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='ZNF136-SRR5197061.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='ZNF136-SRR5197061/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 ZNF136-SRR5197061.hg20-male.36mers.unique.bam Reading in data... Reading data took 4.86220407486 s Creating peak regions... Creating peak regions took 75.3385119438 s Estimating background... Estimating background took 27.2827470303 s Processing ZNF136-SRR5197061.hg20-male.36mers.unique.bam Reading in data... Reading data took 2.54008793831 s Creating peak regions... Creating peak regions took 40.3467531204 s Estimating background... Estimating background took 10.9749391079 s Processing ZNF136-SRR5197061.hg20-male.36mers.unique.bam Reading in data... Reading data took 2.51175689697 s Creating peak regions... Creating peak regions took 37.7676489353 s Estimating background... Estimating background took 11.2895648479 s Processing ZNF136-SRR5197061.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='ZNF136-SRR5197061.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='ZNF136-SRR5197061/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 ZNF136-SRR5197061.hg20-male.36mers.unique.bam Reading in data... Reading data took 4.19766306877 s Creating peak regions... Creating peak regions took 60.1015880108 s Estimating background... Estimating background took 22.7280960083 s Processing ZNF136-SRR5197061.hg20-male.36mers.unique.bam Reading in data... Reading data took 2.64653491974 s Creating peak regions... Creating peak regions took 34.4552938938 s Estimating background... Estimating background took 9.76064419746 s Processing ZNF136-SRR5197061.hg20-male.36mers.unique.bam Reading in data... Reading data took 2.12376117706 s Creating peak regions... Creating peak regions took 34.5770671368 s Estimating background... Estimating background took 10.2851479053 s Processing ZNF136-SRR5197061.hg20-male.36mers.unique.bam Reading in data... Reading data took 2.46138095856 s Creating peak regions... Creating peak regions took 36.9138009548 s Estimating background... Estimating background took 10.9740240574 s Processing ZNF136-SRR5197061.hg20-male.36mers.unique.bam Reading in data... Reading data took 2.33085680008 s Creating peak regions... Creating peak regions took 32.2469539642 s Estimating background... Estimating background took 13.0715329647 s Processing ZNF136-SRR5197061.hg20-male.36mers.unique.bam Reading in data... Reading data took 1.7429318428 s Creating peak regions... Creating peak regions took 26.1914148331 s Estimating background... Estimating background took 7.42039895058 s Processing ZNF136-SRR5197061.hg20-male.36mers.unique.bam Reading in data... Reading data took 1.51548290253 s Creating peak regions... Creating peak regions took 27.6049520969 s Estimating background... Estimating background took 7.38505291939 s Processing ZNF136-SRR5197061.hg20-male.36mers.unique.bam Reading in data... Reading data took 1.46620607376 s Creating peak regions... Creating peak regions took 22.9824998379 s Estimating background... Estimating background took 6.86334586143 s Processing ZNF136-SRR5197061.hg20-male.36mers.unique.bam Reading in data... Reading data took 1.70875787735 s Creating peak regions... Creating peak regions took 23.2888000011 s Estimating background... Estimating background took 8.61501598358 s Processing ZNF136-SRR5197061.hg20-male.36mers.unique.bam Reading in data... Reading data took 1.22830891609 s Creating peak regions... Creating peak regions took 21.9352090359 s Estimating background... Estimating background took 6.07231712341 s Processing ZNF136-SRR5197061.hg20-male.36mers.unique.bam Reading in data... Reading data took 1.05889391899 s Creating peak regions... Creating peak regions took 16.4340348244 s Estimating background... Estimating background took 4.9867169857 s Processing ZNF136-SRR5197061.hg20-male.36mers.unique.bam Reading in data... Reading data took 4.56462097168 s Creating peak regions... Creating peak regions took 64.0779540539 s Estimating background... Estimating background took 18.1530191898 s Processing ZNF136-SRR5197061.hg20-male.36mers.unique.bam Reading in data... Reading data took 1.20926403999 s Creating peak regions... Creating peak regions took 17.8636741638 s Estimating background... Estimating background took 6.29057908058 s Processing ZNF136-SRR5197061.hg20-male.36mers.unique.bam Reading in data... Reading data took 0.695425987244 s Creating peak regions... Creating peak regions took 12.3238799572 s Estimating background... Estimating background took 3.57158684731 s Processing ZNF136-SRR5197061.hg20-male.36mers.unique.bam Reading in data... Reading data took 0.960026979446 s Creating peak regions... Creating peak regions took 13.4566268921 s Estimating background... Estimating background took 5.2743139267 s Processing ZNF136-SRR5197061.hg20-male.36mers.unique.bam Reading in data... Reading data took 3.0854241848 s Creating peak regions... Creating peak regions took 54.4993729591 s Estimating background... Estimating background took 14.8868229389 s Processing ZNF136-SRR5197061.hg20-male.36mers.unique.bam Reading in data... Reading data took 2.87491106987 s Creating peak regions... Creating peak regions took 48.7622740269 s Estimating background... Estimating background took 12.2205851078 s Processing ZNF136-SRR5197061.hg20-male.36mers.unique.bam Reading in data... Reading data took 2.95653009415 s Creating peak regions... Creating peak regions took 49.9241688251 s Estimating background... Estimating background took 13.9633159637 s Processing ZNF136-SRR5197061.hg20-male.36mers.unique.bam Reading in data... Reading data took 3.23489618301 s Creating peak regions... Creating peak regions took 45.2259209156 s Estimating background... Estimating background took 15.3943970203 s Processing ZNF136-SRR5197061.hg20-male.36mers.unique.bam Reading in data... Reading data took 2.81714200974 s Creating peak regions... Creating peak regions took 42.1516368389 s Estimating background... Estimating background took 14.1592998505 s Processing ZNF136-SRR5197061.hg20-male.36mers.unique.bam Reading in data... Reading data took 2.58665299416 s Creating peak regions... Creating peak regions took 37.2074179649 s Estimating background... Estimating background took 10.2093300819 s Processing ZNF136-SRR5197061.hg20-male.36mers.unique.bam Reading in data... Reading data took 2.06695199013 s Creating peak regions... Creating peak regions took 35.2137150764 s Estimating background... Estimating background took 9.70861291885 s Processing ZNF136-SRR5197061.hg20-male.36mers.unique.bam Reading in data... Reading data took 0.0838749408722 s Creating peak regions... Creating peak regions took 0.132372140884 s Estimating background... Estimating background took 0.56042098999 s Processing ZNF136-SRR5197061.hg20-male.36mers.unique.bam Reading in data... Reading data took 2.83883810043 s Creating peak regions... Creating peak regions took 42.8702859879 s Estimating background... Estimating background took 12.6129281521 s Processing ZNF136-SRR5197061.hg20-male.36mers.unique.bam Reading in data... Reading data took 0.10049200058 s Creating peak regions... Creating peak regions took 13.4188859463 s Estimating background... Estimating background took 0.559257030487 s