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Apologies if this has been reported but I can't find it in the forum.
We're in the process of upgrading to GATK v2 but have been using v1.5 and have just noticed a few cases where IndelRealigner suddenly ended without warning or any report of an error. See example below where it ended with only ~50% of the BAM file processed. I'm wondering if it's a memory issue if multiple samples were being run concurrently. But more importantly with no alert it makes it tricky for us to identify when this happens. Is this something that's been fixed in later versions e.g. GATK 2.1 i.e. will Indelrealigner report an error when it finishes but the sample has not been processed to completion?
INFO 16:21:03,120 TraversalEngine - 8:90782004 3.17e+07 3.3 h 6.3 m 47.8% 6.9 h 3.6 h
INFO 16:21:33,939 TraversalEngine - 8:99615949 3.18e+07 3.3 h 6.3 m 48.1% 6.9 h 3.6 h
INFO 16:22:04,047 TraversalEngine - 8:110498944 3.19e+07 3.3 h 6.2 m 48.5% 6.9 h 3.5 h
INFO 16:22:24,484 TraversalEngine - Total runtime 11978.49 secs, 199.64 min, 3.33 hours
INFO 16:22:24,509 TraversalEngine - 0 reads were filtered out during traversal out of 32137673 total (0.00%)
Thank you in advance.