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='LN95_HoxB13_ChIPexo-Rep1-GSM2643249/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='LN95_HoxB13_ChIPexo-Rep1-GSM2643249/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='LN95_HoxB13_ChIPexo-Rep1-GSM2643249/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='LN95_HoxB13_ChIPexo-Rep1-GSM2643249/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 LN95_HoxB13_ChIPexo-Rep1-GSM2643249/aligned.36mers.unique.bam Reading in data... Reading data took 17.8399150372 s Creating peak regions... Creating peak regions took 84.6921839714 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.chrom.sizes', e4='PeakXus', fastq='LN95_HoxB13_ChIPexo-Rep1-GSM2643249/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='LN95_HoxB13_ChIPexo-Rep1-GSM2643249/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 LN95_HoxB13_ChIPexo-Rep1-GSM2643249/aligned.36mers.unique.bam Reading in data... Reading data took 21.4533081055 s Creating peak regions... Creating peak regions took 100.519865036 s Estimating background... Estimating background took 214.991147041 s Processing LN95_HoxB13_ChIPexo-Rep1-GSM2643249/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='LN95_HoxB13_ChIPexo-Rep1-GSM2643249/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='LN95_HoxB13_ChIPexo-Rep1-GSM2643249/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='LN95_HoxB13_ChIPexo-Rep1-GSM2643249/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='LN95_HoxB13_ChIPexo-Rep1-GSM2643249/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 LN95_HoxB13_ChIPexo-Rep1-GSM2643249/aligned.36mers.unique.bam Reading in data... Reading data took 16.1324691772 s Creating peak regions... Creating peak regions took 82.4977378845 s Estimating background... Estimating background took 226.861039877 s Processing LN95_HoxB13_ChIPexo-Rep1-GSM2643249/aligned.36mers.unique.bam Reading in data... Reading data took 9.39037919044 s Creating peak regions... Creating peak regions took 57.6518018246 s Estimating background... Estimating background took 94.6631138325 s Processing LN95_HoxB13_ChIPexo-Rep1-GSM2643249/aligned.36mers.unique.bam Reading in data... Reading data took 10.2117140293 s Creating peak regions... Creating peak regions took 56.7905061245 s Estimating background... Estimating background took 94.3111629486 s Processing LN95_HoxB13_ChIPexo-Rep1-GSM2643249/aligned.36mers.unique.bam Reading in data... Reading data took 9.66644501686 s Creating peak regions... Creating peak regions took 49.2962770462 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='LN95_HoxB13_ChIPexo-Rep1-GSM2643249/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='LN95_HoxB13_ChIPexo-Rep1-GSM2643249/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 LN95_HoxB13_ChIPexo-Rep1-GSM2643249/aligned.36mers.unique.bam Reading in data... Reading data took 15.581179142 s Creating peak regions... Estimating background took 98.1309831142 s Processing LN95_HoxB13_ChIPexo-Rep1-GSM2643249/aligned.36mers.unique.bam Reading in data... Reading data took 5.52174210548 s Creating peak regions... Creating peak regions took 38.9567160606 s Estimating background... Creating peak regions took 82.6126000881 s Estimating background... Estimating background took 50.8163359165 s Processing LN95_HoxB13_ChIPexo-Rep1-GSM2643249/aligned.36mers.unique.bam Reading in data... Reading data took 5.62002897263 s Creating peak regions... Creating peak regions took 37.220236063 s Estimating background... Estimating background took 51.1006400585 s Processing LN95_HoxB13_ChIPexo-Rep1-GSM2643249/aligned.36mers.unique.bam Reading in data... Reading data took 5.24447011948 s Creating peak regions... Creating peak regions took 33.9344220161 s Estimating background... Estimating background took 50.7138500214 s Processing LN95_HoxB13_ChIPexo-Rep1-GSM2643249/aligned.36mers.unique.bam Reading in data... Estimating background took 214.048950911 s Processing LN95_HoxB13_ChIPexo-Rep1-GSM2643249/aligned.36mers.unique.bam Reading in data... Reading data took 4.21128201485 s Creating peak regions... Reading data took 10.2461829185 s Creating peak regions... Creating peak regions took 31.9079048634 s Estimating background... Creating peak regions took 53.095031023 s Estimating background... Estimating background took 28.8605909348 s Processing LN95_HoxB13_ChIPexo-Rep1-GSM2643249/aligned.36mers.unique.bam Reading in data... Reading data took 5.00897502899 s Creating peak regions... Creating peak regions took 31.7905957699 s Estimating background... Estimating background took 49.3670649529 s Processing LN95_HoxB13_ChIPexo-Rep1-GSM2643249/aligned.36mers.unique.bam Reading in data... Estimating background took 91.5609190464 s Processing LN95_HoxB13_ChIPexo-Rep1-GSM2643249/aligned.36mers.unique.bam Reading in data... Reading data took 6.05843305588 s Creating peak regions... Reading data took 10.8714778423 s Creating peak regions... Creating peak regions took 29.2180380821 s Estimating background... Creating peak regions took 63.273622036 s Estimating background... Estimating background took 55.9512829781 s Processing LN95_HoxB13_ChIPexo-Rep1-GSM2643249/aligned.36mers.unique.bam Reading in data... Reading data took 2.16876220703 s Creating peak regions... Creating peak regions took 18.0827181339 s Estimating background... Estimating background took 14.1437420845 s Processing LN95_HoxB13_ChIPexo-Rep1-GSM2643249/aligned.36mers.unique.bam Reading in data... Reading data took 12.9677259922 s Creating peak regions... Estimating background took 97.9810421467 s Processing LN95_HoxB13_ChIPexo-Rep1-GSM2643249/aligned.36mers.unique.bam Reading in data... Reading data took 9.80583095551 s Creating peak regions... Creating peak regions took 83.7213828564 s Estimating background... Creating peak regions took 50.9965889454 s Estimating background... Estimating background took 106.135032177 s Processing LN95_HoxB13_ChIPexo-Rep1-GSM2643249/aligned.36mers.unique.bam Reading in data... Reading data took 6.09134316444 s Creating peak regions... Estimating background took 133.126603127 s Processing LN95_HoxB13_ChIPexo-Rep1-GSM2643249/aligned.36mers.unique.bam Reading in data... Reading data took 3.25276589394 s Creating peak regions... Creating peak regions took 22.6333680153 s Estimating background... Creating peak regions took 44.9690110683 s Estimating background... Estimating background took 31.3350770473 s Processing LN95_HoxB13_ChIPexo-Rep1-GSM2643249/aligned.36mers.unique.bam Reading in data... Reading data took 2.15790295601 s Creating peak regions... Creating peak regions took 15.0853710175 s Estimating background... Estimating background took 48.2280459404 s Processing LN95_HoxB13_ChIPexo-Rep1-GSM2643249/aligned.36mers.unique.bam Reading in data... Estimating background took 18.710313797 s Processing LN95_HoxB13_ChIPexo-Rep1-GSM2643249/aligned.36mers.unique.bam Reading in data... Reading data took 5.73032212257 s Creating peak regions... Reading data took 1.88168311119 s Creating peak regions... Creating peak regions took 16.6482172012 s Estimating background... Estimating background took 12.5208570957 s Processing LN95_HoxB13_ChIPexo-Rep1-GSM2643249/aligned.36mers.unique.bam Reading in data... Creating peak regions took 40.5393981934 s Estimating background... Reading data took 14.6764550209 s Creating peak regions... Estimating background took 52.6362929344 s Processing LN95_HoxB13_ChIPexo-Rep1-GSM2643249/aligned.36mers.unique.bam Reading in data... Reading data took 5.20772314072 s Creating peak regions... Creating peak regions took 76.9467101097 s Estimating background... Creating peak regions took 32.5753688812 s Estimating background... Estimating background took 48.7798051834 s Processing LN95_HoxB13_ChIPexo-Rep1-GSM2643249/aligned.36mers.unique.bam Reading in data... Reading data took 3.75004196167 s Creating peak regions... Creating peak regions took 27.5466430187 s Estimating background... Estimating background took 28.8173160553 s Processing LN95_HoxB13_ChIPexo-Rep1-GSM2643249/aligned.36mers.unique.bam Reading in data... Reading data took 4.82950305939 s Creating peak regions... Estimating background took 151.177032948 s Processing LN95_HoxB13_ChIPexo-Rep1-GSM2643249/aligned.36mers.unique.bam Reading in data... Creating peak regions took 28.8217799664 s Estimating background... Reading data took 12.3888089657 s Creating peak regions... Estimating background took 48.3647038937 s Processing LN95_HoxB13_ChIPexo-Rep1-GSM2643249/aligned.36mers.unique.bam Reading in data... Reading data took 5.32925105095 s Creating peak regions... Creating peak regions took 66.2541861534 s Estimating background... Creating peak regions took 28.3131809235 s Estimating background... Estimating background took 57.6907351017 s Processing LN95_HoxB13_ChIPexo-Rep1-GSM2643249/aligned.36mers.unique.bam Reading in data... Reading data took 2.18512201309 s Creating peak regions... Creating peak regions took 17.9736409187 s Estimating background... Estimating background took 14.1276199818 s Processing LN95_HoxB13_ChIPexo-Rep1-GSM2643249/aligned.36mers.unique.bam Reading in data... Reading data took 13.2052061558 s Creating peak regions... Estimating background took 115.687798023 s Processing LN95_HoxB13_ChIPexo-Rep1-GSM2643249/aligned.36mers.unique.bam Reading in data... Reading data took 13.9359629154 s Creating peak regions... Creating peak regions took 82.2905011177 s Estimating background... Creating peak regions took 64.8424220085 s Estimating background... Estimating background took 131.339384079 s Processing LN95_HoxB13_ChIPexo-Rep1-GSM2643249/aligned.36mers.unique.bam Reading in data... Reading data took 3.3466758728 s Creating peak regions... Estimating background took 151.184293985 s Processing LN95_HoxB13_ChIPexo-Rep1-GSM2643249/aligned.36mers.unique.bam Reading in data... Creating peak regions took 22.133564949 s Estimating background... Reading data took 9.84371495247 s Creating peak regions... Estimating background took 31.8158559799 s Processing LN95_HoxB13_ChIPexo-Rep1-GSM2643249/aligned.36mers.unique.bam Reading in data... Reading data took 2.15898299217 s Creating peak regions... Creating peak regions took 14.6839108467 s Estimating background... Creating peak regions took 58.8623018265 s Estimating background... Estimating background took 18.5653998852 s Processing LN95_HoxB13_ChIPexo-Rep1-GSM2643249/aligned.36mers.unique.bam Reading in data... Reading data took 1.32510495186 s Creating peak regions... Creating peak regions took 13.5667831898 s Estimating background... Estimating background took 11.5056829453 s Processing LN95_HoxB13_ChIPexo-Rep1-GSM2643249/aligned.36mers.unique.bam Reading in data... Reading data took 14.6831269264 s Creating peak regions... Estimating background took 97.6895530224 s Processing LN95_HoxB13_ChIPexo-Rep1-GSM2643249/aligned.36mers.unique.bam Reading in data... Reading data took 11.7183670998 s Creating peak regions... Creating peak regions took 72.2934710979 s Estimating background... Creating peak regions took 60.6118690968 s Estimating background... Estimating background took 149.393427134 s Processing LN95_HoxB13_ChIPexo-Rep1-GSM2643249/aligned.36mers.unique.bam Reading in data... Reading data took 11.6660690308 s Creating peak regions... Estimating background took 109.881901026 s Processing LN95_HoxB13_ChIPexo-Rep1-GSM2643249/aligned.36mers.unique.bam Reading in data... Reading data took 8.6239259243 s Creating peak regions... Creating peak regions took 62.636305809 s Estimating background... Creating peak regions took 52.1221210957 s Estimating background... Estimating background took 74.724725008 s Processing LN95_HoxB13_ChIPexo-Rep1-GSM2643249/aligned.36mers.unique.bam Reading in data... Reading data took 6.59454417229 s Creating peak regions... Estimating background took 125.114444971 s Processing LN95_HoxB13_ChIPexo-Rep1-GSM2643249/aligned.36mers.unique.bam Reading in data... Creating peak regions took 45.7615270615 s Estimating background... Reading data took 16.7115559578 s Creating peak regions... Estimating background took 57.2367889881 s Processing LN95_HoxB13_ChIPexo-Rep1-GSM2643249/aligned.36mers.unique.bam Reading in data... Reading data took 0.853993177414 s Creating peak regions... Creating peak regions took 0.555027961731 s Estimating background... Estimating background took 1.52982091904 s Processing LN95_HoxB13_ChIPexo-Rep1-GSM2643249/aligned.36mers.unique.bam Reading in data... Reading data took 7.85926413536 s Creating peak regions... Creating peak regions took 68.8791861534 s Estimating background... Creating peak regions took 52.6540830135 s Estimating background... Estimating background took 47.0986979008 s Processing LN95_HoxB13_ChIPexo-Rep1-GSM2643249/aligned.36mers.unique.bam Reading in data... Reading data took 0.441582918167 s Creating peak regions... Creating peak regions took 17.6423020363 s Estimating background... Estimating background took 0.878894090652 s Estimating background took 150.418030977 s Processing LN95_HoxB13_ChIPexo-Rep1-GSM2643249/aligned.36mers.unique.bam Reading in data... Reading data took 10.3949670792 s Creating peak regions... Creating peak regions took 58.5360050201 s Estimating background... Estimating background took 100.039751053 s Processing LN95_HoxB13_ChIPexo-Rep1-GSM2643249/aligned.36mers.unique.bam Reading in data... Reading data took 12.1214408875 s Creating peak regions... Creating peak regions took 60.0937700272 s Estimating background... Estimating background took 111.411902905 s Processing LN95_HoxB13_ChIPexo-Rep1-GSM2643249/aligned.36mers.unique.bam Reading in data... Reading data took 8.73515510559 s Creating peak regions... Creating peak regions took 56.6764309406 s Estimating background... Estimating background took 68.6125237942 s Processing LN95_HoxB13_ChIPexo-Rep1-GSM2643249/aligned.36mers.unique.bam Reading in data... Reading data took 6.30305290222 s Creating peak regions... Creating peak regions took 44.8157720566 s Estimating background... Estimating background took 55.5530588627 s Processing LN95_HoxB13_ChIPexo-Rep1-GSM2643249/aligned.36mers.unique.bam Reading in data... Reading data took 0.692018032074 s Creating peak regions... Creating peak regions took 0.352433204651 s Estimating background... Estimating background took 1.33388400078 s Processing LN95_HoxB13_ChIPexo-Rep1-GSM2643249/aligned.36mers.unique.bam Reading in data... Reading data took 7.04413700104 s Creating peak regions... Creating peak regions took 50.4193139076 s Estimating background... Estimating background took 47.2719249725 s Processing LN95_HoxB13_ChIPexo-Rep1-GSM2643249/aligned.36mers.unique.bam Reading in data... Reading data took 0.931694030762 s Creating peak regions... Creating peak regions took 18.0318131447 s Estimating background... Estimating background took 0.830554962158 s