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='ZNF799-SRR5197251.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='ZNF799-SRR5197251/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 ZNF799-SRR5197251.hg20-male.36mers.unique.bam Reading in data... Reading data took 4.04422497749 s Creating peak regions... Creating peak regions took 60.6387739182 s Estimating background... Estimating background took 25.9960720539 s Processing ZNF799-SRR5197251.hg20-male.36mers.unique.bam Reading in data... Reading data took 1.85781311989 s Creating peak regions... Creating peak regions took 32.9033651352 s Estimating background... Estimating background took 11.1021471024 s Processing ZNF799-SRR5197251.hg20-male.36mers.unique.bam Reading in data... Reading data took 1.81321716309 s Creating peak regions... Creating peak regions took 33.7306988239 s Estimating background... Estimating background took 11.2341659069 s Processing ZNF799-SRR5197251.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='ZNF799-SRR5197251.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='ZNF799-SRR5197251/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 ZNF799-SRR5197251.hg20-male.36mers.unique.bam Reading in data... Reading data took 4.10541200638 s Creating peak regions... Creating peak regions took 71.4496400356 s Estimating background... Estimating background took 27.737760067 s Processing ZNF799-SRR5197251.hg20-male.36mers.unique.bam Reading in data... Reading data took 2.12843990326 s Creating peak regions... Creating peak regions took 37.8188641071 s Estimating background... Estimating background took 11.3488581181 s Processing ZNF799-SRR5197251.hg20-male.36mers.unique.bam Reading in data... Reading data took 2.12689208984 s Creating peak regions... Creating peak regions took 40.7008299828 s Estimating background... Estimating background took 10.8739528656 s Processing ZNF799-SRR5197251.hg20-male.36mers.unique.bam Reading in data... Reading data took 2.35900878906 s Creating peak regions... Creating peak regions took 38.5765321255 s Estimating background... Estimating background took 11.6669020653 s Processing ZNF799-SRR5197251.hg20-male.36mers.unique.bam Reading in data... Reading data took 1.77554297447 s Creating peak regions... Creating peak regions took 31.2348890305 s Estimating background... Estimating background took 12.5538167953 s Processing ZNF799-SRR5197251.hg20-male.36mers.unique.bam Reading in data... Reading data took 1.40573191643 s Creating peak regions... Creating peak regions took 31.6728990078 s Estimating background... Estimating background took 7.63381695747 s Processing ZNF799-SRR5197251.hg20-male.36mers.unique.bam Reading in data... Reading data took 1.46685814857 s Creating peak regions... Creating peak regions took 27.4543318748 s Estimating background... Estimating background took 9.40694880486 s Processing ZNF799-SRR5197251.hg20-male.36mers.unique.bam Reading in data... Reading data took 1.37167096138 s Creating peak regions... Creating peak regions took 24.4026610851 s Estimating background... Estimating background took 7.954433918 s Processing ZNF799-SRR5197251.hg20-male.36mers.unique.bam Reading in data... Reading data took 1.50011897087 s Creating peak regions... Creating peak regions took 22.6434161663 s Estimating background... Estimating background took 9.93105006218 s Processing ZNF799-SRR5197251.hg20-male.36mers.unique.bam Reading in data... Reading data took 1.14103412628 s Creating peak regions... Creating peak regions took 22.8916921616 s Estimating background... Estimating background took 6.22169089317 s Processing ZNF799-SRR5197251.hg20-male.36mers.unique.bam Reading in data... Reading data took 1.05111289024 s Creating peak regions... Creating peak regions took 17.185667038 s Estimating background... Estimating background took 6.50995087624 s Processing ZNF799-SRR5197251.hg20-male.36mers.unique.bam Reading in data... Reading data took 3.47378110886 s Creating peak regions... Creating peak regions took 65.7926330566 s Estimating background... Estimating background took 18.271515131 s Processing ZNF799-SRR5197251.hg20-male.36mers.unique.bam Reading in data... Reading data took 1.00958490372 s Creating peak regions... Creating peak regions took 17.9156041145 s Estimating background... Estimating background took 6.15428614616 s Processing ZNF799-SRR5197251.hg20-male.36mers.unique.bam Reading in data... Reading data took 0.540551900864 s Creating peak regions... Creating peak regions took 11.7743558884 s Estimating background... Estimating background took 3.80105900764 s Processing ZNF799-SRR5197251.hg20-male.36mers.unique.bam Reading in data... Reading data took 0.843483924866 s Creating peak regions... Creating peak regions took 14.4825649261 s Estimating background... Estimating background took 6.03113913536 s Processing ZNF799-SRR5197251.hg20-male.36mers.unique.bam Reading in data... Reading data took 2.73055100441 s Creating peak regions... Creating peak regions took 53.9621479511 s Estimating background... Estimating background took 14.3770718575 s Processing ZNF799-SRR5197251.hg20-male.36mers.unique.bam Reading in data... Reading data took 2.26305294037 s Creating peak regions... Creating peak regions took 50.8403849602 s Estimating background... Estimating background took 12.1489651203 s Processing ZNF799-SRR5197251.hg20-male.36mers.unique.bam Reading in data... Reading data took 2.56639790535 s Creating peak regions... Creating peak regions took 49.137057066 s Estimating background... Estimating background took 14.3172330856 s Processing ZNF799-SRR5197251.hg20-male.36mers.unique.bam Reading in data... Reading data took 2.72445702553 s Creating peak regions... Creating peak regions took 47.3609359264 s Estimating background... Estimating background took 15.6577990055 s Processing ZNF799-SRR5197251.hg20-male.36mers.unique.bam Reading in data... Reading data took 2.53117394447 s Creating peak regions... Creating peak regions took 43.5546219349 s Estimating background... Estimating background took 14.0525801182 s Processing ZNF799-SRR5197251.hg20-male.36mers.unique.bam Reading in data... Reading data took 2.28605103493 s Creating peak regions... Creating peak regions took 42.1556658745 s Estimating background... Estimating background took 10.6359820366 s Processing ZNF799-SRR5197251.hg20-male.36mers.unique.bam Reading in data... Reading data took 1.81868815422 s Creating peak regions... Creating peak regions took 39.0998880863 s Estimating background... Estimating background took 10.1074290276 s Processing ZNF799-SRR5197251.hg20-male.36mers.unique.bam Reading in data... Reading data took 0.0760698318481 s Creating peak regions... Creating peak regions took 0.146697998047 s Estimating background... Estimating background took 0.536812782288 s Processing ZNF799-SRR5197251.hg20-male.36mers.unique.bam Reading in data... Reading data took 2.54558086395 s Creating peak regions... Creating peak regions took 45.3670139313 s Estimating background... Estimating background took 13.976514101 s Processing ZNF799-SRR5197251.hg20-male.36mers.unique.bam Reading in data... Reading data took 0.0979161262512 s Creating peak regions... Creating peak regions took 14.1294178963 s Estimating background... Estimating background took 0.573450088501 s