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='ZNF33A-rep2-SRR5197120.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='ZNF33A-rep2-SRR5197120/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 ZNF33A-rep2-SRR5197120.hg20-male.36mers.unique.bam Reading in data... Reading data took 4.14793682098 s Creating peak regions... Creating peak regions took 75.1297278404 s Estimating background... Estimating background took 26.4500451088 s Processing ZNF33A-rep2-SRR5197120.hg20-male.36mers.unique.bam Reading in data... Reading data took 2.02009391785 s Creating peak regions... Creating peak regions took 41.0411438942 s Estimating background... Estimating background took 10.6330509186 s Processing ZNF33A-rep2-SRR5197120.hg20-male.36mers.unique.bam Reading in data... Reading data took 1.94046807289 s Creating peak regions... Creating peak regions took 39.8266150951 s Estimating background... Estimating background took 10.5500659943 s Processing ZNF33A-rep2-SRR5197120.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='ZNF33A-rep2-SRR5197120.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='ZNF33A-rep2-SRR5197120/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 ZNF33A-rep2-SRR5197120.hg20-male.36mers.unique.bam Reading in data... Reading data took 4.30079889297 s Creating peak regions... Creating peak regions took 72.3887050152 s Estimating background... Estimating background took 26.4346609116 s Processing ZNF33A-rep2-SRR5197120.hg20-male.36mers.unique.bam Reading in data... Reading data took 2.14134883881 s Creating peak regions... Creating peak regions took 39.8553569317 s Estimating background... Estimating background took 11.2964260578 s Processing ZNF33A-rep2-SRR5197120.hg20-male.36mers.unique.bam Reading in data... Reading data took 2.16006612778 s Creating peak regions... Creating peak regions took 38.6168570518 s Estimating background... Estimating background took 10.5079519749 s Processing ZNF33A-rep2-SRR5197120.hg20-male.36mers.unique.bam Reading in data... Reading data took 2.22311306 s Creating peak regions... Creating peak regions took 38.9610741138 s Estimating background... Estimating background took 11.9206318855 s Processing ZNF33A-rep2-SRR5197120.hg20-male.36mers.unique.bam Reading in data... Reading data took 1.86531090736 s Creating peak regions... Creating peak regions took 36.3282389641 s Estimating background... Estimating background took 11.5361177921 s Processing ZNF33A-rep2-SRR5197120.hg20-male.36mers.unique.bam Reading in data... Reading data took 1.54554700851 s Creating peak regions... Creating peak regions took 31.1778149605 s Estimating background... Estimating background took 7.29644012451 s Processing ZNF33A-rep2-SRR5197120.hg20-male.36mers.unique.bam Reading in data... Reading data took 1.44974112511 s Creating peak regions... Creating peak regions took 31.0243108273 s Estimating background... Estimating background took 9.19774007797 s Processing ZNF33A-rep2-SRR5197120.hg20-male.36mers.unique.bam Reading in data... Reading data took 1.61271500587 s Creating peak regions... Creating peak regions took 27.4415588379 s Estimating background... Estimating background took 8.09388995171 s Processing ZNF33A-rep2-SRR5197120.hg20-male.36mers.unique.bam Reading in data... Reading data took 1.99002099037 s Creating peak regions... Creating peak regions took 24.3387730122 s Estimating background... Estimating background took 9.65455412865 s Processing ZNF33A-rep2-SRR5197120.hg20-male.36mers.unique.bam Reading in data... Reading data took 0.971485853195 s Creating peak regions... Creating peak regions took 22.0954780579 s Estimating background... Estimating background took 5.5660200119 s Processing ZNF33A-rep2-SRR5197120.hg20-male.36mers.unique.bam Reading in data... Reading data took 1.16170287132 s Creating peak regions... Creating peak regions took 18.2456929684 s Estimating background... Estimating background took 7.01464700699 s Processing ZNF33A-rep2-SRR5197120.hg20-male.36mers.unique.bam Reading in data... Reading data took 3.31134486198 s Creating peak regions... Creating peak regions took 72.4020040035 s Estimating background... Estimating background took 18.6902210712 s Processing ZNF33A-rep2-SRR5197120.hg20-male.36mers.unique.bam Reading in data... Reading data took 0.935407161713 s Creating peak regions... Creating peak regions took 18.469506979 s Estimating background... Estimating background took 6.18423986435 s Processing ZNF33A-rep2-SRR5197120.hg20-male.36mers.unique.bam Reading in data... Reading data took 0.568634033203 s Creating peak regions... Creating peak regions took 13.8746790886 s Estimating background... Estimating background took 3.83350491524 s Processing ZNF33A-rep2-SRR5197120.hg20-male.36mers.unique.bam Reading in data... Reading data took 0.990481138229 s Creating peak regions... Creating peak regions took 16.2911930084 s Estimating background... Estimating background took 6.97737002373 s Processing ZNF33A-rep2-SRR5197120.hg20-male.36mers.unique.bam Reading in data... Reading data took 2.83439421654 s Creating peak regions... Creating peak regions took 58.9484770298 s Estimating background... Estimating background took 13.4984338284 s Processing ZNF33A-rep2-SRR5197120.hg20-male.36mers.unique.bam Reading in data... Reading data took 1.85194516182 s Creating peak regions... Creating peak regions took 57.3314139843 s Estimating background... Estimating background took 11.3192818165 s Processing ZNF33A-rep2-SRR5197120.hg20-male.36mers.unique.bam Reading in data... Reading data took 2.5177719593 s Creating peak regions... Creating peak regions took 55.250936985 s Estimating background... Estimating background took 12.6639459133 s Processing ZNF33A-rep2-SRR5197120.hg20-male.36mers.unique.bam Reading in data... Reading data took 2.86055517197 s Creating peak regions... Creating peak regions took 51.9162259102 s Estimating background... Estimating background took 15.4445798397 s Processing ZNF33A-rep2-SRR5197120.hg20-male.36mers.unique.bam Reading in data... Reading data took 2.61069703102 s Creating peak regions... Creating peak regions took 47.6099050045 s Estimating background... Estimating background took 13.9981110096 s Processing ZNF33A-rep2-SRR5197120.hg20-male.36mers.unique.bam Reading in data... Reading data took 2.22320389748 s Creating peak regions... Creating peak regions took 43.6775839329 s Estimating background... Estimating background took 10.2827370167 s Processing ZNF33A-rep2-SRR5197120.hg20-male.36mers.unique.bam Reading in data... Reading data took 1.95762395859 s Creating peak regions... Creating peak regions took 38.5468189716 s Estimating background... Estimating background took 10.8021459579 s Processing ZNF33A-rep2-SRR5197120.hg20-male.36mers.unique.bam Reading in data... Reading data took 0.0950639247894 s Creating peak regions... Creating peak regions took 0.189327001572 s Estimating background... Estimating background took 0.682906866074 s Processing ZNF33A-rep2-SRR5197120.hg20-male.36mers.unique.bam Reading in data... Reading data took 2.8723950386 s Creating peak regions... Creating peak regions took 45.2466781139 s Estimating background... Estimating background took 14.6963000298 s Processing ZNF33A-rep2-SRR5197120.hg20-male.36mers.unique.bam Reading in data... Reading data took 0.102699041367 s Creating peak regions... Creating peak regions took 16.1328439713 s Estimating background... Estimating background took 0.582705974579 s