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_C19_ChIPexo-Rep2-GSM2643248/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_C19_ChIPexo-Rep2-GSM2643248/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_C19_ChIPexo-Rep2-GSM2643248/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_C19_ChIPexo-Rep2-GSM2643248/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_C19_ChIPexo-Rep2-GSM2643248/aligned.36mers.unique.bam Reading in data... Reading data took 18.478274107 s Creating peak regions... Creating peak regions took 87.8169391155 s Estimating background... Estimating background took 237.530045033 s Processing LN95_C19_ChIPexo-Rep2-GSM2643248/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_C19_ChIPexo-Rep2-GSM2643248/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_C19_ChIPexo-Rep2-GSM2643248/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_C19_ChIPexo-Rep2-GSM2643248/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_C19_ChIPexo-Rep2-GSM2643248/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_C19_ChIPexo-Rep2-GSM2643248/aligned.36mers.unique.bam Reading in data... Reading data took 20.8224089146 s Creating peak regions... Creating peak regions took 86.7986578941 s Estimating background... Estimating background took 240.749087095 s Processing LN95_C19_ChIPexo-Rep2-GSM2643248/aligned.36mers.unique.bam Reading in data... Reading data took 13.5909101963 s Creating peak regions... Creating peak regions took 66.8893830776 s Estimating background... Estimating background took 100.445616007 s Processing LN95_C19_ChIPexo-Rep2-GSM2643248/aligned.36mers.unique.bam Reading in data... Reading data took 12.9539070129 s Creating peak regions... Creating peak regions took 50.6883111 s Estimating background... Estimating background took 114.673280001 s Processing LN95_C19_ChIPexo-Rep2-GSM2643248/aligned.36mers.unique.bam Reading in data... Reading data took 12.6251339912 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_C19_ChIPexo-Rep2-GSM2643248/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_C19_ChIPexo-Rep2-GSM2643248/peakXus/', p3=1.0, p7=1, q2=20, s3=1, skip0=0, t2=1, title5='PeakXus', verbosity=1, w3=5, w4=100, wg7=None)Creating peak regions took 52.5159909725 s Estimating background... Testing that input files exist...done! Processing LN95_C19_ChIPexo-Rep2-GSM2643248/aligned.36mers.unique.bam Reading in data... Reading data took 20.5974237919 s Creating peak regions... Estimating background took 109.585999966 s Processing LN95_C19_ChIPexo-Rep2-GSM2643248/aligned.36mers.unique.bam Reading in data... Reading data took 6.97786593437 s Creating peak regions... Creating peak regions took 97.7797670364 s Estimating background... Creating peak regions took 49.3677139282 s Estimating background... Estimating background took 52.1936779022 s Processing LN95_C19_ChIPexo-Rep2-GSM2643248/aligned.36mers.unique.bam Reading in data... Reading data took 5.88788795471 s Creating peak regions... Creating peak regions took 37.6046779156 s Estimating background... Estimating background took 48.6034858227 s Processing LN95_C19_ChIPexo-Rep2-GSM2643248/aligned.36mers.unique.bam Reading in data... Reading data took 6.75351786613 s Creating peak regions... Creating peak regions took 39.0312759876 s Estimating background... Estimating background took 251.6762321 s Processing LN95_C19_ChIPexo-Rep2-GSM2643248/aligned.36mers.unique.bam Reading in data... Reading data took 13.0606310368 s Creating peak regions... Estimating background took 50.3895308971 s Processing LN95_C19_ChIPexo-Rep2-GSM2643248/aligned.36mers.unique.bam Reading in data... Reading data took 5.35977196693 s Creating peak regions... Creating peak regions took 33.8293960094 s Estimating background... Creating peak regions took 63.695761919 s Estimating background... Estimating background took 35.0990059376 s Processing LN95_C19_ChIPexo-Rep2-GSM2643248/aligned.36mers.unique.bam Reading in data... Reading data took 6.14548397064 s Creating peak regions... Creating peak regions took 33.1905698776 s Estimating background... Estimating background took 95.0020499229 s Processing LN95_C19_ChIPexo-Rep2-GSM2643248/aligned.36mers.unique.bam Reading in data... Reading data took 11.9542899132 s Creating peak regions... Estimating background took 59.8087909222 s Processing LN95_C19_ChIPexo-Rep2-GSM2643248/aligned.36mers.unique.bam Reading in data... Reading data took 7.09746408463 s Creating peak regions... Creating peak regions took 55.4947071075 s Estimating background... Creating peak regions took 31.6096799374 s Estimating background... Estimating background took 65.1397891045 s Processing LN95_C19_ChIPexo-Rep2-GSM2643248/aligned.36mers.unique.bam Reading in data... Reading data took 4.43963694572 s Creating peak regions... Creating peak regions took 25.0197679996 s Estimating background... Estimating background took 113.841956854 s Processing LN95_C19_ChIPexo-Rep2-GSM2643248/aligned.36mers.unique.bam Reading in data... Estimating background took 20.8302540779 s Processing LN95_C19_ChIPexo-Rep2-GSM2643248/aligned.36mers.unique.bam Reading in data... Reading data took 11.4569461346 s Creating peak regions... Reading data took 16.0535821915 s Creating peak regions... Creating peak regions took 53.6704490185 s Estimating background... Creating peak regions took 91.7566900253 s Estimating background... Estimating background took 106.299278021 s Processing LN95_C19_ChIPexo-Rep2-GSM2643248/aligned.36mers.unique.bam Reading in data... Reading data took 6.3644387722 s Creating peak regions... Creating peak regions took 41.4126169682 s Estimating background... Estimating background took 145.573084116 s Processing LN95_C19_ChIPexo-Rep2-GSM2643248/aligned.36mers.unique.bam Reading in data... Reading data took 5.24407100677 s Creating peak regions... Estimating background took 51.755726099 s Processing LN95_C19_ChIPexo-Rep2-GSM2643248/aligned.36mers.unique.bam Reading in data... Reading data took 6.68557405472 s Creating peak regions... Creating peak regions took 31.0096628666 s Estimating background... Creating peak regions took 46.5430510044 s Estimating background... Estimating background took 33.7567591667 s Processing LN95_C19_ChIPexo-Rep2-GSM2643248/aligned.36mers.unique.bam Reading in data... Reading data took 2.94447493553 s Creating peak regions... Creating peak regions took 18.2865788937 s Estimating background... Estimating background took 21.2461719513 s Processing LN95_C19_ChIPexo-Rep2-GSM2643248/aligned.36mers.unique.bam Reading in data... Estimating background took 53.4203629494 s Reading data took 2.1444170475 s Creating peak regions... Processing LN95_C19_ChIPexo-Rep2-GSM2643248/aligned.36mers.unique.bam Reading in data... Reading data took 6.63069391251 s Creating peak regions... Creating peak regions took 19.2047309875 s Estimating background... Estimating background took 14.9813659191 s Processing LN95_C19_ChIPexo-Rep2-GSM2643248/aligned.36mers.unique.bam Reading in data... Creating peak regions took 40.8920099735 s Estimating background... Reading data took 17.2917749882 s Creating peak regions... Estimating background took 51.2829949856 s Processing LN95_C19_ChIPexo-Rep2-GSM2643248/aligned.36mers.unique.bam Reading in data... Reading data took 4.53661894798 s Creating peak regions... Creating peak regions took 72.5683839321 s Estimating background... Creating peak regions took 29.018504858 s Estimating background... Estimating background took 33.9747948647 s Processing LN95_C19_ChIPexo-Rep2-GSM2643248/aligned.36mers.unique.bam Reading in data... Reading data took 6.25637412071 s Creating peak regions... Creating peak regions took 38.8613889217 s Estimating background... Estimating background took 60.9297280312 s Processing LN95_C19_ChIPexo-Rep2-GSM2643248/aligned.36mers.unique.bam Reading in data... Reading data took 6.54676198959 s Creating peak regions... Estimating background took 161.533876896 s Processing LN95_C19_ChIPexo-Rep2-GSM2643248/aligned.36mers.unique.bam Reading in data... Reading data took 15.6952450275 s Creating peak regions... Creating peak regions took 32.3510730267 s Estimating background... Estimating background took 66.7887301445 s Processing LN95_C19_ChIPexo-Rep2-GSM2643248/aligned.36mers.unique.bam Reading in data... Creating peak regions took 77.0980939865 s Estimating background... Reading data took 3.43710613251 s Creating peak regions... Creating peak regions took 19.9542150497 s Estimating background... Estimating background took 20.2400739193 s Processing LN95_C19_ChIPexo-Rep2-GSM2643248/aligned.36mers.unique.bam Reading in data... Reading data took 14.7797429562 s Creating peak regions... Estimating background took 125.173423052 s Processing LN95_C19_ChIPexo-Rep2-GSM2643248/aligned.36mers.unique.bam Reading in data... Reading data took 18.6812520027 s Creating peak regions... Creating peak regions took 87.8827748299 s Estimating background... Creating peak regions took 80.4518220425 s Estimating background... Estimating background took 131.127770901 s Processing LN95_C19_ChIPexo-Rep2-GSM2643248/aligned.36mers.unique.bam Reading in data... Reading data took 4.76317405701 s Creating peak regions... Creating peak regions took 27.5671989918 s Estimating background... Estimating background took 36.8521199226 s Processing LN95_C19_ChIPexo-Rep2-GSM2643248/aligned.36mers.unique.bam Reading in data... Reading data took 2.95433521271 s Creating peak regions... Creating peak regions took 19.0550439358 s Estimating background... Estimating background took 153.834313869 s Processing LN95_C19_ChIPexo-Rep2-GSM2643248/aligned.36mers.unique.bam Reading in data... Estimating background took 19.4357898235 s Processing LN95_C19_ChIPexo-Rep2-GSM2643248/aligned.36mers.unique.bam Reading in data... Reading data took 2.28466320038 s Creating peak regions... Reading data took 14.4252080917 s Creating peak regions... Creating peak regions took 16.5299341679 s Estimating background... Estimating background took 14.0038459301 s Processing LN95_C19_ChIPexo-Rep2-GSM2643248/aligned.36mers.unique.bam Reading in data... Reading data took 15.9547178745 s Creating peak regions... Creating peak regions took 65.1970479488 s Estimating background... Creating peak regions took 77.3090040684 s Estimating background... Estimating background took 94.1059679985 s Processing LN95_C19_ChIPexo-Rep2-GSM2643248/aligned.36mers.unique.bam Reading in data... Reading data took 14.1448330879 s Creating peak regions... Creating peak regions took 68.8797781467 s Estimating background... Estimating background took 169.963249922 s Processing LN95_C19_ChIPexo-Rep2-GSM2643248/aligned.36mers.unique.bam Reading in data... Reading data took 14.7353549004 s Creating peak regions... Estimating background took 121.587417841 s Processing LN95_C19_ChIPexo-Rep2-GSM2643248/aligned.36mers.unique.bam Reading in data... Reading data took 11.3384230137 s Creating peak regions... Creating peak regions took 72.236055851 s Estimating background... Creating peak regions took 61.3254711628 s Estimating background... Estimating background took 129.84484911 s Processing LN95_C19_ChIPexo-Rep2-GSM2643248/aligned.36mers.unique.bam Reading in data... Estimating background took 75.4509940147 s Processing LN95_C19_ChIPexo-Rep2-GSM2643248/aligned.36mers.unique.bam Reading in data... Reading data took 8.20890808105 s Creating peak regions... Reading data took 17.7519621849 s Creating peak regions... Creating peak regions took 48.0575621128 s Estimating background... Creating peak regions took 72.5255229473 s Estimating background... Estimating background took 53.1500039101 s Processing LN95_C19_ChIPexo-Rep2-GSM2643248/aligned.36mers.unique.bam Reading in data... Reading data took 0.672954082489 s Creating peak regions... Creating peak regions took 0.494173049927 s Estimating background... Estimating background took 1.16992282867 s Processing LN95_C19_ChIPexo-Rep2-GSM2643248/aligned.36mers.unique.bam Reading in data... Reading data took 7.09526586533 s Creating peak regions... Creating peak regions took 51.0630581379 s Estimating background... Estimating background took 46.1225130558 s Processing LN95_C19_ChIPexo-Rep2-GSM2643248/aligned.36mers.unique.bam Reading in data... Reading data took 0.611275911331 s Creating peak regions... Creating peak regions took 18.6656110287 s Estimating background... Estimating background took 1.1283659935 s Estimating background took 163.883516073 s Processing LN95_C19_ChIPexo-Rep2-GSM2643248/aligned.36mers.unique.bam Reading in data... Reading data took 12.0556540489 s Creating peak regions... Creating peak regions took 67.8523440361 s Estimating background... Estimating background took 89.2487449646 s Processing LN95_C19_ChIPexo-Rep2-GSM2643248/aligned.36mers.unique.bam Reading in data... Reading data took 13.8129811287 s Creating peak regions... Creating peak regions took 68.2034358978 s Estimating background... Estimating background took 117.122575045 s Processing LN95_C19_ChIPexo-Rep2-GSM2643248/aligned.36mers.unique.bam Reading in data... Reading data took 8.55720877647 s Creating peak regions... Creating peak regions took 50.6607849598 s Estimating background... Estimating background took 71.9032628536 s Processing LN95_C19_ChIPexo-Rep2-GSM2643248/aligned.36mers.unique.bam Reading in data... Reading data took 8.71931099892 s Creating peak regions... Creating peak regions took 49.9143400192 s Estimating background... Estimating background took 57.3618609905 s Processing LN95_C19_ChIPexo-Rep2-GSM2643248/aligned.36mers.unique.bam Reading in data... Reading data took 0.606474161148 s Creating peak regions... Creating peak regions took 0.38639497757 s Estimating background... Estimating background took 1.21743178368 s Processing LN95_C19_ChIPexo-Rep2-GSM2643248/aligned.36mers.unique.bam Reading in data... Reading data took 6.85885500908 s Creating peak regions... Creating peak regions took 46.4982540607 s Estimating background... Estimating background took 42.7708160877 s Processing LN95_C19_ChIPexo-Rep2-GSM2643248/aligned.36mers.unique.bam Reading in data... Reading data took 0.503425121307 s Creating peak regions... Creating peak regions took 14.7908360958 s Estimating background... Estimating background took 0.93610906601 s