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='ZNF701-SRR5197220.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='ZNF701-SRR5197220/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 ZNF701-SRR5197220.hg20-male.36mers.unique.bam Reading in data... Reading data took 6.24720597267 s Creating peak regions... Creating peak regions took 77.2276599407 s Estimating background... Estimating background took 32.4001560211 s Processing ZNF701-SRR5197220.hg20-male.36mers.unique.bam Reading in data... Reading data took 3.10652017593 s Creating peak regions... Creating peak regions took 41.0835168362 s Estimating background... Estimating background took 13.1001179218 s Processing ZNF701-SRR5197220.hg20-male.36mers.unique.bam Reading in data... Reading data took 3.18538689613 s Creating peak regions... Creating peak regions took 38.5307400227 s Estimating background... Estimating background took 12.8248870373 s Processing ZNF701-SRR5197220.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='ZNF701-SRR5197220.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='ZNF701-SRR5197220/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 ZNF701-SRR5197220.hg20-male.36mers.unique.bam Reading in data... Reading data took 5.42598700523 s Creating peak regions... Creating peak regions took 63.5547521114 s Estimating background... Estimating background took 27.3827250004 s Processing ZNF701-SRR5197220.hg20-male.36mers.unique.bam Reading in data... Reading data took 2.77558708191 s Creating peak regions... Creating peak regions took 39.8119840622 s Estimating background... Estimating background took 11.7711219788 s Processing ZNF701-SRR5197220.hg20-male.36mers.unique.bam Reading in data... Reading data took 2.87863302231 s Creating peak regions... Creating peak regions took 37.7707579136 s Estimating background... Estimating background took 11.0633590221 s Processing ZNF701-SRR5197220.hg20-male.36mers.unique.bam Reading in data... Reading data took 2.93872404099 s Creating peak regions... Creating peak regions took 39.4240489006 s Estimating background... Estimating background took 12.6150979996 s Processing ZNF701-SRR5197220.hg20-male.36mers.unique.bam Reading in data... Reading data took 2.63200497627 s Creating peak regions... Creating peak regions took 30.368680954 s Estimating background... Estimating background took 12.8744962215 s Processing ZNF701-SRR5197220.hg20-male.36mers.unique.bam Reading in data... Reading data took 2.17822980881 s Creating peak regions... Creating peak regions took 34.8456368446 s Estimating background... Estimating background took 8.86708593369 s Processing ZNF701-SRR5197220.hg20-male.36mers.unique.bam Reading in data... Reading data took 2.29870891571 s Creating peak regions... Creating peak regions took 31.1020801067 s Estimating background... Estimating background took 8.79453802109 s Processing ZNF701-SRR5197220.hg20-male.36mers.unique.bam Reading in data... Reading data took 2.17303991318 s Creating peak regions... Creating peak regions took 31.0523757935 s Estimating background... Estimating background took 7.6841211319 s Processing ZNF701-SRR5197220.hg20-male.36mers.unique.bam Reading in data... Reading data took 2.29445195198 s Creating peak regions... Creating peak regions took 25.5421698093 s Estimating background... Estimating background took 10.0353860855 s Processing ZNF701-SRR5197220.hg20-male.36mers.unique.bam Reading in data... Reading data took 1.63290905952 s Creating peak regions... Creating peak regions took 22.8256850243 s Estimating background... Estimating background took 7.08289694786 s Processing ZNF701-SRR5197220.hg20-male.36mers.unique.bam Reading in data... Reading data took 1.4517800808 s Creating peak regions... Creating peak regions took 16.9517691135 s Estimating background... Estimating background took 6.0549120903 s Processing ZNF701-SRR5197220.hg20-male.36mers.unique.bam Reading in data... Reading data took 5.29718399048 s Creating peak regions... Creating peak regions took 80.7956578732 s Estimating background... Estimating background took 19.0010550022 s Processing ZNF701-SRR5197220.hg20-male.36mers.unique.bam Reading in data... Reading data took 1.50750589371 s Creating peak regions... Creating peak regions took 19.2154848576 s Estimating background... Estimating background took 6.51432800293 s Processing ZNF701-SRR5197220.hg20-male.36mers.unique.bam Reading in data... Reading data took 1.11872601509 s Creating peak regions... Creating peak regions took 14.1485080719 s Estimating background... Estimating background took 4.46817302704 s Processing ZNF701-SRR5197220.hg20-male.36mers.unique.bam Reading in data... Reading data took 1.2446000576 s Creating peak regions... Creating peak regions took 15.9068260193 s Estimating background... Estimating background took 5.82932686806 s Processing ZNF701-SRR5197220.hg20-male.36mers.unique.bam Reading in data... Reading data took 4.40249705315 s Creating peak regions... Creating peak regions took 61.4536280632 s Estimating background... Estimating background took 16.5052502155 s Processing ZNF701-SRR5197220.hg20-male.36mers.unique.bam Reading in data... Reading data took 3.68972802162 s Creating peak regions... Creating peak regions took 58.7063539028 s Estimating background... Estimating background took 12.0342619419 s Processing ZNF701-SRR5197220.hg20-male.36mers.unique.bam Reading in data... Reading data took 4.13967418671 s Creating peak regions... Creating peak regions took 65.3059160709 s Estimating background... Estimating background took 14.722397089 s Processing ZNF701-SRR5197220.hg20-male.36mers.unique.bam Reading in data... Reading data took 4.13135099411 s Creating peak regions... Creating peak regions took 55.4282701015 s Estimating background... Estimating background took 17.36687994 s Processing ZNF701-SRR5197220.hg20-male.36mers.unique.bam Reading in data... Reading data took 3.29824709892 s Creating peak regions... Creating peak regions took 42.819478035 s Estimating background... Estimating background took 13.9265990257 s Processing ZNF701-SRR5197220.hg20-male.36mers.unique.bam Reading in data... Reading data took 3.31927800179 s Creating peak regions... Creating peak regions took 45.0526502132 s Estimating background... Estimating background took 11.4999959469 s Processing ZNF701-SRR5197220.hg20-male.36mers.unique.bam Reading in data... Reading data took 2.33849906921 s Creating peak regions... Creating peak regions took 37.0217969418 s Estimating background... Estimating background took 11.4870769978 s Processing ZNF701-SRR5197220.hg20-male.36mers.unique.bam Reading in data... Reading data took 0.116084098816 s Creating peak regions... Creating peak regions took 0.188333034515 s Estimating background... Estimating background took 0.677474975586 s Processing ZNF701-SRR5197220.hg20-male.36mers.unique.bam Reading in data... Reading data took 3.59648394585 s Creating peak regions... Creating peak regions took 55.4764649868 s Estimating background... Estimating background took 17.2418069839 s Processing ZNF701-SRR5197220.hg20-male.36mers.unique.bam Reading in data... Reading data took 0.131583929062 s Creating peak regions... Creating peak regions took 16.1623659134 s Estimating background... Estimating background took 0.59453701973 s