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do later versions of GATK (1.5+) warn when Indelrealigner ends prematurely?

mardmard Member
edited September 2012 in Ask the GATK team


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.

Best regards,

Post edited by Geraldine_VdAuwera on


  • Geraldine_VdAuweraGeraldine_VdAuwera Cambridge, MAMember, Administrator, Broadie

    Hi Maria,

    If the tool encounters an error that causes it to fail, it should always produce an error message. This sounds like there may be something wrong with your file -- can you check that there are reads throughout and that the contiguous are properly sorted?

  • Hi Geraldine,

    Thanks for the quick reply.
    The samples were rerun through the same analysis pipeline with no problems (an automated pipeline that processes the samples from fastq to annotated variant calls) so I don't think it's possible for it to be an issue with the bam file content.


  • Geraldine_VdAuweraGeraldine_VdAuwera Cambridge, MAMember, Administrator, Broadie

    Hi Maria,

    If you're not having any other problems with those data files then it's hard to say what might be the issue. All I can say really is that that behavior (quitting without alert) should not happen. It may be related to an older issue that has been fixed since.

    The version of IndelRealigner included with GATK 2 is a completely mature tool; so if you're migrating to v2 anyway my best recommendation is to rerun this with the latest version (2.1-x). Let me know if you still experience this issue.

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