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='ZNF383-SRR5197127.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='ZNF383-SRR5197127/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 ZNF383-SRR5197127.hg20-male.36mers.unique.bam Reading in data... Reading data took 5.68984103203 s Creating peak regions... Creating peak regions took 63.2217111588 s Estimating background... Estimating background took 38.9868900776 s Processing ZNF383-SRR5197127.hg20-male.36mers.unique.bam Reading in data... Reading data took 2.85775184631 s Creating peak regions... Creating peak regions took 34.1019790173 s Estimating background... Estimating background took 16.6224498749 s Processing ZNF383-SRR5197127.hg20-male.36mers.unique.bam Reading in data... Reading data took 2.80711698532 s Creating peak regions... Creating peak regions took 34.9438860416 s Estimating background... Estimating background took 17.2726149559 s Processing ZNF383-SRR5197127.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='ZNF383-SRR5197127.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='ZNF383-SRR5197127/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 ZNF383-SRR5197127.hg20-male.36mers.unique.bam Reading in data... Reading data took 6.0838561058 s Creating peak regions... Creating peak regions took 75.0281500816 s Estimating background... Estimating background took 46.9507198334 s Processing ZNF383-SRR5197127.hg20-male.36mers.unique.bam Reading in data... Reading data took 3.21413803101 s Creating peak regions... Creating peak regions took 42.407709837 s Estimating background... Estimating background took 17.6511650085 s Processing ZNF383-SRR5197127.hg20-male.36mers.unique.bam Reading in data... Reading data took 3.19423699379 s Creating peak regions... Creating peak regions took 41.3301489353 s Estimating background... Estimating background took 20.4853599072 s Processing ZNF383-SRR5197127.hg20-male.36mers.unique.bam Reading in data... Reading data took 3.53322720528 s Creating peak regions... Creating peak regions took 42.1963541508 s Estimating background... Estimating background took 19.3439118862 s Processing ZNF383-SRR5197127.hg20-male.36mers.unique.bam Reading in data... Reading data took 2.35645508766 s Creating peak regions... Creating peak regions took 36.3080170155 s Estimating background... Estimating background took 17.4352359772 s Processing ZNF383-SRR5197127.hg20-male.36mers.unique.bam Reading in data... Reading data took 2.15338492393 s Creating peak regions... Creating peak regions took 31.7875080109 s Estimating background... Estimating background took 12.8971679211 s Processing ZNF383-SRR5197127.hg20-male.36mers.unique.bam Reading in data... Reading data took 2.04826116562 s Creating peak regions... Creating peak regions took 29.3376350403 s Estimating background... Estimating background took 12.3587589264 s Processing ZNF383-SRR5197127.hg20-male.36mers.unique.bam Reading in data... Reading data took 2.21535015106 s Creating peak regions... Creating peak regions took 26.7412781715 s Estimating background... Estimating background took 14.5994400978 s Processing ZNF383-SRR5197127.hg20-male.36mers.unique.bam Reading in data... Reading data took 2.64231109619 s Creating peak regions... Creating peak regions took 26.7979860306 s Estimating background... Estimating background took 18.7288429737 s Processing ZNF383-SRR5197127.hg20-male.36mers.unique.bam Reading in data... Reading data took 1.69169092178 s Creating peak regions... Creating peak regions took 24.8945939541 s Estimating background... Estimating background took 9.04146695137 s Processing ZNF383-SRR5197127.hg20-male.36mers.unique.bam Reading in data... Reading data took 1.42006993294 s Creating peak regions... Creating peak regions took 18.9447090626 s Estimating background... Estimating background took 11.1415088177 s Processing ZNF383-SRR5197127.hg20-male.36mers.unique.bam Reading in data... Reading data took 5.47501206398 s Creating peak regions... Creating peak regions took 75.0780100822 s Estimating background... Estimating background took 32.2474091053 s Processing ZNF383-SRR5197127.hg20-male.36mers.unique.bam Reading in data... Reading data took 2.01805686951 s Creating peak regions... Creating peak regions took 21.2161421776 s Estimating background... Estimating background took 12.1850240231 s Processing ZNF383-SRR5197127.hg20-male.36mers.unique.bam Reading in data... Reading data took 0.90195608139 s Creating peak regions... Creating peak regions took 14.4920048714 s Estimating background... Estimating background took 5.9426150322 s Processing ZNF383-SRR5197127.hg20-male.36mers.unique.bam Reading in data... Reading data took 1.42179703712 s Creating peak regions... Creating peak regions took 16.080851078 s Estimating background... Estimating background took 11.2814760208 s Processing ZNF383-SRR5197127.hg20-male.36mers.unique.bam Reading in data... Reading data took 4.34680199623 s Creating peak regions... Creating peak regions took 60.1541190147 s Estimating background... Estimating background took 23.6087498665 s Processing ZNF383-SRR5197127.hg20-male.36mers.unique.bam Reading in data... Reading data took 3.57550120354 s Creating peak regions... Creating peak regions took 57.0573530197 s Estimating background... Estimating background took 20.3185911179 s Processing ZNF383-SRR5197127.hg20-male.36mers.unique.bam Reading in data... Reading data took 4.17983293533 s Creating peak regions... Creating peak regions took 57.2848730087 s Estimating background... Estimating background took 24.5335030556 s Processing ZNF383-SRR5197127.hg20-male.36mers.unique.bam Reading in data... Reading data took 4.44624304771 s Creating peak regions... Creating peak regions took 54.4269359112 s Estimating background... Estimating background took 26.303237915 s Processing ZNF383-SRR5197127.hg20-male.36mers.unique.bam Reading in data... Reading data took 3.98211193085 s Creating peak regions... Creating peak regions took 48.343118906 s Estimating background... Estimating background took 23.0608401299 s Processing ZNF383-SRR5197127.hg20-male.36mers.unique.bam Reading in data... Reading data took 3.16373705864 s Creating peak regions... Creating peak regions took 42.564868927 s Estimating background... Estimating background took 17.0274322033 s Processing ZNF383-SRR5197127.hg20-male.36mers.unique.bam Reading in data... Reading data took 2.80489206314 s Creating peak regions... Creating peak regions took 36.1913499832 s Estimating background... Estimating background took 14.4967730045 s Processing ZNF383-SRR5197127.hg20-male.36mers.unique.bam Reading in data... Reading data took 0.0986320972443 s Creating peak regions... Creating peak regions took 0.303287982941 s Estimating background... Estimating background took 0.647655963898 s Processing ZNF383-SRR5197127.hg20-male.36mers.unique.bam Reading in data... Reading data took 2.6668279171 s Creating peak regions... Creating peak regions took 40.2145581245 s Estimating background... Estimating background took 19.3423070908 s Processing ZNF383-SRR5197127.hg20-male.36mers.unique.bam Reading in data... Reading data took 0.106737136841 s Creating peak regions... Creating peak regions took 12.104131937 s Estimating background... Estimating background took 0.513051986694 s