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='ZNF30-SRR5197109.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='ZNF30-SRR5197109/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 ZNF30-SRR5197109.hg20-male.36mers.unique.bam Reading in data... Reading data took 6.09060788155 s Creating peak regions... Creating peak regions took 77.3529291153 s Estimating background... Estimating background took 40.2769479752 s Processing ZNF30-SRR5197109.hg20-male.36mers.unique.bam Reading in data... Reading data took 3.03037500381 s Creating peak regions... Creating peak regions took 41.2351019382 s Estimating background... Estimating background took 16.8602859974 s Processing ZNF30-SRR5197109.hg20-male.36mers.unique.bam Reading in data... Reading data took 3.11249303818 s Creating peak regions... Creating peak regions took 39.4115660191 s Estimating background... Estimating background took 16.2226150036 s Processing ZNF30-SRR5197109.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='ZNF30-SRR5197109.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='ZNF30-SRR5197109/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 ZNF30-SRR5197109.hg20-male.36mers.unique.bam Reading in data... Reading data took 5.86127686501 s Creating peak regions... Creating peak regions took 84.6481318474 s Estimating background... Estimating background took 44.6597490311 s Processing ZNF30-SRR5197109.hg20-male.36mers.unique.bam Reading in data... Reading data took 3.13261294365 s Creating peak regions... Creating peak regions took 44.3581860065 s Estimating background... Estimating background took 17.5510678291 s Processing ZNF30-SRR5197109.hg20-male.36mers.unique.bam Reading in data... Reading data took 2.9706799984 s Creating peak regions... Creating peak regions took 45.9559340477 s Estimating background... Estimating background took 18.8700580597 s Processing ZNF30-SRR5197109.hg20-male.36mers.unique.bam Reading in data... Reading data took 3.28518199921 s Creating peak regions... Creating peak regions took 47.4525008202 s Estimating background... Estimating background took 18.9523890018 s Processing ZNF30-SRR5197109.hg20-male.36mers.unique.bam Reading in data... Reading data took 2.47860908508 s Creating peak regions... Creating peak regions took 38.1293919086 s Estimating background... Estimating background took 14.9980978966 s Processing ZNF30-SRR5197109.hg20-male.36mers.unique.bam Reading in data... Reading data took 2.1326341629 s Creating peak regions... Creating peak regions took 36.4147279263 s Estimating background... Estimating background took 11.726416111 s Processing ZNF30-SRR5197109.hg20-male.36mers.unique.bam Reading in data... Reading data took 2.19110989571 s Creating peak regions... Creating peak regions took 32.9167420864 s Estimating background... Estimating background took 15.1357028484 s Processing ZNF30-SRR5197109.hg20-male.36mers.unique.bam Reading in data... Reading data took 2.41995000839 s Creating peak regions... Creating peak regions took 30.7166619301 s Estimating background... Estimating background took 15.4944438934 s Processing ZNF30-SRR5197109.hg20-male.36mers.unique.bam Reading in data... Reading data took 2.79531097412 s Creating peak regions... Creating peak regions took 28.4376609325 s Estimating background... Estimating background took 18.7461459637 s Processing ZNF30-SRR5197109.hg20-male.36mers.unique.bam Reading in data... Reading data took 1.48910307884 s Creating peak regions... Creating peak regions took 26.0684299469 s Estimating background... Estimating background took 8.07852506638 s Processing ZNF30-SRR5197109.hg20-male.36mers.unique.bam Reading in data... Reading data took 2.1233420372 s Creating peak regions... Creating peak regions took 21.8950350285 s Estimating background... Estimating background took 14.4990091324 s Processing ZNF30-SRR5197109.hg20-male.36mers.unique.bam Reading in data... Reading data took 5.04101991653 s Creating peak regions... Creating peak regions took 81.5050501823 s Estimating background... Estimating background took 28.4599018097 s Processing ZNF30-SRR5197109.hg20-male.36mers.unique.bam Reading in data... Reading data took 1.88126802444 s Creating peak regions... Creating peak regions took 22.0651509762 s Estimating background... Estimating background took 11.8340871334 s Processing ZNF30-SRR5197109.hg20-male.36mers.unique.bam Reading in data... Reading data took 0.912396192551 s Creating peak regions... Creating peak regions took 14.8167970181 s Estimating background... Estimating background took 5.58822512627 s Processing ZNF30-SRR5197109.hg20-male.36mers.unique.bam Reading in data... Reading data took 1.75511789322 s Creating peak regions... Creating peak regions took 17.9198570251 s Estimating background... Estimating background took 12.898555994 s Processing ZNF30-SRR5197109.hg20-male.36mers.unique.bam Reading in data... Reading data took 3.93512511253 s Creating peak regions... Creating peak regions took 66.2779140472 s Estimating background... Estimating background took 22.8895728588 s Processing ZNF30-SRR5197109.hg20-male.36mers.unique.bam Reading in data... Reading data took 3.45202803612 s Creating peak regions... Creating peak regions took 61.1451230049 s Estimating background... Estimating background took 15.4864280224 s Processing ZNF30-SRR5197109.hg20-male.36mers.unique.bam Reading in data... Reading data took 3.61380600929 s Creating peak regions... Creating peak regions took 64.8809468746 s Estimating background... Estimating background took 21.4480638504 s Processing ZNF30-SRR5197109.hg20-male.36mers.unique.bam Reading in data... Reading data took 4.00052189827 s Creating peak regions... Creating peak regions took 57.0356869698 s Estimating background... Estimating background took 23.1855740547 s Processing ZNF30-SRR5197109.hg20-male.36mers.unique.bam Reading in data... Reading data took 3.73707795143 s Creating peak regions... Creating peak regions took 51.646613121 s Estimating background... Estimating background took 21.6415219307 s Processing ZNF30-SRR5197109.hg20-male.36mers.unique.bam Reading in data... Reading data took 2.92420601845 s Creating peak regions... Creating peak regions took 42.8370931149 s Estimating background... Estimating background took 13.0198500156 s Processing ZNF30-SRR5197109.hg20-male.36mers.unique.bam Reading in data... Reading data took 2.23548793793 s Creating peak regions... Creating peak regions took 40.1593410969 s Estimating background... Estimating background took 15.2175328732 s Processing ZNF30-SRR5197109.hg20-male.36mers.unique.bam Reading in data... Reading data took 0.086569070816 s Creating peak regions... Creating peak regions took 0.157984972 s Estimating background... Estimating background took 0.654012918472 s Processing ZNF30-SRR5197109.hg20-male.36mers.unique.bam Reading in data... Reading data took 3.20659995079 s Creating peak regions... Creating peak regions took 50.8709988594 s Estimating background... Estimating background took 19.7718429565 s Processing ZNF30-SRR5197109.hg20-male.36mers.unique.bam Reading in data... Reading data took 0.106101036072 s Creating peak regions... Creating peak regions took 16.5899379253 s Estimating background... Estimating background took 0.556313037872 s