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/hg38.blacklist.bed', center6=0, chromnames='/oak/stanford/groups/akundaje/marinovg/genomes/hg20/hg38.chrom.sizes', e4='PeakXus', fastq='ZNF443-SRR5197144.hg20-male.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='ZNF443-SRR5197144/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 ZNF443-SRR5197144.hg20-male.36mers.unique.bam Reading in data... Reading data took 3.9617099762 s Creating peak regions... Creating peak regions took 74.6973268986 s Estimating background... Estimating background took 22.2256500721 s Processing ZNF443-SRR5197144.hg20-male.36mers.unique.bam Reading in data... Reading data took 2.51679182053 s Creating peak regions... Creating peak regions took 38.9360809326 s Estimating background... Estimating background took 9.70407295227 s Processing ZNF443-SRR5197144.hg20-male.36mers.unique.bam Reading in data... Reading data took 1.96574211121 s Creating peak regions... Creating peak regions took 39.1498630047 s Estimating background... Estimating background took 9.51935720444 s Processing ZNF443-SRR5197144.hg20-male.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/hg38.blacklist.bed', center6=0, chromnames='/oak/stanford/groups/akundaje/marinovg/genomes/hg20/hg38-male.chrom.sizes', e4='PeakXus', fastq='ZNF443-SRR5197144.hg20-male.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='ZNF443-SRR5197144/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 ZNF443-SRR5197144.hg20-male.36mers.unique.bam Reading in data... Reading data took 4.05056715012 s Creating peak regions... Creating peak regions took 73.4381608963 s Estimating background... Estimating background took 23.5741200447 s Processing ZNF443-SRR5197144.hg20-male.36mers.unique.bam Reading in data... Reading data took 2.01442694664 s Creating peak regions... Creating peak regions took 39.9016361237 s Estimating background... Estimating background took 8.91151618958 s Processing ZNF443-SRR5197144.hg20-male.36mers.unique.bam Reading in data... Reading data took 1.91546607018 s Creating peak regions... Creating peak regions took 39.1800680161 s Estimating background... Estimating background took 10.0957829952 s Processing ZNF443-SRR5197144.hg20-male.36mers.unique.bam Reading in data... Reading data took 2.27560400963 s Creating peak regions... Creating peak regions took 39.4601449966 s Estimating background... Estimating background took 10.6000461578 s Processing ZNF443-SRR5197144.hg20-male.36mers.unique.bam Reading in data... Reading data took 1.69767594337 s Creating peak regions... Creating peak regions took 35.2522120476 s Estimating background... Estimating background took 10.0379059315 s Processing ZNF443-SRR5197144.hg20-male.36mers.unique.bam Reading in data... Reading data took 1.46737504005 s Creating peak regions... Creating peak regions took 30.3122339249 s Estimating background... Estimating background took 6.8709628582 s Processing ZNF443-SRR5197144.hg20-male.36mers.unique.bam Reading in data... Reading data took 1.23256611824 s Creating peak regions... Creating peak regions took 30.821917057 s Estimating background... Estimating background took 7.1974170208 s Processing ZNF443-SRR5197144.hg20-male.36mers.unique.bam Reading in data... Reading data took 1.38085699081 s Creating peak regions... Creating peak regions took 26.9074089527 s Estimating background... Estimating background took 6.93889307976 s Processing ZNF443-SRR5197144.hg20-male.36mers.unique.bam Reading in data... Reading data took 1.48631000519 s Creating peak regions... Creating peak regions took 24.9235751629 s Estimating background... Estimating background took 9.03367185593 s Processing ZNF443-SRR5197144.hg20-male.36mers.unique.bam Reading in data... Reading data took 1.26534104347 s Creating peak regions... Creating peak regions took 21.5798180103 s Estimating background... Estimating background took 5.40204000473 s Processing ZNF443-SRR5197144.hg20-male.36mers.unique.bam Reading in data... Reading data took 1.1894299984 s Creating peak regions... Creating peak regions took 18.4451107979 s Estimating background... Estimating background took 5.96351408958 s Processing ZNF443-SRR5197144.hg20-male.36mers.unique.bam Reading in data... Reading data took 3.45000290871 s Creating peak regions... Creating peak regions took 75.1998040676 s Estimating background... Estimating background took 15.7963750362 s Processing ZNF443-SRR5197144.hg20-male.36mers.unique.bam Reading in data... Reading data took 1.12812709808 s Creating peak regions... Creating peak regions took 19.9660840034 s Estimating background... Estimating background took 6.60310912132 s Processing ZNF443-SRR5197144.hg20-male.36mers.unique.bam Reading in data... Reading data took 0.743755102158 s Creating peak regions... Creating peak regions took 14.7127430439 s Estimating background... Estimating background took 3.63898897171 s Processing ZNF443-SRR5197144.hg20-male.36mers.unique.bam Reading in data... Reading data took 0.921075820923 s Creating peak regions... Creating peak regions took 16.0661978722 s Estimating background... Estimating background took 5.95758414268 s Processing ZNF443-SRR5197144.hg20-male.36mers.unique.bam Reading in data... Reading data took 3.38483715057 s Creating peak regions... Creating peak regions took 60.8767139912 s Estimating background... Estimating background took 13.5625150204 s Processing ZNF443-SRR5197144.hg20-male.36mers.unique.bam Reading in data... Reading data took 2.47687101364 s Creating peak regions... Creating peak regions took 58.1405258179 s Estimating background... Estimating background took 10.4940969944 s Processing ZNF443-SRR5197144.hg20-male.36mers.unique.bam Reading in data... Reading data took 2.93489289284 s Creating peak regions... Creating peak regions took 50.5723659992 s Estimating background... Estimating background took 12.1735439301 s Processing ZNF443-SRR5197144.hg20-male.36mers.unique.bam Reading in data... Reading data took 2.80898594856 s Creating peak regions... Creating peak regions took 54.3007910252 s Estimating background... Estimating background took 14.2484431267 s Processing ZNF443-SRR5197144.hg20-male.36mers.unique.bam Reading in data... Reading data took 2.99588608742 s Creating peak regions... Creating peak regions took 45.6866607666 s Estimating background... Estimating background took 11.9157979488 s Processing ZNF443-SRR5197144.hg20-male.36mers.unique.bam Reading in data... Reading data took 1.97190785408 s Creating peak regions... Creating peak regions took 42.5918200016 s Estimating background... Estimating background took 9.57112407684 s Processing ZNF443-SRR5197144.hg20-male.36mers.unique.bam Reading in data... Reading data took 1.97138500214 s Creating peak regions... Creating peak regions took 43.1728880405 s Estimating background... Estimating background took 9.64633011818 s Processing ZNF443-SRR5197144.hg20-male.36mers.unique.bam Reading in data... Reading data took 0.143414020538 s Creating peak regions... Creating peak regions took 0.154326915741 s Estimating background... Estimating background took 1.04874300957 s Processing ZNF443-SRR5197144.hg20-male.36mers.unique.bam Reading in data... Reading data took 2.31195998192 s Creating peak regions... Creating peak regions took 45.5909340382 s Estimating background... Estimating background took 11.3972759247 s Processing ZNF443-SRR5197144.hg20-male.36mers.unique.bam Reading in data... Reading data took 0.0948581695557 s Creating peak regions... Creating peak regions took 15.4601631165 s Estimating background... Estimating background took 0.600198984146 s