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='ZNF555-SRR5197176.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='ZNF555-SRR5197176/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 ZNF555-SRR5197176.hg20-male.36mers.unique.bam Reading in data... Reading data took 7.39829707146 s Creating peak regions... Creating peak regions took 78.2036340237 s Estimating background... Estimating background took 48.0629458427 s Processing ZNF555-SRR5197176.hg20-male.36mers.unique.bam Reading in data... Reading data took 3.8411450386 s Creating peak regions... Creating peak regions took 42.659940958 s Estimating background... Estimating background took 20.2700440884 s Processing ZNF555-SRR5197176.hg20-male.36mers.unique.bam Reading in data... Reading data took 3.44264316559 s Creating peak regions... Creating peak regions took 40.4475870132 s Estimating background... Estimating background took 16.3454720974 s Processing ZNF555-SRR5197176.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='ZNF555-SRR5197176.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='ZNF555-SRR5197176/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 ZNF555-SRR5197176.hg20-male.36mers.unique.bam Reading in data... Reading data took 6.84946489334 s Creating peak regions... Creating peak regions took 78.6419959068 s Estimating background... Estimating background took 47.2019510269 s Processing ZNF555-SRR5197176.hg20-male.36mers.unique.bam Reading in data... Reading data took 3.68950581551 s Creating peak regions... Creating peak regions took 43.2058150768 s Estimating background... Estimating background took 19.8616220951 s Processing ZNF555-SRR5197176.hg20-male.36mers.unique.bam Reading in data... Reading data took 3.53777098656 s Creating peak regions... Creating peak regions took 41.8957719803 s Estimating background... Estimating background took 18.0635700226 s Processing ZNF555-SRR5197176.hg20-male.36mers.unique.bam Reading in data... Reading data took 4.07745218277 s Creating peak regions... Creating peak regions took 40.7579731941 s Estimating background... Estimating background took 20.7512359619 s Processing ZNF555-SRR5197176.hg20-male.36mers.unique.bam Reading in data... Reading data took 3.63772511482 s Creating peak regions... Creating peak regions took 35.993721962 s Estimating background... Estimating background took 25.9555828571 s Processing ZNF555-SRR5197176.hg20-male.36mers.unique.bam Reading in data... Reading data took 2.51603794098 s Creating peak regions... Creating peak regions took 32.564111948 s Estimating background... Estimating background took 12.7123470306 s Processing ZNF555-SRR5197176.hg20-male.36mers.unique.bam Reading in data... Reading data took 2.23431396484 s Creating peak regions... Creating peak regions took 32.4134771824 s Estimating background... Estimating background took 13.0040419102 s Processing ZNF555-SRR5197176.hg20-male.36mers.unique.bam Reading in data... Reading data took 2.37557911873 s Creating peak regions... Creating peak regions took 27.0388429165 s Estimating background... Estimating background took 12.7196481228 s Processing ZNF555-SRR5197176.hg20-male.36mers.unique.bam Reading in data... Reading data took 2.6528570652 s Creating peak regions... Creating peak regions took 27.5996408463 s Estimating background... Estimating background took 15.7424271107 s Processing ZNF555-SRR5197176.hg20-male.36mers.unique.bam Reading in data... Reading data took 1.95975494385 s Creating peak regions... Creating peak regions took 25.7592749596 s Estimating background... Estimating background took 10.6705849171 s Processing ZNF555-SRR5197176.hg20-male.36mers.unique.bam Reading in data... Reading data took 1.81102991104 s Creating peak regions... Creating peak regions took 19.5327260494 s Estimating background... Estimating background took 10.4948270321 s Processing ZNF555-SRR5197176.hg20-male.36mers.unique.bam Reading in data... Reading data took 5.93160390854 s Creating peak regions... Creating peak regions took 78.9411420822 s Estimating background... Estimating background took 32.6982049942 s Processing ZNF555-SRR5197176.hg20-male.36mers.unique.bam Reading in data... Reading data took 1.90136909485 s Creating peak regions... Creating peak regions took 21.1388089657 s Estimating background... Estimating background took 10.8288719654 s Processing ZNF555-SRR5197176.hg20-male.36mers.unique.bam Reading in data... Reading data took 1.2325899601 s Creating peak regions... Creating peak regions took 14.2723350525 s Estimating background... Estimating background took 6.87682914734 s Processing ZNF555-SRR5197176.hg20-male.36mers.unique.bam Reading in data... Reading data took 1.41013288498 s Creating peak regions... Creating peak regions took 16.1458370686 s Estimating background... Estimating background took 9.1190598011 s Processing ZNF555-SRR5197176.hg20-male.36mers.unique.bam Reading in data... Reading data took 5.11021494865 s Creating peak regions... Creating peak regions took 64.1005930901 s Estimating background... Estimating background took 26.6286530495 s Processing ZNF555-SRR5197176.hg20-male.36mers.unique.bam Reading in data... Reading data took 4.44887900352 s Creating peak regions... Creating peak regions took 58.0047399998 s Estimating background... Estimating background took 22.7099499702 s Processing ZNF555-SRR5197176.hg20-male.36mers.unique.bam Reading in data... Reading data took 4.83021306992 s Creating peak regions... Creating peak regions took 55.6420359612 s Estimating background... Estimating background took 25.6050438881 s Processing ZNF555-SRR5197176.hg20-male.36mers.unique.bam Reading in data... Reading data took 5.02402710915 s Creating peak regions... Creating peak regions took 53.5494029522 s Estimating background... Estimating background took 28.7879099846 s Processing ZNF555-SRR5197176.hg20-male.36mers.unique.bam Reading in data... Reading data took 4.69792222977 s Creating peak regions... Creating peak regions took 49.3852679729 s Estimating background... Estimating background took 25.6968960762 s Processing ZNF555-SRR5197176.hg20-male.36mers.unique.bam Reading in data... Reading data took 3.88652515411 s Creating peak regions... Creating peak regions took 44.1527769566 s Estimating background... Estimating background took 18.0269510746 s Processing ZNF555-SRR5197176.hg20-male.36mers.unique.bam Reading in data... Reading data took 3.1281440258 s Creating peak regions... Creating peak regions took 43.5814740658 s Estimating background... Estimating background took 16.7252469063 s Processing ZNF555-SRR5197176.hg20-male.36mers.unique.bam Reading in data... Reading data took 0.104377985001 s Creating peak regions... Creating peak regions took 0.181082010269 s Estimating background... Estimating background took 0.541302919388 s Processing ZNF555-SRR5197176.hg20-male.36mers.unique.bam Reading in data... Reading data took 4.5819208622 s Creating peak regions... Creating peak regions took 51.4297449589 s Estimating background... Estimating background took 28.5267059803 s Processing ZNF555-SRR5197176.hg20-male.36mers.unique.bam Reading in data... Reading data took 0.219452857971 s Creating peak regions... Creating peak regions took 16.1675579548 s Estimating background... Estimating background took 0.952038049698 s