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='ZNF483-SRR5197153.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='ZNF483-SRR5197153/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 ZNF483-SRR5197153.hg20-male.36mers.unique.bam Reading in data... Reading data took 4.42086911201 s Creating peak regions... Creating peak regions took 76.2303159237 s Estimating background... Estimating background took 31.2902240753 s Processing ZNF483-SRR5197153.hg20-male.36mers.unique.bam Reading in data... Reading data took 2.24571013451 s Creating peak regions... Creating peak regions took 39.4811708927 s Estimating background... Estimating background took 12.7267241478 s Processing ZNF483-SRR5197153.hg20-male.36mers.unique.bam Reading in data... Reading data took 2.34758806229 s Creating peak regions... Creating peak regions took 39.5460090637 s Estimating background... Estimating background took 12.6901350021 s Processing ZNF483-SRR5197153.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='ZNF483-SRR5197153.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='ZNF483-SRR5197153/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 ZNF483-SRR5197153.hg20-male.36mers.unique.bam Reading in data... Reading data took 4.54056286812 s Creating peak regions... Creating peak regions took 75.0298578739 s Estimating background... Estimating background took 33.4319419861 s Processing ZNF483-SRR5197153.hg20-male.36mers.unique.bam Reading in data... Reading data took 2.34707307816 s Creating peak regions... Creating peak regions took 38.9745750427 s Estimating background... Estimating background took 12.8548312187 s Processing ZNF483-SRR5197153.hg20-male.36mers.unique.bam Reading in data... Reading data took 2.18631410599 s Creating peak regions... Creating peak regions took 39.7646710873 s Estimating background... Estimating background took 13.6684451103 s Processing ZNF483-SRR5197153.hg20-male.36mers.unique.bam Reading in data... Reading data took 2.73706698418 s Creating peak regions... Creating peak regions took 42.4622249603 s Estimating background... Estimating background took 13.2279009819 s Processing ZNF483-SRR5197153.hg20-male.36mers.unique.bam Reading in data... Reading data took 1.76613783836 s Creating peak regions... Creating peak regions took 33.5760800838 s Estimating background... Estimating background took 11.8989450932 s Processing ZNF483-SRR5197153.hg20-male.36mers.unique.bam Reading in data... Reading data took 1.57349395752 s Creating peak regions... Creating peak regions took 30.5314078331 s Estimating background... Estimating background took 8.84253501892 s Processing ZNF483-SRR5197153.hg20-male.36mers.unique.bam Reading in data... Reading data took 1.56574678421 s Creating peak regions... Creating peak regions took 29.4365370274 s Estimating background... Estimating background took 10.1940639019 s Processing ZNF483-SRR5197153.hg20-male.36mers.unique.bam Reading in data... Reading data took 1.51325798035 s Creating peak regions... Creating peak regions took 25.9442269802 s Estimating background... Estimating background took 9.478703022 s Processing ZNF483-SRR5197153.hg20-male.36mers.unique.bam Reading in data... Reading data took 1.80677008629 s Creating peak regions... Creating peak regions took 26.4351019859 s Estimating background... Estimating background took 12.5664570332 s Processing ZNF483-SRR5197153.hg20-male.36mers.unique.bam Reading in data... Reading data took 1.31445097923 s Creating peak regions... Creating peak regions took 23.8402600288 s Estimating background... Estimating background took 6.92340517044 s Processing ZNF483-SRR5197153.hg20-male.36mers.unique.bam Reading in data... Reading data took 1.32110905647 s Creating peak regions... Creating peak regions took 19.0572998524 s Estimating background... Estimating background took 8.64951992035 s Processing ZNF483-SRR5197153.hg20-male.36mers.unique.bam Reading in data... Reading data took 3.79889202118 s Creating peak regions... Creating peak regions took 76.4754259586 s Estimating background... Estimating background took 22.0342550278 s Processing ZNF483-SRR5197153.hg20-male.36mers.unique.bam Reading in data... Reading data took 1.27201008797 s Creating peak regions... Creating peak regions took 20.2481980324 s Estimating background... Estimating background took 7.85361504555 s Processing ZNF483-SRR5197153.hg20-male.36mers.unique.bam Reading in data... Reading data took 0.751242160797 s Creating peak regions... Creating peak regions took 15.0307049751 s Estimating background... Estimating background took 4.78482985497 s Processing ZNF483-SRR5197153.hg20-male.36mers.unique.bam Reading in data... Reading data took 1.18437814713 s Creating peak regions... Creating peak regions took 14.8352620602 s Estimating background... Estimating background took 8.00581502914 s Processing ZNF483-SRR5197153.hg20-male.36mers.unique.bam Reading in data... Reading data took 2.94396305084 s Creating peak regions... Creating peak regions took 61.3596470356 s Estimating background... Estimating background took 16.3071238995 s Processing ZNF483-SRR5197153.hg20-male.36mers.unique.bam Reading in data... Reading data took 2.62805914879 s Creating peak regions... Creating peak regions took 53.1317920685 s Estimating background... Estimating background took 11.9069600105 s Processing ZNF483-SRR5197153.hg20-male.36mers.unique.bam Reading in data... Reading data took 2.75460982323 s Creating peak regions... Creating peak regions took 56.3295099735 s Estimating background... Estimating background took 16.7551298141 s Processing ZNF483-SRR5197153.hg20-male.36mers.unique.bam Reading in data... Reading data took 3.13133621216 s Creating peak regions... Creating peak regions took 49.8238768578 s Estimating background... Estimating background took 17.0343840122 s Processing ZNF483-SRR5197153.hg20-male.36mers.unique.bam Reading in data... Reading data took 2.63568902016 s Creating peak regions... Creating peak regions took 51.409692049 s Estimating background... Estimating background took 17.5083999634 s Processing ZNF483-SRR5197153.hg20-male.36mers.unique.bam Reading in data... Reading data took 2.40681195259 s Creating peak regions... Creating peak regions took 41.4063100815 s Estimating background... Estimating background took 11.8611221313 s Processing ZNF483-SRR5197153.hg20-male.36mers.unique.bam Reading in data... Reading data took 1.99398994446 s Creating peak regions... Creating peak regions took 41.8465909958 s Estimating background... Estimating background took 12.0721271038 s Processing ZNF483-SRR5197153.hg20-male.36mers.unique.bam Reading in data... Reading data took 0.0905690193176 s Creating peak regions... Creating peak regions took 0.159843206406 s Estimating background... Estimating background took 0.704978942871 s Processing ZNF483-SRR5197153.hg20-male.36mers.unique.bam Reading in data... Reading data took 2.90738987923 s Creating peak regions... Creating peak regions took 47.9715828896 s Estimating background... Estimating background took 16.6422169209 s Processing ZNF483-SRR5197153.hg20-male.36mers.unique.bam Reading in data... Reading data took 0.103363037109 s Creating peak regions... Creating peak regions took 13.2411360741 s Estimating background... Estimating background took 0.558715105057 s