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Error running GenomicsDBImport in parallel (java.lang.UnsatisfiedLinkError: no tiledbgenomicsdb)

TracyCTracyC SydneyMember

Hi,

I am using the scatter gather approach to run the Germline short variant discovery workflow. I am using GenomicsDBImport to consolidate GVCFs per scatter interval to allow joint genotyping with GenotypeGVCFs to be run in parallel. I have tested the code for one scatter interval and it works, but when using GNU parallel to run GenomicsDBImport multiple tasks at once for multiple intervals, I get an error that seems to be related to some sort of conflict in the environment.

GATK version: 4.1.0.0 (also tested with 4.1.2.0)
Java runtime: Java HotSpot(TM) 64-Bit Server VM v1.8.0_60-b27

I have tried running each task in a different directory but it doesn't resolve the issue.

The error message is below:

Exception in thread "main" Exception in thread "main" Exception in thread "main" Exception in thread "main" Exception in thread "main" Exception in thread "main" Exception in thread "main" java.lang.ExceptionInInitializerErrorjava.lang.ExceptionInInitializerError
java.lang.ExceptionInInitializerError
at org.broadinstitute.hellbender.tools.genomicsdb.GenomicsDBImport.overwriteOrCreateWorkspace(GenomicsDBImport.java:750)java.lang.ExceptionInInitializerErrorjava.lang.ExceptionInInitializerErrorjava.lang.ExceptionInInitializerError at org.broadinstitute.hellbender.tools.genomicsdb.GenomicsDBImport.overwriteOrCreateWorkspace(GenomicsDBImport.java:750)
java.lang.ExceptionInInitializerError
at org.broadinstitute.hellbender.tools.genomicsdb.GenomicsDBImport.overwriteOrCreateWorkspace(GenomicsDBImport.java:750)java.lang.ExceptionInInitializerError at org.broadinstitute.hellbender.engine.GATKTool.doWork(GATKTool.java:1037)java.lang.ExceptionInInitializerError
java.lang.ExceptionInInitializerError at org.broadinstitute.hellbender.engine.GATKTool.doWork(GATKTool.java:1037)
... 10 moreCaused by: java.lang.UnsatisfiedLinkError: no tiledbgenomicsdb in java.library.pathCaused by: org.genomicsdb.exception.GenomicsDBException: Could not load genomicsdb native library at org.broadinstitute.hellbender.Main.main(Main.java:291) at org.broadinstitute.hellbender.Main.main(Main.java:291) at org.broadinstitute.hellbender.Main.main(Main.java:291)
Caused by: java.lang.UnsatisfiedLinkError: no tiledbgenomicsdb in java.library.pathCaused by: org.genomicsdb.exception.GenomicsDBException: Could not load genomicsdb native library at java.lang.ClassLoader.loadLibrary(ClassLoader.java:1864)Caused by: org.genomicsdb.exception.GenomicsDBException: Could not load genomicsdb native library at org.genomicsdb.GenomicsDBUtilsJni.(GenomicsDBUtilsJni.java:33)
... 10 moreCaused by: java.lang.UnsatisfiedLinkError: no tiledbgenomicsdb in java.library.path
Caused by: java.lang.UnsatisfiedLinkError: no tiledbgenomicsdb in java.library.path at java.lang.Runtime.loadLibrary0(Runtime.java:870)
at org.genomicsdb.GenomicsDBLibLoader.loadLibrary(GenomicsDBLibLoader.java:43)Caused by: java.lang.UnsatisfiedLinkError: no tiledbgenomicsdb in java.library.path at org.genomicsdb.GenomicsDBUtilsJni.(GenomicsDBUtilsJni.java:30) ... 10 more
Caused by: java.lang.UnsatisfiedLinkError: no tiledbgenomicsdb in java.library.path ... 10 more
at java.lang.ClassLoader.loadLibrary(ClassLoader.java:1864) at java.lang.Runtime.loadLibrary0(Runtime.java:870) at org.genomicsdb.GenomicsDBLibLoader.loadLibrary(GenomicsDBLibLoader.java:43)Caused by: java.lang.UnsatisfiedLinkError: no tiledbgenomicsdb in java.library.path ... 10 more
Caused by: java.lang.UnsatisfiedLinkError: no tiledbgenomicsdb in java.library.path
Caused by: java.lang.UnsatisfiedLinkError: no tiledbgenomicsdb in java.library.path at org.genomicsdb.GenomicsDBUtilsJni.(GenomicsDBUtilsJni.java:30)
Caused by: java.lang.UnsatisfiedLinkError: no tiledbgenomicsdb in java.library.path at java.lang.ClassLoader.loadLibrary(ClassLoader.java:1864)

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