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='ZNF419-SRR5197132.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='ZNF419-SRR5197132/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 ZNF419-SRR5197132.hg20-male.36mers.unique.bam Reading in data... Reading data took 8.66928291321 s Creating peak regions... Creating peak regions took 84.1052069664 s Estimating background... Estimating background took 93.4328610897 s Processing ZNF419-SRR5197132.hg20-male.36mers.unique.bam Reading in data... Reading data took 4.69002079964 s Creating peak regions... Creating peak regions took 46.1690850258 s Estimating background... Estimating background took 35.7145249844 s Processing ZNF419-SRR5197132.hg20-male.36mers.unique.bam Reading in data... Reading data took 4.15532302856 s Creating peak regions... Creating peak regions took 41.9504239559 s Estimating background... Estimating background took 33.2440209389 s Processing ZNF419-SRR5197132.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='ZNF419-SRR5197132.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='ZNF419-SRR5197132/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 ZNF419-SRR5197132.hg20-male.36mers.unique.bam Reading in data... Reading data took 8.72841596603 s Creating peak regions... Creating peak regions took 81.9663090706 s Estimating background... Estimating background took 92.7688879967 s Processing ZNF419-SRR5197132.hg20-male.36mers.unique.bam Reading in data... Reading data took 4.52780604362 s Creating peak regions... Creating peak regions took 45.2153031826 s Estimating background... Estimating background took 38.9246439934 s Processing ZNF419-SRR5197132.hg20-male.36mers.unique.bam Reading in data... Reading data took 4.63372302055 s Creating peak regions... Creating peak regions took 43.971255064 s Estimating background... Estimating background took 38.0236439705 s Processing ZNF419-SRR5197132.hg20-male.36mers.unique.bam Reading in data... Reading data took 4.82416701317 s Creating peak regions... Creating peak regions took 42.8015739918 s Estimating background... Estimating background took 37.2265751362 s Processing ZNF419-SRR5197132.hg20-male.36mers.unique.bam Reading in data... Reading data took 3.62139987946 s Creating peak regions... Creating peak regions took 37.9296917915 s Estimating background... Estimating background took 36.0782968998 s Processing ZNF419-SRR5197132.hg20-male.36mers.unique.bam Reading in data... Reading data took 3.28332304955 s Creating peak regions... Creating peak regions took 34.0114271641 s Estimating background... Estimating background took 24.0825190544 s Processing ZNF419-SRR5197132.hg20-male.36mers.unique.bam Reading in data... Reading data took 2.80118083954 s Creating peak regions... Creating peak regions took 32.565707922 s Estimating background... Estimating background took 28.271075964 s Processing ZNF419-SRR5197132.hg20-male.36mers.unique.bam Reading in data... Reading data took 3.16527700424 s Creating peak regions... Creating peak regions took 30.0258879662 s Estimating background... Estimating background took 27.4216678143 s Processing ZNF419-SRR5197132.hg20-male.36mers.unique.bam Reading in data... Reading data took 4.14833688736 s Creating peak regions... Creating peak regions took 27.1626989841 s Estimating background... Estimating background took 34.9122340679 s Processing ZNF419-SRR5197132.hg20-male.36mers.unique.bam Reading in data... Reading data took 2.30581307411 s Creating peak regions... Creating peak regions took 25.8707458973 s Estimating background... Estimating background took 17.2866330147 s Processing ZNF419-SRR5197132.hg20-male.36mers.unique.bam Reading in data... Reading data took 2.41292715073 s Creating peak regions... Creating peak regions took 19.1346650124 s Estimating background... Estimating background took 23.3959329128 s Processing ZNF419-SRR5197132.hg20-male.36mers.unique.bam Reading in data... Reading data took 7.30375409126 s Creating peak regions... Creating peak regions took 80.0789308548 s Estimating background... Estimating background took 60.9439930916 s Processing ZNF419-SRR5197132.hg20-male.36mers.unique.bam Reading in data... Reading data took 2.73322510719 s Creating peak regions... Creating peak regions took 23.8790328503 s Estimating background... Estimating background took 23.2191128731 s Processing ZNF419-SRR5197132.hg20-male.36mers.unique.bam Reading in data... Reading data took 1.46591687202 s Creating peak regions... Creating peak regions took 15.6691379547 s Estimating background... Estimating background took 12.0494801998 s Processing ZNF419-SRR5197132.hg20-male.36mers.unique.bam Reading in data... Reading data took 2.07706713676 s Creating peak regions... Creating peak regions took 16.3507709503 s Estimating background... Estimating background took 22.7030630112 s Processing ZNF419-SRR5197132.hg20-male.36mers.unique.bam Reading in data... Reading data took 5.80723905563 s Creating peak regions... Creating peak regions took 63.681923151 s Estimating background... Estimating background took 46.1563868523 s Processing ZNF419-SRR5197132.hg20-male.36mers.unique.bam Reading in data... Reading data took 4.30779194832 s Creating peak regions... Creating peak regions took 52.6530790329 s Estimating background... Estimating background took 32.7190670967 s Processing ZNF419-SRR5197132.hg20-male.36mers.unique.bam Reading in data... Reading data took 5.64663887024 s Creating peak regions... Creating peak regions took 57.0136129856 s Estimating background... Estimating background took 41.5568659306 s Processing ZNF419-SRR5197132.hg20-male.36mers.unique.bam Reading in data... Reading data took 5.22887396812 s Creating peak regions... Creating peak regions took 45.3245558739 s Estimating background... Estimating background took 42.30894804 s Processing ZNF419-SRR5197132.hg20-male.36mers.unique.bam Reading in data... Reading data took 4.44387388229 s Creating peak regions... Creating peak regions took 43.9269621372 s Estimating background... Estimating background took 39.9358150959 s Processing ZNF419-SRR5197132.hg20-male.36mers.unique.bam Reading in data... Reading data took 3.53318309784 s Creating peak regions... Creating peak regions took 39.2189719677 s Estimating background... Estimating background took 25.8855879307 s Processing ZNF419-SRR5197132.hg20-male.36mers.unique.bam Reading in data... Reading data took 2.98455691338 s Creating peak regions... Creating peak regions took 36.7815918922 s Estimating background... Estimating background took 27.0504221916 s Processing ZNF419-SRR5197132.hg20-male.36mers.unique.bam Reading in data... Reading data took 0.101716995239 s Creating peak regions... Creating peak regions took 0.193390846252 s Estimating background... Estimating background took 0.561720848083 s Processing ZNF419-SRR5197132.hg20-male.36mers.unique.bam Reading in data... Reading data took 4.52864599228 s Creating peak regions... Creating peak regions took 42.3159358501 s Estimating background... Estimating background took 39.8188760281 s Processing ZNF419-SRR5197132.hg20-male.36mers.unique.bam Reading in data... Reading data took 0.244882106781 s Creating peak regions... Creating peak regions took 14.2665860653 s Estimating background... Estimating background took 0.760237932205 s