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='ZNF662-SRR5197206.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='ZNF662-SRR5197206/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 ZNF662-SRR5197206.hg20-male.36mers.unique.bam Reading in data... Reading data took 6.63122701645 s Creating peak regions... Creating peak regions took 79.3229320049 s Estimating background... Estimating background took 55.378729105 s Processing ZNF662-SRR5197206.hg20-male.36mers.unique.bam Reading in data... Reading data took 3.36786389351 s Creating peak regions... Creating peak regions took 42.1481142044 s Estimating background... Estimating background took 19.9714360237 s Processing ZNF662-SRR5197206.hg20-male.36mers.unique.bam Reading in data... Reading data took 3.2590470314 s Creating peak regions... Creating peak regions took 38.0404551029 s Estimating background... Estimating background took 17.2179749012 s Processing ZNF662-SRR5197206.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='ZNF662-SRR5197206.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='ZNF662-SRR5197206/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 ZNF662-SRR5197206.hg20-male.36mers.unique.bam Reading in data... Reading data took 6.60892510414 s Creating peak regions... Creating peak regions took 77.0490419865 s Estimating background... Estimating background took 52.4046700001 s Processing ZNF662-SRR5197206.hg20-male.36mers.unique.bam Reading in data... Reading data took 3.27501821518 s Creating peak regions... Creating peak regions took 40.7995119095 s Estimating background... Estimating background took 19.5133030415 s Processing ZNF662-SRR5197206.hg20-male.36mers.unique.bam Reading in data... Reading data took 3.6756529808 s Creating peak regions... Creating peak regions took 41.1520140171 s Estimating background... Estimating background took 20.3930568695 s Processing ZNF662-SRR5197206.hg20-male.36mers.unique.bam Reading in data... Reading data took 3.67092514038 s Creating peak regions... Creating peak regions took 40.2649478912 s Estimating background... Estimating background took 22.5499930382 s Processing ZNF662-SRR5197206.hg20-male.36mers.unique.bam Reading in data... Reading data took 3.36976099014 s Creating peak regions... Creating peak regions took 33.7135839462 s Estimating background... Estimating background took 28.353566885 s Processing ZNF662-SRR5197206.hg20-male.36mers.unique.bam Reading in data... Reading data took 2.40894508362 s Creating peak regions... Creating peak regions took 30.5549929142 s Estimating background... Estimating background took 14.246819973 s Processing ZNF662-SRR5197206.hg20-male.36mers.unique.bam Reading in data... Reading data took 2.58682608604 s Creating peak regions... Creating peak regions took 30.2298431396 s Estimating background... Estimating background took 18.247205019 s Processing ZNF662-SRR5197206.hg20-male.36mers.unique.bam Reading in data... Reading data took 2.51334905624 s Creating peak regions... Creating peak regions took 26.8817839622 s Estimating background... Estimating background took 13.1143610477 s Processing ZNF662-SRR5197206.hg20-male.36mers.unique.bam Reading in data... Reading data took 2.34008002281 s Creating peak regions... Creating peak regions took 26.7933938503 s Estimating background... Estimating background took 16.2189772129 s Processing ZNF662-SRR5197206.hg20-male.36mers.unique.bam Reading in data... Reading data took 1.85690283775 s Creating peak regions... Creating peak regions took 24.0239679813 s Estimating background... Estimating background took 11.5407390594 s Processing ZNF662-SRR5197206.hg20-male.36mers.unique.bam Reading in data... Reading data took 1.68035292625 s Creating peak regions... Creating peak regions took 18.9427511692 s Estimating background... Estimating background took 9.18794512749 s Processing ZNF662-SRR5197206.hg20-male.36mers.unique.bam Reading in data... Reading data took 5.8523068428 s Creating peak regions... Creating peak regions took 77.2681641579 s Estimating background... Estimating background took 36.5937840939 s Processing ZNF662-SRR5197206.hg20-male.36mers.unique.bam Reading in data... Reading data took 1.61823582649 s Creating peak regions... Creating peak regions took 20.3378119469 s Estimating background... Estimating background took 10.3485150337 s Processing ZNF662-SRR5197206.hg20-male.36mers.unique.bam Reading in data... Reading data took 0.997766017914 s Creating peak regions... Creating peak regions took 14.1083610058 s Estimating background... Estimating background took 6.52750301361 s Processing ZNF662-SRR5197206.hg20-male.36mers.unique.bam Reading in data... Reading data took 1.21563601494 s Creating peak regions... Creating peak regions took 15.829308033 s Estimating background... Estimating background took 9.2114648819 s Processing ZNF662-SRR5197206.hg20-male.36mers.unique.bam Reading in data... Reading data took 4.53013110161 s Creating peak regions... Creating peak regions took 62.7434191704 s Estimating background... Estimating background took 28.8260650635 s Processing ZNF662-SRR5197206.hg20-male.36mers.unique.bam Reading in data... Reading data took 3.91191506386 s Creating peak regions... Creating peak regions took 57.4581329823 s Estimating background... Estimating background took 22.8449149132 s Processing ZNF662-SRR5197206.hg20-male.36mers.unique.bam Reading in data... Reading data took 4.45069408417 s Creating peak regions... Creating peak regions took 58.1794579029 s Estimating background... Estimating background took 27.0687618256 s Processing ZNF662-SRR5197206.hg20-male.36mers.unique.bam Reading in data... Reading data took 4.64398002625 s Creating peak regions... Creating peak regions took 53.0553741455 s Estimating background... Estimating background took 29.7002718449 s Processing ZNF662-SRR5197206.hg20-male.36mers.unique.bam Reading in data... Reading data took 4.43205308914 s Creating peak regions... Creating peak regions took 48.7105789185 s Estimating background... Estimating background took 26.5230782032 s Processing ZNF662-SRR5197206.hg20-male.36mers.unique.bam Reading in data... Reading data took 3.53555417061 s Creating peak regions... Creating peak regions took 43.3869650364 s Estimating background... Estimating background took 20.2019331455 s Processing ZNF662-SRR5197206.hg20-male.36mers.unique.bam Reading in data... Reading data took 2.4794459343 s Creating peak regions... Creating peak regions took 39.9639089108 s Estimating background... Estimating background took 15.7260220051 s Processing ZNF662-SRR5197206.hg20-male.36mers.unique.bam Reading in data... Reading data took 0.102497816086 s Creating peak regions... Creating peak regions took 0.18662405014 s Estimating background... Estimating background took 0.760308027267 s Processing ZNF662-SRR5197206.hg20-male.36mers.unique.bam Reading in data... Reading data took 4.41942214966 s Creating peak regions... Creating peak regions took 48.463752985 s Estimating background... Estimating background took 30.8135530949 s Processing ZNF662-SRR5197206.hg20-male.36mers.unique.bam Reading in data... Reading data took 0.244396924973 s Creating peak regions... Creating peak regions took 14.7064549923 s Estimating background... Estimating background took 0.704951047897 s