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GenomicsDBImport java.lang.ExceptionInInitializerError #6122

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bhanugandham opened this issue Aug 26, 2019 · 5 comments
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GenomicsDBImport java.lang.ExceptionInInitializerError #6122

bhanugandham opened this issue Aug 26, 2019 · 5 comments
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@nalinigans
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@bhanugandham
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GATK version: GATK 4.1.3.0
docker container used: quay.io/biocontainers/gatk4:4.1.3.0--0

Please find below the error report from a GATK user:

20:06:25.036 INFO GenomicsDBImport - GCS max retries/reopens: 20
20:06:25.036 INFO GenomicsDBImport - Requester pays: disabled
20:06:25.037 INFO GenomicsDBImport - Initializing engine
20:07:32.463 INFO FeatureManager - Using codec IntervalListCodec to read file file:///gscmnt/gc2560/core/model_data/2887491634/build21f22873ebe0486c8e6f69c15435aa96/GRCh38_autosomal.interval_list
20:07:32.555 INFO IntervalArgumentCollection - Processing 2875001522 bp from intervals
20:07:32.792 INFO GenomicsDBImport - Done initializing engine
20:07:33.106 INFO GenomicsDBImport - Shutting down engine
[August 22, 2019 8:07:33 PM GMT] org.broadinstitute.hellbender.tools.genomicsdb.GenomicsDBImport done. Elapsed time: 1.17 minutes.
Runtime.totalMemory()=253493248
Exception in thread "main" java.lang.ExceptionInInitializerError
at org.genomicsdb.GenomicsDBUtils.createTileDBWorkspace(GenomicsDBUtils.java:37)
at org.broadinstitute.hellbender.tools.genomicsdb.GenomicsDBImport.overwriteCreateOrCheckWorkspace(GenomicsDBImport.java:883)
at org.broadinstitute.hellbender.tools.genomicsdb.GenomicsDBImport.onTraversalStart(GenomicsDBImport.java:605)
at org.broadinstitute.hellbender.engine.GATKTool.doWork(GATKTool.java:1046)
at org.broadinstitute.hellbender.cmdline.CommandLineProgram.runTool(CommandLineProgram.java:139)
at org.broadinstitute.hellbender.cmdline.CommandLineProgram.instanceMainPostParseArgs(CommandLineProgram.java:191)
at org.broadinstitute.hellbender.cmdline.CommandLineProgram.instanceMain(CommandLineProgram.java:210)
at org.broadinstitute.hellbender.Main.runCommandLineProgram(Main.java:162)
at org.broadinstitute.hellbender.Main.mainEntry(Main.java:205)
at org.broadinstitute.hellbender.Main.main(Main.java:291)
Caused by: org.genomicsdb.exception.GenomicsDBException: Could not load genomicsdb native library
at org.genomicsdb.GenomicsDBUtilsJni.(GenomicsDBUtilsJni.java:33)
... 10 more
Caused by: java.lang.UnsatisfiedLinkError: /tmp/libtiledbgenomicsdb8918780584607909502.so: libcurl.so.4: cannot open shared object file: No such file or directory
at java.lang.ClassLoader$NativeLibrary.load(Native Method)
at java.lang.ClassLoader.loadLibrary0(ClassLoader.java:1941)
at java.lang.ClassLoader.loadLibrary(ClassLoader.java:1824)
at java.lang.Runtime.load0(Runtime.java:809)
at java.lang.System.load(System.java:1086)
at org.genomicsdb.GenomicsDBLibLoader.loadLibraryFromJar(GenomicsDBLibLoader.java:147)
at org.genomicsdb.GenomicsDBLibLoader.loadLibrary(GenomicsDBLibLoader.java:47)
at org.genomicsdb.GenomicsDBUtilsJni.(GenomicsDBUtilsJni.java:30)
... 10 more

This Issue was generated from your [forums]
[forums]: https://gatkforums.broadinstitute.org/gatk/discussion/24378/error-while-running-genomicsdbimport/p1
@bhanugandham
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Hi @nalinigans

I have created a issue ticket as discussed during the office hrs. Please let me know if there is any other information you may need.

@nalinigans
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nalinigans commented Aug 27, 2019 •
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I am working on a fix. Meanwhile, here are the commands to work around the issue -
On Ubuntu: sudo apt-get update && sudo apt-get install libcurl4
On Centos: sudo yum install libcurl

nalinigans added a commit that referenced this issue Sep 15, 2019
@nalinigans
Move to 1.1.1 version of genomicsdb to fix Forum Issue 59636 and Issue …
dffe9e0 
…#6122
@nalinigans nalinigans mentioned this issue Sep 26, 2019
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droazen pushed a commit that referenced this issue Sep 27, 2019
@nalinigans @droazen
Move to GenomicsDB 1.1.2 (#6188)
712bfc4 
Changes relevant to GATK:

* Allow changes for allele specific and other annotations to vid file via GenomicsDBImporter without hardcoding them in genomicsdb. See GenomicsDB Fix 39. Thanks @mlathara.

* Fix for BUGreportGATK-07-19-19 reported by @bshifaw where a large ploidy + number of genotypes was leading to math overflow. The overflow is now caught and GenomicsDB stops enumerating genotypes for this case. Thanks @kgururaj.

* Fix for missing libcurl in the native GenomicsDB library - Issue #6122

* Fix to avoid crashing when vcfbufferstream from htslib happens to be invalid. This check was put in response to the Forum Issue 59667. Note that the test vcfs sample2, sample3 and sample4 had to be changed to be htslib compliant for importing and to run org.broadinstitute.hellbender.tools.walkers.mutect.CreateSomaticPanelOfNormalsIntegrationTest successfully.

* Allow for native GenomicsDBExceptions to be propagated as java IOExceptions to allow gatk to gracefully handle the exception by printing out relevant information. See GenomicsDB Fix 68.

* Fix for issues using vid protobuf interface to pass vid information and there is more than one config. Thanks @mlathara.
@lbergelson
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@droazen This is fixed now?

@droazen
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droazen commented Nov 27, 2019

I believe this was fixed in GenomicsDB version 1.1.2

@droazen
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droazen commented Nov 27, 2019

(according to #6188)

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