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/wgEncodeDacMapabilityConsensusExcludable.bed', center6=0, chromnames='/oak/stanford/groups/akundaje/marinovg/genomes/hg19/hg19.chrom.sizes', e4='PeakXus', fastq='CTCF_3-50bp_fragment.36mers.hg19-female.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='peakXus-CTCF_3-50bp_fragment/', p3=1.0, p7=1, q2=20, s3=1, skip0=0, t2=1, title5='PeakXus', verbosity=1, w3=5, w4=100, wg7=None)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/wgEncodeDacMapabilityConsensusExcludable.bed', center6=0, chromnames='/oak/stanford/groups/akundaje/marinovg/genomes/hg19/hg19.chrom.sizes', e4='PeakXus', fastq='CTCF_3-50bp_fragment.36mers.hg19-female.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='./peakXus-CTCF_3-50bp_fragment/', p3=1.0, p7=1, q2=20, s3=1, skip0=0, t2=1, title5='PeakXus', verbosity=1, w3=5, w4=100, wg7=None)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/wgEncodeDacMapabilityConsensusExcludable.bed', center6=0, chromnames='/oak/stanford/groups/akundaje/marinovg/genomes/hg19/hg19.chrom.sizes', e4='PeakXus', fastq='CTCF_3-50bp_fragment.36mers.hg19-female.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='/oak/stanford/groups/akundaje/marinovg/various/2018-01-08-DamID-ChIPexo-ChEC/06-human-K562-CTCF-ChIP-exo/peakXus-CTCF_3-50bp_fragment/', p3=1.0, p7=1, q2=20, s3=1, skip0=0, t2=1, title5='PeakXus', verbosity=1, w3=5, w4=100, wg7=None)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/wgEncodeDacMapabilityConsensusExcludable.bed', center6=0, chromnames='/oak/stanford/groups/akundaje/marinovg/genomes/hg19/hg19.chrom.sizes', e4='PeakXus', fastq='CTCF_3-50bp_fragment.36mers.hg19-female.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='/oak/stanford/groups/akundaje/marinovg/various/2018-01-08-DamID-ChIPexo-ChEC/06-human-K562-CTCF-ChIP-exo/peakXus-CTCF_3-50bp_fragment/', p3=1.0, p7=1, q2=20, s3=1, skip0=0, t2=1, title5='PeakXus', verbosity=1, w3=5, w4=100, wg7=None)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/wgEncodeDacMapabilityConsensusExcludable.bed', center6=0, chromnames='/oak/stanford/groups/akundaje/marinovg/genomes/hg19/hg19.chrom.sizes', e4='PeakXus', fastq='CTCF_3-50bp_fragment.36mers.hg19-female.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='/oak/stanford/groups/akundaje/marinovg/various/2018-01-08-DamID-ChIPexo-ChEC/06-human-K562-CTCF-ChIP-exo/peakXus-CTCF_3-50bp_fragment/', p3=1.0, p7=1, q2=20, s3=1, skip0=0, t2=1, title5='PeakXus', verbosity=1, w3=5, w4=100, wg7=None)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/wgEncodeDacMapabilityConsensusExcludable.bed', center6=0, chromnames='/oak/stanford/groups/akundaje/marinovg/genomes/hg19/hg19.chrom.sizes', e4='PeakXus', fastq='CTCF_3-50bp_fragment.36mers.hg19-female.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='/oak/stanford/groups/akundaje/marinovg/various/2018-01-08-DamID-ChIPexo-ChEC/06-human-K562-CTCF-ChIP-exo/peakXus-CTCF_3-50bp_fragment/', 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 CTCF_3-50bp_fragment.36mers.hg19-female.unique.bam Reading in data... Reading data took 9.76643610001 s Creating peak regions... Creating peak regions took 45.194961071 s Estimating background... Estimating background took 29.253921032 s Processing CTCF_3-50bp_fragment.36mers.hg19-female.unique.bam Reading in data... Reading data took 12.4160380363 s Creating peak regions... Creating peak regions took 49.9969389439 s Estimating background... Estimating background took 37.6964890957 s Processing CTCF_3-50bp_fragment.36mers.hg19-female.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/wgEncodeDacMapabilityConsensusExcludable.bed', center6=0, chromnames='/oak/stanford/groups/akundaje/marinovg/genomes/hg19/female.hg19.chrom.sizes', e4='PeakXus', fastq='CTCF_3-50bp_fragment.36mers.hg19-female.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='/oak/stanford/groups/akundaje/marinovg/various/2018-01-08-DamID-ChIPexo-ChEC/06-human-K562-CTCF-ChIP-exo/peakXus-CTCF_3-50bp_fragment/', 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 CTCF_3-50bp_fragment.36mers.hg19-female.unique.bam Reading in data... Reading data took 15.5295910835 s Creating peak regions... Creating peak regions took 98.4133460522 s Estimating background... Estimating background took 72.7325940132 s Processing CTCF_3-50bp_fragment.36mers.hg19-female.unique.bam Reading in data... Reading data took 11.3043179512 s Creating peak regions... Creating peak regions took 94.5799012184 s Estimating background... Estimating background took 54.5079820156 s Processing CTCF_3-50bp_fragment.36mers.hg19-female.unique.bam Reading in data... Reading data took 11.2848899364 s Creating peak regions... Creating peak regions took 78.4599239826 s Estimating background... Estimating background took 52.6546571255 s Processing CTCF_3-50bp_fragment.36mers.hg19-female.unique.bam Reading in data... Reading data took 7.40349197388 s Creating peak regions... Creating peak regions took 72.5599570274 s Estimating background... Estimating background took 33.9690029621 s Processing CTCF_3-50bp_fragment.36mers.hg19-female.unique.bam Reading in data... Reading data took 10.4033389091 s Creating peak regions... Creating peak regions took 69.7168109417 s Estimating background... Estimating background took 52.1632540226 s Processing CTCF_3-50bp_fragment.36mers.hg19-female.unique.bam Reading in data... Reading data took 9.42526984215 s Creating peak regions... Creating peak regions took 68.3594579697 s Estimating background... Estimating background took 43.793653965 s Processing CTCF_3-50bp_fragment.36mers.hg19-female.unique.bam Reading in data... Reading data took 8.61829400063 s Creating peak regions... Creating peak regions took 62.4736168385 s Estimating background... Estimating background took 40.2211859226 s Processing CTCF_3-50bp_fragment.36mers.hg19-female.unique.bam Reading in data... Reading data took 8.52839803696 s Creating peak regions... Creating peak regions took 58.4984059334 s Estimating background... Estimating background took 39.4974970818 s Processing CTCF_3-50bp_fragment.36mers.hg19-female.unique.bam Reading in data... Reading data took 7.46223306656 s Creating peak regions... Creating peak regions took 54.1802411079 s Estimating background... Estimating background took 35.2047200203 s Processing CTCF_3-50bp_fragment.36mers.hg19-female.unique.bam Reading in data... Reading data took 7.11165118217 s Creating peak regions... Creating peak regions took 52.5672299862 s Estimating background... Estimating background took 34.2714140415 s Processing CTCF_3-50bp_fragment.36mers.hg19-female.unique.bam Reading in data... Reading data took 8.84898400307 s Creating peak regions... Creating peak regions took 53.9991707802 s Estimating background... Estimating background took 42.5862808228 s Processing CTCF_3-50bp_fragment.36mers.hg19-female.unique.bam Reading in data... Reading data took 8.42072677612 s Creating peak regions... Creating peak regions took 53.0583930016 s Estimating background... Estimating background took 40.1283128262 s Processing CTCF_3-50bp_fragment.36mers.hg19-female.unique.bam Reading in data... Reading data took 5.12926101685 s Creating peak regions... Creating peak regions took 44.5247261524 s Estimating background... Estimating background took 21.9682219028 s Processing CTCF_3-50bp_fragment.36mers.hg19-female.unique.bam Reading in data... Reading data took 5.22623682022 s Creating peak regions... Creating peak regions took 40.7849559784 s Estimating background... Estimating background took 25.9436569214 s Processing CTCF_3-50bp_fragment.36mers.hg19-female.unique.bam Reading in data... Reading data took 6.01096916199 s Creating peak regions... Creating peak regions took 39.0350930691 s Estimating background... Estimating background took 29.1529991627 s Processing CTCF_3-50bp_fragment.36mers.hg19-female.unique.bam Reading in data... Reading data took 4.82899808884 s Creating peak regions... Creating peak regions took 34.2164208889 s Estimating background... Estimating background took 22.400195837 s Processing CTCF_3-50bp_fragment.36mers.hg19-female.unique.bam Reading in data... Reading data took 5.74683904648 s Creating peak regions... Creating peak regions took 32.9638259411 s Estimating background... Estimating background took 27.2334079742 s Processing CTCF_3-50bp_fragment.36mers.hg19-female.unique.bam Reading in data... Reading data took 4.30493187904 s Creating peak regions... Creating peak regions took 30.205851078 s Estimating background... Estimating background took 18.9717681408 s Processing CTCF_3-50bp_fragment.36mers.hg19-female.unique.bam Reading in data... Reading data took 3.92538499832 s Creating peak regions... Creating peak regions took 22.5125098228 s Estimating background... Estimating background took 19.1897110939 s Processing CTCF_3-50bp_fragment.36mers.hg19-female.unique.bam Reading in data... Reading data took 4.35088396072 s Creating peak regions... Creating peak regions took 24.288588047 s Estimating background... Estimating background took 20.0038588047 s Processing CTCF_3-50bp_fragment.36mers.hg19-female.unique.bam Reading in data... Reading data took 2.13509297371 s Creating peak regions... Creating peak regions took 17.9717059135 s Estimating background... Estimating background took 10.2494039536 s Processing CTCF_3-50bp_fragment.36mers.hg19-female.unique.bam Reading in data... Reading data took 1.82555913925 s Creating peak regions... Creating peak regions took 18.4360349178 s Estimating background... Estimating background took 9.93960213661 s Processing CTCF_3-50bp_fragment.36mers.hg19-female.unique.bam Reading in data... Reading data took 6.39756321907 s Creating peak regions... Creating peak regions took 59.8368580341 s Estimating background... Estimating background took 30.5851509571 s Processing CTCF_3-50bp_fragment.36mers.hg19-female.unique.bam Reading in data... Reading data took 0.25515294075 s Creating peak regions... Creating peak regions took 0.467283964157 s Estimating background... Estimating background took 0.835694074631 s