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='ZNF671-SRR5197209.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='ZNF671-SRR5197209/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 ZNF671-SRR5197209.hg20-male.36mers.unique.bam Reading in data... Reading data took 3.82640910149 s Creating peak regions... Creating peak regions took 75.1832289696 s Estimating background... Estimating background took 25.2708261013 s Processing ZNF671-SRR5197209.hg20-male.36mers.unique.bam Reading in data... Reading data took 2.09635400772 s Creating peak regions... Creating peak regions took 38.9043850899 s Estimating background... Estimating background took 12.4769282341 s Processing ZNF671-SRR5197209.hg20-male.36mers.unique.bam Reading in data... Reading data took 2.00691318512 s Creating peak regions... Creating peak regions took 39.4263780117 s Estimating background... Estimating background took 10.6311810017 s Processing ZNF671-SRR5197209.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='ZNF671-SRR5197209.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='ZNF671-SRR5197209/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 ZNF671-SRR5197209.hg20-male.36mers.unique.bam Reading in data... Reading data took 3.81621694565 s Creating peak regions... Creating peak regions took 72.9295890331 s Estimating background... Estimating background took 24.8206958771 s Processing ZNF671-SRR5197209.hg20-male.36mers.unique.bam Reading in data... Reading data took 2.09169006348 s Creating peak regions... Creating peak regions took 37.866008997 s Estimating background... Estimating background took 12.4215979576 s Processing ZNF671-SRR5197209.hg20-male.36mers.unique.bam Reading in data... Reading data took 2.20976018906 s Creating peak regions... Creating peak regions took 37.9535839558 s Estimating background... Estimating background took 10.3589010239 s Processing ZNF671-SRR5197209.hg20-male.36mers.unique.bam Reading in data... Reading data took 1.96917819977 s Creating peak regions... Creating peak regions took 40.4768109322 s Estimating background... Estimating background took 11.0952529907 s Processing ZNF671-SRR5197209.hg20-male.36mers.unique.bam Reading in data... Reading data took 1.94530892372 s Creating peak regions... Creating peak regions took 34.5882730484 s Estimating background... Estimating background took 10.7841329575 s Processing ZNF671-SRR5197209.hg20-male.36mers.unique.bam Reading in data... Reading data took 1.43512392044 s Creating peak regions... Creating peak regions took 31.5985639095 s Estimating background... Estimating background took 7.4182331562 s Processing ZNF671-SRR5197209.hg20-male.36mers.unique.bam Reading in data... Reading data took 1.3009750843 s Creating peak regions... Creating peak regions took 28.2652750015 s Estimating background... Estimating background took 8.30300402641 s Processing ZNF671-SRR5197209.hg20-male.36mers.unique.bam Reading in data... Reading data took 1.37861013412 s Creating peak regions... Creating peak regions took 25.4200971127 s Estimating background... Estimating background took 7.55937218666 s Processing ZNF671-SRR5197209.hg20-male.36mers.unique.bam Reading in data... Reading data took 1.57460093498 s Creating peak regions... Creating peak regions took 25.2339301109 s Estimating background... Estimating background took 10.6733961105 s Processing ZNF671-SRR5197209.hg20-male.36mers.unique.bam Reading in data... Reading data took 1.02241706848 s Creating peak regions... Creating peak regions took 23.8836679459 s Estimating background... Estimating background took 5.44258594513 s Processing ZNF671-SRR5197209.hg20-male.36mers.unique.bam Reading in data... Reading data took 0.975373029709 s Creating peak regions... Creating peak regions took 17.605766058 s Estimating background... Estimating background took 6.5090610981 s Processing ZNF671-SRR5197209.hg20-male.36mers.unique.bam Reading in data... Reading data took 3.30297112465 s Creating peak regions... Creating peak regions took 73.2755551338 s Estimating background... Estimating background took 18.066395998 s Processing ZNF671-SRR5197209.hg20-male.36mers.unique.bam Reading in data... Reading data took 1.20207500458 s Creating peak regions... Creating peak regions took 20.2281839848 s Estimating background... Estimating background took 7.27711105347 s Processing ZNF671-SRR5197209.hg20-male.36mers.unique.bam Reading in data... Reading data took 0.756572008133 s Creating peak regions... Creating peak regions took 13.2427170277 s Estimating background... Estimating background took 5.78124690056 s Processing ZNF671-SRR5197209.hg20-male.36mers.unique.bam Reading in data... Reading data took 0.935961961746 s Creating peak regions... Creating peak regions took 15.6466999054 s Estimating background... Estimating background took 5.9129858017 s Processing ZNF671-SRR5197209.hg20-male.36mers.unique.bam Reading in data... Reading data took 2.62546801567 s Creating peak regions... Creating peak regions took 59.3896970749 s Estimating background... Estimating background took 14.0947420597 s Processing ZNF671-SRR5197209.hg20-male.36mers.unique.bam Reading in data... Reading data took 2.38511896133 s Creating peak regions... Creating peak regions took 53.0088729858 s Estimating background... Estimating background took 12.1811730862 s Processing ZNF671-SRR5197209.hg20-male.36mers.unique.bam Reading in data... Reading data took 2.56729412079 s Creating peak regions... Creating peak regions took 51.45885396 s Estimating background... Estimating background took 13.7713558674 s Processing ZNF671-SRR5197209.hg20-male.36mers.unique.bam Reading in data... Reading data took 2.67000603676 s Creating peak regions... Creating peak regions took 52.2272908688 s Estimating background... Estimating background took 15.5138270855 s Processing ZNF671-SRR5197209.hg20-male.36mers.unique.bam Reading in data... Reading data took 2.51634001732 s Creating peak regions... Creating peak regions took 45.8041069508 s Estimating background... Estimating background took 13.4530689716 s Processing ZNF671-SRR5197209.hg20-male.36mers.unique.bam Reading in data... Reading data took 1.99063205719 s Creating peak regions... Creating peak regions took 43.7855129242 s Estimating background... Estimating background took 10.0600678921 s Processing ZNF671-SRR5197209.hg20-male.36mers.unique.bam Reading in data... Reading data took 1.79278993607 s Creating peak regions... Creating peak regions took 38.8266608715 s Estimating background... Estimating background took 9.92552185059 s Processing ZNF671-SRR5197209.hg20-male.36mers.unique.bam Reading in data... Reading data took 0.074070930481 s Creating peak regions... Creating peak regions took 0.160556077957 s Estimating background... Estimating background took 0.54842710495 s Processing ZNF671-SRR5197209.hg20-male.36mers.unique.bam Reading in data... Reading data took 2.50846004486 s Creating peak regions... Creating peak regions took 47.710381031 s Estimating background... Estimating background took 12.7810869217 s Processing ZNF671-SRR5197209.hg20-male.36mers.unique.bam Reading in data... Reading data took 0.517338037491 s Creating peak regions... Creating peak regions took 17.0362670422 s Estimating background... Estimating background took 2.55161309242 s