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='ZNF573-SRR5197187.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='ZNF573-SRR5197187/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 ZNF573-SRR5197187.hg20-male.36mers.unique.bam Reading in data... Reading data took 12.6104881763 s Creating peak regions... Creating peak regions took 84.0333659649 s Estimating background... Estimating background took 99.1346991062 s Processing ZNF573-SRR5197187.hg20-male.36mers.unique.bam Reading in data... Reading data took 6.93841314316 s Creating peak regions... Creating peak regions took 46.0027940273 s Estimating background... Estimating background took 33.7980749607 s Processing ZNF573-SRR5197187.hg20-male.36mers.unique.bam Reading in data... Reading data took 5.37602806091 s Creating peak regions... Creating peak regions took 37.5950241089 s Estimating background... Estimating background took 32.2533278465 s Processing ZNF573-SRR5197187.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='ZNF573-SRR5197187.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='ZNF573-SRR5197187/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 ZNF573-SRR5197187.hg20-male.36mers.unique.bam Reading in data... Reading data took 12.9418029785 s Creating peak regions... Creating peak regions took 82.2087380886 s Estimating background... Estimating background took 97.0051810741 s Processing ZNF573-SRR5197187.hg20-male.36mers.unique.bam Reading in data... Reading data took 6.65212202072 s Creating peak regions... Creating peak regions took 46.7928919792 s Estimating background... Estimating background took 37.7855529785 s Processing ZNF573-SRR5197187.hg20-male.36mers.unique.bam Reading in data... Reading data took 6.61626005173 s Creating peak regions... Creating peak regions took 44.3908889294 s Estimating background... Estimating background took 38.7796308994 s Processing ZNF573-SRR5197187.hg20-male.36mers.unique.bam Reading in data... Reading data took 6.84070396423 s Creating peak regions... Creating peak regions took 44.3608670235 s Estimating background... Estimating background took 41.2609660625 s Processing ZNF573-SRR5197187.hg20-male.36mers.unique.bam Reading in data... Reading data took 5.78636598587 s Creating peak regions... Creating peak regions took 37.4959638119 s Estimating background... Estimating background took 39.0460579395 s Processing ZNF573-SRR5197187.hg20-male.36mers.unique.bam Reading in data... Reading data took 4.42851996422 s Creating peak regions... Creating peak regions took 34.7953188419 s Estimating background... Estimating background took 25.0411779881 s Processing ZNF573-SRR5197187.hg20-male.36mers.unique.bam Reading in data... Reading data took 4.38811802864 s Creating peak regions... Creating peak regions took 31.7274060249 s Estimating background... Estimating background took 28.4070911407 s Processing ZNF573-SRR5197187.hg20-male.36mers.unique.bam Reading in data... Reading data took 4.53233790398 s Creating peak regions... Creating peak regions took 29.4654159546 s Estimating background... Estimating background took 27.4772779942 s Processing ZNF573-SRR5197187.hg20-male.36mers.unique.bam Reading in data... Reading data took 5.25717115402 s Creating peak regions... Creating peak regions took 28.5712189674 s Estimating background... Estimating background took 36.8984889984 s Processing ZNF573-SRR5197187.hg20-male.36mers.unique.bam Reading in data... Reading data took 3.54499793053 s Creating peak regions... Creating peak regions took 26.1786708832 s Estimating background... Estimating background took 18.5481131077 s Processing ZNF573-SRR5197187.hg20-male.36mers.unique.bam Reading in data... Reading data took 3.54566502571 s Creating peak regions... Creating peak regions took 20.0634438992 s Estimating background... Estimating background took 22.8088819981 s Processing ZNF573-SRR5197187.hg20-male.36mers.unique.bam Reading in data... Reading data took 10.7449529171 s Creating peak regions... Creating peak regions took 78.8215899467 s Estimating background... Estimating background took 63.3996050358 s Processing ZNF573-SRR5197187.hg20-male.36mers.unique.bam Reading in data... Reading data took 3.72042298317 s Creating peak regions... Creating peak regions took 23.5130660534 s Estimating background... Estimating background took 22.4423959255 s Processing ZNF573-SRR5197187.hg20-male.36mers.unique.bam Reading in data... Reading data took 2.01152396202 s Creating peak regions... Creating peak regions took 15.0565280914 s Estimating background... Estimating background took 11.0488321781 s Processing ZNF573-SRR5197187.hg20-male.36mers.unique.bam Reading in data... Reading data took 3.01776099205 s Creating peak regions... Creating peak regions took 17.502918005 s Estimating background... Estimating background took 22.340526104 s Processing ZNF573-SRR5197187.hg20-male.36mers.unique.bam Reading in data... Reading data took 8.76762485504 s Creating peak regions... Creating peak regions took 64.0608229637 s Estimating background... Estimating background took 50.054931879 s Processing ZNF573-SRR5197187.hg20-male.36mers.unique.bam Reading in data... Reading data took 7.31689786911 s Creating peak regions... Creating peak regions took 60.6269881725 s Estimating background... Estimating background took 36.2281961441 s Processing ZNF573-SRR5197187.hg20-male.36mers.unique.bam Reading in data... Reading data took 8.15600705147 s Creating peak regions... Creating peak regions took 58.3703417778 s Estimating background... Estimating background took 46.2624881268 s Processing ZNF573-SRR5197187.hg20-male.36mers.unique.bam Reading in data... Reading data took 8.40842103958 s Creating peak regions... Creating peak regions took 53.8010621071 s Estimating background... Estimating background took 50.4709019661 s Processing ZNF573-SRR5197187.hg20-male.36mers.unique.bam Reading in data... Reading data took 7.33512711525 s Creating peak regions... Creating peak regions took 50.4669699669 s Estimating background... Estimating background took 43.4775340557 s Processing ZNF573-SRR5197187.hg20-male.36mers.unique.bam Reading in data... Reading data took 5.56586909294 s Creating peak regions... Creating peak regions took 39.7983841896 s Estimating background... Estimating background took 28.8981890678 s Processing ZNF573-SRR5197187.hg20-male.36mers.unique.bam Reading in data... Reading data took 4.70569300652 s Creating peak regions... Creating peak regions took 37.8106179237 s Estimating background... Estimating background took 28.8827869892 s Processing ZNF573-SRR5197187.hg20-male.36mers.unique.bam Reading in data... Reading data took 0.171601057053 s Creating peak regions... Creating peak regions took 0.234936952591 s Estimating background... Estimating background took 0.814815044403 s Processing ZNF573-SRR5197187.hg20-male.36mers.unique.bam Reading in data... Reading data took 5.94099593163 s Creating peak regions... Creating peak regions took 42.2902619839 s Estimating background... Estimating background took 38.6119248867 s Processing ZNF573-SRR5197187.hg20-male.36mers.unique.bam Reading in data... Reading data took 0.229221105576 s Creating peak regions... Creating peak regions took 14.3687150478 s Estimating background... Estimating background took 0.810271978378 s