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='A17_V7_ChIPexo-GSM2643264/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='A17_V7_ChIPexo-GSM2643264/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='A17_V7_ChIPexo-GSM2643264/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='A17_V7_ChIPexo-GSM2643264/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 A17_V7_ChIPexo-GSM2643264/aligned.36mers.unique.bam Reading in data... Reading data took 23.1898708344 s Creating peak regions... Creating peak regions took 97.5852560997 s Estimating background... Estimating background took 370.128964186 s Processing A17_V7_ChIPexo-GSM2643264/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='A17_V7_ChIPexo-GSM2643264/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='A17_V7_ChIPexo-GSM2643264/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='A17_V7_ChIPexo-GSM2643264/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='A17_V7_ChIPexo-GSM2643264/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 A17_V7_ChIPexo-GSM2643264/aligned.36mers.unique.bam Reading in data... Reading data took 22.6235849857 s Creating peak regions... Creating peak regions took 97.4570109844 s Estimating background... Estimating background took 378.604214907 s Processing A17_V7_ChIPexo-GSM2643264/aligned.36mers.unique.bam Reading in data... Reading data took 16.9746830463 s Creating peak regions... Creating peak regions took 69.0395009518 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='A17_V7_ChIPexo-GSM2643264/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='A17_V7_ChIPexo-GSM2643264/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 A17_V7_ChIPexo-GSM2643264/aligned.36mers.unique.bam Reading in data... Reading data took 22.2479548454 s Creating peak regions... Estimating background took 227.946566105 s Processing A17_V7_ChIPexo-GSM2643264/aligned.36mers.unique.bam Reading in data... Reading data took 20.5200369358 s Creating peak regions... Creating peak regions took 92.4313268661 s Estimating background... Creating peak regions took 71.7772989273 s Estimating background... Estimating background took 299.818614006 s Processing A17_V7_ChIPexo-GSM2643264/aligned.36mers.unique.bam Reading in data... Reading data took 20.6692070961 s Creating peak regions... Estimating background took 374.944777966 s Processing A17_V7_ChIPexo-GSM2643264/aligned.36mers.unique.bam Reading in data... Reading data took 17.650354147 s Creating peak regions... Creating peak regions took 73.2030851841 s Estimating background... Creating peak regions took 70.9007089138 s Estimating background... Estimating background took 206.661820889 s Processing A17_V7_ChIPexo-GSM2643264/aligned.36mers.unique.bam Reading in data... Estimating background took 280.908457994 s Processing A17_V7_ChIPexo-GSM2643264/aligned.36mers.unique.bam Reading in data... Reading data took 17.1418881416 s Creating peak regions... Reading data took 10.3948588371 s Creating peak regions... Creating peak regions took 56.5788960457 s Estimating background... Creating peak regions took 67.8892970085 s Estimating background... Estimating background took 109.097792149 s Processing A17_V7_ChIPexo-GSM2643264/aligned.36mers.unique.bam Reading in data... Reading data took 9.7091050148 s Creating peak regions... Creating peak regions took 46.2249629498 s Estimating background... Estimating background took 266.35506916 s Processing A17_V7_ChIPexo-GSM2643264/aligned.36mers.unique.bam Reading in data... Reading data took 18.423812151 s Creating peak regions... Estimating background took 133.940600872 s Processing A17_V7_ChIPexo-GSM2643264/aligned.36mers.unique.bam Reading in data... Reading data took 9.95025587082 s Creating peak regions... Creating peak regions took 47.3959710598 s Estimating background... Creating peak regions took 65.6272740364 s Estimating background... Estimating background took 113.373870134 s Processing A17_V7_ChIPexo-GSM2643264/aligned.36mers.unique.bam Reading in data... Reading data took 9.55811309814 s Creating peak regions... Creating peak regions took 40.4163751602 s Estimating background... Estimating background took 99.882614851 s Processing A17_V7_ChIPexo-GSM2643264/aligned.36mers.unique.bam Reading in data... Estimating background took 266.498800039 s Processing A17_V7_ChIPexo-GSM2643264/aligned.36mers.unique.bam Reading in data... Reading data took 8.53656792641 s Creating peak regions... Reading data took 9.12249088287 s Creating peak regions... Creating peak regions took 36.4475779533 s Estimating background... Creating peak regions took 47.1653950214 s Estimating background... Estimating background took 87.2982258797 s Processing A17_V7_ChIPexo-GSM2643264/aligned.36mers.unique.bam Reading in data... Reading data took 13.9002768993 s Creating peak regions... Estimating background took 91.9879560471 s Processing A17_V7_ChIPexo-GSM2643264/aligned.36mers.unique.bam Reading in data... Reading data took 9.91863584518 s Creating peak regions... Creating peak regions took 51.4280161858 s Estimating background... Creating peak regions took 43.8103950024 s Estimating background... Estimating background took 118.087167025 s Processing A17_V7_ChIPexo-GSM2643264/aligned.36mers.unique.bam Reading in data... Reading data took 9.31151008606 s Creating peak regions... Estimating background took 167.241494894 s Processing A17_V7_ChIPexo-GSM2643264/aligned.36mers.unique.bam Reading in data... Reading data took 5.21836400032 s Creating peak regions... Creating peak regions took 37.3580610752 s Estimating background... Creating peak regions took 27.219684124 s Estimating background... Estimating background took 49.3221049309 s Processing A17_V7_ChIPexo-GSM2643264/aligned.36mers.unique.bam Reading in data... Estimating background took 101.182295084 s Processing A17_V7_ChIPexo-GSM2643264/aligned.36mers.unique.bam Reading in data... Reading data took 31.2261900902 s Creating peak regions... Reading data took 9.24268889427 s Creating peak regions... Creating peak regions took 37.4980919361 s Estimating background... Creating peak regions took 126.636830091 s Estimating background... Estimating background took 90.2213292122 s Processing A17_V7_ChIPexo-GSM2643264/aligned.36mers.unique.bam Reading in data... Reading data took 7.34920120239 s Creating peak regions... Creating peak regions took 35.0681090355 s Estimating background... Estimating background took 75.5197880268 s Processing A17_V7_ChIPexo-GSM2643264/aligned.36mers.unique.bam Reading in data... Reading data took 10.5761210918 s Creating peak regions... Creating peak regions took 39.2572360039 s Estimating background... Estimating background took 163.310035944 s Processing A17_V7_ChIPexo-GSM2643264/aligned.36mers.unique.bam Reading in data... Reading data took 4.90099310875 s Creating peak regions... Creating peak regions took 25.9747469425 s Estimating background... Estimating background took 46.1521430016 s Processing A17_V7_ChIPexo-GSM2643264/aligned.36mers.unique.bam Reading in data... Reading data took 33.4494888783 s Creating peak regions... Creating peak regions took 108.950690985 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='A17_V7_ChIPexo-GSM2643264/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='A17_V7_ChIPexo-GSM2643264/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 A17_V7_ChIPexo-GSM2643264/aligned.36mers.unique.bam Reading in data... Reading data took 25.277451992 s Creating peak regions... Creating peak regions took 94.8975031376 s Estimating background... Estimating background took 386.663561821 s Processing A17_V7_ChIPexo-GSM2643264/aligned.36mers.unique.bam Reading in data... Reading data took 16.9838681221 s Creating peak regions... Creating peak regions took 73.0822160244 s Estimating background... Estimating background took 225.100384951 s Processing A17_V7_ChIPexo-GSM2643264/aligned.36mers.unique.bam Reading in data... Reading data took 19.8179059029 s Creating peak regions... Creating peak regions took 78.203963995 s Estimating background... Estimating background took 300.138802052 s Processing A17_V7_ChIPexo-GSM2643264/aligned.36mers.unique.bam Reading in data... Reading data took 21.4813828468 s Creating peak regions... Creating peak regions took 85.5380010605 s Estimating background... Estimating background took 273.230993032 s Processing A17_V7_ChIPexo-GSM2643264/aligned.36mers.unique.bam Reading in data... Reading data took 9.98147916794 s Creating peak regions... Creating peak regions took 53.5147550106 s Estimating background... Estimating background took 98.234815836 s Processing A17_V7_ChIPexo-GSM2643264/aligned.36mers.unique.bam Reading in data... Reading data took 10.2447340488 s Creating peak regions... Creating peak regions took 51.2517800331 s Estimating background... Estimating background took 130.051632881 s Processing A17_V7_ChIPexo-GSM2643264/aligned.36mers.unique.bam Reading in data... Reading data took 10.5473029613 s Creating peak regions... Creating peak regions took 56.516381979 s Estimating background... Estimating background took 116.762798071 s Processing A17_V7_ChIPexo-GSM2643264/aligned.36mers.unique.bam Reading in data... Reading data took 9.78197002411 s Creating peak regions... Creating peak regions took 49.8048501015 s Estimating background... Estimating background took 101.865286112 s Processing A17_V7_ChIPexo-GSM2643264/aligned.36mers.unique.bam Reading in data... Reading data took 8.35797691345 s Creating peak regions... Creating peak regions took 39.1327910423 s Estimating background... Estimating background took 84.5618350506 s Processing A17_V7_ChIPexo-GSM2643264/aligned.36mers.unique.bam Reading in data... Reading data took 13.0493450165 s Creating peak regions... Creating peak regions took 45.9199159145 s Estimating background... Estimating background took 160.235621929 s Processing A17_V7_ChIPexo-GSM2643264/aligned.36mers.unique.bam Reading in data... Reading data took 5.76113295555 s Creating peak regions... Creating peak regions took 29.8693580627 s Estimating background... Estimating background took 49.3752961159 s Processing A17_V7_ChIPexo-GSM2643264/aligned.36mers.unique.bam Reading in data... Reading data took 30.6509637833 s Creating peak regions... Creating peak regions took 125.479275942 s Estimating background...