GATK doesn't work on Java 1.9

[tseemann]

I was getting this error:

##### ERROR MESSAGE: Invalid command line: Malformed walker argument: Could not find walker with name: RealignerTargetCreator

Tracked it down to here:

https://gatkforums.broadinstitute.org/gatk/discussion/10464/invalid-command-line-malformed-walker-argument

it seems it needs older Java 1.8 :-(

PS. picard seems to be ok

[cutpatel]

Yes, gatk unfortunately requires JAVA 8 and no other version is allowed.

[tseemann]

Are you able to add a --java option or honour a MTBSEQ_JAVA environment variable?
As Java 9 is now standard.

[elbakrifz]

I get the same error when I running : java -jar /Users/mac/Downloads/package-archive-gatk-GenomeAnalysisTK-3.7-0-gcfedb67/GenomeAnalysisTK.jar -T RealignerTargetCreator -R /Users/mac/Desktop/LmjFwholegenome_20070731_V5.2.fasta -I /Users/mac/Desktop/NGS/marked-duplicates42.bam -O SRR6369642_realtarget.list with the java 8 update 251, how can I fix it please

[elbakrifz]

with java 1.8