java -jar ../../diCal2.jar --paramFile mutRec.param  --vcfFile contig.0.vcf --vcfFilterPassString PASS --vcfReferenceFile output.ref --lociPerHmmStep 1000 --configFile three_populations.config --demoFile three_populations.demo --intervalType loguniform --intervalParams '8,0.01,4'  --compositeLikelihood lol --metaStartFile three_populations.start --bounds '0.02,20;0.02,20' --numberIterationsEM 4 --numberIterationsMstep 2 --metaNumIterations 3 --metaKeepBest 2 --metaNumPoints 5 --seed 4711 --verbose
