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_HoxB13_ChIPexo-Rep2-GSM2643244/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_HoxB13_ChIPexo-Rep2-GSM2643244/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_HoxB13_ChIPexo-Rep2-GSM2643244/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_HoxB13_ChIPexo-Rep2-GSM2643244/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_HoxB13_ChIPexo-Rep2-GSM2643244/aligned.36mers.unique.bam Reading in data... Reading data took 18.7113928795 s Creating peak regions... Creating peak regions took 83.8121390343 s Estimating background... Estimating background took 265.414824963 s Processing 22RV1_HoxB13_ChIPexo-Rep2-GSM2643244/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_HoxB13_ChIPexo-Rep2-GSM2643244/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_HoxB13_ChIPexo-Rep2-GSM2643244/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_HoxB13_ChIPexo-Rep2-GSM2643244/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_HoxB13_ChIPexo-Rep2-GSM2643244/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_HoxB13_ChIPexo-Rep2-GSM2643244/aligned.36mers.unique.bam Reading in data... Reading data took 17.5646078587 s Creating peak regions... Creating peak regions took 86.6352088451 s Estimating background... Estimating background took 287.245646954 s Processing 22RV1_HoxB13_ChIPexo-Rep2-GSM2643244/aligned.36mers.unique.bam Reading in data... Reading data took 10.0462489128 s Creating peak regions... Creating peak regions took 49.0663280487 s Estimating background... Estimating background took 79.9281330109 s Processing 22RV1_HoxB13_ChIPexo-Rep2-GSM2643244/aligned.36mers.unique.bam Reading in data... Reading data took 9.50962209702 s Creating peak regions... Creating peak regions took 47.2281060219 s Estimating background... Estimating background took 91.4535269737 s Processing 22RV1_HoxB13_ChIPexo-Rep2-GSM2643244/aligned.36mers.unique.bam Reading in data... Reading data took 15.3465559483 s Creating peak regions... Creating peak regions took 62.7685539722 s Estimating background... Estimating background took 187.910392046 s Processing 22RV1_HoxB13_ChIPexo-Rep2-GSM2643244/aligned.36mers.unique.bam Reading in data... Reading data took 10.9602210522 s Creating peak regions... Creating peak regions took 54.8363080025 s Estimating background... Estimating background took 92.4066309929 s Processing 22RV1_HoxB13_ChIPexo-Rep2-GSM2643244/aligned.36mers.unique.bam Reading in data... Reading data took 7.44955897331 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='22RV1_HoxB13_ChIPexo-Rep2-GSM2643244/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_HoxB13_ChIPexo-Rep2-GSM2643244/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_HoxB13_ChIPexo-Rep2-GSM2643244/aligned.36mers.unique.bam Reading in data... Creating peak regions took 49.4784760475 s Estimating background... Reading data took 16.9944369793 s Creating peak regions... Estimating background took 66.3152339458 s Processing 22RV1_HoxB13_ChIPexo-Rep2-GSM2643244/aligned.36mers.unique.bam Reading in data... Reading data took 5.19624185562 s Creating peak regions... Creating peak regions took 80.520742178 s Estimating background... Creating peak regions took 34.1313450336 s Estimating background... Estimating background took 49.2965049744 s Processing 22RV1_HoxB13_ChIPexo-Rep2-GSM2643244/aligned.36mers.unique.bam Reading in data... Reading data took 4.94807505608 s Creating peak regions... Creating peak regions took 32.5966739655 s Estimating background... Estimating background took 33.2197470665 s Processing 22RV1_HoxB13_ChIPexo-Rep2-GSM2643244/aligned.36mers.unique.bam Reading in data... Reading data took 4.10920405388 s Creating peak regions... Creating peak regions took 30.4258990288 s Estimating background... Estimating background took 36.0105268955 s Processing 22RV1_HoxB13_ChIPexo-Rep2-GSM2643244/aligned.36mers.unique.bam Reading in data... Reading data took 5.8811750412 s Creating peak regions... Creating peak regions took 30.1270611286 s Estimating background... Estimating background took 255.656601906 s Processing 22RV1_HoxB13_ChIPexo-Rep2-GSM2643244/aligned.36mers.unique.bam Reading in data... Reading data took 10.0325109959 s Creating peak regions... Estimating background took 60.6818430424 s Processing 22RV1_HoxB13_ChIPexo-Rep2-GSM2643244/aligned.36mers.unique.bam Reading in data... Reading data took 3.08360099792 s Creating peak regions... Creating peak regions took 47.0049641132 s Estimating background... Creating peak regions took 23.6566801071 s Estimating background... Estimating background took 17.0846309662 s Processing 22RV1_HoxB13_ChIPexo-Rep2-GSM2643244/aligned.36mers.unique.bam Reading in data... Reading data took 13.7248260975 s Creating peak regions... Estimating background took 73.4599211216 s Processing 22RV1_HoxB13_ChIPexo-Rep2-GSM2643244/aligned.36mers.unique.bam Reading in data... Reading data took 8.64499497414 s Creating peak regions... Creating peak regions took 86.8340628147 s Estimating background... Creating peak regions took 48.7354059219 s Estimating background... Estimating background took 80.5916190147 s Processing 22RV1_HoxB13_ChIPexo-Rep2-GSM2643244/aligned.36mers.unique.bam Reading in data... Reading data took 13.6494441032 s Creating peak regions... Estimating background took 151.277760983 s Creating peak regions took 56.0193190575 s Estimating background... Processing 22RV1_HoxB13_ChIPexo-Rep2-GSM2643244/aligned.36mers.unique.bam Reading in data... Reading data took 3.77752995491 s Creating peak regions... Creating peak regions took 23.7358491421 s Estimating background... Estimating background took 29.5889310837 s Processing 22RV1_HoxB13_ChIPexo-Rep2-GSM2643244/aligned.36mers.unique.bam Reading in data... Reading data took 3.74544095993 s Creating peak regions... Creating peak regions took 19.0666968822 s Estimating background... Estimating background took 30.8785340786 s Processing 22RV1_HoxB13_ChIPexo-Rep2-GSM2643244/aligned.36mers.unique.bam Reading in data... Reading data took 1.42701601982 s Creating peak regions... Creating peak regions took 16.4284539223 s Estimating background... Estimating background took 11.9304080009 s Processing 22RV1_HoxB13_ChIPexo-Rep2-GSM2643244/aligned.36mers.unique.bam Reading in data... Reading data took 21.749147892 s Creating peak regions... Estimating background took 162.900779963 s Processing 22RV1_HoxB13_ChIPexo-Rep2-GSM2643244/aligned.36mers.unique.bam Reading in data... Reading data took 9.47697901726 s Creating peak regions... Creating peak regions took 45.0763831139 s Estimating background... Creating peak regions took 89.2852289677 s Estimating background... Estimating background took 93.7371449471 s Processing 22RV1_HoxB13_ChIPexo-Rep2-GSM2643244/aligned.36mers.unique.bam Reading in data... Reading data took 6.91579699516 s Creating peak regions... Creating peak regions took 36.799492836 s Estimating background... Estimating background took 63.7502520084 s Processing 22RV1_HoxB13_ChIPexo-Rep2-GSM2643244/aligned.36mers.unique.bam Reading in data... Reading data took 4.72616386414 s Creating peak regions... Creating peak regions took 33.7368910313 s Estimating background... Estimating background took 43.0763218403 s Processing 22RV1_HoxB13_ChIPexo-Rep2-GSM2643244/aligned.36mers.unique.bam Reading in data... Reading data took 3.61663007736 s Creating peak regions... Estimating background took 272.185107946 s Processing 22RV1_HoxB13_ChIPexo-Rep2-GSM2643244/aligned.36mers.unique.bam Reading in data... Creating peak regions took 25.3774199486 s Estimating background... Reading data took 20.3075740337 s Creating peak regions... Estimating background took 29.8755459785 s Processing 22RV1_HoxB13_ChIPexo-Rep2-GSM2643244/aligned.36mers.unique.bam Reading in data... Reading data took 4.14559006691 s Creating peak regions... Creating peak regions took 28.7421891689 s Estimating background... Estimating background took 35.5783920288 s Processing 22RV1_HoxB13_ChIPexo-Rep2-GSM2643244/aligned.36mers.unique.bam Reading in data... Creating peak regions took 89.2221341133 s Estimating background... Reading data took 5.88277101517 s Creating peak regions... Creating peak regions took 32.248344183 s Estimating background... Estimating background took 50.8936750889 s Processing 22RV1_HoxB13_ChIPexo-Rep2-GSM2643244/aligned.36mers.unique.bam Reading in data... Reading data took 2.64898300171 s Creating peak regions... Creating peak regions took 18.7471759319 s Estimating background... Estimating background took 15.302311182 s Processing 22RV1_HoxB13_ChIPexo-Rep2-GSM2643244/aligned.36mers.unique.bam Reading in data... Reading data took 14.1707689762 s Creating peak regions... Estimating background took 189.392076015 s Processing 22RV1_HoxB13_ChIPexo-Rep2-GSM2643244/aligned.36mers.unique.bam Reading in data... Reading data took 16.4658670425 s Creating peak regions... Creating peak regions took 80.2207531929 s Estimating background... Creating peak regions took 77.8976640701 s Estimating background... Estimating background took 142.756029844 s Processing 22RV1_HoxB13_ChIPexo-Rep2-GSM2643244/aligned.36mers.unique.bam Reading in data... Reading data took 3.17817902565 s Creating peak regions... Creating peak regions took 21.4460940361 s Estimating background... Estimating background took 26.9085288048 s Processing 22RV1_HoxB13_ChIPexo-Rep2-GSM2643244/aligned.36mers.unique.bam Reading in data... Reading data took 3.07010006905 s Creating peak regions... Creating peak regions took 18.7156538963 s Estimating background... Estimating background took 148.652760983 s Processing 22RV1_HoxB13_ChIPexo-Rep2-GSM2643244/aligned.36mers.unique.bam Reading in data... Reading data took 13.6216549873 s Creating peak regions... Estimating background took 28.5032417774 s Processing 22RV1_HoxB13_ChIPexo-Rep2-GSM2643244/aligned.36mers.unique.bam Reading in data... Reading data took 1.52426481247 s Creating peak regions... Creating peak regions took 15.983725071 s Estimating background... Estimating background took 10.1005511284 s Processing 22RV1_HoxB13_ChIPexo-Rep2-GSM2643244/aligned.36mers.unique.bam Reading in data... Reading data took 18.6359889507 s Creating peak regions... Creating peak regions took 64.8366839886 s Estimating background... Creating peak regions took 81.3797140121 s Estimating background... Estimating background took 148.239444017 s Processing 22RV1_HoxB13_ChIPexo-Rep2-GSM2643244/aligned.36mers.unique.bam Reading in data... Reading data took 16.0294380188 s Creating peak regions... Creating peak regions took 69.8544409275 s Estimating background... Estimating background took 252.142879963 s Processing 22RV1_HoxB13_ChIPexo-Rep2-GSM2643244/aligned.36mers.unique.bam Reading in data... Reading data took 14.4044260979 s Creating peak regions... Creating peak regions took 64.5019938946 s Estimating background... Estimating background took 205.71577692 s Processing 22RV1_HoxB13_ChIPexo-Rep2-GSM2643244/aligned.36mers.unique.bam Reading in data... Reading data took 15.1599941254 s Creating peak regions... Creating peak regions took 64.4765789509 s Estimating background... Estimating background took 172.626541138 s Processing 22RV1_HoxB13_ChIPexo-Rep2-GSM2643244/aligned.36mers.unique.bam Reading in data... Reading data took 14.1431629658 s Creating peak regions... Creating peak regions took 81.9360048771 s Estimating background... Estimating background took 184.940917015 s Processing 22RV1_HoxB13_ChIPexo-Rep2-GSM2643244/aligned.36mers.unique.bam Reading in data... Reading data took 8.21871709824 s Creating peak regions... Creating peak regions took 50.5442390442 s Estimating background... Estimating background took 133.00561595 s Processing 22RV1_HoxB13_ChIPexo-Rep2-GSM2643244/aligned.36mers.unique.bam Reading in data... Reading data took 11.8499999046 s Creating peak regions... Estimating background took 81.9028038979 s Processing 22RV1_HoxB13_ChIPexo-Rep2-GSM2643244/aligned.36mers.unique.bam Reading in data... Reading data took 0.879417896271 s Creating peak regions... Creating peak regions took 0.691895961761 s Estimating background... Estimating background took 1.22524690628 s Processing 22RV1_HoxB13_ChIPexo-Rep2-GSM2643244/aligned.36mers.unique.bam Reading in data... Reading data took 6.77731609344 s Creating peak regions... Creating peak regions took 63.5329129696 s Estimating background... Creating peak regions took 52.797396183 s Estimating background... Estimating background took 43.8731720448 s Processing 22RV1_HoxB13_ChIPexo-Rep2-GSM2643244/aligned.36mers.unique.bam Reading in data... Reading data took 0.958221912384 s Creating peak regions... Creating peak regions took 18.7374589443 s Estimating background... Estimating background took 3.97568392754 s Estimating background took 130.997125864 s Processing 22RV1_HoxB13_ChIPexo-Rep2-GSM2643244/aligned.36mers.unique.bam Reading in data... Reading data took 14.9391272068 s Creating peak regions... Creating peak regions took 62.5943908691 s Estimating background... Estimating background took 191.354522943 s Processing 22RV1_HoxB13_ChIPexo-Rep2-GSM2643244/aligned.36mers.unique.bam Reading in data... Reading data took 16.4498200417 s Creating peak regions... Creating peak regions took 63.6389558315 s Estimating background... Estimating background took 174.68698287 s Processing 22RV1_HoxB13_ChIPexo-Rep2-GSM2643244/aligned.36mers.unique.bam Reading in data... Reading data took 7.77289009094 s Creating peak regions... Creating peak regions took 47.7124471664 s Estimating background... Estimating background took 69.9280629158 s Processing 22RV1_HoxB13_ChIPexo-Rep2-GSM2643244/aligned.36mers.unique.bam Reading in data... Reading data took 0.51617193222 s Creating peak regions... Creating peak regions took 0.444441080093 s Estimating background... Estimating background took 1.07980394363 s Processing 22RV1_HoxB13_ChIPexo-Rep2-GSM2643244/aligned.36mers.unique.bam Reading in data... Reading data took 6.67709207535 s Creating peak regions... Creating peak regions took 47.2829680443 s Estimating background... Estimating background took 37.6221420765 s Processing 22RV1_HoxB13_ChIPexo-Rep2-GSM2643244/aligned.36mers.unique.bam Reading in data... Reading data took 0.973958969116 s Creating peak regions... Creating peak regions took 17.3527851105 s Estimating background... Estimating background took 6.29626083374 s