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='ZNF311-SRR5197110.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='ZNF311-SRR5197110/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 ZNF311-SRR5197110.hg20-male.36mers.unique.bam Reading in data... Reading data took 4.33631587029 s Creating peak regions... Creating peak regions took 76.3344929218 s Estimating background... Estimating background took 30.446048975 s Processing ZNF311-SRR5197110.hg20-male.36mers.unique.bam Reading in data... Reading data took 2.31223487854 s Creating peak regions... Creating peak regions took 39.4735300541 s Estimating background... Estimating background took 12.0001609325 s Processing ZNF311-SRR5197110.hg20-male.36mers.unique.bam Reading in data... Reading data took 2.32012605667 s Creating peak regions... Creating peak regions took 39.4593360424 s Estimating background... Estimating background took 12.2293391228 s Processing ZNF311-SRR5197110.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='ZNF311-SRR5197110.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='ZNF311-SRR5197110/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 ZNF311-SRR5197110.hg20-male.36mers.unique.bam Reading in data... Reading data took 4.50378799438 s Creating peak regions... Creating peak regions took 76.8698270321 s Estimating background... Estimating background took 32.3926680088 s Processing ZNF311-SRR5197110.hg20-male.36mers.unique.bam Reading in data... Reading data took 2.28021788597 s Creating peak regions... Creating peak regions took 41.9088490009 s Estimating background... Estimating background took 12.8711879253 s Processing ZNF311-SRR5197110.hg20-male.36mers.unique.bam Reading in data... Reading data took 2.23262095451 s Creating peak regions... Creating peak regions took 41.8555321693 s Estimating background... Estimating background took 12.9983980656 s Processing ZNF311-SRR5197110.hg20-male.36mers.unique.bam Reading in data... Reading data took 3.01736903191 s Creating peak regions... Creating peak regions took 41.7162630558 s Estimating background... Estimating background took 13.8223309517 s Processing ZNF311-SRR5197110.hg20-male.36mers.unique.bam Reading in data... Reading data took 2.06799006462 s Creating peak regions... Creating peak regions took 35.0628521442 s Estimating background... Estimating background took 15.1079568863 s Processing ZNF311-SRR5197110.hg20-male.36mers.unique.bam Reading in data... Reading data took 1.62541985512 s Creating peak regions... Creating peak regions took 30.9417130947 s Estimating background... Estimating background took 8.75061583519 s Processing ZNF311-SRR5197110.hg20-male.36mers.unique.bam Reading in data... Reading data took 1.48416900635 s Creating peak regions... Creating peak regions took 32.8054389954 s Estimating background... Estimating background took 10.2870671749 s Processing ZNF311-SRR5197110.hg20-male.36mers.unique.bam Reading in data... Reading data took 1.39659500122 s Creating peak regions... Creating peak regions took 28.3443689346 s Estimating background... Estimating background took 8.19135904312 s Processing ZNF311-SRR5197110.hg20-male.36mers.unique.bam Reading in data... Reading data took 1.66987299919 s Creating peak regions... Creating peak regions took 25.8269898891 s Estimating background... Estimating background took 11.8682000637 s Processing ZNF311-SRR5197110.hg20-male.36mers.unique.bam Reading in data... Reading data took 1.22039318085 s Creating peak regions... Creating peak regions took 25.0199899673 s Estimating background... Estimating background took 7.3452231884 s Processing ZNF311-SRR5197110.hg20-male.36mers.unique.bam Reading in data... Reading data took 1.38447904587 s Creating peak regions... Creating peak regions took 19.0706031322 s Estimating background... Estimating background took 7.90508389473 s Processing ZNF311-SRR5197110.hg20-male.36mers.unique.bam Reading in data... Reading data took 3.94365000725 s Creating peak regions... Creating peak regions took 75.0184719563 s Estimating background... Estimating background took 22.4616010189 s Processing ZNF311-SRR5197110.hg20-male.36mers.unique.bam Reading in data... Reading data took 1.32058095932 s Creating peak regions... Creating peak regions took 21.1092979908 s Estimating background... Estimating background took 7.42428302765 s Processing ZNF311-SRR5197110.hg20-male.36mers.unique.bam Reading in data... Reading data took 0.698790073395 s Creating peak regions... Creating peak regions took 15.3286659718 s Estimating background... Estimating background took 4.55906796455 s Processing ZNF311-SRR5197110.hg20-male.36mers.unique.bam Reading in data... Reading data took 1.09960484505 s Creating peak regions... Creating peak regions took 16.2975080013 s Estimating background... Estimating background took 7.33624482155 s Processing ZNF311-SRR5197110.hg20-male.36mers.unique.bam Reading in data... Reading data took 3.68468999863 s Creating peak regions... Creating peak regions took 61.5433459282 s Estimating background... Estimating background took 16.8049669266 s Processing ZNF311-SRR5197110.hg20-male.36mers.unique.bam Reading in data... Reading data took 2.69485282898 s Creating peak regions... Creating peak regions took 56.8473870754 s Estimating background... Estimating background took 13.0657999516 s Processing ZNF311-SRR5197110.hg20-male.36mers.unique.bam Reading in data... Reading data took 2.92735981941 s Creating peak regions... Creating peak regions took 57.4997050762 s Estimating background... Estimating background took 17.1500720978 s Processing ZNF311-SRR5197110.hg20-male.36mers.unique.bam Reading in data... Reading data took 3.67061305046 s Creating peak regions... Creating peak regions took 52.985311985 s Estimating background... Estimating background took 17.7361521721 s Processing ZNF311-SRR5197110.hg20-male.36mers.unique.bam Reading in data... Reading data took 2.99982213974 s Creating peak regions... Creating peak regions took 53.7007279396 s Estimating background... Estimating background took 17.6112120152 s Processing ZNF311-SRR5197110.hg20-male.36mers.unique.bam Reading in data... Reading data took 2.41214799881 s Creating peak regions... Creating peak regions took 47.2348320484 s Estimating background... Estimating background took 12.4368300438 s Processing ZNF311-SRR5197110.hg20-male.36mers.unique.bam Reading in data... Reading data took 2.1333360672 s Creating peak regions... Creating peak regions took 45.0744171143 s Estimating background... Estimating background took 12.0694739819 s Processing ZNF311-SRR5197110.hg20-male.36mers.unique.bam Reading in data... Reading data took 0.0796511173248 s Creating peak regions... Creating peak regions took 0.166085958481 s Estimating background... Estimating background took 0.549324989319 s Processing ZNF311-SRR5197110.hg20-male.36mers.unique.bam Reading in data... Reading data took 3.2974460125 s Creating peak regions... Creating peak regions took 51.1358568668 s Estimating background... Estimating background took 16.0685319901 s Processing ZNF311-SRR5197110.hg20-male.36mers.unique.bam Reading in data... Reading data took 0.103622913361 s Creating peak regions... Creating peak regions took 13.1118841171 s Estimating background... Estimating background took 0.531544923782 s