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='ZNF441-SRR5197142.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='ZNF441-SRR5197142/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 ZNF441-SRR5197142.hg20-male.36mers.unique.bam Reading in data... Reading data took 3.95734786987 s Creating peak regions... Creating peak regions took 74.6523649693 s Estimating background... Estimating background took 26.2703499794 s Processing ZNF441-SRR5197142.hg20-male.36mers.unique.bam Reading in data... Reading data took 2.12075400352 s Creating peak regions... Creating peak regions took 39.0587208271 s Estimating background... Estimating background took 10.9057137966 s Processing ZNF441-SRR5197142.hg20-male.36mers.unique.bam Reading in data... Reading data took 2.09025096893 s Creating peak regions... Creating peak regions took 37.2712159157 s Estimating background... Estimating background took 10.6049580574 s Processing ZNF441-SRR5197142.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='ZNF441-SRR5197142.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='ZNF441-SRR5197142/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 ZNF441-SRR5197142.hg20-male.36mers.unique.bam Reading in data... Reading data took 3.84216284752 s Creating peak regions... Creating peak regions took 75.2563688755 s Estimating background... Estimating background took 28.0296320915 s Processing ZNF441-SRR5197142.hg20-male.36mers.unique.bam Reading in data... Reading data took 2.03059506416 s Creating peak regions... Creating peak regions took 40.6570720673 s Estimating background... Estimating background took 10.0799529552 s Processing ZNF441-SRR5197142.hg20-male.36mers.unique.bam Reading in data... Reading data took 1.92351293564 s Creating peak regions... Creating peak regions took 39.2814629078 s Estimating background... Estimating background took 11.5161440372 s Processing ZNF441-SRR5197142.hg20-male.36mers.unique.bam Reading in data... Reading data took 2.30712008476 s Creating peak regions... Creating peak regions took 40.0205690861 s Estimating background... Estimating background took 11.9816110134 s Processing ZNF441-SRR5197142.hg20-male.36mers.unique.bam Reading in data... Reading data took 1.73300790787 s Creating peak regions... Creating peak regions took 33.9928138256 s Estimating background... Estimating background took 10.3226180077 s Processing ZNF441-SRR5197142.hg20-male.36mers.unique.bam Reading in data... Reading data took 1.47997188568 s Creating peak regions... Creating peak regions took 31.4978199005 s Estimating background... Estimating background took 7.74408102036 s Processing ZNF441-SRR5197142.hg20-male.36mers.unique.bam Reading in data... Reading data took 1.40796804428 s Creating peak regions... Creating peak regions took 29.6404139996 s Estimating background... Estimating background took 8.97835302353 s Processing ZNF441-SRR5197142.hg20-male.36mers.unique.bam Reading in data... Reading data took 1.55733394623 s Creating peak regions... Creating peak regions took 26.3561389446 s Estimating background... Estimating background took 8.1805331707 s Processing ZNF441-SRR5197142.hg20-male.36mers.unique.bam Reading in data... Reading data took 1.65143799782 s Creating peak regions... Creating peak regions took 25.3459060192 s Estimating background... Estimating background took 10.8571441174 s Processing ZNF441-SRR5197142.hg20-male.36mers.unique.bam Reading in data... Reading data took 0.946580171585 s Creating peak regions... Creating peak regions took 23.5274069309 s Estimating background... Estimating background took 5.69681692123 s Processing ZNF441-SRR5197142.hg20-male.36mers.unique.bam Reading in data... Reading data took 1.43642902374 s Creating peak regions... Creating peak regions took 19.3635828495 s Estimating background... Estimating background took 8.8805539608 s Processing ZNF441-SRR5197142.hg20-male.36mers.unique.bam Reading in data... Reading data took 3.50293803215 s Creating peak regions... Creating peak regions took 72.4322628975 s Estimating background... Estimating background took 18.3337311745 s Processing ZNF441-SRR5197142.hg20-male.36mers.unique.bam Reading in data... Reading data took 1.13347196579 s Creating peak regions... Creating peak regions took 21.4484779835 s Estimating background... Estimating background took 6.78733086586 s Processing ZNF441-SRR5197142.hg20-male.36mers.unique.bam Reading in data... Reading data took 0.838875055313 s Creating peak regions... Creating peak regions took 14.8855719566 s Estimating background... Estimating background took 3.87392020226 s Processing ZNF441-SRR5197142.hg20-male.36mers.unique.bam Reading in data... Reading data took 0.985143899918 s Creating peak regions... Creating peak regions took 16.4183168411 s Estimating background... Estimating background took 7.33954310417 s Processing ZNF441-SRR5197142.hg20-male.36mers.unique.bam Reading in data... Reading data took 2.68274903297 s Creating peak regions... Creating peak regions took 58.6905658245 s Estimating background... Estimating background took 14.1407339573 s Processing ZNF441-SRR5197142.hg20-male.36mers.unique.bam Reading in data... Reading data took 2.37524104118 s Creating peak regions... Creating peak regions took 58.363888979 s Estimating background... Estimating background took 10.9253151417 s Processing ZNF441-SRR5197142.hg20-male.36mers.unique.bam Reading in data... Reading data took 2.45337104797 s Creating peak regions... Creating peak regions took 55.2737100124 s Estimating background... Estimating background took 13.9460270405 s Processing ZNF441-SRR5197142.hg20-male.36mers.unique.bam Reading in data... Reading data took 2.69653582573 s Creating peak regions... Creating peak regions took 55.2383368015 s Estimating background... Estimating background took 15.8967950344 s Processing ZNF441-SRR5197142.hg20-male.36mers.unique.bam Reading in data... Reading data took 3.11758208275 s Creating peak regions... Creating peak regions took 47.6839489937 s Estimating background... Estimating background took 14.4107038975 s Processing ZNF441-SRR5197142.hg20-male.36mers.unique.bam Reading in data... Reading data took 2.01108384132 s Creating peak regions... Creating peak regions took 46.806773901 s Estimating background... Estimating background took 10.5350990295 s Processing ZNF441-SRR5197142.hg20-male.36mers.unique.bam Reading in data... Reading data took 1.79798603058 s Creating peak regions... Creating peak regions took 39.5383980274 s Estimating background... Estimating background took 10.1606318951 s Processing ZNF441-SRR5197142.hg20-male.36mers.unique.bam Reading in data... Reading data took 0.0810031890869 s Creating peak regions... Creating peak regions took 0.167417049408 s Estimating background... Estimating background took 0.645336866379 s Processing ZNF441-SRR5197142.hg20-male.36mers.unique.bam Reading in data... Reading data took 2.37627696991 s Creating peak regions... Creating peak regions took 46.5208599567 s Estimating background... Estimating background took 12.5570168495 s Processing ZNF441-SRR5197142.hg20-male.36mers.unique.bam Reading in data... Reading data took 0.0907249450684 s Creating peak regions... Creating peak regions took 15.3696370125 s Estimating background... Estimating background took 0.435067176819 s