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='ZNF860-SRR5197262.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='ZNF860-SRR5197262/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 ZNF860-SRR5197262.hg20-male.36mers.unique.bam Reading in data... Reading data took 4.24048995972 s Creating peak regions... Creating peak regions took 75.4946959019 s Estimating background... Estimating background took 27.3477771282 s Processing ZNF860-SRR5197262.hg20-male.36mers.unique.bam Reading in data... Reading data took 2.1252579689 s Creating peak regions... Creating peak regions took 39.3395521641 s Estimating background... Estimating background took 11.5261080265 s Processing ZNF860-SRR5197262.hg20-male.36mers.unique.bam Reading in data... Reading data took 2.18899607658 s Creating peak regions... Creating peak regions took 42.050673008 s Estimating background... Estimating background took 11.8406569958 s Processing ZNF860-SRR5197262.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='ZNF860-SRR5197262.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='ZNF860-SRR5197262/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 ZNF860-SRR5197262.hg20-male.36mers.unique.bam Reading in data... Reading data took 4.30986499786 s Creating peak regions... Creating peak regions took 75.8699691296 s Estimating background... Estimating background took 27.0347080231 s Processing ZNF860-SRR5197262.hg20-male.36mers.unique.bam Reading in data... Reading data took 2.06649899483 s Creating peak regions... Creating peak regions took 39.1779689789 s Estimating background... Estimating background took 11.3722231388 s Processing ZNF860-SRR5197262.hg20-male.36mers.unique.bam Reading in data... Reading data took 2.15016412735 s Creating peak regions... Creating peak regions took 41.7843859196 s Estimating background... Estimating background took 11.7907938957 s Processing ZNF860-SRR5197262.hg20-male.36mers.unique.bam Reading in data... Reading data took 2.42298007011 s Creating peak regions... Creating peak regions took 40.8193690777 s Estimating background... Estimating background took 12.1427390575 s Processing ZNF860-SRR5197262.hg20-male.36mers.unique.bam Reading in data... Reading data took 1.68699097633 s Creating peak regions... Creating peak regions took 35.1767389774 s Estimating background... Estimating background took 10.3992609978 s Processing ZNF860-SRR5197262.hg20-male.36mers.unique.bam Reading in data... Reading data took 1.67629384995 s Creating peak regions... Creating peak regions took 32.1644279957 s Estimating background... Estimating background took 8.22141814232 s Processing ZNF860-SRR5197262.hg20-male.36mers.unique.bam Reading in data... Reading data took 1.43646883965 s Creating peak regions... Creating peak regions took 28.9141018391 s Estimating background... Estimating background took 8.80868005753 s Processing ZNF860-SRR5197262.hg20-male.36mers.unique.bam Reading in data... Reading data took 1.50543689728 s Creating peak regions... Creating peak regions took 25.8817470074 s Estimating background... Estimating background took 8.97212910652 s Processing ZNF860-SRR5197262.hg20-male.36mers.unique.bam Reading in data... Reading data took 1.86761593819 s Creating peak regions... Creating peak regions took 24.7643930912 s Estimating background... Estimating background took 11.0401139259 s Processing ZNF860-SRR5197262.hg20-male.36mers.unique.bam Reading in data... Reading data took 1.18642807007 s Creating peak regions... Creating peak regions took 24.5583109856 s Estimating background... Estimating background took 5.74734902382 s Processing ZNF860-SRR5197262.hg20-male.36mers.unique.bam Reading in data... Reading data took 1.28327202797 s Creating peak regions... Creating peak regions took 17.9940431118 s Estimating background... Estimating background took 8.11076021194 s Processing ZNF860-SRR5197262.hg20-male.36mers.unique.bam Reading in data... Reading data took 3.52217698097 s Creating peak regions... Creating peak regions took 71.0533699989 s Estimating background... Estimating background took 18.3478229046 s Processing ZNF860-SRR5197262.hg20-male.36mers.unique.bam Reading in data... Reading data took 1.18039894104 s Creating peak regions... Creating peak regions took 21.0156040192 s Estimating background... Estimating background took 6.93428683281 s Processing ZNF860-SRR5197262.hg20-male.36mers.unique.bam Reading in data... Reading data took 0.612692117691 s Creating peak regions... Creating peak regions took 14.2251219749 s Estimating background... Estimating background took 3.81921100616 s Processing ZNF860-SRR5197262.hg20-male.36mers.unique.bam Reading in data... Reading data took 0.990957975388 s Creating peak regions... Creating peak regions took 15.9681050777 s Estimating background... Estimating background took 7.41300296783 s Processing ZNF860-SRR5197262.hg20-male.36mers.unique.bam Reading in data... Reading data took 2.86394810677 s Creating peak regions... Creating peak regions took 58.2300908566 s Estimating background... Estimating background took 14.7009038925 s Processing ZNF860-SRR5197262.hg20-male.36mers.unique.bam Reading in data... Reading data took 2.4375898838 s Creating peak regions... Creating peak regions took 54.167014122 s Estimating background... Estimating background took 11.3071169853 s Processing ZNF860-SRR5197262.hg20-male.36mers.unique.bam Reading in data... Reading data took 2.84546399117 s Creating peak regions... Creating peak regions took 52.4750859737 s Estimating background... Estimating background took 14.347028017 s Processing ZNF860-SRR5197262.hg20-male.36mers.unique.bam Reading in data... Reading data took 2.68896198273 s Creating peak regions... Creating peak regions took 50.1005501747 s Estimating background... Estimating background took 15.6377489567 s Processing ZNF860-SRR5197262.hg20-male.36mers.unique.bam Reading in data... Reading data took 2.76392006874 s Creating peak regions... Creating peak regions took 46.3058540821 s Estimating background... Estimating background took 14.3853449821 s Processing ZNF860-SRR5197262.hg20-male.36mers.unique.bam Reading in data... Reading data took 2.07341098785 s Creating peak regions... Creating peak regions took 44.8672969341 s Estimating background... Estimating background took 10.1585259438 s Processing ZNF860-SRR5197262.hg20-male.36mers.unique.bam Reading in data... Reading data took 1.9900970459 s Creating peak regions... Creating peak regions took 39.647767067 s Estimating background... Estimating background took 10.6255528927 s Processing ZNF860-SRR5197262.hg20-male.36mers.unique.bam Reading in data... Reading data took 0.0868239402771 s Creating peak regions... Creating peak regions took 0.160185813904 s Estimating background... Estimating background took 0.645051002502 s Processing ZNF860-SRR5197262.hg20-male.36mers.unique.bam Reading in data... Reading data took 2.62512779236 s Creating peak regions... Creating peak regions took 48.448900938 s Estimating background... Estimating background took 13.6219549179 s Processing ZNF860-SRR5197262.hg20-male.36mers.unique.bam Reading in data... Reading data took 0.0928580760956 s Creating peak regions... Creating peak regions took 16.0254380703 s Estimating background... Estimating background took 0.54937505722 s