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='LN95_C19_ChIPexo-Rep1-GSM2643247/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='LN95_C19_ChIPexo-Rep1-GSM2643247/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='LN95_C19_ChIPexo-Rep1-GSM2643247/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='LN95_C19_ChIPexo-Rep1-GSM2643247/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 LN95_C19_ChIPexo-Rep1-GSM2643247/aligned.36mers.unique.bam Reading in data... Reading data took 19.0218820572 s Creating peak regions... Creating peak regions took 90.6738660336 s Estimating background... Estimating background took 271.147949934 s Processing LN95_C19_ChIPexo-Rep1-GSM2643247/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='LN95_C19_ChIPexo-Rep1-GSM2643247/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='LN95_C19_ChIPexo-Rep1-GSM2643247/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='LN95_C19_ChIPexo-Rep1-GSM2643247/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='LN95_C19_ChIPexo-Rep1-GSM2643247/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 LN95_C19_ChIPexo-Rep1-GSM2643247/aligned.36mers.unique.bam Reading in data... Reading data took 22.7517988682 s Creating peak regions... Creating peak regions took 96.173099041 s Estimating background... Estimating background took 256.692535877 s Processing LN95_C19_ChIPexo-Rep1-GSM2643247/aligned.36mers.unique.bam Reading in data... Reading data took 12.9877829552 s Creating peak regions... Creating peak regions took 58.6889808178 s Estimating background... Estimating background took 107.796061039 s Processing LN95_C19_ChIPexo-Rep1-GSM2643247/aligned.36mers.unique.bam Reading in data... Reading data took 11.1975448132 s Creating peak regions... Creating peak regions took 52.8042919636 s Estimating background... Estimating background took 113.891314983 s Processing LN95_C19_ChIPexo-Rep1-GSM2643247/aligned.36mers.unique.bam Reading in data... Reading data took 11.4116911888 s Creating peak regions... Creating peak regions took 53.7917900085 s Estimating background... Estimating background took 126.566661835 s Processing LN95_C19_ChIPexo-Rep1-GSM2643247/aligned.36mers.unique.bam Reading in data... Reading data took 7.25634789467 s Creating peak regions... Creating peak regions took 44.6346101761 s Estimating background... Estimating background took 58.2930319309 s Processing LN95_C19_ChIPexo-Rep1-GSM2643247/aligned.36mers.unique.bam Reading in data... Reading data took 6.97514104843 s Creating peak regions... Creating peak regions took 39.9395442009 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='LN95_C19_ChIPexo-Rep1-GSM2643247/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='LN95_C19_ChIPexo-Rep1-GSM2643247/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 LN95_C19_ChIPexo-Rep1-GSM2643247/aligned.36mers.unique.bam Reading in data... Estimating background took 59.3366019726 s Processing LN95_C19_ChIPexo-Rep1-GSM2643247/aligned.36mers.unique.bam Reading in data... Reading data took 6.28796696663 s Creating peak regions... Reading data took 18.7156848907 s Creating peak regions... Creating peak regions took 35.4357409477 s Estimating background... Estimating background took 56.3185927868 s Processing LN95_C19_ChIPexo-Rep1-GSM2643247/aligned.36mers.unique.bam Reading in data... Creating peak regions took 85.2273869514 s Estimating background... Reading data took 4.58911705017 s Creating peak regions... Creating peak regions took 29.5046420097 s Estimating background... Estimating background took 36.4074599743 s Processing LN95_C19_ChIPexo-Rep1-GSM2643247/aligned.36mers.unique.bam Reading in data... Reading data took 6.35896706581 s Creating peak regions... Creating peak regions took 31.1420328617 s Estimating background... Estimating background took 64.3471679688 s Processing LN95_C19_ChIPexo-Rep1-GSM2643247/aligned.36mers.unique.bam Reading in data... Reading data took 6.65898108482 s Creating peak regions... Creating peak regions took 30.3668808937 s Estimating background... Estimating background took 260.140835047 s Processing LN95_C19_ChIPexo-Rep1-GSM2643247/aligned.36mers.unique.bam Reading in data... Reading data took 11.0388300419 s Creating peak regions... Estimating background took 67.6628160477 s Processing LN95_C19_ChIPexo-Rep1-GSM2643247/aligned.36mers.unique.bam Reading in data... Reading data took 3.52108097076 s Creating peak regions... Creating peak regions took 18.6379678249 s Estimating background... Estimating background took 20.4702351093 s Processing LN95_C19_ChIPexo-Rep1-GSM2643247/aligned.36mers.unique.bam Reading in data... Creating peak regions took 51.5258460045 s Estimating background... Reading data took 19.1045999527 s Creating peak regions... Estimating background took 104.582130909 s Processing LN95_C19_ChIPexo-Rep1-GSM2643247/aligned.36mers.unique.bam Reading in data... Reading data took 10.66527915 s Creating peak regions... Creating peak regions took 109.930297136 s Estimating background... Creating peak regions took 46.1884641647 s Estimating background... Estimating background took 148.859260082 s Processing LN95_C19_ChIPexo-Rep1-GSM2643247/aligned.36mers.unique.bam Reading in data... Estimating background took 113.902794123 s Processing LN95_C19_ChIPexo-Rep1-GSM2643247/aligned.36mers.unique.bam Reading in data... Reading data took 4.45856785774 s Creating peak regions... Reading data took 11.2977449894 s Creating peak regions... Creating peak regions took 26.487555027 s Estimating background... Creating peak regions took 50.6654369831 s Estimating background... Estimating background took 39.3417310715 s Processing LN95_C19_ChIPexo-Rep1-GSM2643247/aligned.36mers.unique.bam Reading in data... Reading data took 2.68306803703 s Creating peak regions... Creating peak regions took 16.2627360821 s Estimating background... Estimating background took 21.7364270687 s Processing LN95_C19_ChIPexo-Rep1-GSM2643247/aligned.36mers.unique.bam Reading in data... Reading data took 2.25414705276 s Creating peak regions... Creating peak regions took 15.7675879002 s Estimating background... Estimating background took 15.7064311504 s Processing LN95_C19_ChIPexo-Rep1-GSM2643247/aligned.36mers.unique.bam Reading in data... Reading data took 16.0831549168 s Creating peak regions... Estimating background took 121.264034033 s Processing LN95_C19_ChIPexo-Rep1-GSM2643247/aligned.36mers.unique.bam Reading in data... Reading data took 6.64899587631 s Creating peak regions... Creating peak regions took 40.6799030304 s Estimating background... Creating peak regions took 77.7488880157 s Estimating background... Estimating background took 55.4782459736 s Processing LN95_C19_ChIPexo-Rep1-GSM2643247/aligned.36mers.unique.bam Reading in data... Reading data took 6.08348894119 s Creating peak regions... Creating peak regions took 33.1140458584 s Estimating background... Estimating background took 52.2210359573 s Processing LN95_C19_ChIPexo-Rep1-GSM2643247/aligned.36mers.unique.bam Reading in data... Reading data took 5.90262103081 s Creating peak regions... Estimating background took 172.508924007 s Processing LN95_C19_ChIPexo-Rep1-GSM2643247/aligned.36mers.unique.bam Reading in data... Creating peak regions took 34.1614179611 s Estimating background... Reading data took 14.2524461746 s Creating peak regions... Estimating background took 54.264013052 s Processing LN95_C19_ChIPexo-Rep1-GSM2643247/aligned.36mers.unique.bam Reading in data... Reading data took 4.66062879562 s Creating peak regions... Creating peak regions took 27.7143208981 s Estimating background... Creating peak regions took 90.0041761398 s Estimating background... Estimating background took 36.0845298767 s Processing LN95_C19_ChIPexo-Rep1-GSM2643247/aligned.36mers.unique.bam Reading in data... Reading data took 6.70135402679 s Creating peak regions... Creating peak regions took 30.933041811 s Estimating background... Estimating background took 63.2839179039 s Processing LN95_C19_ChIPexo-Rep1-GSM2643247/aligned.36mers.unique.bam Reading in data... Estimating background took 129.232019901 s Processing LN95_C19_ChIPexo-Rep1-GSM2643247/aligned.36mers.unique.bam Reading in data... Reading data took 7.68585395813 s Creating peak regions... Reading data took 15.7936139107 s Creating peak regions... Creating peak regions took 33.2545177937 s Estimating background... Creating peak regions took 83.3230628967 s Estimating background... Estimating background took 66.4757738113 s Processing LN95_C19_ChIPexo-Rep1-GSM2643247/aligned.36mers.unique.bam Reading in data... Reading data took 3.2120578289 s Creating peak regions... Creating peak regions took 19.2037010193 s Estimating background... Estimating background took 20.4012601376 s Processing LN95_C19_ChIPexo-Rep1-GSM2643247/aligned.36mers.unique.bam Reading in data... Reading data took 14.1814651489 s Creating peak regions... Creating peak regions took 79.8014988899 s Estimating background... Estimating background took 165.063755989 s Processing LN95_C19_ChIPexo-Rep1-GSM2643247/aligned.36mers.unique.bam Reading in data... Reading data took 13.3067491055 s Creating peak regions... Creating peak regions took 70.4180629253 s Estimating background... Estimating background took 142.012502909 s Processing LN95_C19_ChIPexo-Rep1-GSM2643247/aligned.36mers.unique.bam Reading in data... Reading data took 4.50460505486 s Creating peak regions... Creating peak regions took 24.5335731506 s Estimating background... Estimating background took 38.7546770573 s Processing LN95_C19_ChIPexo-Rep1-GSM2643247/aligned.36mers.unique.bam Reading in data... Reading data took 2.60432887077 s Creating peak regions... Estimating background took 108.552681923 s Processing LN95_C19_ChIPexo-Rep1-GSM2643247/aligned.36mers.unique.bam Reading in data... Reading data took 14.4196639061 s Creating peak regions... Creating peak regions took 14.9813580513 s Estimating background... Estimating background took 21.2815179825 s Processing LN95_C19_ChIPexo-Rep1-GSM2643247/aligned.36mers.unique.bam Reading in data... Reading data took 2.35946893692 s Creating peak regions... Creating peak regions took 15.7641739845 s Estimating background... Estimating background took 14.9048137665 s Processing LN95_C19_ChIPexo-Rep1-GSM2643247/aligned.36mers.unique.bam Reading in data... Reading data took 16.9006979465 s Creating peak regions... Creating peak regions took 72.5552418232 s Estimating background... Creating peak regions took 76.3563330173 s Estimating background... Estimating background took 143.458353996 s Processing LN95_C19_ChIPexo-Rep1-GSM2643247/aligned.36mers.unique.bam Reading in data... Reading data took 10.8586258888 s Creating peak regions... Creating peak regions took 68.1132280827 s Estimating background... Estimating background took 174.350882053 s Processing LN95_C19_ChIPexo-Rep1-GSM2643247/aligned.36mers.unique.bam Reading in data... Reading data took 14.5046219826 s Creating peak regions... Estimating background took 81.445089817 s Processing LN95_C19_ChIPexo-Rep1-GSM2643247/aligned.36mers.unique.bam Reading in data... Reading data took 8.70580911636 s Creating peak regions... Creating peak regions took 64.9281039238 s Estimating background... Creating peak regions took 51.1238241196 s Estimating background... Estimating background took 63.3192811012 s Processing LN95_C19_ChIPexo-Rep1-GSM2643247/aligned.36mers.unique.bam Reading in data... Reading data took 0.870312929153 s Creating peak regions... Creating peak regions took 0.464023113251 s Estimating background... Estimating background took 1.25898909569 s Processing LN95_C19_ChIPexo-Rep1-GSM2643247/aligned.36mers.unique.bam Reading in data... Reading data took 8.12147092819 s Creating peak regions... Estimating background took 129.741667986 s Processing LN95_C19_ChIPexo-Rep1-GSM2643247/aligned.36mers.unique.bam Reading in data... Reading data took 17.5757060051 s Creating peak regions... Creating peak regions took 50.5401780605 s Estimating background... Estimating background took 51.8666870594 s Processing LN95_C19_ChIPexo-Rep1-GSM2643247/aligned.36mers.unique.bam Reading in data... Reading data took 0.711016893387 s Creating peak regions... Creating peak regions took 71.1529018879 s Estimating background... Creating peak regions took 17.524889946 s Estimating background... Estimating background took 1.16774892807 s Estimating background took 159.144860983 s Processing LN95_C19_ChIPexo-Rep1-GSM2643247/aligned.36mers.unique.bam Reading in data... Reading data took 13.2589011192 s Creating peak regions... Creating peak regions took 61.9780888557 s Estimating background... Estimating background took 106.151908159 s Processing LN95_C19_ChIPexo-Rep1-GSM2643247/aligned.36mers.unique.bam Reading in data... Reading data took 14.0957071781 s Creating peak regions... Creating peak regions took 61.1934978962 s Estimating background... Estimating background took 121.421194077 s Processing LN95_C19_ChIPexo-Rep1-GSM2643247/aligned.36mers.unique.bam Reading in data... Reading data took 10.6856369972 s Creating peak regions... Creating peak regions took 59.9780099392 s Estimating background... Estimating background took 84.5143978596 s Processing LN95_C19_ChIPexo-Rep1-GSM2643247/aligned.36mers.unique.bam Reading in data... Reading data took 7.4456179142 s Creating peak regions... Creating peak regions took 43.621502161 s Estimating background... Estimating background took 59.8286669254 s Processing LN95_C19_ChIPexo-Rep1-GSM2643247/aligned.36mers.unique.bam Reading in data... Reading data took 1.22834706306 s Creating peak regions... Creating peak regions took 1.00528407097 s Estimating background... Estimating background took 1.40345978737 s Processing LN95_C19_ChIPexo-Rep1-GSM2643247/aligned.36mers.unique.bam Reading in data... Reading data took 9.29859519005 s Creating peak regions... Creating peak regions took 56.6422019005 s Estimating background... Estimating background took 54.4112079144 s Processing LN95_C19_ChIPexo-Rep1-GSM2643247/aligned.36mers.unique.bam Reading in data... Reading data took 0.581645965576 s Creating peak regions... Creating peak regions took 16.4753201008 s Estimating background... Estimating background took 0.892555952072 s