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='ZNF613-SRR5197195.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='ZNF613-SRR5197195/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 ZNF613-SRR5197195.hg20-male.36mers.unique.bam Reading in data... Reading data took 5.23416399956 s Creating peak regions... Creating peak regions took 77.8984019756 s Estimating background... Estimating background took 38.0175020695 s Processing ZNF613-SRR5197195.hg20-male.36mers.unique.bam Reading in data... Reading data took 2.72365188599 s Creating peak regions... Creating peak regions took 39.8133189678 s Estimating background... Estimating background took 14.4137699604 s Processing ZNF613-SRR5197195.hg20-male.36mers.unique.bam Reading in data... Reading data took 2.95000290871 s Creating peak regions... Creating peak regions took 39.8562481403 s Estimating background... Estimating background took 13.8567500114 s Processing ZNF613-SRR5197195.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='ZNF613-SRR5197195.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='ZNF613-SRR5197195/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 ZNF613-SRR5197195.hg20-male.36mers.unique.bam Reading in data... Reading data took 5.55144691467 s Creating peak regions... Creating peak regions took 75.0179378986 s Estimating background... Estimating background took 37.1593267918 s Processing ZNF613-SRR5197195.hg20-male.36mers.unique.bam Reading in data... Reading data took 2.65458893776 s Creating peak regions... Creating peak regions took 37.7446551323 s Estimating background... Estimating background took 12.1801571846 s Processing ZNF613-SRR5197195.hg20-male.36mers.unique.bam Reading in data... Reading data took 2.34710788727 s Creating peak regions... Creating peak regions took 40.8230490685 s Estimating background... Estimating background took 11.8181529045 s Processing ZNF613-SRR5197195.hg20-male.36mers.unique.bam Reading in data... Reading data took 2.54964208603 s Creating peak regions... Creating peak regions took 41.8986608982 s Estimating background... Estimating background took 13.4012749195 s Processing ZNF613-SRR5197195.hg20-male.36mers.unique.bam Reading in data... Reading data took 2.63459181786 s Creating peak regions... Creating peak regions took 33.8136918545 s Estimating background... Estimating background took 14.5054450035 s Processing ZNF613-SRR5197195.hg20-male.36mers.unique.bam Reading in data... Reading data took 1.67417883873 s Creating peak regions... Creating peak regions took 26.5436739922 s Estimating background... Estimating background took 8.46372413635 s Processing ZNF613-SRR5197195.hg20-male.36mers.unique.bam Reading in data... Reading data took 2.06180286407 s Creating peak regions... Creating peak regions took 33.9105088711 s Estimating background... Estimating background took 10.9753820896 s Processing ZNF613-SRR5197195.hg20-male.36mers.unique.bam Reading in data... Reading data took 1.7140250206 s Creating peak regions... Creating peak regions took 27.7583019733 s Estimating background... Estimating background took 9.13157296181 s Processing ZNF613-SRR5197195.hg20-male.36mers.unique.bam Reading in data... Reading data took 1.93103003502 s Creating peak regions... Creating peak regions took 26.463752985 s Estimating background... Estimating background took 10.9921791553 s Processing ZNF613-SRR5197195.hg20-male.36mers.unique.bam Reading in data... Reading data took 1.53768801689 s Creating peak regions... Creating peak regions took 24.8696300983 s Estimating background... Estimating background took 7.16422700882 s Processing ZNF613-SRR5197195.hg20-male.36mers.unique.bam Reading in data... Reading data took 1.2536380291 s Creating peak regions... Creating peak regions took 17.4849281311 s Estimating background... Estimating background took 7.14463305473 s Processing ZNF613-SRR5197195.hg20-male.36mers.unique.bam Reading in data... Reading data took 4.7393860817 s Creating peak regions... Creating peak regions took 73.4871909618 s Estimating background... Estimating background took 22.6792809963 s Processing ZNF613-SRR5197195.hg20-male.36mers.unique.bam Reading in data... Reading data took 1.44050383568 s Creating peak regions... Creating peak regions took 20.3553740978 s Estimating background... Estimating background took 7.43115901947 s Processing ZNF613-SRR5197195.hg20-male.36mers.unique.bam Reading in data... Reading data took 0.821765899658 s Creating peak regions... Creating peak regions took 13.7116110325 s Estimating background... Estimating background took 4.60014891624 s Processing ZNF613-SRR5197195.hg20-male.36mers.unique.bam Reading in data... Reading data took 1.08759689331 s Creating peak regions... Creating peak regions took 16.5402648449 s Estimating background... Estimating background took 6.82038283348 s Processing ZNF613-SRR5197195.hg20-male.36mers.unique.bam Reading in data... Reading data took 3.82916617393 s Creating peak regions... Creating peak regions took 59.9328918457 s Estimating background... Estimating background took 19.6720480919 s Processing ZNF613-SRR5197195.hg20-male.36mers.unique.bam Reading in data... Reading data took 3.40168881416 s Creating peak regions... Creating peak regions took 55.8513588905 s Estimating background... Estimating background took 13.9331679344 s Processing ZNF613-SRR5197195.hg20-male.36mers.unique.bam Reading in data... Reading data took 4.08376598358 s Creating peak regions... Creating peak regions took 54.1336300373 s Estimating background... Estimating background took 19.0499119759 s Processing ZNF613-SRR5197195.hg20-male.36mers.unique.bam Reading in data... Reading data took 4.19846200943 s Creating peak regions... Creating peak regions took 51.8232929707 s Estimating background... Estimating background took 21.9079630375 s Processing ZNF613-SRR5197195.hg20-male.36mers.unique.bam Reading in data... Reading data took 3.60298514366 s Creating peak regions... Creating peak regions took 48.1581118107 s Estimating background... Estimating background took 17.986301899 s Processing ZNF613-SRR5197195.hg20-male.36mers.unique.bam Reading in data... Reading data took 3.26793909073 s Creating peak regions... Creating peak regions took 41.4092030525 s Estimating background... Estimating background took 12.6906540394 s Processing ZNF613-SRR5197195.hg20-male.36mers.unique.bam Reading in data... Reading data took 2.6080288887 s Creating peak regions... Creating peak regions took 39.703797102 s Estimating background... Estimating background took 11.9832060337 s Processing ZNF613-SRR5197195.hg20-male.36mers.unique.bam Reading in data... Reading data took 0.106527090073 s Creating peak regions... Creating peak regions took 0.233366966248 s Estimating background... Estimating background took 0.558317899704 s Processing ZNF613-SRR5197195.hg20-male.36mers.unique.bam Reading in data... Reading data took 3.79070496559 s Creating peak regions... Creating peak regions took 47.4156320095 s Estimating background... Estimating background took 17.8756639957 s Processing ZNF613-SRR5197195.hg20-male.36mers.unique.bam Reading in data... Reading data took 0.168130874634 s Creating peak regions... Creating peak regions took 16.236415863 s Estimating background... Estimating background took 0.539197921753 s