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='ZNF333-SRR5197116.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='ZNF333-SRR5197116/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 ZNF333-SRR5197116.hg20-male.36mers.unique.bam Reading in data... Reading data took 3.70872092247 s Creating peak regions... Creating peak regions took 60.9190049171 s Estimating background... Estimating background took 23.9276931286 s Processing ZNF333-SRR5197116.hg20-male.36mers.unique.bam Reading in data... Reading data took 1.7071788311 s Creating peak regions... Creating peak regions took 32.4398829937 s Estimating background... Estimating background took 10.184470892 s Processing ZNF333-SRR5197116.hg20-male.36mers.unique.bam Reading in data... Reading data took 1.78224015236 s Creating peak regions... Creating peak regions took 34.9808571339 s Estimating background... Estimating background took 10.6696751118 s Processing ZNF333-SRR5197116.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='ZNF333-SRR5197116.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='ZNF333-SRR5197116/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 ZNF333-SRR5197116.hg20-male.36mers.unique.bam Reading in data... Reading data took 4.46928620338 s Creating peak regions... Creating peak regions took 73.2705800533 s Estimating background... Estimating background took 29.4432530403 s Processing ZNF333-SRR5197116.hg20-male.36mers.unique.bam Reading in data... Reading data took 2.2366809845 s Creating peak regions... Creating peak regions took 40.7174940109 s Estimating background... Estimating background took 12.9427399635 s Processing ZNF333-SRR5197116.hg20-male.36mers.unique.bam Reading in data... Reading data took 2.30446505547 s Creating peak regions... Creating peak regions took 41.6124978065 s Estimating background... Estimating background took 12.4861459732 s Processing ZNF333-SRR5197116.hg20-male.36mers.unique.bam Reading in data... Reading data took 2.27339911461 s Creating peak regions... Creating peak regions took 42.0032160282 s Estimating background... Estimating background took 14.000797987 s Processing ZNF333-SRR5197116.hg20-male.36mers.unique.bam Reading in data... Reading data took 1.92359089851 s Creating peak regions... Creating peak regions took 34.3961489201 s Estimating background... Estimating background took 12.4303369522 s Processing ZNF333-SRR5197116.hg20-male.36mers.unique.bam Reading in data... Reading data took 1.65204787254 s Creating peak regions... Creating peak regions took 29.900851965 s Estimating background... Estimating background took 8.72405791283 s Processing ZNF333-SRR5197116.hg20-male.36mers.unique.bam Reading in data... Reading data took 1.47162294388 s Creating peak regions... Creating peak regions took 29.5561521053 s Estimating background... Estimating background took 10.0265870094 s Processing ZNF333-SRR5197116.hg20-male.36mers.unique.bam Reading in data... Reading data took 1.49014091492 s Creating peak regions... Creating peak regions took 26.3121869564 s Estimating background... Estimating background took 9.41259694099 s Processing ZNF333-SRR5197116.hg20-male.36mers.unique.bam Reading in data... Reading data took 1.86498498917 s Creating peak regions... Creating peak regions took 26.0033040047 s Estimating background... Estimating background took 11.5879511833 s Processing ZNF333-SRR5197116.hg20-male.36mers.unique.bam Reading in data... Reading data took 1.1459710598 s Creating peak regions... Creating peak regions took 21.8579909801 s Estimating background... Estimating background took 6.36146903038 s Processing ZNF333-SRR5197116.hg20-male.36mers.unique.bam Reading in data... Reading data took 1.23505687714 s Creating peak regions... Creating peak regions took 18.8735821247 s Estimating background... Estimating background took 8.66959786415 s Processing ZNF333-SRR5197116.hg20-male.36mers.unique.bam Reading in data... Reading data took 3.75153493881 s Creating peak regions... Creating peak regions took 71.8762149811 s Estimating background... Estimating background took 20.1885049343 s Processing ZNF333-SRR5197116.hg20-male.36mers.unique.bam Reading in data... Reading data took 1.36046719551 s Creating peak regions... Creating peak regions took 19.7770040035 s Estimating background... Estimating background took 8.1359500885 s Processing ZNF333-SRR5197116.hg20-male.36mers.unique.bam Reading in data... Reading data took 0.676291942596 s Creating peak regions... Creating peak regions took 14.680423975 s Estimating background... Estimating background took 4.55834889412 s Processing ZNF333-SRR5197116.hg20-male.36mers.unique.bam Reading in data... Reading data took 1.19775819778 s Creating peak regions... Creating peak regions took 16.4306509495 s Estimating background... Estimating background took 8.41412496567 s Processing ZNF333-SRR5197116.hg20-male.36mers.unique.bam Reading in data... Reading data took 2.98026895523 s Creating peak regions... Creating peak regions took 55.512346983 s Estimating background... Estimating background took 17.1331920624 s Processing ZNF333-SRR5197116.hg20-male.36mers.unique.bam Reading in data... Reading data took 2.4782140255 s Creating peak regions... Creating peak regions took 55.171102047 s Estimating background... Estimating background took 12.6182620525 s Processing ZNF333-SRR5197116.hg20-male.36mers.unique.bam Reading in data... Reading data took 2.67875814438 s Creating peak regions... Creating peak regions took 54.3895339966 s Estimating background... Estimating background took 14.9731860161 s Processing ZNF333-SRR5197116.hg20-male.36mers.unique.bam Reading in data... Reading data took 2.95101213455 s Creating peak regions... Creating peak regions took 51.1566698551 s Estimating background... Estimating background took 18.3217709064 s Processing ZNF333-SRR5197116.hg20-male.36mers.unique.bam Reading in data... Reading data took 2.79780292511 s Creating peak regions... Creating peak regions took 47.1696341038 s Estimating background... Estimating background took 15.6467680931 s Processing ZNF333-SRR5197116.hg20-male.36mers.unique.bam Reading in data... Reading data took 2.09484982491 s Creating peak regions... Creating peak regions took 43.4978289604 s Estimating background... Estimating background took 11.5642828941 s Processing ZNF333-SRR5197116.hg20-male.36mers.unique.bam Reading in data... Reading data took 2.04686808586 s Creating peak regions... Creating peak regions took 44.0014650822 s Estimating background... Estimating background took 10.7990739346 s Processing ZNF333-SRR5197116.hg20-male.36mers.unique.bam Reading in data... Reading data took 0.087660074234 s Creating peak regions... Creating peak regions took 0.163563966751 s Estimating background... Estimating background took 0.651026964188 s Processing ZNF333-SRR5197116.hg20-male.36mers.unique.bam Reading in data... Reading data took 2.59852409363 s Creating peak regions... Creating peak regions took 48.7113528252 s Estimating background... Estimating background took 14.6623091698 s Processing ZNF333-SRR5197116.hg20-male.36mers.unique.bam Reading in data... Reading data took 0.116524934769 s Creating peak regions... Creating peak regions took 16.1884679794 s Estimating background... Estimating background took 0.748697042465 s