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='ZNF684-SRR5197217.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='ZNF684-SRR5197217/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 ZNF684-SRR5197217.hg20-male.36mers.unique.bam Reading in data... Reading data took 5.06525397301 s Creating peak regions... Creating peak regions took 77.9734740257 s Estimating background... Estimating background took 42.5791499615 s Processing ZNF684-SRR5197217.hg20-male.36mers.unique.bam Reading in data... Reading data took 2.6778690815 s Creating peak regions... Creating peak regions took 40.9015510082 s Estimating background... Estimating background took 17.466520071 s Processing ZNF684-SRR5197217.hg20-male.36mers.unique.bam Reading in data... Reading data took 2.6318731308 s Creating peak regions... Creating peak regions took 42.4587271214 s Estimating background... Estimating background took 15.8426580429 s Processing ZNF684-SRR5197217.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='ZNF684-SRR5197217.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='ZNF684-SRR5197217/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 ZNF684-SRR5197217.hg20-male.36mers.unique.bam Reading in data... Reading data took 5.52958393097 s Creating peak regions... Creating peak regions took 72.932723999 s Estimating background... Estimating background took 37.8249700069 s Processing ZNF684-SRR5197217.hg20-male.36mers.unique.bam Reading in data... Reading data took 2.9330239296 s Creating peak regions... Creating peak regions took 41.8717250824 s Estimating background... Estimating background took 16.6251070499 s Processing ZNF684-SRR5197217.hg20-male.36mers.unique.bam Reading in data... Reading data took 2.66633796692 s Creating peak regions... Creating peak regions took 39.0042099953 s Estimating background... Estimating background took 15.4286899567 s Processing ZNF684-SRR5197217.hg20-male.36mers.unique.bam Reading in data... Reading data took 2.71154284477 s Creating peak regions... Creating peak regions took 40.2158308029 s Estimating background... Estimating background took 15.1267931461 s Processing ZNF684-SRR5197217.hg20-male.36mers.unique.bam Reading in data... Reading data took 2.25788617134 s Creating peak regions... Creating peak regions took 33.8505260944 s Estimating background... Estimating background took 15.8209159374 s Processing ZNF684-SRR5197217.hg20-male.36mers.unique.bam Reading in data... Reading data took 1.92130684853 s Creating peak regions... Creating peak regions took 30.1478807926 s Estimating background... Estimating background took 10.778594017 s Processing ZNF684-SRR5197217.hg20-male.36mers.unique.bam Reading in data... Reading data took 1.89705681801 s Creating peak regions... Creating peak regions took 30.019644022 s Estimating background... Estimating background took 12.1559169292 s Processing ZNF684-SRR5197217.hg20-male.36mers.unique.bam Reading in data... Reading data took 1.8474650383 s Creating peak regions... Creating peak regions took 27.0266869068 s Estimating background... Estimating background took 11.5960111618 s Processing ZNF684-SRR5197217.hg20-male.36mers.unique.bam Reading in data... Reading data took 2.3307030201 s Creating peak regions... Creating peak regions took 28.1641139984 s Estimating background... Estimating background took 14.2646119595 s Processing ZNF684-SRR5197217.hg20-male.36mers.unique.bam Reading in data... Reading data took 1.42992401123 s Creating peak regions... Creating peak regions took 24.7697229385 s Estimating background... Estimating background took 7.68760085106 s Processing ZNF684-SRR5197217.hg20-male.36mers.unique.bam Reading in data... Reading data took 1.75223302841 s Creating peak regions... Creating peak regions took 18.7752599716 s Estimating background... Estimating background took 10.2331721783 s Processing ZNF684-SRR5197217.hg20-male.36mers.unique.bam Reading in data... Reading data took 4.78711295128 s Creating peak regions... Creating peak regions took 81.7889690399 s Estimating background... Estimating background took 26.8118159771 s Processing ZNF684-SRR5197217.hg20-male.36mers.unique.bam Reading in data... Reading data took 1.5868871212 s Creating peak regions... Creating peak regions took 21.0768249035 s Estimating background... Estimating background took 9.81569194794 s Processing ZNF684-SRR5197217.hg20-male.36mers.unique.bam Reading in data... Reading data took 0.890064954758 s Creating peak regions... Creating peak regions took 14.0161600113 s Estimating background... Estimating background took 5.13161110878 s Processing ZNF684-SRR5197217.hg20-male.36mers.unique.bam Reading in data... Reading data took 1.20521211624 s Creating peak regions... Creating peak regions took 17.3973019123 s Estimating background... Estimating background took 9.73744297028 s Processing ZNF684-SRR5197217.hg20-male.36mers.unique.bam Reading in data... Reading data took 4.07355999947 s Creating peak regions... Creating peak regions took 66.0796501637 s Estimating background... Estimating background took 21.4025809765 s Processing ZNF684-SRR5197217.hg20-male.36mers.unique.bam Reading in data... Reading data took 3.35817217827 s Creating peak regions... Creating peak regions took 54.2165031433 s Estimating background... Estimating background took 16.4980800152 s Processing ZNF684-SRR5197217.hg20-male.36mers.unique.bam Reading in data... Reading data took 3.59561896324 s Creating peak regions... Creating peak regions took 58.5003709793 s Estimating background... Estimating background took 20.2084980011 s Processing ZNF684-SRR5197217.hg20-male.36mers.unique.bam Reading in data... Reading data took 4.12267184258 s Creating peak regions... Creating peak regions took 58.9879469872 s Estimating background... Estimating background took 24.3565359116 s Processing ZNF684-SRR5197217.hg20-male.36mers.unique.bam Reading in data... Reading data took 3.50338315964 s Creating peak regions... Creating peak regions took 48.6690080166 s Estimating background... Estimating background took 21.7229309082 s Processing ZNF684-SRR5197217.hg20-male.36mers.unique.bam Reading in data... Reading data took 2.83962893486 s Creating peak regions... Creating peak regions took 46.5008809566 s Estimating background... Estimating background took 14.4679169655 s Processing ZNF684-SRR5197217.hg20-male.36mers.unique.bam Reading in data... Reading data took 2.42499494553 s Creating peak regions... Creating peak regions took 41.2117750645 s Estimating background... Estimating background took 14.050057888 s Processing ZNF684-SRR5197217.hg20-male.36mers.unique.bam Reading in data... Reading data took 0.124804973602 s Creating peak regions... Creating peak regions took 0.213526964188 s Estimating background... Estimating background took 0.788896083832 s Processing ZNF684-SRR5197217.hg20-male.36mers.unique.bam Reading in data... Reading data took 3.56901288033 s Creating peak regions... Creating peak regions took 46.9530320168 s Estimating background... Estimating background took 21.8456640244 s Processing ZNF684-SRR5197217.hg20-male.36mers.unique.bam Reading in data... Reading data took 0.174067974091 s Creating peak regions... Creating peak regions took 16.8317949772 s Estimating background... Estimating background took 0.68744301796 s