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='ZNF543-SRR5197169.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='ZNF543-SRR5197169/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 ZNF543-SRR5197169.hg20-male.36mers.unique.bam Reading in data... Reading data took 6.94040894508 s Creating peak regions... Creating peak regions took 79.7932910919 s Estimating background... Estimating background took 52.7358109951 s Processing ZNF543-SRR5197169.hg20-male.36mers.unique.bam Reading in data... Reading data took 3.55963110924 s Creating peak regions... Creating peak regions took 42.0848720074 s Estimating background... Estimating background took 21.164591074 s Processing ZNF543-SRR5197169.hg20-male.36mers.unique.bam Reading in data... Reading data took 3.39401197433 s Creating peak regions... Creating peak regions took 40.7237288952 s Estimating background... Estimating background took 21.3675410748 s Processing ZNF543-SRR5197169.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='ZNF543-SRR5197169.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='ZNF543-SRR5197169/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 ZNF543-SRR5197169.hg20-male.36mers.unique.bam Reading in data... Reading data took 6.52459716797 s Creating peak regions... Creating peak regions took 79.3048191071 s Estimating background... Estimating background took 53.9472539425 s Processing ZNF543-SRR5197169.hg20-male.36mers.unique.bam Reading in data... Reading data took 3.39791488647 s Creating peak regions... Creating peak regions took 42.7280180454 s Estimating background... Estimating background took 22.4136869907 s Processing ZNF543-SRR5197169.hg20-male.36mers.unique.bam Reading in data... Reading data took 3.79125809669 s Creating peak regions... Creating peak regions took 45.5781781673 s Estimating background... Estimating background took 20.872824192 s Processing ZNF543-SRR5197169.hg20-male.36mers.unique.bam Reading in data... Reading data took 3.62217903137 s Creating peak regions... Creating peak regions took 41.4264709949 s Estimating background... Estimating background took 22.8811740875 s Processing ZNF543-SRR5197169.hg20-male.36mers.unique.bam Reading in data... Reading data took 3.09600520134 s Creating peak regions... Creating peak regions took 35.8313210011 s Estimating background... Estimating background took 22.2274119854 s Processing ZNF543-SRR5197169.hg20-male.36mers.unique.bam Reading in data... Reading data took 2.23148703575 s Creating peak regions... Creating peak regions took 29.8461148739 s Estimating background... Estimating background took 14.3620429039 s Processing ZNF543-SRR5197169.hg20-male.36mers.unique.bam Reading in data... Reading data took 2.17388606071 s Creating peak regions... Creating peak regions took 33.3530888557 s Estimating background... Estimating background took 16.369740963 s Processing ZNF543-SRR5197169.hg20-male.36mers.unique.bam Reading in data... Reading data took 2.37109994888 s Creating peak regions... Creating peak regions took 30.0435988903 s Estimating background... Estimating background took 14.9135279655 s Processing ZNF543-SRR5197169.hg20-male.36mers.unique.bam Reading in data... Reading data took 2.58083987236 s Creating peak regions... Creating peak regions took 27.1637060642 s Estimating background... Estimating background took 19.328263998 s Processing ZNF543-SRR5197169.hg20-male.36mers.unique.bam Reading in data... Reading data took 1.87829899788 s Creating peak regions... Creating peak regions took 25.0604240894 s Estimating background... Estimating background took 11.6982998848 s Processing ZNF543-SRR5197169.hg20-male.36mers.unique.bam Reading in data... Reading data took 1.79466700554 s Creating peak regions... Creating peak regions took 20.0478889942 s Estimating background... Estimating background took 12.7020881176 s Processing ZNF543-SRR5197169.hg20-male.36mers.unique.bam Reading in data... Reading data took 5.66272091866 s Creating peak regions... Creating peak regions took 76.1083731651 s Estimating background... Estimating background took 36.0622308254 s Processing ZNF543-SRR5197169.hg20-male.36mers.unique.bam Reading in data... Reading data took 2.01770186424 s Creating peak regions... Creating peak regions took 21.1763939857 s Estimating background... Estimating background took 11.6961979866 s Processing ZNF543-SRR5197169.hg20-male.36mers.unique.bam Reading in data... Reading data took 1.07543802261 s Creating peak regions... Creating peak regions took 13.2296338081 s Estimating background... Estimating background took 6.78740692139 s Processing ZNF543-SRR5197169.hg20-male.36mers.unique.bam Reading in data... Reading data took 1.44014787674 s Creating peak regions... Creating peak regions took 15.3242630959 s Estimating background... Estimating background took 11.9785261154 s Processing ZNF543-SRR5197169.hg20-male.36mers.unique.bam Reading in data... Reading data took 4.86846494675 s Creating peak regions... Creating peak regions took 66.6359531879 s Estimating background... Estimating background took 28.5621972084 s Processing ZNF543-SRR5197169.hg20-male.36mers.unique.bam Reading in data... Reading data took 3.79010105133 s Creating peak regions... Creating peak regions took 58.6072978973 s Estimating background... Estimating background took 21.6327579021 s Processing ZNF543-SRR5197169.hg20-male.36mers.unique.bam Reading in data... Reading data took 4.62988591194 s Creating peak regions... Creating peak regions took 55.9415009022 s Estimating background... Estimating background took 28.5862998962 s Processing ZNF543-SRR5197169.hg20-male.36mers.unique.bam Reading in data... Reading data took 4.61072707176 s Creating peak regions... Creating peak regions took 53.9535148144 s Estimating background... Estimating background took 30.5681521893 s Processing ZNF543-SRR5197169.hg20-male.36mers.unique.bam Reading in data... Reading data took 4.16132998466 s Creating peak regions... Creating peak regions took 41.2999441624 s Estimating background... Estimating background took 22.8135490417 s Processing ZNF543-SRR5197169.hg20-male.36mers.unique.bam Reading in data... Reading data took 2.72357296944 s Creating peak regions... Creating peak regions took 36.729156971 s Estimating background... Estimating background took 15.5259339809 s Processing ZNF543-SRR5197169.hg20-male.36mers.unique.bam Reading in data... Reading data took 2.47237491608 s Creating peak regions... Creating peak regions took 34.3798708916 s Estimating background... Estimating background took 16.16406703 s Processing ZNF543-SRR5197169.hg20-male.36mers.unique.bam Reading in data... Reading data took 0.0949189662933 s Creating peak regions... Creating peak regions took 0.175053834915 s Estimating background... Estimating background took 0.525911092758 s Processing ZNF543-SRR5197169.hg20-male.36mers.unique.bam Reading in data... Reading data took 3.46864104271 s Creating peak regions... Creating peak regions took 39.7487201691 s Estimating background... Estimating background took 24.1853358746 s Processing ZNF543-SRR5197169.hg20-male.36mers.unique.bam Reading in data... Reading data took 0.136916160583 s Creating peak regions... Creating peak regions took 13.5512912273 s Estimating background... Estimating background took 0.654902935028 s