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='ZNF552-SRR5197175.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='ZNF552-SRR5197175/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 ZNF552-SRR5197175.hg20-male.36mers.unique.bam Reading in data... Reading data took 4.72442793846 s Creating peak regions... Creating peak regions took 77.4744532108 s Estimating background... Estimating background took 32.8388299942 s Processing ZNF552-SRR5197175.hg20-male.36mers.unique.bam Reading in data... Reading data took 2.90771102905 s Creating peak regions... Creating peak regions took 40.271064043 s Estimating background... Estimating background took 12.8546860218 s Processing ZNF552-SRR5197175.hg20-male.36mers.unique.bam Reading in data... Reading data took 2.53654909134 s Creating peak regions... Creating peak regions took 40.4698500633 s Estimating background... Estimating background took 13.3066608906 s Processing ZNF552-SRR5197175.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='ZNF552-SRR5197175.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='ZNF552-SRR5197175/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 ZNF552-SRR5197175.hg20-male.36mers.unique.bam Reading in data... Reading data took 4.73150396347 s Creating peak regions... Creating peak regions took 76.4338901043 s Estimating background... Estimating background took 32.0382399559 s Processing ZNF552-SRR5197175.hg20-male.36mers.unique.bam Reading in data... Reading data took 2.53562879562 s Creating peak regions... Creating peak regions took 40.1860969067 s Estimating background... Estimating background took 12.7955129147 s Processing ZNF552-SRR5197175.hg20-male.36mers.unique.bam Reading in data... Reading data took 2.61490297318 s Creating peak regions... Creating peak regions took 40.4268209934 s Estimating background... Estimating background took 13.308041811 s Processing ZNF552-SRR5197175.hg20-male.36mers.unique.bam Reading in data... Reading data took 2.48648905754 s Creating peak regions... Creating peak regions took 39.7820599079 s Estimating background... Estimating background took 14.1132938862 s Processing ZNF552-SRR5197175.hg20-male.36mers.unique.bam Reading in data... Reading data took 2.35662102699 s Creating peak regions... Creating peak regions took 36.4571549892 s Estimating background... Estimating background took 16.255535841 s Processing ZNF552-SRR5197175.hg20-male.36mers.unique.bam Reading in data... Reading data took 1.8441491127 s Creating peak regions... Creating peak regions took 32.8153450489 s Estimating background... Estimating background took 9.06756091118 s Processing ZNF552-SRR5197175.hg20-male.36mers.unique.bam Reading in data... Reading data took 1.64706206322 s Creating peak regions... Creating peak regions took 31.7047331333 s Estimating background... Estimating background took 9.97247219086 s Processing ZNF552-SRR5197175.hg20-male.36mers.unique.bam Reading in data... Reading data took 1.60329413414 s Creating peak regions... Creating peak regions took 27.9002258778 s Estimating background... Estimating background took 8.76634001732 s Processing ZNF552-SRR5197175.hg20-male.36mers.unique.bam Reading in data... Reading data took 1.79485988617 s Creating peak regions... Creating peak regions took 24.005535841 s Estimating background... Estimating background took 10.8068449497 s Processing ZNF552-SRR5197175.hg20-male.36mers.unique.bam Reading in data... Reading data took 1.50284194946 s Creating peak regions... Creating peak regions took 25.0688679218 s Estimating background... Estimating background took 7.48817396164 s Processing ZNF552-SRR5197175.hg20-male.36mers.unique.bam Reading in data... Reading data took 1.23396205902 s Creating peak regions... Creating peak regions took 17.5634300709 s Estimating background... Estimating background took 6.50954699516 s Processing ZNF552-SRR5197175.hg20-male.36mers.unique.bam Reading in data... Reading data took 4.22320604324 s Creating peak regions... Creating peak regions took 76.0923070908 s Estimating background... Estimating background took 22.529487133 s Processing ZNF552-SRR5197175.hg20-male.36mers.unique.bam Reading in data... Reading data took 1.30284500122 s Creating peak regions... Creating peak regions took 20.0260491371 s Estimating background... Estimating background took 7.65649390221 s Processing ZNF552-SRR5197175.hg20-male.36mers.unique.bam Reading in data... Reading data took 0.99215388298 s Creating peak regions... Creating peak regions took 14.732336998 s Estimating background... Estimating background took 4.5561170578 s Processing ZNF552-SRR5197175.hg20-male.36mers.unique.bam Reading in data... Reading data took 0.924546003342 s Creating peak regions... Creating peak regions took 15.9979031086 s Estimating background... Estimating background took 6.65942311287 s Processing ZNF552-SRR5197175.hg20-male.36mers.unique.bam Reading in data... Reading data took 3.463504076 s Creating peak regions... Creating peak regions took 58.8865480423 s Estimating background... Estimating background took 17.9891700745 s Processing ZNF552-SRR5197175.hg20-male.36mers.unique.bam Reading in data... Reading data took 3.01124811172 s Creating peak regions... Creating peak regions took 56.162017107 s Estimating background... Estimating background took 14.7541370392 s Processing ZNF552-SRR5197175.hg20-male.36mers.unique.bam Reading in data... Reading data took 3.66706609726 s Creating peak regions... Creating peak regions took 51.5000770092 s Estimating background... Estimating background took 17.63717103 s Processing ZNF552-SRR5197175.hg20-male.36mers.unique.bam Reading in data... Reading data took 3.46101093292 s Creating peak regions... Creating peak regions took 51.8654448986 s Estimating background... Estimating background took 19.4100768566 s Processing ZNF552-SRR5197175.hg20-male.36mers.unique.bam Reading in data... Reading data took 3.11727905273 s Creating peak regions... Creating peak regions took 47.4303848743 s Estimating background... Estimating background took 16.8616769314 s Processing ZNF552-SRR5197175.hg20-male.36mers.unique.bam Reading in data... Reading data took 2.56748914719 s Creating peak regions... Creating peak regions took 45.5801408291 s Estimating background... Estimating background took 12.4292838573 s Processing ZNF552-SRR5197175.hg20-male.36mers.unique.bam Reading in data... Reading data took 2.33673095703 s Creating peak regions... Creating peak regions took 43.005325079 s Estimating background... Estimating background took 12.0636701584 s Processing ZNF552-SRR5197175.hg20-male.36mers.unique.bam Reading in data... Reading data took 0.0966591835022 s Creating peak regions... Creating peak regions took 0.220882892609 s Estimating background... Estimating background took 0.657344818115 s Processing ZNF552-SRR5197175.hg20-male.36mers.unique.bam Reading in data... Reading data took 3.31072711945 s Creating peak regions... Creating peak regions took 49.8043329716 s Estimating background... Estimating background took 19.3735518456 s Processing ZNF552-SRR5197175.hg20-male.36mers.unique.bam Reading in data... Reading data took 0.119719028473 s Creating peak regions... Creating peak regions took 16.2118930817 s Estimating background... Estimating background took 0.5494389534 s