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='ZNF154-SRR5197063.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='ZNF154-SRR5197063/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 ZNF154-SRR5197063.hg20-male.36mers.unique.bam Reading in data... Reading data took 3.89650797844 s Creating peak regions... Creating peak regions took 74.5556731224 s Estimating background... Estimating background took 23.4416329861 s Processing ZNF154-SRR5197063.hg20-male.36mers.unique.bam Reading in data... Reading data took 1.92966008186 s Creating peak regions... Creating peak regions took 41.6038150787 s Estimating background... Estimating background took 9.73507499695 s Processing ZNF154-SRR5197063.hg20-male.36mers.unique.bam Reading in data... Reading data took 2.0929210186 s Creating peak regions... Creating peak regions took 39.169107914 s Estimating background... Estimating background took 8.97403120995 s Processing ZNF154-SRR5197063.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='ZNF154-SRR5197063.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='ZNF154-SRR5197063/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 ZNF154-SRR5197063.hg20-male.36mers.unique.bam Reading in data... Reading data took 3.2347779274 s Creating peak regions... Creating peak regions took 66.8433551788 s Estimating background... Estimating background took 19.949409008 s Processing ZNF154-SRR5197063.hg20-male.36mers.unique.bam Reading in data... Reading data took 1.58125686646 s Creating peak regions... Creating peak regions took 34.1838490963 s Estimating background... Estimating background took 8.17224097252 s Processing ZNF154-SRR5197063.hg20-male.36mers.unique.bam Reading in data... Reading data took 1.60936403275 s Creating peak regions... Creating peak regions took 33.8288440704 s Estimating background... Estimating background took 8.02689695358 s Processing ZNF154-SRR5197063.hg20-male.36mers.unique.bam Reading in data... Reading data took 1.67604112625 s Creating peak regions... Creating peak regions took 34.9220268726 s Estimating background... Estimating background took 9.52792811394 s Processing ZNF154-SRR5197063.hg20-male.36mers.unique.bam Reading in data... Reading data took 1.80881094933 s Creating peak regions... Creating peak regions took 32.7171461582 s Estimating background... Estimating background took 10.641602993 s Processing ZNF154-SRR5197063.hg20-male.36mers.unique.bam Reading in data... Reading data took 1.36014413834 s Creating peak regions... Creating peak regions took 31.2235820293 s Estimating background... Estimating background took 6.65942502022 s Processing ZNF154-SRR5197063.hg20-male.36mers.unique.bam Reading in data... Reading data took 1.22416114807 s Creating peak regions... Creating peak regions took 30.2031459808 s Estimating background... Estimating background took 6.73936510086 s Processing ZNF154-SRR5197063.hg20-male.36mers.unique.bam Reading in data... Reading data took 1.25910115242 s Creating peak regions... Creating peak regions took 26.9291388988 s Estimating background... Estimating background took 6.35847306252 s Processing ZNF154-SRR5197063.hg20-male.36mers.unique.bam Reading in data... Reading data took 1.36563205719 s Creating peak regions... Creating peak regions took 25.2784130573 s Estimating background... Estimating background took 7.11468195915 s Processing ZNF154-SRR5197063.hg20-male.36mers.unique.bam Reading in data... Reading data took 0.94744682312 s Creating peak regions... Creating peak regions took 22.4485208988 s Estimating background... Estimating background took 5.09549307823 s Processing ZNF154-SRR5197063.hg20-male.36mers.unique.bam Reading in data... Reading data took 0.858861923218 s Creating peak regions... Creating peak regions took 16.0811138153 s Estimating background... Estimating background took 4.88586091995 s Processing ZNF154-SRR5197063.hg20-male.36mers.unique.bam Reading in data... Reading data took 3.13440704346 s Creating peak regions... Creating peak regions took 73.0609538555 s Estimating background... Estimating background took 15.367536068 s Processing ZNF154-SRR5197063.hg20-male.36mers.unique.bam Reading in data... Reading data took 1.05641889572 s Creating peak regions... Creating peak regions took 19.243885994 s Estimating background... Estimating background took 5.30633211136 s Processing ZNF154-SRR5197063.hg20-male.36mers.unique.bam Reading in data... Reading data took 0.554102182388 s Creating peak regions... Creating peak regions took 14.1733720303 s Estimating background... Estimating background took 2.25954318047 s Processing ZNF154-SRR5197063.hg20-male.36mers.unique.bam Reading in data... Reading data took 0.956212997437 s Creating peak regions... Creating peak regions took 15.3589780331 s Estimating background... Estimating background took 4.8482439518 s Processing ZNF154-SRR5197063.hg20-male.36mers.unique.bam Reading in data... Reading data took 2.50684714317 s Creating peak regions... Creating peak regions took 59.2482068539 s Estimating background... Estimating background took 12.343818903 s Processing ZNF154-SRR5197063.hg20-male.36mers.unique.bam Reading in data... Reading data took 2.22422885895 s Creating peak regions... Creating peak regions took 57.0943179131 s Estimating background... Estimating background took 10.7168190479 s Processing ZNF154-SRR5197063.hg20-male.36mers.unique.bam Reading in data... Reading data took 2.44624614716 s Creating peak regions... Creating peak regions took 50.2921290398 s Estimating background... Estimating background took 12.0904300213 s Processing ZNF154-SRR5197063.hg20-male.36mers.unique.bam Reading in data... Reading data took 2.68040108681 s Creating peak regions... Creating peak regions took 52.6961128712 s Estimating background... Estimating background took 12.9656128883 s Processing ZNF154-SRR5197063.hg20-male.36mers.unique.bam Reading in data... Reading data took 2.49769806862 s Creating peak regions... Creating peak regions took 46.7615129948 s Estimating background... Estimating background took 11.8336498737 s Processing ZNF154-SRR5197063.hg20-male.36mers.unique.bam Reading in data... Reading data took 2.20252394676 s Creating peak regions... Creating peak regions took 43.8344960213 s Estimating background... Estimating background took 9.30458712578 s Processing ZNF154-SRR5197063.hg20-male.36mers.unique.bam Reading in data... Reading data took 1.75885605812 s Creating peak regions... Creating peak regions took 38.9398858547 s Estimating background... Estimating background took 8.67032814026 s Processing ZNF154-SRR5197063.hg20-male.36mers.unique.bam Reading in data... Reading data took 0.099781036377 s Creating peak regions... Creating peak regions took 0.197599887848 s Estimating background... Estimating background took 0.776012897491 s Processing ZNF154-SRR5197063.hg20-male.36mers.unique.bam Reading in data... Reading data took 2.68648791313 s Creating peak regions... Creating peak regions took 47.619120121 s Estimating background... Estimating background took 14.0339038372 s Processing ZNF154-SRR5197063.hg20-male.36mers.unique.bam Reading in data... Reading data took 0.107404947281 s Creating peak regions... Creating peak regions took 15.9570608139 s Estimating background... Estimating background took 0.530725955963 s