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_C19_ChIPexo-Rep1-GSM2643241/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_C19_ChIPexo-Rep1-GSM2643241/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_C19_ChIPexo-Rep1-GSM2643241/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_C19_ChIPexo-Rep1-GSM2643241/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_C19_ChIPexo-Rep1-GSM2643241/aligned.36mers.unique.bam Reading in data... Reading data took 17.626237154 s Creating peak regions... Creating peak regions took 81.1241719723 s Estimating background... Estimating background took 203.323628902 s Processing 22RV1_C19_ChIPexo-Rep1-GSM2643241/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_C19_ChIPexo-Rep1-GSM2643241/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_C19_ChIPexo-Rep1-GSM2643241/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_C19_ChIPexo-Rep1-GSM2643241/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_C19_ChIPexo-Rep1-GSM2643241/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_C19_ChIPexo-Rep1-GSM2643241/aligned.36mers.unique.bam Reading in data... Reading data took 18.7582850456 s Creating peak regions... Creating peak regions took 83.1444821358 s Estimating background... Estimating background took 225.933542013 s Processing 22RV1_C19_ChIPexo-Rep1-GSM2643241/aligned.36mers.unique.bam Reading in data... Reading data took 8.91543889046 s Creating peak regions... Creating peak regions took 42.6578249931 s Estimating background... Estimating background took 61.9407198429 s Processing 22RV1_C19_ChIPexo-Rep1-GSM2643241/aligned.36mers.unique.bam Reading in data... Reading data took 9.42708301544 s Creating peak regions... Creating peak regions took 46.9568989277 s Estimating background... Estimating background took 67.1786930561 s Processing 22RV1_C19_ChIPexo-Rep1-GSM2643241/aligned.36mers.unique.bam Reading in data... Reading data took 13.327684164 s Creating peak regions... Creating peak regions took 52.1047868729 s Estimating background... Estimating background took 134.090180159 s Processing 22RV1_C19_ChIPexo-Rep1-GSM2643241/aligned.36mers.unique.bam Reading in data... Reading data took 8.04958486557 s Creating peak regions... Creating peak regions took 41.4156908989 s Estimating background... Estimating background took 59.7942979336 s Processing 22RV1_C19_ChIPexo-Rep1-GSM2643241/aligned.36mers.unique.bam Reading in data... Reading data took 7.12222099304 s Creating peak regions... Creating peak regions took 38.3230900764 s Estimating background... Estimating background took 46.0256710052 s Processing 22RV1_C19_ChIPexo-Rep1-GSM2643241/aligned.36mers.unique.bam Reading in data... Reading data took 5.61411309242 s Creating peak regions... Creating peak regions took 32.0056169033 s Estimating background... Estimating background took 35.917124033 s Processing 22RV1_C19_ChIPexo-Rep1-GSM2643241/aligned.36mers.unique.bam Reading in data... Reading data took 5.0359890461 s Creating peak regions... Creating peak regions took 32.8609309196 s Estimating background... Estimating background took 32.0009760857 s Processing 22RV1_C19_ChIPexo-Rep1-GSM2643241/aligned.36mers.unique.bam Reading in data... Reading data took 4.78063511848 s Creating peak regions... Creating peak regions took 26.1267139912 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_C19_ChIPexo-Rep1-GSM2643241/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_C19_ChIPexo-Rep1-GSM2643241/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_C19_ChIPexo-Rep1-GSM2643241/aligned.36mers.unique.bam Reading in data... Estimating background took 32.9963779449 s Processing 22RV1_C19_ChIPexo-Rep1-GSM2643241/aligned.36mers.unique.bam Reading in data... Reading data took 20.4449830055 s Creating peak regions... Reading data took 6.25853013992 s Creating peak regions... Creating peak regions took 29.405834198 s Estimating background... Estimating background took 41.7262420654 s Processing 22RV1_C19_ChIPexo-Rep1-GSM2643241/aligned.36mers.unique.bam Reading in data... Reading data took 3.81116986275 s Creating peak regions... Creating peak regions took 98.9106419086 s Estimating background... Creating peak regions took 18.2672929764 s Estimating background... Estimating background took 19.6091551781 s Processing 22RV1_C19_ChIPexo-Rep1-GSM2643241/aligned.36mers.unique.bam Reading in data... Reading data took 13.0424289703 s Creating peak regions... Creating peak regions took 79.7824590206 s Estimating background... Estimating background took 105.904552937 s Processing 22RV1_C19_ChIPexo-Rep1-GSM2643241/aligned.36mers.unique.bam Reading in data... Reading data took 4.96758508682 s Creating peak regions... Estimating background took 231.920655012 s Processing 22RV1_C19_ChIPexo-Rep1-GSM2643241/aligned.36mers.unique.bam Reading in data... Reading data took 9.10354089737 s Creating peak regions... Creating peak regions took 25.965736866 s Estimating background... Estimating background took 29.3526859283 s Processing 22RV1_C19_ChIPexo-Rep1-GSM2643241/aligned.36mers.unique.bam Reading in data... Reading data took 2.87917304039 s Creating peak regions... Creating peak regions took 51.7917070389 s Estimating background... Creating peak regions took 18.045758009 s Estimating background... Estimating background took 19.5722720623 s Processing 22RV1_C19_ChIPexo-Rep1-GSM2643241/aligned.36mers.unique.bam Reading in data... Reading data took 2.02784109116 s Creating peak regions... Creating peak regions took 16.2821528912 s Estimating background... Estimating background took 12.8787529469 s Processing 22RV1_C19_ChIPexo-Rep1-GSM2643241/aligned.36mers.unique.bam Reading in data... Estimating background took 70.2318608761 s Processing 22RV1_C19_ChIPexo-Rep1-GSM2643241/aligned.36mers.unique.bam Reading in data... Reading data took 16.7824170589 s Creating peak regions... Reading data took 9.80164599419 s Creating peak regions... Creating peak regions took 50.5529739857 s Estimating background... Creating peak regions took 76.1533560753 s Estimating background... Estimating background took 70.9251949787 s Processing 22RV1_C19_ChIPexo-Rep1-GSM2643241/aligned.36mers.unique.bam Reading in data... Reading data took 13.7094159126 s Creating peak regions... Creating peak regions took 57.524271965 s Estimating background... Estimating background took 170.073325872 s Processing 22RV1_C19_ChIPexo-Rep1-GSM2643241/aligned.36mers.unique.bam Reading in data... Reading data took 13.1174769402 s Creating peak regions... Creating peak regions took 64.9369421005 s Estimating background... Estimating background took 142.097113132 s Processing 22RV1_C19_ChIPexo-Rep1-GSM2643241/aligned.36mers.unique.bam Reading in data... Reading data took 8.78999114037 s Creating peak regions... Creating peak regions took 45.507627964 s Estimating background... Estimating background took 105.878921032 s Processing 22RV1_C19_ChIPexo-Rep1-GSM2643241/aligned.36mers.unique.bam Reading in data... Reading data took 12.0727570057 s Creating peak regions... Estimating background took 61.4045548439 s Processing 22RV1_C19_ChIPexo-Rep1-GSM2643241/aligned.36mers.unique.bam Reading in data... Reading data took 7.39926886559 s Creating peak regions... Creating peak regions took 62.8981728554 s Estimating background... Creating peak regions took 41.8643529415 s Estimating background... Estimating background took 48.1395270824 s Processing 22RV1_C19_ChIPexo-Rep1-GSM2643241/aligned.36mers.unique.bam Reading in data... Reading data took 5.76301813126 s Creating peak regions... Creating peak regions took 37.5098121166 s Estimating background... Estimating background took 104.290838003 s Processing 22RV1_C19_ChIPexo-Rep1-GSM2643241/aligned.36mers.unique.bam Reading in data... Reading data took 14.4116618633 s Creating peak regions... Estimating background took 40.3755497932 s Processing 22RV1_C19_ChIPexo-Rep1-GSM2643241/aligned.36mers.unique.bam Reading in data... Reading data took 4.78417301178 s Creating peak regions... Creating peak regions took 30.9920198917 s Estimating background... Creating peak regions took 62.8744311333 s Estimating background... Estimating background took 32.3870270252 s Processing 22RV1_C19_ChIPexo-Rep1-GSM2643241/aligned.36mers.unique.bam Reading in data... Reading data took 5.01396799088 s Creating peak regions... Creating peak regions took 29.1059389114 s Estimating background... Estimating background took 34.4460110664 s Processing 22RV1_C19_ChIPexo-Rep1-GSM2643241/aligned.36mers.unique.bam Reading in data... Reading data took 6.53906416893 s Creating peak regions... Estimating background took 97.8250539303 s Processing 22RV1_C19_ChIPexo-Rep1-GSM2643241/aligned.36mers.unique.bam Reading in data... Reading data took 14.4885828495 s Creating peak regions... Creating peak regions took 32.9010090828 s Estimating background... Estimating background took 45.169244051 s Processing 22RV1_C19_ChIPexo-Rep1-GSM2643241/aligned.36mers.unique.bam Reading in data... Creating peak regions took 60.9828820229 s Estimating background... Reading data took 3.72573208809 s Creating peak regions... Creating peak regions took 20.3279030323 s Estimating background... Estimating background took 22.4346790314 s Processing 22RV1_C19_ChIPexo-Rep1-GSM2643241/aligned.36mers.unique.bam Reading in data... Reading data took 13.2641530037 s Creating peak regions... Creating peak regions took 83.2203860283 s Estimating background... Estimating background took 156.336493015 s Processing 22RV1_C19_ChIPexo-Rep1-GSM2643241/aligned.36mers.unique.bam Reading in data... Reading data took 14.6226620674 s Creating peak regions... Creating peak regions took 61.3193700314 s Estimating background... Estimating background took 110.538878918 s Processing 22RV1_C19_ChIPexo-Rep1-GSM2643241/aligned.36mers.unique.bam Reading in data... Reading data took 4.55857992172 s Creating peak regions... Creating peak regions took 29.6983590126 s Estimating background... Estimating background took 28.2613060474 s Processing 22RV1_C19_ChIPexo-Rep1-GSM2643241/aligned.36mers.unique.bam Reading in data... Reading data took 3.19196581841 s Creating peak regions... Creating peak regions took 19.763780117 s Estimating background... Estimating background took 22.443887949 s Processing 22RV1_C19_ChIPexo-Rep1-GSM2643241/aligned.36mers.unique.bam Reading in data... Reading data took 2.56363511086 s Creating peak regions... Estimating background took 139.331854105 s Processing 22RV1_C19_ChIPexo-Rep1-GSM2643241/aligned.36mers.unique.bam Reading in data... Creating peak regions took 17.2764611244 s Estimating background... Reading data took 8.70103192329 s Creating peak regions... Estimating background took 14.2687699795 s Processing 22RV1_C19_ChIPexo-Rep1-GSM2643241/aligned.36mers.unique.bam Reading in data... Reading data took 19.0632209778 s Creating peak regions... Creating peak regions took 51.2548408508 s Estimating background... Estimating background took 58.972452879 s Processing 22RV1_C19_ChIPexo-Rep1-GSM2643241/aligned.36mers.unique.bam Reading in data... Reading data took 0.683256864548 s Creating peak regions... Creating peak regions took 0.497323989868 s Estimating background... Estimating background took 1.18469190598 s Processing 22RV1_C19_ChIPexo-Rep1-GSM2643241/aligned.36mers.unique.bam Reading in data... Creating peak regions took 85.1199309826 s Estimating background... Reading data took 6.2737569809 s Creating peak regions... Creating peak regions took 48.0925829411 s Estimating background... Estimating background took 27.218640089 s Processing 22RV1_C19_ChIPexo-Rep1-GSM2643241/aligned.36mers.unique.bam Reading in data... Reading data took 1.16476798058 s Creating peak regions... Creating peak regions took 18.3734018803 s Estimating background... Estimating background took 3.29466295242 s Estimating background took 190.648125887 s Processing 22RV1_C19_ChIPexo-Rep1-GSM2643241/aligned.36mers.unique.bam Reading in data... Reading data took 14.8267240524 s Creating peak regions... Creating peak regions took 80.97199893 s Estimating background... Estimating background took 114.076378107 s Processing 22RV1_C19_ChIPexo-Rep1-GSM2643241/aligned.36mers.unique.bam Reading in data... Reading data took 13.5454490185 s Creating peak regions... Creating peak regions took 71.1515951157 s Estimating background... Estimating background took 111.518859148 s Processing 22RV1_C19_ChIPexo-Rep1-GSM2643241/aligned.36mers.unique.bam Reading in data... Reading data took 14.1754539013 s Creating peak regions... Creating peak regions took 66.394149065 s Estimating background... Estimating background took 98.3787600994 s Processing 22RV1_C19_ChIPexo-Rep1-GSM2643241/aligned.36mers.unique.bam Reading in data... Reading data took 17.0386509895 s Creating peak regions... Creating peak regions took 74.0250849724 s Estimating background... Estimating background took 153.182195187 s Processing 22RV1_C19_ChIPexo-Rep1-GSM2643241/aligned.36mers.unique.bam Reading in data... Reading data took 16.8743839264 s Creating peak regions... Creating peak regions took 69.0561459064 s Estimating background... Estimating background took 144.531281948 s Processing 22RV1_C19_ChIPexo-Rep1-GSM2643241/aligned.36mers.unique.bam Reading in data... Reading data took 9.85076212883 s Creating peak regions... Creating peak regions took 55.2297258377 s Estimating background... Estimating background took 57.4681601524 s Processing 22RV1_C19_ChIPexo-Rep1-GSM2643241/aligned.36mers.unique.bam Reading in data... Reading data took 0.6439640522 s Creating peak regions... Creating peak regions took 0.455842018127 s Estimating background... Estimating background took 1.19813513756 s Processing 22RV1_C19_ChIPexo-Rep1-GSM2643241/aligned.36mers.unique.bam Reading in data... Reading data took 6.30757284164 s Creating peak regions... Creating peak regions took 49.8889601231 s Estimating background... Estimating background took 28.1610820293 s Processing 22RV1_C19_ChIPexo-Rep1-GSM2643241/aligned.36mers.unique.bam Reading in data... Reading data took 0.991420984268 s Creating peak regions... Creating peak regions took 23.7128098011 s Estimating background... Estimating background took 5.9858880043 s