWithMateCigar Found 0 optical duplicate clusters.
INFO 2019-12-16 10:53:28 MarkDuplicatesWithMateCigar Processed 11567680 records
INFO 2019-12-16 10:53:28 MarkDuplicatesWithMateCigar Marking 0 records as duplicates.


Where as when I GroupReadsByUMI, the tool works and gives me a record of the UMI

Alsop, is there a way to get a list of duplicate sets or the UMI Sets as a different file?

Answers

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