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Creating temporary directory for auto-index files

Hello,
I am running GATK on a core server that has the GATK resource bundle available in a read only directory. For many processes I get the warning flag saying that a index is out of date (such as dbsnp) and it will create a new index. However since I don't have write permission to the folder, GATK creates a copy in memory. This isn't a problem running most GATK commands. However, when I try and run VariantRecalibrator, I have been unable to run it without using the --disable_auto_index_creation_and_locking_when_reading_rods flag. I am guessing that trying to hold 5 indices in memory at once is the problem. Is there a way to have the updated indices written to a temporary folder? Does it even matter?

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