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='ZNF765-SRR5197234.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='ZNF765-SRR5197234/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 ZNF765-SRR5197234.hg20-male.36mers.unique.bam Reading in data... Reading data took 8.70727396011 s Creating peak regions... Creating peak regions took 82.5745558739 s Estimating background... Estimating background took 95.063685894 s Processing ZNF765-SRR5197234.hg20-male.36mers.unique.bam Reading in data... Reading data took 4.69903302193 s Creating peak regions... Creating peak regions took 47.2600569725 s Estimating background... Estimating background took 34.9910640717 s Processing ZNF765-SRR5197234.hg20-male.36mers.unique.bam Reading in data... Reading data took 4.05137705803 s Creating peak regions... Creating peak regions took 40.0356249809 s Estimating background... Estimating background took 32.8242909908 s Processing ZNF765-SRR5197234.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='ZNF765-SRR5197234.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='ZNF765-SRR5197234/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 ZNF765-SRR5197234.hg20-male.36mers.unique.bam Reading in data... Reading data took 8.89066290855 s Creating peak regions... Creating peak regions took 82.8923521042 s Estimating background... Estimating background took 92.8632998466 s Processing ZNF765-SRR5197234.hg20-male.36mers.unique.bam Reading in data... Reading data took 4.42473697662 s Creating peak regions... Creating peak regions took 45.4453039169 s Estimating background... Estimating background took 37.9084599018 s Processing ZNF765-SRR5197234.hg20-male.36mers.unique.bam Reading in data... Reading data took 4.91332912445 s Creating peak regions... Creating peak regions took 43.9276759624 s Estimating background... Estimating background took 39.3250501156 s Processing ZNF765-SRR5197234.hg20-male.36mers.unique.bam Reading in data... Reading data took 4.72500896454 s Creating peak regions... Creating peak regions took 44.2609159946 s Estimating background... Estimating background took 41.4323568344 s Processing ZNF765-SRR5197234.hg20-male.36mers.unique.bam Reading in data... Reading data took 4.26077413559 s Creating peak regions... Creating peak regions took 37.4919989109 s Estimating background... Estimating background took 38.4753181934 s Processing ZNF765-SRR5197234.hg20-male.36mers.unique.bam Reading in data... Reading data took 3.40973091125 s Creating peak regions... Creating peak regions took 34.5763239861 s Estimating background... Estimating background took 25.1859540939 s Processing ZNF765-SRR5197234.hg20-male.36mers.unique.bam Reading in data... Reading data took 3.31229019165 s Creating peak regions... Creating peak regions took 32.8369879723 s Estimating background... Estimating background took 30.2711348534 s Processing ZNF765-SRR5197234.hg20-male.36mers.unique.bam Reading in data... Reading data took 3.23819088936 s Creating peak regions... Creating peak regions took 29.4393591881 s Estimating background... Estimating background took 27.9759049416 s Processing ZNF765-SRR5197234.hg20-male.36mers.unique.bam Reading in data... Reading data took 3.77057409286 s Creating peak regions... Creating peak regions took 28.8873360157 s Estimating background... Estimating background took 38.1759500504 s Processing ZNF765-SRR5197234.hg20-male.36mers.unique.bam Reading in data... Reading data took 2.5174369812 s Creating peak regions... Creating peak regions took 26.1136300564 s Estimating background... Estimating background took 18.8110210896 s Processing ZNF765-SRR5197234.hg20-male.36mers.unique.bam Reading in data... Reading data took 2.78237819672 s Creating peak regions... Creating peak regions took 20.1370198727 s Estimating background... Estimating background took 25.7517549992 s Processing ZNF765-SRR5197234.hg20-male.36mers.unique.bam Reading in data... Reading data took 7.45841908455 s Creating peak regions... Creating peak regions took 79.157913208 s Estimating background... Estimating background took 63.3437149525 s Processing ZNF765-SRR5197234.hg20-male.36mers.unique.bam Reading in data... Reading data took 2.88898301125 s Creating peak regions... Creating peak regions took 23.7067060471 s Estimating background... Estimating background took 24.4356369972 s Processing ZNF765-SRR5197234.hg20-male.36mers.unique.bam Reading in data... Reading data took 1.48036909103 s Creating peak regions... Creating peak regions took 14.9536678791 s Estimating background... Estimating background took 11.7306799889 s Processing ZNF765-SRR5197234.hg20-male.36mers.unique.bam Reading in data... Reading data took 2.23820400238 s Creating peak regions... Creating peak regions took 17.8827850819 s Estimating background... Estimating background took 24.1713900566 s Processing ZNF765-SRR5197234.hg20-male.36mers.unique.bam Reading in data... Reading data took 6.0865020752 s Creating peak regions... Creating peak regions took 63.8893811703 s Estimating background... Estimating background took 48.851555109 s Processing ZNF765-SRR5197234.hg20-male.36mers.unique.bam Reading in data... Reading data took 5.33646798134 s Creating peak regions... Creating peak regions took 59.686262846 s Estimating background... Estimating background took 33.1927700043 s Processing ZNF765-SRR5197234.hg20-male.36mers.unique.bam Reading in data... Reading data took 5.49996900558 s Creating peak regions... Creating peak regions took 58.5339589119 s Estimating background... Estimating background took 46.8897850513 s Processing ZNF765-SRR5197234.hg20-male.36mers.unique.bam Reading in data... Reading data took 6.02134490013 s Creating peak regions... Creating peak regions took 57.411536932 s Estimating background... Estimating background took 52.8363740444 s Processing ZNF765-SRR5197234.hg20-male.36mers.unique.bam Reading in data... Reading data took 5.59526181221 s Creating peak regions... Creating peak regions took 52.2641119957 s Estimating background... Estimating background took 47.656473875 s Processing ZNF765-SRR5197234.hg20-male.36mers.unique.bam Reading in data... Reading data took 4.48775005341 s Creating peak regions... Creating peak regions took 44.3707559109 s Estimating background... Estimating background took 31.5745289326 s Processing ZNF765-SRR5197234.hg20-male.36mers.unique.bam Reading in data... Reading data took 3.70286083221 s Creating peak regions... Creating peak regions took 38.5350058079 s Estimating background... Estimating background took 31.0210340023 s Processing ZNF765-SRR5197234.hg20-male.36mers.unique.bam Reading in data... Reading data took 0.143447160721 s Creating peak regions... Creating peak regions took 0.224711894989 s Estimating background... Estimating background took 0.698013067245 s Processing ZNF765-SRR5197234.hg20-male.36mers.unique.bam Reading in data... Reading data took 4.835324049 s Creating peak regions... Creating peak regions took 46.3461019993 s Estimating background... Estimating background took 44.0142550468 s Processing ZNF765-SRR5197234.hg20-male.36mers.unique.bam Reading in data... Reading data took 0.270151138306 s Creating peak regions... Creating peak regions took 15.3111920357 s Estimating background... Estimating background took 0.762714147568 s