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/hg19/wgEncodeHg19ConsensusSignalArtifactRegions.bed', center6=0, chromnames='/oak/stanford/groups/akundaje/marinovg/genomes/hg19/female.hg19.chrom.sizes', e4='PeakXus', fastq='A31_V7_ChIPexo-GSM2643266/aligned.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='A31_V7_ChIPexo-GSM2643266/peakXus/', 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/hg19/wgEncodeHg19ConsensusSignalArtifactRegions.bed', center6=0, chromnames='/oak/stanford/groups/akundaje/marinovg/genomes/hg19/hg19.chrom.sizes', e4='PeakXus', fastq='A31_V7_ChIPexo-GSM2643266/aligned.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='A31_V7_ChIPexo-GSM2643266/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 A31_V7_ChIPexo-GSM2643266/aligned.36mers.unique.bam Reading in data... Reading data took 16.2574310303 s Creating peak regions... Creating peak regions took 83.209059 s Estimating background... Estimating background took 208.577836037 s Processing A31_V7_ChIPexo-GSM2643266/aligned.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/hg19/wgEncodeHg19ConsensusSignalArtifactRegions.bed', center6=0, chromnames='/oak/stanford/groups/akundaje/marinovg/genomes/hg19/hg19-male.chrom.sizes', e4='PeakXus', fastq='A31_V7_ChIPexo-GSM2643266/alignments.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='A31_V7_ChIPexo-GSM2643266/peakXus/', 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/hg19/wgEncodeHg19ConsensusSignalArtifactRegions.bed', center6=0, chromnames='/oak/stanford/groups/akundaje/marinovg/genomes/hg19/hg19-male.chrom.sizes', e4='PeakXus', fastq='A31_V7_ChIPexo-GSM2643266/aligned.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='A31_V7_ChIPexo-GSM2643266/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 A31_V7_ChIPexo-GSM2643266/aligned.36mers.unique.bam Reading in data... Reading data took 16.1375181675 s Creating peak regions... Creating peak regions took 82.5614302158 s Estimating background... Estimating background took 211.55385685 s Processing A31_V7_ChIPexo-GSM2643266/aligned.36mers.unique.bam Reading in data... Reading data took 14.1764290333 s Creating peak regions... Creating peak regions took 62.1022810936 s Estimating background... Estimating background took 159.563898802 s Processing A31_V7_ChIPexo-GSM2643266/aligned.36mers.unique.bam Reading in data... Reading data took 12.1179008484 s Creating peak regions... Creating peak regions took 60.8153209686 s Estimating background... Estimating background took 130.500355959 s Processing A31_V7_ChIPexo-GSM2643266/aligned.36mers.unique.bam Reading in data... Reading data took 18.2316019535 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/hg19/wgEncodeHg19ConsensusSignalArtifactRegions.bed', center6=0, chromnames='/oak/stanford/groups/akundaje/marinovg/genomes/hg19/hg19-male.chrom.sizes', e4='PeakXus', fastq='A31_V7_ChIPexo-GSM2643266/aligned.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='A31_V7_ChIPexo-GSM2643266/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 A31_V7_ChIPexo-GSM2643266/aligned.36mers.unique.bam Reading in data... Reading data took 16.9086399078 s Creating peak regions... Creating peak regions took 72.7222459316 s Estimating background... Creating peak regions took 87.5801429749 s Estimating background... Estimating background took 201.669700861 s Processing A31_V7_ChIPexo-GSM2643266/aligned.36mers.unique.bam Reading in data... Estimating background took 244.439385891 s Processing A31_V7_ChIPexo-GSM2643266/aligned.36mers.unique.bam Reading in data... Reading data took 9.37332892418 s Creating peak regions... Reading data took 14.5064609051 s Creating peak regions... Creating peak regions took 46.235255003 s Estimating background... Creating peak regions took 64.1287658215 s Estimating background... Estimating background took 73.5570318699 s Processing A31_V7_ChIPexo-GSM2643266/aligned.36mers.unique.bam Reading in data... Reading data took 9.71573400497 s Creating peak regions... Creating peak regions took 47.3083310127 s Estimating background... Estimating background took 159.980818033 s Processing A31_V7_ChIPexo-GSM2643266/aligned.36mers.unique.bam Reading in data... Reading data took 11.6303191185 s Creating peak regions... Estimating background took 108.0911901 s Processing A31_V7_ChIPexo-GSM2643266/aligned.36mers.unique.bam Reading in data... Creating peak regions took 54.0695281029 s Estimating background... Reading data took 8.98717594147 s Creating peak regions... Creating peak regions took 48.2640578747 s Estimating background... Estimating background took 119.874997854 s Processing A31_V7_ChIPexo-GSM2643266/aligned.36mers.unique.bam Reading in data... Estimating background took 70.6944248676 s Processing A31_V7_ChIPexo-GSM2643266/aligned.36mers.unique.bam Reading in data... Reading data took 7.4122159481 s Creating peak regions... Reading data took 17.4872879982 s Creating peak regions... Creating peak regions took 37.960267067 s Estimating background... Creating peak regions took 62.2576491833 s Estimating background... Estimating background took 60.6068241596 s Processing A31_V7_ChIPexo-GSM2643266/aligned.36mers.unique.bam Reading in data... Reading data took 7.02090501785 s Creating peak regions... Creating peak regions took 33.1158790588 s Estimating background... Estimating background took 77.8206250668 s Processing A31_V7_ChIPexo-GSM2643266/aligned.36mers.unique.bam Reading in data... Reading data took 10.3865699768 s Creating peak regions... Creating peak regions took 38.298746109 s Estimating background... Estimating background took 232.651532888 s Processing A31_V7_ChIPexo-GSM2643266/aligned.36mers.unique.bam Reading in data... Reading data took 8.66886997223 s Creating peak regions... Creating peak regions took 42.0363550186 s Estimating background... Estimating background took 122.364696026 s Processing A31_V7_ChIPexo-GSM2643266/aligned.36mers.unique.bam Reading in data... Reading data took 4.43212795258 s Creating peak regions... Creating peak regions took 24.2702989578 s Estimating background... Estimating background took 78.0872750282 s Processing A31_V7_ChIPexo-GSM2643266/aligned.36mers.unique.bam Reading in data... Reading data took 9.15603494644 s Creating peak regions... Estimating background took 31.2412970066 s Processing A31_V7_ChIPexo-GSM2643266/aligned.36mers.unique.bam Reading in data... Reading data took 24.8158910275 s Creating peak regions... Creating peak regions took 43.3509030342 s Estimating background... Estimating background took 93.8565940857 s Processing A31_V7_ChIPexo-GSM2643266/aligned.36mers.unique.bam Reading in data... Reading data took 7.53375697136 s Creating peak regions... Creating peak regions took 116.842288017 s Estimating background... Creating peak regions took 37.2589528561 s Estimating background... Estimating background took 75.8263268471 s Processing A31_V7_ChIPexo-GSM2643266/aligned.36mers.unique.bam Reading in data... Reading data took 7.22126889229 s Creating peak regions... Creating peak regions took 35.5891518593 s Estimating background... Estimating background took 55.5811588764 s Processing A31_V7_ChIPexo-GSM2643266/aligned.36mers.unique.bam Reading in data... Reading data took 7.68729901314 s Creating peak regions... Creating peak regions took 34.840362072 s Estimating background... Estimating background took 77.0925228596 s Processing A31_V7_ChIPexo-GSM2643266/aligned.36mers.unique.bam Reading in data... Reading data took 10.0956881046 s Creating peak regions... Creating peak regions took 41.3374650478 s Estimating background... Estimating background took 109.777287006 s Processing A31_V7_ChIPexo-GSM2643266/aligned.36mers.unique.bam Reading in data... Reading data took 3.800563097 s Creating peak regions... Creating peak regions took 21.3606989384 s Estimating background... Estimating background took 28.2114720345 s Processing A31_V7_ChIPexo-GSM2643266/aligned.36mers.unique.bam Reading in data... Reading data took 24.0161161423 s Creating peak regions... Creating peak regions took 100.227615118 s Estimating background... 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/hg19/wgEncodeHg19ConsensusSignalArtifactRegions.bed', center6=0, chromnames='/oak/stanford/groups/akundaje/marinovg/genomes/hg19/hg19-male.chrom.sizes', e4='PeakXus', fastq='A31_V7_ChIPexo-GSM2643266/aligned.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='A31_V7_ChIPexo-GSM2643266/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 A31_V7_ChIPexo-GSM2643266/aligned.36mers.unique.bam Reading in data... Reading data took 16.0960350037 s Creating peak regions... Creating peak regions took 82.1966300011 s Estimating background... Estimating background took 210.911879063 s Processing A31_V7_ChIPexo-GSM2643266/aligned.36mers.unique.bam Reading in data... Reading data took 13.6769640446 s Creating peak regions... Creating peak regions took 65.7092478275 s Estimating background... Estimating background took 157.817909002 s Processing A31_V7_ChIPexo-GSM2643266/aligned.36mers.unique.bam Reading in data... Reading data took 11.7927098274 s Creating peak regions... Creating peak regions took 57.6835138798 s Estimating background... Estimating background took 127.944409132 s Processing A31_V7_ChIPexo-GSM2643266/aligned.36mers.unique.bam Reading in data... Reading data took 19.2665741444 s Creating peak regions... Creating peak regions took 64.9665970802 s Estimating background... Estimating background took 250.399492025 s Processing A31_V7_ChIPexo-GSM2643266/aligned.36mers.unique.bam Reading in data... Reading data took 7.57144403458 s Creating peak regions... Creating peak regions took 44.5114369392 s Estimating background... Estimating background took 83.8929328918 s Processing A31_V7_ChIPexo-GSM2643266/aligned.36mers.unique.bam Reading in data... Reading data took 8.69875407219 s Creating peak regions... Creating peak regions took 45.0966100693 s Estimating background... Estimating background took 100.326711893 s Processing A31_V7_ChIPexo-GSM2643266/aligned.36mers.unique.bam Reading in data... Reading data took 7.26780080795 s Creating peak regions... Creating peak regions took 37.7013998032 s Estimating background... Estimating background took 76.995429039 s Processing A31_V7_ChIPexo-GSM2643266/aligned.36mers.unique.bam Reading in data... Reading data took 6.3462460041 s Creating peak regions... Creating peak regions took 34.5929458141 s Estimating background... Estimating background took 58.1977920532 s Processing A31_V7_ChIPexo-GSM2643266/aligned.36mers.unique.bam Reading in data... Reading data took 7.30236911774 s Creating peak regions... Creating peak regions took 34.1641960144 s Estimating background... Estimating background took 75.2440028191 s Processing A31_V7_ChIPexo-GSM2643266/aligned.36mers.unique.bam Reading in data... Reading data took 9.05804491043 s Creating peak regions... Creating peak regions took 34.1647970676 s Estimating background... Estimating background took 113.128798962 s Processing A31_V7_ChIPexo-GSM2643266/aligned.36mers.unique.bam Reading in data... Reading data took 3.9546289444 s Creating peak regions... Creating peak regions took 21.9503340721 s Estimating background... Estimating background took 28.3965668678 s Processing A31_V7_ChIPexo-GSM2643266/aligned.36mers.unique.bam Reading in data... Reading data took 25.0683991909 s Creating peak regions... Creating peak regions took 109.444173098 s Estimating background...