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='A3_HoxB13_ChIPexo-GSM2643267/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='A3_HoxB13_ChIPexo-GSM2643267/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='A3_HoxB13_ChIPexo-GSM2643267/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='A3_HoxB13_ChIPexo-GSM2643267/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 A3_HoxB13_ChIPexo-GSM2643267/aligned.36mers.unique.bam Reading in data... Reading data took 21.8180019855 s Creating peak regions... Creating peak regions took 98.0704629421 s Estimating background... Estimating background took 324.744330883 s Processing A3_HoxB13_ChIPexo-GSM2643267/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='A3_HoxB13_ChIPexo-GSM2643267/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='A3_HoxB13_ChIPexo-GSM2643267/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='A3_HoxB13_ChIPexo-GSM2643267/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='A3_HoxB13_ChIPexo-GSM2643267/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 A3_HoxB13_ChIPexo-GSM2643267/aligned.36mers.unique.bam Reading in data... Reading data took 21.6987659931 s Creating peak regions... Creating peak regions took 93.9767279625 s Estimating background... Estimating background took 358.958276033 s Processing A3_HoxB13_ChIPexo-GSM2643267/aligned.36mers.unique.bam Reading in data... Reading data took 16.754805088 s Creating peak regions... Creating peak regions took 70.9792971611 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='A3_HoxB13_ChIPexo-GSM2643267/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='A3_HoxB13_ChIPexo-GSM2643267/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 A3_HoxB13_ChIPexo-GSM2643267/aligned.36mers.unique.bam Reading in data... Estimating background took 213.179279089 s Processing A3_HoxB13_ChIPexo-GSM2643267/aligned.36mers.unique.bam Reading in data... Reading data took 20.5819969177 s Creating peak regions... Reading data took 17.9336979389 s Creating peak regions... Creating peak regions took 64.9589970112 s Estimating background... Creating peak regions took 92.427836895 s Estimating background... Estimating background took 260.435976028 s Processing A3_HoxB13_ChIPexo-GSM2643267/aligned.36mers.unique.bam Reading in data... Reading data took 18.4817728996 s Creating peak regions... Estimating background took 314.667483091 s Processing A3_HoxB13_ChIPexo-GSM2643267/aligned.36mers.unique.bam Reading in data... Reading data took 15.9425001144 s Creating peak regions... Creating peak regions took 77.0587038994 s Estimating background... Creating peak regions took 63.705190897 s Estimating background... Estimating background took 181.914654016 s Processing A3_HoxB13_ChIPexo-GSM2643267/aligned.36mers.unique.bam Reading in data... Reading data took 17.6732749939 s Creating peak regions... Estimating background took 264.271435976 s Processing A3_HoxB13_ChIPexo-GSM2643267/aligned.36mers.unique.bam Reading in data... Reading data took 14.0402669907 s Creating peak regions... Creating peak regions took 65.0344128609 s Estimating background... Creating peak regions took 62.0137221813 s Estimating background... Estimating background took 128.823876143 s Processing A3_HoxB13_ChIPexo-GSM2643267/aligned.36mers.unique.bam Reading in data... Reading data took 15.8328738213 s Creating peak regions... Creating peak regions took 58.1733767986 s Estimating background... Estimating background took 221.524194956 s Processing A3_HoxB13_ChIPexo-GSM2643267/aligned.36mers.unique.bam Reading in data... Reading data took 17.693529129 s Creating peak regions... Creating peak regions took 70.8235509396 s Estimating background... Estimating background took 209.152379036 s Processing A3_HoxB13_ChIPexo-GSM2643267/aligned.36mers.unique.bam Reading in data... Reading data took 9.97447896004 s Creating peak regions... Creating peak regions took 44.1314110756 s Estimating background... Estimating background took 230.12658 s Processing A3_HoxB13_ChIPexo-GSM2643267/aligned.36mers.unique.bam Reading in data... Reading data took 11.9256460667 s Creating peak regions... Estimating background took 108.491919994 s Processing A3_HoxB13_ChIPexo-GSM2643267/aligned.36mers.unique.bam Reading in data... Reading data took 9.45398688316 s Creating peak regions... Creating peak regions took 54.3665750027 s Estimating background... Creating peak regions took 38.0146491528 s Estimating background... Estimating background took 120.31764102 s Processing A3_HoxB13_ChIPexo-GSM2643267/aligned.36mers.unique.bam Reading in data... Estimating background took 93.463755846 s Processing A3_HoxB13_ChIPexo-GSM2643267/aligned.36mers.unique.bam Reading in data... Reading data took 12.4107019901 s Creating peak regions... Reading data took 12.3830242157 s Creating peak regions... Creating peak regions took 41.5504140854 s Estimating background... Creating peak regions took 51.1722631454 s Estimating background... Estimating background took 162.685853004 s Processing A3_HoxB13_ChIPexo-GSM2643267/aligned.36mers.unique.bam Reading in data... Reading data took 11.805357933 s Creating peak regions... Estimating background took 171.680491924 s Processing A3_HoxB13_ChIPexo-GSM2643267/aligned.36mers.unique.bam Reading in data... Reading data took 8.14342999458 s Creating peak regions... Creating peak regions took 40.599132061 s Estimating background... Creating peak regions took 38.7734749317 s Estimating background... Estimating background took 88.4265182018 s Processing A3_HoxB13_ChIPexo-GSM2643267/aligned.36mers.unique.bam Reading in data... Reading data took 8.14739584923 s Creating peak regions... Creating peak regions took 35.6810870171 s Estimating background... Estimating background took 182.435711861 s Processing A3_HoxB13_ChIPexo-GSM2643267/aligned.36mers.unique.bam Reading in data... Reading data took 7.73215293884 s Creating peak regions... Estimating background took 69.9320161343 s Processing A3_HoxB13_ChIPexo-GSM2643267/aligned.36mers.unique.bam Reading in data... Creating peak regions took 27.5996410847 s Estimating background... Reading data took 10.3342888355 s Creating peak regions... Creating peak regions took 39.715610981 s Estimating background... Estimating background took 78.7740499973 s Processing A3_HoxB13_ChIPexo-GSM2643267/aligned.36mers.unique.bam Reading in data... Reading data took 24.9823310375 s Creating peak regions... Estimating background took 149.197931051 s Processing A3_HoxB13_ChIPexo-GSM2643267/aligned.36mers.unique.bam Reading in data... Reading data took 13.2920150757 s Creating peak regions... Creating peak regions took 107.294380188 s Estimating background... Creating peak regions took 47.9824800491 s Estimating background... Estimating background took 164.215962172 s Processing A3_HoxB13_ChIPexo-GSM2643267/aligned.36mers.unique.bam Reading in data... Reading data took 7.01122188568 s Creating peak regions... Creating peak regions took 27.9703700542 s Estimating background... Estimating background took 70.010654211 s Processing A3_HoxB13_ChIPexo-GSM2643267/aligned.36mers.unique.bam Reading in data... Reading data took 24.1863560677 s Creating peak regions... Creating peak regions took 101.460572958 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='A3_HoxB13_ChIPexo-GSM2643267/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='A3_HoxB13_ChIPexo-GSM2643267/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 A3_HoxB13_ChIPexo-GSM2643267/aligned.36mers.unique.bam Reading in data... Reading data took 20.7218329906 s Creating peak regions... Creating peak regions took 90.4246900082 s Estimating background... Estimating background took 302.264772892 s Processing A3_HoxB13_ChIPexo-GSM2643267/aligned.36mers.unique.bam Reading in data... Reading data took 15.5600278378 s Creating peak regions... Creating peak regions took 66.4732830524 s Estimating background... Estimating background took 173.64440608 s Processing A3_HoxB13_ChIPexo-GSM2643267/aligned.36mers.unique.bam Reading in data... Reading data took 17.3867380619 s Creating peak regions... Creating peak regions took 79.875921011 s Estimating background... Estimating background took 232.858016968 s Processing A3_HoxB13_ChIPexo-GSM2643267/aligned.36mers.unique.bam Reading in data... Reading data took 17.5123989582 s Creating peak regions... Creating peak regions took 68.280987978 s Estimating background... Estimating background took 219.420900106 s Processing A3_HoxB13_ChIPexo-GSM2643267/aligned.36mers.unique.bam Reading in data... Reading data took 10.4023780823 s Creating peak regions... Creating peak regions took 53.1789529324 s Estimating background... Estimating background took 121.131849051 s Processing A3_HoxB13_ChIPexo-GSM2643267/aligned.36mers.unique.bam Reading in data... Reading data took 11.2402029037 s Creating peak regions... Creating peak regions took 48.0427119732 s Estimating background... Estimating background took 171.660194159 s Processing A3_HoxB13_ChIPexo-GSM2643267/aligned.36mers.unique.bam Reading in data... Reading data took 9.30513286591 s Creating peak regions... Creating peak regions took 44.981757164 s Estimating background... Estimating background took 88.3179519176 s Processing A3_HoxB13_ChIPexo-GSM2643267/aligned.36mers.unique.bam Reading in data... Reading data took 7.73841714859 s Creating peak regions... Creating peak regions took 36.029597044 s Estimating background... Estimating background took 69.703250885 s Processing A3_HoxB13_ChIPexo-GSM2643267/aligned.36mers.unique.bam Reading in data... Reading data took 11.2297768593 s Creating peak regions... Creating peak regions took 42.2765130997 s Estimating background... Estimating background took 145.214646101 s Processing A3_HoxB13_ChIPexo-GSM2643267/aligned.36mers.unique.bam Reading in data... Reading data took 14.2198829651 s Creating peak regions... Creating peak regions took 45.0023579597 s Estimating background... Estimating background took 163.306903124 s Processing A3_HoxB13_ChIPexo-GSM2643267/aligned.36mers.unique.bam Reading in data... Reading data took 8.02586698532 s Creating peak regions... Creating peak regions took 31.3770840168 s Estimating background... Estimating background took 72.8814799786 s Processing A3_HoxB13_ChIPexo-GSM2643267/aligned.36mers.unique.bam Reading in data... Reading data took 23.7481138706 s Creating peak regions... Creating peak regions took 103.146921873 s Estimating background...