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='22RV1_HoxB13_ChIPexo-Rep1-GSM2643243/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='22RV1_HoxB13_ChIPexo-Rep1-GSM2643243/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='22RV1_HoxB13_ChIPexo-Rep1-GSM2643243/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='22RV1_HoxB13_ChIPexo-Rep1-GSM2643243/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 22RV1_HoxB13_ChIPexo-Rep1-GSM2643243/aligned.36mers.unique.bam Reading in data... Reading data took 18.4351301193 s Creating peak regions... Creating peak regions took 85.4857099056 s Estimating background... Estimating background took 276.972227097 s Processing 22RV1_HoxB13_ChIPexo-Rep1-GSM2643243/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='22RV1_HoxB13_ChIPexo-Rep1-GSM2643243/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='22RV1_HoxB13_ChIPexo-Rep1-GSM2643243/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='22RV1_HoxB13_ChIPexo-Rep1-GSM2643243/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='22RV1_HoxB13_ChIPexo-Rep1-GSM2643243/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 22RV1_HoxB13_ChIPexo-Rep1-GSM2643243/aligned.36mers.unique.bam Reading in data... Reading data took 19.4704167843 s Creating peak regions... Creating peak regions took 94.4143819809 s Estimating background... Estimating background took 318.447447062 s Processing 22RV1_HoxB13_ChIPexo-Rep1-GSM2643243/aligned.36mers.unique.bam Reading in data... Reading data took 9.44240617752 s Creating peak regions... Creating peak regions took 54.9706809521 s Estimating background... Estimating background took 91.5148849487 s Processing 22RV1_HoxB13_ChIPexo-Rep1-GSM2643243/aligned.36mers.unique.bam Reading in data... Reading data took 9.18782401085 s Creating peak regions... Creating peak regions took 50.6004319191 s Estimating background... Estimating background took 98.8190999031 s Processing 22RV1_HoxB13_ChIPexo-Rep1-GSM2643243/aligned.36mers.unique.bam Reading in data... Reading data took 15.3991510868 s Creating peak regions... Creating peak regions took 63.2402119637 s Estimating background... Estimating background took 192.410830975 s Processing 22RV1_HoxB13_ChIPexo-Rep1-GSM2643243/aligned.36mers.unique.bam Reading in data... Reading data took 11.5951800346 s Creating peak regions... Creating peak regions took 53.0296459198 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='22RV1_HoxB13_ChIPexo-Rep1-GSM2643243/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='22RV1_HoxB13_ChIPexo-Rep1-GSM2643243/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 22RV1_HoxB13_ChIPexo-Rep1-GSM2643243/aligned.36mers.unique.bam Reading in data... Reading data took 19.356153965 s Creating peak regions... Estimating background took 111.700549126 s Processing 22RV1_HoxB13_ChIPexo-Rep1-GSM2643243/aligned.36mers.unique.bam Reading in data... Reading data took 7.93329501152 s Creating peak regions... Creating peak regions took 45.043803215 s Estimating background... Creating peak regions took 87.4832668304 s Estimating background... Estimating background took 77.2185080051 s Processing 22RV1_HoxB13_ChIPexo-Rep1-GSM2643243/aligned.36mers.unique.bam Reading in data... Reading data took 5.45595407486 s Creating peak regions... Creating peak regions took 38.6509070396 s Estimating background... Estimating background took 53.6555328369 s Processing 22RV1_HoxB13_ChIPexo-Rep1-GSM2643243/aligned.36mers.unique.bam Reading in data... Reading data took 5.04924297333 s Creating peak regions... Creating peak regions took 31.1087398529 s Estimating background... Estimating background took 37.0033779144 s Processing 22RV1_HoxB13_ChIPexo-Rep1-GSM2643243/aligned.36mers.unique.bam Reading in data... Reading data took 5.17356491089 s Creating peak regions... Creating peak regions took 31.5123429298 s Estimating background... Estimating background took 309.975353956 s Processing 22RV1_HoxB13_ChIPexo-Rep1-GSM2643243/aligned.36mers.unique.bam Reading in data... Estimating background took 40.2659809589 s Processing 22RV1_HoxB13_ChIPexo-Rep1-GSM2643243/aligned.36mers.unique.bam Reading in data... Reading data took 9.32324004173 s Creating peak regions... Reading data took 7.41204404831 s Creating peak regions... Creating peak regions took 34.3933250904 s Estimating background... Creating peak regions took 48.4592580795 s Estimating background... Estimating background took 66.4373519421 s Processing 22RV1_HoxB13_ChIPexo-Rep1-GSM2643243/aligned.36mers.unique.bam Reading in data... Reading data took 2.86490392685 s Creating peak regions... Creating peak regions took 19.7005209923 s Estimating background... Estimating background took 95.7528018951 s Processing 22RV1_HoxB13_ChIPexo-Rep1-GSM2643243/aligned.36mers.unique.bam Reading in data... Estimating background took 19.4081380367 s Processing 22RV1_HoxB13_ChIPexo-Rep1-GSM2643243/aligned.36mers.unique.bam Reading in data... Reading data took 9.83307099342 s Creating peak regions... Reading data took 14.8807830811 s Creating peak regions... Creating peak regions took 53.1501119137 s Estimating background... Creating peak regions took 91.9768538475 s Estimating background... Estimating background took 98.5519330502 s Processing 22RV1_HoxB13_ChIPexo-Rep1-GSM2643243/aligned.36mers.unique.bam Reading in data... Reading data took 14.7917881012 s Creating peak regions... Creating peak regions took 61.3009049892 s Estimating background... Estimating background took 166.924181938 s Processing 22RV1_HoxB13_ChIPexo-Rep1-GSM2643243/aligned.36mers.unique.bam Reading in data... Reading data took 4.56910395622 s Creating peak regions... Creating peak regions took 28.2958059311 s Estimating background... Estimating background took 29.8496968746 s Processing 22RV1_HoxB13_ChIPexo-Rep1-GSM2643243/aligned.36mers.unique.bam Reading in data... Reading data took 3.60566496849 s Creating peak regions... Creating peak regions took 18.666312933 s Estimating background... Estimating background took 34.5969250202 s Processing 22RV1_HoxB13_ChIPexo-Rep1-GSM2643243/aligned.36mers.unique.bam Reading in data... Reading data took 1.81610798836 s Creating peak regions... Creating peak regions took 17.3527579308 s Estimating background... Estimating background took 11.9776890278 s Processing 22RV1_HoxB13_ChIPexo-Rep1-GSM2643243/aligned.36mers.unique.bam Reading in data... Estimating background took 195.259303808 s Processing 22RV1_HoxB13_ChIPexo-Rep1-GSM2643243/aligned.36mers.unique.bam Reading in data... Reading data took 9.08160805702 s Creating peak regions... Reading data took 21.9196231365 s Creating peak regions... Creating peak regions took 48.4760298729 s Estimating background... Creating peak regions took 90.3365058899 s Estimating background... Estimating background took 111.637206078 s Processing 22RV1_HoxB13_ChIPexo-Rep1-GSM2643243/aligned.36mers.unique.bam Reading in data... Reading data took 7.30296301842 s Creating peak regions... Creating peak regions took 37.850301981 s Estimating background... Estimating background took 71.5183448792 s Processing 22RV1_HoxB13_ChIPexo-Rep1-GSM2643243/aligned.36mers.unique.bam Reading in data... Reading data took 5.80139780045 s Creating peak regions... Creating peak regions took 35.5490121841 s Estimating background... Estimating background took 52.8436999321 s Processing 22RV1_HoxB13_ChIPexo-Rep1-GSM2643243/aligned.36mers.unique.bam Reading in data... Reading data took 4.79954910278 s Creating peak regions... Estimating background took 299.003327847 s Processing 22RV1_HoxB13_ChIPexo-Rep1-GSM2643243/aligned.36mers.unique.bam Reading in data... Creating peak regions took 34.0944399834 s Estimating background... Reading data took 19.2280039787 s Creating peak regions... Estimating background took 36.4475870132 s Processing 22RV1_HoxB13_ChIPexo-Rep1-GSM2643243/aligned.36mers.unique.bam Reading in data... Reading data took 4.6370818615 s Creating peak regions... Creating peak regions took 27.8357961178 s Estimating background... Creating peak regions took 88.7276248932 s Estimating background... Estimating background took 38.1777658463 s Processing 22RV1_HoxB13_ChIPexo-Rep1-GSM2643243/aligned.36mers.unique.bam Reading in data... Reading data took 5.64462280273 s Creating peak regions... Creating peak regions took 27.0262589455 s Estimating background... Estimating background took 69.2972309589 s Processing 22RV1_HoxB13_ChIPexo-Rep1-GSM2643243/aligned.36mers.unique.bam Reading in data... Reading data took 2.82787394524 s Creating peak regions... Creating peak regions took 23.9126999378 s Estimating background... Estimating background took 19.9680218697 s Processing 22RV1_HoxB13_ChIPexo-Rep1-GSM2643243/aligned.36mers.unique.bam Reading in data... Reading data took 15.7835481167 s Creating peak regions... Estimating background took 201.005784988 s Processing 22RV1_HoxB13_ChIPexo-Rep1-GSM2643243/aligned.36mers.unique.bam Reading in data... Reading data took 18.278979063 s Creating peak regions... Creating peak regions took 96.0803358555 s Estimating background... Creating peak regions took 79.3806848526 s Estimating background... Estimating background took 161.857910872 s Processing 22RV1_HoxB13_ChIPexo-Rep1-GSM2643243/aligned.36mers.unique.bam Reading in data... Reading data took 4.12397909164 s Creating peak regions... Estimating background took 168.831927776 s Processing 22RV1_HoxB13_ChIPexo-Rep1-GSM2643243/aligned.36mers.unique.bam Reading in data... Creating peak regions took 28.7538511753 s Estimating background... Reading data took 14.0914301872 s Creating peak regions... Estimating background took 29.8460278511 s Processing 22RV1_HoxB13_ChIPexo-Rep1-GSM2643243/aligned.36mers.unique.bam Reading in data... Reading data took 3.71669387817 s Creating peak regions... Creating peak regions took 19.3284268379 s Estimating background... Creating peak regions took 69.506207943 s Estimating background... Estimating background took 36.7787160873 s Processing 22RV1_HoxB13_ChIPexo-Rep1-GSM2643243/aligned.36mers.unique.bam Reading in data... Reading data took 1.85021686554 s Creating peak regions... Creating peak regions took 16.6351351738 s Estimating background... Estimating background took 12.804142952 s Processing 22RV1_HoxB13_ChIPexo-Rep1-GSM2643243/aligned.36mers.unique.bam Reading in data... Reading data took 23.1302690506 s Creating peak regions... Creating peak regions took 87.6186180115 s Estimating background... Estimating background took 168.189006805 s Processing 22RV1_HoxB13_ChIPexo-Rep1-GSM2643243/aligned.36mers.unique.bam Reading in data... Reading data took 19.1526629925 s Creating peak regions... Creating peak regions took 70.0886521339 s Estimating background... Estimating background took 300.802809954 s Processing 22RV1_HoxB13_ChIPexo-Rep1-GSM2643243/aligned.36mers.unique.bam Reading in data... Reading data took 19.5411570072 s Creating peak regions... Estimating background took 226.767655849 s Processing 22RV1_HoxB13_ChIPexo-Rep1-GSM2643243/aligned.36mers.unique.bam Reading in data... Reading data took 16.7352349758 s Creating peak regions... Creating peak regions took 86.3154668808 s Estimating background... Creating peak regions took 67.590898037 s Estimating background... Estimating background took 203.019431114 s Processing 22RV1_HoxB13_ChIPexo-Rep1-GSM2643243/aligned.36mers.unique.bam Reading in data... Estimating background took 199.448750019 s Processing 22RV1_HoxB13_ChIPexo-Rep1-GSM2643243/aligned.36mers.unique.bam Reading in data... Reading data took 18.0945100784 s Creating peak regions... Reading data took 10.3296329975 s Creating peak regions... Creating peak regions took 55.4059491158 s Estimating background... Creating peak regions took 76.634540081 s Estimating background... Estimating background took 85.0398340225 s Processing 22RV1_HoxB13_ChIPexo-Rep1-GSM2643243/aligned.36mers.unique.bam Reading in data... Reading data took 0.717446804047 s Creating peak regions... Creating peak regions took 0.558877944946 s Estimating background... Estimating background took 1.33175706863 s Processing 22RV1_HoxB13_ChIPexo-Rep1-GSM2643243/aligned.36mers.unique.bam Reading in data... Reading data took 7.82662582397 s Creating peak regions... Creating peak regions took 53.3135349751 s Estimating background... Estimating background took 167.119307041 s Processing 22RV1_HoxB13_ChIPexo-Rep1-GSM2643243/aligned.36mers.unique.bam Reading in data... Estimating background took 48.8546111584 s Processing 22RV1_HoxB13_ChIPexo-Rep1-GSM2643243/aligned.36mers.unique.bam Reading in data... Reading data took 1.3855111599 s Creating peak regions... Reading data took 19.5411739349 s Creating peak regions... Creating peak regions took 17.9180748463 s Estimating background... Estimating background took 7.07632803917 s Creating peak regions took 66.7692558765 s Estimating background... Estimating background took 168.980267048 s Processing 22RV1_HoxB13_ChIPexo-Rep1-GSM2643243/aligned.36mers.unique.bam Reading in data... Reading data took 20.4293110371 s Creating peak regions... Creating peak regions took 65.5943889618 s Estimating background... Estimating background took 207.451915026 s Processing 22RV1_HoxB13_ChIPexo-Rep1-GSM2643243/aligned.36mers.unique.bam Reading in data... Reading data took 17.8466570377 s Creating peak regions... Creating peak regions took 62.5826690197 s Estimating background... Estimating background took 178.409451008 s Processing 22RV1_HoxB13_ChIPexo-Rep1-GSM2643243/aligned.36mers.unique.bam Reading in data... Reading data took 8.76851606369 s Creating peak regions... Creating peak regions took 51.2815728188 s Estimating background... Estimating background took 71.854872942 s Processing 22RV1_HoxB13_ChIPexo-Rep1-GSM2643243/aligned.36mers.unique.bam Reading in data... Reading data took 0.909462928772 s Creating peak regions... Creating peak regions took 0.542952060699 s Estimating background... Estimating background took 1.1700489521 s Processing 22RV1_HoxB13_ChIPexo-Rep1-GSM2643243/aligned.36mers.unique.bam Reading in data... Reading data took 6.90603303909 s Creating peak regions... Creating peak regions took 51.9336869717 s Estimating background... Estimating background took 41.3417210579 s Processing 22RV1_HoxB13_ChIPexo-Rep1-GSM2643243/aligned.36mers.unique.bam Reading in data... Reading data took 0.924337148666 s Creating peak regions... Creating peak regions took 16.6456558704 s Estimating background... Estimating background took 3.51671004295 s