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='ZNF300-SRR5197106.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='ZNF300-SRR5197106/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 ZNF300-SRR5197106.hg20-male.36mers.unique.bam Reading in data... Reading data took 4.8854238987 s Creating peak regions... Creating peak regions took 73.4515199661 s Estimating background... Estimating background took 15.551306963 s Processing ZNF300-SRR5197106.hg20-male.36mers.unique.bam Reading in data... Reading data took 2.45153188705 s Creating peak regions... Creating peak regions took 38.0326571465 s Estimating background... Estimating background took 6.48506402969 s Processing ZNF300-SRR5197106.hg20-male.36mers.unique.bam Reading in data... Reading data took 2.43501091003 s Creating peak regions... Creating peak regions took 40.2260091305 s Estimating background... Estimating background took 6.66411995888 s Processing ZNF300-SRR5197106.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='ZNF300-SRR5197106.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='ZNF300-SRR5197106/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 ZNF300-SRR5197106.hg20-male.36mers.unique.bam Reading in data... Reading data took 4.72610998154 s Creating peak regions... Creating peak regions took 73.3190419674 s Estimating background... Estimating background took 15.4296429157 s Processing ZNF300-SRR5197106.hg20-male.36mers.unique.bam Reading in data... Reading data took 2.31991815567 s Creating peak regions... Creating peak regions took 40.0672659874 s Estimating background... Estimating background took 6.98857808113 s Processing ZNF300-SRR5197106.hg20-male.36mers.unique.bam Reading in data... Reading data took 2.40733098984 s Creating peak regions... Creating peak regions took 42.8580050468 s Estimating background... Estimating background took 6.90378308296 s Processing ZNF300-SRR5197106.hg20-male.36mers.unique.bam Reading in data... Reading data took 2.13682293892 s Creating peak regions... Creating peak regions took 40.7333290577 s Estimating background... Estimating background took 7.40834903717 s Processing ZNF300-SRR5197106.hg20-male.36mers.unique.bam Reading in data... Reading data took 2.24057412148 s Creating peak regions... Creating peak regions took 35.9325740337 s Estimating background... Estimating background took 8.10317707062 s Processing ZNF300-SRR5197106.hg20-male.36mers.unique.bam Reading in data... Reading data took 2.029047966 s Creating peak regions... Creating peak regions took 31.4605879784 s Estimating background... Estimating background took 5.62193012238 s Processing ZNF300-SRR5197106.hg20-male.36mers.unique.bam Reading in data... Reading data took 1.81992101669 s Creating peak regions... Creating peak regions took 27.924407959 s Estimating background... Estimating background took 5.20469713211 s Processing ZNF300-SRR5197106.hg20-male.36mers.unique.bam Reading in data... Reading data took 1.59923791885 s Creating peak regions... Creating peak regions took 27.620372057 s Estimating background... Estimating background took 4.85427880287 s Processing ZNF300-SRR5197106.hg20-male.36mers.unique.bam Reading in data... Reading data took 1.70022892952 s Creating peak regions... Creating peak regions took 25.9016671181 s Estimating background... Estimating background took 5.0628900528 s Processing ZNF300-SRR5197106.hg20-male.36mers.unique.bam Reading in data... Reading data took 1.36832690239 s Creating peak regions... Creating peak regions took 24.5078699589 s Estimating background... Estimating background took 3.83575487137 s Processing ZNF300-SRR5197106.hg20-male.36mers.unique.bam Reading in data... Reading data took 1.43398594856 s Creating peak regions... Creating peak regions took 17.738861084 s Estimating background... Estimating background took 3.44459104538 s Processing ZNF300-SRR5197106.hg20-male.36mers.unique.bam Reading in data... Reading data took 4.15829014778 s Creating peak regions... Creating peak regions took 74.9227280617 s Estimating background... Estimating background took 12.1958599091 s Processing ZNF300-SRR5197106.hg20-male.36mers.unique.bam Reading in data... Reading data took 1.42917299271 s Creating peak regions... Creating peak regions took 19.7906918526 s Estimating background... Estimating background took 4.40476799011 s Processing ZNF300-SRR5197106.hg20-male.36mers.unique.bam Reading in data... Reading data took 0.757261037827 s Creating peak regions... Creating peak regions took 13.606014967 s Estimating background... Estimating background took 2.74170589447 s Processing ZNF300-SRR5197106.hg20-male.36mers.unique.bam Reading in data... Reading data took 1.09342598915 s Creating peak regions... Creating peak regions took 14.3705120087 s Estimating background... Estimating background took 3.58350586891 s Processing ZNF300-SRR5197106.hg20-male.36mers.unique.bam Reading in data... Reading data took 3.45480704308 s Creating peak regions... Creating peak regions took 61.9070448875 s Estimating background... Estimating background took 9.95338988304 s Processing ZNF300-SRR5197106.hg20-male.36mers.unique.bam Reading in data... Reading data took 2.99864792824 s Creating peak regions... Creating peak regions took 58.5654549599 s Estimating background... Estimating background took 8.12913703918 s Processing ZNF300-SRR5197106.hg20-male.36mers.unique.bam Reading in data... Reading data took 3.19597792625 s Creating peak regions... Creating peak regions took 56.1419239044 s Estimating background... Estimating background took 8.82151699066 s Processing ZNF300-SRR5197106.hg20-male.36mers.unique.bam Reading in data... Reading data took 3.36202001572 s Creating peak regions... Creating peak regions took 53.0851180553 s Estimating background... Estimating background took 9.09407711029 s Processing ZNF300-SRR5197106.hg20-male.36mers.unique.bam Reading in data... Reading data took 2.88736820221 s Creating peak regions... Creating peak regions took 46.6906690598 s Estimating background... Estimating background took 8.91181612015 s Processing ZNF300-SRR5197106.hg20-male.36mers.unique.bam Reading in data... Reading data took 2.56844997406 s Creating peak regions... Creating peak regions took 44.0965018272 s Estimating background... Estimating background took 7.32500100136 s Processing ZNF300-SRR5197106.hg20-male.36mers.unique.bam Reading in data... Reading data took 2.1878991127 s Creating peak regions... Creating peak regions took 39.9347071648 s Estimating background... Estimating background took 6.22852015495 s Processing ZNF300-SRR5197106.hg20-male.36mers.unique.bam Reading in data... Reading data took 0.0711741447449 s Creating peak regions... Creating peak regions took 0.132886886597 s Estimating background... Estimating background took 0.407385826111 s Processing ZNF300-SRR5197106.hg20-male.36mers.unique.bam Reading in data... Reading data took 3.52009797096 s Creating peak regions... Creating peak regions took 49.493461132 s Estimating background... Estimating background took 10.0854389668 s Processing ZNF300-SRR5197106.hg20-male.36mers.unique.bam Reading in data... Reading data took 0.135968208313 s Creating peak regions... Creating peak regions took 16.2340710163 s Estimating background... Estimating background took 0.430448055267 s