INPUT PARAMETERS: Namespace(B2=None, N4=1000, N6=1000, S4=1, UMIs=None, adapters1=None, b3=0.05, blacklist='/oak/stanford/groups/akundaje/marinovg/genomes/blacklists/hg38.blacklist.bed', center6=0, chromnames='/oak/stanford/groups/akundaje/marinovg/genomes/hg20/hg38.chrom.sizes', e4='PeakXus', fastq='ZNF549-rep2-SRR5197173.hg20-male.36mers.unique.bam', genome2=None, k4=4, l3=5, l6='PeakXus', l_l3=60, m4=10, m5=20, m6=100, matrixhits=None, maxw7=50, minw7=4, ml4=17, ms4=-8, n3=1, n4=1, o5=1, outdir='ZNF549-rep2-SRR5197173/peakXus/', p3=1.0, p7=1, q2=20, s3=1, skip0=0, t2=1, title5='PeakXus', verbosity=1, w3=5, w4=100, wg7=None)Testing that input files exist...done! Processing ZNF549-rep2-SRR5197173.hg20-male.36mers.unique.bam Reading in data... Reading data took 8.98865699768 s Creating peak regions... Creating peak regions took 70.4960939884 s Estimating background... Estimating background took 103.22633791 s Processing ZNF549-rep2-SRR5197173.hg20-male.36mers.unique.bam Reading in data... Reading data took 4.59630703926 s Creating peak regions... Creating peak regions took 38.1542010307 s Estimating background... Estimating background took 38.0157399178 s Processing ZNF549-rep2-SRR5197173.hg20-male.36mers.unique.bam Reading in data... Reading data took 4.55826711655 s Creating peak regions... Creating peak regions took 37.5467560291 s Estimating background... Estimating background took 39.1128849983 s Processing ZNF549-rep2-SRR5197173.hg20-male.36mers.unique.bam Reading in data... INPUT PARAMETERS: Namespace(B2=None, N4=1000, N6=1000, S4=1, UMIs=None, adapters1=None, b3=0.05, blacklist='/oak/stanford/groups/akundaje/marinovg/genomes/blacklists/hg38.blacklist.bed', center6=0, chromnames='/oak/stanford/groups/akundaje/marinovg/genomes/hg20/hg38-male.chrom.sizes', e4='PeakXus', fastq='ZNF549-rep2-SRR5197173.hg20-male.36mers.unique.bam', genome2=None, k4=4, l3=5, l6='PeakXus', l_l3=60, m4=10, m5=20, m6=100, matrixhits=None, maxw7=50, minw7=4, ml4=17, ms4=-8, n3=1, n4=1, o5=1, outdir='ZNF549-rep2-SRR5197173/peakXus/', p3=1.0, p7=1, q2=20, s3=1, skip0=0, t2=1, title5='PeakXus', verbosity=1, w3=5, w4=100, wg7=None)Testing that input files exist...done! Processing ZNF549-rep2-SRR5197173.hg20-male.36mers.unique.bam Reading in data... Reading data took 9.38492107391 s Creating peak regions... Creating peak regions took 80.035875082 s Estimating background... Estimating background took 111.525719881 s Processing ZNF549-rep2-SRR5197173.hg20-male.36mers.unique.bam Reading in data... Reading data took 6.07447314262 s Creating peak regions... Creating peak regions took 53.8331310749 s Estimating background... Estimating background took 41.4782910347 s Processing ZNF549-rep2-SRR5197173.hg20-male.36mers.unique.bam Reading in data... Reading data took 5.58418703079 s Creating peak regions... Creating peak regions took 47.6363341808 s Estimating background... Estimating background took 43.3133909702 s Processing ZNF549-rep2-SRR5197173.hg20-male.36mers.unique.bam Reading in data... Reading data took 5.3639550209 s Creating peak regions... Creating peak regions took 46.2821991444 s Estimating background... Estimating background took 48.2622818947 s Processing ZNF549-rep2-SRR5197173.hg20-male.36mers.unique.bam Reading in data... Reading data took 5.5840818882 s Creating peak regions... Creating peak regions took 42.8679640293 s Estimating background... Estimating background took 54.2690069675 s Processing ZNF549-rep2-SRR5197173.hg20-male.36mers.unique.bam Reading in data... Reading data took 4.2855219841 s Creating peak regions... Creating peak regions took 38.5484018326 s Estimating background... Estimating background took 30.079458952 s Processing ZNF549-rep2-SRR5197173.hg20-male.36mers.unique.bam Reading in data... Reading data took 4.184278965 s Creating peak regions... Creating peak regions took 41.3372302055 s Estimating background... Estimating background took 33.3246200085 s Processing ZNF549-rep2-SRR5197173.hg20-male.36mers.unique.bam Reading in data... Reading data took 3.79844498634 s Creating peak regions... Creating peak regions took 31.5524661541 s Estimating background... Estimating background took 30.2769198418 s Processing ZNF549-rep2-SRR5197173.hg20-male.36mers.unique.bam Reading in data... Reading data took 4.22618699074 s Creating peak regions... Creating peak regions took 32.0697510242 s Estimating background... Estimating background took 37.6412799358 s Processing ZNF549-rep2-SRR5197173.hg20-male.36mers.unique.bam Reading in data... Reading data took 3.30048584938 s Creating peak regions... Creating peak regions took 28.8468549252 s Estimating background... Estimating background took 23.4077038765 s Processing ZNF549-rep2-SRR5197173.hg20-male.36mers.unique.bam Reading in data... Reading data took 2.98082590103 s Creating peak regions... Creating peak regions took 23.5901069641 s Estimating background... Estimating background took 26.0117669106 s Processing ZNF549-rep2-SRR5197173.hg20-male.36mers.unique.bam Reading in data... Reading data took 9.61744403839 s Creating peak regions... Creating peak regions took 89.4811549187 s Estimating background... Estimating background took 77.7497498989 s Processing ZNF549-rep2-SRR5197173.hg20-male.36mers.unique.bam Reading in data... Reading data took 2.92456293106 s Creating peak regions... Creating peak regions took 25.3184969425 s Estimating background... Estimating background took 24.9626801014 s Processing ZNF549-rep2-SRR5197173.hg20-male.36mers.unique.bam Reading in data... Reading data took 1.85477805138 s Creating peak regions... Creating peak regions took 16.4317080975 s Estimating background... Estimating background took 13.6513969898 s Processing ZNF549-rep2-SRR5197173.hg20-male.36mers.unique.bam Reading in data... Reading data took 2.46119809151 s Creating peak regions... Creating peak regions took 18.0390281677 s Estimating background... Estimating background took 21.4825739861 s Processing ZNF549-rep2-SRR5197173.hg20-male.36mers.unique.bam Reading in data... Reading data took 8.65892100334 s Creating peak regions... Creating peak regions took 85.3190619946 s Estimating background... Estimating background took 64.8743779659 s Processing ZNF549-rep2-SRR5197173.hg20-male.36mers.unique.bam Reading in data... Reading data took 7.40814304352 s Creating peak regions... Creating peak regions took 74.9933829308 s Estimating background... Estimating background took 53.4783251286 s Processing ZNF549-rep2-SRR5197173.hg20-male.36mers.unique.bam Reading in data... Reading data took 7.25775408745 s Creating peak regions... Creating peak regions took 65.6042969227 s Estimating background... Estimating background took 56.6367981434 s Processing ZNF549-rep2-SRR5197173.hg20-male.36mers.unique.bam Reading in data... Reading data took 7.75833320618 s Creating peak regions... Creating peak regions took 76.8610329628 s Estimating background... Estimating background took 65.6809420586 s Processing ZNF549-rep2-SRR5197173.hg20-male.36mers.unique.bam Reading in data... Reading data took 8.07332992554 s Creating peak regions... Creating peak regions took 59.9539120197 s Estimating background... Estimating background took 61.5660810471 s Processing ZNF549-rep2-SRR5197173.hg20-male.36mers.unique.bam Reading in data... Reading data took 6.07289099693 s Creating peak regions... Creating peak regions took 52.4492528439 s Estimating background... Estimating background took 40.9832401276 s Processing ZNF549-rep2-SRR5197173.hg20-male.36mers.unique.bam Reading in data... Reading data took 5.09566307068 s Creating peak regions... Creating peak regions took 47.8251190186 s Estimating background... Estimating background took 41.6245319843 s Processing ZNF549-rep2-SRR5197173.hg20-male.36mers.unique.bam Reading in data... Reading data took 0.494976043701 s Creating peak regions... Creating peak regions took 0.659981966019 s Estimating background... Estimating background took 0.933668136597 s Processing ZNF549-rep2-SRR5197173.hg20-male.36mers.unique.bam Reading in data... Reading data took 7.06962490082 s Creating peak regions... Creating peak regions took 59.3679380417 s Estimating background... Estimating background took 66.5518159866 s Processing ZNF549-rep2-SRR5197173.hg20-male.36mers.unique.bam Reading in data... Reading data took 0.502207040787 s Creating peak regions... Creating peak regions took 17.4870519638 s Estimating background... Estimating background took 0.944218158722 s