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='ZNF282-SRR5197098.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='ZNF282-SRR5197098/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 ZNF282-SRR5197098.hg20-male.36mers.unique.bam Reading in data... Reading data took 6.54669117928 s Creating peak regions... Creating peak regions took 62.2629699707 s Estimating background... Estimating background took 30.7790839672 s Processing ZNF282-SRR5197098.hg20-male.36mers.unique.bam Reading in data... Reading data took 2.86786222458 s Creating peak regions... Creating peak regions took 32.4639029503 s Estimating background... Estimating background took 12.4448409081 s Processing ZNF282-SRR5197098.hg20-male.36mers.unique.bam Reading in data... Reading data took 2.96708607674 s Creating peak regions... Creating peak regions took 33.1900191307 s Estimating background... Estimating background took 13.3973460197 s Processing ZNF282-SRR5197098.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='ZNF282-SRR5197098.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='ZNF282-SRR5197098/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 ZNF282-SRR5197098.hg20-male.36mers.unique.bam Reading in data... Reading data took 7.75805401802 s Creating peak regions... Creating peak regions took 74.6173219681 s Estimating background... Estimating background took 39.9861819744 s Processing ZNF282-SRR5197098.hg20-male.36mers.unique.bam Reading in data... Reading data took 3.83564591408 s Creating peak regions... Creating peak regions took 37.5130310059 s Estimating background... Estimating background took 12.8561730385 s Processing ZNF282-SRR5197098.hg20-male.36mers.unique.bam Reading in data... Reading data took 3.10740399361 s Creating peak regions... Creating peak regions took 40.6846768856 s Estimating background... Estimating background took 15.4014611244 s Processing ZNF282-SRR5197098.hg20-male.36mers.unique.bam Reading in data... Reading data took 3.93952012062 s Creating peak regions... Creating peak regions took 40.096927166 s Estimating background... Estimating background took 16.5539851189 s Processing ZNF282-SRR5197098.hg20-male.36mers.unique.bam Reading in data... Reading data took 3.46642494202 s Creating peak regions... Creating peak regions took 36.774066925 s Estimating background... Estimating background took 16.5321040154 s Processing ZNF282-SRR5197098.hg20-male.36mers.unique.bam Reading in data... Reading data took 2.66496109962 s Creating peak regions... Creating peak regions took 30.2310299873 s Estimating background... Estimating background took 10.6623210907 s Processing ZNF282-SRR5197098.hg20-male.36mers.unique.bam Reading in data... Reading data took 2.38600993156 s Creating peak regions... Creating peak regions took 29.5658462048 s Estimating background... Estimating background took 11.0148568153 s Processing ZNF282-SRR5197098.hg20-male.36mers.unique.bam Reading in data... Reading data took 2.64317297935 s Creating peak regions... Creating peak regions took 28.1097180843 s Estimating background... Estimating background took 10.8356659412 s Processing ZNF282-SRR5197098.hg20-male.36mers.unique.bam Reading in data... Reading data took 2.67436814308 s Creating peak regions... Creating peak regions took 26.7653419971 s Estimating background... Estimating background took 13.7405819893 s Processing ZNF282-SRR5197098.hg20-male.36mers.unique.bam Reading in data... Reading data took 2.13921880722 s Creating peak regions... Creating peak regions took 23.5494070053 s Estimating background... Estimating background took 8.18839621544 s Processing ZNF282-SRR5197098.hg20-male.36mers.unique.bam Reading in data... Reading data took 1.93209505081 s Creating peak regions... Creating peak regions took 17.4834179878 s Estimating background... Estimating background took 9.58417916298 s Processing ZNF282-SRR5197098.hg20-male.36mers.unique.bam Reading in data... Reading data took 6.29376506805 s Creating peak regions... Creating peak regions took 72.9265320301 s Estimating background... Estimating background took 26.1752579212 s Processing ZNF282-SRR5197098.hg20-male.36mers.unique.bam Reading in data... Reading data took 1.81374192238 s Creating peak regions... Creating peak regions took 20.0015060902 s Estimating background... Estimating background took 7.89847707748 s Processing ZNF282-SRR5197098.hg20-male.36mers.unique.bam Reading in data... Reading data took 1.14755296707 s Creating peak regions... Creating peak regions took 13.9544689655 s Estimating background... Estimating background took 5.06061005592 s Processing ZNF282-SRR5197098.hg20-male.36mers.unique.bam Reading in data... Reading data took 1.60294604301 s Creating peak regions... Creating peak regions took 15.9685459137 s Estimating background... Estimating background took 8.12700915337 s Processing ZNF282-SRR5197098.hg20-male.36mers.unique.bam Reading in data... Reading data took 5.18886494637 s Creating peak regions... Creating peak regions took 59.3833270073 s Estimating background... Estimating background took 20.3444201946 s Processing ZNF282-SRR5197098.hg20-male.36mers.unique.bam Reading in data... Reading data took 4.12145090103 s Creating peak regions... Creating peak regions took 56.290874958 s Estimating background... Estimating background took 14.7352468967 s Processing ZNF282-SRR5197098.hg20-male.36mers.unique.bam Reading in data... Reading data took 4.98539805412 s Creating peak regions... Creating peak regions took 54.1069359779 s Estimating background... Estimating background took 20.2053639889 s Processing ZNF282-SRR5197098.hg20-male.36mers.unique.bam Reading in data... Reading data took 5.28047704697 s Creating peak regions... Creating peak regions took 51.813131094 s Estimating background... Estimating background took 22.2086219788 s Processing ZNF282-SRR5197098.hg20-male.36mers.unique.bam Reading in data... Reading data took 4.82750988007 s Creating peak regions... Creating peak regions took 48.2738211155 s Estimating background... Estimating background took 19.2757110596 s Processing ZNF282-SRR5197098.hg20-male.36mers.unique.bam Reading in data... Reading data took 3.47027897835 s Creating peak regions... Creating peak regions took 43.4867928028 s Estimating background... Estimating background took 13.2009501457 s Processing ZNF282-SRR5197098.hg20-male.36mers.unique.bam Reading in data... Reading data took 3.42688584328 s Creating peak regions... Creating peak regions took 43.9146630764 s Estimating background... Estimating background took 14.1955149174 s Processing ZNF282-SRR5197098.hg20-male.36mers.unique.bam Reading in data... Reading data took 0.0983469486237 s Creating peak regions... Creating peak regions took 0.142356872559 s Estimating background... Estimating background took 0.778521060944 s Processing ZNF282-SRR5197098.hg20-male.36mers.unique.bam Reading in data... Reading data took 4.71939182281 s Creating peak regions... Creating peak regions took 47.3533661366 s Estimating background... Estimating background took 20.0549609661 s Processing ZNF282-SRR5197098.hg20-male.36mers.unique.bam Reading in data... Reading data took 0.137582063675 s Creating peak regions... Creating peak regions took 15.481128931 s Estimating background... Estimating background took 0.546674013138 s