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='ZNF737-SRR5197228.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='ZNF737-SRR5197228/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 ZNF737-SRR5197228.hg20-male.36mers.unique.bam Reading in data... Reading data took 3.22014284134 s Creating peak regions... Creating peak regions took 60.8851480484 s Estimating background... Estimating background took 17.9496188164 s Processing ZNF737-SRR5197228.hg20-male.36mers.unique.bam Reading in data... Reading data took 1.45353794098 s Creating peak regions... Creating peak regions took 32.0757410526 s Estimating background... Estimating background took 8.32675981522 s Processing ZNF737-SRR5197228.hg20-male.36mers.unique.bam Reading in data... Reading data took 1.45184993744 s Creating peak regions... Creating peak regions took 32.7074911594 s Estimating background... Estimating background took 8.36205601692 s Processing ZNF737-SRR5197228.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='ZNF737-SRR5197228.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='ZNF737-SRR5197228/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 ZNF737-SRR5197228.hg20-male.36mers.unique.bam Reading in data... Reading data took 4.12085700035 s Creating peak regions... Creating peak regions took 75.7423670292 s Estimating background... Estimating background took 22.7412359715 s Processing ZNF737-SRR5197228.hg20-male.36mers.unique.bam Reading in data... Reading data took 1.98225808144 s Creating peak regions... Creating peak regions took 38.8093450069 s Estimating background... Estimating background took 9.90083909035 s Processing ZNF737-SRR5197228.hg20-male.36mers.unique.bam Reading in data... Reading data took 1.87210607529 s Creating peak regions... Creating peak regions took 38.4398519993 s Estimating background... Estimating background took 9.70707607269 s Processing ZNF737-SRR5197228.hg20-male.36mers.unique.bam Reading in data... Reading data took 2.07499098778 s Creating peak regions... Creating peak regions took 38.316947937 s Estimating background... Estimating background took 10.0434200764 s Processing ZNF737-SRR5197228.hg20-male.36mers.unique.bam Reading in data... Reading data took 1.77440190315 s Creating peak regions... Creating peak regions took 33.0265600681 s Estimating background... Estimating background took 10.0613460541 s Processing ZNF737-SRR5197228.hg20-male.36mers.unique.bam Reading in data... Reading data took 1.39651083946 s Creating peak regions... Creating peak regions took 32.2157509327 s Estimating background... Estimating background took 6.76829218864 s Processing ZNF737-SRR5197228.hg20-male.36mers.unique.bam Reading in data... Reading data took 1.23163700104 s Creating peak regions... Creating peak regions took 30.5410840511 s Estimating background... Estimating background took 7.15850186348 s Processing ZNF737-SRR5197228.hg20-male.36mers.unique.bam Reading in data... Reading data took 1.38178515434 s Creating peak regions... Creating peak regions took 27.5416810513 s Estimating background... Estimating background took 7.12784123421 s Processing ZNF737-SRR5197228.hg20-male.36mers.unique.bam Reading in data... Reading data took 1.50980997086 s Creating peak regions... Creating peak regions took 24.1612131596 s Estimating background... Estimating background took 8.27970790863 s Processing ZNF737-SRR5197228.hg20-male.36mers.unique.bam Reading in data... Reading data took 1.04327392578 s Creating peak regions... Creating peak regions took 24.4826431274 s Estimating background... Estimating background took 5.42353796959 s Processing ZNF737-SRR5197228.hg20-male.36mers.unique.bam Reading in data... Reading data took 1.0728290081 s Creating peak regions... Creating peak regions took 17.7840919495 s Estimating background... Estimating background took 5.76813411713 s Processing ZNF737-SRR5197228.hg20-male.36mers.unique.bam Reading in data... Reading data took 3.25942397118 s Creating peak regions... Creating peak regions took 74.5845849514 s Estimating background... Estimating background took 16.0197839737 s Processing ZNF737-SRR5197228.hg20-male.36mers.unique.bam Reading in data... Reading data took 1.21882796288 s Creating peak regions... Creating peak regions took 19.2100789547 s Estimating background... Estimating background took 5.62893390656 s Processing ZNF737-SRR5197228.hg20-male.36mers.unique.bam Reading in data... Reading data took 0.56166100502 s Creating peak regions... Creating peak regions took 14.5789980888 s Estimating background... Estimating background took 3.47505879402 s Processing ZNF737-SRR5197228.hg20-male.36mers.unique.bam Reading in data... Reading data took 0.872229814529 s Creating peak regions... Creating peak regions took 14.5374560356 s Estimating background... Estimating background took 5.59132099152 s Processing ZNF737-SRR5197228.hg20-male.36mers.unique.bam Reading in data... Reading data took 2.66616106033 s Creating peak regions... Creating peak regions took 61.4424269199 s Estimating background... Estimating background took 13.0052790642 s Processing ZNF737-SRR5197228.hg20-male.36mers.unique.bam Reading in data... Reading data took 2.23777604103 s Creating peak regions... Creating peak regions took 57.5985369682 s Estimating background... Estimating background took 10.5329329967 s Processing ZNF737-SRR5197228.hg20-male.36mers.unique.bam Reading in data... Reading data took 2.50403499603 s Creating peak regions... Creating peak regions took 52.1034240723 s Estimating background... Estimating background took 12.7393360138 s Processing ZNF737-SRR5197228.hg20-male.36mers.unique.bam Reading in data... Reading data took 2.72244811058 s Creating peak regions... Creating peak regions took 52.471200943 s Estimating background... Estimating background took 13.3394870758 s Processing ZNF737-SRR5197228.hg20-male.36mers.unique.bam Reading in data... Reading data took 2.39840221405 s Creating peak regions... Creating peak regions took 49.2554781437 s Estimating background... Estimating background took 12.2768371105 s Processing ZNF737-SRR5197228.hg20-male.36mers.unique.bam Reading in data... Reading data took 1.90513586998 s Creating peak regions... Creating peak regions took 44.7699151039 s Estimating background... Estimating background took 9.02885699272 s Processing ZNF737-SRR5197228.hg20-male.36mers.unique.bam Reading in data... Reading data took 1.68586492538 s Creating peak regions... Creating peak regions took 37.2184929848 s Estimating background... Estimating background took 9.02686095238 s Processing ZNF737-SRR5197228.hg20-male.36mers.unique.bam Reading in data... Reading data took 0.0816941261292 s Creating peak regions... Creating peak regions took 0.147411108017 s Estimating background... Estimating background took 0.527930021286 s Processing ZNF737-SRR5197228.hg20-male.36mers.unique.bam Reading in data... Reading data took 2.48936891556 s Creating peak regions... Creating peak regions took 47.7380971909 s Estimating background... Estimating background took 12.8048629761 s Processing ZNF737-SRR5197228.hg20-male.36mers.unique.bam Reading in data... Reading data took 0.0965421199799 s Creating peak regions... Creating peak regions took 15.0481789112 s Estimating background... Estimating background took 0.574499130249 s