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_V7_ChIPexo-Rep1-GSM2643245/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_V7_ChIPexo-Rep1-GSM2643245/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_V7_ChIPexo-Rep1-GSM2643245/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_V7_ChIPexo-Rep1-GSM2643245/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_V7_ChIPexo-Rep1-GSM2643245/aligned.36mers.unique.bam Reading in data... Reading data took 12.5331668854 s Creating peak regions... Creating peak regions took 78.0280809402 s Estimating background... Estimating background took 139.472949028 s Processing LN95_V7_ChIPexo-Rep1-GSM2643245/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_V7_ChIPexo-Rep1-GSM2643245/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_V7_ChIPexo-Rep1-GSM2643245/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_V7_ChIPexo-Rep1-GSM2643245/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_V7_ChIPexo-Rep1-GSM2643245/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_V7_ChIPexo-Rep1-GSM2643245/aligned.36mers.unique.bam Reading in data... Reading data took 12.8968369961 s Creating peak regions... Creating peak regions took 75.4689338207 s Estimating background... Estimating background took 131.207149982 s Processing LN95_V7_ChIPexo-Rep1-GSM2643245/aligned.36mers.unique.bam Reading in data... Reading data took 8.23806214333 s Creating peak regions... Creating peak regions took 52.4000399113 s Estimating background... Estimating background took 51.1435489655 s Processing LN95_V7_ChIPexo-Rep1-GSM2643245/aligned.36mers.unique.bam Reading in data... Reading data took 7.90731310844 s Creating peak regions... Creating peak regions took 49.3868319988 s Estimating background... Estimating background took 59.5992631912 s Processing LN95_V7_ChIPexo-Rep1-GSM2643245/aligned.36mers.unique.bam Reading in data... Reading data took 9.04961681366 s Creating peak regions... Creating peak regions took 48.0185539722 s Estimating background... Estimating background took 58.6215410233 s Processing LN95_V7_ChIPexo-Rep1-GSM2643245/aligned.36mers.unique.bam Reading in data... Reading data took 4.77953696251 s Creating peak regions... Creating peak regions took 39.9424321651 s Estimating background... Estimating background took 27.7865149975 s Processing LN95_V7_ChIPexo-Rep1-GSM2643245/aligned.36mers.unique.bam Reading in data... Reading data took 4.64388895035 s Creating peak regions... Creating peak regions took 35.4511420727 s Estimating background... Estimating background took 27.2799298763 s Processing LN95_V7_ChIPexo-Rep1-GSM2643245/aligned.36mers.unique.bam Reading in data... Reading data took 4.4664311409 s Creating peak regions... Creating peak regions took 33.6539840698 s Estimating background... Estimating background took 29.8969070911 s Processing LN95_V7_ChIPexo-Rep1-GSM2643245/aligned.36mers.unique.bam Reading in data... Reading data took 3.25704908371 s Creating peak regions... Creating peak regions took 27.9490590096 s Estimating background... Estimating background took 17.9170939922 s Processing LN95_V7_ChIPexo-Rep1-GSM2643245/aligned.36mers.unique.bam Reading in data... Reading data took 4.78390097618 s Creating peak regions... Creating peak regions took 30.3961808681 s Estimating background... Estimating background took 32.4712710381 s Processing LN95_V7_ChIPexo-Rep1-GSM2643245/aligned.36mers.unique.bam Reading in data... Reading data took 5.33133816719 s Creating peak regions... Creating peak regions took 29.8101398945 s Estimating background... Estimating background took 38.8047060966 s Processing LN95_V7_ChIPexo-Rep1-GSM2643245/aligned.36mers.unique.bam Reading in data... Reading data took 2.34771800041 s Creating peak regions... Creating peak regions took 19.2949140072 s Estimating background... Estimating background took 11.3016340733 s Processing LN95_V7_ChIPexo-Rep1-GSM2643245/aligned.36mers.unique.bam Reading in data... Reading data took 10.835971117 s Creating peak regions... Creating peak regions took 80.4693620205 s Estimating background... Estimating background took 75.369852066 s Processing LN95_V7_ChIPexo-Rep1-GSM2643245/aligned.36mers.unique.bam Reading in data... Reading data took 3.9135119915 s Creating peak regions... 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_V7_ChIPexo-Rep1-GSM2643245/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_V7_ChIPexo-Rep1-GSM2643245/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_V7_ChIPexo-Rep1-GSM2643245/aligned.36mers.unique.bam Reading in data... Reading data took 12.5079269409 s Creating peak regions... Creating peak regions took 27.5673420429 s Estimating background... Estimating background took 20.8372461796 s Processing LN95_V7_ChIPexo-Rep1-GSM2643245/aligned.36mers.unique.bam Reading in data... Reading data took 2.04746103287 s Creating peak regions... Creating peak regions took 14.5692579746 s Estimating background... Estimating background took 11.018337965 s Processing LN95_V7_ChIPexo-Rep1-GSM2643245/aligned.36mers.unique.bam Reading in data... Reading data took 1.66416192055 s Creating peak regions... Creating peak regions took 70.5671970844 s Estimating background... Creating peak regions took 16.9038009644 s Estimating background... Estimating background took 7.65416693687 s Processing LN95_V7_ChIPexo-Rep1-GSM2643245/aligned.36mers.unique.bam Reading in data... Reading data took 11.8394758701 s Creating peak regions... Creating peak regions took 76.6604979038 s Estimating background... Estimating background took 135.295536995 s Processing LN95_V7_ChIPexo-Rep1-GSM2643245/aligned.36mers.unique.bam Reading in data... Reading data took 7.6265308857 s Creating peak regions... Creating peak regions took 47.0499699116 s Estimating background... Estimating background took 88.1780400276 s Processing LN95_V7_ChIPexo-Rep1-GSM2643245/aligned.36mers.unique.bam Reading in data... Reading data took 11.4273378849 s Creating peak regions... Estimating background took 49.8142960072 s Processing LN95_V7_ChIPexo-Rep1-GSM2643245/aligned.36mers.unique.bam Reading in data... Reading data took 8.54405498505 s Creating peak regions... Creating peak regions took 70.5575010777 s Estimating background... Creating peak regions took 46.3464860916 s Estimating background... Estimating background took 67.6838879585 s Processing LN95_V7_ChIPexo-Rep1-GSM2643245/aligned.36mers.unique.bam Reading in data... Estimating background took 57.969563961 s Processing LN95_V7_ChIPexo-Rep1-GSM2643245/aligned.36mers.unique.bam Reading in data... Reading data took 12.0784740448 s Creating peak regions... Reading data took 7.73916697502 s Creating peak regions... Creating peak regions took 49.6888110638 s Estimating background... Creating peak regions took 70.3834290504 s Estimating background... Estimating background took 59.0548019409 s Processing LN95_V7_ChIPexo-Rep1-GSM2643245/aligned.36mers.unique.bam Reading in data... Reading data took 4.69052505493 s Creating peak regions... Creating peak regions took 35.888532877 s Estimating background... Estimating background took 86.3561489582 s Processing LN95_V7_ChIPexo-Rep1-GSM2643245/aligned.36mers.unique.bam Reading in data... Reading data took 10.1619799137 s Creating peak regions... Estimating background took 27.2352621555 s Processing LN95_V7_ChIPexo-Rep1-GSM2643245/aligned.36mers.unique.bam Reading in data... Reading data took 3.63398909569 s Creating peak regions... Creating peak regions took 29.6445469856 s Estimating background... Creating peak regions took 67.5199010372 s Estimating background... Estimating background took 26.5698490143 s Processing LN95_V7_ChIPexo-Rep1-GSM2643245/aligned.36mers.unique.bam Reading in data... Reading data took 3.91736912727 s Creating peak regions... Creating peak regions took 28.7101309299 s Estimating background... Estimating background took 53.0077280998 s Processing LN95_V7_ChIPexo-Rep1-GSM2643245/aligned.36mers.unique.bam Reading in data... Reading data took 9.81602597237 s Creating peak regions... Estimating background took 25.7673521042 s Processing LN95_V7_ChIPexo-Rep1-GSM2643245/aligned.36mers.unique.bam Reading in data... Reading data took 3.25821709633 s Creating peak regions... Creating peak regions took 28.1194918156 s Estimating background... Estimating background took 18.057197094 s Processing LN95_V7_ChIPexo-Rep1-GSM2643245/aligned.36mers.unique.bam Reading in data... Creating peak regions took 57.0079050064 s Estimating background... Reading data took 4.22587585449 s Creating peak regions... Creating peak regions took 27.0195529461 s Estimating background... Estimating background took 33.041301012 s Processing LN95_V7_ChIPexo-Rep1-GSM2643245/aligned.36mers.unique.bam Reading in data... Reading data took 4.62483310699 s Creating peak regions... Estimating background took 71.3511388302 s Processing LN95_V7_ChIPexo-Rep1-GSM2643245/aligned.36mers.unique.bam Reading in data... Reading data took 7.04503488541 s Creating peak regions... Creating peak regions took 25.1223621368 s Estimating background... Estimating background took 33.0024130344 s Processing LN95_V7_ChIPexo-Rep1-GSM2643245/aligned.36mers.unique.bam Reading in data... Reading data took 2.08488678932 s Creating peak regions... Creating peak regions took 49.9324960709 s Estimating background... Creating peak regions took 17.4604709148 s Estimating background... Estimating background took 10.1880369186 s Processing LN95_V7_ChIPexo-Rep1-GSM2643245/aligned.36mers.unique.bam Reading in data... Reading data took 11.1596889496 s Creating peak regions... Estimating background took 39.3933820724 s Processing LN95_V7_ChIPexo-Rep1-GSM2643245/aligned.36mers.unique.bam Reading in data... Reading data took 5.37416982651 s Creating peak regions... Creating peak regions took 42.9003639221 s Estimating background... Creating peak regions took 77.2389330864 s Estimating background... Estimating background took 31.4704010487 s Processing LN95_V7_ChIPexo-Rep1-GSM2643245/aligned.36mers.unique.bam Reading in data... Reading data took 0.691910982132 s Creating peak regions... Creating peak regions took 0.508358955383 s Estimating background... Estimating background took 1.49662303925 s Processing LN95_V7_ChIPexo-Rep1-GSM2643245/aligned.36mers.unique.bam Reading in data... Reading data took 7.07319402695 s Creating peak regions... Creating peak regions took 53.3022048473 s Estimating background... Estimating background took 70.9087450504 s Processing LN95_V7_ChIPexo-Rep1-GSM2643245/aligned.36mers.unique.bam Reading in data... Reading data took 3.42472195625 s Creating peak regions... Creating peak regions took 21.7545659542 s Estimating background... Estimating background took 28.6300549507 s Processing LN95_V7_ChIPexo-Rep1-GSM2643245/aligned.36mers.unique.bam Reading in data... Reading data took 0.423938035965 s Creating peak regions... Estimating background took 20.0732200146 s Processing LN95_V7_ChIPexo-Rep1-GSM2643245/aligned.36mers.unique.bam Reading in data... Creating peak regions took 17.8539140224 s Estimating background... Estimating background took 0.993527889252 s Reading data took 1.90896010399 s Creating peak regions... Creating peak regions took 14.6744000912 s Estimating background... Estimating background took 10.7794878483 s Processing LN95_V7_ChIPexo-Rep1-GSM2643245/aligned.36mers.unique.bam Reading in data... Reading data took 1.23759198189 s Creating peak regions... Creating peak regions took 11.9797420502 s Estimating background... Estimating background took 6.60055112839 s Processing LN95_V7_ChIPexo-Rep1-GSM2643245/aligned.36mers.unique.bam Reading in data... Reading data took 9.86591386795 s Creating peak regions... Creating peak regions took 66.0828790665 s Estimating background... Estimating background took 85.6229269505 s Processing LN95_V7_ChIPexo-Rep1-GSM2643245/aligned.36mers.unique.bam Reading in data... Reading data took 9.76353096962 s Creating peak regions... Creating peak regions took 61.3021559715 s Estimating background... Estimating background took 63.7132229805 s Processing LN95_V7_ChIPexo-Rep1-GSM2643245/aligned.36mers.unique.bam Reading in data... Reading data took 10.1185450554 s Creating peak regions... Creating peak regions took 59.4737200737 s Estimating background... Estimating background took 84.7256350517 s Processing LN95_V7_ChIPexo-Rep1-GSM2643245/aligned.36mers.unique.bam Reading in data... Reading data took 10.555768013 s Creating peak regions... Creating peak regions took 71.3879508972 s Estimating background... Estimating background took 50.7856931686 s Processing LN95_V7_ChIPexo-Rep1-GSM2643245/aligned.36mers.unique.bam Reading in data... Reading data took 9.08002209663 s Creating peak regions... Creating peak regions took 52.004983902 s Estimating background... Estimating background took 66.7659640312 s Processing LN95_V7_ChIPexo-Rep1-GSM2643245/aligned.36mers.unique.bam Reading in data... Reading data took 7.92998600006 s Creating peak regions... Creating peak regions took 48.6612451077 s Estimating background... Estimating background took 38.5777249336 s Processing LN95_V7_ChIPexo-Rep1-GSM2643245/aligned.36mers.unique.bam Reading in data... Reading data took 5.54047203064 s Creating peak regions... Creating peak regions took 43.2633459568 s Estimating background... Estimating background took 32.5330350399 s Processing LN95_V7_ChIPexo-Rep1-GSM2643245/aligned.36mers.unique.bam Reading in data... Reading data took 0.49977684021 s Creating peak regions... Creating peak regions took 0.372818946838 s Estimating background... Estimating background took 1.38686800003 s Processing LN95_V7_ChIPexo-Rep1-GSM2643245/aligned.36mers.unique.bam Reading in data... Reading data took 6.57715201378 s Creating peak regions... Creating peak regions took 52.1555449963 s Estimating background... Estimating background took 24.9501729012 s Processing LN95_V7_ChIPexo-Rep1-GSM2643245/aligned.36mers.unique.bam Reading in data... Reading data took 0.281565904617 s Creating peak regions... Creating peak regions took 13.8473660946 s Estimating background... Estimating background took 0.672475814819 s