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='ZKSCAN3-SRR5197048.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='ZKSCAN3-SRR5197048/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 ZKSCAN3-SRR5197048.hg20-male.36mers.unique.bam Reading in data... Reading data took 5.29928302765 s Creating peak regions... Creating peak regions took 67.724943161 s Estimating background... Estimating background took 37.0452508926 s Processing ZKSCAN3-SRR5197048.hg20-male.36mers.unique.bam Reading in data... Reading data took 2.45097184181 s Creating peak regions... Creating peak regions took 35.9788730145 s Estimating background... Estimating background took 15.1449577808 s Processing ZKSCAN3-SRR5197048.hg20-male.36mers.unique.bam Reading in data... Reading data took 2.74379014969 s Creating peak regions... Creating peak regions took 38.1921751499 s Estimating background... Estimating background took 15.5983598232 s Processing ZKSCAN3-SRR5197048.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='ZKSCAN3-SRR5197048.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='ZKSCAN3-SRR5197048/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 ZKSCAN3-SRR5197048.hg20-male.36mers.unique.bam Reading in data... Reading data took 5.65661907196 s Creating peak regions... Creating peak regions took 72.4038329124 s Estimating background... Estimating background took 39.9661009312 s Processing ZKSCAN3-SRR5197048.hg20-male.36mers.unique.bam Reading in data... Reading data took 2.85975885391 s Creating peak regions... Creating peak regions took 36.8571951389 s Estimating background... Estimating background took 16.1078119278 s Processing ZKSCAN3-SRR5197048.hg20-male.36mers.unique.bam Reading in data... Reading data took 2.9540438652 s Creating peak regions... Creating peak regions took 39.9621500969 s Estimating background... Estimating background took 16.2904698849 s Processing ZKSCAN3-SRR5197048.hg20-male.36mers.unique.bam Reading in data... Reading data took 3.27921104431 s Creating peak regions... Creating peak regions took 36.5050780773 s Estimating background... Estimating background took 16.6510000229 s Processing ZKSCAN3-SRR5197048.hg20-male.36mers.unique.bam Reading in data... Reading data took 2.57766008377 s Creating peak regions... Creating peak regions took 32.4936621189 s Estimating background... Estimating background took 18.6847848892 s Processing ZKSCAN3-SRR5197048.hg20-male.36mers.unique.bam Reading in data... Reading data took 2.16183590889 s Creating peak regions... Creating peak regions took 29.1048989296 s Estimating background... Estimating background took 11.1319200993 s Processing ZKSCAN3-SRR5197048.hg20-male.36mers.unique.bam Reading in data... Reading data took 1.86791992188 s Creating peak regions... Creating peak regions took 26.9691028595 s Estimating background... Estimating background took 12.0196881294 s Processing ZKSCAN3-SRR5197048.hg20-male.36mers.unique.bam Reading in data... Reading data took 2.11735916138 s Creating peak regions... Creating peak regions took 24.2084782124 s Estimating background... Estimating background took 11.3669731617 s Processing ZKSCAN3-SRR5197048.hg20-male.36mers.unique.bam Reading in data... Reading data took 1.99305510521 s Creating peak regions... Creating peak regions took 23.7152431011 s Estimating background... Estimating background took 13.0681769848 s Processing ZKSCAN3-SRR5197048.hg20-male.36mers.unique.bam Reading in data... Reading data took 1.48555612564 s Creating peak regions... Creating peak regions took 20.7678489685 s Estimating background... Estimating background took 8.54913496971 s Processing ZKSCAN3-SRR5197048.hg20-male.36mers.unique.bam Reading in data... Reading data took 1.51146793365 s Creating peak regions... Creating peak regions took 16.0753731728 s Estimating background... Estimating background took 8.5041642189 s Processing ZKSCAN3-SRR5197048.hg20-male.36mers.unique.bam Reading in data... Reading data took 4.73247814178 s Creating peak regions... Creating peak regions took 70.8696730137 s Estimating background... Estimating background took 26.6282849312 s Processing ZKSCAN3-SRR5197048.hg20-male.36mers.unique.bam Reading in data... Reading data took 1.77749013901 s Creating peak regions... Creating peak regions took 19.1692540646 s Estimating background... Estimating background took 9.34511113167 s Processing ZKSCAN3-SRR5197048.hg20-male.36mers.unique.bam Reading in data... Reading data took 0.876378059387 s Creating peak regions... Creating peak regions took 13.7824680805 s Estimating background... Estimating background took 5.27413606644 s Processing ZKSCAN3-SRR5197048.hg20-male.36mers.unique.bam Reading in data... Reading data took 1.16022086143 s Creating peak regions... Creating peak regions took 14.7858819962 s Estimating background... Estimating background took 8.35955500603 s Processing ZKSCAN3-SRR5197048.hg20-male.36mers.unique.bam Reading in data... Reading data took 3.84131598473 s Creating peak regions... Creating peak regions took 59.3343071938 s Estimating background... Estimating background took 23.2297348976 s Processing ZKSCAN3-SRR5197048.hg20-male.36mers.unique.bam Reading in data... Reading data took 3.77004289627 s Creating peak regions... Creating peak regions took 51.9273908138 s Estimating background... Estimating background took 17.2204661369 s Processing ZKSCAN3-SRR5197048.hg20-male.36mers.unique.bam Reading in data... Reading data took 3.96603512764 s Creating peak regions... Creating peak regions took 50.5420589447 s Estimating background... Estimating background took 20.3800878525 s Processing ZKSCAN3-SRR5197048.hg20-male.36mers.unique.bam Reading in data... Reading data took 4.08248496056 s Creating peak regions... Creating peak regions took 48.4345769882 s Estimating background... Estimating background took 22.9679272175 s Processing ZKSCAN3-SRR5197048.hg20-male.36mers.unique.bam Reading in data... Reading data took 3.5684440136 s Creating peak regions... Creating peak regions took 44.1681568623 s Estimating background... Estimating background took 20.1910459995 s Processing ZKSCAN3-SRR5197048.hg20-male.36mers.unique.bam Reading in data... Reading data took 2.94389104843 s Creating peak regions... Creating peak regions took 42.7304458618 s Estimating background... Estimating background took 16.215512991 s Processing ZKSCAN3-SRR5197048.hg20-male.36mers.unique.bam Reading in data... Reading data took 2.60010886192 s Creating peak regions... Creating peak regions took 40.8900430202 s Estimating background... Estimating background took 14.4820420742 s Processing ZKSCAN3-SRR5197048.hg20-male.36mers.unique.bam Reading in data... Reading data took 0.0834100246429 s Creating peak regions... Creating peak regions took 0.140903949738 s Estimating background... Estimating background took 0.530992031097 s Processing ZKSCAN3-SRR5197048.hg20-male.36mers.unique.bam Reading in data... Reading data took 4.18871998787 s Creating peak regions... Creating peak regions took 43.4534220695 s Estimating background... Estimating background took 25.490858078 s Processing ZKSCAN3-SRR5197048.hg20-male.36mers.unique.bam Reading in data... Reading data took 0.175866127014 s Creating peak regions... Creating peak regions took 15.3859419823 s Estimating background... Estimating background took 0.793943881989 s