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GATK and SGE

RadRad CAMember

Hello

A quick question about GATK and SGE clusters. I need to run a set of GATK commands on our cluster but I think this was tied with the usage of Queue (may be I am wrong)

I tried to run it through a job manager I use for all the tools I have but I have a memory issue with GATK commands

Invalid maximum heap size: -Xmx4g -jar
Error: Could not create the Java Virtual Machine.
Error: A fatal exception has occurred. Program will exit.

Using this memory size on local node works great but not in cluster mode.

My question is : can I run GATK on GE without using scala or Queue ?

Thanks

Rad

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