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Hi, just wanted to ask again if FASTEST_AVAILABLE can be different depending on the server, i.e., can a faster server have a different FASTEST_AVAILABLE than a slower server? The issue persists when using the same number of threads on both the serv…
Is there a document that describes what these different options for --pair-hmm-implementation do? Also, can we know what the default value FASTEST_AVAILABLE is for a given analysis - it doesn't seem to be in the log files. Will the FASTEST_AVAILAB…
Ok we can have a look at the different options for the Pair HMM implementation. The detailed feedback is much appreciated!
I don't know if we can try that as it would be a significant deviation from our pipeline, but could you please provide some info on how we would go about invoking the Java implementation? Also as the Java versions are different in the two servers, …
This is what we see in the log from one server: 20:01:36.550 WARN IntelPairHmm - Flush-to-zero (FTZ) is enabled when running PairHMM 20:01:36.551 INFO IntelPairHmm - Available threads: 2 20:01:36.551 INFO IntelPairHmm - Requested threads: 4 …
The two servers both have x86_64, but there are significant differences in the number of CPUs (2 vs 40), Threads per core (1 vs 2), and cores per socket (1 vs 10). Not sure how I can find the pair hmm acceleration used by GATK. Let me know what ot…
Hi, did anyone here get the 'actual observed frequency' referred to above? I'm surprised it's not part of the default outputs, or can it be now added with some command-line option or another tool? I am using the latest version of GATK. Thank you.