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GATK on Power8

vsimavsima DelftMember


I am trying to run GATK on Power8 and getting the following error:

INFO  08:30:18,423 HelpFormatter - Executing as [email protected] on Linux 3.16.0-44-generic ppc64le; IBM J9 VM pxl6470_27sr3fp10-20150708_01 (SR3 FP10).
INFO  08:30:18,424 HelpFormatter - Date/Time: 2015/10/14 08:30:18
INFO  08:30:18,424 HelpFormatter - ---------------------------------------------------------------------------------
INFO  08:30:18,424 HelpFormatter - ---------------------------------------------------------------------------------
##### ERROR ------------------------------------------------------------------------------------------
##### ERROR stack trace
org.broadinstitute.gatk.utils.exceptions.ReviewedGATKException: Couldn't decrypt AWS keys, something is wrong with the GATK distribution
    at org.broadinstitute.gatk.engine.phonehome.GATKRunReport.checkAWSAreValid(GATKRunReport.java:471)
    at org.broadinstitute.gatk.engine.GenomeAnalysisEngine.execute(GenomeAnalysisEngine.java:252)
    at org.broadinstitute.gatk.engine.CommandLineExecutable.execute(CommandLineExecutable.java:121)
    at org.broadinstitute.gatk.utils.commandline.CommandLineProgram.start(CommandLineProgram.java:248)
    at org.broadinstitute.gatk.utils.commandline.CommandLineProgram.start(CommandLineProgram.java:155)
    at org.broadinstitute.gatk.engine.CommandLineGATK.main(CommandLineGATK.java:106)
##### ERROR ------------------------------------------------------------------------------------------
##### ERROR A GATK RUNTIME ERROR has occurred (version 3.4-46-gbc02625):

The Java available on that machine is:

java version "1.7.0"
Java(TM) SE Runtime Environment (build pxl6470_27sr3fp10-20150708_01(SR3 FP10))
IBM J9 VM (build 2.7, JRE 1.7.0 Linux ppc64le-64 Compressed References 20150630_255653 (JIT enabled, AOT enabled)
J9VM - R27_Java727_SR3_20150630_2236_B255653
JIT  - tr.r13.java_20150623_94888.01
GC   - R27_Java727_SR3_20150630_2236_B255653_CMPRSS
J9CL - 20150630_255653)
JCL - 20150628_01 based on Oracle jdk7u85-b15

At this link (http://gatkforums.broadinstitute.org/discussion/4833/speed-up-haplotypecaller-on-ibm-power8-systems) it is mentioned that GATK was run on Power8 before.

I tried to look for an Oracle Power8 JDK but could not find any except the IBM JDK.

Could you please advise on how to run GATK on Power8?




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