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='ZNF529-SRR5197165.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='ZNF529-SRR5197165/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 ZNF529-SRR5197165.hg20-male.36mers.unique.bam Reading in data... Reading data took 12.1606729031 s Creating peak regions... Creating peak regions took 87.3508999348 s Estimating background... Estimating background took 123.449918985 s Processing ZNF529-SRR5197165.hg20-male.36mers.unique.bam Reading in data... Reading data took 6.14813804626 s Creating peak regions... Creating peak regions took 46.9728829861 s Estimating background... Estimating background took 45.1034121513 s Processing ZNF529-SRR5197165.hg20-male.36mers.unique.bam Reading in data... Reading data took 5.2963309288 s Creating peak regions... Creating peak regions took 38.8540558815 s Estimating background... Estimating background took 39.2671101093 s Processing ZNF529-SRR5197165.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='ZNF529-SRR5197165.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='ZNF529-SRR5197165/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 ZNF529-SRR5197165.hg20-male.36mers.unique.bam Reading in data... Reading data took 11.9090008736 s Creating peak regions... Creating peak regions took 88.6964399815 s Estimating background... Estimating background took 129.569399834 s Processing ZNF529-SRR5197165.hg20-male.36mers.unique.bam Reading in data... Reading data took 6.39678382874 s Creating peak regions... Creating peak regions took 46.9242939949 s Estimating background... Estimating background took 50.598649025 s Processing ZNF529-SRR5197165.hg20-male.36mers.unique.bam Reading in data... Reading data took 6.06893396378 s Creating peak regions... Creating peak regions took 46.3190169334 s Estimating background... Estimating background took 47.1566159725 s Processing ZNF529-SRR5197165.hg20-male.36mers.unique.bam Reading in data... Reading data took 6.36836600304 s Creating peak regions... Creating peak regions took 46.9951648712 s Estimating background... Estimating background took 55.3893687725 s Processing ZNF529-SRR5197165.hg20-male.36mers.unique.bam Reading in data... Reading data took 6.72428107262 s Creating peak regions... Creating peak regions took 41.6204669476 s Estimating background... Estimating background took 81.6212201118 s Processing ZNF529-SRR5197165.hg20-male.36mers.unique.bam Reading in data... Reading data took 4.65084910393 s Creating peak regions... Creating peak regions took 35.9775569439 s Estimating background... Estimating background took 33.6427021027 s Processing ZNF529-SRR5197165.hg20-male.36mers.unique.bam Reading in data... Reading data took 4.09647607803 s Creating peak regions... Creating peak regions took 32.204171896 s Estimating background... Estimating background took 33.0884189606 s Processing ZNF529-SRR5197165.hg20-male.36mers.unique.bam Reading in data... Reading data took 3.52823495865 s Creating peak regions... Creating peak regions took 27.7910749912 s Estimating background... Estimating background took 25.9210908413 s Processing ZNF529-SRR5197165.hg20-male.36mers.unique.bam Reading in data... Reading data took 3.90257310867 s Creating peak regions... Creating peak regions took 28.3439221382 s Estimating background... Estimating background took 34.0142571926 s Processing ZNF529-SRR5197165.hg20-male.36mers.unique.bam Reading in data... Reading data took 3.68925595284 s Creating peak regions... Creating peak regions took 27.8842608929 s Estimating background... Estimating background took 28.1549959183 s Processing ZNF529-SRR5197165.hg20-male.36mers.unique.bam Reading in data... Reading data took 2.51587200165 s Creating peak regions... Creating peak regions took 19.7837510109 s Estimating background... Estimating background took 18.1074850559 s Processing ZNF529-SRR5197165.hg20-male.36mers.unique.bam Reading in data... Reading data took 10.7422418594 s Creating peak regions... Creating peak regions took 83.1475770473 s Estimating background... Estimating background took 89.1674969196 s Processing ZNF529-SRR5197165.hg20-male.36mers.unique.bam Reading in data... Reading data took 2.77535390854 s Creating peak regions... Creating peak regions took 23.1974937916 s Estimating background... Estimating background took 21.7949640751 s Processing ZNF529-SRR5197165.hg20-male.36mers.unique.bam Reading in data... Reading data took 1.79594898224 s Creating peak regions... Creating peak regions took 12.9587740898 s Estimating background... Estimating background took 12.5034170151 s Processing ZNF529-SRR5197165.hg20-male.36mers.unique.bam Reading in data... Reading data took 1.65803813934 s Creating peak regions... Creating peak regions took 14.4061510563 s Estimating background... Estimating background took 14.846198082 s Processing ZNF529-SRR5197165.hg20-male.36mers.unique.bam Reading in data... Reading data took 7.2149848938 s Creating peak regions... Creating peak regions took 55.2192201614 s Estimating background... Estimating background took 60.134458065 s Processing ZNF529-SRR5197165.hg20-male.36mers.unique.bam Reading in data... Reading data took 6.35460281372 s Creating peak regions... Creating peak regions took 51.2021260262 s Estimating background... Estimating background took 49.9173378944 s Processing ZNF529-SRR5197165.hg20-male.36mers.unique.bam Reading in data... Reading data took 6.85724306107 s Creating peak regions... Creating peak regions took 52.2171909809 s Estimating background... Estimating background took 56.7169029713 s Processing ZNF529-SRR5197165.hg20-male.36mers.unique.bam Reading in data... Reading data took 7.17826318741 s Creating peak regions... Creating peak regions took 51.3504519463 s Estimating background... Estimating background took 65.9825158119 s Processing ZNF529-SRR5197165.hg20-male.36mers.unique.bam Reading in data... Reading data took 6.11938095093 s Creating peak regions... Creating peak regions took 46.8101799488 s Estimating background... Estimating background took 52.795719862 s Processing ZNF529-SRR5197165.hg20-male.36mers.unique.bam Reading in data... Reading data took 5.1015560627 s Creating peak regions... Creating peak regions took 42.2819831371 s Estimating background... Estimating background took 40.4356460571 s Processing ZNF529-SRR5197165.hg20-male.36mers.unique.bam Reading in data... Reading data took 4.3833770752 s Creating peak regions... Creating peak regions took 38.097358942 s Estimating background... Estimating background took 35.5146179199 s Processing ZNF529-SRR5197165.hg20-male.36mers.unique.bam Reading in data... Reading data took 0.160180807114 s Creating peak regions... Creating peak regions took 0.285228967667 s Estimating background... Estimating background took 0.755801200867 s Processing ZNF529-SRR5197165.hg20-male.36mers.unique.bam Reading in data... Reading data took 6.51946902275 s Creating peak regions... Creating peak regions took 45.6618189812 s Estimating background... Estimating background took 66.6469368935 s Processing ZNF529-SRR5197165.hg20-male.36mers.unique.bam Reading in data... Reading data took 0.457129001617 s Creating peak regions... Creating peak regions took 15.0039229393 s Estimating background... Estimating background took 0.928807973862 s