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='ZNF823-SRR5197258.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='ZNF823-SRR5197258/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 ZNF823-SRR5197258.hg20-male.36mers.unique.bam Reading in data... Reading data took 6.40076780319 s Creating peak regions... Creating peak regions took 75.2985179424 s Estimating background... Estimating background took 22.0850689411 s Processing ZNF823-SRR5197258.hg20-male.36mers.unique.bam Reading in data... Reading data took 2.96941494942 s Creating peak regions... Creating peak regions took 38.7268359661 s Estimating background... Estimating background took 9.71641087532 s Processing ZNF823-SRR5197258.hg20-male.36mers.unique.bam Reading in data... Reading data took 2.99692106247 s Creating peak regions... Creating peak regions took 39.3412480354 s Estimating background... Estimating background took 9.51719999313 s Processing ZNF823-SRR5197258.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='ZNF823-SRR5197258.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='ZNF823-SRR5197258/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 ZNF823-SRR5197258.hg20-male.36mers.unique.bam Reading in data... Reading data took 5.98850297928 s Creating peak regions... Creating peak regions took 75.000483036 s Estimating background... Estimating background took 22.4582779408 s Processing ZNF823-SRR5197258.hg20-male.36mers.unique.bam Reading in data... Reading data took 2.95134806633 s Creating peak regions... Creating peak regions took 39.1406171322 s Estimating background... Estimating background took 9.90339803696 s Processing ZNF823-SRR5197258.hg20-male.36mers.unique.bam Reading in data... Reading data took 3.09610009193 s Creating peak regions... Creating peak regions took 39.4602589607 s Estimating background... Estimating background took 9.56381011009 s Processing ZNF823-SRR5197258.hg20-male.36mers.unique.bam Reading in data... Reading data took 3.18776798248 s Creating peak regions... Creating peak regions took 38.6119699478 s Estimating background... Estimating background took 9.93002700806 s Processing ZNF823-SRR5197258.hg20-male.36mers.unique.bam Reading in data... Reading data took 2.81001091003 s Creating peak regions... Creating peak regions took 33.4747581482 s Estimating background... Estimating background took 11.7763960361 s Processing ZNF823-SRR5197258.hg20-male.36mers.unique.bam Reading in data... Reading data took 2.32900595665 s Creating peak regions... Creating peak regions took 32.148581028 s Estimating background... Estimating background took 6.79018187523 s Processing ZNF823-SRR5197258.hg20-male.36mers.unique.bam Reading in data... Reading data took 1.99173092842 s Creating peak regions... Creating peak regions took 29.004584074 s Estimating background... Estimating background took 6.71203494072 s Processing ZNF823-SRR5197258.hg20-male.36mers.unique.bam Reading in data... Reading data took 1.92194104195 s Creating peak regions... Creating peak regions took 26.9902501106 s Estimating background... Estimating background took 6.07160902023 s Processing ZNF823-SRR5197258.hg20-male.36mers.unique.bam Reading in data... Reading data took 2.14670205116 s Creating peak regions... Creating peak regions took 25.53627491 s Estimating background... Estimating background took 7.099629879 s Processing ZNF823-SRR5197258.hg20-male.36mers.unique.bam Reading in data... Reading data took 1.67951798439 s Creating peak regions... Creating peak regions took 24.1657390594 s Estimating background... Estimating background took 5.42474198341 s Processing ZNF823-SRR5197258.hg20-male.36mers.unique.bam Reading in data... Reading data took 1.36372804642 s Creating peak regions... Creating peak regions took 17.8977310658 s Estimating background... Estimating background took 4.87670111656 s Processing ZNF823-SRR5197258.hg20-male.36mers.unique.bam Reading in data... Reading data took 5.43046379089 s Creating peak regions... Creating peak regions took 74.97579813 s Estimating background... Estimating background took 16.7008240223 s Processing ZNF823-SRR5197258.hg20-male.36mers.unique.bam Reading in data... Reading data took 1.44076490402 s Creating peak regions... Creating peak regions took 19.1321029663 s Estimating background... Estimating background took 4.90620303154 s Processing ZNF823-SRR5197258.hg20-male.36mers.unique.bam Reading in data... Reading data took 1.08444690704 s Creating peak regions... Creating peak regions took 14.1768710613 s Estimating background... Estimating background took 2.17235302925 s Processing ZNF823-SRR5197258.hg20-male.36mers.unique.bam Reading in data... Reading data took 1.27953481674 s Creating peak regions... Creating peak regions took 14.3222630024 s Estimating background... Estimating background took 4.34866714478 s Processing ZNF823-SRR5197258.hg20-male.36mers.unique.bam Reading in data... Reading data took 4.26934313774 s Creating peak regions... Creating peak regions took 61.1972248554 s Estimating background... Estimating background took 13.3846838474 s Processing ZNF823-SRR5197258.hg20-male.36mers.unique.bam Reading in data... Reading data took 3.83115911484 s Creating peak regions... Creating peak regions took 57.4221601486 s Estimating background... Estimating background took 11.6827030182 s Processing ZNF823-SRR5197258.hg20-male.36mers.unique.bam Reading in data... Reading data took 4.15239310265 s Creating peak regions... Creating peak regions took 55.9107899666 s Estimating background... Estimating background took 12.9770100117 s Processing ZNF823-SRR5197258.hg20-male.36mers.unique.bam Reading in data... Reading data took 4.35356688499 s Creating peak regions... Creating peak regions took 53.1252100468 s Estimating background... Estimating background took 14.8656129837 s Processing ZNF823-SRR5197258.hg20-male.36mers.unique.bam Reading in data... Reading data took 3.7217028141 s Creating peak regions... Creating peak regions took 46.9586830139 s Estimating background... Estimating background took 12.2414810658 s Processing ZNF823-SRR5197258.hg20-male.36mers.unique.bam Reading in data... Reading data took 3.08948802948 s Creating peak regions... Creating peak regions took 41.8912761211 s Estimating background... Estimating background took 9.77159786224 s Processing ZNF823-SRR5197258.hg20-male.36mers.unique.bam Reading in data... Reading data took 3.47903513908 s Creating peak regions... Creating peak regions took 39.8020720482 s Estimating background... Estimating background took 9.32592892647 s Processing ZNF823-SRR5197258.hg20-male.36mers.unique.bam Reading in data... Reading data took 0.112134933472 s Creating peak regions... Creating peak regions took 0.175258874893 s Estimating background... Estimating background took 0.647747993469 s Processing ZNF823-SRR5197258.hg20-male.36mers.unique.bam Reading in data... Reading data took 3.99385595322 s Creating peak regions... Creating peak regions took 48.3821699619 s Estimating background... Estimating background took 13.874464035 s Processing ZNF823-SRR5197258.hg20-male.36mers.unique.bam Reading in data... Reading data took 0.165993928909 s Creating peak regions... Creating peak regions took 15.8054890633 s Estimating background... Estimating background took 0.549551963806 s