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='ZNF468-SRR5197150.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='ZNF468-SRR5197150/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 ZNF468-SRR5197150.hg20-male.36mers.unique.bam Reading in data... Reading data took 3.87757301331 s Creating peak regions... Creating peak regions took 75.3526051044 s Estimating background... Estimating background took 29.1051430702 s Processing ZNF468-SRR5197150.hg20-male.36mers.unique.bam Reading in data... Reading data took 1.96248602867 s Creating peak regions... Creating peak regions took 37.357339859 s Estimating background... Estimating background took 12.4629411697 s Processing ZNF468-SRR5197150.hg20-male.36mers.unique.bam Reading in data... Reading data took 2.01292896271 s Creating peak regions... Creating peak regions took 40.8655180931 s Estimating background... Estimating background took 12.0100169182 s Processing ZNF468-SRR5197150.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='ZNF468-SRR5197150.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='ZNF468-SRR5197150/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 ZNF468-SRR5197150.hg20-male.36mers.unique.bam Reading in data... Reading data took 4.14871501923 s Creating peak regions... Creating peak regions took 65.4113950729 s Estimating background... Estimating background took 26.0523540974 s Processing ZNF468-SRR5197150.hg20-male.36mers.unique.bam Reading in data... Reading data took 1.75992488861 s Creating peak regions... Creating peak regions took 33.7642560005 s Estimating background... Estimating background took 11.091242075 s Processing ZNF468-SRR5197150.hg20-male.36mers.unique.bam Reading in data... Reading data took 1.7246940136 s Creating peak regions... Creating peak regions took 37.2998609543 s Estimating background... Estimating background took 10.8514199257 s Processing ZNF468-SRR5197150.hg20-male.36mers.unique.bam Reading in data... Reading data took 1.89754891396 s Creating peak regions... Creating peak regions took 36.626709938 s Estimating background... Estimating background took 11.8410379887 s Processing ZNF468-SRR5197150.hg20-male.36mers.unique.bam Reading in data... Reading data took 1.34891915321 s Creating peak regions... Creating peak regions took 28.9841780663 s Estimating background... Estimating background took 9.52919316292 s Processing ZNF468-SRR5197150.hg20-male.36mers.unique.bam Reading in data... Reading data took 1.16324806213 s Creating peak regions... Creating peak regions took 26.9124610424 s Estimating background... Estimating background took 7.35666799545 s Processing ZNF468-SRR5197150.hg20-male.36mers.unique.bam Reading in data... Reading data took 1.14049005508 s Creating peak regions... Creating peak regions took 25.9993300438 s Estimating background... Estimating background took 7.9769141674 s Processing ZNF468-SRR5197150.hg20-male.36mers.unique.bam Reading in data... Reading data took 1.33495116234 s Creating peak regions... Creating peak regions took 23.2707850933 s Estimating background... Estimating background took 8.29193711281 s Processing ZNF468-SRR5197150.hg20-male.36mers.unique.bam Reading in data... Reading data took 1.49037003517 s Creating peak regions... Creating peak regions took 21.9998009205 s Estimating background... Estimating background took 11.0435020924 s Processing ZNF468-SRR5197150.hg20-male.36mers.unique.bam Reading in data... Reading data took 0.826997041702 s Creating peak regions... Creating peak regions took 20.1974000931 s Estimating background... Estimating background took 5.32725691795 s Processing ZNF468-SRR5197150.hg20-male.36mers.unique.bam Reading in data... Reading data took 1.12381100655 s Creating peak regions... Creating peak regions took 15.7084000111 s Estimating background... Estimating background took 8.81894183159 s Processing ZNF468-SRR5197150.hg20-male.36mers.unique.bam Reading in data... Reading data took 2.79223799706 s Creating peak regions... Creating peak regions took 66.3623199463 s Estimating background... Estimating background took 16.7174229622 s Processing ZNF468-SRR5197150.hg20-male.36mers.unique.bam Reading in data... Reading data took 0.951431035995 s Creating peak regions... Creating peak regions took 18.6089949608 s Estimating background... Estimating background took 6.7818710804 s Processing ZNF468-SRR5197150.hg20-male.36mers.unique.bam Reading in data... Reading data took 0.651376008987 s Creating peak regions... Creating peak regions took 11.8814210892 s Estimating background... Estimating background took 3.83721208572 s Processing ZNF468-SRR5197150.hg20-male.36mers.unique.bam Reading in data... Reading data took 0.908286094666 s Creating peak regions... Creating peak regions took 14.2397220135 s Estimating background... Estimating background took 7.00712203979 s Processing ZNF468-SRR5197150.hg20-male.36mers.unique.bam Reading in data... Reading data took 2.18209910393 s Creating peak regions... Creating peak regions took 50.7232151031 s Estimating background... Estimating background took 13.6162700653 s Processing ZNF468-SRR5197150.hg20-male.36mers.unique.bam Reading in data... Reading data took 1.95384407043 s Creating peak regions... Creating peak regions took 48.038061142 s Estimating background... Estimating background took 11.2788250446 s Processing ZNF468-SRR5197150.hg20-male.36mers.unique.bam Reading in data... Reading data took 2.1505241394 s Creating peak regions... Creating peak regions took 46.7429351807 s Estimating background... Estimating background took 12.8901050091 s Processing ZNF468-SRR5197150.hg20-male.36mers.unique.bam Reading in data... Reading data took 2.21436595917 s Creating peak regions... Creating peak regions took 46.8923761845 s Estimating background... Estimating background took 14.3676781654 s Processing ZNF468-SRR5197150.hg20-male.36mers.unique.bam Reading in data... Reading data took 2.19927692413 s Creating peak regions... Creating peak regions took 40.7899529934 s Estimating background... Estimating background took 14.0549440384 s Processing ZNF468-SRR5197150.hg20-male.36mers.unique.bam Reading in data... Reading data took 1.76555585861 s Creating peak regions... Creating peak regions took 36.8398098946 s Estimating background... Estimating background took 9.22998809814 s Processing ZNF468-SRR5197150.hg20-male.36mers.unique.bam Reading in data... Reading data took 1.47771501541 s Creating peak regions... Creating peak regions took 37.4525570869 s Estimating background... Estimating background took 10.1884498596 s Processing ZNF468-SRR5197150.hg20-male.36mers.unique.bam Reading in data... Reading data took 0.0901989936829 s Creating peak regions... Creating peak regions took 0.170055150986 s Estimating background... Estimating background took 0.678071022034 s Processing ZNF468-SRR5197150.hg20-male.36mers.unique.bam Reading in data... Reading data took 2.24790692329 s Creating peak regions... Creating peak regions took 42.3487198353 s Estimating background... Estimating background took 12.1139848232 s Processing ZNF468-SRR5197150.hg20-male.36mers.unique.bam Reading in data... Reading data took 0.092885017395 s Creating peak regions... Creating peak regions took 13.5307209492 s Estimating background... Estimating background took 0.417377948761 s