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='ZNF223-SRR5197083.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='ZNF223-SRR5197083/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 ZNF223-SRR5197083.hg20-male.36mers.unique.bam Reading in data... Reading data took 9.94271802902 s Creating peak regions... Creating peak regions took 78.2190082073 s Estimating background... Estimating background took 87.7152249813 s Processing ZNF223-SRR5197083.hg20-male.36mers.unique.bam Reading in data... Reading data took 5.03141689301 s Creating peak regions... Creating peak regions took 41.6562728882 s Estimating background... Estimating background took 31.539618969 s Processing ZNF223-SRR5197083.hg20-male.36mers.unique.bam Reading in data... Reading data took 4.66207504272 s Creating peak regions... Creating peak regions took 35.6628749371 s Estimating background... Estimating background took 30.8833739758 s Processing ZNF223-SRR5197083.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='ZNF223-SRR5197083.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='ZNF223-SRR5197083/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 ZNF223-SRR5197083.hg20-male.36mers.unique.bam Reading in data... Reading data took 10.1549038887 s Creating peak regions... Creating peak regions took 80.9770619869 s Estimating background... Estimating background took 76.2922542095 s Processing ZNF223-SRR5197083.hg20-male.36mers.unique.bam Reading in data... Reading data took 4.31171011925 s Creating peak regions... Creating peak regions took 37.6902458668 s Estimating background... Estimating background took 29.6936039925 s Processing ZNF223-SRR5197083.hg20-male.36mers.unique.bam Reading in data... Reading data took 4.12647008896 s Creating peak regions... Creating peak regions took 37.0124468803 s Estimating background... Estimating background took 30.8859791756 s Processing ZNF223-SRR5197083.hg20-male.36mers.unique.bam Reading in data... Reading data took 4.41837501526 s Creating peak regions... Creating peak regions took 37.0968840122 s Estimating background... Estimating background took 33.1077318192 s Processing ZNF223-SRR5197083.hg20-male.36mers.unique.bam Reading in data... Reading data took 4.61385607719 s Creating peak regions... Creating peak regions took 33.1547949314 s Estimating background... Estimating background took 45.7686500549 s Processing ZNF223-SRR5197083.hg20-male.36mers.unique.bam Reading in data... Reading data took 3.18850398064 s Creating peak regions... Creating peak regions took 29.4355220795 s Estimating background... Estimating background took 21.6337120533 s Processing ZNF223-SRR5197083.hg20-male.36mers.unique.bam Reading in data... Reading data took 2.50107598305 s Creating peak regions... Creating peak regions took 27.1791939735 s Estimating background... Estimating background took 19.5316340923 s Processing ZNF223-SRR5197083.hg20-male.36mers.unique.bam Reading in data... Reading data took 2.56357812881 s Creating peak regions... Creating peak regions took 23.984142065 s Estimating background... Estimating background took 17.4741828442 s Processing ZNF223-SRR5197083.hg20-male.36mers.unique.bam Reading in data... Reading data took 2.77643013 s Creating peak regions... Creating peak regions took 22.8905160427 s Estimating background... Estimating background took 20.8352398872 s Processing ZNF223-SRR5197083.hg20-male.36mers.unique.bam Reading in data... Reading data took 2.56420707703 s Creating peak regions... Creating peak regions took 21.5817379951 s Estimating background... Estimating background took 18.2691679001 s Processing ZNF223-SRR5197083.hg20-male.36mers.unique.bam Reading in data... Reading data took 1.86761617661 s Creating peak regions... Creating peak regions took 16.2173540592 s Estimating background... Estimating background took 11.6214160919 s Processing ZNF223-SRR5197083.hg20-male.36mers.unique.bam Reading in data... Reading data took 7.34577488899 s Creating peak regions... Creating peak regions took 71.1360011101 s Estimating background... Estimating background took 56.3596260548 s Processing ZNF223-SRR5197083.hg20-male.36mers.unique.bam Reading in data... Reading data took 2.10253500938 s Creating peak regions... Creating peak regions took 19.3230669498 s Estimating background... Estimating background took 15.6346449852 s Processing ZNF223-SRR5197083.hg20-male.36mers.unique.bam Reading in data... Reading data took 1.69768190384 s Creating peak regions... Creating peak regions took 12.0306799412 s Estimating background... Estimating background took 9.98746085167 s Processing ZNF223-SRR5197083.hg20-male.36mers.unique.bam Reading in data... Reading data took 1.37638401985 s Creating peak regions... Creating peak regions took 13.4845740795 s Estimating background... Estimating background took 11.3380770683 s Processing ZNF223-SRR5197083.hg20-male.36mers.unique.bam Reading in data... Reading data took 6.16220211983 s Creating peak regions... Creating peak regions took 54.2120771408 s Estimating background... Estimating background took 48.2270209789 s Processing ZNF223-SRR5197083.hg20-male.36mers.unique.bam Reading in data... Reading data took 5.46728301048 s Creating peak regions... Creating peak regions took 52.6591880322 s Estimating background... Estimating background took 38.4961938858 s Processing ZNF223-SRR5197083.hg20-male.36mers.unique.bam Reading in data... Reading data took 6.21545314789 s Creating peak regions... Creating peak regions took 50.863476038 s Estimating background... Estimating background took 46.0044369698 s Processing ZNF223-SRR5197083.hg20-male.36mers.unique.bam Reading in data... Reading data took 6.42811608315 s Creating peak regions... Creating peak regions took 50.8197610378 s Estimating background... Estimating background took 51.4204220772 s Processing ZNF223-SRR5197083.hg20-male.36mers.unique.bam Reading in data... Reading data took 5.4764881134 s Creating peak regions... Creating peak regions took 43.4374821186 s Estimating background... Estimating background took 41.0651471615 s Processing ZNF223-SRR5197083.hg20-male.36mers.unique.bam Reading in data... Reading data took 4.4245018959 s Creating peak regions... Creating peak regions took 40.5738549232 s Estimating background... Estimating background took 31.1541121006 s Processing ZNF223-SRR5197083.hg20-male.36mers.unique.bam Reading in data... Reading data took 3.79343008995 s Creating peak regions... Creating peak regions took 37.5832769871 s Estimating background... Estimating background took 27.7579450607 s Processing ZNF223-SRR5197083.hg20-male.36mers.unique.bam Reading in data... Reading data took 0.190223932266 s Creating peak regions... Creating peak regions took 0.273451089859 s Estimating background... Estimating background took 0.748505115509 s Processing ZNF223-SRR5197083.hg20-male.36mers.unique.bam Reading in data... Reading data took 5.78845596313 s Creating peak regions... Creating peak regions took 44.7867870331 s Estimating background... Estimating background took 51.3361990452 s Processing ZNF223-SRR5197083.hg20-male.36mers.unique.bam Reading in data... Reading data took 0.379400014877 s Creating peak regions... Creating peak regions took 14.4487030506 s Estimating background... Estimating background took 0.770662784576 s