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='ZNF496-SRR5197159.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='ZNF496-SRR5197159/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 ZNF496-SRR5197159.hg20-male.36mers.unique.bam Reading in data... Reading data took 8.56750297546 s Creating peak regions... Creating peak regions took 75.8460857868 s Estimating background... Estimating background took 35.4679000378 s Processing ZNF496-SRR5197159.hg20-male.36mers.unique.bam Reading in data... Reading data took 4.16184401512 s Creating peak regions... Creating peak regions took 39.9088540077 s Estimating background... Estimating background took 14.4390389919 s Processing ZNF496-SRR5197159.hg20-male.36mers.unique.bam Reading in data... Reading data took 4.37918901443 s Creating peak regions... Creating peak regions took 40.1284818649 s Estimating background... Estimating background took 13.0392119884 s Processing ZNF496-SRR5197159.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='ZNF496-SRR5197159.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='ZNF496-SRR5197159/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 ZNF496-SRR5197159.hg20-male.36mers.unique.bam Reading in data... Reading data took 8.28240609169 s Creating peak regions... Creating peak regions took 75.537405014 s Estimating background... Estimating background took 36.7127678394 s Processing ZNF496-SRR5197159.hg20-male.36mers.unique.bam Reading in data... Reading data took 3.49588489532 s Creating peak regions... Creating peak regions took 39.6630680561 s Estimating background... Estimating background took 14.8623640537 s Processing ZNF496-SRR5197159.hg20-male.36mers.unique.bam Reading in data... Reading data took 4.22187805176 s Creating peak regions... Creating peak regions took 40.9708838463 s Estimating background... Estimating background took 14.527312994 s Processing ZNF496-SRR5197159.hg20-male.36mers.unique.bam Reading in data... Reading data took 4.45774698257 s Creating peak regions... Creating peak regions took 39.2373039722 s Estimating background... Estimating background took 15.363795042 s Processing ZNF496-SRR5197159.hg20-male.36mers.unique.bam Reading in data... Reading data took 3.90823698044 s Creating peak regions... Creating peak regions took 34.1942842007 s Estimating background... Estimating background took 16.8226249218 s Processing ZNF496-SRR5197159.hg20-male.36mers.unique.bam Reading in data... Reading data took 2.86183404922 s Creating peak regions... Creating peak regions took 29.6674931049 s Estimating background... Estimating background took 9.65779018402 s Processing ZNF496-SRR5197159.hg20-male.36mers.unique.bam Reading in data... Reading data took 2.73147797585 s Creating peak regions... Creating peak regions took 28.477339983 s Estimating background... Estimating background took 10.6324050426 s Processing ZNF496-SRR5197159.hg20-male.36mers.unique.bam Reading in data... Reading data took 2.57975196838 s Creating peak regions... Creating peak regions took 29.0132510662 s Estimating background... Estimating background took 9.97004699707 s Processing ZNF496-SRR5197159.hg20-male.36mers.unique.bam Reading in data... Reading data took 3.18112182617 s Creating peak regions... Creating peak regions took 27.379057169 s Estimating background... Estimating background took 12.3626761436 s Processing ZNF496-SRR5197159.hg20-male.36mers.unique.bam Reading in data... Reading data took 2.30152392387 s Creating peak regions... Creating peak regions took 23.0376839638 s Estimating background... Estimating background took 7.75446605682 s Processing ZNF496-SRR5197159.hg20-male.36mers.unique.bam Reading in data... Reading data took 1.88840579987 s Creating peak regions... Creating peak regions took 18.3891990185 s Estimating background... Estimating background took 7.71778702736 s Processing ZNF496-SRR5197159.hg20-male.36mers.unique.bam Reading in data... Reading data took 7.20278906822 s Creating peak regions... Creating peak regions took 73.9300808907 s Estimating background... Estimating background took 23.5939700603 s Processing ZNF496-SRR5197159.hg20-male.36mers.unique.bam Reading in data... Reading data took 2.32581305504 s Creating peak regions... Creating peak regions took 21.3903169632 s Estimating background... Estimating background took 8.50477695465 s Processing ZNF496-SRR5197159.hg20-male.36mers.unique.bam Reading in data... Reading data took 1.14537191391 s Creating peak regions... Creating peak regions took 13.7016370296 s Estimating background... Estimating background took 4.62153816223 s Processing ZNF496-SRR5197159.hg20-male.36mers.unique.bam Reading in data... Reading data took 1.63804984093 s Creating peak regions... Creating peak regions took 16.1584100723 s Estimating background... Estimating background took 7.6262550354 s Processing ZNF496-SRR5197159.hg20-male.36mers.unique.bam Reading in data... Reading data took 5.74281811714 s Creating peak regions... Creating peak regions took 58.6142339706 s Estimating background... Estimating background took 19.6112780571 s Processing ZNF496-SRR5197159.hg20-male.36mers.unique.bam Reading in data... Reading data took 4.88702893257 s Creating peak regions... Creating peak regions took 57.2079401016 s Estimating background... Estimating background took 16.302740097 s Processing ZNF496-SRR5197159.hg20-male.36mers.unique.bam Reading in data... Reading data took 5.58340215683 s Creating peak regions... Creating peak regions took 57.0642359257 s Estimating background... Estimating background took 18.4497768879 s Processing ZNF496-SRR5197159.hg20-male.36mers.unique.bam Reading in data... Reading data took 5.804489851 s Creating peak regions... Creating peak regions took 56.8531091213 s Estimating background... Estimating background took 21.9323120117 s Processing ZNF496-SRR5197159.hg20-male.36mers.unique.bam Reading in data... Reading data took 5.02955508232 s Creating peak regions... Creating peak regions took 48.4419209957 s Estimating background... Estimating background took 18.5081810951 s Processing ZNF496-SRR5197159.hg20-male.36mers.unique.bam Reading in data... Reading data took 4.43818116188 s Creating peak regions... Creating peak regions took 45.9149410725 s Estimating background... Estimating background took 13.6192550659 s Processing ZNF496-SRR5197159.hg20-male.36mers.unique.bam Reading in data... Reading data took 3.64215803146 s Creating peak regions... Creating peak regions took 37.3223259449 s Estimating background... Estimating background took 10.9410400391 s Processing ZNF496-SRR5197159.hg20-male.36mers.unique.bam Reading in data... Reading data took 0.0849049091339 s Creating peak regions... Creating peak regions took 0.164209127426 s Estimating background... Estimating background took 0.573258876801 s Processing ZNF496-SRR5197159.hg20-male.36mers.unique.bam Reading in data... Reading data took 4.58387899399 s Creating peak regions... Creating peak regions took 41.5270779133 s Estimating background... Estimating background took 16.8545978069 s Processing ZNF496-SRR5197159.hg20-male.36mers.unique.bam Reading in data... Reading data took 0.120162010193 s Creating peak regions... Creating peak regions took 12.7419278622 s Estimating background... Estimating background took 0.559297084808 s