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GATK and Berkeley Lab Checkpoint/Restart, RUNTIME ERROR, runtime must be >= 0

tommycarstensentommycarstensen United KingdomMember Posts: 404 ✭✭✭

I am using GATK 2.7 HC with Berkeley Lab Checkpoint/Restart (BLCR). After I checkpoint and restart my job on the cluster I get the stdout and stderr shown below. I think I got it, because the restart happened after midnight. Usually I just get incorrect estimates on total remaining runtime. Would it be possible to make GATK fully compatible with the use of BLCR? Thank you.

stdout:
INFO 01:15:01,258 ProgressMeter - 1:28001706 0.00e+00 -4690921.0 s -9223372036.0 s 80.0% -5862401.0 s -1171480.0 s

stderr:

ERROR ------------------------------------------------------------------------------------------
ERROR stack trace

java.lang.IllegalArgumentException: runtime must be >= 0 but got -4690951902384272
at org.broadinstitute.sting.gatk.GenomeAnalysisEngine.exceedsRuntimeLimit(GenomeAnalysisEngine.java:1200)
at org.broadinstitute.sting.gatk.traversals.TraverseActiveRegions$ActiveRegionIterator.hasNext(TraverseActiveRegions.java:329)
at org.broadinstitute.sting.utils.nanoScheduler.NanoScheduler.executeSingleThreaded(NanoScheduler.java:268)
at org.broadinstitute.sting.utils.nanoScheduler.NanoScheduler.execute(NanoScheduler.java:245)
at org.broadinstitute.sting.gatk.traversals.TraverseActiveRegions.traverse(TraverseActiveRegions.java:273)
at org.broadinstitute.sting.gatk.traversals.TraverseActiveRegions.traverse(TraverseActiveRegions.java:78)
at org.broadinstitute.sting.gatk.executive.LinearMicroScheduler.execute(LinearMicroScheduler.java:99)
at org.broadinstitute.sting.gatk.GenomeAnalysisEngine.execute(GenomeAnalysisEngine.java:313)
at org.broadinstitute.sting.gatk.CommandLineExecutable.execute(CommandLineExecutable.java:113)
at org.broadinstitute.sting.commandline.CommandLineProgram.start(CommandLineProgram.java:245)
at org.broadinstitute.sting.commandline.CommandLineProgram.start(CommandLineProgram.java:152)
at org.broadinstitute.sting.gatk.CommandLineGATK.main(CommandLineGATK.java:91)

ERROR ------------------------------------------------------------------------------------------
ERROR A GATK RUNTIME ERROR has occurred (version 2.7-2-g6bda569):
ERROR
ERROR This might be a bug. Please check the documentation guide to see if this is a known problem.
ERROR If not, please post the error message, with stack trace, to the GATK forum.
ERROR Visit our website and forum for extensive documentation and answers to
ERROR commonly asked questions http://www.broadinstitute.org/gatk
ERROR
ERROR MESSAGE: runtime must be >= 0 but got -4690951902384272
ERROR ------------------------------------------------------------------------------------------

Best Answer

Answers

  • tommycarstensentommycarstensen United KingdomMember Posts: 404 ✭✭✭

    Thanks Geraldine. I might have to be that 3rd party developer myself.

  • tommycarstensentommycarstensen United KingdomMember Posts: 404 ✭✭✭

    Geraldine, just wanted to let you - and everyone else reading this thread - know, that a pull request dealing with the above mentioned issue can be found at https://github.com/broadgsa/gatk-protected/pull/4 Thank you to everyone, who contributed to solving this problem.

  • Geraldine_VdAuweraGeraldine_VdAuwera Cambridge, MAMember, Administrator, Broadie Posts: 11,669 admin

    Thanks @tommycarstensen! I believe this is going through code review at the moment.

    Geraldine Van der Auwera, PhD

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