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='Rev-erbalpha_ChIP-exo_rep1-GSM1659703/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='Rev-erbalpha_ChIP-exo_rep1-GSM1659703/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 Rev-erbalpha_ChIP-exo_rep1-GSM1659703/alignments.36mers.unique.bam Reading in data... Reading data took 8.96127104759 s Creating peak regions... Creating peak regions took 37.4625759125 s Estimating background... Estimating background took 41.5340368748 s Processing Rev-erbalpha_ChIP-exo_rep1-GSM1659703/alignments.36mers.unique.bam Reading in data... Reading data took 11.1281490326 s Creating peak regions... Creating peak regions took 40.1827859879 s Estimating background... Estimating background took 52.8946239948 s Processing Rev-erbalpha_ChIP-exo_rep1-GSM1659703/alignments.36mers.unique.bam Reading in data... Reading data took 8.29006195068 s Creating peak regions... Creating peak regions took 35.2794349194 s Estimating background... Estimating background took 32.4605648518 s Processing Rev-erbalpha_ChIP-exo_rep1-GSM1659703/alignments.36mers.unique.bam Reading in data... Reading data took 8.02537488937 s Creating peak regions... Creating peak regions took 33.791806221 s Estimating background... Estimating background took 34.2490670681 s Processing Rev-erbalpha_ChIP-exo_rep1-GSM1659703/alignments.36mers.unique.bam Reading in data... Reading data took 7.8325688839 s Creating peak regions... Creating peak regions took 35.931000948 s Estimating background... Estimating background took 30.1819751263 s Processing Rev-erbalpha_ChIP-exo_rep1-GSM1659703/alignments.36mers.unique.bam Reading in data... Reading data took 7.18017292023 s Creating peak regions... Creating peak regions took 28.012611866 s Estimating background... Estimating background took 32.0770759583 s Processing Rev-erbalpha_ChIP-exo_rep1-GSM1659703/alignments.36mers.unique.bam Reading in data... Reading data took 6.09128308296 s Creating peak regions... Creating peak regions took 29.2060980797 s Estimating background... Estimating background took 27.4624209404 s Processing Rev-erbalpha_ChIP-exo_rep1-GSM1659703/alignments.36mers.unique.bam Reading in data... Reading data took 6.58328199387 s Creating peak regions... Creating peak regions took 27.4666450024 s Estimating background... Estimating background took 30.8460719585 s Processing Rev-erbalpha_ChIP-exo_rep1-GSM1659703/alignments.36mers.unique.bam Reading in data... Reading data took 5.54230713844 s Creating peak regions... Creating peak regions took 25.1603929996 s Estimating background... Estimating background took 23.6835148335 s Processing Rev-erbalpha_ChIP-exo_rep1-GSM1659703/alignments.36mers.unique.bam Reading in data... Reading data took 5.22479295731 s Creating peak regions... Creating peak regions took 19.4310281277 s Estimating background... Estimating background took 27.1480140686 s Processing Rev-erbalpha_ChIP-exo_rep1-GSM1659703/alignments.36mers.unique.bam Reading in data... Reading data took 13.3189067841 s Creating peak regions... Creating peak regions took 56.6217229366 s Estimating background... Estimating background took 54.5141050816 s Processing Rev-erbalpha_ChIP-exo_rep1-GSM1659703/alignments.36mers.unique.bam Reading in data... Reading data took 0.177972793579 s Creating peak regions... Creating peak regions took 0.419828891754 s Estimating background... Estimating background took 0.263978004456 s Processing Rev-erbalpha_ChIP-exo_rep1-GSM1659703/alignments.36mers.unique.bam Reading in data... Reading data took 0.0807828903198 s Creating peak regions... Creating peak regions took 0.322564125061 s Estimating background... Estimating background took 0.259141921997 s Processing Rev-erbalpha_ChIP-exo_rep1-GSM1659703/alignments.36mers.unique.bam Reading in data... Reading data took 0.0668859481812 s Creating peak regions... Creating peak regions took 0.207230806351 s Estimating background... Estimating background took 0.274068832397 s Processing Rev-erbalpha_ChIP-exo_rep1-GSM1659703/alignments.36mers.unique.bam Reading in data... Processing Rev-erbalpha_ChIP-exo_rep1-GSM1659703/alignments.36mers.unique.bam Reading in data... Reading data took 0.0501959323883 s Creating peak regions... Creating peak regions took 0.256838083267 s Estimating background... Estimating background took 0.259178161621 s Processing Rev-erbalpha_ChIP-exo_rep1-GSM1659703/alignments.36mers.unique.bam Reading in data... Reading data took 14.4809908867 s Creating peak regions... Creating peak regions took 52.7087118626 s Estimating background... Estimating background took 60.8957560062 s Processing Rev-erbalpha_ChIP-exo_rep1-GSM1659703/alignments.36mers.unique.bam Reading in data... Reading data took 10.6492791176 s Creating peak regions... Creating peak regions took 48.3606259823 s Estimating background... Estimating background took 43.9711670876 s Processing Rev-erbalpha_ChIP-exo_rep1-GSM1659703/alignments.36mers.unique.bam Reading in data... Reading data took 12.1745080948 s Creating peak regions... Creating peak regions took 51.6741440296 s Estimating background... Estimating background took 56.8679602146 s Processing Rev-erbalpha_ChIP-exo_rep1-GSM1659703/alignments.36mers.unique.bam Reading in data... Reading data took 0.3267390728 s Creating peak regions... Creating peak regions took 0.266631126404 s Estimating background... Estimating background took 0.351897954941 s Processing Rev-erbalpha_ChIP-exo_rep1-GSM1659703/alignments.36mers.unique.bam Reading in data... Processing Rev-erbalpha_ChIP-exo_rep1-GSM1659703/alignments.36mers.unique.bam Reading in data... Reading data took 0.0539259910583 s Creating peak regions... Creating peak regions took 0.0231781005859 s Estimating background... Estimating background took 0.370035886765 s Processing Rev-erbalpha_ChIP-exo_rep1-GSM1659703/alignments.36mers.unique.bam Reading in data... Processing Rev-erbalpha_ChIP-exo_rep1-GSM1659703/alignments.36mers.unique.bam Reading in data... Processing Rev-erbalpha_ChIP-exo_rep1-GSM1659703/alignments.36mers.unique.bam Reading in data... Reading data took 0.0613899230957 s Creating peak regions... Creating peak regions took 0.00292015075684 s Estimating background... Estimating background took 0.352066993713 s Processing Rev-erbalpha_ChIP-exo_rep1-GSM1659703/alignments.36mers.unique.bam Reading in data... Reading data took 11.9248230457 s Creating peak regions... Creating peak regions took 46.6910920143 s Estimating background... Estimating background took 51.5096750259 s Processing Rev-erbalpha_ChIP-exo_rep1-GSM1659703/alignments.36mers.unique.bam Reading in data... Reading data took 0.399708986282 s Creating peak regions... Creating peak regions took 0.330407857895 s Estimating background... Estimating background took 0.33895111084 s Processing Rev-erbalpha_ChIP-exo_rep1-GSM1659703/alignments.36mers.unique.bam Reading in data... Reading data took 0.0735011100769 s Creating peak regions... Creating peak regions took 0.264535903931 s Estimating background... Estimating background took 0.35177898407 s Processing Rev-erbalpha_ChIP-exo_rep1-GSM1659703/alignments.36mers.unique.bam Reading in data... Reading data took 0.0514049530029 s Creating peak regions... Creating peak regions took 0.221341133118 s Estimating background... Estimating background took 0.346543073654 s Processing Rev-erbalpha_ChIP-exo_rep1-GSM1659703/alignments.36mers.unique.bam Reading in data... Processing Rev-erbalpha_ChIP-exo_rep1-GSM1659703/alignments.36mers.unique.bam Reading in data... Reading data took 0.055281162262 s Creating peak regions... Creating peak regions took 1.11607003212 s Estimating background... Estimating background took 0.3797519207 s Processing Rev-erbalpha_ChIP-exo_rep1-GSM1659703/alignments.36mers.unique.bam Reading in data... Reading data took 11.2838759422 s Creating peak regions... Creating peak regions took 48.8152639866 s Estimating background... Estimating background took 49.8782539368 s Processing Rev-erbalpha_ChIP-exo_rep1-GSM1659703/alignments.36mers.unique.bam Reading in data... Reading data took 11.1223809719 s Creating peak regions... Creating peak regions took 44.9376451969 s Estimating background... Estimating background took 47.1122908592 s Processing Rev-erbalpha_ChIP-exo_rep1-GSM1659703/alignments.36mers.unique.bam Reading in data... Processing Rev-erbalpha_ChIP-exo_rep1-GSM1659703/alignments.36mers.unique.bam Reading in data... Reading data took 8.975522995 s Creating peak regions... Creating peak regions took 37.9821500778 s Estimating background... Estimating background took 44.4909198284 s Processing Rev-erbalpha_ChIP-exo_rep1-GSM1659703/alignments.36mers.unique.bam Reading in data... Reading data took 10.3812940121 s Creating peak regions... Creating peak regions took 38.0594658852 s Estimating background... Estimating background took 45.9256689548 s Processing Rev-erbalpha_ChIP-exo_rep1-GSM1659703/alignments.36mers.unique.bam Reading in data... Reading data took 1.02979898453 s Creating peak regions... Creating peak regions took 0.267624139786 s Estimating background... Estimating background took 1.71649980545 s Processing Rev-erbalpha_ChIP-exo_rep1-GSM1659703/alignments.36mers.unique.bam Reading in data... Reading data took 0.0775079727173 s Creating peak regions... Creating peak regions took 0.0685079097748 s Estimating background... Estimating background took 0.364732027054 s Processing Rev-erbalpha_ChIP-exo_rep1-GSM1659703/alignments.36mers.unique.bam Reading in data... Reading data took 0.0589570999146 s Creating peak regions... Creating peak regions took 0.0588600635529 s Estimating background... Estimating background took 0.377551078796 s Processing Rev-erbalpha_ChIP-exo_rep1-GSM1659703/alignments.36mers.unique.bam Reading in data... Reading data took 0.0557808876038 s Creating peak regions... Creating peak regions took 0.053551197052 s Estimating background... Estimating background took 0.372576951981 s Processing Rev-erbalpha_ChIP-exo_rep1-GSM1659703/alignments.36mers.unique.bam Reading in data... Reading data took 0.0789639949799 s Creating peak regions... Creating peak regions took 0.0843069553375 s Estimating background... Estimating background took 0.352790117264 s Processing Rev-erbalpha_ChIP-exo_rep1-GSM1659703/alignments.36mers.unique.bam Reading in data... Reading data took 0.0830888748169 s Creating peak regions... Creating peak regions took 0.0736758708954 s Estimating background... Estimating background took 0.364928007126 s Processing Rev-erbalpha_ChIP-exo_rep1-GSM1659703/alignments.36mers.unique.bam Reading in data... Reading data took 0.0833270549774 s Creating peak regions... Creating peak regions took 0.032900094986 s Estimating background... Estimating background took 0.367751121521 s Processing Rev-erbalpha_ChIP-exo_rep1-GSM1659703/alignments.36mers.unique.bam Reading in data... Reading data took 0.0796749591827 s Creating peak regions... Creating peak regions took 0.0424201488495 s Estimating background... Estimating background took 0.37136888504 s Processing Rev-erbalpha_ChIP-exo_rep1-GSM1659703/alignments.36mers.unique.bam Reading in data... Reading data took 0.0833089351654 s Creating peak regions... Creating peak regions took 0.0440080165863 s Estimating background... Estimating background took 0.413063049316 s Processing Rev-erbalpha_ChIP-exo_rep1-GSM1659703/alignments.36mers.unique.bam Reading in data... Reading data took 0.0858438014984 s Creating peak regions... Creating peak regions took 0.0562269687653 s Estimating background... Estimating background took 0.364773988724 s Processing Rev-erbalpha_ChIP-exo_rep1-GSM1659703/alignments.36mers.unique.bam Reading in data... Reading data took 0.0591430664062 s Creating peak regions... Creating peak regions took 0.112077951431 s Estimating background... Estimating background took 0.367630004883 s Processing Rev-erbalpha_ChIP-exo_rep1-GSM1659703/alignments.36mers.unique.bam Reading in data... Reading data took 0.054967880249 s Creating peak regions... Creating peak regions took 0.0364849567413 s Estimating background... Estimating background took 0.345072031021 s Processing Rev-erbalpha_ChIP-exo_rep1-GSM1659703/alignments.36mers.unique.bam Reading in data... Reading data took 0.0587551593781 s Creating peak regions... Creating peak regions took 0.0325090885162 s Estimating background... Estimating background took 0.355142116547 s Processing Rev-erbalpha_ChIP-exo_rep1-GSM1659703/alignments.36mers.unique.bam Reading in data... Reading data took 0.111012220383 s Creating peak regions... Creating peak regions took 0.101356983185 s Estimating background... Estimating background took 0.356727838516 s Processing Rev-erbalpha_ChIP-exo_rep1-GSM1659703/alignments.36mers.unique.bam Reading in data... Reading data took 0.0830979347229 s Creating peak regions... Creating peak regions took 0.0530569553375 s Estimating background... Estimating background took 0.370079040527 s Processing Rev-erbalpha_ChIP-exo_rep1-GSM1659703/alignments.36mers.unique.bam Reading in data... Reading data took 0.0792298316956 s Creating peak regions... Creating peak regions took 0.0408630371094 s Estimating background... Estimating background took 0.369114875793 s Processing Rev-erbalpha_ChIP-exo_rep1-GSM1659703/alignments.36mers.unique.bam Reading in data... Reading data took 0.31737780571 s Creating peak regions... Creating peak regions took 0.0591561794281 s Estimating background... Estimating background took 0.463387012482 s Processing Rev-erbalpha_ChIP-exo_rep1-GSM1659703/alignments.36mers.unique.bam Reading in data... Reading data took 0.0689158439636 s Creating peak regions... Creating peak regions took 0.0674331188202 s Estimating background... Estimating background took 0.354240894318 s Processing Rev-erbalpha_ChIP-exo_rep1-GSM1659703/alignments.36mers.unique.bam Reading in data... Reading data took 0.130802869797 s Creating peak regions... Creating peak regions took 0.0470290184021 s Estimating background... Estimating background took 0.326678037643 s Processing Rev-erbalpha_ChIP-exo_rep1-GSM1659703/alignments.36mers.unique.bam Reading in data... Reading data took 0.0771930217743 s Creating peak regions... Creating peak regions took 0.114806890488 s Estimating background... Estimating background took 0.331328868866 s Processing Rev-erbalpha_ChIP-exo_rep1-GSM1659703/alignments.36mers.unique.bam Reading in data... Reading data took 0.0540449619293 s Creating peak regions... Creating peak regions took 0.034921169281 s Estimating background... Estimating background took 0.354841947556 s Processing Rev-erbalpha_ChIP-exo_rep1-GSM1659703/alignments.36mers.unique.bam Reading in data... Reading data took 0.090390920639 s Creating peak regions... Creating peak regions took 0.0730469226837 s Estimating background... Estimating background took 0.354650020599 s Processing Rev-erbalpha_ChIP-exo_rep1-GSM1659703/alignments.36mers.unique.bam Reading in data... Reading data took 0.233342170715 s Creating peak regions... Creating peak regions took 0.179358005524 s Estimating background... Estimating background took 0.861763000488 s Processing Rev-erbalpha_ChIP-exo_rep1-GSM1659703/alignments.36mers.unique.bam Reading in data... Reading data took 5.45988512039 s Creating peak regions... Creating peak regions took 57.9322311878 s Estimating background... Estimating background took 7.83471393585 s Processing Rev-erbalpha_ChIP-exo_rep1-GSM1659703/alignments.36mers.unique.bam Reading in data... Reading data took 0.502882957458 s Creating peak regions... Creating peak regions took 0.512732982635 s Estimating background... Estimating background took 0.372544050217 s Processing Rev-erbalpha_ChIP-exo_rep1-GSM1659703/alignments.36mers.unique.bam Reading in data... Reading data took 0.247840881348 s Creating peak regions... Creating peak regions took 32.8437421322 s Estimating background... Estimating background took 0.56230711937 s Processing Rev-erbalpha_ChIP-exo_rep1-GSM1659703/alignments.36mers.unique.bam Reading in data... Processing Rev-erbalpha_ChIP-exo_rep1-GSM1659703/alignments.36mers.unique.bam Reading in data... Processing Rev-erbalpha_ChIP-exo_rep1-GSM1659703/alignments.36mers.unique.bam Reading in data... Processing Rev-erbalpha_ChIP-exo_rep1-GSM1659703/alignments.36mers.unique.bam Reading in data...