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='ZNF487-SRR5197157.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='ZNF487-SRR5197157/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 ZNF487-SRR5197157.hg20-male.36mers.unique.bam Reading in data... Reading data took 3.31018280983 s Creating peak regions... Creating peak regions took 73.299849987 s Estimating background... Estimating background took 13.9483790398 s Processing ZNF487-SRR5197157.hg20-male.36mers.unique.bam Reading in data... Reading data took 2.06921696663 s Creating peak regions... Creating peak regions took 39.4461698532 s Estimating background... Estimating background took 6.14450407028 s Processing ZNF487-SRR5197157.hg20-male.36mers.unique.bam Reading in data... Reading data took 1.8389840126 s Creating peak regions... Creating peak regions took 40.5740869045 s Estimating background... Estimating background took 6.34172081947 s Processing ZNF487-SRR5197157.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='ZNF487-SRR5197157.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='ZNF487-SRR5197157/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 ZNF487-SRR5197157.hg20-male.36mers.unique.bam Reading in data... Reading data took 3.55009293556 s Creating peak regions... Creating peak regions took 72.2115600109 s Estimating background... Estimating background took 14.670017004 s Processing ZNF487-SRR5197157.hg20-male.36mers.unique.bam Reading in data... Reading data took 1.7480070591 s Creating peak regions... Creating peak regions took 40.8981230259 s Estimating background... Estimating background took 6.37137889862 s Processing ZNF487-SRR5197157.hg20-male.36mers.unique.bam Reading in data... Reading data took 1.64872097969 s Creating peak regions... Creating peak regions took 39.7965149879 s Estimating background... Estimating background took 6.50590419769 s Processing ZNF487-SRR5197157.hg20-male.36mers.unique.bam Reading in data... Reading data took 1.84536719322 s Creating peak regions... Creating peak regions took 40.747658968 s Estimating background... Estimating background took 6.86026716232 s Processing ZNF487-SRR5197157.hg20-male.36mers.unique.bam Reading in data... Reading data took 1.80149698257 s Creating peak regions... Creating peak regions took 35.1768968105 s Estimating background... Estimating background took 7.22565793991 s Processing ZNF487-SRR5197157.hg20-male.36mers.unique.bam Reading in data... Reading data took 1.25541901588 s Creating peak regions... Creating peak regions took 29.8940308094 s Estimating background... Estimating background took 4.72239303589 s Processing ZNF487-SRR5197157.hg20-male.36mers.unique.bam Reading in data... Reading data took 1.04057598114 s Creating peak regions... Creating peak regions took 28.4004290104 s Estimating background... Estimating background took 4.82295298576 s Processing ZNF487-SRR5197157.hg20-male.36mers.unique.bam Reading in data... Reading data took 1.07464003563 s Creating peak regions... Creating peak regions took 26.5655319691 s Estimating background... Estimating background took 4.30718398094 s Processing ZNF487-SRR5197157.hg20-male.36mers.unique.bam Reading in data... Reading data took 1.37553787231 s Creating peak regions... Creating peak regions took 24.5834710598 s Estimating background... Estimating background took 4.4452931881 s Processing ZNF487-SRR5197157.hg20-male.36mers.unique.bam Reading in data... Reading data took 0.911666154861 s Creating peak regions... Creating peak regions took 23.1699669361 s Estimating background... Estimating background took 3.42833590508 s Processing ZNF487-SRR5197157.hg20-male.36mers.unique.bam Reading in data... Reading data took 0.877321958542 s Creating peak regions... Creating peak regions took 17.0939669609 s Estimating background... Estimating background took 1.63029313087 s Processing ZNF487-SRR5197157.hg20-male.36mers.unique.bam Reading in data... Reading data took 2.98000812531 s Creating peak regions... Creating peak regions took 67.9550960064 s Estimating background... Estimating background took 11.543637991 s Processing ZNF487-SRR5197157.hg20-male.36mers.unique.bam Reading in data... Reading data took 1.07823896408 s Creating peak regions... Creating peak regions took 19.5145130157 s Estimating background... Estimating background took 3.06581091881 s Processing ZNF487-SRR5197157.hg20-male.36mers.unique.bam Reading in data... Reading data took 0.519592046738 s Creating peak regions... Creating peak regions took 13.7785758972 s Estimating background... Estimating background took 3.17663693428 s Processing ZNF487-SRR5197157.hg20-male.36mers.unique.bam Reading in data... Reading data took 0.656769990921 s Creating peak regions... Creating peak regions took 14.1085338593 s Estimating background... Estimating background took 2.88594603539 s Processing ZNF487-SRR5197157.hg20-male.36mers.unique.bam Reading in data... Reading data took 2.45606088638 s Creating peak regions... Creating peak regions took 58.3268620968 s Estimating background... Estimating background took 9.20481395721 s Processing ZNF487-SRR5197157.hg20-male.36mers.unique.bam Reading in data... Reading data took 2.23257708549 s Creating peak regions... Creating peak regions took 56.8710711002 s Estimating background... Estimating background took 8.25746107101 s Processing ZNF487-SRR5197157.hg20-male.36mers.unique.bam Reading in data... Reading data took 2.4854362011 s Creating peak regions... Creating peak regions took 54.4259009361 s Estimating background... Estimating background took 8.60983300209 s Processing ZNF487-SRR5197157.hg20-male.36mers.unique.bam Reading in data... Reading data took 2.43633294106 s Creating peak regions... Creating peak regions took 51.0988850594 s Estimating background... Estimating background took 9.08196902275 s Processing ZNF487-SRR5197157.hg20-male.36mers.unique.bam Reading in data... Reading data took 2.38172507286 s Creating peak regions... Creating peak regions took 45.9450109005 s Estimating background... Estimating background took 8.60045599937 s Processing ZNF487-SRR5197157.hg20-male.36mers.unique.bam Reading in data... Reading data took 1.7761080265 s Creating peak regions... Creating peak regions took 44.9776351452 s Estimating background... Estimating background took 6.61789512634 s Processing ZNF487-SRR5197157.hg20-male.36mers.unique.bam Reading in data... Reading data took 1.57948803902 s Creating peak regions... Creating peak regions took 40.4935879707 s Estimating background... Estimating background took 6.56732010841 s Processing ZNF487-SRR5197157.hg20-male.36mers.unique.bam Reading in data... Reading data took 0.0855388641357 s Creating peak regions... Creating peak regions took 0.157853841782 s Estimating background... Estimating background took 0.684357881546 s Processing ZNF487-SRR5197157.hg20-male.36mers.unique.bam Reading in data... Reading data took 2.57270908356 s Creating peak regions... Creating peak regions took 49.1174359322 s Estimating background... Estimating background took 10.00761199 s Processing ZNF487-SRR5197157.hg20-male.36mers.unique.bam Reading in data... Reading data took 0.125059127808 s Creating peak regions... Creating peak regions took 16.1282939911 s Estimating background... Estimating background took 0.450578927994 s