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='ZNF584-SRR5197189.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='ZNF584-SRR5197189/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 ZNF584-SRR5197189.hg20-male.36mers.unique.bam Reading in data... Reading data took 5.88818097115 s Creating peak regions... Creating peak regions took 78.8820660114 s Estimating background... Estimating background took 42.8973932266 s Processing ZNF584-SRR5197189.hg20-male.36mers.unique.bam Reading in data... Reading data took 2.84703302383 s Creating peak regions... Creating peak regions took 43.2916309834 s Estimating background... Estimating background took 15.9274041653 s Processing ZNF584-SRR5197189.hg20-male.36mers.unique.bam Reading in data... Reading data took 2.85677814484 s Creating peak regions... Creating peak regions took 40.6148340702 s Estimating background... Estimating background took 14.7586681843 s Processing ZNF584-SRR5197189.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='ZNF584-SRR5197189.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='ZNF584-SRR5197189/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 ZNF584-SRR5197189.hg20-male.36mers.unique.bam Reading in data... Reading data took 6.04459691048 s Creating peak regions... Creating peak regions took 78.9504480362 s Estimating background... Estimating background took 42.3744430542 s Processing ZNF584-SRR5197189.hg20-male.36mers.unique.bam Reading in data... Reading data took 2.94328808784 s Creating peak regions... Creating peak regions took 42.6192440987 s Estimating background... Estimating background took 15.875715971 s Processing ZNF584-SRR5197189.hg20-male.36mers.unique.bam Reading in data... Reading data took 2.8614320755 s Creating peak regions... Creating peak regions took 40.8514771461 s Estimating background... Estimating background took 15.6495301723 s Processing ZNF584-SRR5197189.hg20-male.36mers.unique.bam Reading in data... Reading data took 3.07203602791 s Creating peak regions... Creating peak regions took 40.5531458855 s Estimating background... Estimating background took 16.9046211243 s Processing ZNF584-SRR5197189.hg20-male.36mers.unique.bam Reading in data... Reading data took 2.80077600479 s Creating peak regions... Creating peak regions took 36.8032019138 s Estimating background... Estimating background took 20.1542952061 s Processing ZNF584-SRR5197189.hg20-male.36mers.unique.bam Reading in data... Reading data took 2.09106421471 s Creating peak regions... Creating peak regions took 31.8881750107 s Estimating background... Estimating background took 10.8840110302 s Processing ZNF584-SRR5197189.hg20-male.36mers.unique.bam Reading in data... Reading data took 2.05440402031 s Creating peak regions... Creating peak regions took 31.8637490273 s Estimating background... Estimating background took 11.1864020824 s Processing ZNF584-SRR5197189.hg20-male.36mers.unique.bam Reading in data... Reading data took 1.87016201019 s Creating peak regions... Creating peak regions took 28.4991891384 s Estimating background... Estimating background took 10.0244400501 s Processing ZNF584-SRR5197189.hg20-male.36mers.unique.bam Reading in data... Reading data took 1.89801502228 s Creating peak regions... Creating peak regions took 26.6712150574 s Estimating background... Estimating background took 10.7488629818 s Processing ZNF584-SRR5197189.hg20-male.36mers.unique.bam Reading in data... Reading data took 1.62338805199 s Creating peak regions... Creating peak regions took 25.0325469971 s Estimating background... Estimating background took 8.71916913986 s Processing ZNF584-SRR5197189.hg20-male.36mers.unique.bam Reading in data... Reading data took 1.46591496468 s Creating peak regions... Creating peak regions took 18.8149189949 s Estimating background... Estimating background took 8.01234102249 s Processing ZNF584-SRR5197189.hg20-male.36mers.unique.bam Reading in data... Reading data took 5.08162999153 s Creating peak regions... Creating peak regions took 74.0937469006 s Estimating background... Estimating background took 27.169798851 s Processing ZNF584-SRR5197189.hg20-male.36mers.unique.bam Reading in data... Reading data took 1.66634297371 s Creating peak regions... Creating peak regions took 20.7220160961 s Estimating background... Estimating background took 8.39508891106 s Processing ZNF584-SRR5197189.hg20-male.36mers.unique.bam Reading in data... Reading data took 0.968930006027 s Creating peak regions... Creating peak regions took 15.1273357868 s Estimating background... Estimating background took 5.15176796913 s Processing ZNF584-SRR5197189.hg20-male.36mers.unique.bam Reading in data... Reading data took 1.16632413864 s Creating peak regions... Creating peak regions took 16.0415000916 s Estimating background... Estimating background took 7.5681078434 s Processing ZNF584-SRR5197189.hg20-male.36mers.unique.bam Reading in data... Reading data took 4.05513095856 s Creating peak regions... Creating peak regions took 60.2512159348 s Estimating background... Estimating background took 21.3731400967 s Processing ZNF584-SRR5197189.hg20-male.36mers.unique.bam Reading in data... Reading data took 3.47800803185 s Creating peak regions... Creating peak regions took 57.4991137981 s Estimating background... Estimating background took 18.379778862 s Processing ZNF584-SRR5197189.hg20-male.36mers.unique.bam Reading in data... Reading data took 4.03958010674 s Creating peak regions... Creating peak regions took 55.4265019894 s Estimating background... Estimating background took 21.2765378952 s Processing ZNF584-SRR5197189.hg20-male.36mers.unique.bam Reading in data... Reading data took 4.10274815559 s Creating peak regions... Creating peak regions took 53.2061581612 s Estimating background... Estimating background took 23.5846440792 s Processing ZNF584-SRR5197189.hg20-male.36mers.unique.bam Reading in data... Reading data took 3.84913182259 s Creating peak regions... Creating peak regions took 49.5952029228 s Estimating background... Estimating background took 21.0026509762 s Processing ZNF584-SRR5197189.hg20-male.36mers.unique.bam Reading in data... Reading data took 3.11719584465 s Creating peak regions... Creating peak regions took 44.2280468941 s Estimating background... Estimating background took 14.9693028927 s Processing ZNF584-SRR5197189.hg20-male.36mers.unique.bam Reading in data... Reading data took 2.55519318581 s Creating peak regions... Creating peak regions took 40.9192359447 s Estimating background... Estimating background took 13.949411869 s Processing ZNF584-SRR5197189.hg20-male.36mers.unique.bam Reading in data... Reading data took 0.0962178707123 s Creating peak regions... Creating peak regions took 0.173655033112 s Estimating background... Estimating background took 0.81406712532 s Processing ZNF584-SRR5197189.hg20-male.36mers.unique.bam Reading in data... Reading data took 3.90730309486 s Creating peak regions... Creating peak regions took 50.0199701786 s Estimating background... Estimating background took 22.5952060223 s Processing ZNF584-SRR5197189.hg20-male.36mers.unique.bam Reading in data... Reading data took 0.134412050247 s Creating peak regions... Creating peak regions took 15.5351610184 s Estimating background... Estimating background took 0.691207170486 s