I was wondering if anything can be done to get CNNScoreVariants to run faster. There doesn't seem to be a Spark version of it yet. The documentation mentions the arguments "--inter-op-threads" and "--intra-op-threads" - could these help on a multi-core system?
At present I am running GATK 184.108.40.206 on a laptop with multiple cores and just going through the materials from the Costa Rica workshop about CNNScoreVariants on the laptop. (It is likely I will ultimately run the production job using CNNScoreVariant on a cluster which has multi-core nodes.) I am also running the related 3-gatk-cnn-tutorial notebook on Terra. It seems to have run for at least half an hour on that platform already; so it would be useful to have some sort of typical estimate for the run time for the first "run the default 1D model" example on that platform (e.g. in a computer lab would this have been allowed to run during the lunch break or overnight?)
Please sign in to leave a comment.