Question: GATK recalibrator aborted/ended without any summery report
gravatar for Yingzi Zhang
15 months ago by
Yingzi Zhang60
Yingzi Zhang60 wrote:

Dear all, I successfully built index of pig's vcf file and applied them to do GATK recalibrator. My input bam file size was about 20G, My baserecalibrator ran and didn't report any error. It only warned that "Feature file 'sus_scrofa.vcf' appears to contain no sequence dictionary. Attempting to retrieve a sequence dictionary from the associated index file" and it started traversal. (befpre all these, I have successfully built vcf index using IndexFeatureFile) However. And the recalibrator begain output log file like this:

21:34:59.056 INFO ProgressMeter - Starting traversal 21:34:59.056 INFO ProgressMeter - Current Locus Elapsed Minutes Reads Processed Reads/Minute

21:35:13.018 INFO ProgressMeter - 4:53125217 0.2 1000 4297.7

21:35:24.142 INFO ProgressMeter - 10:38467706 0.4 2000 4783.5

21:35:34.879 INFO ProgressMeter - 6:38745010 0.6 3000 5024.7

21:35:52.362 INFO ProgressMeter - 13:174891640 0.9 5000 5627.9

21:36:06.822 INFO ProgressMeter - 13:76857766 1.1 7000 6197.9

21:36:19.541 INFO ProgressMeter - 16:35570996 1.3 9000 6709.4

21:36:30.035 INFO ProgressMeter - 3:17489359 1.5 11000 7254.4

21:36:40.240 INFO ProgressMeter - 17:39409077 1.7 13000 7708.8"

However, it kept output like this and aborted/ended (I don't know) after almost 72h. Why? How was that please. Is there any help please? Thank you.


gatk recalibrator error • 395 views
ADD COMMENTlink modified 15 months ago • written 15 months ago by Yingzi Zhang60

Any error messages? Sometimes GATK could give error messages that are hard to spot from the output. The other thing you could try is to switch to a newer version of GATK (possibly java, too), assuming the VCF and BAM files are perfectly fine.

ADD REPLYlink written 11 months ago by Vitis2.3k
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