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='ZNF93-SRR5197268.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='ZNF93-SRR5197268/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 ZNF93-SRR5197268.hg20-male.36mers.unique.bam Reading in data... Reading data took 5.34456515312 s Creating peak regions... Creating peak regions took 71.0351390839 s Estimating background... Estimating background took 35.6730208397 s Processing ZNF93-SRR5197268.hg20-male.36mers.unique.bam Reading in data... Reading data took 2.67009997368 s Creating peak regions... Creating peak regions took 38.3732218742 s Estimating background... Estimating background took 13.8603639603 s Processing ZNF93-SRR5197268.hg20-male.36mers.unique.bam Reading in data... Reading data took 2.53169512749 s Creating peak regions... Creating peak regions took 36.4551370144 s Estimating background... Estimating background took 13.6006231308 s Processing ZNF93-SRR5197268.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='ZNF93-SRR5197268.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='ZNF93-SRR5197268/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 ZNF93-SRR5197268.hg20-male.36mers.unique.bam Reading in data... Reading data took 5.85183310509 s Creating peak regions... Creating peak regions took 68.0584199429 s Estimating background... Estimating background took 34.1699159145 s Processing ZNF93-SRR5197268.hg20-male.36mers.unique.bam Reading in data... Reading data took 3.35390305519 s Creating peak regions... Creating peak regions took 39.4844279289 s Estimating background... Estimating background took 15.7574090958 s Processing ZNF93-SRR5197268.hg20-male.36mers.unique.bam Reading in data... Reading data took 3.28373098373 s Creating peak regions... Creating peak regions took 40.216960907 s Estimating background... Estimating background took 16.2795801163 s Processing ZNF93-SRR5197268.hg20-male.36mers.unique.bam Reading in data... Reading data took 3.56387019157 s Creating peak regions... Creating peak regions took 39.1150200367 s Estimating background... Estimating background took 15.5713598728 s Processing ZNF93-SRR5197268.hg20-male.36mers.unique.bam Reading in data... Reading data took 3.22895503044 s Creating peak regions... Creating peak regions took 34.4771478176 s Estimating background... Estimating background took 19.5785179138 s Processing ZNF93-SRR5197268.hg20-male.36mers.unique.bam Reading in data... Reading data took 2.56006503105 s Creating peak regions... Creating peak regions took 31.465952158 s Estimating background... Estimating background took 12.8920059204 s Processing ZNF93-SRR5197268.hg20-male.36mers.unique.bam Reading in data... Reading data took 3.11244511604 s Creating peak regions... 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='ZNF93-SRR5197268.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='ZNF93-SRR5197268/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 ZNF93-SRR5197268.hg20-male.36mers.unique.bam Reading in data... Reading data took 4.56599211693 s Creating peak regions... Creating peak regions took 64.852134943 s Estimating background... Estimating background took 32.4121949673 s Processing ZNF93-SRR5197268.hg20-male.36mers.unique.bam Reading in data... Reading data took 2.37573719025 s Creating peak regions... Creating peak regions took 34.6280350685 s Estimating background... Estimating background took 13.2535538673 s Processing ZNF93-SRR5197268.hg20-male.36mers.unique.bam Reading in data... Reading data took 2.23667311668 s Creating peak regions... Creating peak regions took 34.4637730122 s Estimating background... Estimating background took 12.9584197998 s Processing ZNF93-SRR5197268.hg20-male.36mers.unique.bam Reading in data... Reading data took 2.44111800194 s Creating peak regions... Creating peak regions took 34.349686861 s Estimating background... Estimating background took 14.5050837994 s Processing ZNF93-SRR5197268.hg20-male.36mers.unique.bam Reading in data... Reading data took 2.24968099594 s Creating peak regions... Creating peak regions took 29.8835039139 s Estimating background... Estimating background took 17.2192280293 s Processing ZNF93-SRR5197268.hg20-male.36mers.unique.bam Reading in data... Reading data took 1.63324093819 s Creating peak regions... Creating peak regions took 26.9639780521 s Estimating background... Estimating background took 9.13912510872 s Processing ZNF93-SRR5197268.hg20-male.36mers.unique.bam Reading in data... Reading data took 1.86426496506 s Creating peak regions... Creating peak regions took 26.6231400967 s Estimating background... Estimating background took 13.4315290451 s Processing ZNF93-SRR5197268.hg20-male.36mers.unique.bam Reading in data... Reading data took 1.51651597023 s Creating peak regions... Creating peak regions took 24.2855370045 s Estimating background... Estimating background took 8.72653388977 s Processing ZNF93-SRR5197268.hg20-male.36mers.unique.bam Reading in data... Reading data took 1.91628789902 s Creating peak regions... Creating peak regions took 23.2430269718 s Estimating background... Estimating background took 12.0987370014 s Processing ZNF93-SRR5197268.hg20-male.36mers.unique.bam Reading in data... Reading data took 1.36773705482 s Creating peak regions... Creating peak regions took 20.1999680996 s Estimating background... Estimating background took 7.70254611969 s Processing ZNF93-SRR5197268.hg20-male.36mers.unique.bam Reading in data... Reading data took 1.14187192917 s Creating peak regions... Creating peak regions took 15.1374418736 s Estimating background... Estimating background took 6.7144100666 s Processing ZNF93-SRR5197268.hg20-male.36mers.unique.bam Reading in data... Reading data took 4.27007699013 s Creating peak regions... Creating peak regions took 62.618350029 s Estimating background... Estimating background took 23.5607838631 s Processing ZNF93-SRR5197268.hg20-male.36mers.unique.bam Reading in data... Reading data took 1.21233487129 s Creating peak regions... Creating peak regions took 17.5155310631 s Estimating background... Estimating background took 7.21684408188 s Processing ZNF93-SRR5197268.hg20-male.36mers.unique.bam Reading in data... Reading data took 0.749866962433 s Creating peak regions... Creating peak regions took 12.9138700962 s Estimating background... Estimating background took 4.42935991287 s Processing ZNF93-SRR5197268.hg20-male.36mers.unique.bam Reading in data... Reading data took 1.10296010971 s Creating peak regions... Creating peak regions took 13.6942601204 s Estimating background... Estimating background took 6.86996603012 s Processing ZNF93-SRR5197268.hg20-male.36mers.unique.bam Reading in data... Reading data took 3.23272800446 s Creating peak regions... Creating peak regions took 50.2159471512 s Estimating background... Estimating background took 18.1620740891 s Processing ZNF93-SRR5197268.hg20-male.36mers.unique.bam Reading in data... Reading data took 2.91343688965 s Creating peak regions... Creating peak regions took 48.3029100895 s Estimating background... Estimating background took 15.0086019039 s Processing ZNF93-SRR5197268.hg20-male.36mers.unique.bam Reading in data... Reading data took 3.45403194427 s Creating peak regions... Creating peak regions took 46.7059218884 s Estimating background... Estimating background took 17.5660481453 s Processing ZNF93-SRR5197268.hg20-male.36mers.unique.bam Reading in data... Reading data took 3.49923205376 s Creating peak regions... Creating peak regions took 44.9785671234 s Estimating background... Estimating background took 21.2628490925 s Processing ZNF93-SRR5197268.hg20-male.36mers.unique.bam Reading in data... Reading data took 3.21326398849 s Creating peak regions... Creating peak regions took 41.8935201168 s Estimating background... Estimating background took 18.2926111221 s Processing ZNF93-SRR5197268.hg20-male.36mers.unique.bam Reading in data... Reading data took 2.68458509445 s Creating peak regions... Creating peak regions took 37.5620629787 s Estimating background... Estimating background took 13.2458910942 s Processing ZNF93-SRR5197268.hg20-male.36mers.unique.bam Reading in data... Reading data took 2.19114899635 s Creating peak regions... Creating peak regions took 37.2092180252 s Estimating background... Estimating background took 12.3990211487 s Processing ZNF93-SRR5197268.hg20-male.36mers.unique.bam Reading in data... Reading data took 0.0944530963898 s Creating peak regions... Creating peak regions took 0.163625001907 s Estimating background... Estimating background took 0.642471075058 s Processing ZNF93-SRR5197268.hg20-male.36mers.unique.bam Reading in data... Reading data took 3.09632515907 s Creating peak regions... Creating peak regions took 41.3055720329 s Estimating background... Estimating background took 19.2323601246 s Processing ZNF93-SRR5197268.hg20-male.36mers.unique.bam Reading in data... Reading data took 0.141273975372 s Creating peak regions... Creating peak regions took 13.6125340462 s Estimating background... Estimating background took 0.57977104187 s