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this is a followup of /discussion/5304/haplotypecaller-treatment-of-scaffolds
I am using Joint Genotyping on a row of ~80 individuals (scaffoldwise).
I am using -nt 16
I have following problems:
A| I'm getting a lot of these warnings (I didn't have so many when I did Haplotype Caller) - Do I need to worry?
ExactAFCalculator - this tool is currently set to genotype at most 6 alternate alleles in a given context, but the context at scaffold_3:4434354 has 7 alternate alleles so only the top alleles will be used; see the --max_alternate_alleles argument
B| The job ends with following
INFO 04:11:46,918 ProgressMeter - scaffold_3:6037801 5037839.0 2.3 h 27.1 m 10.4% 21.8 h 19.5 h
INFO 04:11:54,984 ProgressMeter - done 6037839.0 2.3 h 22.6 m 10.4% 21.8 h 19.5 h
INFO 04:11:54,984 ProgressMeter - Total runtime 8198.11 secs, 136.64 min, 2.28 hours
So: Time elapsed 2.3h and done, but 19.5 h to go. Is there a problem with multithreading?