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='ZNF566-SRR5197183.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='ZNF566-SRR5197183/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 ZNF566-SRR5197183.hg20-male.36mers.unique.bam Reading in data... Reading data took 4.84372115135 s Creating peak regions... Creating peak regions took 78.3680830002 s Estimating background... Estimating background took 40.6829640865 s Processing ZNF566-SRR5197183.hg20-male.36mers.unique.bam Reading in data... Reading data took 2.52450990677 s Creating peak regions... Creating peak regions took 40.8980481625 s Estimating background... Estimating background took 16.2572770119 s Processing ZNF566-SRR5197183.hg20-male.36mers.unique.bam Reading in data... Reading data took 2.56942391396 s Creating peak regions... Creating peak regions took 40.5580160618 s Estimating background... Estimating background took 15.8854148388 s Processing ZNF566-SRR5197183.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='ZNF566-SRR5197183.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='ZNF566-SRR5197183/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 ZNF566-SRR5197183.hg20-male.36mers.unique.bam Reading in data... Reading data took 4.64420104027 s Creating peak regions... Creating peak regions took 67.9140729904 s Estimating background... Estimating background took 35.5036718845 s Processing ZNF566-SRR5197183.hg20-male.36mers.unique.bam Reading in data... Reading data took 2.36882996559 s Creating peak regions... Creating peak regions took 36.2025210857 s Estimating background... Estimating background took 14.3669781685 s Processing ZNF566-SRR5197183.hg20-male.36mers.unique.bam Reading in data... Reading data took 2.46305179596 s Creating peak regions... Creating peak regions took 35.706371069 s Estimating background... Estimating background took 14.9636750221 s Processing ZNF566-SRR5197183.hg20-male.36mers.unique.bam Reading in data... Reading data took 2.45592999458 s Creating peak regions... Creating peak regions took 35.8245968819 s Estimating background... Estimating background took 15.4564158916 s Processing ZNF566-SRR5197183.hg20-male.36mers.unique.bam Reading in data... Reading data took 2.39129495621 s Creating peak regions... Creating peak regions took 33.1709849834 s Estimating background... Estimating background took 16.0645489693 s Processing ZNF566-SRR5197183.hg20-male.36mers.unique.bam Reading in data... Reading data took 1.584223032 s Creating peak regions... Creating peak regions took 26.867773056 s Estimating background... Estimating background took 10.1394541264 s Processing ZNF566-SRR5197183.hg20-male.36mers.unique.bam Reading in data... Reading data took 1.64339399338 s Creating peak regions... Creating peak regions took 26.3987309933 s Estimating background... Estimating background took 10.6798222065 s Processing ZNF566-SRR5197183.hg20-male.36mers.unique.bam Reading in data... Reading data took 1.64585900307 s Creating peak regions... Creating peak regions took 25.7655699253 s Estimating background... Estimating background took 11.3130049706 s Processing ZNF566-SRR5197183.hg20-male.36mers.unique.bam Reading in data... Reading data took 1.8674890995 s Creating peak regions... Creating peak regions took 23.2224359512 s Estimating background... Estimating background took 13.9521110058 s Processing ZNF566-SRR5197183.hg20-male.36mers.unique.bam Reading in data... Reading data took 1.19383811951 s Creating peak regions... Creating peak regions took 20.4236750603 s Estimating background... Estimating background took 7.88516902924 s Processing ZNF566-SRR5197183.hg20-male.36mers.unique.bam Reading in data... Reading data took 1.35170102119 s Creating peak regions... Creating peak regions took 16.2831418514 s Estimating background... Estimating background took 9.92193102837 s Processing ZNF566-SRR5197183.hg20-male.36mers.unique.bam Reading in data... Reading data took 3.94283390045 s Creating peak regions... Creating peak regions took 69.0182631016 s Estimating background... Estimating background took 24.6680021286 s Processing ZNF566-SRR5197183.hg20-male.36mers.unique.bam Reading in data... Reading data took 1.2756729126 s Creating peak regions... Creating peak regions took 18.310254097 s Estimating background... Estimating background took 8.67620706558 s Processing ZNF566-SRR5197183.hg20-male.36mers.unique.bam Reading in data... Reading data took 0.827921867371 s Creating peak regions... Creating peak regions took 12.6813750267 s Estimating background... Estimating background took 4.899518013 s Processing ZNF566-SRR5197183.hg20-male.36mers.unique.bam Reading in data... Reading data took 1.07209920883 s Creating peak regions... Creating peak regions took 14.7974820137 s Estimating background... Estimating background took 9.40104699135 s Processing ZNF566-SRR5197183.hg20-male.36mers.unique.bam Reading in data... Reading data took 3.20057296753 s Creating peak regions... Creating peak regions took 52.9173738956 s Estimating background... Estimating background took 19.3433670998 s Processing ZNF566-SRR5197183.hg20-male.36mers.unique.bam Reading in data... Reading data took 2.76619100571 s Creating peak regions... Creating peak regions took 50.0127649307 s Estimating background... Estimating background took 15.7361650467 s Processing ZNF566-SRR5197183.hg20-male.36mers.unique.bam Reading in data... Reading data took 2.82113289833 s Creating peak regions... Creating peak regions took 48.2448458672 s Estimating background... Estimating background took 17.8320088387 s Processing ZNF566-SRR5197183.hg20-male.36mers.unique.bam Reading in data... Reading data took 3.22060894966 s Creating peak regions... Creating peak regions took 47.3479959965 s Estimating background... Estimating background took 21.3289318085 s Processing ZNF566-SRR5197183.hg20-male.36mers.unique.bam Reading in data... Reading data took 3.08848190308 s Creating peak regions... Creating peak regions took 44.1489021778 s Estimating background... Estimating background took 20.4673159122 s Processing ZNF566-SRR5197183.hg20-male.36mers.unique.bam Reading in data... Reading data took 2.34018707275 s Creating peak regions... Creating peak regions took 39.2568979263 s Estimating background... Estimating background took 13.8320548534 s Processing ZNF566-SRR5197183.hg20-male.36mers.unique.bam Reading in data... Reading data took 2.24332499504 s Creating peak regions... Creating peak regions took 36.4880049229 s Estimating background... Estimating background took 13.5316650867 s Processing ZNF566-SRR5197183.hg20-male.36mers.unique.bam Reading in data... Reading data took 0.0929849147797 s Creating peak regions... Creating peak regions took 0.16686296463 s Estimating background... Estimating background took 0.668260097504 s Processing ZNF566-SRR5197183.hg20-male.36mers.unique.bam Reading in data... Reading data took 2.77687096596 s Creating peak regions... Creating peak regions took 41.99218297 s Estimating background... Estimating background took 17.977959156 s Processing ZNF566-SRR5197183.hg20-male.36mers.unique.bam Reading in data... Reading data took 0.119819164276 s Creating peak regions... Creating peak regions took 13.522341013 s Estimating background... Estimating background took 0.559053897858 s