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='ZNF561-SRR5197179.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='ZNF561-SRR5197179/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 ZNF561-SRR5197179.hg20-male.36mers.unique.bam Reading in data... Reading data took 7.22279787064 s Creating peak regions... Creating peak regions took 80.023209095 s Estimating background... Estimating background took 59.4355452061 s Processing ZNF561-SRR5197179.hg20-male.36mers.unique.bam Reading in data... Reading data took 3.56275892258 s Creating peak regions... Creating peak regions took 44.5780479908 s Estimating background... Estimating background took 22.9647769928 s Processing ZNF561-SRR5197179.hg20-male.36mers.unique.bam Reading in data... Reading data took 3.42990899086 s Creating peak regions... Creating peak regions took 38.9063029289 s Estimating background... Estimating background took 19.9479470253 s Processing ZNF561-SRR5197179.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='ZNF561-SRR5197179.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='ZNF561-SRR5197179/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 ZNF561-SRR5197179.hg20-male.36mers.unique.bam Reading in data... Reading data took 6.48943114281 s Creating peak regions... Creating peak regions took 79.9563350677 s Estimating background... Estimating background took 59.3529620171 s Processing ZNF561-SRR5197179.hg20-male.36mers.unique.bam Reading in data... Reading data took 3.59532904625 s Creating peak regions... Creating peak regions took 44.3434050083 s Estimating background... Estimating background took 23.0269529819 s Processing ZNF561-SRR5197179.hg20-male.36mers.unique.bam Reading in data... Reading data took 3.34991288185 s Creating peak regions... Creating peak regions took 41.9380691051 s Estimating background... Estimating background took 23.9690439701 s Processing ZNF561-SRR5197179.hg20-male.36mers.unique.bam Reading in data... Reading data took 3.52115917206 s Creating peak regions... Creating peak regions took 41.4221940041 s Estimating background... Estimating background took 24.6293430328 s Processing ZNF561-SRR5197179.hg20-male.36mers.unique.bam Reading in data... Reading data took 2.96978998184 s Creating peak regions... Creating peak regions took 35.9881398678 s Estimating background... Estimating background took 24.4774179459 s Processing ZNF561-SRR5197179.hg20-male.36mers.unique.bam Reading in data... Reading data took 2.46658992767 s Creating peak regions... Creating peak regions took 31.1372349262 s Estimating background... Estimating background took 15.4795629978 s Processing ZNF561-SRR5197179.hg20-male.36mers.unique.bam Reading in data... Reading data took 2.24731302261 s Creating peak regions... Creating peak regions took 29.9672148228 s Estimating background... Estimating background took 16.9399030209 s Processing ZNF561-SRR5197179.hg20-male.36mers.unique.bam Reading in data... Reading data took 2.29568195343 s Creating peak regions... Creating peak regions took 28.0119349957 s Estimating background... Estimating background took 16.825494051 s Processing ZNF561-SRR5197179.hg20-male.36mers.unique.bam Reading in data... Reading data took 2.73694205284 s Creating peak regions... Creating peak regions took 27.0532109737 s Estimating background... Estimating background took 22.3286201954 s Processing ZNF561-SRR5197179.hg20-male.36mers.unique.bam Reading in data... Reading data took 1.82323718071 s Creating peak regions... Creating peak regions took 24.8031680584 s Estimating background... Estimating background took 11.676954031 s Processing ZNF561-SRR5197179.hg20-male.36mers.unique.bam Reading in data... Reading data took 1.87516999245 s Creating peak regions... Creating peak regions took 18.9188930988 s Estimating background... Estimating background took 15.3850648403 s Processing ZNF561-SRR5197179.hg20-male.36mers.unique.bam Reading in data... Reading data took 5.65743207932 s Creating peak regions... Creating peak regions took 75.3953378201 s Estimating background... Estimating background took 38.5767309666 s Processing ZNF561-SRR5197179.hg20-male.36mers.unique.bam Reading in data... Reading data took 2.0764939785 s Creating peak regions... Creating peak regions took 21.4906020164 s Estimating background... Estimating background took 14.2686200142 s Processing ZNF561-SRR5197179.hg20-male.36mers.unique.bam Reading in data... Reading data took 1.0143430233 s Creating peak regions... Creating peak regions took 14.4603040218 s Estimating background... Estimating background took 7.68027806282 s Processing ZNF561-SRR5197179.hg20-male.36mers.unique.bam Reading in data... Reading data took 1.47819900513 s Creating peak regions... Creating peak regions took 16.0039038658 s Estimating background... Estimating background took 14.0283901691 s Processing ZNF561-SRR5197179.hg20-male.36mers.unique.bam Reading in data... Reading data took 4.43699121475 s Creating peak regions... Creating peak regions took 66.2857410908 s Estimating background... Estimating background took 29.7266559601 s Processing ZNF561-SRR5197179.hg20-male.36mers.unique.bam Reading in data... Reading data took 4.03716397285 s Creating peak regions... Creating peak regions took 58.3373978138 s Estimating background... Estimating background took 23.31767416 s Processing ZNF561-SRR5197179.hg20-male.36mers.unique.bam Reading in data... Reading data took 4.27487421036 s Creating peak regions... Creating peak regions took 55.6883111 s Estimating background... Estimating background took 29.2279970646 s Processing ZNF561-SRR5197179.hg20-male.36mers.unique.bam Reading in data... Reading data took 4.57646393776 s Creating peak regions... Creating peak regions took 51.7275090218 s Estimating background... Estimating background took 32.4198141098 s Processing ZNF561-SRR5197179.hg20-male.36mers.unique.bam Reading in data... Reading data took 4.41634917259 s Creating peak regions... Creating peak regions took 50.0061891079 s Estimating background... Estimating background took 30.3640680313 s Processing ZNF561-SRR5197179.hg20-male.36mers.unique.bam Reading in data... Reading data took 3.28198194504 s Creating peak regions... Creating peak regions took 44.4452860355 s Estimating background... Estimating background took 20.7574989796 s Processing ZNF561-SRR5197179.hg20-male.36mers.unique.bam Reading in data... Reading data took 2.86311388016 s Creating peak regions... Creating peak regions took 41.7860360146 s Estimating background... Estimating background took 20.8723499775 s Processing ZNF561-SRR5197179.hg20-male.36mers.unique.bam Reading in data... Reading data took 0.107151985168 s Creating peak regions... Creating peak regions took 0.190710067749 s Estimating background... Estimating background took 0.707690000534 s Processing ZNF561-SRR5197179.hg20-male.36mers.unique.bam Reading in data... Reading data took 4.0271859169 s Creating peak regions... Creating peak regions took 47.4534599781 s Estimating background... Estimating background took 28.834895134 s Processing ZNF561-SRR5197179.hg20-male.36mers.unique.bam Reading in data... Reading data took 0.167390108109 s Creating peak regions... Creating peak regions took 14.9731168747 s Estimating background... Estimating background took 0.761708021164 s