GATK error on HPC clusters

Question

[princy149]

I run GATK pipeline but at stage of BaseRecalibrator step , I got this error :

Unrecognized VM option 'PrintGCTimeStamps'
Error: Could not create the Java Virtual Machine.

How could I solve this error. is anyone have idea. highly appreciate for your help.

Thank you

Answer 1

[ATpoint]

Check the GATK documentation for the expected Java version and then make sure that version is available. Or simpler, get conda going and isntall GATK via this so you have dependencies right.

[princy149]

thank you