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='ZKSCAN5-SRR5197049.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='ZKSCAN5-SRR5197049/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 ZKSCAN5-SRR5197049.hg20-male.36mers.unique.bam Reading in data... Reading data took 5.60960388184 s Creating peak regions... Creating peak regions took 68.9754149914 s Estimating background... Estimating background took 50.7788629532 s Processing ZKSCAN5-SRR5197049.hg20-male.36mers.unique.bam Reading in data... Reading data took 3.02895998955 s Creating peak regions... Creating peak regions took 36.9664509296 s Estimating background... Estimating background took 20.3603520393 s Processing ZKSCAN5-SRR5197049.hg20-male.36mers.unique.bam Reading in data... Reading data took 2.80453395844 s Creating peak regions... Creating peak regions took 36.9948129654 s Estimating background... Estimating background took 20.1008279324 s Processing ZKSCAN5-SRR5197049.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='ZKSCAN5-SRR5197049.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='ZKSCAN5-SRR5197049/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 ZKSCAN5-SRR5197049.hg20-male.36mers.unique.bam Reading in data... Reading data took 6.83684301376 s Creating peak regions... Creating peak regions took 78.2488999367 s Estimating background... Estimating background took 56.9948971272 s Processing ZKSCAN5-SRR5197049.hg20-male.36mers.unique.bam Reading in data... Reading data took 3.59259414673 s Creating peak regions... Creating peak regions took 42.1655020714 s Estimating background... Estimating background took 22.4903798103 s Processing ZKSCAN5-SRR5197049.hg20-male.36mers.unique.bam Reading in data... Reading data took 3.43535780907 s Creating peak regions... Creating peak regions took 41.6005849838 s Estimating background... Estimating background took 23.1624360085 s Processing ZKSCAN5-SRR5197049.hg20-male.36mers.unique.bam Reading in data... Reading data took 3.54889011383 s Creating peak regions... Creating peak regions took 41.3110170364 s Estimating background... Estimating background took 25.5027019978 s Processing ZKSCAN5-SRR5197049.hg20-male.36mers.unique.bam Reading in data... Reading data took 3.26676607132 s Creating peak regions... Creating peak regions took 36.0100679398 s Estimating background... Estimating background took 26.0789139271 s Processing ZKSCAN5-SRR5197049.hg20-male.36mers.unique.bam Reading in data... Reading data took 2.46269607544 s Creating peak regions... Creating peak regions took 32.6924140453 s Estimating background... Estimating background took 15.7376818657 s Processing ZKSCAN5-SRR5197049.hg20-male.36mers.unique.bam Reading in data... Reading data took 2.69260311127 s Creating peak regions... Creating peak regions took 31.1003801823 s Estimating background... Estimating background took 22.8180160522 s Processing ZKSCAN5-SRR5197049.hg20-male.36mers.unique.bam Reading in data... Reading data took 2.4135260582 s Creating peak regions... Creating peak regions took 27.9517791271 s Estimating background... Estimating background took 16.1393449306 s Processing ZKSCAN5-SRR5197049.hg20-male.36mers.unique.bam Reading in data... Reading data took 3.02171707153 s Creating peak regions... Creating peak regions took 26.9370100498 s Estimating background... Estimating background took 22.330520153 s Processing ZKSCAN5-SRR5197049.hg20-male.36mers.unique.bam Reading in data... Reading data took 1.74479198456 s Creating peak regions... Creating peak regions took 23.5619900227 s Estimating background... Estimating background took 11.1825959682 s Processing ZKSCAN5-SRR5197049.hg20-male.36mers.unique.bam Reading in data... Reading data took 1.85457611084 s Creating peak regions... Creating peak regions took 17.5859131813 s Estimating background... Estimating background took 12.6035108566 s Processing ZKSCAN5-SRR5197049.hg20-male.36mers.unique.bam Reading in data... Reading data took 5.02844119072 s Creating peak regions... Creating peak regions took 67.411689043 s Estimating background... Estimating background took 39.2405509949 s Processing ZKSCAN5-SRR5197049.hg20-male.36mers.unique.bam Reading in data... Reading data took 1.92587304115 s Creating peak regions... Creating peak regions took 22.2127048969 s Estimating background... Estimating background took 12.9427158833 s Processing ZKSCAN5-SRR5197049.hg20-male.36mers.unique.bam Reading in data... Reading data took 1.13283205032 s Creating peak regions... Creating peak regions took 15.5335130692 s Estimating background... Estimating background took 7.28818917274 s Processing ZKSCAN5-SRR5197049.hg20-male.36mers.unique.bam Reading in data... Reading data took 1.43768286705 s Creating peak regions... Creating peak regions took 15.0260207653 s Estimating background... Estimating background took 12.889647007 s Processing ZKSCAN5-SRR5197049.hg20-male.36mers.unique.bam Reading in data... Reading data took 4.40514492989 s Creating peak regions... Creating peak regions took 60.8847558498 s Estimating background... Estimating background took 30.6154630184 s Processing ZKSCAN5-SRR5197049.hg20-male.36mers.unique.bam Reading in data... Reading data took 3.98282694817 s Creating peak regions... Creating peak regions took 58.3696777821 s Estimating background... Estimating background took 23.2954630852 s Processing ZKSCAN5-SRR5197049.hg20-male.36mers.unique.bam Reading in data... Reading data took 4.29697704315 s Creating peak regions... Creating peak regions took 56.2535018921 s Estimating background... Estimating background took 28.595099926 s Processing ZKSCAN5-SRR5197049.hg20-male.36mers.unique.bam Reading in data... Reading data took 4.71112108231 s Creating peak regions... Creating peak regions took 54.4207279682 s Estimating background... Estimating background took 34.7040660381 s Processing ZKSCAN5-SRR5197049.hg20-male.36mers.unique.bam Reading in data... Reading data took 4.36011505127 s Creating peak regions... Creating peak regions took 50.3202769756 s Estimating background... Estimating background took 29.7877838612 s Processing ZKSCAN5-SRR5197049.hg20-male.36mers.unique.bam Reading in data... Reading data took 3.50514221191 s Creating peak regions... Creating peak regions took 45.7413198948 s Estimating background... Estimating background took 21.9063868523 s Processing ZKSCAN5-SRR5197049.hg20-male.36mers.unique.bam Reading in data... Reading data took 3.2880859375 s Creating peak regions... Creating peak regions took 42.7656888962 s Estimating background... Estimating background took 21.5222420692 s Processing ZKSCAN5-SRR5197049.hg20-male.36mers.unique.bam Reading in data... Reading data took 0.136404037476 s Creating peak regions... Creating peak regions took 0.270903110504 s Estimating background... Estimating background took 0.668514966965 s Processing ZKSCAN5-SRR5197049.hg20-male.36mers.unique.bam Reading in data... Reading data took 4.23556518555 s Creating peak regions... Creating peak regions took 49.6275720596 s Estimating background... Estimating background took 33.2414219379 s Processing ZKSCAN5-SRR5197049.hg20-male.36mers.unique.bam Reading in data... Reading data took 0.342057943344 s Creating peak regions... Creating peak regions took 16.9000020027 s Estimating background... Estimating background took 1.09740400314 s