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After GenotypeGVCFs crash, I restart it. The ProgressMeter does NOT start from the beginning !!!

sheep_gamesheep_game ChinaMember
edited July 2015 in Ask the GATK team

The GenotypeGVCFs crash for some reasons I am not clear !
it throws the message below:
...
(many lines here)
...
INFO 17:25:12,879 ProgressMeter - 1:58001 0.0 12.3 m 1224.3 w 0.0% 7.9 w 7.9 w
INFO 17:28:21,843 ProgressMeter - 1:58001 0.0 13.5 m 1339.8 w 0.0% 8.6 w 8.6 w
INFO 17:30:43,033 ProgressMeter - 1:58001 0.0 17.8 m 1770.2 w 0.0% 11.4 w 11.4 w

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

java.lang.RuntimeException: java.lang.reflect.InvocationTargetException
at htsjdk.tribble.index.IndexFactory.loadIndex(IndexFactory.java:189)
at org.broadinstitute.gatk.utils.refdata.tracks.RMDTrackBuilder.loadFromDisk(RMDTrackBuilder.java:335)
at org.broadinstitute.gatk.utils.refdata.tracks.RMDTrackBuilder.attemptToLockAndLoadIndexFromDisk(RMDTrackBuilder.java:319)
at org.broadinstitute.gatk.utils.refdata.tracks.RMDTrackBuilder.loadIndex(RMDTrackBuilder.java:278)
at org.broadinstitute.gatk.utils.refdata.tracks.RMDTrackBuilder.getFeatureSource(RMDTrackBuilder.java:224)
at org.broadinstitute.gatk.utils.refdata.tracks.RMDTrackBuilder.createInstanceOfTrack(RMDTrackBuilder.java:147)
at org.broadinstitute.gatk.engine.datasources.rmd.ReferenceOrderedQueryDataPool.createNewResource(ReferenceOrderedDataSource.java:226)
at org.broadinstitute.gatk.engine.datasources.rmd.ReferenceOrderedQueryDataPool.createNewResource(ReferenceOrderedDataSource.java:185)
at org.broadinstitute.gatk.engine.datasources.rmd.ResourcePool.iterator(ResourcePool.java:84)
at org.broadinstitute.gatk.engine.datasources.rmd.ReferenceOrderedDataSource.seek(ReferenceOrderedDataSource.java:168)
at org.broadinstitute.gatk.engine.datasources.providers.RodLocusView.(RodLocusView.java:82)
at org.broadinstitute.gatk.engine.traversals.TraverseLociNano.getLocusView(TraverseLociNano.java:129)
at org.broadinstitute.gatk.engine.traversals.TraverseLociNano.traverse(TraverseLociNano.java:80)
at org.broadinstitute.gatk.engine.traversals.TraverseLociNano.traverse(TraverseLociNano.java:48)
at org.broadinstitute.gatk.engine.executive.ShardTraverser.call(ShardTraverser.java:98)
at java.util.concurrent.FutureTask.run(FutureTask.java:266)
at java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1142)
at java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:617)
at java.lang.Thread.run(Thread.java:745)
Caused by: java.lang.reflect.InvocationTargetException
at sun.reflect.GeneratedConstructorAccessor16.newInstance(Unknown Source)
at sun.reflect.DelegatingConstructorAccessorImpl.newInstance(DelegatingConstructorAccessorImpl.java:45)
at java.lang.reflect.Constructor.newInstance(Constructor.java:408)
at htsjdk.tribble.index.IndexFactory.loadIndex(IndexFactory.java:185)
... 18 more
Caused by: java.lang.OutOfMemoryError: GC overhead limit exceeded
at htsjdk.tribble.index.interval.IntervalTreeIndex$ChrIndex.read(IntervalTreeIndex.java:206)
at htsjdk.tribble.index.AbstractIndex.read(AbstractIndex.java:364)
at htsjdk.tribble.index.interval.IntervalTreeIndex.(IntervalTreeIndex.java:52)
... 22 more

ERROR ------------------------------------------------------------------------------------------
ERROR A GATK RUNTIME ERROR has occurred (version 3.4-46-gbc02625):
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: java.lang.reflect.InvocationTargetException
ERROR ------------------------------------------------------------------------------------------

And I restart the program GenotypeGVCFs at the SAME position and SAME Arguments.
The starting ProgressMeter is far from the beginning position,like this:
...
...
INFO 17:38:37,766 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
INFO 17:38:37,766 ProgressMeter - | processed | time | per 1M | | total | remaining
INFO 17:38:37,767 ProgressMeter - Location | sites | elapsed | sites | completed | runtime | runtime
INFO 17:38:37,888 GenotypeGVCFs - Notice that the -ploidy parameter is ignored in GenotypeGVCFs tool as this is automatically determined by the input variant files
INFO 17:39:17,370 ProgressMeter - Starting 0.0 39.0 s 65.5 w 100.0% 39.0 s 0.0 s
INFO 17:40:01,886 ProgressMeter - 1:3000101 0.0 84.0 s 139.1 w 0.8% 2.9 h 2.9 h
...
...

Is it a BUG or NOT ???

By the way, after a half hour, The GenotypeGVCFs crash again at another position because of java.lang.reflect.InvocationTargetException
...
INFO 17:58:52,940 ProgressMeter - 1:3054001 0.0 20.3 m 2009.2 w 0.8% 41.2 h 40.9 h

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

java.lang.RuntimeException: java.lang.reflect.InvocationTargetException
...

Could you give me any suggestion? THX

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