Error when using GenotypeGVCFs with GenomicsDB

Hi,

I'm using GATK 4.0.10.0 and when running GenotypeGVCFs with a GenomicsDB workspace as input, I get the following error:

11:22:14.094 INFO GenotypeGVCFs - ------------------------------------------------------------
11:22:14.094 INFO GenotypeGVCFs - The Genome Analysis Toolkit (GATK) v4.0.10.0
11:22:14.094 INFO GenotypeGVCFs - For support and documentation go to
11:22:14.095 INFO GenotypeGVCFs - Executing as [email protected] on Linux v2.6.32-696.13.2.el6.Bull.128.x86_64 amd64
11:22:14.095 INFO GenotypeGVCFs - Java runtime: Java HotSpot(TM) 64-Bit Server VM v1.8.0_102-b14
11:22:14.095 INFO GenotypeGVCFs - Start Date/Time: October 19, 2018 11:22:13 AM CEST
11:22:14.095 INFO GenotypeGVCFs - ------------------------------------------------------------
11:22:14.095 INFO GenotypeGVCFs - ------------------------------------------------------------
11:22:14.096 INFO GenotypeGVCFs - HTSJDK Version: 2.16.1
11:22:14.096 INFO GenotypeGVCFs - Picard Version: 2.18.13
11:22:14.096 INFO GenotypeGVCFs - HTSJDK Defaults.COMPRESSION_LEVEL : 2
11:22:14.096 INFO GenotypeGVCFs - HTSJDK Defaults.USE_ASYNC_IO_READ_FOR_SAMTOOLS : false
11:22:14.096 INFO GenotypeGVCFs - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_SAMTOOLS : true
11:22:14.096 INFO GenotypeGVCFs - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_TRIBBLE : false
11:22:14.096 INFO GenotypeGVCFs - Deflater: IntelDeflater
11:22:14.096 INFO GenotypeGVCFs - Inflater: IntelInflater
11:22:14.096 INFO GenotypeGVCFs - GCS max retries/reopens: 20
11:22:14.096 INFO GenotypeGVCFs - Requester pays: disabled
11:22:14.096 INFO GenotypeGVCFs - Initializing engine
11:22:14.669 INFO GenotypeGVCFs - Shutting down engine
[October 19, 2018 11:22:14 AM CEST] org.broadinstitute.hellbender.tools.walkers.GenotypeGVCFs done. Elapsed time: 0.02 minutes.
Runtime.totalMemory()=963117056
Exception in thread "main" java.lang.ExceptionInInitializerError
at com.intel.genomicsdb.reader.GenomicsDBFeatureReader.generateHeadersForQueryGivenQueryJSONFile(GenomicsDBFeatureReader.java:206)
at com.intel.genomicsdb.reader.GenomicsDBFeatureReader.generateHeadersForQuery(GenomicsDBFeatureReader.java:201)
at com.intel.genomicsdb.reader.GenomicsDBFeatureReader.(GenomicsDBFeatureReader.java:76)
at org.broadinstitute.hellbender.engine.FeatureDataSource.getGenomicsDBFeatureReader(FeatureDataSource.java:401)
at org.broadinstitute.hellbender.engine.FeatureDataSource.getFeatureReader(FeatureDataSource.java:311)
at org.broadinstitute.hellbender.engine.FeatureDataSource.(FeatureDataSource.java:267)
at org.broadinstitute.hellbender.engine.VariantWalker.initializeDrivingVariants(VariantWalker.java:55)
at org.broadinstitute.hellbender.engine.VariantWalkerBase.initializeFeatures(VariantWalkerBase.java:49)
at org.broadinstitute.hellbender.engine.GATKTool.onStartup(GATKTool.java:638)
at org.broadinstitute.hellbender.engine.VariantWalker.onStartup(VariantWalker.java:43)
at org.broadinstitute.hellbender.cmdline.CommandLineProgram.runTool(CommandLineProgram.java:137)
at org.broadinstitute.hellbender.cmdline.CommandLineProgram.instanceMainPostParseArgs(CommandLineProgram.java:192)
at org.broadinstitute.hellbender.cmdline.CommandLineProgram.instanceMain(CommandLineProgram.java:211)
at org.broadinstitute.hellbender.Main.runCommandLineProgram(Main.java:160)
at org.broadinstitute.hellbender.Main.mainEntry(Main.java:203)
at org.broadinstitute.hellbender.Main.main(Main.java:289)
Caused by: com.intel.genomicsdb.exception.GenomicsDBException: Could not load genomicsdb native library
at com.intel.genomicsdb.reader.GenomicsDBQueryStream.(GenomicsDBQueryStream.java:48)
... 16 more
Caused by: java.lang.UnsatisfiedLinkError: com.intel.genomicsdb.GenomicsDBLibLoader.jniGenomicsDBOneTimeInitialize()I
at com.intel.genomicsdb.GenomicsDBLibLoader.jniGenomicsDBOneTimeInitialize(Native Method)
at com.intel.genomicsdb.GenomicsDBLibLoader.loadLibrary(GenomicsDBLibLoader.java:53)
at com.intel.genomicsdb.reader.GenomicsDBQueryStream.(GenomicsDBQueryStream.java:45)
... 16 more

In previous GATK versions I ran into some problems with file locking and Lustre, but in this case, it shouldn't be a problem since it doesn't even work when disabling file locking.

Thank you,

Cristina.

Answers

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