Notice:
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.

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

Sign In or Register to comment.