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='ZNF254-SRR5197088.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='ZNF254-SRR5197088/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 ZNF254-SRR5197088.hg20-male.36mers.unique.bam Reading in data... Reading data took 6.51647901535 s Creating peak regions... Creating peak regions took 79.2000758648 s Estimating background... Estimating background took 49.5376009941 s Processing ZNF254-SRR5197088.hg20-male.36mers.unique.bam Reading in data... Reading data took 3.37886404991 s Creating peak regions... Creating peak regions took 43.8052759171 s Estimating background... Estimating background took 19.7750658989 s Processing ZNF254-SRR5197088.hg20-male.36mers.unique.bam Reading in data... Reading data took 3.30645298958 s Creating peak regions... Creating peak regions took 37.7489249706 s Estimating background... Estimating background took 15.9623250961 s Processing ZNF254-SRR5197088.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='ZNF254-SRR5197088.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='ZNF254-SRR5197088/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 ZNF254-SRR5197088.hg20-male.36mers.unique.bam Reading in data... Reading data took 6.24744105339 s Creating peak regions... Creating peak regions took 76.3143160343 s Estimating background... Estimating background took 50.793596983 s Processing ZNF254-SRR5197088.hg20-male.36mers.unique.bam Reading in data... Reading data took 3.36147379875 s Creating peak regions... Creating peak regions took 42.707141161 s Estimating background... Estimating background took 18.7880489826 s Processing ZNF254-SRR5197088.hg20-male.36mers.unique.bam Reading in data... Reading data took 3.03746294975 s Creating peak regions... Creating peak regions took 41.9734489918 s Estimating background... Estimating background took 20.249256134 s Processing ZNF254-SRR5197088.hg20-male.36mers.unique.bam Reading in data... Reading data took 3.46723413467 s Creating peak regions... Creating peak regions took 42.1290140152 s Estimating background... Estimating background took 19.5649840832 s Processing ZNF254-SRR5197088.hg20-male.36mers.unique.bam Reading in data... Reading data took 2.81691789627 s Creating peak regions... Creating peak regions took 34.971009016 s Estimating background... Estimating background took 22.1602199078 s Processing ZNF254-SRR5197088.hg20-male.36mers.unique.bam Reading in data... Reading data took 2.27339506149 s Creating peak regions... Creating peak regions took 32.0702109337 s Estimating background... Estimating background took 12.8042891026 s Processing ZNF254-SRR5197088.hg20-male.36mers.unique.bam Reading in data... Reading data took 1.9015879631 s Creating peak regions... Creating peak regions took 28.7986221313 s Estimating background... Estimating background took 13.9775111675 s Processing ZNF254-SRR5197088.hg20-male.36mers.unique.bam Reading in data... Reading data took 2.0396490097 s Creating peak regions... Creating peak regions took 27.3837358952 s Estimating background... Estimating background took 13.9041759968 s Processing ZNF254-SRR5197088.hg20-male.36mers.unique.bam Reading in data... Reading data took 2.39605998993 s Creating peak regions... Creating peak regions took 26.4705321789 s Estimating background... Estimating background took 16.9239189625 s Processing ZNF254-SRR5197088.hg20-male.36mers.unique.bam Reading in data... Reading data took 1.81643199921 s Creating peak regions... Creating peak regions took 23.7648980618 s Estimating background... Estimating background took 10.5307059288 s Processing ZNF254-SRR5197088.hg20-male.36mers.unique.bam Reading in data... Reading data took 1.51615405083 s Creating peak regions... Creating peak regions took 17.9758720398 s Estimating background... Estimating background took 10.9917881489 s Processing ZNF254-SRR5197088.hg20-male.36mers.unique.bam Reading in data... Reading data took 5.39514279366 s Creating peak regions... Creating peak regions took 81.2759838104 s Estimating background... Estimating background took 32.6745810509 s Processing ZNF254-SRR5197088.hg20-male.36mers.unique.bam Reading in data... Reading data took 1.78383517265 s Creating peak regions... Creating peak regions took 20.9039239883 s Estimating background... Estimating background took 11.0261781216 s Processing ZNF254-SRR5197088.hg20-male.36mers.unique.bam Reading in data... Reading data took 0.967451095581 s Creating peak regions... Creating peak regions took 14.0456018448 s Estimating background... Estimating background took 6.4251101017 s Processing ZNF254-SRR5197088.hg20-male.36mers.unique.bam Reading in data... Reading data took 1.31891083717 s Creating peak regions... Creating peak regions took 16.5419330597 s Estimating background... Estimating background took 9.97287487984 s Processing ZNF254-SRR5197088.hg20-male.36mers.unique.bam Reading in data... Reading data took 4.31720209122 s Creating peak regions... Creating peak regions took 61.9658288956 s Estimating background... Estimating background took 27.1003508568 s Processing ZNF254-SRR5197088.hg20-male.36mers.unique.bam Reading in data... Reading data took 3.65163993835 s Creating peak regions... Creating peak regions took 58.3138480186 s Estimating background... Estimating background took 17.851028204 s Processing ZNF254-SRR5197088.hg20-male.36mers.unique.bam Reading in data... Reading data took 4.0471329689 s Creating peak regions... Creating peak regions took 58.9377689362 s Estimating background... Estimating background took 27.1830701828 s Processing ZNF254-SRR5197088.hg20-male.36mers.unique.bam Reading in data... Reading data took 4.58322000504 s Creating peak regions... Creating peak regions took 52.8929300308 s Estimating background... Estimating background took 29.8274738789 s Processing ZNF254-SRR5197088.hg20-male.36mers.unique.bam Reading in data... Reading data took 3.94112491608 s Creating peak regions... Creating peak regions took 49.4342141151 s Estimating background... Estimating background took 25.9333748817 s Processing ZNF254-SRR5197088.hg20-male.36mers.unique.bam Reading in data... Reading data took 2.99312496185 s Creating peak regions... Creating peak regions took 41.6813728809 s Estimating background... Estimating background took 14.691783905 s Processing ZNF254-SRR5197088.hg20-male.36mers.unique.bam Reading in data... Reading data took 2.17319107056 s Creating peak regions... Creating peak regions took 34.3686728477 s Estimating background... Estimating background took 14.750138998 s Processing ZNF254-SRR5197088.hg20-male.36mers.unique.bam Reading in data... Reading data took 0.097874879837 s Creating peak regions... Creating peak regions took 0.174420118332 s Estimating background... Estimating background took 0.656985044479 s Processing ZNF254-SRR5197088.hg20-male.36mers.unique.bam Reading in data... Reading data took 3.24467802048 s Creating peak regions... Creating peak regions took 40.146517992 s Estimating background... Estimating background took 23.2118699551 s Processing ZNF254-SRR5197088.hg20-male.36mers.unique.bam Reading in data... Reading data took 0.152415037155 s Creating peak regions... Creating peak regions took 13.7551348209 s Estimating background... Estimating background took 0.665959119797 s