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_V7_ChIPexo-Rep1-GSM2643239/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_V7_ChIPexo-Rep1-GSM2643239/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_V7_ChIPexo-Rep1-GSM2643239/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_V7_ChIPexo-Rep1-GSM2643239/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_V7_ChIPexo-Rep1-GSM2643239/aligned.36mers.unique.bam Reading in data... Reading data took 18.8492929935 s Creating peak regions... Creating peak regions took 73.5998380184 s Estimating background... Estimating background took 131.485788107 s Processing 22RV1_V7_ChIPexo-Rep1-GSM2643239/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_V7_ChIPexo-Rep1-GSM2643239/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_V7_ChIPexo-Rep1-GSM2643239/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_V7_ChIPexo-Rep1-GSM2643239/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_V7_ChIPexo-Rep1-GSM2643239/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_V7_ChIPexo-Rep1-GSM2643239/aligned.36mers.unique.bam Reading in data... Reading data took 19.1429638863 s Creating peak regions... Creating peak regions took 74.4921638966 s Estimating background... Estimating background took 157.197135925 s Processing 22RV1_V7_ChIPexo-Rep1-GSM2643239/aligned.36mers.unique.bam Reading in data... Reading data took 8.8703558445 s Creating peak regions... Creating peak regions took 48.0009200573 s Estimating background... Estimating background took 41.6219220161 s Processing 22RV1_V7_ChIPexo-Rep1-GSM2643239/aligned.36mers.unique.bam Reading in data... Reading data took 8.97683095932 s Creating peak regions... Creating peak regions took 45.0552370548 s Estimating background... Estimating background took 43.9442830086 s Processing 22RV1_V7_ChIPexo-Rep1-GSM2643239/aligned.36mers.unique.bam Reading in data... Reading data took 13.901009798 s Creating peak regions... Creating peak regions took 48.3057010174 s Estimating background... Estimating background took 94.4987230301 s Processing 22RV1_V7_ChIPexo-Rep1-GSM2643239/aligned.36mers.unique.bam Reading in data... Reading data took 8.10496902466 s Creating peak regions... Creating peak regions took 38.8383908272 s Estimating background... Estimating background took 40.7864348888 s Processing 22RV1_V7_ChIPexo-Rep1-GSM2643239/aligned.36mers.unique.bam Reading in data... Reading data took 6.80503201485 s Creating peak regions... Creating peak regions took 34.6845998764 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_V7_ChIPexo-Rep1-GSM2643239/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_V7_ChIPexo-Rep1-GSM2643239/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_V7_ChIPexo-Rep1-GSM2643239/aligned.36mers.unique.bam Reading in data... Estimating background took 32.8791530132 s Processing 22RV1_V7_ChIPexo-Rep1-GSM2643239/aligned.36mers.unique.bam Reading in data... Reading data took 5.64597201347 s Creating peak regions... Reading data took 22.7850999832 s Creating peak regions... Creating peak regions took 32.2984490395 s Estimating background... Estimating background took 23.3886108398 s Processing 22RV1_V7_ChIPexo-Rep1-GSM2643239/aligned.36mers.unique.bam Reading in data... Reading data took 5.20120811462 s Creating peak regions... Creating peak regions took 26.2492640018 s Estimating background... Creating peak regions took 88.5995328426 s Estimating background... Estimating background took 20.6143991947 s Processing 22RV1_V7_ChIPexo-Rep1-GSM2643239/aligned.36mers.unique.bam Reading in data... Reading data took 4.66336917877 s Creating peak regions... Creating peak regions took 25.8482751846 s Estimating background... Estimating background took 20.3457400799 s Processing 22RV1_V7_ChIPexo-Rep1-GSM2643239/aligned.36mers.unique.bam Reading in data... Reading data took 5.59982299805 s Creating peak regions... Creating peak regions took 27.2264049053 s Estimating background... Estimating background took 28.1176359653 s Processing 22RV1_V7_ChIPexo-Rep1-GSM2643239/aligned.36mers.unique.bam Reading in data... Reading data took 3.58319401741 s Creating peak regions... Creating peak regions took 20.0036950111 s Estimating background... Estimating background took 156.415276051 s Processing 22RV1_V7_ChIPexo-Rep1-GSM2643239/aligned.36mers.unique.bam Reading in data... Estimating background took 12.5240600109 s Processing 22RV1_V7_ChIPexo-Rep1-GSM2643239/aligned.36mers.unique.bam Reading in data... Reading data took 10.2180831432 s Creating peak regions... Reading data took 15.1754381657 s Creating peak regions... Creating peak regions took 46.7935698032 s Estimating background... Estimating background took 45.3528499603 s Creating peak regions took 83.962033987 s Estimating background... Processing 22RV1_V7_ChIPexo-Rep1-GSM2643239/aligned.36mers.unique.bam Reading in data... Reading data took 9.93085002899 s Creating peak regions... Creating peak regions took 47.3452100754 s Estimating background... Estimating background took 65.3512790203 s Processing 22RV1_V7_ChIPexo-Rep1-GSM2643239/aligned.36mers.unique.bam Reading in data... Reading data took 5.0997710228 s Creating peak regions... Creating peak regions took 24.1825180054 s Estimating background... Estimating background took 47.4410178661 s Processing 22RV1_V7_ChIPexo-Rep1-GSM2643239/aligned.36mers.unique.bam Reading in data... Estimating background took 17.7356801033 s Processing 22RV1_V7_ChIPexo-Rep1-GSM2643239/aligned.36mers.unique.bam Reading in data... Reading data took 3.48898911476 s Creating peak regions... Reading data took 15.3315031528 s Creating peak regions... Creating peak regions took 17.0074179173 s Estimating background... Estimating background took 12.9717581272 s Processing 22RV1_V7_ChIPexo-Rep1-GSM2643239/aligned.36mers.unique.bam Reading in data... Reading data took 1.93156599998 s Creating peak regions... Creating peak regions took 15.3820610046 s Estimating background... Creating peak regions took 48.9838349819 s Estimating background... Estimating background took 7.96832704544 s Processing 22RV1_V7_ChIPexo-Rep1-GSM2643239/aligned.36mers.unique.bam Reading in data... Reading data took 17.3797650337 s Creating peak regions... Creating peak regions took 71.3973038197 s Estimating background... Estimating background took 97.3902599812 s Processing 22RV1_V7_ChIPexo-Rep1-GSM2643239/aligned.36mers.unique.bam Reading in data... Reading data took 8.86179709435 s Creating peak regions... Creating peak regions took 41.4939088821 s Estimating background... Estimating background took 41.0456199646 s Processing 22RV1_V7_ChIPexo-Rep1-GSM2643239/aligned.36mers.unique.bam Reading in data... Reading data took 7.02145195007 s Creating peak regions... Estimating background took 118.016016006 s Processing 22RV1_V7_ChIPexo-Rep1-GSM2643239/aligned.36mers.unique.bam Reading in data... Reading data took 16.2911789417 s Creating peak regions... Creating peak regions took 35.4122760296 s Estimating background... Estimating background took 33.4264800549 s Processing 22RV1_V7_ChIPexo-Rep1-GSM2643239/aligned.36mers.unique.bam Reading in data... Reading data took 6.07288908958 s Creating peak regions... Creating peak regions took 70.6795370579 s Estimating background... Creating peak regions took 33.3056480885 s Estimating background... Estimating background took 27.7743659019 s Processing 22RV1_V7_ChIPexo-Rep1-GSM2643239/aligned.36mers.unique.bam Reading in data... Reading data took 6.04756593704 s Creating peak regions... Creating peak regions took 32.8032300472 s Estimating background... Estimating background took 77.2002301216 s Processing 22RV1_V7_ChIPexo-Rep1-GSM2643239/aligned.36mers.unique.bam Reading in data... Reading data took 13.9870531559 s Creating peak regions... Estimating background took 20.9596049786 s Processing 22RV1_V7_ChIPexo-Rep1-GSM2643239/aligned.36mers.unique.bam Reading in data... Reading data took 5.21742892265 s Creating peak regions... Creating peak regions took 26.3702759743 s Estimating background... Estimating background took 21.6459228992 s Processing 22RV1_V7_ChIPexo-Rep1-GSM2643239/aligned.36mers.unique.bam Reading in data... Creating peak regions took 59.9661159515 s Estimating background... Reading data took 6.37165498734 s Creating peak regions... Creating peak regions took 24.6297969818 s Estimating background... Estimating background took 29.2511470318 s Processing 22RV1_V7_ChIPexo-Rep1-GSM2643239/aligned.36mers.unique.bam Reading in data... Reading data took 4.05566692352 s Creating peak regions... Estimating background took 70.2725970745 s Processing 22RV1_V7_ChIPexo-Rep1-GSM2643239/aligned.36mers.unique.bam Reading in data... Reading data took 14.6615269184 s Creating peak regions... Creating peak regions took 23.5225329399 s Estimating background... Estimating background took 12.5742249489 s Processing 22RV1_V7_ChIPexo-Rep1-GSM2643239/aligned.36mers.unique.bam Reading in data... Reading data took 15.8580310345 s Creating peak regions... Creating peak regions took 63.8903999329 s Estimating background... Creating peak regions took 84.5400679111 s Estimating background... Estimating background took 59.9199779034 s Processing 22RV1_V7_ChIPexo-Rep1-GSM2643239/aligned.36mers.unique.bam Reading in data... Reading data took 15.171257019 s Creating peak regions... Estimating background took 71.0759198666 s Processing 22RV1_V7_ChIPexo-Rep1-GSM2643239/aligned.36mers.unique.bam Reading in data... Reading data took 4.63053798676 s Creating peak regions... Creating peak regions took 57.4522900581 s Estimating background... Creating peak regions took 22.7935600281 s Estimating background... Estimating background took 17.8613209724 s Processing 22RV1_V7_ChIPexo-Rep1-GSM2643239/aligned.36mers.unique.bam Reading in data... Reading data took 3.6929359436 s Creating peak regions... Creating peak regions took 18.1474239826 s Estimating background... Estimating background took 15.1017620564 s Processing 22RV1_V7_ChIPexo-Rep1-GSM2643239/aligned.36mers.unique.bam Reading in data... Reading data took 2.35520887375 s Creating peak regions... Creating peak regions took 17.5184719563 s Estimating background... Estimating background took 97.2714781761 s Processing 22RV1_V7_ChIPexo-Rep1-GSM2643239/aligned.36mers.unique.bam Reading in data... Estimating background took 8.47390508652 s Processing 22RV1_V7_ChIPexo-Rep1-GSM2643239/aligned.36mers.unique.bam Reading in data... Reading data took 15.0041439533 s Creating peak regions... Reading data took 20.07914114 s Creating peak regions... Creating peak regions took 55.889744997 s Estimating background... Creating peak regions took 77.6585271358 s Estimating background... Estimating background took 97.6796329021 s Processing 22RV1_V7_ChIPexo-Rep1-GSM2643239/aligned.36mers.unique.bam Reading in data... Reading data took 9.01208305359 s Creating peak regions... Creating peak regions took 45.7247321606 s Estimating background... Estimating background took 126.590910912 s Processing 22RV1_V7_ChIPexo-Rep1-GSM2643239/aligned.36mers.unique.bam Reading in data... Reading data took 18.9495978355 s Creating peak regions... Estimating background took 37.2986741066 s Processing 22RV1_V7_ChIPexo-Rep1-GSM2643239/aligned.36mers.unique.bam Reading in data... Reading data took 0.50398683548 s Creating peak regions... Creating peak regions took 0.389519929886 s Estimating background... Estimating background took 1.19734597206 s Processing 22RV1_V7_ChIPexo-Rep1-GSM2643239/aligned.36mers.unique.bam Reading in data... Reading data took 7.60204386711 s Creating peak regions... Creating peak regions took 75.5237030983 s Estimating background... Creating peak regions took 54.4624199867 s Estimating background... Estimating background took 19.1031458378 s Processing 22RV1_V7_ChIPexo-Rep1-GSM2643239/aligned.36mers.unique.bam Reading in data... Reading data took 1.01185894012 s Creating peak regions... Creating peak regions took 16.6775820255 s Estimating background... Estimating background took 2.25254607201 s Estimating background took 83.1665599346 s Processing 22RV1_V7_ChIPexo-Rep1-GSM2643239/aligned.36mers.unique.bam Reading in data... Reading data took 15.5853581429 s Creating peak regions... Creating peak regions took 67.4011871815 s Estimating background... Estimating background took 76.2419729233 s Processing 22RV1_V7_ChIPexo-Rep1-GSM2643239/aligned.36mers.unique.bam Reading in data... Reading data took 15.1518909931 s Creating peak regions... Creating peak regions took 66.0301170349 s Estimating background... Estimating background took 69.2678399086 s Processing 22RV1_V7_ChIPexo-Rep1-GSM2643239/aligned.36mers.unique.bam Reading in data... Reading data took 17.9692921638 s Creating peak regions... Creating peak regions took 64.9050080776 s Estimating background... Estimating background took 111.246567011 s Processing 22RV1_V7_ChIPexo-Rep1-GSM2643239/aligned.36mers.unique.bam Reading in data... Reading data took 17.2263391018 s Creating peak regions... Creating peak regions took 61.847222805 s Estimating background... Estimating background took 105.703009844 s Processing 22RV1_V7_ChIPexo-Rep1-GSM2643239/aligned.36mers.unique.bam Reading in data... Reading data took 9.84022903442 s Creating peak regions... Creating peak regions took 52.0549438 s Estimating background... Estimating background took 40.364481926 s Processing 22RV1_V7_ChIPexo-Rep1-GSM2643239/aligned.36mers.unique.bam Reading in data... Reading data took 0.581649065018 s Creating peak regions... Creating peak regions took 0.492264986038 s Estimating background... Estimating background took 1.23618006706 s Processing 22RV1_V7_ChIPexo-Rep1-GSM2643239/aligned.36mers.unique.bam Reading in data... Reading data took 7.62940716743 s Creating peak regions... Creating peak regions took 52.4389150143 s Estimating background... Estimating background took 20.6607410908 s Processing 22RV1_V7_ChIPexo-Rep1-GSM2643239/aligned.36mers.unique.bam Reading in data... Reading data took 1.02079319954 s Creating peak regions... Creating peak regions took 19.7635519505 s Estimating background... Estimating background took 5.31989383698 s