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='ZNF891-SRR5197265.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='ZNF891-SRR5197265/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 ZNF891-SRR5197265.hg20-male.36mers.unique.bam Reading in data... Reading data took 2.99208807945 s Creating peak regions... Creating peak regions took 68.134442091 s Estimating background... Estimating background took 16.9980940819 s Processing ZNF891-SRR5197265.hg20-male.36mers.unique.bam Reading in data... Reading data took 1.60096597672 s Creating peak regions... Creating peak regions took 37.3022918701 s Estimating background... Estimating background took 8.22487688065 s Processing ZNF891-SRR5197265.hg20-male.36mers.unique.bam Reading in data... Reading data took 1.73046708107 s Creating peak regions... Creating peak regions took 35.8889629841 s Estimating background... Estimating background took 8.13706493378 s Processing ZNF891-SRR5197265.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='ZNF891-SRR5197265.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='ZNF891-SRR5197265/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 ZNF891-SRR5197265.hg20-male.36mers.unique.bam Reading in data... Reading data took 3.18205022812 s Creating peak regions... Creating peak regions took 59.3709971905 s Estimating background... Estimating background took 15.2962579727 s Processing ZNF891-SRR5197265.hg20-male.36mers.unique.bam Reading in data... Reading data took 1.30276298523 s Creating peak regions... Creating peak regions took 32.6654989719 s Estimating background... Estimating background took 7.12756800652 s Processing ZNF891-SRR5197265.hg20-male.36mers.unique.bam Reading in data... Reading data took 1.24832201004 s Creating peak regions... Creating peak regions took 31.1105790138 s Estimating background... Estimating background took 7.2629840374 s Processing ZNF891-SRR5197265.hg20-male.36mers.unique.bam Reading in data... Reading data took 1.38283705711 s Creating peak regions... Creating peak regions took 33.412966013 s Estimating background... Estimating background took 7.59931087494 s Processing ZNF891-SRR5197265.hg20-male.36mers.unique.bam Reading in data... Reading data took 1.04702687263 s Creating peak regions... Creating peak regions took 26.2888860703 s Estimating background... Estimating background took 6.94385790825 s Processing ZNF891-SRR5197265.hg20-male.36mers.unique.bam Reading in data... Reading data took 0.884652137756 s Creating peak regions... Creating peak regions took 24.2833991051 s Estimating background... Estimating background took 5.20164704323 s Processing ZNF891-SRR5197265.hg20-male.36mers.unique.bam Reading in data... Reading data took 0.858155965805 s Creating peak regions... Creating peak regions took 24.7535831928 s Estimating background... Estimating background took 5.47738790512 s Processing ZNF891-SRR5197265.hg20-male.36mers.unique.bam Reading in data... Reading data took 0.861727952957 s Creating peak regions... Creating peak regions took 22.1936588287 s Estimating background... Estimating background took 5.39126586914 s Processing ZNF891-SRR5197265.hg20-male.36mers.unique.bam Reading in data... Reading data took 1.09405994415 s Creating peak regions... Creating peak regions took 21.0603299141 s Estimating background... Estimating background took 7.02579903603 s Processing ZNF891-SRR5197265.hg20-male.36mers.unique.bam Reading in data... Reading data took 0.613083124161 s Creating peak regions... Creating peak regions took 18.3420939445 s Estimating background... Estimating background took 4.00996804237 s Processing ZNF891-SRR5197265.hg20-male.36mers.unique.bam Reading in data... Reading data took 0.813395023346 s Creating peak regions... Creating peak regions took 14.8198359013 s Estimating background... Estimating background took 4.74070906639 s Processing ZNF891-SRR5197265.hg20-male.36mers.unique.bam Reading in data... Reading data took 2.11240911484 s Creating peak regions... Creating peak regions took 60.5414431095 s Estimating background... Estimating background took 11.5297648907 s Processing ZNF891-SRR5197265.hg20-male.36mers.unique.bam Reading in data... Reading data took 0.749104976654 s Creating peak regions... Creating peak regions took 17.1330060959 s Estimating background... Estimating background took 4.91807103157 s Processing ZNF891-SRR5197265.hg20-male.36mers.unique.bam Reading in data... Reading data took 0.442260980606 s Creating peak regions... Creating peak regions took 11.535861969 s Estimating background... Estimating background took 2.85122895241 s Processing ZNF891-SRR5197265.hg20-male.36mers.unique.bam Reading in data... Reading data took 0.681668043137 s Creating peak regions... Creating peak regions took 11.7038989067 s Estimating background... Estimating background took 4.63634896278 s Processing ZNF891-SRR5197265.hg20-male.36mers.unique.bam Reading in data... Reading data took 1.8117442131 s Creating peak regions... Creating peak regions took 49.2657849789 s Estimating background... Estimating background took 9.06453704834 s Processing ZNF891-SRR5197265.hg20-male.36mers.unique.bam Reading in data... Reading data took 1.38034081459 s Creating peak regions... Creating peak regions took 41.4117181301 s Estimating background... Estimating background took 7.65093207359 s Processing ZNF891-SRR5197265.hg20-male.36mers.unique.bam Reading in data... Reading data took 1.55971384048 s Creating peak regions... Creating peak regions took 44.6949808598 s Estimating background... Estimating background took 9.11872720718 s Processing ZNF891-SRR5197265.hg20-male.36mers.unique.bam Reading in data... Reading data took 2.21875596046 s Creating peak regions... Creating peak regions took 39.3395578861 s Estimating background... Estimating background took 9.64217114449 s Processing ZNF891-SRR5197265.hg20-male.36mers.unique.bam Reading in data... Reading data took 1.57560396194 s Creating peak regions... Creating peak regions took 37.5185661316 s Estimating background... Estimating background took 9.25581002235 s Processing ZNF891-SRR5197265.hg20-male.36mers.unique.bam Reading in data... Reading data took 1.20253300667 s Creating peak regions... Creating peak regions took 35.7782139778 s Estimating background... Estimating background took 6.69058203697 s Processing ZNF891-SRR5197265.hg20-male.36mers.unique.bam Reading in data... Reading data took 1.08827209473 s Creating peak regions... Creating peak regions took 33.86343503 s Estimating background... Estimating background took 6.75033020973 s Processing ZNF891-SRR5197265.hg20-male.36mers.unique.bam Reading in data... Reading data took 0.0670728683472 s Creating peak regions... Creating peak regions took 0.123877048492 s Estimating background... Estimating background took 0.523711204529 s Processing ZNF891-SRR5197265.hg20-male.36mers.unique.bam Reading in data... Reading data took 1.55253601074 s Creating peak regions... Creating peak regions took 38.6861579418 s Estimating background... Estimating background took 8.16231489182 s Processing ZNF891-SRR5197265.hg20-male.36mers.unique.bam Reading in data... Reading data took 0.0755250453949 s Creating peak regions... Creating peak regions took 12.3769681454 s Estimating background... Estimating background took 0.415504932404 s