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='ZNF789-SRR5197245.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='ZNF789-SRR5197245/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 ZNF789-SRR5197245.hg20-male.36mers.unique.bam Reading in data... Reading data took 5.2911798954 s Creating peak regions... Creating peak regions took 78.671587944 s Estimating background... Estimating background took 45.3914310932 s Processing ZNF789-SRR5197245.hg20-male.36mers.unique.bam Reading in data... Reading data took 2.76739811897 s Creating peak regions... Creating peak regions took 41.3699498177 s Estimating background... Estimating background took 17.849684 s Processing ZNF789-SRR5197245.hg20-male.36mers.unique.bam Reading in data... Reading data took 2.7325630188 s Creating peak regions... Creating peak regions took 39.6579008102 s Estimating background... Estimating background took 15.972135067 s Processing ZNF789-SRR5197245.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='ZNF789-SRR5197245.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='ZNF789-SRR5197245/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 ZNF789-SRR5197245.hg20-male.36mers.unique.bam Reading in data... Reading data took 5.67609906197 s Creating peak regions... Creating peak regions took 75.1613788605 s Estimating background... Estimating background took 41.4942150116 s Processing ZNF789-SRR5197245.hg20-male.36mers.unique.bam Reading in data... Reading data took 2.79978299141 s Creating peak regions... Creating peak regions took 39.3564090729 s Estimating background... Estimating background took 16.5747330189 s Processing ZNF789-SRR5197245.hg20-male.36mers.unique.bam Reading in data... Reading data took 2.98827290535 s Creating peak regions... Creating peak regions took 39.1905679703 s Estimating background... Estimating background took 17.1196141243 s Processing ZNF789-SRR5197245.hg20-male.36mers.unique.bam Reading in data... Reading data took 2.8462741375 s Creating peak regions... Creating peak regions took 38.9609510899 s Estimating background... Estimating background took 18.1647160053 s Processing ZNF789-SRR5197245.hg20-male.36mers.unique.bam Reading in data... Reading data took 2.4220199585 s Creating peak regions... Creating peak regions took 33.054787159 s Estimating background... Estimating background took 17.3778111935 s Processing ZNF789-SRR5197245.hg20-male.36mers.unique.bam Reading in data... Reading data took 1.895581007 s Creating peak regions... Creating peak regions took 30.5338470936 s Estimating background... Estimating background took 11.7409830093 s Processing ZNF789-SRR5197245.hg20-male.36mers.unique.bam Reading in data... Reading data took 1.78388118744 s Creating peak regions... Creating peak regions took 30.7797889709 s Estimating background... Estimating background took 13.234940052 s Processing ZNF789-SRR5197245.hg20-male.36mers.unique.bam Reading in data... Reading data took 1.97074890137 s Creating peak regions... Creating peak regions took 25.7642569542 s Estimating background... Estimating background took 12.5118980408 s Processing ZNF789-SRR5197245.hg20-male.36mers.unique.bam Reading in data... Reading data took 2.03810310364 s Creating peak regions... Creating peak regions took 24.9848380089 s Estimating background... Estimating background took 16.264193058 s Processing ZNF789-SRR5197245.hg20-male.36mers.unique.bam Reading in data... Reading data took 1.42640304565 s Creating peak regions... Creating peak regions took 23.5669929981 s Estimating background... Estimating background took 8.62831997871 s Processing ZNF789-SRR5197245.hg20-male.36mers.unique.bam Reading in data... Reading data took 1.52014398575 s Creating peak regions... Creating peak regions took 18.7365298271 s Estimating background... Estimating background took 11.4391858578 s Processing ZNF789-SRR5197245.hg20-male.36mers.unique.bam Reading in data... Reading data took 4.45251703262 s Creating peak regions... Creating peak regions took 70.976804018 s Estimating background... Estimating background took 28.7665748596 s Processing ZNF789-SRR5197245.hg20-male.36mers.unique.bam Reading in data... Reading data took 1.64963293076 s Creating peak regions... Creating peak regions took 19.9842669964 s Estimating background... Estimating background took 11.1465978622 s Processing ZNF789-SRR5197245.hg20-male.36mers.unique.bam Reading in data... Reading data took 0.84925198555 s Creating peak regions... Creating peak regions took 14.2853360176 s Estimating background... Estimating background took 5.78298282623 s Processing ZNF789-SRR5197245.hg20-male.36mers.unique.bam Reading in data... Reading data took 1.25968694687 s Creating peak regions... Creating peak regions took 16.0273098946 s Estimating background... Estimating background took 10.5926411152 s Processing ZNF789-SRR5197245.hg20-male.36mers.unique.bam Reading in data... Reading data took 3.62034893036 s Creating peak regions... Creating peak regions took 57.500232935 s Estimating background... Estimating background took 21.3062791824 s Processing ZNF789-SRR5197245.hg20-male.36mers.unique.bam Reading in data... Reading data took 3.19095993042 s Creating peak regions... Creating peak regions took 54.1403090954 s Estimating background... Estimating background took 17.2281000614 s Processing ZNF789-SRR5197245.hg20-male.36mers.unique.bam Reading in data... Reading data took 3.44583797455 s Creating peak regions... Creating peak regions took 52.5609331131 s Estimating background... Estimating background took 21.4244990349 s Processing ZNF789-SRR5197245.hg20-male.36mers.unique.bam Reading in data... Reading data took 3.70954012871 s Creating peak regions... Creating peak regions took 51.2459270954 s Estimating background... Estimating background took 24.0562431812 s Processing ZNF789-SRR5197245.hg20-male.36mers.unique.bam Reading in data... Reading data took 3.4490339756 s Creating peak regions... Creating peak regions took 47.4166929722 s Estimating background... Estimating background took 22.128549099 s Processing ZNF789-SRR5197245.hg20-male.36mers.unique.bam Reading in data... Reading data took 2.84884595871 s Creating peak regions... Creating peak regions took 42.303319931 s Estimating background... Estimating background took 15.3973240852 s Processing ZNF789-SRR5197245.hg20-male.36mers.unique.bam Reading in data... Reading data took 2.55936694145 s Creating peak regions... Creating peak regions took 42.0919780731 s Estimating background... Estimating background took 15.5831038952 s Processing ZNF789-SRR5197245.hg20-male.36mers.unique.bam Reading in data... Reading data took 0.0922989845276 s Creating peak regions... Creating peak regions took 0.177525043488 s Estimating background... Estimating background took 0.709306001663 s Processing ZNF789-SRR5197245.hg20-male.36mers.unique.bam Reading in data... Reading data took 3.37366604805 s Creating peak regions... Creating peak regions took 45.067262888 s Estimating background... Estimating background took 21.5703320503 s Processing ZNF789-SRR5197245.hg20-male.36mers.unique.bam Reading in data... Reading data took 0.116725921631 s Creating peak regions... Creating peak regions took 15.0791261196 s Estimating background... Estimating background took 0.682407140732 s