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Error while running GenomicsDBImport

What does this error mean:

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

How do i rectify this error?

Issue · Github
by bhanuGandham

Issue Number
6122
State
open
Last Updated
Assignee
Array

Answers

  • bhanuGandhambhanuGandham Cambridge MAMember, Administrator, Broadie, Moderator admin

    HI @saimukund

    Please post the version of gatk you are using and the exact command.

  • saimukundsaimukund Member

    This is the docker container i used: quay.io/biocontainers/gatk4:4.1.3.0--0. So i am guessing its GATK 4.1.3.0.

    This is the exact command i ran:
    gatk GenomicsDBImport -R /gscmnt/gc2560/core/model_data/2887491634/build21f22873ebe0486c8e6f69c15435aa96/all_sequences.fa -L /gscmnt/gc2560/core/model_data/2887491634/build21f22873ebe0486c8e6f69c15435aa96/GRCh38_autosomal.interval_list --genomicsdb-workspace-path pon_db -V /gscmnt/gc2708/info/medseq/ppg/saimukund/CWLs/Mutect/1_for_pon.vcf.gz -V /gscmnt/gc2708/info/medseq/ppg/saimukund/CWLs/Mutect/10_for_pon.vcf.gz -V /gscmnt/gc2708/info/medseq/ppg/saimukund/CWLs/Mutect/11_for_pon.vcf.gz -V /gscmnt/gc2708/info/medseq/ppg/saimukund/CWLs/Mutect/12_for_pon.vcf.gz -V /gscmnt/gc2708/info/medseq/ppg/saimukund/CWLs/Mutect/13_for_pon.vcf.gz -V /gscmnt/gc2708/info/medseq/ppg/saimukund/CWLs/Mutect/14_for_pon.vcf.gz -V /gscmnt/gc2708/info/medseq/ppg/saimukund/CWLs/Mutect/15_for_pon.vcf.gz -V /gscmnt/gc2708/info/medseq/ppg/saimukund/CWLs/Mutect/16_for_pon.vcf.gz -V /gscmnt/gc2708/info/medseq/ppg/saimukund/CWLs/Mutect/17_for_pon.vcf.gz -V /gscmnt/gc2708/info/medseq/ppg/saimukund/CWLs/Mutect/18_for_pon.vcf.gz -V /gscmnt/gc2708/info/medseq/ppg/saimukund/CWLs/Mutect/19_for_pon.vcf.gz -V /gscmnt/gc2708/info/medseq/ppg/saimukund/CWLs/Mutect/2_for_pon.vcf.gz -V /gscmnt/gc2708/info/medseq/ppg/saimukund/CWLs/Mutect/20_for_pon.vcf.gz -V /gscmnt/gc2708/info/medseq/ppg/saimukund/CWLs/Mutect/21_for_pon.vcf.gz -V /gscmnt/gc2708/info/medseq/ppg/saimukund/CWLs/Mutect/22_for_pon.vcf.gz -V /gscmnt/gc2708/info/medseq/ppg/saimukund/CWLs/Mutect/23_for_pon.vcf.gz -V /gscmnt/gc2708/info/medseq/ppg/saimukund/CWLs/Mutect/24_for_pon.vcf.gz -V /gscmnt/gc2708/info/medseq/ppg/saimukund/CWLs/Mutect/26_for_pon.vcf.gz -V /gscmnt/gc2708/info/medseq/ppg/saimukund/CWLs/Mutect/27_for_pon.vcf.gz -V /gscmnt/gc2708/info/medseq/ppg/saimukund/CWLs/Mutect/28_for_pon.vcf.gz -V /gscmnt/gc2708/info/medseq/ppg/saimukund/CWLs/Mutect/29_for_pon.vcf.gz -V /gscmnt/gc2708/info/medseq/ppg/saimukund/CWLs/Mutect/3_for_pon.vcf.gz -V /gscmnt/gc2708/info/medseq/ppg/saimukund/CWLs/Mutect/30_for_pon.vcf.gz -V /gscmnt/gc2708/info/medseq/ppg/saimukund/CWLs/Mutect/31_for_pon.vcf.gz -V /gscmnt/gc2708/info/medseq/ppg/saimukund/CWLs/Mutect/32_for_pon.vcf.gz -V /gscmnt/gc2708/info/medseq/ppg/saimukund/CWLs/Mutect/33_for_pon.vcf.gz -V /gscmnt/gc2708/info/medseq/ppg/saimukund/CWLs/Mutect/34_for_pon.vcf.gz -V /gscmnt/gc2708/info/medseq/ppg/saimukund/CWLs/Mutect/35_for_pon.vcf.gz -V /gscmnt/gc2708/info/medseq/ppg/saimukund/CWLs/Mutect/36_for_pon.vcf.gz -V /gscmnt/gc2708/info/medseq/ppg/saimukund/CWLs/Mutect/37_for_pon.vcf.gz -V /gscmnt/gc2708/info/medseq/ppg/saimukund/CWLs/Mutect/4_for_pon.vcf.gz -V /gscmnt/gc2708/info/medseq/ppg/saimukund/CWLs/Mutect/5_for_pon.vcf.gz -V /gscmnt/gc2708/info/medseq/ppg/saimukund/CWLs/Mutect/6_for_pon.vcf.gz -V /gscmnt/gc2708/info/medseq/ppg/saimukund/CWLs/Mutect/7_for_pon.vcf.gz -V /gscmnt/gc2708/info/medseq/ppg/saimukund/CWLs/Mutect/8_for_pon.vcf.gz -V /gscmnt/gc2708/info/medseq/ppg/saimukund/CWLs/Mutect/9_for_pon.vcf.gz

  • bhanuGandhambhanuGandham Cambridge MAMember, Administrator, Broadie, Moderator admin

    Hi @saimukund

    This looks like a big and I have created a issue ticket for it here: https://github.com/broadinstitute/gatk/issues/6122

    You can track this github ticket for progress on this issue.

  • bhanuGandhambhanuGandham Cambridge MAMember, Administrator, Broadie, Moderator admin

    Hi @saimukund

    Here is a workaround for the error in the meantime.

    On Ubuntu:
    sudo apt-get update && sudo apt-get install libcurl4
    On Centos:
    sudo yum install libcurl

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