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='A3_V7_ChIPexo-GSM2643268/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='A3_V7_ChIPexo-GSM2643268/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='A3_V7_ChIPexo-GSM2643268/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='A3_V7_ChIPexo-GSM2643268/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 A3_V7_ChIPexo-GSM2643268/aligned.36mers.unique.bam Reading in data... Reading data took 16.8221931458 s Creating peak regions... Creating peak regions took 85.7059469223 s Estimating background... Estimating background took 204.205128193 s Processing A3_V7_ChIPexo-GSM2643268/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='A3_V7_ChIPexo-GSM2643268/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='A3_V7_ChIPexo-GSM2643268/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='A3_V7_ChIPexo-GSM2643268/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='A3_V7_ChIPexo-GSM2643268/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 A3_V7_ChIPexo-GSM2643268/aligned.36mers.unique.bam Reading in data... Reading data took 16.4373879433 s Creating peak regions... Creating peak regions took 88.8380880356 s Estimating background... Estimating background took 218.310135841 s Processing A3_V7_ChIPexo-GSM2643268/aligned.36mers.unique.bam Reading in data... Reading data took 12.0496330261 s Creating peak regions... Creating peak regions took 62.813421011 s Estimating background... Estimating background took 120.61344099 s Processing A3_V7_ChIPexo-GSM2643268/aligned.36mers.unique.bam Reading in data... Reading data took 14.3600430489 s Creating peak regions... Creating peak regions took 64.406550169 s Estimating background... Estimating background took 162.23032999 s Processing A3_V7_ChIPexo-GSM2643268/aligned.36mers.unique.bam Reading in data... Reading data took 14.2116189003 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='A3_V7_ChIPexo-GSM2643268/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='A3_V7_ChIPexo-GSM2643268/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 A3_V7_ChIPexo-GSM2643268/aligned.36mers.unique.bam Reading in data... Reading data took 15.6985888481 s Creating peak regions... Creating peak regions took 58.6847119331 s Estimating background... Creating peak regions took 83.1377968788 s Estimating background... Estimating background took 147.995780945 s Processing A3_V7_ChIPexo-GSM2643268/aligned.36mers.unique.bam Reading in data... Reading data took 8.2427880764 s Creating peak regions... Creating peak regions took 45.3213851452 s Estimating background... Estimating background took 208.658472061 s Processing A3_V7_ChIPexo-GSM2643268/aligned.36mers.unique.bam Reading in data... Reading data took 10.9027760029 s Creating peak regions... Estimating background took 74.615033865 s Processing A3_V7_ChIPexo-GSM2643268/aligned.36mers.unique.bam Reading in data... Reading data took 9.48387217522 s Creating peak regions... Creating peak regions took 45.3025949001 s Estimating background... Creating peak regions took 67.8081159592 s Estimating background... Estimating background took 114.531069994 s Processing A3_V7_ChIPexo-GSM2643268/aligned.36mers.unique.bam Reading in data... Reading data took 6.31835222244 s Creating peak regions... Estimating background took 118.042259932 s Processing A3_V7_ChIPexo-GSM2643268/aligned.36mers.unique.bam Reading in data... Reading data took 12.8396360874 s Creating peak regions... Creating peak regions took 40.8857409954 s Estimating background... Creating peak regions took 62.1586699486 s Estimating background... Estimating background took 56.9031310081 s Processing A3_V7_ChIPexo-GSM2643268/aligned.36mers.unique.bam Reading in data... Reading data took 6.45981311798 s Creating peak regions... Creating peak regions took 37.9535357952 s Estimating background... Estimating background took 47.1989130974 s Processing A3_V7_ChIPexo-GSM2643268/aligned.36mers.unique.bam Reading in data... Reading data took 7.8432559967 s Creating peak regions... Creating peak regions took 34.0400650501 s Estimating background... Estimating background took 154.209982872 s Processing A3_V7_ChIPexo-GSM2643268/aligned.36mers.unique.bam Reading in data... Reading data took 12.4278879166 s Creating peak regions... Creating peak regions took 56.0947711468 s Estimating background... Estimating background took 90.9945709705 s Processing A3_V7_ChIPexo-GSM2643268/aligned.36mers.unique.bam Reading in data... Reading data took 10.0788700581 s Creating peak regions... Creating peak regions took 39.784309864 s Estimating background... Estimating background took 163.160546064 s Processing A3_V7_ChIPexo-GSM2643268/aligned.36mers.unique.bam Reading in data... Reading data took 8.49375605583 s Creating peak regions... Estimating background took 113.000061035 s Processing A3_V7_ChIPexo-GSM2643268/aligned.36mers.unique.bam Reading in data... Reading data took 5.82258319855 s Creating peak regions... Creating peak regions took 44.5806190968 s Estimating background... Creating peak regions took 26.884087801 s Estimating background... Estimating background took 46.4674720764 s Processing A3_V7_ChIPexo-GSM2643268/aligned.36mers.unique.bam Reading in data... Reading data took 19.8131392002 s Creating peak regions... Estimating background took 72.103374958 s Processing A3_V7_ChIPexo-GSM2643268/aligned.36mers.unique.bam Reading in data... Reading data took 8.81267595291 s Creating peak regions... Creating peak regions took 45.5960350037 s Estimating background... Creating peak regions took 103.534955025 s Estimating background... Estimating background took 118.403510809 s Processing A3_V7_ChIPexo-GSM2643268/aligned.36mers.unique.bam Reading in data... Reading data took 8.07920598984 s Creating peak regions... Creating peak regions took 41.6099469662 s Estimating background... Estimating background took 53.5610198975 s Processing A3_V7_ChIPexo-GSM2643268/aligned.36mers.unique.bam Reading in data... Reading data took 5.45143604279 s Creating peak regions... Creating peak regions took 34.8129680157 s Estimating background... Estimating background took 217.503584146 s Processing A3_V7_ChIPexo-GSM2643268/aligned.36mers.unique.bam Reading in data... Reading data took 8.02140212059 s Creating peak regions... Creating peak regions took 32.3470611572 s Estimating background... Estimating background took 47.8494410515 s Processing A3_V7_ChIPexo-GSM2643268/aligned.36mers.unique.bam Reading in data... Reading data took 7.31912016869 s Creating peak regions... Creating peak regions took 34.6270051003 s Estimating background... Estimating background took 71.9925010204 s Processing A3_V7_ChIPexo-GSM2643268/aligned.36mers.unique.bam Reading in data... Reading data took 5.90407800674 s Creating peak regions... Creating peak regions took 21.692027092 s Estimating background... Estimating background took 90.5935239792 s Processing A3_V7_ChIPexo-GSM2643268/aligned.36mers.unique.bam Reading in data... Reading data took 9.16663980484 s Creating peak regions... Estimating background took 58.3819458485 s Processing A3_V7_ChIPexo-GSM2643268/aligned.36mers.unique.bam Reading in data... Reading data took 2.57245492935 s Creating peak regions... Creating peak regions took 17.5171940327 s Estimating background... Creating peak regions took 35.9332230091 s Estimating background... Estimating background took 19.4912700653 s Processing A3_V7_ChIPexo-GSM2643268/aligned.36mers.unique.bam Reading in data... Reading data took 21.7339258194 s Creating peak regions... Estimating background took 111.236648798 s Processing A3_V7_ChIPexo-GSM2643268/aligned.36mers.unique.bam Reading in data... Reading data took 4.89656090736 s Creating peak regions... Creating peak regions took 94.395829916 s Estimating background... Creating peak regions took 24.5747461319 s Estimating background... Estimating background took 49.9077889919 s Processing A3_V7_ChIPexo-GSM2643268/aligned.36mers.unique.bam Reading in data... Reading data took 18.8199179173 s Creating peak regions... Creating peak regions took 92.0231220722 s Estimating background... Estimating background took 272.109854937 s Processing A3_V7_ChIPexo-GSM2643268/aligned.36mers.unique.bam Reading in data... Reading data took 16.6344821453 s Creating peak regions... Creating peak regions took 79.1170270443 s Estimating background... Estimating background took 211.101742029 s Processing A3_V7_ChIPexo-GSM2643268/aligned.36mers.unique.bam Reading in data... Reading data took 7.14511108398 s Creating peak regions... Creating peak regions took 34.8211028576 s Estimating background... Estimating background took 76.262983799 s Processing A3_V7_ChIPexo-GSM2643268/aligned.36mers.unique.bam Reading in data... Reading data took 4.96140599251 s Creating peak regions... Estimating background took 146.379305124 s Processing A3_V7_ChIPexo-GSM2643268/aligned.36mers.unique.bam Reading in data... Creating peak regions took 22.3660001755 s Estimating background... Reading data took 18.4845130444 s Creating peak regions... Estimating background took 55.0881419182 s Processing A3_V7_ChIPexo-GSM2643268/aligned.36mers.unique.bam Reading in data... Reading data took 2.72945904732 s Creating peak regions... Creating peak regions took 17.0973181725 s Estimating background... Creating peak regions took 84.9171750546 s Estimating background... Estimating background took 19.8413250446 s Processing A3_V7_ChIPexo-GSM2643268/aligned.36mers.unique.bam Reading in data... Reading data took 17.680357933 s Creating peak regions... Creating peak regions took 79.8887281418 s Estimating background... Estimating background took 203.367126942 s Processing A3_V7_ChIPexo-GSM2643268/aligned.36mers.unique.bam Reading in data... Reading data took 19.4316420555 s Creating peak regions... Creating peak regions took 78.5623569489 s Estimating background... Estimating background took 263.960120201 s Processing A3_V7_ChIPexo-GSM2643268/aligned.36mers.unique.bam Reading in data... Reading data took 15.2265841961 s Creating peak regions... Creating peak regions took 78.5793850422 s Estimating background... Estimating background took 172.614681005 s Processing A3_V7_ChIPexo-GSM2643268/aligned.36mers.unique.bam Reading in data... Reading data took 19.7798960209 s Creating peak regions... Creating peak regions took 77.9007658958 s Estimating background... Estimating background took 136.61126399 s Processing A3_V7_ChIPexo-GSM2643268/aligned.36mers.unique.bam Reading in data... Reading data took 14.676404953 s Creating peak regions... Creating peak regions took 68.6663529873 s Estimating background... Estimating background took 239.78259778 s Processing A3_V7_ChIPexo-GSM2643268/aligned.36mers.unique.bam Reading in data... Reading data took 33.0005819798 s Creating peak regions... Estimating background took 171.711433887 s Processing A3_V7_ChIPexo-GSM2643268/aligned.36mers.unique.bam Reading in data... Reading data took 14.6535730362 s Creating peak regions... Creating peak regions took 69.030151844 s Estimating background... Creating peak regions took 99.5147621632 s Estimating background... Estimating background took 138.01709199 s Processing A3_V7_ChIPexo-GSM2643268/aligned.36mers.unique.bam Reading in data... Reading data took 15.5398910046 s Creating peak regions... Creating peak regions took 64.5198500156 s Estimating background... Estimating background took 202.110255957 s Processing A3_V7_ChIPexo-GSM2643268/aligned.36mers.unique.bam Reading in data... Reading data took 28.0239210129 s Creating peak regions... Estimating background took 505.036442041 s Processing A3_V7_ChIPexo-GSM2643268/aligned.36mers.unique.bam Reading in data... Reading data took 17.3371460438 s Creating peak regions... Creating peak regions took 85.676281929 s Estimating background... Creating peak regions took 79.7204301357 s Estimating background... Estimating background took 164.375590086 s Processing A3_V7_ChIPexo-GSM2643268/aligned.36mers.unique.bam Reading in data... Reading data took 1.20631194115 s Creating peak regions... Creating peak regions took 0.535789012909 s Estimating background... Estimating background took 1.52710604668 s Processing A3_V7_ChIPexo-GSM2643268/aligned.36mers.unique.bam Reading in data... Reading data took 11.5195729733 s Creating peak regions... Creating peak regions took 56.4592440128 s Estimating background... Estimating background took 79.4252688885 s Processing A3_V7_ChIPexo-GSM2643268/aligned.36mers.unique.bam Reading in data... Reading data took 2.10764288902 s Creating peak regions... Estimating background took 400.315402985 s Processing A3_V7_ChIPexo-GSM2643268/aligned.36mers.unique.bam Reading in data... Reading data took 12.4337770939 s Creating peak regions... Creating peak regions took 32.0533089638 s Estimating background... Estimating background took 10.6828739643 s Creating peak regions took 57.5666210651 s Estimating background... Estimating background took 145.29962492 s Processing A3_V7_ChIPexo-GSM2643268/aligned.36mers.unique.bam Reading in data... Reading data took 1.08477497101 s Creating peak regions... Creating peak regions took 0.612847089767 s Estimating background... Estimating background took 1.2574660778 s Processing A3_V7_ChIPexo-GSM2643268/aligned.36mers.unique.bam Reading in data... Reading data took 9.83536815643 s Creating peak regions... Creating peak regions took 53.0304169655 s Estimating background... Estimating background took 62.8274829388 s Processing A3_V7_ChIPexo-GSM2643268/aligned.36mers.unique.bam Reading in data... Reading data took 1.28225493431 s Creating peak regions... Creating peak regions took 17.1353690624 s Estimating background... Estimating background took 5.2575750351 s