If you happen to see a question you know the answer to, please do chime in and help your fellow community members. We encourage our fourm members to be more involved, jump in and help out your fellow researchers with their questions. GATK forum is a community forum and helping each other with using GATK tools and research is the cornerstone of our success as a genomics research community.We appreciate your help!
Test-drive the GATK tools and Best Practices pipelines on Terra
Check out this blog post to learn how you can get started with GATK and try out the pipelines in preconfigured workspaces (with a user-friendly interface!) without having to install anything.
Clock drift error
I'm trying to use genotypeGCFs on 350 small gVCF files (from bacterial genomes) and I'm getting this "clock drift" error:
INFO 13:02:46,006 ProgressMeter - chr1:44001 0.0 3.0 h 15250.3 w 2.0% 6.3 d 6.2 d
INFO 13:06:30,421 ProgressMeter - chr1:44001 0.0 3.0 h 15250.3 w 2.0% 6.4 d 6.3 d
INFO 14:38:28,521 ProgressMeter - chr1:44001 0.0 3.1 h 15250.3 w 2.0% 6.6 d 6.5 d
WARN 16:24:14,924 SimpleTimer - Clock drift of -1,425,286,806,691,525,163 - -1,425,286,778,358,860,637 = 28,332,664,526 nanoseconds detected, vs. max allowable drift of 5,000,000,000. Assuming checkpoint/restart event.
WARN 18:23:08,307 SimpleTimer - Clock drift of -1,425,286,778,358,827,793 - -1,425,286,806,691,525,163 = 28,332,697,370 nanoseconds detected, vs. max allowable drift of 5,000,000,000. Assuming checkpoint/restart event.
INFO 22:55:24,502 ProgressMeter - chr1:44001 0.0 0.0 s 0.0 s 2.0% 0.0 s 0.0 s
INFO 02:46:17,060 ProgressMeter - chr1:44001 0.0 14.1 h 15250.3 w 2.0% 4.3 w 4.2 w
Any ideas what that is?