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='ZNF285-SRR5197102.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='ZNF285-SRR5197102/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 ZNF285-SRR5197102.hg20-male.36mers.unique.bam Reading in data... Reading data took 2.7970468998 s Creating peak regions... Creating peak regions took 59.8862228394 s Estimating background... Estimating background took 13.6272249222 s Processing ZNF285-SRR5197102.hg20-male.36mers.unique.bam Reading in data... Reading data took 1.36680102348 s Creating peak regions... Creating peak regions took 29.2672538757 s Estimating background... Estimating background took 6.26076698303 s Processing ZNF285-SRR5197102.hg20-male.36mers.unique.bam Reading in data... Reading data took 1.35075902939 s Creating peak regions... Creating peak regions took 33.3483541012 s Estimating background... Estimating background took 6.74447107315 s Processing ZNF285-SRR5197102.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='ZNF285-SRR5197102.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='ZNF285-SRR5197102/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 ZNF285-SRR5197102.hg20-male.36mers.unique.bam Reading in data... Reading data took 3.58228182793 s Creating peak regions... Creating peak regions took 71.2255468369 s Estimating background... Estimating background took 17.6585381031 s Processing ZNF285-SRR5197102.hg20-male.36mers.unique.bam Reading in data... Reading data took 1.83704400063 s Creating peak regions... Creating peak regions took 36.7896640301 s Estimating background... Estimating background took 7.30109906197 s Processing ZNF285-SRR5197102.hg20-male.36mers.unique.bam Reading in data... Reading data took 1.50947618484 s Creating peak regions... Creating peak regions took 38.4432320595 s Estimating background... Estimating background took 7.91517090797 s Processing ZNF285-SRR5197102.hg20-male.36mers.unique.bam Reading in data... Reading data took 1.82900595665 s Creating peak regions... Creating peak regions took 39.2770550251 s Estimating background... Estimating background took 7.87166500092 s Processing ZNF285-SRR5197102.hg20-male.36mers.unique.bam Reading in data... Reading data took 1.51041412354 s Creating peak regions... Creating peak regions took 34.1552660465 s Estimating background... Estimating background took 7.1008439064 s Processing ZNF285-SRR5197102.hg20-male.36mers.unique.bam Reading in data... Reading data took 1.25623607635 s Creating peak regions... Creating peak regions took 31.4387638569 s Estimating background... Estimating background took 5.59493494034 s Processing ZNF285-SRR5197102.hg20-male.36mers.unique.bam Reading in data... Reading data took 1.29042196274 s Creating peak regions... Creating peak regions took 29.8673701286 s Estimating background... Estimating background took 5.55452990532 s Processing ZNF285-SRR5197102.hg20-male.36mers.unique.bam Reading in data... Reading data took 1.3023378849 s Creating peak regions... Creating peak regions took 26.5205359459 s Estimating background... Estimating background took 5.82235217094 s Processing ZNF285-SRR5197102.hg20-male.36mers.unique.bam Reading in data... Reading data took 1.48330593109 s Creating peak regions... Creating peak regions took 25.1281890869 s Estimating background... Estimating background took 7.20591306686 s Processing ZNF285-SRR5197102.hg20-male.36mers.unique.bam Reading in data... Reading data took 0.928145885468 s Creating peak regions... Creating peak regions took 22.068723917 s Estimating background... Estimating background took 4.27956199646 s Processing ZNF285-SRR5197102.hg20-male.36mers.unique.bam Reading in data... Reading data took 1.03965997696 s Creating peak regions... Creating peak regions took 16.7184898853 s Estimating background... Estimating background took 4.93533611298 s Processing ZNF285-SRR5197102.hg20-male.36mers.unique.bam Reading in data... Reading data took 2.9866631031 s Creating peak regions... Creating peak regions took 72.985547781 s Estimating background... Estimating background took 12.0665221214 s Processing ZNF285-SRR5197102.hg20-male.36mers.unique.bam Reading in data... Reading data took 1.19234609604 s Creating peak regions... Creating peak regions took 18.9731040001 s Estimating background... Estimating background took 5.2901289463 s Processing ZNF285-SRR5197102.hg20-male.36mers.unique.bam Reading in data... Reading data took 0.564666032791 s Creating peak regions... Creating peak regions took 13.8772230148 s Estimating background... Estimating background took 1.94679808617 s Processing ZNF285-SRR5197102.hg20-male.36mers.unique.bam Reading in data... Reading data took 1.01447105408 s Creating peak regions... Creating peak regions took 15.6016228199 s Estimating background... Estimating background took 4.68868303299 s Processing ZNF285-SRR5197102.hg20-male.36mers.unique.bam Reading in data... Reading data took 2.49410915375 s Creating peak regions... Creating peak regions took 60.1794600487 s Estimating background... Estimating background took 10.5996959209 s Processing ZNF285-SRR5197102.hg20-male.36mers.unique.bam Reading in data... Reading data took 2.06699919701 s Creating peak regions... Creating peak regions took 53.2186088562 s Estimating background... Estimating background took 8.30934619904 s Processing ZNF285-SRR5197102.hg20-male.36mers.unique.bam Reading in data... Reading data took 2.32344889641 s Creating peak regions... Creating peak regions took 54.5417070389 s Estimating background... Estimating background took 9.58066391945 s Processing ZNF285-SRR5197102.hg20-male.36mers.unique.bam Reading in data... Reading data took 2.43202614784 s Creating peak regions... Creating peak regions took 46.6134979725 s Estimating background... Estimating background took 10.250923872 s Processing ZNF285-SRR5197102.hg20-male.36mers.unique.bam Reading in data... Reading data took 2.3957400322 s Creating peak regions... Creating peak regions took 47.8435909748 s Estimating background... Estimating background took 9.67811393738 s Processing ZNF285-SRR5197102.hg20-male.36mers.unique.bam Reading in data... Reading data took 1.69927716255 s Creating peak regions... Creating peak regions took 41.3082830906 s Estimating background... Estimating background took 7.33054900169 s Processing ZNF285-SRR5197102.hg20-male.36mers.unique.bam Reading in data... Reading data took 1.63157296181 s Creating peak regions... Creating peak regions took 41.2343609333 s Estimating background... Estimating background took 7.42177605629 s Processing ZNF285-SRR5197102.hg20-male.36mers.unique.bam Reading in data... Reading data took 0.0866310596466 s Creating peak regions... Creating peak regions took 0.141661882401 s Estimating background... Estimating background took 0.649616956711 s Processing ZNF285-SRR5197102.hg20-male.36mers.unique.bam Reading in data... Reading data took 2.16583204269 s Creating peak regions... Creating peak regions took 46.9932329655 s Estimating background... Estimating background took 8.81443595886 s Processing ZNF285-SRR5197102.hg20-male.36mers.unique.bam Reading in data... Reading data took 0.0937120914459 s Creating peak regions... Creating peak regions took 15.0270390511 s Estimating background... Estimating background took 0.434172153473 s