java -jar ../../diCal2.jar --paramFile mutRec.param --vcfFile contig.0.vcf --vcfFilterPassString PASS --vcfReferenceFile output.ref --lociPerHmmStep 1000 --configFile introgression.config --demoFile introgression.demo --intervalType loguniform --intervalParams '8,0.01,4' --compositeLikelihood lol --metaGridStart --metaNumStartPoints 10 --bounds '0.002,20;0.01,0.99' --numberIterationsEM 0 --seed 4711 --verbose --useEigenCore
