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='ZNF442-SRR5197143.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='ZNF442-SRR5197143/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 ZNF442-SRR5197143.hg20-male.36mers.unique.bam Reading in data... Reading data took 6.875633955 s Creating peak regions... Creating peak regions took 81.9200520515 s Estimating background... Estimating background took 69.8688688278 s Processing ZNF442-SRR5197143.hg20-male.36mers.unique.bam Reading in data... Reading data took 3.65225815773 s Creating peak regions... Creating peak regions took 43.1834568977 s Estimating background... Estimating background took 24.10612607 s Processing ZNF442-SRR5197143.hg20-male.36mers.unique.bam Reading in data... Reading data took 3.27367901802 s Creating peak regions... Creating peak regions took 37.4962799549 s Estimating background... Estimating background took 23.283313036 s Processing ZNF442-SRR5197143.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='ZNF442-SRR5197143.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='ZNF442-SRR5197143/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 ZNF442-SRR5197143.hg20-male.36mers.unique.bam Reading in data... Reading data took 7.16285204887 s Creating peak regions... Creating peak regions took 78.7357940674 s Estimating background... Estimating background took 70.6935708523 s Processing ZNF442-SRR5197143.hg20-male.36mers.unique.bam Reading in data... Reading data took 3.35052013397 s Creating peak regions... Creating peak regions took 42.585575819 s Estimating background... Estimating background took 26.7234721184 s Processing ZNF442-SRR5197143.hg20-male.36mers.unique.bam Reading in data... Reading data took 3.73078417778 s Creating peak regions... Creating peak regions took 43.3435330391 s Estimating background... Estimating background took 25.8385419846 s Processing ZNF442-SRR5197143.hg20-male.36mers.unique.bam Reading in data... Reading data took 3.96171402931 s Creating peak regions... Creating peak regions took 41.8865599632 s Estimating background... Estimating background took 28.5783288479 s Processing ZNF442-SRR5197143.hg20-male.36mers.unique.bam Reading in data... Reading data took 3.42527794838 s Creating peak regions... Creating peak regions took 36.0750830173 s Estimating background... Estimating background took 29.2140939236 s Processing ZNF442-SRR5197143.hg20-male.36mers.unique.bam Reading in data... Reading data took 2.35644984245 s Creating peak regions... Creating peak regions took 32.7502880096 s Estimating background... Estimating background took 18.5612750053 s Processing ZNF442-SRR5197143.hg20-male.36mers.unique.bam Reading in data... Reading data took 2.62835383415 s Creating peak regions... Creating peak regions took 32.2903158665 s Estimating background... Estimating background took 22.5084178448 s Processing ZNF442-SRR5197143.hg20-male.36mers.unique.bam Reading in data... Reading data took 2.52479696274 s Creating peak regions... Creating peak regions took 27.9464321136 s Estimating background... Estimating background took 17.8935391903 s Processing ZNF442-SRR5197143.hg20-male.36mers.unique.bam Reading in data... Reading data took 2.84950613976 s Creating peak regions... Creating peak regions took 27.3805720806 s Estimating background... Estimating background took 24.582928896 s Processing ZNF442-SRR5197143.hg20-male.36mers.unique.bam Reading in data... Reading data took 2.08044505119 s Creating peak regions... Creating peak regions took 25.7033689022 s Estimating background... Estimating background took 14.6644818783 s Processing ZNF442-SRR5197143.hg20-male.36mers.unique.bam Reading in data... Reading data took 2.02725291252 s Creating peak regions... Creating peak regions took 18.4854440689 s Estimating background... Estimating background took 14.6518681049 s Processing ZNF442-SRR5197143.hg20-male.36mers.unique.bam Reading in data... Reading data took 6.35310101509 s Creating peak regions... Creating peak regions took 76.3536059856 s Estimating background... Estimating background took 43.77282691 s Processing ZNF442-SRR5197143.hg20-male.36mers.unique.bam Reading in data... Reading data took 1.98713517189 s Creating peak regions... Creating peak regions took 21.5359220505 s Estimating background... Estimating background took 15.6040079594 s Processing ZNF442-SRR5197143.hg20-male.36mers.unique.bam Reading in data... Reading data took 1.25218391418 s Creating peak regions... Creating peak regions took 14.7108979225 s Estimating background... Estimating background took 8.60983204842 s Processing ZNF442-SRR5197143.hg20-male.36mers.unique.bam Reading in data... Reading data took 1.79338693619 s Creating peak regions... Creating peak regions took 17.3289580345 s Estimating background... Estimating background took 14.8767859936 s Processing ZNF442-SRR5197143.hg20-male.36mers.unique.bam Reading in data... Reading data took 5.05419015884 s Creating peak regions... Creating peak regions took 64.6348898411 s Estimating background... Estimating background took 35.328343153 s Processing ZNF442-SRR5197143.hg20-male.36mers.unique.bam Reading in data... Reading data took 4.53303408623 s Creating peak regions... Creating peak regions took 60.6122970581 s Estimating background... Estimating background took 27.0565400124 s Processing ZNF442-SRR5197143.hg20-male.36mers.unique.bam Reading in data... Reading data took 4.98705601692 s Creating peak regions... Creating peak regions took 57.8473680019 s Estimating background... Estimating background took 33.6121928692 s Processing ZNF442-SRR5197143.hg20-male.36mers.unique.bam Reading in data... Reading data took 5.13335800171 s Creating peak regions... Creating peak regions took 48.0451068878 s Estimating background... Estimating background took 31.5322749615 s Processing ZNF442-SRR5197143.hg20-male.36mers.unique.bam Reading in data... Reading data took 3.88681983948 s Creating peak regions... Creating peak regions took 41.8363339901 s Estimating background... Estimating background took 27.1141190529 s Processing ZNF442-SRR5197143.hg20-male.36mers.unique.bam Reading in data... Reading data took 2.88201713562 s Creating peak regions... Creating peak regions took 35.55448699 s Estimating background... Estimating background took 19.9729950428 s Processing ZNF442-SRR5197143.hg20-male.36mers.unique.bam Reading in data... Reading data took 2.47694706917 s Creating peak regions... Creating peak regions took 34.9977121353 s Estimating background... Estimating background took 19.0703399181 s Processing ZNF442-SRR5197143.hg20-male.36mers.unique.bam Reading in data... Reading data took 0.107519865036 s Creating peak regions... Creating peak regions took 0.193795919418 s Estimating background... Estimating background took 0.745015144348 s Processing ZNF442-SRR5197143.hg20-male.36mers.unique.bam Reading in data... Reading data took 3.66052603722 s Creating peak regions... Creating peak regions took 40.7826690674 s Estimating background... Estimating background took 30.8627209663 s Processing ZNF442-SRR5197143.hg20-male.36mers.unique.bam Reading in data... Reading data took 0.230187892914 s Creating peak regions... Creating peak regions took 14.3820340633 s Estimating background... Estimating background took 0.774006128311 s