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='ZNF425-SRR5197134.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='ZNF425-SRR5197134/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 ZNF425-SRR5197134.hg20-male.36mers.unique.bam Reading in data... Reading data took 4.31679987907 s Creating peak regions... Creating peak regions took 76.6028270721 s Estimating background... Estimating background took 31.1014330387 s Processing ZNF425-SRR5197134.hg20-male.36mers.unique.bam Reading in data... Reading data took 2.19910883904 s Creating peak regions... Creating peak regions took 39.0983848572 s Estimating background... Estimating background took 12.3923480511 s Processing ZNF425-SRR5197134.hg20-male.36mers.unique.bam Reading in data... Reading data took 2.1476829052 s Creating peak regions... Creating peak regions took 39.2673778534 s Estimating background... Estimating background took 12.6793670654 s Processing ZNF425-SRR5197134.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='ZNF425-SRR5197134.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='ZNF425-SRR5197134/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 ZNF425-SRR5197134.hg20-male.36mers.unique.bam Reading in data... Reading data took 4.11372804642 s Creating peak regions... Creating peak regions took 74.3936181068 s Estimating background... Estimating background took 32.7950909138 s Processing ZNF425-SRR5197134.hg20-male.36mers.unique.bam Reading in data... Reading data took 2.28833794594 s Creating peak regions... Creating peak regions took 38.7311160564 s Estimating background... Estimating background took 12.3618481159 s Processing ZNF425-SRR5197134.hg20-male.36mers.unique.bam Reading in data... Reading data took 2.07688784599 s Creating peak regions... Creating peak regions took 39.567579031 s Estimating background... Estimating background took 13.4148170948 s Processing ZNF425-SRR5197134.hg20-male.36mers.unique.bam Reading in data... Reading data took 2.62960505486 s Creating peak regions... Creating peak regions took 42.0321011543 s Estimating background... Estimating background took 13.9903728962 s Processing ZNF425-SRR5197134.hg20-male.36mers.unique.bam Reading in data... Reading data took 1.53007984161 s Creating peak regions... Creating peak regions took 32.9631700516 s Estimating background... Estimating background took 12.0066931248 s Processing ZNF425-SRR5197134.hg20-male.36mers.unique.bam Reading in data... Reading data took 1.55524516106 s Creating peak regions... Creating peak regions took 32.364068985 s Estimating background... Estimating background took 8.77808213234 s Processing ZNF425-SRR5197134.hg20-male.36mers.unique.bam Reading in data... Reading data took 1.52228307724 s Creating peak regions... Creating peak regions took 29.1558070183 s Estimating background... Estimating background took 9.86561203003 s Processing ZNF425-SRR5197134.hg20-male.36mers.unique.bam Reading in data... Reading data took 1.43706393242 s Creating peak regions... Creating peak regions took 26.0748951435 s Estimating background... Estimating background took 8.92643117905 s Processing ZNF425-SRR5197134.hg20-male.36mers.unique.bam Reading in data... Reading data took 1.70969200134 s Creating peak regions... Creating peak regions took 26.7187860012 s Estimating background... Estimating background took 13.0361030102 s Processing ZNF425-SRR5197134.hg20-male.36mers.unique.bam Reading in data... Reading data took 1.23229789734 s Creating peak regions... Creating peak regions took 23.7211940289 s Estimating background... Estimating background took 6.68109583855 s Processing ZNF425-SRR5197134.hg20-male.36mers.unique.bam Reading in data... Reading data took 1.26638913155 s Creating peak regions... Creating peak regions took 19.0549259186 s Estimating background... Estimating background took 9.42916202545 s Processing ZNF425-SRR5197134.hg20-male.36mers.unique.bam Reading in data... Reading data took 3.67345905304 s Creating peak regions... Creating peak regions took 71.5621869564 s Estimating background... Estimating background took 22.0509381294 s Processing ZNF425-SRR5197134.hg20-male.36mers.unique.bam Reading in data... Reading data took 1.40560507774 s Creating peak regions... Creating peak regions took 20.2588970661 s Estimating background... Estimating background took 8.14353489876 s Processing ZNF425-SRR5197134.hg20-male.36mers.unique.bam Reading in data... Reading data took 0.656080007553 s Creating peak regions... Creating peak regions took 14.9260160923 s Estimating background... Estimating background took 3.76922607422 s Processing ZNF425-SRR5197134.hg20-male.36mers.unique.bam Reading in data... Reading data took 0.789375066757 s Creating peak regions... Creating peak regions took 15.7301061153 s Estimating background... Estimating background took 7.8222630024 s Processing ZNF425-SRR5197134.hg20-male.36mers.unique.bam Reading in data... Reading data took 2.75386691093 s Creating peak regions... Creating peak regions took 55.4998159409 s Estimating background... Estimating background took 16.301295042 s Processing ZNF425-SRR5197134.hg20-male.36mers.unique.bam Reading in data... Reading data took 2.45798993111 s Creating peak regions... Creating peak regions took 53.0382609367 s Estimating background... Estimating background took 12.575868845 s Processing ZNF425-SRR5197134.hg20-male.36mers.unique.bam Reading in data... Reading data took 2.75559186935 s Creating peak regions... Creating peak regions took 56.6230700016 s Estimating background... Estimating background took 16.3406350613 s Processing ZNF425-SRR5197134.hg20-male.36mers.unique.bam Reading in data... Reading data took 2.85579299927 s Creating peak regions... Creating peak regions took 48.9770078659 s Estimating background... Estimating background took 17.5082879066 s Processing ZNF425-SRR5197134.hg20-male.36mers.unique.bam Reading in data... Reading data took 2.88107085228 s Creating peak regions... Creating peak regions took 48.4289000034 s Estimating background... Estimating background took 17.1415100098 s Processing ZNF425-SRR5197134.hg20-male.36mers.unique.bam Reading in data... Reading data took 2.2898440361 s Creating peak regions... Creating peak regions took 44.1153581142 s Estimating background... Estimating background took 11.6943998337 s Processing ZNF425-SRR5197134.hg20-male.36mers.unique.bam Reading in data... Reading data took 1.92845392227 s Creating peak regions... Creating peak regions took 42.2237319946 s Estimating background... Estimating background took 11.381649971 s Processing ZNF425-SRR5197134.hg20-male.36mers.unique.bam Reading in data... Reading data took 0.129835128784 s Creating peak regions... Creating peak regions took 0.162389993668 s Estimating background... Estimating background took 0.576597929001 s Processing ZNF425-SRR5197134.hg20-male.36mers.unique.bam Reading in data... Reading data took 2.50636005402 s Creating peak regions... Creating peak regions took 47.5044238567 s Estimating background... Estimating background took 13.3483729362 s Processing ZNF425-SRR5197134.hg20-male.36mers.unique.bam Reading in data... Reading data took 0.131586074829 s Creating peak regions... Creating peak regions took 13.0907249451 s Estimating background... Estimating background took 0.42098903656 s