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='ZNF433-SRR5197139.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='ZNF433-SRR5197139/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 ZNF433-SRR5197139.hg20-male.36mers.unique.bam Reading in data... Reading data took 5.17097806931 s Creating peak regions... Creating peak regions took 73.8415379524 s Estimating background... Estimating background took 33.4587790966 s Processing ZNF433-SRR5197139.hg20-male.36mers.unique.bam Reading in data... Reading data took 2.48888111115 s Creating peak regions... Creating peak regions took 39.5204617977 s Estimating background... Estimating background took 13.8608970642 s Processing ZNF433-SRR5197139.hg20-male.36mers.unique.bam Reading in data... Reading data took 2.49775791168 s Creating peak regions... Creating peak regions took 39.4666411877 s Estimating background... Estimating background took 13.9538550377 s Processing ZNF433-SRR5197139.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='ZNF433-SRR5197139.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='ZNF433-SRR5197139/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 ZNF433-SRR5197139.hg20-male.36mers.unique.bam Reading in data... Reading data took 4.98746013641 s Creating peak regions... Creating peak regions took 75.4045779705 s Estimating background... Estimating background took 36.6523280144 s Processing ZNF433-SRR5197139.hg20-male.36mers.unique.bam Reading in data... Reading data took 2.70458292961 s Creating peak regions... Creating peak regions took 38.8779160976 s Estimating background... Estimating background took 14.1522600651 s Processing ZNF433-SRR5197139.hg20-male.36mers.unique.bam Reading in data... Reading data took 2.74198794365 s Creating peak regions... Creating peak regions took 39.1635229588 s Estimating background... Estimating background took 14.9030659199 s Processing ZNF433-SRR5197139.hg20-male.36mers.unique.bam Reading in data... Reading data took 2.87808609009 s Creating peak regions... Creating peak regions took 40.7623050213 s Estimating background... Estimating background took 14.3339669704 s Processing ZNF433-SRR5197139.hg20-male.36mers.unique.bam Reading in data... Reading data took 2.36527895927 s Creating peak regions... Creating peak regions took 33.8751029968 s Estimating background... Estimating background took 16.0096158981 s Processing ZNF433-SRR5197139.hg20-male.36mers.unique.bam Reading in data... Reading data took 1.82678484917 s Creating peak regions... Creating peak regions took 31.5776391029 s Estimating background... Estimating background took 10.0061631203 s Processing ZNF433-SRR5197139.hg20-male.36mers.unique.bam Reading in data... Reading data took 1.92653989792 s Creating peak regions... Creating peak regions took 28.3621709347 s Estimating background... Estimating background took 11.7566559315 s Processing ZNF433-SRR5197139.hg20-male.36mers.unique.bam Reading in data... Reading data took 1.82418298721 s Creating peak regions... Creating peak regions took 26.5102231503 s Estimating background... Estimating background took 10.076846838 s Processing ZNF433-SRR5197139.hg20-male.36mers.unique.bam Reading in data... Reading data took 2.12921285629 s Creating peak regions... Creating peak regions took 26.7460510731 s Estimating background... Estimating background took 14.2579698563 s Processing ZNF433-SRR5197139.hg20-male.36mers.unique.bam Reading in data... Reading data took 1.51820802689 s Creating peak regions... Creating peak regions took 24.1018509865 s Estimating background... Estimating background took 8.26212787628 s Processing ZNF433-SRR5197139.hg20-male.36mers.unique.bam Reading in data... Reading data took 1.56648206711 s Creating peak regions... Creating peak regions took 18.1642999649 s Estimating background... Estimating background took 8.89201211929 s Processing ZNF433-SRR5197139.hg20-male.36mers.unique.bam Reading in data... Reading data took 3.71551513672 s Creating peak regions... Creating peak regions took 72.4995219707 s Estimating background... Estimating background took 25.5790669918 s Processing ZNF433-SRR5197139.hg20-male.36mers.unique.bam Reading in data... Reading data took 1.62112188339 s Creating peak regions... Creating peak regions took 20.6169919968 s Estimating background... Estimating background took 8.87827706337 s Processing ZNF433-SRR5197139.hg20-male.36mers.unique.bam Reading in data... Reading data took 0.912425041199 s Creating peak regions... Creating peak regions took 13.1195340157 s Estimating background... Estimating background took 4.68976998329 s Processing ZNF433-SRR5197139.hg20-male.36mers.unique.bam Reading in data... Reading data took 1.24010682106 s Creating peak regions... Creating peak regions took 15.541793108 s Estimating background... Estimating background took 8.70543813705 s Processing ZNF433-SRR5197139.hg20-male.36mers.unique.bam Reading in data... Reading data took 3.80332899094 s Creating peak regions... Creating peak regions took 59.3487169743 s Estimating background... Estimating background took 18.5683300495 s Processing ZNF433-SRR5197139.hg20-male.36mers.unique.bam Reading in data... Reading data took 2.94207286835 s Creating peak regions... Creating peak regions took 54.0061490536 s Estimating background... Estimating background took 14.9432611465 s Processing ZNF433-SRR5197139.hg20-male.36mers.unique.bam Reading in data... Reading data took 3.41594004631 s Creating peak regions... Creating peak regions took 54.8963141441 s Estimating background... Estimating background took 18.5885999203 s Processing ZNF433-SRR5197139.hg20-male.36mers.unique.bam Reading in data... Reading data took 3.86272382736 s Creating peak regions... Creating peak regions took 54.7983469963 s Estimating background... Estimating background took 22.1041219234 s Processing ZNF433-SRR5197139.hg20-male.36mers.unique.bam Reading in data... Reading data took 3.37542796135 s Creating peak regions... Creating peak regions took 49.6336700916 s Estimating background... Estimating background took 18.4191110134 s Processing ZNF433-SRR5197139.hg20-male.36mers.unique.bam Reading in data... Reading data took 2.04341697693 s Creating peak regions... Creating peak regions took 45.3393158913 s Estimating background... Estimating background took 13.3078649044 s Processing ZNF433-SRR5197139.hg20-male.36mers.unique.bam Reading in data... Reading data took 2.35902786255 s Creating peak regions... Creating peak regions took 40.6936490536 s Estimating background... Estimating background took 13.1722779274 s Processing ZNF433-SRR5197139.hg20-male.36mers.unique.bam Reading in data... Reading data took 0.0994930267334 s Creating peak regions... Creating peak regions took 0.159500837326 s Estimating background... Estimating background took 0.598989963531 s Processing ZNF433-SRR5197139.hg20-male.36mers.unique.bam Reading in data... Reading data took 3.2694978714 s Creating peak regions... Creating peak regions took 43.901870966 s Estimating background... Estimating background took 14.6444242001 s Processing ZNF433-SRR5197139.hg20-male.36mers.unique.bam Reading in data... Reading data took 0.0954627990723 s Creating peak regions... Creating peak regions took 14.3923580647 s Estimating background... Estimating background took 0.467893838882 s