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_C19_ChIPexo-Rep2-GSM2643242/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_C19_ChIPexo-Rep2-GSM2643242/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_C19_ChIPexo-Rep2-GSM2643242/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_C19_ChIPexo-Rep2-GSM2643242/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_C19_ChIPexo-Rep2-GSM2643242/aligned.36mers.unique.bam Reading in data... Reading data took 13.9858798981 s Creating peak regions... Creating peak regions took 77.0267739296 s Estimating background... Estimating background took 149.51752305 s Processing 22RV1_C19_ChIPexo-Rep2-GSM2643242/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_C19_ChIPexo-Rep2-GSM2643242/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_C19_ChIPexo-Rep2-GSM2643242/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_C19_ChIPexo-Rep2-GSM2643242/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_C19_ChIPexo-Rep2-GSM2643242/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_C19_ChIPexo-Rep2-GSM2643242/aligned.36mers.unique.bam Reading in data... Reading data took 15.1728169918 s Creating peak regions... Creating peak regions took 84.7267580032 s Estimating background... Estimating background took 175.797402859 s Processing 22RV1_C19_ChIPexo-Rep2-GSM2643242/aligned.36mers.unique.bam Reading in data... Reading data took 7.7517991066 s Creating peak regions... Creating peak regions took 58.697273016 s Estimating background... Estimating background took 52.5853939056 s Processing 22RV1_C19_ChIPexo-Rep2-GSM2643242/aligned.36mers.unique.bam Reading in data... Reading data took 9.54919195175 s Creating peak regions... Creating peak regions took 46.3574779034 s Estimating background... Estimating background took 52.406017065 s Processing 22RV1_C19_ChIPexo-Rep2-GSM2643242/aligned.36mers.unique.bam Reading in data... Reading data took 10.3957850933 s Creating peak regions... Creating peak regions took 54.638684988 s Estimating background... Estimating background took 108.253475904 s Processing 22RV1_C19_ChIPexo-Rep2-GSM2643242/aligned.36mers.unique.bam Reading in data... Reading data took 6.77351307869 s Creating peak regions... Creating peak regions took 48.3153409958 s Estimating background... Estimating background took 44.9051389694 s Processing 22RV1_C19_ChIPexo-Rep2-GSM2643242/aligned.36mers.unique.bam Reading in data... Reading data took 6.01829910278 s Creating peak regions... Creating peak regions took 38.24969697 s Estimating background... Estimating background took 37.1139979362 s Processing 22RV1_C19_ChIPexo-Rep2-GSM2643242/aligned.36mers.unique.bam Reading in data... Reading data took 5.19383001328 s Creating peak regions... Creating peak regions took 43.8256549835 s Estimating background... Estimating background took 33.3049371243 s Processing 22RV1_C19_ChIPexo-Rep2-GSM2643242/aligned.36mers.unique.bam Reading in data... Reading data took 4.92973303795 s Creating peak regions... Creating peak regions took 31.9907178879 s Estimating background... Estimating background took 27.8926019669 s Processing 22RV1_C19_ChIPexo-Rep2-GSM2643242/aligned.36mers.unique.bam Reading in data... Reading data took 4.12510585785 s Creating peak regions... Creating peak regions took 27.247522831 s Estimating background... Estimating background took 27.7208898067 s Processing 22RV1_C19_ChIPexo-Rep2-GSM2643242/aligned.36mers.unique.bam Reading in data... Reading data took 4.9510819912 s Creating peak regions... Creating peak regions took 26.6489360332 s Estimating background... Estimating background took 33.1429760456 s Processing 22RV1_C19_ChIPexo-Rep2-GSM2643242/aligned.36mers.unique.bam Reading in data... Reading data took 2.90484786034 s Creating peak regions... Creating peak regions took 19.2164838314 s Estimating background... Estimating background took 18.5697109699 s Processing 22RV1_C19_ChIPexo-Rep2-GSM2643242/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_C19_ChIPexo-Rep2-GSM2643242/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_C19_ChIPexo-Rep2-GSM2643242/peakXus/', p3=1.0, p7=1, q2=20, s3=1, skip0=0, t2=1, title5='PeakXus', verbosity=1, w3=5, w4=100, wg7=None)Reading data took 10.9957950115 s Creating peak regions... Testing that input files exist...done! Processing 22RV1_C19_ChIPexo-Rep2-GSM2643242/aligned.36mers.unique.bam Reading in data... Reading data took 15.8125939369 s Creating peak regions... Creating peak regions took 77.4208521843 s Estimating background... Creating peak regions took 86.0421509743 s Estimating background... Estimating background took 76.4350788593 s Processing 22RV1_C19_ChIPexo-Rep2-GSM2643242/aligned.36mers.unique.bam Reading in data... Reading data took 3.85210895538 s Creating peak regions... Creating peak regions took 29.4010818005 s Estimating background... Estimating background took 23.5832400322 s Processing 22RV1_C19_ChIPexo-Rep2-GSM2643242/aligned.36mers.unique.bam Reading in data... Reading data took 2.96926593781 s Creating peak regions... Creating peak regions took 20.2336039543 s Estimating background... Estimating background took 17.3023040295 s Processing 22RV1_C19_ChIPexo-Rep2-GSM2643242/aligned.36mers.unique.bam Reading in data... Reading data took 2.01291704178 s Creating peak regions... Estimating background took 168.657054186 s Processing 22RV1_C19_ChIPexo-Rep2-GSM2643242/aligned.36mers.unique.bam Reading in data... Creating peak regions took 18.7378852367 s Estimating background... Reading data took 8.83047199249 s Creating peak regions... Estimating background took 11.4125828743 s Processing 22RV1_C19_ChIPexo-Rep2-GSM2643242/aligned.36mers.unique.bam Reading in data... Reading data took 14.0972838402 s Creating peak regions... Creating peak regions took 53.0848259926 s Estimating background... Creating peak regions took 81.7549510002 s Estimating background... Estimating background took 49.841616869 s Processing 22RV1_C19_ChIPexo-Rep2-GSM2643242/aligned.36mers.unique.bam Reading in data... Reading data took 7.66592693329 s Creating peak regions... Creating peak regions took 50.4691390991 s Estimating background... Estimating background took 51.4308059216 s Processing 22RV1_C19_ChIPexo-Rep2-GSM2643242/aligned.36mers.unique.bam Reading in data... Reading data took 11.0105030537 s Creating peak regions... Estimating background took 132.204632998 s Processing 22RV1_C19_ChIPexo-Rep2-GSM2643242/aligned.36mers.unique.bam Reading in data... Reading data took 11.8419108391 s Creating peak regions... Creating peak regions took 55.6739690304 s Estimating background... Creating peak regions took 75.9871969223 s Estimating background... Estimating background took 102.130823851 s Processing 22RV1_C19_ChIPexo-Rep2-GSM2643242/aligned.36mers.unique.bam Reading in data... Reading data took 6.19753289223 s Creating peak regions... Estimating background took 85.0330069065 s Processing 22RV1_C19_ChIPexo-Rep2-GSM2643242/aligned.36mers.unique.bam Reading in data... Reading data took 12.8963229656 s Creating peak regions... Creating peak regions took 39.9492690563 s Estimating background... Estimating background took 43.0610358715 s Processing 22RV1_C19_ChIPexo-Rep2-GSM2643242/aligned.36mers.unique.bam Reading in data... Reading data took 5.3265171051 s Creating peak regions... Creating peak regions took 71.460599184 s Estimating background... Creating peak regions took 40.5392100811 s Estimating background... Estimating background took 37.175522089 s Processing 22RV1_C19_ChIPexo-Rep2-GSM2643242/aligned.36mers.unique.bam Reading in data... Reading data took 4.93748402596 s Creating peak regions... Estimating background took 75.0496878624 s Processing 22RV1_C19_ChIPexo-Rep2-GSM2643242/aligned.36mers.unique.bam Reading in data... Reading data took 9.77611207962 s Creating peak regions... Creating peak regions took 30.6475918293 s Estimating background... Estimating background took 30.2719419003 s Processing 22RV1_C19_ChIPexo-Rep2-GSM2643242/aligned.36mers.unique.bam Reading in data... Reading data took 4.22022795677 s Creating peak regions... Creating peak regions took 59.7203431129 s Estimating background... Creating peak regions took 29.7014801502 s Estimating background... Estimating background took 25.3814239502 s Processing 22RV1_C19_ChIPexo-Rep2-GSM2643242/aligned.36mers.unique.bam Reading in data... Reading data took 4.14765119553 s Creating peak regions... Estimating background took 70.9686040878 s Processing 22RV1_C19_ChIPexo-Rep2-GSM2643242/aligned.36mers.unique.bam Reading in data... Creating peak regions took 26.1167259216 s Estimating background... Reading data took 12.3496060371 s Creating peak regions... Estimating background took 26.7494649887 s Processing 22RV1_C19_ChIPexo-Rep2-GSM2643242/aligned.36mers.unique.bam Reading in data... Reading data took 5.00493884087 s Creating peak regions... Creating peak regions took 30.4511938095 s Estimating background... Creating peak regions took 66.0425949097 s Estimating background... Estimating background took 30.2129678726 s Processing 22RV1_C19_ChIPexo-Rep2-GSM2643242/aligned.36mers.unique.bam Reading in data... Reading data took 2.83313703537 s Creating peak regions... Creating peak regions took 19.502972126 s Estimating background... Estimating background took 17.4114468098 s Processing 22RV1_C19_ChIPexo-Rep2-GSM2643242/aligned.36mers.unique.bam Reading in data... Reading data took 10.2452859879 s Creating peak regions... Estimating background took 122.36272192 s Processing 22RV1_C19_ChIPexo-Rep2-GSM2643242/aligned.36mers.unique.bam Reading in data... Reading data took 12.8930268288 s Creating peak regions... Creating peak regions took 81.5055599213 s Estimating background... Creating peak regions took 59.6184699535 s Estimating background... Estimating background took 78.5984699726 s Processing 22RV1_C19_ChIPexo-Rep2-GSM2643242/aligned.36mers.unique.bam Reading in data... Reading data took 3.52929711342 s Creating peak regions... Creating peak regions took 25.993710041 s Estimating background... Estimating background took 23.0928018093 s Processing 22RV1_C19_ChIPexo-Rep2-GSM2643242/aligned.36mers.unique.bam Reading in data... Reading data took 2.34242606163 s Creating peak regions... Creating peak regions took 16.6516358852 s Estimating background... Estimating background took 107.778731108 s Processing 22RV1_C19_ChIPexo-Rep2-GSM2643242/aligned.36mers.unique.bam Reading in data... Reading data took 6.95109796524 s Creating peak regions... Estimating background took 15.2007279396 s Processing 22RV1_C19_ChIPexo-Rep2-GSM2643242/aligned.36mers.unique.bam Reading in data... Reading data took 1.93845701218 s Creating peak regions... Creating peak regions took 16.1999709606 s Estimating background... Estimating background took 10.3544919491 s Processing 22RV1_C19_ChIPexo-Rep2-GSM2643242/aligned.36mers.unique.bam Reading in data... Creating peak regions took 49.201941967 s Estimating background... Reading data took 13.9483041763 s Creating peak regions... Estimating background took 46.8236470222 s Processing 22RV1_C19_ChIPexo-Rep2-GSM2643242/aligned.36mers.unique.bam Reading in data... Reading data took 0.487329006195 s Creating peak regions... Creating peak regions took 0.566087961197 s Estimating background... Estimating background took 1.34284186363 s Processing 22RV1_C19_ChIPexo-Rep2-GSM2643242/aligned.36mers.unique.bam Reading in data... Reading data took 6.30527806282 s Creating peak regions... Creating peak regions took 74.0095469952 s Estimating background... Creating peak regions took 52.7910029888 s Estimating background... Estimating background took 20.9749968052 s Processing 22RV1_C19_ChIPexo-Rep2-GSM2643242/aligned.36mers.unique.bam Reading in data... Reading data took 0.750174999237 s Creating peak regions... Creating peak regions took 17.3216888905 s Estimating background... Estimating background took 3.04597306252 s Estimating background took 134.723259211 s Processing 22RV1_C19_ChIPexo-Rep2-GSM2643242/aligned.36mers.unique.bam Reading in data... Reading data took 11.4739189148 s Creating peak regions... Creating peak regions took 70.4784269333 s Estimating background... Estimating background took 80.8688700199 s Processing 22RV1_C19_ChIPexo-Rep2-GSM2643242/aligned.36mers.unique.bam Reading in data... Reading data took 11.6841299534 s Creating peak regions... Creating peak regions took 70.7334840298 s Estimating background... Estimating background took 79.2699520588 s Processing 22RV1_C19_ChIPexo-Rep2-GSM2643242/aligned.36mers.unique.bam Reading in data... Reading data took 10.4927120209 s Creating peak regions... Creating peak regions took 67.6279270649 s Estimating background... Estimating background took 70.0890769958 s Processing 22RV1_C19_ChIPexo-Rep2-GSM2643242/aligned.36mers.unique.bam Reading in data... Reading data took 11.6796290874 s Creating peak regions... Creating peak regions took 62.9921631813 s Estimating background... Estimating background took 118.259258032 s Processing 22RV1_C19_ChIPexo-Rep2-GSM2643242/aligned.36mers.unique.bam Reading in data... Reading data took 11.8197641373 s Creating peak regions... Creating peak regions took 59.3512117863 s Estimating background... Estimating background took 106.46122694 s Processing 22RV1_C19_ChIPexo-Rep2-GSM2643242/aligned.36mers.unique.bam Reading in data... Reading data took 7.04807305336 s Creating peak regions... Creating peak regions took 49.5583899021 s Estimating background... Estimating background took 42.2023239136 s Processing 22RV1_C19_ChIPexo-Rep2-GSM2643242/aligned.36mers.unique.bam Reading in data... Reading data took 0.485593080521 s Creating peak regions... Creating peak regions took 0.537515878677 s Estimating background... Estimating background took 1.10196304321 s Processing 22RV1_C19_ChIPexo-Rep2-GSM2643242/aligned.36mers.unique.bam Reading in data... Reading data took 5.35905003548 s Creating peak regions... Creating peak regions took 50.5494029522 s Estimating background... Estimating background took 21.0686640739 s Processing 22RV1_C19_ChIPexo-Rep2-GSM2643242/aligned.36mers.unique.bam Reading in data... Reading data took 0.726974964142 s Creating peak regions... Creating peak regions took 16.985065937 s Estimating background... Estimating background took 5.32748198509 s