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='exo_BATF_rep2-GSM2259185/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='exo_BATF_rep2-GSM2259185/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 exo_BATF_rep2-GSM2259185/aligned.36mers.unique.bam Reading in data... Reading data took 3.63102293015 s Creating peak regions... Creating peak regions took 34.1217548847 s Estimating background... Estimating background took 17.0933229923 s Processing exo_BATF_rep2-GSM2259185/aligned.36mers.unique.bam Reading in data... Reading data took 3.70552301407 s Creating peak regions... Creating peak regions took 32.0521409512 s Estimating background... Estimating background took 18.2806861401 s Processing exo_BATF_rep2-GSM2259185/aligned.36mers.unique.bam Reading in data... Reading data took 3.47397017479 s Creating peak regions... Creating peak regions took 33.8700578213 s Estimating background... Estimating background took 13.6154191494 s Processing exo_BATF_rep2-GSM2259185/aligned.36mers.unique.bam Reading in data... Reading data took 2.76429486275 s Creating peak regions... Creating peak regions took 29.4073610306 s Estimating background... Estimating background took 14.962033987 s Processing exo_BATF_rep2-GSM2259185/aligned.36mers.unique.bam Reading in data... Reading data took 2.73036599159 s Creating peak regions... Creating peak regions took 35.3427610397 s Estimating background... Estimating background took 12.3733448982 s Processing exo_BATF_rep2-GSM2259185/aligned.36mers.unique.bam Reading in data... Reading data took 2.82938194275 s Creating peak regions... Creating peak regions took 32.1668968201 s Estimating background... Estimating background took 12.8598690033 s Processing exo_BATF_rep2-GSM2259185/aligned.36mers.unique.bam Reading in data... Reading data took 2.97727203369 s Creating peak regions... Creating peak regions took 28.4412369728 s Estimating background... Estimating background took 12.6251480579 s Processing exo_BATF_rep2-GSM2259185/aligned.36mers.unique.bam Reading in data... Reading data took 2.55654907227 s Creating peak regions... Creating peak regions took 29.2130949497 s Estimating background... Estimating background took 12.4118411541 s Processing exo_BATF_rep2-GSM2259185/aligned.36mers.unique.bam Reading in data... Reading data took 2.41247200966 s Creating peak regions... Creating peak regions took 26.2290768623 s Estimating background... Estimating background took 10.3572788239 s Processing exo_BATF_rep2-GSM2259185/aligned.36mers.unique.bam Reading in data... Reading data took 1.88800001144 s Creating peak regions... Creating peak regions took 19.2202708721 s Estimating background... Estimating background took 8.21775197983 s Processing exo_BATF_rep2-GSM2259185/aligned.36mers.unique.bam Reading in data... Reading data took 5.40299606323 s Creating peak regions... Creating peak regions took 57.3922669888 s Estimating background... Estimating background took 22.8982231617 s Processing exo_BATF_rep2-GSM2259185/aligned.36mers.unique.bam Reading in data... Reading data took 0.0939340591431 s Creating peak regions... Creating peak regions took 0.345017194748 s Estimating background... Estimating background took 0.268582105637 s Processing exo_BATF_rep2-GSM2259185/aligned.36mers.unique.bam Reading in data... Reading data took 0.0776438713074 s Creating peak regions... Creating peak regions took 0.353723049164 s Estimating background... Estimating background took 0.275882005692 s Processing exo_BATF_rep2-GSM2259185/aligned.36mers.unique.bam Reading in data... Reading data took 0.0795359611511 s Creating peak regions... Creating peak regions took 0.265691041946 s Estimating background... Estimating background took 0.287327051163 s Processing exo_BATF_rep2-GSM2259185/aligned.36mers.unique.bam Reading in data... Processing exo_BATF_rep2-GSM2259185/aligned.36mers.unique.bam Reading in data... Reading data took 0.0516669750214 s Creating peak regions... Creating peak regions took 0.306376934052 s Estimating background... Estimating background took 0.268656015396 s Processing exo_BATF_rep2-GSM2259185/aligned.36mers.unique.bam Reading in data... Reading data took 5.89632701874 s Creating peak regions... Creating peak regions took 50.5116579533 s Estimating background... Estimating background took 24.575507164 s Processing exo_BATF_rep2-GSM2259185/aligned.36mers.unique.bam Reading in data... Reading data took 4.45838093758 s Creating peak regions... Creating peak regions took 47.985886097 s Estimating background... Estimating background took 19.1563489437 s Processing exo_BATF_rep2-GSM2259185/aligned.36mers.unique.bam Reading in data... Reading data took 4.23690915108 s Creating peak regions... Creating peak regions took 48.3065259457 s Estimating background... Estimating background took 18.3143458366 s Processing exo_BATF_rep2-GSM2259185/aligned.36mers.unique.bam Reading in data... Reading data took 0.242264986038 s Creating peak regions... Creating peak regions took 0.315033912659 s Estimating background... Estimating background took 0.339551925659 s Processing exo_BATF_rep2-GSM2259185/aligned.36mers.unique.bam Reading in data... Processing exo_BATF_rep2-GSM2259185/aligned.36mers.unique.bam Reading in data... Reading data took 0.0475430488586 s Creating peak regions... Creating peak regions took 0.019504070282 s Estimating background... Estimating background took 0.344915866852 s Processing exo_BATF_rep2-GSM2259185/aligned.36mers.unique.bam Reading in data... Processing exo_BATF_rep2-GSM2259185/aligned.36mers.unique.bam Reading in data... Processing exo_BATF_rep2-GSM2259185/aligned.36mers.unique.bam Reading in data... Reading data took 0.053307056427 s Creating peak regions... Creating peak regions took 0.00313496589661 s Estimating background... Estimating background took 0.330371856689 s Processing exo_BATF_rep2-GSM2259185/aligned.36mers.unique.bam Reading in data... Reading data took 4.80415582657 s Creating peak regions... Creating peak regions took 43.8563349247 s Estimating background... Estimating background took 17.8304970264 s Processing exo_BATF_rep2-GSM2259185/aligned.36mers.unique.bam Reading in data... Reading data took 0.265141010284 s Creating peak regions... Creating peak regions took 0.320536136627 s Estimating background... Estimating background took 0.323237895966 s Processing exo_BATF_rep2-GSM2259185/aligned.36mers.unique.bam Reading in data... Processing exo_BATF_rep2-GSM2259185/aligned.36mers.unique.bam Reading in data... Processing exo_BATF_rep2-GSM2259185/aligned.36mers.unique.bam Reading in data... Processing exo_BATF_rep2-GSM2259185/aligned.36mers.unique.bam Reading in data... Reading data took 0.0652809143066 s Creating peak regions... Creating peak regions took 1.08329892159 s Estimating background... Estimating background took 0.33830499649 s Processing exo_BATF_rep2-GSM2259185/aligned.36mers.unique.bam Reading in data... Reading data took 4.36495089531 s Creating peak regions... Creating peak regions took 47.3516719341 s Estimating background... Estimating background took 18.6783299446 s Processing exo_BATF_rep2-GSM2259185/aligned.36mers.unique.bam Reading in data... Reading data took 3.99732398987 s Creating peak regions... Creating peak regions took 46.1095819473 s Estimating background... Estimating background took 19.4495251179 s Processing exo_BATF_rep2-GSM2259185/aligned.36mers.unique.bam Reading in data... Processing exo_BATF_rep2-GSM2259185/aligned.36mers.unique.bam Reading in data... Reading data took 3.30920600891 s Creating peak regions... Creating peak regions took 35.788323164 s Estimating background... Estimating background took 14.4307780266 s Processing exo_BATF_rep2-GSM2259185/aligned.36mers.unique.bam Reading in data... Reading data took 4.24877595901 s Creating peak regions... Creating peak regions took 38.5286169052 s Estimating background... Estimating background took 18.1852779388 s Processing exo_BATF_rep2-GSM2259185/aligned.36mers.unique.bam Reading in data... Reading data took 0.25841999054 s Creating peak regions... Creating peak regions took 0.225899934769 s Estimating background... Estimating background took 0.862601995468 s Processing exo_BATF_rep2-GSM2259185/aligned.36mers.unique.bam Reading in data... Reading data took 0.0607621669769 s Creating peak regions... Creating peak regions took 0.0725300312042 s Estimating background... Estimating background took 0.334753036499 s Processing exo_BATF_rep2-GSM2259185/aligned.36mers.unique.bam Reading in data... Reading data took 0.0782179832458 s Creating peak regions... Creating peak regions took 0.0377850532532 s Estimating background... Estimating background took 0.348153114319 s Processing exo_BATF_rep2-GSM2259185/aligned.36mers.unique.bam Reading in data... Reading data took 0.0559577941895 s Creating peak regions... Creating peak regions took 0.0498809814453 s Estimating background... Estimating background took 0.355094909668 s Processing exo_BATF_rep2-GSM2259185/aligned.36mers.unique.bam Reading in data... Reading data took 0.06276512146 s Creating peak regions... Creating peak regions took 0.0678758621216 s Estimating background... Estimating background took 0.35164809227 s Processing exo_BATF_rep2-GSM2259185/aligned.36mers.unique.bam Reading in data... Reading data took 0.0833721160889 s Creating peak regions... Creating peak regions took 0.0969960689545 s Estimating background... Estimating background took 0.367030143738 s Processing exo_BATF_rep2-GSM2259185/aligned.36mers.unique.bam Reading in data... Reading data took 0.0794358253479 s Creating peak regions... Creating peak regions took 0.0367498397827 s Estimating background... Estimating background took 0.351802825928 s Processing exo_BATF_rep2-GSM2259185/aligned.36mers.unique.bam Reading in data... Reading data took 0.0595269203186 s Creating peak regions... Creating peak regions took 0.0415959358215 s Estimating background... Estimating background took 0.351131916046 s Processing exo_BATF_rep2-GSM2259185/aligned.36mers.unique.bam Reading in data... Reading data took 0.075474023819 s Creating peak regions... Creating peak regions took 0.0577530860901 s Estimating background... Estimating background took 0.355458021164 s Processing exo_BATF_rep2-GSM2259185/aligned.36mers.unique.bam Reading in data... Reading data took 0.05721616745 s Creating peak regions... Creating peak regions took 0.0459940433502 s Estimating background... Estimating background took 0.366279125214 s Processing exo_BATF_rep2-GSM2259185/aligned.36mers.unique.bam Reading in data... Reading data took 0.0587289333344 s Creating peak regions... Creating peak regions took 0.132817029953 s Estimating background... Estimating background took 0.360545158386 s Processing exo_BATF_rep2-GSM2259185/aligned.36mers.unique.bam Reading in data... Reading data took 0.0568389892578 s Creating peak regions... Creating peak regions took 0.040155172348 s Estimating background... Estimating background took 0.353074073792 s Processing exo_BATF_rep2-GSM2259185/aligned.36mers.unique.bam Reading in data... Reading data took 0.0566000938416 s Creating peak regions... Creating peak regions took 0.0441699028015 s Estimating background... Estimating background took 0.359784841537 s Processing exo_BATF_rep2-GSM2259185/aligned.36mers.unique.bam Reading in data... Reading data took 0.0732340812683 s Creating peak regions... Creating peak regions took 0.074581861496 s Estimating background... Estimating background took 0.357490062714 s Processing exo_BATF_rep2-GSM2259185/aligned.36mers.unique.bam Reading in data... Reading data took 0.056382894516 s Creating peak regions... Creating peak regions took 0.0502879619598 s Estimating background... Estimating background took 0.356915950775 s Processing exo_BATF_rep2-GSM2259185/aligned.36mers.unique.bam Reading in data... Reading data took 0.05677485466 s Creating peak regions... Creating peak regions took 0.0406088829041 s Estimating background... Estimating background took 0.366065979004 s Processing exo_BATF_rep2-GSM2259185/aligned.36mers.unique.bam Reading in data... Reading data took 0.293430089951 s Creating peak regions... Creating peak regions took 0.040431022644 s Estimating background... Estimating background took 0.458349943161 s Processing exo_BATF_rep2-GSM2259185/aligned.36mers.unique.bam Reading in data... Reading data took 0.0729849338531 s Creating peak regions... Creating peak regions took 0.0713729858398 s Estimating background... Estimating background took 0.337080955505 s Processing exo_BATF_rep2-GSM2259185/aligned.36mers.unique.bam Reading in data... Reading data took 0.130883932114 s Creating peak regions... Creating peak regions took 0.0488622188568 s Estimating background... Estimating background took 0.415951967239 s Processing exo_BATF_rep2-GSM2259185/aligned.36mers.unique.bam Reading in data... Reading data took 0.0594480037689 s Creating peak regions... Creating peak regions took 0.117416858673 s Estimating background... Estimating background took 0.310068130493 s Processing exo_BATF_rep2-GSM2259185/aligned.36mers.unique.bam Reading in data... Reading data took 0.0782730579376 s Creating peak regions... Creating peak regions took 0.0418770313263 s Estimating background... Estimating background took 0.311280965805 s Processing exo_BATF_rep2-GSM2259185/aligned.36mers.unique.bam Reading in data... Reading data took 0.0871818065643 s Creating peak regions... Creating peak regions took 0.0819931030273 s Estimating background... Estimating background took 0.320784807205 s Processing exo_BATF_rep2-GSM2259185/aligned.36mers.unique.bam Reading in data... Reading data took 0.122365951538 s Creating peak regions... Creating peak regions took 0.215586900711 s Estimating background... Estimating background took 0.613487958908 s Processing exo_BATF_rep2-GSM2259185/aligned.36mers.unique.bam Reading in data... Reading data took 3.43546295166 s Creating peak regions... Creating peak regions took 41.6123039722 s Estimating background... Estimating background took 12.4019041061 s Processing exo_BATF_rep2-GSM2259185/aligned.36mers.unique.bam Reading in data... Reading data took 0.108458995819 s Creating peak regions... Creating peak regions took 0.494080066681 s Estimating background... Estimating background took 0.366631984711 s Processing exo_BATF_rep2-GSM2259185/aligned.36mers.unique.bam Reading in data... Reading data took 0.0588030815125 s Creating peak regions... Creating peak regions took 23.7857558727 s Estimating background... Estimating background took 0.33030796051 s Processing exo_BATF_rep2-GSM2259185/aligned.36mers.unique.bam Reading in data... Processing exo_BATF_rep2-GSM2259185/aligned.36mers.unique.bam Reading in data... Processing exo_BATF_rep2-GSM2259185/aligned.36mers.unique.bam Reading in data... Processing exo_BATF_rep2-GSM2259185/aligned.36mers.unique.bam Reading in data...