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='ZNF780A-SRR5197240.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='ZNF780A-SRR5197240/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 ZNF780A-SRR5197240.hg20-male.36mers.unique.bam Reading in data... Reading data took 5.49789595604 s Creating peak regions... Creating peak regions took 64.0218138695 s Estimating background... Estimating background took 39.8132679462 s Processing ZNF780A-SRR5197240.hg20-male.36mers.unique.bam Reading in data... Reading data took 2.6648709774 s Creating peak regions... Creating peak regions took 35.234639883 s Estimating background... Estimating background took 16.636318922 s Processing ZNF780A-SRR5197240.hg20-male.36mers.unique.bam Reading in data... Reading data took 2.57159590721 s Creating peak regions... Creating peak regions took 34.7520768642 s Estimating background... Estimating background took 16.4266469479 s Processing ZNF780A-SRR5197240.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='ZNF780A-SRR5197240.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='ZNF780A-SRR5197240/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 ZNF780A-SRR5197240.hg20-male.36mers.unique.bam Reading in data... Reading data took 6.44186711311 s Creating peak regions... Creating peak regions took 76.4943990707 s Estimating background... Estimating background took 45.3943750858 s Processing ZNF780A-SRR5197240.hg20-male.36mers.unique.bam Reading in data... Reading data took 3.18590688705 s Creating peak regions... Creating peak regions took 40.275758028 s Estimating background... Estimating background took 18.4179401398 s Processing ZNF780A-SRR5197240.hg20-male.36mers.unique.bam Reading in data... Reading data took 3.13087081909 s Creating peak regions... Creating peak regions took 39.5983889103 s Estimating background... Estimating background took 18.5138909817 s Processing ZNF780A-SRR5197240.hg20-male.36mers.unique.bam Reading in data... Reading data took 3.15472221375 s Creating peak regions... Creating peak regions took 39.0419669151 s Estimating background... Estimating background took 19.7048728466 s Processing ZNF780A-SRR5197240.hg20-male.36mers.unique.bam Reading in data... Reading data took 2.88471698761 s Creating peak regions... Creating peak regions took 34.3491339684 s Estimating background... Estimating background took 20.9826500416 s Processing ZNF780A-SRR5197240.hg20-male.36mers.unique.bam Reading in data... Reading data took 2.3584189415 s Creating peak regions... Creating peak regions took 31.3162779808 s Estimating background... Estimating background took 12.5132379532 s Processing ZNF780A-SRR5197240.hg20-male.36mers.unique.bam Reading in data... Reading data took 2.20297503471 s Creating peak regions... Creating peak regions took 29.3024170399 s Estimating background... Estimating background took 13.9870040417 s Processing ZNF780A-SRR5197240.hg20-male.36mers.unique.bam Reading in data... Reading data took 2.08329606056 s Creating peak regions... Creating peak regions took 24.3143258095 s Estimating background... Estimating background took 12.0473148823 s Processing ZNF780A-SRR5197240.hg20-male.36mers.unique.bam Reading in data... Reading data took 2.34008002281 s Creating peak regions... Creating peak regions took 25.2709310055 s Estimating background... Estimating background took 16.3847670555 s Processing ZNF780A-SRR5197240.hg20-male.36mers.unique.bam Reading in data... Reading data took 1.75505399704 s Creating peak regions... Creating peak regions took 23.4567408562 s Estimating background... Estimating background took 9.77259922028 s Processing ZNF780A-SRR5197240.hg20-male.36mers.unique.bam Reading in data... Reading data took 1.50554800034 s Creating peak regions... Creating peak regions took 18.8857240677 s Estimating background... Estimating background took 9.5309650898 s Processing ZNF780A-SRR5197240.hg20-male.36mers.unique.bam Reading in data... Reading data took 4.99991393089 s Creating peak regions... Creating peak regions took 76.0122339725 s Estimating background... Estimating background took 31.207280159 s Processing ZNF780A-SRR5197240.hg20-male.36mers.unique.bam Reading in data... Reading data took 1.64293408394 s Creating peak regions... Creating peak regions took 20.1277160645 s Estimating background... Estimating background took 10.6258199215 s Processing ZNF780A-SRR5197240.hg20-male.36mers.unique.bam Reading in data... Reading data took 1.02172899246 s Creating peak regions... Creating peak regions took 13.7401530743 s Estimating background... Estimating background took 5.81451416016 s Processing ZNF780A-SRR5197240.hg20-male.36mers.unique.bam Reading in data... Reading data took 1.15118789673 s Creating peak regions... Creating peak regions took 15.9358069897 s Estimating background... Estimating background took 9.20006012917 s Processing ZNF780A-SRR5197240.hg20-male.36mers.unique.bam Reading in data... Reading data took 4.1410779953 s Creating peak regions... Creating peak regions took 62.4142420292 s Estimating background... Estimating background took 25.3448491096 s Processing ZNF780A-SRR5197240.hg20-male.36mers.unique.bam Reading in data... Reading data took 3.54189777374 s Creating peak regions... Creating peak regions took 55.028275013 s Estimating background... Estimating background took 19.6218271255 s Processing ZNF780A-SRR5197240.hg20-male.36mers.unique.bam Reading in data... Reading data took 4.00081300735 s Creating peak regions... Creating peak regions took 53.9248309135 s Estimating background... Estimating background took 23.5603458881 s Processing ZNF780A-SRR5197240.hg20-male.36mers.unique.bam Reading in data... Reading data took 4.42027807236 s Creating peak regions... Creating peak regions took 52.2952849865 s Estimating background... Estimating background took 28.2023668289 s Processing ZNF780A-SRR5197240.hg20-male.36mers.unique.bam Reading in data... Reading data took 3.84317398071 s Creating peak regions... Creating peak regions took 48.1050322056 s Estimating background... Estimating background took 24.1984829903 s Processing ZNF780A-SRR5197240.hg20-male.36mers.unique.bam Reading in data... Reading data took 3.20892310143 s Creating peak regions... Creating peak regions took 41.1028490067 s Estimating background... Estimating background took 16.8393640518 s Processing ZNF780A-SRR5197240.hg20-male.36mers.unique.bam Reading in data... Reading data took 2.74953198433 s Creating peak regions... Creating peak regions took 38.7704598904 s Estimating background... Estimating background took 16.5963191986 s Processing ZNF780A-SRR5197240.hg20-male.36mers.unique.bam Reading in data... Reading data took 0.110748052597 s Creating peak regions... Creating peak regions took 0.370450973511 s Estimating background... Estimating background took 0.904402971268 s Processing ZNF780A-SRR5197240.hg20-male.36mers.unique.bam Reading in data... Reading data took 3.436398983 s Creating peak regions... Creating peak regions took 46.6384050846 s Estimating background... Estimating background took 24.1491410732 s Processing ZNF780A-SRR5197240.hg20-male.36mers.unique.bam Reading in data... Reading data took 0.12292098999 s Creating peak regions... Creating peak regions took 14.3320028782 s Estimating background... Estimating background took 0.716051101685 s