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='ZNF398-SRR5197128.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='ZNF398-SRR5197128/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 ZNF398-SRR5197128.hg20-male.36mers.unique.bam Reading in data... Reading data took 4.50677800179 s Creating peak regions... Creating peak regions took 63.7041978836 s Estimating background... Estimating background took 30.5637869835 s Processing ZNF398-SRR5197128.hg20-male.36mers.unique.bam Reading in data... Reading data took 2.25378108025 s Creating peak regions... Creating peak regions took 33.8450419903 s Estimating background... Estimating background took 12.1558032036 s Processing ZNF398-SRR5197128.hg20-male.36mers.unique.bam Reading in data... Reading data took 2.3318400383 s Creating peak regions... Creating peak regions took 32.042181015 s Estimating background... Estimating background took 12.662966013 s Processing ZNF398-SRR5197128.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='ZNF398-SRR5197128.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='ZNF398-SRR5197128/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 ZNF398-SRR5197128.hg20-male.36mers.unique.bam Reading in data... Reading data took 5.73369193077 s Creating peak regions... Creating peak regions took 75.9023220539 s Estimating background... Estimating background took 39.1612541676 s Processing ZNF398-SRR5197128.hg20-male.36mers.unique.bam Reading in data... Reading data took 3.05288982391 s Creating peak regions... Creating peak regions took 40.1306889057 s Estimating background... Estimating background took 13.8677051067 s Processing ZNF398-SRR5197128.hg20-male.36mers.unique.bam Reading in data... Reading data took 3.00599789619 s Creating peak regions... Creating peak regions took 38.8576271534 s Estimating background... Estimating background took 14.9989631176 s Processing ZNF398-SRR5197128.hg20-male.36mers.unique.bam Reading in data... Reading data took 3.12173390388 s Creating peak regions... Creating peak regions took 43.6920201778 s Estimating background... Estimating background took 14.5984787941 s Processing ZNF398-SRR5197128.hg20-male.36mers.unique.bam Reading in data... Reading data took 2.52052783966 s Creating peak regions... Creating peak regions took 36.8787529469 s Estimating background... Estimating background took 19.5634338856 s Processing ZNF398-SRR5197128.hg20-male.36mers.unique.bam Reading in data... Reading data took 2.11054587364 s Creating peak regions... Creating peak regions took 30.3389070034 s Estimating background... Estimating background took 10.6271789074 s Processing ZNF398-SRR5197128.hg20-male.36mers.unique.bam Reading in data... Reading data took 1.99807715416 s Creating peak regions... Creating peak regions took 29.8212590218 s Estimating background... Estimating background took 10.8586239815 s Processing ZNF398-SRR5197128.hg20-male.36mers.unique.bam Reading in data... Reading data took 1.90914797783 s Creating peak regions... Creating peak regions took 27.8043818474 s Estimating background... Estimating background took 9.58491897583 s Processing ZNF398-SRR5197128.hg20-male.36mers.unique.bam Reading in data... Reading data took 2.15981388092 s Creating peak regions... Creating peak regions took 27.3719270229 s Estimating background... Estimating background took 11.3863730431 s Processing ZNF398-SRR5197128.hg20-male.36mers.unique.bam Reading in data... Reading data took 1.56419706345 s Creating peak regions... Creating peak regions took 26.0114550591 s Estimating background... Estimating background took 8.74499797821 s Processing ZNF398-SRR5197128.hg20-male.36mers.unique.bam Reading in data... Reading data took 1.5693230629 s Creating peak regions... Creating peak regions took 17.8204979897 s Estimating background... Estimating background took 7.28150010109 s Processing ZNF398-SRR5197128.hg20-male.36mers.unique.bam Reading in data... Reading data took 4.91198205948 s Creating peak regions... Creating peak regions took 73.7565159798 s Estimating background... Estimating background took 26.5638887882 s Processing ZNF398-SRR5197128.hg20-male.36mers.unique.bam Reading in data... Reading data took 1.55844902992 s Creating peak regions... Creating peak regions took 21.0161569118 s Estimating background... Estimating background took 8.19373989105 s Processing ZNF398-SRR5197128.hg20-male.36mers.unique.bam Reading in data... Reading data took 0.917541980743 s Creating peak regions... Creating peak regions took 14.001937151 s Estimating background... Estimating background took 4.96315288544 s Processing ZNF398-SRR5197128.hg20-male.36mers.unique.bam Reading in data... Reading data took 1.21830797195 s Creating peak regions... Creating peak regions took 16.2269349098 s Estimating background... Estimating background took 7.58373808861 s Processing ZNF398-SRR5197128.hg20-male.36mers.unique.bam Reading in data... Reading data took 4.06216001511 s Creating peak regions... Creating peak regions took 59.8355028629 s Estimating background... Estimating background took 19.4960551262 s Processing ZNF398-SRR5197128.hg20-male.36mers.unique.bam Reading in data... Reading data took 3.51634287834 s Creating peak regions... Creating peak regions took 56.7027099133 s Estimating background... Estimating background took 17.7222208977 s Processing ZNF398-SRR5197128.hg20-male.36mers.unique.bam Reading in data... Reading data took 4.07850909233 s Creating peak regions... Creating peak regions took 59.5614850521 s Estimating background... Estimating background took 19.1672580242 s Processing ZNF398-SRR5197128.hg20-male.36mers.unique.bam Reading in data... Reading data took 4.00945091248 s Creating peak regions... Creating peak regions took 52.9558780193 s Estimating background... Estimating background took 23.1670851707 s Processing ZNF398-SRR5197128.hg20-male.36mers.unique.bam Reading in data... Reading data took 3.80527305603 s Creating peak regions... Creating peak regions took 48.5742340088 s Estimating background... Estimating background took 19.6671919823 s Processing ZNF398-SRR5197128.hg20-male.36mers.unique.bam Reading in data... Reading data took 2.97802996635 s Creating peak regions... Creating peak regions took 43.9429550171 s Estimating background... Estimating background took 14.4882369041 s Processing ZNF398-SRR5197128.hg20-male.36mers.unique.bam Reading in data... Reading data took 2.57213282585 s Creating peak regions... Creating peak regions took 40.890761137 s Estimating background... Estimating background took 12.2588100433 s Processing ZNF398-SRR5197128.hg20-male.36mers.unique.bam Reading in data... Reading data took 0.0999429225922 s Creating peak regions... Creating peak regions took 0.177669048309 s Estimating background... Estimating background took 0.632520198822 s Processing ZNF398-SRR5197128.hg20-male.36mers.unique.bam Reading in data... Reading data took 3.04991602898 s Creating peak regions... Creating peak regions took 39.5205800533 s Estimating background... Estimating background took 17.9741740227 s Processing ZNF398-SRR5197128.hg20-male.36mers.unique.bam Reading in data... Reading data took 0.118705034256 s Creating peak regions... Creating peak regions took 13.7727119923 s Estimating background... Estimating background took 2.49476480484 s