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='ZNF157-SRR5197064.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='ZNF157-SRR5197064/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 ZNF157-SRR5197064.hg20-male.36mers.unique.bam Reading in data... Reading data took 5.74851489067 s Creating peak regions... Creating peak regions took 64.1171889305 s Estimating background... Estimating background took 45.8247170448 s Processing ZNF157-SRR5197064.hg20-male.36mers.unique.bam Reading in data... Reading data took 2.79019498825 s Creating peak regions... Creating peak regions took 34.4198491573 s Estimating background... Estimating background took 19.5174100399 s Processing ZNF157-SRR5197064.hg20-male.36mers.unique.bam Reading in data... Reading data took 2.9514541626 s Creating peak regions... Creating peak regions took 35.0428171158 s Estimating background... Estimating background took 20.0916850567 s Processing ZNF157-SRR5197064.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='ZNF157-SRR5197064.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='ZNF157-SRR5197064/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 ZNF157-SRR5197064.hg20-male.36mers.unique.bam Reading in data... Reading data took 6.34748911858 s Creating peak regions... Creating peak regions took 70.9850320816 s Estimating background... Estimating background took 49.8770620823 s Processing ZNF157-SRR5197064.hg20-male.36mers.unique.bam Reading in data... Reading data took 3.1335709095 s Creating peak regions... Creating peak regions took 37.521479845 s Estimating background... Estimating background took 21.1614358425 s Processing ZNF157-SRR5197064.hg20-male.36mers.unique.bam Reading in data... Reading data took 3.17973899841 s Creating peak regions... Creating peak regions took 38.2615280151 s Estimating background... Estimating background took 22.0246610641 s Processing ZNF157-SRR5197064.hg20-male.36mers.unique.bam Reading in data... Reading data took 3.88866376877 s Creating peak regions... Creating peak regions took 36.9120638371 s Estimating background... Estimating background took 22.4735019207 s Processing ZNF157-SRR5197064.hg20-male.36mers.unique.bam Reading in data... Reading data took 2.84990096092 s Creating peak regions... Creating peak regions took 31.3428850174 s Estimating background... Estimating background took 20.21727705 s Processing ZNF157-SRR5197064.hg20-male.36mers.unique.bam Reading in data... Reading data took 2.36327385902 s Creating peak regions... Creating peak regions took 28.9876949787 s Estimating background... Estimating background took 14.16705513 s Processing ZNF157-SRR5197064.hg20-male.36mers.unique.bam Reading in data... Reading data took 2.15189099312 s Creating peak regions... Creating peak regions took 26.9722559452 s Estimating background... Estimating background took 16.2685642242 s Processing ZNF157-SRR5197064.hg20-male.36mers.unique.bam Reading in data... Reading data took 2.20088386536 s Creating peak regions... Creating peak regions took 23.9235761166 s Estimating background... Estimating background took 16.7783827782 s Processing ZNF157-SRR5197064.hg20-male.36mers.unique.bam Reading in data... Reading data took 2.74219799042 s Creating peak regions... Creating peak regions took 24.0768949986 s Estimating background... Estimating background took 21.9189460278 s Processing ZNF157-SRR5197064.hg20-male.36mers.unique.bam Reading in data... Reading data took 1.77579593658 s Creating peak regions... Creating peak regions took 21.8565349579 s Estimating background... Estimating background took 10.1541409492 s Processing ZNF157-SRR5197064.hg20-male.36mers.unique.bam Reading in data... Reading data took 2.05203104019 s Creating peak regions... Creating peak regions took 18.0364968777 s Estimating background... Estimating background took 15.6963720322 s Processing ZNF157-SRR5197064.hg20-male.36mers.unique.bam Reading in data... Reading data took 5.33600497246 s Creating peak regions... Creating peak regions took 66.5470371246 s Estimating background... Estimating background took 34.1770660877 s Processing ZNF157-SRR5197064.hg20-male.36mers.unique.bam Reading in data... Reading data took 1.97313499451 s Creating peak regions... Creating peak regions took 19.1531281471 s Estimating background... Estimating background took 13.8270671368 s Processing ZNF157-SRR5197064.hg20-male.36mers.unique.bam Reading in data... Reading data took 1.04969501495 s Creating peak regions... Creating peak regions took 13.0128519535 s Estimating background... Estimating background took 7.03201818466 s Processing ZNF157-SRR5197064.hg20-male.36mers.unique.bam Reading in data... Reading data took 1.9735250473 s Creating peak regions... Creating peak regions took 14.6834189892 s Estimating background... Estimating background took 14.5602722168 s Processing ZNF157-SRR5197064.hg20-male.36mers.unique.bam Reading in data... Reading data took 4.07803583145 s Creating peak regions... Creating peak regions took 57.5584871769 s Estimating background... Estimating background took 26.5753629208 s Processing ZNF157-SRR5197064.hg20-male.36mers.unique.bam Reading in data... Reading data took 3.48070597649 s Creating peak regions... Creating peak regions took 51.2565560341 s Estimating background... Estimating background took 20.183385849 s Processing ZNF157-SRR5197064.hg20-male.36mers.unique.bam Reading in data... Reading data took 3.926019907 s Creating peak regions... Creating peak regions took 49.6704940796 s Estimating background... Estimating background took 25.8088378906 s Processing ZNF157-SRR5197064.hg20-male.36mers.unique.bam Reading in data... Reading data took 4.24183297157 s Creating peak regions... Creating peak regions took 47.950371027 s Estimating background... Estimating background took 28.9160239697 s Processing ZNF157-SRR5197064.hg20-male.36mers.unique.bam Reading in data... Reading data took 3.99824404716 s Creating peak regions... Creating peak regions took 45.5285089016 s Estimating background... Estimating background took 28.1369068623 s Processing ZNF157-SRR5197064.hg20-male.36mers.unique.bam Reading in data... Reading data took 3.24778795242 s Creating peak regions... Creating peak regions took 40.2917890549 s Estimating background... Estimating background took 18.7276368141 s Processing ZNF157-SRR5197064.hg20-male.36mers.unique.bam Reading in data... Reading data took 2.84660577774 s Creating peak regions... Creating peak regions took 37.6207289696 s Estimating background... Estimating background took 19.4458339214 s Processing ZNF157-SRR5197064.hg20-male.36mers.unique.bam Reading in data... Reading data took 0.0988509654999 s Creating peak regions... Creating peak regions took 0.179347038269 s Estimating background... Estimating background took 0.570874929428 s Processing ZNF157-SRR5197064.hg20-male.36mers.unique.bam Reading in data... Reading data took 3.95159602165 s Creating peak regions... Creating peak regions took 43.2020590305 s Estimating background... Estimating background took 25.8295691013 s Processing ZNF157-SRR5197064.hg20-male.36mers.unique.bam Reading in data... Reading data took 0.152230024338 s Creating peak regions... Creating peak regions took 14.778649807 s Estimating background... Estimating background took 0.674653053284 s