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/mm10.blacklist.bed', center6=0, chromnames='/oak/stanford/groups/akundaje/marinovg/genomes/mm10/mm10.chrom.sizes', e4='PeakXus', fastq='Mouse_ChIP_Exo-GSM1582728/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='Mouse_ChIP_Exo-GSM1582728/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/mm10.blacklist.bed', center6=0, chromnames='/oak/stanford/groups/akundaje/marinovg/genomes/mm10/mm10.chrom.sizes', e4='PeakXus', fastq='Mouse_ChIP_Exo-GSM1582728/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='Mouse_ChIP_Exo-GSM1582728/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 Mouse_ChIP_Exo-GSM1582728/aligned.36mers.unique.bam Reading in data... Reading data took 10.2643430233 s Creating peak regions... Creating peak regions took 34.4808158875 s Estimating background... Estimating background took 27.3640780449 s Processing Mouse_ChIP_Exo-GSM1582728/aligned.36mers.unique.bam Reading in data... Reading data took 9.5234310627 s Creating peak regions... Creating peak regions took 32.3811578751 s Estimating background... Estimating background took 25.8491268158 s Processing Mouse_ChIP_Exo-GSM1582728/aligned.36mers.unique.bam Reading in data... Reading data took 8.79347610474 s Creating peak regions... Creating peak regions took 36.3455297947 s Estimating background... Estimating background took 24.8362510204 s Processing Mouse_ChIP_Exo-GSM1582728/aligned.36mers.unique.bam Reading in data... Reading data took 10.1327149868 s Creating peak regions... Creating peak regions took 40.127117157 s Estimating background... Estimating background took 25.8122839928 s Processing Mouse_ChIP_Exo-GSM1582728/aligned.36mers.unique.bam Reading in data... Reading data took 9.50730013847 s Creating peak regions... Creating peak regions took 33.8852250576 s Estimating background... Estimating background took 24.7399349213 s Processing Mouse_ChIP_Exo-GSM1582728/aligned.36mers.unique.bam Reading in data... Reading data took 8.58312296867 s Creating peak regions... Creating peak regions took 28.9139540195 s Estimating background... Estimating background took 22.1329090595 s Processing Mouse_ChIP_Exo-GSM1582728/aligned.36mers.unique.bam Reading in data... Reading data took 8.52691698074 s Creating peak regions... Creating peak regions took 30.743792057 s Estimating background... Estimating background took 23.1036229134 s Processing Mouse_ChIP_Exo-GSM1582728/aligned.36mers.unique.bam Reading in data... Reading data took 7.72822284698 s Creating peak regions... Creating peak regions took 28.1088871956 s Estimating background... Estimating background took 19.5183060169 s Processing Mouse_ChIP_Exo-GSM1582728/aligned.36mers.unique.bam Reading in data... Reading data took 7.59608006477 s Creating peak regions... Creating peak regions took 25.941986084 s Estimating background... Estimating background took 19.2049160004 s Processing Mouse_ChIP_Exo-GSM1582728/aligned.36mers.unique.bam Reading in data... Reading data took 5.72342896461 s Creating peak regions... Creating peak regions took 17.8419599533 s Estimating background... Estimating background took 13.835586071 s Processing Mouse_ChIP_Exo-GSM1582728/aligned.36mers.unique.bam Reading in data... Reading data took 15.9424550533 s Creating peak regions... Creating peak regions took 59.519477129 s Estimating background... Estimating background took 44.8150610924 s Processing Mouse_ChIP_Exo-GSM1582728/aligned.36mers.unique.bam Reading in data... Reading data took 0.295079946518 s Creating peak regions... Creating peak regions took 1.11804318428 s Estimating background... Estimating background took 0.329559087753 s Processing Mouse_ChIP_Exo-GSM1582728/aligned.36mers.unique.bam Reading in data... Reading data took 0.0839238166809 s Creating peak regions... Creating peak regions took 0.436252117157 s Estimating background... Estimating background took 0.322607040405 s Processing Mouse_ChIP_Exo-GSM1582728/aligned.36mers.unique.bam Reading in data... Reading data took 0.0627701282501 s Creating peak regions... Creating peak regions took 0.26079916954 s Estimating background... Estimating background took 0.321847915649 s Processing Mouse_ChIP_Exo-GSM1582728/aligned.36mers.unique.bam Reading in data... Processing Mouse_ChIP_Exo-GSM1582728/aligned.36mers.unique.bam Reading in data... Reading data took 0.0605010986328 s Creating peak regions... Creating peak regions took 0.329274177551 s Estimating background... Estimating background took 0.309334039688 s Processing Mouse_ChIP_Exo-GSM1582728/aligned.36mers.unique.bam Reading in data... Reading data took 19.471763134 s Creating peak regions... Creating peak regions took 55.1225509644 s Estimating background... Estimating background took 41.9117882252 s Processing Mouse_ChIP_Exo-GSM1582728/aligned.36mers.unique.bam Reading in data... Reading data took 13.6438510418 s Creating peak regions... Creating peak regions took 51.0253210068 s Estimating background... Estimating background took 36.4855568409 s Processing Mouse_ChIP_Exo-GSM1582728/aligned.36mers.unique.bam Reading in data... Reading data took 13.2964098454 s Creating peak regions... Creating peak regions took 48.0599889755 s Estimating background... Estimating background took 35.2091360092 s Processing Mouse_ChIP_Exo-GSM1582728/aligned.36mers.unique.bam Reading in data... Reading data took 0.354686975479 s Creating peak regions... Creating peak regions took 0.301698923111 s Estimating background... Estimating background took 0.330441951752 s Processing Mouse_ChIP_Exo-GSM1582728/aligned.36mers.unique.bam Reading in data... Processing Mouse_ChIP_Exo-GSM1582728/aligned.36mers.unique.bam Reading in data... Reading data took 0.0436978340149 s Creating peak regions... Creating peak regions took 0.0219171047211 s Estimating background... Estimating background took 0.313478946686 s Processing Mouse_ChIP_Exo-GSM1582728/aligned.36mers.unique.bam Reading in data... Processing Mouse_ChIP_Exo-GSM1582728/aligned.36mers.unique.bam Reading in data... Processing Mouse_ChIP_Exo-GSM1582728/aligned.36mers.unique.bam Reading in data... Reading data took 0.0504310131073 s Creating peak regions... Creating peak regions took 0.00253415107727 s Estimating background... Estimating background took 0.311918973923 s Processing Mouse_ChIP_Exo-GSM1582728/aligned.36mers.unique.bam Reading in data... Reading data took 14.2035610676 s Creating peak regions... Creating peak regions took 45.418211937 s Estimating background... Estimating background took 34.4382100105 s Processing Mouse_ChIP_Exo-GSM1582728/aligned.36mers.unique.bam Reading in data... Reading data took 0.542727947235 s Creating peak regions... Creating peak regions took 0.545331954956 s Estimating background... Estimating background took 0.367523908615 s Processing Mouse_ChIP_Exo-GSM1582728/aligned.36mers.unique.bam Reading in data... Reading data took 0.0733411312103 s Creating peak regions... Creating peak regions took 0.277931928635 s Estimating background... Estimating background took 0.351284980774 s Processing Mouse_ChIP_Exo-GSM1582728/aligned.36mers.unique.bam Reading in data... Reading data took 0.0818741321564 s Creating peak regions... Creating peak regions took 0.337294101715 s Estimating background... Estimating background took 0.360970973969 s Processing Mouse_ChIP_Exo-GSM1582728/aligned.36mers.unique.bam Reading in data... Processing Mouse_ChIP_Exo-GSM1582728/aligned.36mers.unique.bam Reading in data... Reading data took 0.0606591701508 s Creating peak regions... Creating peak regions took 1.9787209034 s Estimating background... Estimating background took 0.352313995361 s Processing Mouse_ChIP_Exo-GSM1582728/aligned.36mers.unique.bam Reading in data... Reading data took 14.1360588074 s Creating peak regions... Creating peak regions took 47.4297599792 s Estimating background... Estimating background took 34.4069750309 s Processing Mouse_ChIP_Exo-GSM1582728/aligned.36mers.unique.bam Reading in data... Reading data took 10.0154919624 s Creating peak regions... Creating peak regions took 38.5173761845 s Estimating background... Estimating background took 28.535599947 s Processing Mouse_ChIP_Exo-GSM1582728/aligned.36mers.unique.bam Reading in data... Processing Mouse_ChIP_Exo-GSM1582728/aligned.36mers.unique.bam Reading in data... Reading data took 9.86325311661 s Creating peak regions... Creating peak regions took 37.2200548649 s Estimating background... Estimating background took 27.5170071125 s Processing Mouse_ChIP_Exo-GSM1582728/aligned.36mers.unique.bam Reading in data... Reading data took 10.3262090683 s Creating peak regions... Creating peak regions took 36.0595037937 s Estimating background... Estimating background took 28.422878027 s Processing Mouse_ChIP_Exo-GSM1582728/aligned.36mers.unique.bam Reading in data... Reading data took 0.622386932373 s Creating peak regions... Creating peak regions took 0.374840021133 s Estimating background... Estimating background took 0.39734005928 s Processing Mouse_ChIP_Exo-GSM1582728/aligned.36mers.unique.bam Reading in data... Reading data took 0.0999228954315 s Creating peak regions... Creating peak regions took 0.0820271968842 s Estimating background... Estimating background took 0.362362146378 s Processing Mouse_ChIP_Exo-GSM1582728/aligned.36mers.unique.bam Reading in data... Reading data took 0.0571889877319 s Creating peak regions... Creating peak regions took 0.0422449111938 s Estimating background... Estimating background took 0.397691011429 s Processing Mouse_ChIP_Exo-GSM1582728/aligned.36mers.unique.bam Reading in data... Reading data took 0.0726139545441 s Creating peak regions... Creating peak regions took 0.061558008194 s Estimating background... Estimating background took 0.338891983032 s Processing Mouse_ChIP_Exo-GSM1582728/aligned.36mers.unique.bam Reading in data... Reading data took 0.0813457965851 s Creating peak regions... Creating peak regions took 0.0860180854797 s Estimating background... Estimating background took 0.377169132233 s Processing Mouse_ChIP_Exo-GSM1582728/aligned.36mers.unique.bam Reading in data... Reading data took 0.0875511169434 s Creating peak regions... Creating peak regions took 0.10090303421 s Estimating background... Estimating background took 0.391133069992 s Processing Mouse_ChIP_Exo-GSM1582728/aligned.36mers.unique.bam Reading in data... Reading data took 0.078006029129 s Creating peak regions... Creating peak regions took 0.0352118015289 s Estimating background... Estimating background took 0.375053882599 s Processing Mouse_ChIP_Exo-GSM1582728/aligned.36mers.unique.bam Reading in data... Reading data took 0.066535949707 s Creating peak regions... Creating peak regions took 0.0817539691925 s Estimating background... Estimating background took 0.38699388504 s Processing Mouse_ChIP_Exo-GSM1582728/aligned.36mers.unique.bam Reading in data... Reading data took 0.0770189762115 s Creating peak regions... Creating peak regions took 0.0457789897919 s Estimating background... Estimating background took 0.340112924576 s Processing Mouse_ChIP_Exo-GSM1582728/aligned.36mers.unique.bam Reading in data... Reading data took 0.0840058326721 s Creating peak regions... Creating peak regions took 0.0746819972992 s Estimating background... Estimating background took 0.340731859207 s Processing Mouse_ChIP_Exo-GSM1582728/aligned.36mers.unique.bam Reading in data... Reading data took 0.0828931331635 s Creating peak regions... Creating peak regions took 0.1190969944 s Estimating background... Estimating background took 0.341346025467 s Processing Mouse_ChIP_Exo-GSM1582728/aligned.36mers.unique.bam Reading in data... Reading data took 0.0822348594666 s Creating peak regions... Creating peak regions took 0.0464079380035 s Estimating background... Estimating background took 0.340563058853 s Processing Mouse_ChIP_Exo-GSM1582728/aligned.36mers.unique.bam Reading in data... Reading data took 0.0808539390564 s Creating peak regions... Creating peak regions took 0.0376269817352 s Estimating background... Estimating background took 0.372838020325 s Processing Mouse_ChIP_Exo-GSM1582728/aligned.36mers.unique.bam Reading in data... Reading data took 0.147763967514 s Creating peak regions... Creating peak regions took 0.0729959011078 s Estimating background... Estimating background took 0.515910148621 s Processing Mouse_ChIP_Exo-GSM1582728/aligned.36mers.unique.bam Reading in data... Reading data took 0.0704250335693 s Creating peak regions... Creating peak regions took 0.0590651035309 s Estimating background... Estimating background took 0.41003704071 s Processing Mouse_ChIP_Exo-GSM1582728/aligned.36mers.unique.bam Reading in data... Reading data took 0.0710990428925 s Creating peak regions... Creating peak regions took 0.0555210113525 s Estimating background... Estimating background took 0.411206007004 s Processing Mouse_ChIP_Exo-GSM1582728/aligned.36mers.unique.bam Reading in data... Reading data took 0.669622182846 s Creating peak regions... Creating peak regions took 0.0324580669403 s Estimating background... Estimating background took 0.598758935928 s Processing Mouse_ChIP_Exo-GSM1582728/aligned.36mers.unique.bam Reading in data... Reading data took 0.0952498912811 s Creating peak regions... Creating peak regions took 0.0518741607666 s Estimating background... Estimating background took 0.343101978302 s Processing Mouse_ChIP_Exo-GSM1582728/aligned.36mers.unique.bam Reading in data... Reading data took 0.299868106842 s Creating peak regions... Creating peak regions took 0.0280110836029 s Estimating background... Estimating background took 0.449194908142 s Processing Mouse_ChIP_Exo-GSM1582728/aligned.36mers.unique.bam Reading in data... Reading data took 0.116816043854 s Creating peak regions... Creating peak regions took 0.0924241542816 s Estimating background... Estimating background took 0.34154009819 s Processing Mouse_ChIP_Exo-GSM1582728/aligned.36mers.unique.bam Reading in data... Reading data took 0.0807750225067 s Creating peak regions... Creating peak regions took 0.0443449020386 s Estimating background... Estimating background took 0.341694831848 s Processing Mouse_ChIP_Exo-GSM1582728/aligned.36mers.unique.bam Reading in data... Reading data took 0.108212947845 s Creating peak regions... Creating peak regions took 0.0492348670959 s Estimating background... Estimating background took 0.337697029114 s Processing Mouse_ChIP_Exo-GSM1582728/aligned.36mers.unique.bam Reading in data... Reading data took 0.349786996841 s Creating peak regions... Creating peak regions took 0.17954993248 s Estimating background... Estimating background took 0.861138105392 s Processing Mouse_ChIP_Exo-GSM1582728/aligned.36mers.unique.bam Reading in data... Reading data took 7.97553896904 s Creating peak regions... Creating peak regions took 46.1243400574 s Estimating background... Estimating background took 13.4364352226 s Processing Mouse_ChIP_Exo-GSM1582728/aligned.36mers.unique.bam Reading in data... Reading data took 0.191203117371 s Creating peak regions... Creating peak regions took 0.391760110855 s Estimating background... Estimating background took 0.347741127014 s Processing Mouse_ChIP_Exo-GSM1582728/aligned.36mers.unique.bam Reading in data... Reading data took 0.497435092926 s Creating peak regions... Creating peak regions took 26.6443858147 s Estimating background... Estimating background took 4.20175504684 s Processing Mouse_ChIP_Exo-GSM1582728/aligned.36mers.unique.bam Reading in data... Processing Mouse_ChIP_Exo-GSM1582728/aligned.36mers.unique.bam Reading in data... Processing Mouse_ChIP_Exo-GSM1582728/aligned.36mers.unique.bam Reading in data... Processing Mouse_ChIP_Exo-GSM1582728/aligned.36mers.unique.bam Reading in data...