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='ZNF558-SRR5197178.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='ZNF558-SRR5197178/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 ZNF558-SRR5197178.hg20-male.36mers.unique.bam Reading in data... Reading data took 6.44717502594 s Creating peak regions... Creating peak regions took 77.7542359829 s Estimating background... Estimating background took 48.0401771069 s Processing ZNF558-SRR5197178.hg20-male.36mers.unique.bam Reading in data... Reading data took 3.38668894768 s Creating peak regions... Creating peak regions took 42.9706602097 s Estimating background... Estimating background took 18.9055058956 s Processing ZNF558-SRR5197178.hg20-male.36mers.unique.bam Reading in data... Reading data took 3.36461901665 s Creating peak regions... Creating peak regions took 40.0935120583 s Estimating background... Estimating background took 17.2567288876 s Processing ZNF558-SRR5197178.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='ZNF558-SRR5197178.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='ZNF558-SRR5197178/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 ZNF558-SRR5197178.hg20-male.36mers.unique.bam Reading in data... Reading data took 6.10779809952 s Creating peak regions... Creating peak regions took 78.0242440701 s Estimating background... Estimating background took 47.4248490334 s Processing ZNF558-SRR5197178.hg20-male.36mers.unique.bam Reading in data... Reading data took 3.04029798508 s Creating peak regions... Creating peak regions took 41.8594181538 s Estimating background... Estimating background took 19.1884498596 s Processing ZNF558-SRR5197178.hg20-male.36mers.unique.bam Reading in data... Reading data took 3.10396981239 s Creating peak regions... Creating peak regions took 40.9078040123 s Estimating background... Estimating background took 19.5619139671 s Processing ZNF558-SRR5197178.hg20-male.36mers.unique.bam Reading in data... Reading data took 3.06458902359 s Creating peak regions... Creating peak regions took 40.744289875 s Estimating background... Estimating background took 20.0586290359 s Processing ZNF558-SRR5197178.hg20-male.36mers.unique.bam Reading in data... Reading data took 2.62466907501 s Creating peak regions... Creating peak regions took 34.5495018959 s Estimating background... Estimating background took 16.6292309761 s Processing ZNF558-SRR5197178.hg20-male.36mers.unique.bam Reading in data... Reading data took 2.11339306831 s Creating peak regions... Creating peak regions took 33.457597971 s Estimating background... Estimating background took 12.7266530991 s Processing ZNF558-SRR5197178.hg20-male.36mers.unique.bam Reading in data... Reading data took 2.20727801323 s Creating peak regions... Creating peak regions took 30.1106522083 s Estimating background... Estimating background took 14.9560530186 s Processing ZNF558-SRR5197178.hg20-male.36mers.unique.bam Reading in data... Reading data took 2.25501322746 s Creating peak regions... Creating peak regions took 27.1459739208 s Estimating background... Estimating background took 15.5689070225 s Processing ZNF558-SRR5197178.hg20-male.36mers.unique.bam Reading in data... Reading data took 2.71878695488 s Creating peak regions... Creating peak regions took 26.2515530586 s Estimating background... Estimating background took 19.8847548962 s Processing ZNF558-SRR5197178.hg20-male.36mers.unique.bam Reading in data... Reading data took 1.61227798462 s Creating peak regions... Creating peak regions took 23.8923330307 s Estimating background... Estimating background took 8.88770985603 s Processing ZNF558-SRR5197178.hg20-male.36mers.unique.bam Reading in data... Reading data took 2.18377399445 s Creating peak regions... Creating peak regions took 18.4237978458 s Estimating background... Estimating background took 15.4422807693 s Processing ZNF558-SRR5197178.hg20-male.36mers.unique.bam Reading in data... Reading data took 4.99458813667 s Creating peak regions... Creating peak regions took 73.1570379734 s Estimating background... Estimating background took 31.1099720001 s Processing ZNF558-SRR5197178.hg20-male.36mers.unique.bam Reading in data... Reading data took 1.75315308571 s Creating peak regions... Creating peak regions took 20.698526144 s Estimating background... Estimating background took 12.2372179031 s Processing ZNF558-SRR5197178.hg20-male.36mers.unique.bam Reading in data... Reading data took 0.950877189636 s Creating peak regions... Creating peak regions took 13.95429492 s Estimating background... Estimating background took 6.11156511307 s Processing ZNF558-SRR5197178.hg20-male.36mers.unique.bam Reading in data... Reading data took 1.64640402794 s Creating peak regions... Creating peak regions took 16.6258859634 s Estimating background... Estimating background took 13.5075719357 s Processing ZNF558-SRR5197178.hg20-male.36mers.unique.bam Reading in data... Reading data took 4.01092386246 s Creating peak regions... Creating peak regions took 56.6503469944 s Estimating background... Estimating background took 22.9958860874 s Processing ZNF558-SRR5197178.hg20-male.36mers.unique.bam Reading in data... Reading data took 3.23521304131 s Creating peak regions... Creating peak regions took 59.5613148212 s Estimating background... Estimating background took 17.1455619335 s Processing ZNF558-SRR5197178.hg20-male.36mers.unique.bam Reading in data... Reading data took 3.7214319706 s Creating peak regions... Creating peak regions took 57.84562397 s Estimating background... Estimating background took 22.7185800076 s Processing ZNF558-SRR5197178.hg20-male.36mers.unique.bam Reading in data... Reading data took 3.97598195076 s Creating peak regions... Creating peak regions took 51.6692578793 s Estimating background... Estimating background took 25.1126220226 s Processing ZNF558-SRR5197178.hg20-male.36mers.unique.bam Reading in data... Reading data took 3.84280896187 s Creating peak regions... Creating peak regions took 48.3785860538 s Estimating background... Estimating background took 24.7628259659 s Processing ZNF558-SRR5197178.hg20-male.36mers.unique.bam Reading in data... Reading data took 3.00394701958 s Creating peak regions... Creating peak regions took 42.6744241714 s Estimating background... Estimating background took 16.6849179268 s Processing ZNF558-SRR5197178.hg20-male.36mers.unique.bam Reading in data... Reading data took 2.83743786812 s Creating peak regions... Creating peak regions took 41.3812220097 s Estimating background... Estimating background took 17.9801459312 s Processing ZNF558-SRR5197178.hg20-male.36mers.unique.bam Reading in data... Reading data took 0.100471973419 s Creating peak regions... Creating peak regions took 0.188727855682 s Estimating background... Estimating background took 0.693769931793 s Processing ZNF558-SRR5197178.hg20-male.36mers.unique.bam Reading in data... Reading data took 3.49309706688 s Creating peak regions... Creating peak regions took 46.5653569698 s Estimating background... Estimating background took 21.7303390503 s Processing ZNF558-SRR5197178.hg20-male.36mers.unique.bam Reading in data... Reading data took 0.172752857208 s Creating peak regions... Creating peak regions took 15.1410648823 s Estimating background... Estimating background took 0.550422906876 s