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='ZNF304-SRR5197108.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='ZNF304-SRR5197108/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 ZNF304-SRR5197108.hg20-male.36mers.unique.bam Reading in data... Reading data took 6.56711292267 s Creating peak regions... Creating peak regions took 79.7806539536 s Estimating background... Estimating background took 54.828111887 s Processing ZNF304-SRR5197108.hg20-male.36mers.unique.bam Reading in data... Reading data took 3.55122208595 s Creating peak regions... Creating peak regions took 43.5936021805 s Estimating background... Estimating background took 22.1403369904 s Processing ZNF304-SRR5197108.hg20-male.36mers.unique.bam Reading in data... Reading data took 3.44038796425 s Creating peak regions... Creating peak regions took 41.7129130363 s Estimating background... Estimating background took 19.4196720123 s Processing ZNF304-SRR5197108.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='ZNF304-SRR5197108.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='ZNF304-SRR5197108/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 ZNF304-SRR5197108.hg20-male.36mers.unique.bam Reading in data... Reading data took 6.65647602081 s Creating peak regions... Creating peak regions took 77.4764490128 s Estimating background... Estimating background took 56.8324320316 s Processing ZNF304-SRR5197108.hg20-male.36mers.unique.bam Reading in data... Reading data took 3.44358205795 s Creating peak regions... Creating peak regions took 41.0018079281 s Estimating background... Estimating background took 21.4653930664 s Processing ZNF304-SRR5197108.hg20-male.36mers.unique.bam Reading in data... Reading data took 3.25972414017 s Creating peak regions... Creating peak regions took 43.7303748131 s Estimating background... Estimating background took 22.0348680019 s Processing ZNF304-SRR5197108.hg20-male.36mers.unique.bam Reading in data... Reading data took 3.5574119091 s Creating peak regions... Creating peak regions took 41.629021883 s Estimating background... Estimating background took 23.6818180084 s Processing ZNF304-SRR5197108.hg20-male.36mers.unique.bam Reading in data... Reading data took 3.05976104736 s Creating peak regions... Creating peak regions took 36.3529889584 s Estimating background... Estimating background took 25.8171751499 s Processing ZNF304-SRR5197108.hg20-male.36mers.unique.bam Reading in data... Reading data took 2.39159297943 s Creating peak regions... Creating peak regions took 30.7702360153 s Estimating background... Estimating background took 14.4893450737 s Processing ZNF304-SRR5197108.hg20-male.36mers.unique.bam Reading in data... Reading data took 2.59972286224 s Creating peak regions... Creating peak regions took 29.0683541298 s Estimating background... Estimating background took 17.0563950539 s Processing ZNF304-SRR5197108.hg20-male.36mers.unique.bam Reading in data... Reading data took 2.17965102196 s Creating peak regions... Creating peak regions took 30.0972959995 s Estimating background... Estimating background took 14.9305870533 s Processing ZNF304-SRR5197108.hg20-male.36mers.unique.bam Reading in data... Reading data took 2.62694501877 s Creating peak regions... Creating peak regions took 26.97727108 s Estimating background... Estimating background took 17.0987279415 s Processing ZNF304-SRR5197108.hg20-male.36mers.unique.bam Reading in data... Reading data took 1.66202688217 s Creating peak regions... Creating peak regions took 24.1478719711 s Estimating background... Estimating background took 11.7977671623 s Processing ZNF304-SRR5197108.hg20-male.36mers.unique.bam Reading in data... Reading data took 1.71220898628 s Creating peak regions... Creating peak regions took 18.8021979332 s Estimating background... Estimating background took 11.5907468796 s Processing ZNF304-SRR5197108.hg20-male.36mers.unique.bam Reading in data... Reading data took 5.80881714821 s Creating peak regions... Creating peak regions took 79.5347859859 s Estimating background... Estimating background took 36.9684782028 s Processing ZNF304-SRR5197108.hg20-male.36mers.unique.bam Reading in data... Reading data took 1.73186302185 s Creating peak regions... Creating peak regions took 21.3740119934 s Estimating background... Estimating background took 12.0398890972 s Processing ZNF304-SRR5197108.hg20-male.36mers.unique.bam Reading in data... Reading data took 0.942610025406 s Creating peak regions... Creating peak regions took 14.3745958805 s Estimating background... Estimating background took 6.54781603813 s Processing ZNF304-SRR5197108.hg20-male.36mers.unique.bam Reading in data... Reading data took 1.32491397858 s Creating peak regions... Creating peak regions took 16.0236830711 s Estimating background... Estimating background took 10.6001989841 s Processing ZNF304-SRR5197108.hg20-male.36mers.unique.bam Reading in data... Reading data took 3.98691701889 s Creating peak regions... Creating peak regions took 64.9853339195 s Estimating background... Estimating background took 30.9488298893 s Processing ZNF304-SRR5197108.hg20-male.36mers.unique.bam Reading in data... Reading data took 4.1337389946 s Creating peak regions... Creating peak regions took 57.9348709583 s Estimating background... Estimating background took 23.4726321697 s Processing ZNF304-SRR5197108.hg20-male.36mers.unique.bam Reading in data... Reading data took 4.44679808617 s Creating peak regions... Creating peak regions took 57.9475300312 s Estimating background... Estimating background took 29.1535611153 s Processing ZNF304-SRR5197108.hg20-male.36mers.unique.bam Reading in data... Reading data took 4.21941304207 s Creating peak regions... Creating peak regions took 54.1863050461 s Estimating background... Estimating background took 33.2022769451 s Processing ZNF304-SRR5197108.hg20-male.36mers.unique.bam Reading in data... Reading data took 4.23029994965 s Creating peak regions... Creating peak regions took 49.7210459709 s Estimating background... Estimating background took 24.0898890495 s Processing ZNF304-SRR5197108.hg20-male.36mers.unique.bam Reading in data... Reading data took 2.8598279953 s Creating peak regions... Creating peak regions took 37.9468901157 s Estimating background... Estimating background took 18.0126001835 s Processing ZNF304-SRR5197108.hg20-male.36mers.unique.bam Reading in data... Reading data took 2.57822799683 s Creating peak regions... Creating peak regions took 39.63235116 s Estimating background... Estimating background took 19.0791239738 s Processing ZNF304-SRR5197108.hg20-male.36mers.unique.bam Reading in data... Reading data took 0.0975430011749 s Creating peak regions... Creating peak regions took 0.175890922546 s Estimating background... Estimating background took 0.795189857483 s Processing ZNF304-SRR5197108.hg20-male.36mers.unique.bam Reading in data... Reading data took 4.41782093048 s Creating peak regions... Creating peak regions took 47.8185789585 s Estimating background... Estimating background took 28.2789590359 s Processing ZNF304-SRR5197108.hg20-male.36mers.unique.bam Reading in data... Reading data took 0.148044109344 s Creating peak regions... Creating peak regions took 14.8900530338 s Estimating background... Estimating background took 0.65984416008 s