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='ZNF782-SRR5197241.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='ZNF782-SRR5197241/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 ZNF782-SRR5197241.hg20-male.36mers.unique.bam Reading in data... Reading data took 4.13657188416 s Creating peak regions... Creating peak regions took 75.8511240482 s Estimating background... Estimating background took 27.4604051113 s Processing ZNF782-SRR5197241.hg20-male.36mers.unique.bam Reading in data... Reading data took 2.25288200378 s Creating peak regions... Creating peak regions took 40.3300888538 s Estimating background... Estimating background took 11.3073401451 s Processing ZNF782-SRR5197241.hg20-male.36mers.unique.bam Reading in data... Reading data took 2.11923789978 s Creating peak regions... Creating peak regions took 39.7556979656 s Estimating background... Estimating background took 11.6110069752 s Processing ZNF782-SRR5197241.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='ZNF782-SRR5197241.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='ZNF782-SRR5197241/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 ZNF782-SRR5197241.hg20-male.36mers.unique.bam Reading in data... Reading data took 4.16533398628 s Creating peak regions... Creating peak regions took 73.0023508072 s Estimating background... Estimating background took 25.4449608326 s Processing ZNF782-SRR5197241.hg20-male.36mers.unique.bam Reading in data... Reading data took 1.97443199158 s Creating peak regions... Creating peak regions took 38.0708100796 s Estimating background... Estimating background took 10.8239579201 s Processing ZNF782-SRR5197241.hg20-male.36mers.unique.bam Reading in data... Reading data took 1.94829893112 s Creating peak regions... Creating peak regions took 38.0927181244 s Estimating background... Estimating background took 10.8695049286 s Processing ZNF782-SRR5197241.hg20-male.36mers.unique.bam Reading in data... Reading data took 2.2681491375 s Creating peak regions... Creating peak regions took 40.1094419956 s Estimating background... Estimating background took 11.3537359238 s Processing ZNF782-SRR5197241.hg20-male.36mers.unique.bam Reading in data... Reading data took 1.75486421585 s Creating peak regions... Creating peak regions took 34.5216488838 s Estimating background... Estimating background took 11.5924890041 s Processing ZNF782-SRR5197241.hg20-male.36mers.unique.bam Reading in data... Reading data took 1.38532805443 s Creating peak regions... Creating peak regions took 31.5120379925 s Estimating background... Estimating background took 7.4966750145 s Processing ZNF782-SRR5197241.hg20-male.36mers.unique.bam Reading in data... Reading data took 1.35053992271 s Creating peak regions... Creating peak regions took 28.3386540413 s Estimating background... Estimating background took 8.50001001358 s Processing ZNF782-SRR5197241.hg20-male.36mers.unique.bam Reading in data... Reading data took 1.27688503265 s Creating peak regions... Creating peak regions took 25.3469469547 s Estimating background... Estimating background took 7.74473285675 s Processing ZNF782-SRR5197241.hg20-male.36mers.unique.bam Reading in data... Reading data took 1.69768810272 s Creating peak regions... Creating peak regions took 25.3139469624 s Estimating background... Estimating background took 9.97617816925 s Processing ZNF782-SRR5197241.hg20-male.36mers.unique.bam Reading in data... Reading data took 1.17867207527 s Creating peak regions... Creating peak regions took 23.2697172165 s Estimating background... Estimating background took 5.60135602951 s Processing ZNF782-SRR5197241.hg20-male.36mers.unique.bam Reading in data... Reading data took 1.05806589127 s Creating peak regions... Creating peak regions took 16.7716741562 s Estimating background... Estimating background took 6.60474300385 s Processing ZNF782-SRR5197241.hg20-male.36mers.unique.bam Reading in data... Reading data took 3.39543914795 s Creating peak regions... Creating peak regions took 69.1388049126 s Estimating background... Estimating background took 18.460652113 s Processing ZNF782-SRR5197241.hg20-male.36mers.unique.bam Reading in data... Reading data took 1.30966615677 s Creating peak regions... Creating peak regions took 19.1200561523 s Estimating background... Estimating background took 7.10633897781 s Processing ZNF782-SRR5197241.hg20-male.36mers.unique.bam Reading in data... Reading data took 0.591341018677 s Creating peak regions... Creating peak regions took 13.0859730244 s Estimating background... Estimating background took 3.83583116531 s Processing ZNF782-SRR5197241.hg20-male.36mers.unique.bam Reading in data... Reading data took 1.07730793953 s Creating peak regions... Creating peak regions took 14.6305809021 s Estimating background... Estimating background took 6.3012368679 s Processing ZNF782-SRR5197241.hg20-male.36mers.unique.bam Reading in data... Reading data took 2.78499507904 s Creating peak regions... Creating peak regions took 56.0564310551 s Estimating background... Estimating background took 14.1998791695 s Processing ZNF782-SRR5197241.hg20-male.36mers.unique.bam Reading in data... Reading data took 2.27288103104 s Creating peak regions... Creating peak regions took 56.431317091 s Estimating background... Estimating background took 11.8506400585 s Processing ZNF782-SRR5197241.hg20-male.36mers.unique.bam Reading in data... Reading data took 2.58917403221 s Creating peak regions... Creating peak regions took 51.5990998745 s Estimating background... Estimating background took 13.9738340378 s Processing ZNF782-SRR5197241.hg20-male.36mers.unique.bam Reading in data... Reading data took 2.76344609261 s Creating peak regions... Creating peak regions took 48.6751029491 s Estimating background... Estimating background took 14.8997900486 s Processing ZNF782-SRR5197241.hg20-male.36mers.unique.bam Reading in data... Reading data took 2.50322794914 s Creating peak regions... Creating peak regions took 45.4139211178 s Estimating background... Estimating background took 13.8384690285 s Processing ZNF782-SRR5197241.hg20-male.36mers.unique.bam Reading in data... Reading data took 2.07509899139 s Creating peak regions... Creating peak regions took 43.6127550602 s Estimating background... Estimating background took 10.3363239765 s Processing ZNF782-SRR5197241.hg20-male.36mers.unique.bam Reading in data... Reading data took 1.81268405914 s Creating peak regions... Creating peak regions took 40.9647951126 s Estimating background... Estimating background took 10.2193789482 s Processing ZNF782-SRR5197241.hg20-male.36mers.unique.bam Reading in data... Reading data took 0.0788910388947 s Creating peak regions... Creating peak regions took 0.140257120132 s Estimating background... Estimating background took 0.583760023117 s Processing ZNF782-SRR5197241.hg20-male.36mers.unique.bam Reading in data... Reading data took 2.62077999115 s Creating peak regions... Creating peak regions took 46.9432718754 s Estimating background... Estimating background took 14.4831490517 s Processing ZNF782-SRR5197241.hg20-male.36mers.unique.bam Reading in data... Reading data took 0.109642028809 s Creating peak regions... Creating peak regions took 14.7023379803 s Estimating background... Estimating background took 0.535645961761 s