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/hg19/wgEncodeHg19ConsensusSignalArtifactRegions.bed', center6=0, chromnames='/oak/stanford/groups/akundaje/marinovg/genomes/hg19/female.hg19.chrom.sizes', e4='PeakXus', fastq='A31_HoxB13_ChIPexo-GSM2643265/aligned.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='A31_HoxB13_ChIPexo-GSM2643265/peakXus/', p3=1.0, p7=1, q2=20, s3=1, skip0=0, t2=1, title5='PeakXus', verbosity=1, w3=5, w4=100, wg7=None)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/hg19/wgEncodeHg19ConsensusSignalArtifactRegions.bed', center6=0, chromnames='/oak/stanford/groups/akundaje/marinovg/genomes/hg19/hg19.chrom.sizes', e4='PeakXus', fastq='A31_HoxB13_ChIPexo-GSM2643265/aligned.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='A31_HoxB13_ChIPexo-GSM2643265/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 A31_HoxB13_ChIPexo-GSM2643265/aligned.36mers.unique.bam Reading in data... Reading data took 21.0272610188 s Creating peak regions... Creating peak regions took 94.8841888905 s Estimating background... Estimating background took 346.152017832 s Processing A31_HoxB13_ChIPexo-GSM2643265/aligned.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/hg19/wgEncodeHg19ConsensusSignalArtifactRegions.bed', center6=0, chromnames='/oak/stanford/groups/akundaje/marinovg/genomes/hg19/hg19-male.chrom.sizes', e4='PeakXus', fastq='A31_HoxB13_ChIPexo-GSM2643265/alignments.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='A31_HoxB13_ChIPexo-GSM2643265/peakXus/', p3=1.0, p7=1, q2=20, s3=1, skip0=0, t2=1, title5='PeakXus', verbosity=1, w3=5, w4=100, wg7=None)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/hg19/wgEncodeHg19ConsensusSignalArtifactRegions.bed', center6=0, chromnames='/oak/stanford/groups/akundaje/marinovg/genomes/hg19/hg19-male.chrom.sizes', e4='PeakXus', fastq='A31_HoxB13_ChIPexo-GSM2643265/aligned.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='A31_HoxB13_ChIPexo-GSM2643265/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 A31_HoxB13_ChIPexo-GSM2643265/aligned.36mers.unique.bam Reading in data... Reading data took 21.3789319992 s Creating peak regions... Creating peak regions took 93.6708409786 s Estimating background... Estimating background took 334.229443073 s Processing A31_HoxB13_ChIPexo-GSM2643265/aligned.36mers.unique.bam Reading in data... Reading data took 21.5706040859 s Creating peak regions... Creating peak regions took 72.6143729687 s Estimating background... 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/hg19/wgEncodeHg19ConsensusSignalArtifactRegions.bed', center6=0, chromnames='/oak/stanford/groups/akundaje/marinovg/genomes/hg19/hg19-male.chrom.sizes', e4='PeakXus', fastq='A31_HoxB13_ChIPexo-GSM2643265/aligned.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='A31_HoxB13_ChIPexo-GSM2643265/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 A31_HoxB13_ChIPexo-GSM2643265/aligned.36mers.unique.bam Reading in data... Reading data took 22.9719078541 s Creating peak regions... Estimating background took 263.315935135 s Processing A31_HoxB13_ChIPexo-GSM2643265/aligned.36mers.unique.bam Reading in data... Reading data took 14.8711531162 s Creating peak regions... Creating peak regions took 62.5468430519 s Estimating background... Creating peak regions took 94.1282470226 s Estimating background... Estimating background took 211.602716923 s Processing A31_HoxB13_ChIPexo-GSM2643265/aligned.36mers.unique.bam Reading in data... Reading data took 23.3567349911 s Creating peak regions... Creating peak regions took 89.2827038765 s Estimating background... Estimating background took 327.630606174 s Processing A31_HoxB13_ChIPexo-GSM2643265/aligned.36mers.unique.bam Reading in data... Reading data took 18.5115530491 s Creating peak regions... Creating peak regions took 78.494934082 s Estimating background... Estimating background took 252.943700075 s Processing A31_HoxB13_ChIPexo-GSM2643265/aligned.36mers.unique.bam Reading in data... Estimating background took 364.237154007 s Processing A31_HoxB13_ChIPexo-GSM2643265/aligned.36mers.unique.bam Reading in data... Reading data took 14.2521579266 s Creating peak regions... Reading data took 10.4091980457 s Creating peak regions... Creating peak regions took 53.0457799435 s Estimating background... Creating peak regions took 64.057518959 s Estimating background... Estimating background took 113.38530612 s Processing A31_HoxB13_ChIPexo-GSM2643265/aligned.36mers.unique.bam Reading in data... Reading data took 12.759237051 s Creating peak regions... Creating peak regions took 50.4192471504 s Estimating background... Estimating background took 200.390644073 s Processing A31_HoxB13_ChIPexo-GSM2643265/aligned.36mers.unique.bam Reading in data... Reading data took 22.6073708534 s Creating peak regions... Creating peak regions took 80.1208770275 s Estimating background... Estimating background took 154.164072037 s Processing A31_HoxB13_ChIPexo-GSM2643265/aligned.36mers.unique.bam Reading in data... Reading data took 10.086482048 s Creating peak regions... Creating peak regions took 46.1726551056 s Estimating background... Estimating background took 115.61689496 s Processing A31_HoxB13_ChIPexo-GSM2643265/aligned.36mers.unique.bam Reading in data... Reading data took 10.3866159916 s Creating peak regions... Creating peak regions took 43.9878330231 s Estimating background... Estimating background took 107.741750002 s Processing A31_HoxB13_ChIPexo-GSM2643265/aligned.36mers.unique.bam Reading in data... Estimating background took 358.983043909 s Processing A31_HoxB13_ChIPexo-GSM2643265/aligned.36mers.unique.bam Reading in data... Reading data took 10.9675121307 s Creating peak regions... Reading data took 11.1357460022 s Creating peak regions... Creating peak regions took 41.8175289631 s Estimating background... Creating peak regions took 54.7207739353 s Estimating background... Estimating background took 128.183665991 s Processing A31_HoxB13_ChIPexo-GSM2643265/aligned.36mers.unique.bam Reading in data... Estimating background took 118.229985952 s Processing A31_HoxB13_ChIPexo-GSM2643265/aligned.36mers.unique.bam Reading in data... Reading data took 11.6057579517 s Creating peak regions... Reading data took 11.8832881451 s Creating peak regions... Creating peak regions took 39.725851059 s Estimating background... Creating peak regions took 50.7626640797 s Estimating background... Estimating background took 165.165749073 s Processing A31_HoxB13_ChIPexo-GSM2643265/aligned.36mers.unique.bam Reading in data... Estimating background took 149.534852982 s Processing A31_HoxB13_ChIPexo-GSM2643265/aligned.36mers.unique.bam Reading in data... Reading data took 6.13809108734 s Creating peak regions... Reading data took 8.76731991768 s Creating peak regions... Creating peak regions took 27.286096096 s Estimating background... Creating peak regions took 41.9431080818 s Estimating background... Estimating background took 50.7645511627 s Processing A31_HoxB13_ChIPexo-GSM2643265/aligned.36mers.unique.bam Reading in data... Reading data took 32.3802769184 s Creating peak regions... Estimating background took 114.075248003 s Processing A31_HoxB13_ChIPexo-GSM2643265/aligned.36mers.unique.bam Reading in data... Reading data took 10.1688988209 s Creating peak regions... Creating peak regions took 42.8659698963 s Estimating background... Creating peak regions took 122.676163912 s Estimating background... Estimating background took 101.153650045 s Processing A31_HoxB13_ChIPexo-GSM2643265/aligned.36mers.unique.bam Reading in data... Reading data took 10.5238261223 s Creating peak regions... Creating peak regions took 46.8942320347 s Estimating background... Estimating background took 126.437470913 s Processing A31_HoxB13_ChIPexo-GSM2643265/aligned.36mers.unique.bam Reading in data... Reading data took 10.8602302074 s Creating peak regions... Creating peak regions took 41.1591529846 s Estimating background... Estimating background took 159.474175215 s Processing A31_HoxB13_ChIPexo-GSM2643265/aligned.36mers.unique.bam Reading in data... Reading data took 5.82258009911 s Creating peak regions... Creating peak regions took 27.2049479485 s Estimating background... Estimating background took 56.8812589645 s Processing A31_HoxB13_ChIPexo-GSM2643265/aligned.36mers.unique.bam Reading in data... Reading data took 33.7336139679 s Creating peak regions... Creating peak regions took 122.651932001 s Estimating background... 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/hg19/wgEncodeHg19ConsensusSignalArtifactRegions.bed', center6=0, chromnames='/oak/stanford/groups/akundaje/marinovg/genomes/hg19/hg19-male.chrom.sizes', e4='PeakXus', fastq='A31_HoxB13_ChIPexo-GSM2643265/aligned.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='A31_HoxB13_ChIPexo-GSM2643265/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 A31_HoxB13_ChIPexo-GSM2643265/aligned.36mers.unique.bam Reading in data... Reading data took 20.9513969421 s Creating peak regions... Creating peak regions took 90.6542010307 s Estimating background... Estimating background took 318.699234009 s Processing A31_HoxB13_ChIPexo-GSM2643265/aligned.36mers.unique.bam Reading in data... Reading data took 18.509529829 s Creating peak regions... Creating peak regions took 73.7548220158 s Estimating background... Estimating background took 247.722162008 s Processing A31_HoxB13_ChIPexo-GSM2643265/aligned.36mers.unique.bam Reading in data... Reading data took 15.9669139385 s Creating peak regions... Creating peak regions took 69.3808369637 s Estimating background... Estimating background took 189.487737894 s Processing A31_HoxB13_ChIPexo-GSM2643265/aligned.36mers.unique.bam Reading in data... Reading data took 22.3489181995 s Creating peak regions... Creating peak regions took 80.9899599552 s Estimating background... Estimating background took 350.010457039 s Processing A31_HoxB13_ChIPexo-GSM2643265/aligned.36mers.unique.bam Reading in data... Reading data took 9.63761997223 s Creating peak regions... Creating peak regions took 48.5391628742 s Estimating background... Estimating background took 110.270303965 s Processing A31_HoxB13_ChIPexo-GSM2643265/aligned.36mers.unique.bam Reading in data... Reading data took 11.6388721466 s Creating peak regions... Creating peak regions took 50.721175909 s Estimating background... Estimating background took 142.401634932 s Processing A31_HoxB13_ChIPexo-GSM2643265/aligned.36mers.unique.bam Reading in data... Reading data took 8.94876098633 s Creating peak regions... Creating peak regions took 42.0473198891 s Estimating background... Estimating background took 101.996478081 s Processing A31_HoxB13_ChIPexo-GSM2643265/aligned.36mers.unique.bam Reading in data... Reading data took 8.13838791847 s Creating peak regions... Creating peak regions took 43.0938110352 s Estimating background... Estimating background took 100.278832912 s Processing A31_HoxB13_ChIPexo-GSM2643265/aligned.36mers.unique.bam Reading in data... Reading data took 10.2764430046 s Creating peak regions... Creating peak regions took 41.699434042 s Estimating background... Estimating background took 126.367481947 s Processing A31_HoxB13_ChIPexo-GSM2643265/aligned.36mers.unique.bam Reading in data... Reading data took 14.1083049774 s Creating peak regions... Creating peak regions took 46.8623030186 s Estimating background... Estimating background took 153.353674889 s Processing A31_HoxB13_ChIPexo-GSM2643265/aligned.36mers.unique.bam Reading in data... Reading data took 5.37625813484 s Creating peak regions... Creating peak regions took 24.869656086 s Estimating background... Estimating background took 48.4806029797 s Processing A31_HoxB13_ChIPexo-GSM2643265/aligned.36mers.unique.bam Reading in data... Reading data took 30.3060619831 s Creating peak regions... Creating peak regions took 138.130903959 s Estimating background...