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_HoxB13_ChIPexo-Rep2-GSM2643250/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_HoxB13_ChIPexo-Rep2-GSM2643250/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_HoxB13_ChIPexo-Rep2-GSM2643250/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_HoxB13_ChIPexo-Rep2-GSM2643250/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_HoxB13_ChIPexo-Rep2-GSM2643250/aligned.36mers.unique.bam Reading in data... Reading data took 19.0094509125 s Creating peak regions... Creating peak regions took 95.3635110855 s Estimating background... Estimating background took 212.103741884 s Processing LN95_HoxB13_ChIPexo-Rep2-GSM2643250/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_HoxB13_ChIPexo-Rep2-GSM2643250/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_HoxB13_ChIPexo-Rep2-GSM2643250/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_HoxB13_ChIPexo-Rep2-GSM2643250/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_HoxB13_ChIPexo-Rep2-GSM2643250/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_HoxB13_ChIPexo-Rep2-GSM2643250/aligned.36mers.unique.bam Reading in data... Reading data took 15.002810955 s Creating peak regions... Creating peak regions took 78.4490470886 s Estimating background... Estimating background took 196.399217129 s Processing LN95_HoxB13_ChIPexo-Rep2-GSM2643250/aligned.36mers.unique.bam Reading in data... Reading data took 10.1955058575 s Creating peak regions... Creating peak regions took 53.335018158 s Estimating background... Estimating background took 75.865655899 s Processing LN95_HoxB13_ChIPexo-Rep2-GSM2643250/aligned.36mers.unique.bam Reading in data... Reading data took 9.45007395744 s Creating peak regions... Creating peak regions took 52.3749527931 s Estimating background... Estimating background took 89.680243969 s Processing LN95_HoxB13_ChIPexo-Rep2-GSM2643250/aligned.36mers.unique.bam Reading in data... Reading data took 9.0241689682 s Creating peak regions... Creating peak regions took 49.3458900452 s Estimating background... Estimating background took 89.4897968769 s Processing LN95_HoxB13_ChIPexo-Rep2-GSM2643250/aligned.36mers.unique.bam Reading in data... Reading data took 6.10229301453 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_HoxB13_ChIPexo-Rep2-GSM2643250/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_HoxB13_ChIPexo-Rep2-GSM2643250/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 44.9128820896 s Estimating background... Testing that input files exist...done! Processing LN95_HoxB13_ChIPexo-Rep2-GSM2643250/aligned.36mers.unique.bam Reading in data... Reading data took 14.3542180061 s Creating peak regions... Estimating background took 46.6017420292 s Processing LN95_HoxB13_ChIPexo-Rep2-GSM2643250/aligned.36mers.unique.bam Reading in data... Reading data took 5.28093695641 s Creating peak regions... Creating peak regions took 34.3714010715 s Estimating background... Creating peak regions took 80.3339660168 s Estimating background... Estimating background took 44.9640340805 s Processing LN95_HoxB13_ChIPexo-Rep2-GSM2643250/aligned.36mers.unique.bam Reading in data... Reading data took 4.97581291199 s Creating peak regions... Creating peak regions took 34.8115170002 s Estimating background... Estimating background took 43.2758290768 s Processing LN95_HoxB13_ChIPexo-Rep2-GSM2643250/aligned.36mers.unique.bam Reading in data... Reading data took 3.81087803841 s Creating peak regions... Creating peak regions took 29.390253067 s Estimating background... Estimating background took 24.3461620808 s Processing LN95_HoxB13_ChIPexo-Rep2-GSM2643250/aligned.36mers.unique.bam Reading in data... Reading data took 4.75301718712 s Creating peak regions... Estimating background took 194.28438592 s Processing LN95_HoxB13_ChIPexo-Rep2-GSM2643250/aligned.36mers.unique.bam Reading in data... Reading data took 9.72373795509 s Creating peak regions... Creating peak regions took 31.3113069534 s Estimating background... Estimating background took 42.3308401108 s Processing LN95_HoxB13_ChIPexo-Rep2-GSM2643250/aligned.36mers.unique.bam Reading in data... Reading data took 5.47854685783 s Creating peak regions... Creating peak regions took 66.0747740269 s Estimating background... Creating peak regions took 30.0516889095 s Estimating background... Estimating background took 50.6124520302 s Processing LN95_HoxB13_ChIPexo-Rep2-GSM2643250/aligned.36mers.unique.bam Reading in data... Reading data took 2.36515498161 s Creating peak regions... Estimating background took 80.3628540039 s Processing LN95_HoxB13_ChIPexo-Rep2-GSM2643250/aligned.36mers.unique.bam Reading in data... Creating peak regions took 18.5114979744 s Estimating background... Reading data took 9.95449113846 s Creating peak regions... Estimating background took 10.8775830269 s Processing LN95_HoxB13_ChIPexo-Rep2-GSM2643250/aligned.36mers.unique.bam Reading in data... Reading data took 13.3448941708 s Creating peak regions... Creating peak regions took 54.2962479591 s Estimating background... Creating peak regions took 86.3512279987 s Estimating background... Estimating background took 89.8994960785 s Processing LN95_HoxB13_ChIPexo-Rep2-GSM2643250/aligned.36mers.unique.bam Reading in data... Reading data took 9.72819399834 s Creating peak regions... Creating peak regions took 55.4036622047 s Estimating background... Estimating background took 118.628593922 s Processing LN95_HoxB13_ChIPexo-Rep2-GSM2643250/aligned.36mers.unique.bam Reading in data... Reading data took 4.93564510345 s Creating peak regions... Creating peak regions took 26.5474691391 s Estimating background... Estimating background took 29.3609409332 s Processing LN95_HoxB13_ChIPexo-Rep2-GSM2643250/aligned.36mers.unique.bam Reading in data... Reading data took 2.22447800636 s Creating peak regions... Estimating background took 93.1622669697 s Processing LN95_HoxB13_ChIPexo-Rep2-GSM2643250/aligned.36mers.unique.bam Reading in data... Creating peak regions took 15.5364539623 s Estimating background... Reading data took 5.71953511238 s Creating peak regions... Estimating background took 16.922852993 s Processing LN95_HoxB13_ChIPexo-Rep2-GSM2643250/aligned.36mers.unique.bam Reading in data... Reading data took 1.50494599342 s Creating peak regions... Creating peak regions took 14.4701440334 s Estimating background... Estimating background took 10.879322052 s Processing LN95_HoxB13_ChIPexo-Rep2-GSM2643250/aligned.36mers.unique.bam Reading in data... Creating peak regions took 39.921284914 s Estimating background... Reading data took 12.1860020161 s Creating peak regions... Estimating background took 44.089564085 s Processing LN95_HoxB13_ChIPexo-Rep2-GSM2643250/aligned.36mers.unique.bam Reading in data... Reading data took 4.53231096268 s Creating peak regions... Creating peak regions took 64.2236790657 s Estimating background... Creating peak regions took 34.7296788692 s Estimating background... Estimating background took 43.3463590145 s Processing LN95_HoxB13_ChIPexo-Rep2-GSM2643250/aligned.36mers.unique.bam Reading in data... Reading data took 4.56913089752 s Creating peak regions... Creating peak regions took 33.2698428631 s Estimating background... Estimating background took 134.12175107 s Estimating background took 45.7475309372 s Processing LN95_HoxB13_ChIPexo-Rep2-GSM2643250/aligned.36mers.unique.bam Reading in data... Processing LN95_HoxB13_ChIPexo-Rep2-GSM2643250/aligned.36mers.unique.bam Reading in data... Reading data took 3.6672129631 s Creating peak regions... Reading data took 10.7755839825 s Creating peak regions... Creating peak regions took 28.9329791069 s Estimating background... Estimating background took 27.6788220406 s Processing LN95_HoxB13_ChIPexo-Rep2-GSM2643250/aligned.36mers.unique.bam Reading in data... Reading data took 4.49959802628 s Creating peak regions... Creating peak regions took 63.9600319862 s Estimating background... Creating peak regions took 27.4594449997 s Estimating background... Estimating background took 44.7845489979 s Processing LN95_HoxB13_ChIPexo-Rep2-GSM2643250/aligned.36mers.unique.bam Reading in data... Reading data took 4.87799406052 s Creating peak regions... Creating peak regions took 25.5195550919 s Estimating background... Estimating background took 107.047632933 s Processing LN95_HoxB13_ChIPexo-Rep2-GSM2643250/aligned.36mers.unique.bam Reading in data... Reading data took 13.1951470375 s Creating peak regions... Estimating background took 51.7083828449 s Processing LN95_HoxB13_ChIPexo-Rep2-GSM2643250/aligned.36mers.unique.bam Reading in data... Reading data took 1.9881541729 s Creating peak regions... Creating peak regions took 18.3555219173 s Estimating background... Estimating background took 12.4706850052 s Processing LN95_HoxB13_ChIPexo-Rep2-GSM2643250/aligned.36mers.unique.bam Reading in data... Reading data took 11.4111759663 s Creating peak regions... Creating peak regions took 70.74812603 s Estimating background... Creating peak regions took 81.292498827 s Estimating background... Estimating background took 133.673336029 s Processing LN95_HoxB13_ChIPexo-Rep2-GSM2643250/aligned.36mers.unique.bam Reading in data... Reading data took 11.663779974 s Creating peak regions... Estimating background took 122.919950962 s Processing LN95_HoxB13_ChIPexo-Rep2-GSM2643250/aligned.36mers.unique.bam Reading in data... Reading data took 3.13840913773 s Creating peak regions... Creating peak regions took 63.6598329544 s Estimating background... Creating peak regions took 22.867483139 s Estimating background... Estimating background took 27.7575199604 s Processing LN95_HoxB13_ChIPexo-Rep2-GSM2643250/aligned.36mers.unique.bam Reading in data... Reading data took 1.91935896873 s Creating peak regions... Creating peak regions took 14.8076529503 s Estimating background... Estimating background took 17.971091032 s Processing LN95_HoxB13_ChIPexo-Rep2-GSM2643250/aligned.36mers.unique.bam Reading in data... Reading data took 1.4033010006 s Creating peak regions... Estimating background took 90.7101590633 s Processing LN95_HoxB13_ChIPexo-Rep2-GSM2643250/aligned.36mers.unique.bam Reading in data... Creating peak regions took 15.3987739086 s Estimating background... Reading data took 10.4160089493 s Creating peak regions... Estimating background took 9.96448493004 s Processing LN95_HoxB13_ChIPexo-Rep2-GSM2643250/aligned.36mers.unique.bam Reading in data... Reading data took 11.3634579182 s Creating peak regions... Creating peak regions took 54.0223960876 s Estimating background... Creating peak regions took 70.3047468662 s Estimating background... Estimating background took 101.282196999 s Processing LN95_HoxB13_ChIPexo-Rep2-GSM2643250/aligned.36mers.unique.bam Reading in data... Reading data took 8.21784210205 s Creating peak regions... Creating peak regions took 52.4215221405 s Estimating background... Estimating background took 138.018394947 s Processing LN95_HoxB13_ChIPexo-Rep2-GSM2643250/aligned.36mers.unique.bam Reading in data... Reading data took 11.6318440437 s Creating peak regions... Estimating background took 66.247148037 s Processing LN95_HoxB13_ChIPexo-Rep2-GSM2643250/aligned.36mers.unique.bam Reading in data... Reading data took 6.77924895287 s Creating peak regions... Creating peak regions took 67.1845510006 s Estimating background... Creating peak regions took 51.8928809166 s Estimating background... Estimating background took 52.7904160023 s Processing LN95_HoxB13_ChIPexo-Rep2-GSM2643250/aligned.36mers.unique.bam Reading in data... Reading data took 0.823685884476 s Creating peak regions... Creating peak regions took 0.453892946243 s Estimating background... Estimating background took 1.50416088104 s Processing LN95_HoxB13_ChIPexo-Rep2-GSM2643250/aligned.36mers.unique.bam Reading in data... Reading data took 7.75230002403 s Creating peak regions... Estimating background took 104.213031054 s Processing LN95_HoxB13_ChIPexo-Rep2-GSM2643250/aligned.36mers.unique.bam Reading in data... Reading data took 12.6879799366 s Creating peak regions... Creating peak regions took 56.6103918552 s Estimating background... Creating peak regions took 74.8378880024 s Estimating background... Estimating background took 46.5087800026 s Processing LN95_HoxB13_ChIPexo-Rep2-GSM2643250/aligned.36mers.unique.bam Reading in data... Reading data took 0.546881914139 s Creating peak regions... Creating peak regions took 20.0558578968 s Estimating background... Estimating background took 0.964024066925 s Estimating background took 131.292433023 s Processing LN95_HoxB13_ChIPexo-Rep2-GSM2643250/aligned.36mers.unique.bam Reading in data... Reading data took 8.79902005196 s Creating peak regions... Creating peak regions took 62.34628582 s Estimating background... Estimating background took 90.7718379498 s Processing LN95_HoxB13_ChIPexo-Rep2-GSM2643250/aligned.36mers.unique.bam Reading in data... Reading data took 10.6396689415 s Creating peak regions... Creating peak regions took 61.4561109543 s Estimating background... Estimating background took 108.304535151 s Processing LN95_HoxB13_ChIPexo-Rep2-GSM2643250/aligned.36mers.unique.bam Reading in data... Reading data took 8.06628584862 s Creating peak regions... Creating peak regions took 48.5517020226 s Estimating background... Estimating background took 67.1978268623 s Processing LN95_HoxB13_ChIPexo-Rep2-GSM2643250/aligned.36mers.unique.bam Reading in data... Reading data took 6.5470969677 s Creating peak regions... Creating peak regions took 46.5467908382 s Estimating background... Estimating background took 49.1048648357 s Processing LN95_HoxB13_ChIPexo-Rep2-GSM2643250/aligned.36mers.unique.bam Reading in data... Reading data took 0.613608837128 s Creating peak regions... Creating peak regions took 0.467615842819 s Estimating background... Estimating background took 3.15963411331 s Processing LN95_HoxB13_ChIPexo-Rep2-GSM2643250/aligned.36mers.unique.bam Reading in data... Reading data took 4.98572587967 s Creating peak regions... Creating peak regions took 48.398444891 s Estimating background... Estimating background took 41.4856741428 s Processing LN95_HoxB13_ChIPexo-Rep2-GSM2643250/aligned.36mers.unique.bam Reading in data... Reading data took 0.145424127579 s Creating peak regions... Creating peak regions took 14.5196139812 s Estimating background... Estimating background took 0.793915987015 s