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='ZNF792-SRR5197248.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='ZNF792-SRR5197248/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 ZNF792-SRR5197248.hg20-male.36mers.unique.bam Reading in data... Reading data took 10.1181390285 s Creating peak regions... Creating peak regions took 80.3676919937 s Estimating background... Estimating background took 72.3252561092 s Processing ZNF792-SRR5197248.hg20-male.36mers.unique.bam Reading in data... Reading data took 5.327480793 s Creating peak regions... Creating peak regions took 46.4141609669 s Estimating background... Estimating background took 24.4493079185 s Processing ZNF792-SRR5197248.hg20-male.36mers.unique.bam Reading in data... Reading data took 4.08668398857 s Creating peak regions... Creating peak regions took 36.469825983 s Estimating background... Estimating background took 22.5484700203 s Processing ZNF792-SRR5197248.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='ZNF792-SRR5197248.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='ZNF792-SRR5197248/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 ZNF792-SRR5197248.hg20-male.36mers.unique.bam Reading in data... Reading data took 9.35048890114 s Creating peak regions... Creating peak regions took 77.0934579372 s Estimating background... Estimating background took 67.0331299305 s Processing ZNF792-SRR5197248.hg20-male.36mers.unique.bam Reading in data... Reading data took 4.74686813354 s Creating peak regions... Creating peak regions took 42.1469910145 s Estimating background... Estimating background took 24.5728490353 s Processing ZNF792-SRR5197248.hg20-male.36mers.unique.bam Reading in data... Reading data took 4.68461179733 s Creating peak regions... Creating peak regions took 38.2929918766 s Estimating background... Estimating background took 24.7219088078 s Processing ZNF792-SRR5197248.hg20-male.36mers.unique.bam Reading in data... Reading data took 4.87330794334 s Creating peak regions... Creating peak regions took 39.2900359631 s Estimating background... Estimating background took 27.4243240356 s Processing ZNF792-SRR5197248.hg20-male.36mers.unique.bam Reading in data... Reading data took 4.48266196251 s Creating peak regions... Creating peak regions took 35.4463710785 s Estimating background... Estimating background took 35.0094490051 s Processing ZNF792-SRR5197248.hg20-male.36mers.unique.bam Reading in data... Reading data took 3.29397010803 s Creating peak regions... Creating peak regions took 31.6090760231 s Estimating background... Estimating background took 17.1583859921 s Processing ZNF792-SRR5197248.hg20-male.36mers.unique.bam Reading in data... Reading data took 3.03639006615 s Creating peak regions... Creating peak regions took 29.5315761566 s Estimating background... Estimating background took 18.0498359203 s Processing ZNF792-SRR5197248.hg20-male.36mers.unique.bam Reading in data... Reading data took 2.78726792336 s Creating peak regions... Creating peak regions took 25.3995008469 s Estimating background... Estimating background took 14.7180821896 s Processing ZNF792-SRR5197248.hg20-male.36mers.unique.bam Reading in data... Reading data took 3.00203895569 s Creating peak regions... Creating peak regions took 24.3325381279 s Estimating background... Estimating background took 18.6029720306 s Processing ZNF792-SRR5197248.hg20-male.36mers.unique.bam Reading in data... Reading data took 2.5753839016 s Creating peak regions... Creating peak regions took 23.687556982 s Estimating background... Estimating background took 14.4836649895 s Processing ZNF792-SRR5197248.hg20-male.36mers.unique.bam Reading in data... Reading data took 2.16743803024 s Creating peak regions... Creating peak regions took 17.7266499996 s Estimating background... Estimating background took 11.6080548763 s Processing ZNF792-SRR5197248.hg20-male.36mers.unique.bam Reading in data... Reading data took 7.78437209129 s Creating peak regions... Creating peak regions took 71.966771841 s Estimating background... Estimating background took 44.2677080631 s Processing ZNF792-SRR5197248.hg20-male.36mers.unique.bam Reading in data... Reading data took 2.36021614075 s Creating peak regions... Creating peak regions took 20.6099469662 s Estimating background... Estimating background took 13.5747909546 s Processing ZNF792-SRR5197248.hg20-male.36mers.unique.bam Reading in data... Reading data took 1.61334609985 s Creating peak regions... Creating peak regions took 14.75030303 s Estimating background... Estimating background took 8.14718389511 s Processing ZNF792-SRR5197248.hg20-male.36mers.unique.bam Reading in data... Reading data took 1.69833803177 s Creating peak regions... Creating peak regions took 15.7660429478 s Estimating background... Estimating background took 11.0583188534 s Processing ZNF792-SRR5197248.hg20-male.36mers.unique.bam Reading in data... Reading data took 6.07634091377 s Creating peak regions... Creating peak regions took 58.4501399994 s Estimating background... Estimating background took 35.7721378803 s Processing ZNF792-SRR5197248.hg20-male.36mers.unique.bam Reading in data... Reading data took 5.94774198532 s Creating peak regions... Creating peak regions took 55.5392940044 s Estimating background... Estimating background took 28.9509818554 s Processing ZNF792-SRR5197248.hg20-male.36mers.unique.bam Reading in data... Reading data took 6.46385598183 s Creating peak regions... Creating peak regions took 54.0969519615 s Estimating background... Estimating background took 34.7495617867 s Processing ZNF792-SRR5197248.hg20-male.36mers.unique.bam Reading in data... Reading data took 6.04476118088 s Creating peak regions... Creating peak regions took 51.529088974 s Estimating background... Estimating background took 36.5607349873 s Processing ZNF792-SRR5197248.hg20-male.36mers.unique.bam Reading in data... Reading data took 5.92213106155 s Creating peak regions... Creating peak regions took 48.0399050713 s Estimating background... Estimating background took 33.130975008 s Processing ZNF792-SRR5197248.hg20-male.36mers.unique.bam Reading in data... Reading data took 4.52452802658 s Creating peak regions... Creating peak regions took 42.3420209885 s Estimating background... Estimating background took 24.6053738594 s Processing ZNF792-SRR5197248.hg20-male.36mers.unique.bam Reading in data... Reading data took 3.89626002312 s Creating peak regions... Creating peak regions took 39.0837309361 s Estimating background... Estimating background took 21.6320648193 s Processing ZNF792-SRR5197248.hg20-male.36mers.unique.bam Reading in data... Reading data took 0.135087013245 s Creating peak regions... Creating peak regions took 0.206017971039 s Estimating background... Estimating background took 0.700567007065 s Processing ZNF792-SRR5197248.hg20-male.36mers.unique.bam Reading in data... Reading data took 5.79520106316 s Creating peak regions... Creating peak regions took 44.8232469559 s Estimating background... Estimating background took 39.5268120766 s Processing ZNF792-SRR5197248.hg20-male.36mers.unique.bam Reading in data... Reading data took 0.306959152222 s Creating peak regions... Creating peak regions took 14.8562200069 s Estimating background... Estimating background took 0.874861001968 s