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='ZNF222-SRR5197082.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='ZNF222-SRR5197082/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 ZNF222-SRR5197082.hg20-male.36mers.unique.bam Reading in data... Reading data took 3.980864048 s Creating peak regions... Creating peak regions took 78.6645951271 s Estimating background... Estimating background took 26.6603248119 s Processing ZNF222-SRR5197082.hg20-male.36mers.unique.bam Reading in data... Reading data took 1.95260715485 s Creating peak regions... Creating peak regions took 41.3400068283 s Estimating background... Estimating background took 10.9835369587 s Processing ZNF222-SRR5197082.hg20-male.36mers.unique.bam Reading in data... Reading data took 1.84977817535 s Creating peak regions... Creating peak regions took 43.8782191277 s Estimating background... Estimating background took 10.8531980515 s Processing ZNF222-SRR5197082.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='ZNF222-SRR5197082.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='ZNF222-SRR5197082/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 ZNF222-SRR5197082.hg20-male.36mers.unique.bam Reading in data... Reading data took 4.24100518227 s Creating peak regions... Creating peak regions took 74.6237089634 s Estimating background... Estimating background took 22.7365541458 s Processing ZNF222-SRR5197082.hg20-male.36mers.unique.bam Reading in data... Reading data took 1.96242809296 s Creating peak regions... Creating peak regions took 39.079816103 s Estimating background... Estimating background took 11.227244854 s Processing ZNF222-SRR5197082.hg20-male.36mers.unique.bam Reading in data... Reading data took 1.95135498047 s Creating peak regions... Creating peak regions took 41.4784059525 s Estimating background... Estimating background took 11.7869539261 s Processing ZNF222-SRR5197082.hg20-male.36mers.unique.bam Reading in data... Reading data took 2.2003569603 s Creating peak regions... Creating peak regions took 45.2772419453 s Estimating background... Estimating background took 12.2266330719 s Processing ZNF222-SRR5197082.hg20-male.36mers.unique.bam Reading in data... Reading data took 1.75359106064 s Creating peak regions... Creating peak regions took 35.3534300327 s Estimating background... Estimating background took 10.8665411472 s Processing ZNF222-SRR5197082.hg20-male.36mers.unique.bam Reading in data... Reading data took 1.40082502365 s Creating peak regions... Creating peak regions took 32.0569400787 s Estimating background... Estimating background took 7.8739938736 s Processing ZNF222-SRR5197082.hg20-male.36mers.unique.bam Reading in data... Reading data took 1.51974105835 s Creating peak regions... Creating peak regions took 29.0418608189 s Estimating background... Estimating background took 9.01364898682 s Processing ZNF222-SRR5197082.hg20-male.36mers.unique.bam Reading in data... Reading data took 1.4007730484 s Creating peak regions... Creating peak regions took 25.9233431816 s Estimating background... Estimating background took 8.42240405083 s Processing ZNF222-SRR5197082.hg20-male.36mers.unique.bam Reading in data... Reading data took 1.69188690186 s Creating peak regions... Creating peak regions took 26.3577780724 s Estimating background... Estimating background took 10.756870985 s Processing ZNF222-SRR5197082.hg20-male.36mers.unique.bam Reading in data... Reading data took 1.11839199066 s Creating peak regions... Creating peak regions took 24.2881069183 s Estimating background... Estimating background took 5.83518719673 s Processing ZNF222-SRR5197082.hg20-male.36mers.unique.bam Reading in data... Reading data took 1.29556584358 s Creating peak regions... Creating peak regions took 18.6180639267 s Estimating background... Estimating background took 8.22223591805 s Processing ZNF222-SRR5197082.hg20-male.36mers.unique.bam Reading in data... Reading data took 3.40726613998 s Creating peak regions... Creating peak regions took 70.7476551533 s Estimating background... Estimating background took 18.3628969193 s Processing ZNF222-SRR5197082.hg20-male.36mers.unique.bam Reading in data... Reading data took 1.33347606659 s Creating peak regions... Creating peak regions took 20.0670859814 s Estimating background... Estimating background took 7.08962702751 s Processing ZNF222-SRR5197082.hg20-male.36mers.unique.bam Reading in data... Reading data took 0.596726894379 s Creating peak regions... Creating peak regions took 13.5216228962 s Estimating background... Estimating background took 3.85521507263 s Processing ZNF222-SRR5197082.hg20-male.36mers.unique.bam Reading in data... Reading data took 0.936044216156 s Creating peak regions... Creating peak regions took 14.9377579689 s Estimating background... Estimating background took 7.10282087326 s Processing ZNF222-SRR5197082.hg20-male.36mers.unique.bam Reading in data... Reading data took 2.5859708786 s Creating peak regions... Creating peak regions took 57.7516708374 s Estimating background... Estimating background took 13.7996630669 s Processing ZNF222-SRR5197082.hg20-male.36mers.unique.bam Reading in data... Reading data took 2.26311802864 s Creating peak regions... Creating peak regions took 59.0036058426 s Estimating background... Estimating background took 11.396905899 s Processing ZNF222-SRR5197082.hg20-male.36mers.unique.bam Reading in data... Reading data took 2.63728690147 s Creating peak regions... Creating peak regions took 56.1107759476 s Estimating background... Estimating background took 14.177385807 s Processing ZNF222-SRR5197082.hg20-male.36mers.unique.bam Reading in data... Reading data took 2.76347184181 s Creating peak regions... Creating peak regions took 50.2899198532 s Estimating background... Estimating background took 15.8471720219 s Processing ZNF222-SRR5197082.hg20-male.36mers.unique.bam Reading in data... Reading data took 2.65907907486 s Creating peak regions... Creating peak regions took 50.1486570835 s Estimating background... Estimating background took 15.0167379379 s Processing ZNF222-SRR5197082.hg20-male.36mers.unique.bam Reading in data... Reading data took 1.97813487053 s Creating peak regions... Creating peak regions took 40.2244288921 s Estimating background... Estimating background took 10.5177209377 s Processing ZNF222-SRR5197082.hg20-male.36mers.unique.bam Reading in data... Reading data took 1.9703309536 s Creating peak regions... Creating peak regions took 39.954210043 s Estimating background... Estimating background took 11.1742079258 s Processing ZNF222-SRR5197082.hg20-male.36mers.unique.bam Reading in data... Reading data took 0.0771489143372 s Creating peak regions... Creating peak regions took 0.148581027985 s Estimating background... Estimating background took 0.538208007812 s Processing ZNF222-SRR5197082.hg20-male.36mers.unique.bam Reading in data... Reading data took 2.37421798706 s Creating peak regions... Creating peak regions took 45.8088469505 s Estimating background... Estimating background took 12.344285965 s Processing ZNF222-SRR5197082.hg20-male.36mers.unique.bam Reading in data... Reading data took 0.0947678089142 s Creating peak regions... Creating peak regions took 15.1213541031 s Estimating background... Estimating background took 0.613079071045 s