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='22RV1_V7_ChIPexo-Rep2-GSM2643240/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='22RV1_V7_ChIPexo-Rep2-GSM2643240/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='22RV1_V7_ChIPexo-Rep2-GSM2643240/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='22RV1_V7_ChIPexo-Rep2-GSM2643240/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 22RV1_V7_ChIPexo-Rep2-GSM2643240/aligned.36mers.unique.bam Reading in data... Reading data took 12.3264689445 s Creating peak regions... Creating peak regions took 68.7311089039 s Estimating background... Estimating background took 84.2822480202 s Processing 22RV1_V7_ChIPexo-Rep2-GSM2643240/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='22RV1_V7_ChIPexo-Rep2-GSM2643240/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='22RV1_V7_ChIPexo-Rep2-GSM2643240/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='22RV1_V7_ChIPexo-Rep2-GSM2643240/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='22RV1_V7_ChIPexo-Rep2-GSM2643240/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 22RV1_V7_ChIPexo-Rep2-GSM2643240/aligned.36mers.unique.bam Reading in data... Reading data took 13.0626809597 s Creating peak regions... Creating peak regions took 70.4219238758 s Estimating background... Estimating background took 87.8427429199 s Processing 22RV1_V7_ChIPexo-Rep2-GSM2643240/aligned.36mers.unique.bam Reading in data... Reading data took 6.24867892265 s Creating peak regions... Creating peak regions took 43.0242819786 s Estimating background... Estimating background took 26.3537099361 s Processing 22RV1_V7_ChIPexo-Rep2-GSM2643240/aligned.36mers.unique.bam Reading in data... Reading data took 6.52643704414 s Creating peak regions... Creating peak regions took 45.9609048367 s Estimating background... Estimating background took 26.5465049744 s Processing 22RV1_V7_ChIPexo-Rep2-GSM2643240/aligned.36mers.unique.bam Reading in data... Reading data took 9.50144600868 s Creating peak regions... Creating peak regions took 46.4239809513 s Estimating background... Estimating background took 61.2184028625 s Processing 22RV1_V7_ChIPexo-Rep2-GSM2643240/aligned.36mers.unique.bam Reading in data... Reading data took 5.88638997078 s Creating peak regions... Creating peak regions took 36.117647171 s Estimating background... Estimating background took 24.3279149532 s Processing 22RV1_V7_ChIPexo-Rep2-GSM2643240/aligned.36mers.unique.bam Reading in data... Reading data took 4.81570410728 s Creating peak regions... Creating peak regions took 34.3904440403 s Estimating background... Estimating background took 20.015212059 s Processing 22RV1_V7_ChIPexo-Rep2-GSM2643240/aligned.36mers.unique.bam Reading in data... Reading data took 3.61698698997 s Creating peak regions... Creating peak regions took 28.0336771011 s Estimating background... Estimating background took 14.937915802 s Processing 22RV1_V7_ChIPexo-Rep2-GSM2643240/aligned.36mers.unique.bam Reading in data... Reading data took 3.31028795242 s Creating peak regions... Creating peak regions took 28.2439260483 s Estimating background... Estimating background took 12.1312642097 s Processing 22RV1_V7_ChIPexo-Rep2-GSM2643240/aligned.36mers.unique.bam Reading in data... Reading data took 3.59821414948 s Creating peak regions... Creating peak regions took 23.0608620644 s Estimating background... Estimating background took 13.6641230583 s Processing 22RV1_V7_ChIPexo-Rep2-GSM2643240/aligned.36mers.unique.bam Reading in data... Reading data took 3.94676685333 s Creating peak regions... Creating peak regions took 22.2481579781 s Estimating background... Estimating background took 16.952051878 s Processing 22RV1_V7_ChIPexo-Rep2-GSM2643240/aligned.36mers.unique.bam Reading in data... Reading data took 2.31342196465 s Creating peak regions... Creating peak regions took 16.2662298679 s Estimating background... Estimating background took 7.99460291862 s Processing 22RV1_V7_ChIPexo-Rep2-GSM2643240/aligned.36mers.unique.bam Reading in data... Reading data took 8.99072694778 s Creating peak regions... Creating peak regions took 69.6741440296 s Estimating background... Estimating background took 41.7173609734 s Processing 22RV1_V7_ChIPexo-Rep2-GSM2643240/aligned.36mers.unique.bam Reading in data... Reading data took 2.90099000931 s Creating peak regions... Creating peak regions took 18.3003330231 s Estimating background... Estimating background took 10.6498949528 s Processing 22RV1_V7_ChIPexo-Rep2-GSM2643240/aligned.36mers.unique.bam Reading in data... Reading data took 1.95296502113 s Creating peak regions... Creating peak regions took 13.2147018909 s Estimating background... Estimating background took 8.95936584473 s Processing 22RV1_V7_ChIPexo-Rep2-GSM2643240/aligned.36mers.unique.bam Reading in data... Reading data took 1.23199105263 s Creating peak regions... Creating peak regions took 14.357475996 s Estimating background... Estimating background took 5.43658590317 s Processing 22RV1_V7_ChIPexo-Rep2-GSM2643240/aligned.36mers.unique.bam Reading in data... Reading data took 11.8095998764 s Creating peak regions... Creating peak regions took 63.8185489178 s Estimating background... Estimating background took 71.5078449249 s Processing 22RV1_V7_ChIPexo-Rep2-GSM2643240/aligned.36mers.unique.bam Reading in data... Reading data took 9.9882478714 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='22RV1_V7_ChIPexo-Rep2-GSM2643240/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='22RV1_V7_ChIPexo-Rep2-GSM2643240/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 22RV1_V7_ChIPexo-Rep2-GSM2643240/aligned.36mers.unique.bam Reading in data... Reading data took 15.1621510983 s Creating peak regions... Creating peak regions took 64.1585187912 s Estimating background... Estimating background took 46.1691880226 s Processing 22RV1_V7_ChIPexo-Rep2-GSM2643240/aligned.36mers.unique.bam Reading in data... Reading data took 9.48815894127 s Creating peak regions... Creating peak regions took 77.3638949394 s Estimating background... Creating peak regions took 54.8467040062 s Estimating background... Estimating background took 38.8894939423 s Processing 22RV1_V7_ChIPexo-Rep2-GSM2643240/aligned.36mers.unique.bam Reading in data... Estimating background took 94.3069989681 s Processing 22RV1_V7_ChIPexo-Rep2-GSM2643240/aligned.36mers.unique.bam Reading in data... Reading data took 7.98055005074 s Creating peak regions... Reading data took 6.66227507591 s Creating peak regions... Creating peak regions took 43.0940070152 s Estimating background... Creating peak regions took 49.5330028534 s Estimating background... Estimating background took 28.5633118153 s Processing 22RV1_V7_ChIPexo-Rep2-GSM2643240/aligned.36mers.unique.bam Reading in data... Reading data took 6.79611992836 s Creating peak regions... Estimating background took 41.603427887 s Processing 22RV1_V7_ChIPexo-Rep2-GSM2643240/aligned.36mers.unique.bam Reading in data... Reading data took 11.8664708138 s Creating peak regions... Creating peak regions took 44.2031941414 s Estimating background... Estimating background took 29.5476219654 s Processing 22RV1_V7_ChIPexo-Rep2-GSM2643240/aligned.36mers.unique.bam Reading in data... Creating peak regions took 59.1852321625 s Estimating background... Reading data took 11.3780338764 s Creating peak regions... Creating peak regions took 54.1837551594 s Estimating background... Estimating background took 64.8671970367 s Processing 22RV1_V7_ChIPexo-Rep2-GSM2643240/aligned.36mers.unique.bam Reading in data... Reading data took 10.6911950111 s Creating peak regions... Estimating background took 63.8696219921 s Processing 22RV1_V7_ChIPexo-Rep2-GSM2643240/aligned.36mers.unique.bam Reading in data... Creating peak regions took 50.4326810837 s Estimating background... Reading data took 7.06073594093 s Creating peak regions... Creating peak regions took 40.5126750469 s Estimating background... Estimating background took 58.5809309483 s Processing 22RV1_V7_ChIPexo-Rep2-GSM2643240/aligned.36mers.unique.bam Reading in data... Reading data took 5.63104009628 s Creating peak regions... Estimating background took 26.9597699642 s Processing 22RV1_V7_ChIPexo-Rep2-GSM2643240/aligned.36mers.unique.bam Reading in data... Reading data took 5.46401000023 s Creating peak regions... Creating peak regions took 42.206788063 s Estimating background... Creating peak regions took 35.0251588821 s Estimating background... Estimating background took 23.1325128078 s Processing 22RV1_V7_ChIPexo-Rep2-GSM2643240/aligned.36mers.unique.bam Reading in data... Reading data took 0.348410129547 s Creating peak regions... Creating peak regions took 0.298305988312 s Estimating background... Estimating background took 1.03690385818 s Processing 22RV1_V7_ChIPexo-Rep2-GSM2643240/aligned.36mers.unique.bam Reading in data... Estimating background took 22.0595421791 s Processing 22RV1_V7_ChIPexo-Rep2-GSM2643240/aligned.36mers.unique.bam Reading in data... Reading data took 4.57093000412 s Creating peak regions... Reading data took 4.01056981087 s Creating peak regions... Creating peak regions took 32.1792900562 s Estimating background... Creating peak regions took 42.4024579525 s Estimating background... Estimating background took 16.9402010441 s Processing 22RV1_V7_ChIPexo-Rep2-GSM2643240/aligned.36mers.unique.bam Reading in data... Reading data took 3.38289690018 s Creating peak regions... Estimating background took 14.00415802 s Processing 22RV1_V7_ChIPexo-Rep2-GSM2643240/aligned.36mers.unique.bam Reading in data... Reading data took 1.12142205238 s Creating peak regions... Creating peak regions took 19.4774270058 s Estimating background... Estimating background took 1.52121901512 s Creating peak regions took 27.1121511459 s Estimating background... Estimating background took 13.0037770271 s Processing 22RV1_V7_ChIPexo-Rep2-GSM2643240/aligned.36mers.unique.bam Reading in data... Reading data took 4.11533808708 s Creating peak regions... Creating peak regions took 28.3223800659 s Estimating background... Estimating background took 14.117939949 s Processing 22RV1_V7_ChIPexo-Rep2-GSM2643240/aligned.36mers.unique.bam Reading in data... Reading data took 4.39693117142 s Creating peak regions... Creating peak regions took 29.0759341717 s Estimating background... Estimating background took 18.776320219 s Processing 22RV1_V7_ChIPexo-Rep2-GSM2643240/aligned.36mers.unique.bam Reading in data... Reading data took 2.65464615822 s Creating peak regions... Creating peak regions took 24.0071251392 s Estimating background... Estimating background took 8.89234018326 s Processing 22RV1_V7_ChIPexo-Rep2-GSM2643240/aligned.36mers.unique.bam Reading in data... Reading data took 10.4581079483 s Creating peak regions... Creating peak regions took 73.6269259453 s Estimating background... Estimating background took 45.8485531807 s Processing 22RV1_V7_ChIPexo-Rep2-GSM2643240/aligned.36mers.unique.bam Reading in data... Reading data took 3.6582930088 s Creating peak regions... Creating peak regions took 21.5579781532 s Estimating background... Estimating background took 12.1496491432 s Processing 22RV1_V7_ChIPexo-Rep2-GSM2643240/aligned.36mers.unique.bam Reading in data... Reading data took 2.18322610855 s Creating peak regions... Creating peak regions took 19.1397349834 s Estimating background... Estimating background took 10.1712081432 s Processing 22RV1_V7_ChIPexo-Rep2-GSM2643240/aligned.36mers.unique.bam Reading in data... Reading data took 1.66923689842 s Creating peak regions... Creating peak regions took 15.6885089874 s Estimating background... Estimating background took 5.71249604225 s Processing 22RV1_V7_ChIPexo-Rep2-GSM2643240/aligned.36mers.unique.bam Reading in data... Reading data took 14.4994699955 s Creating peak regions... Creating peak regions took 64.1416170597 s Estimating background... Estimating background took 78.5213699341 s Processing 22RV1_V7_ChIPexo-Rep2-GSM2643240/aligned.36mers.unique.bam Reading in data... Reading data took 11.1204400063 s Creating peak regions... Creating peak regions took 65.177423954 s Estimating background... Estimating background took 53.1302628517 s Processing 22RV1_V7_ChIPexo-Rep2-GSM2643240/aligned.36mers.unique.bam Reading in data... Reading data took 10.4289932251 s Creating peak regions... Creating peak regions took 57.3210999966 s Estimating background... Estimating background took 45.2286410332 s Processing 22RV1_V7_ChIPexo-Rep2-GSM2643240/aligned.36mers.unique.bam Reading in data... Reading data took 9.22817802429 s Creating peak regions... Creating peak regions took 56.6415669918 s Estimating background... Estimating background took 43.3947491646 s Processing 22RV1_V7_ChIPexo-Rep2-GSM2643240/aligned.36mers.unique.bam Reading in data... Reading data took 12.957310915 s Creating peak regions... Creating peak regions took 56.1063230038 s Estimating background... Estimating background took 66.6986570358 s Processing 22RV1_V7_ChIPexo-Rep2-GSM2643240/aligned.36mers.unique.bam Reading in data... Reading data took 11.1874799728 s Creating peak regions... Creating peak regions took 56.0418422222 s Estimating background... Estimating background took 63.4341509342 s Processing 22RV1_V7_ChIPexo-Rep2-GSM2643240/aligned.36mers.unique.bam Reading in data... Reading data took 6.62900590897 s Creating peak regions... Creating peak regions took 45.5277090073 s Estimating background... Estimating background took 26.9522721767 s Processing 22RV1_V7_ChIPexo-Rep2-GSM2643240/aligned.36mers.unique.bam Reading in data... Reading data took 0.432747840881 s Creating peak regions... Creating peak regions took 0.488299846649 s Estimating background... Estimating background took 1.07272696495 s Processing 22RV1_V7_ChIPexo-Rep2-GSM2643240/aligned.36mers.unique.bam Reading in data... Reading data took 5.2609629631 s Creating peak regions... Creating peak regions took 47.3985319138 s Estimating background... Estimating background took 13.4749898911 s Processing 22RV1_V7_ChIPexo-Rep2-GSM2643240/aligned.36mers.unique.bam Reading in data... Reading data took 1.49110603333 s Creating peak regions... Creating peak regions took 19.2030980587 s Estimating background... Estimating background took 3.86963510513 s