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_rep4-GSM2259187/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_rep4-GSM2259187/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_rep4-GSM2259187/aligned.36mers.unique.bam Reading in data... Reading data took 3.63601517677 s Creating peak regions... Creating peak regions took 33.8477869034 s Estimating background... Estimating background took 10.1238741875 s Processing exo_BATF_rep4-GSM2259187/aligned.36mers.unique.bam Reading in data... Reading data took 3.55982303619 s Creating peak regions... Creating peak regions took 33.142925024 s Estimating background... Estimating background took 11.0337848663 s Processing exo_BATF_rep4-GSM2259187/aligned.36mers.unique.bam Reading in data... Reading data took 3.02577209473 s Creating peak regions... Creating peak regions took 34.1804039478 s Estimating background... Estimating background took 8.27790212631 s Processing exo_BATF_rep4-GSM2259187/aligned.36mers.unique.bam Reading in data... Reading data took 2.85950684547 s Creating peak regions... Creating peak regions took 31.495445013 s Estimating background... Estimating background took 9.14144897461 s Processing exo_BATF_rep4-GSM2259187/aligned.36mers.unique.bam Reading in data... Reading data took 2.97594118118 s Creating peak regions... Creating peak regions took 31.4704871178 s Estimating background... Estimating background took 8.25524997711 s Processing exo_BATF_rep4-GSM2259187/aligned.36mers.unique.bam Reading in data... Reading data took 2.58628487587 s Creating peak regions... Creating peak regions took 26.472258091 s Estimating background... Estimating background took 7.92433810234 s Processing exo_BATF_rep4-GSM2259187/aligned.36mers.unique.bam Reading in data... Reading data took 2.72580003738 s Creating peak regions... Creating peak regions took 25.4615800381 s Estimating background... Estimating background took 7.35632491112 s Processing exo_BATF_rep4-GSM2259187/aligned.36mers.unique.bam Reading in data... Reading data took 2.23561406136 s Creating peak regions... Creating peak regions took 23.9330108166 s Estimating background... Estimating background took 7.13999009132 s Processing exo_BATF_rep4-GSM2259187/aligned.36mers.unique.bam Reading in data... Reading data took 2.4368519783 s Creating peak regions... Creating peak regions took 23.3338220119 s Estimating background... Estimating background took 5.88755202293 s Processing exo_BATF_rep4-GSM2259187/aligned.36mers.unique.bam Reading in data... Reading data took 1.66831684113 s Creating peak regions... Creating peak regions took 16.5779731274 s Estimating background... Estimating background took 5.3473610878 s Processing exo_BATF_rep4-GSM2259187/aligned.36mers.unique.bam Reading in data... Reading data took 4.65419507027 s Creating peak regions... Creating peak regions took 53.1404099464 s Estimating background... Estimating background took 13.5414988995 s Processing exo_BATF_rep4-GSM2259187/aligned.36mers.unique.bam Reading in data... Reading data took 0.0558850765228 s Creating peak regions... Creating peak regions took 0.273485183716 s Estimating background... Estimating background took 0.322245121002 s Processing exo_BATF_rep4-GSM2259187/aligned.36mers.unique.bam Reading in data... Reading data took 0.0814719200134 s Creating peak regions... Creating peak regions took 0.323702096939 s Estimating background... Estimating background took 0.339629888535 s Processing exo_BATF_rep4-GSM2259187/aligned.36mers.unique.bam Reading in data... Reading data took 0.0580260753632 s Creating peak regions... Creating peak regions took 0.252273082733 s Estimating background... Estimating background took 0.333645105362 s Processing exo_BATF_rep4-GSM2259187/aligned.36mers.unique.bam Reading in data... Processing exo_BATF_rep4-GSM2259187/aligned.36mers.unique.bam Reading in data... Reading data took 0.0501170158386 s Creating peak regions... Creating peak regions took 0.274949073792 s Estimating background... Estimating background took 0.329162836075 s Processing exo_BATF_rep4-GSM2259187/aligned.36mers.unique.bam Reading in data... Reading data took 6.05671596527 s Creating peak regions... Creating peak regions took 50.7169880867 s Estimating background... Estimating background took 14.5894749165 s Processing exo_BATF_rep4-GSM2259187/aligned.36mers.unique.bam Reading in data... Reading data took 3.95713996887 s Creating peak regions... Creating peak regions took 41.9088461399 s Estimating background... Estimating background took 11.0285749435 s Processing exo_BATF_rep4-GSM2259187/aligned.36mers.unique.bam Reading in data... Reading data took 3.50039792061 s Creating peak regions... Creating peak regions took 50.033769846 s Estimating background... Estimating background took 10.7679920197 s Processing exo_BATF_rep4-GSM2259187/aligned.36mers.unique.bam Reading in data... Reading data took 0.103967189789 s Creating peak regions... Creating peak regions took 0.209496021271 s Estimating background... Estimating background took 0.313359975815 s Processing exo_BATF_rep4-GSM2259187/aligned.36mers.unique.bam Reading in data... Processing exo_BATF_rep4-GSM2259187/aligned.36mers.unique.bam Reading in data... Reading data took 0.0486719608307 s Creating peak regions... Creating peak regions took 0.0209519863129 s Estimating background... Estimating background took 0.316797971725 s Processing exo_BATF_rep4-GSM2259187/aligned.36mers.unique.bam Reading in data... Processing exo_BATF_rep4-GSM2259187/aligned.36mers.unique.bam Reading in data... Processing exo_BATF_rep4-GSM2259187/aligned.36mers.unique.bam Reading in data... Reading data took 0.0437779426575 s Creating peak regions... Creating peak regions took 0.00294208526611 s Estimating background... Estimating background took 0.356297969818 s Processing exo_BATF_rep4-GSM2259187/aligned.36mers.unique.bam Reading in data... Reading data took 3.90499401093 s Creating peak regions... Creating peak regions took 42.9014830589 s Estimating background... Estimating background took 9.63813185692 s Processing exo_BATF_rep4-GSM2259187/aligned.36mers.unique.bam Reading in data... Reading data took 0.0660769939423 s Creating peak regions... Creating peak regions took 0.205942869186 s Estimating background... Estimating background took 0.30064702034 s Processing exo_BATF_rep4-GSM2259187/aligned.36mers.unique.bam Reading in data... Processing exo_BATF_rep4-GSM2259187/aligned.36mers.unique.bam Reading in data... Processing exo_BATF_rep4-GSM2259187/aligned.36mers.unique.bam Reading in data... Processing exo_BATF_rep4-GSM2259187/aligned.36mers.unique.bam Reading in data... Reading data took 0.0360760688782 s Creating peak regions... Creating peak regions took 0.603844881058 s Estimating background... Estimating background took 0.29945898056 s Processing exo_BATF_rep4-GSM2259187/aligned.36mers.unique.bam Reading in data... Reading data took 3.52805709839 s Creating peak regions... Creating peak regions took 40.7743098736 s Estimating background... Estimating background took 10.4987430573 s Processing exo_BATF_rep4-GSM2259187/aligned.36mers.unique.bam Reading in data... Reading data took 3.50011181831 s Creating peak regions... Creating peak regions took 44.4315237999 s Estimating background... Estimating background took 10.8165390491 s Processing exo_BATF_rep4-GSM2259187/aligned.36mers.unique.bam Reading in data... Processing exo_BATF_rep4-GSM2259187/aligned.36mers.unique.bam Reading in data... Reading data took 2.76183009148 s Creating peak regions... Creating peak regions took 35.1044750214 s Estimating background... Estimating background took 8.22719597816 s Processing exo_BATF_rep4-GSM2259187/aligned.36mers.unique.bam Reading in data... Reading data took 3.35230922699 s Creating peak regions... Creating peak regions took 30.9997489452 s Estimating background... Estimating background took 10.1909718513 s Processing exo_BATF_rep4-GSM2259187/aligned.36mers.unique.bam Reading in data... Reading data took 0.0967869758606 s Creating peak regions... Creating peak regions took 0.172222852707 s Estimating background... Estimating background took 0.658699035645 s Processing exo_BATF_rep4-GSM2259187/aligned.36mers.unique.bam Reading in data... Reading data took 0.0720250606537 s Creating peak regions... Creating peak regions took 0.0655038356781 s Estimating background... Estimating background took 0.343052148819 s Processing exo_BATF_rep4-GSM2259187/aligned.36mers.unique.bam Reading in data... Reading data took 0.0735001564026 s Creating peak regions... Creating peak regions took 0.033928155899 s Estimating background... Estimating background took 0.314753055573 s Processing exo_BATF_rep4-GSM2259187/aligned.36mers.unique.bam Reading in data... Reading data took 0.0736789703369 s Creating peak regions... Creating peak regions took 0.0491590499878 s Estimating background... Estimating background took 0.312175989151 s Processing exo_BATF_rep4-GSM2259187/aligned.36mers.unique.bam Reading in data... Reading data took 0.0735828876495 s Creating peak regions... Creating peak regions took 0.0676341056824 s Estimating background... Estimating background took 0.323889017105 s Processing exo_BATF_rep4-GSM2259187/aligned.36mers.unique.bam Reading in data... Reading data took 0.0517861843109 s Creating peak regions... Creating peak regions took 0.0572571754456 s Estimating background... Estimating background took 0.341511964798 s Processing exo_BATF_rep4-GSM2259187/aligned.36mers.unique.bam Reading in data... Reading data took 0.0750720500946 s Creating peak regions... Creating peak regions took 0.0332159996033 s Estimating background... Estimating background took 0.34467291832 s Processing exo_BATF_rep4-GSM2259187/aligned.36mers.unique.bam Reading in data... Reading data took 0.0518431663513 s Creating peak regions... Creating peak regions took 0.0368030071259 s Estimating background... Estimating background took 0.322668790817 s Processing exo_BATF_rep4-GSM2259187/aligned.36mers.unique.bam Reading in data... Reading data took 0.0725061893463 s Creating peak regions... Creating peak regions took 0.0471680164337 s Estimating background... Estimating background took 0.320120096207 s Processing exo_BATF_rep4-GSM2259187/aligned.36mers.unique.bam Reading in data... Reading data took 0.0505650043488 s Creating peak regions... Creating peak regions took 0.0379111766815 s Estimating background... Estimating background took 0.325902938843 s Processing exo_BATF_rep4-GSM2259187/aligned.36mers.unique.bam Reading in data... Reading data took 0.20733499527 s Creating peak regions... Creating peak regions took 0.1413230896 s Estimating background... Estimating background took 0.317317962646 s Processing exo_BATF_rep4-GSM2259187/aligned.36mers.unique.bam Reading in data... Reading data took 0.0506570339203 s Creating peak regions... Creating peak regions took 0.0372459888458 s Estimating background... Estimating background took 0.312561988831 s Processing exo_BATF_rep4-GSM2259187/aligned.36mers.unique.bam Reading in data... Reading data took 0.0743339061737 s Creating peak regions... Creating peak regions took 0.0384650230408 s Estimating background... Estimating background took 0.321381092072 s Processing exo_BATF_rep4-GSM2259187/aligned.36mers.unique.bam Reading in data... Reading data took 0.0865259170532 s Creating peak regions... Creating peak regions took 0.0929119586945 s Estimating background... Estimating background took 0.344676017761 s Processing exo_BATF_rep4-GSM2259187/aligned.36mers.unique.bam Reading in data... Reading data took 0.0727441310883 s Creating peak regions... Creating peak regions took 0.0411729812622 s Estimating background... Estimating background took 0.375864028931 s Processing exo_BATF_rep4-GSM2259187/aligned.36mers.unique.bam Reading in data... Reading data took 0.07470703125 s Creating peak regions... Creating peak regions took 0.0380599498749 s Estimating background... Estimating background took 0.36887383461 s Processing exo_BATF_rep4-GSM2259187/aligned.36mers.unique.bam Reading in data... Reading data took 0.28898692131 s Creating peak regions... Creating peak regions took 0.0537469387054 s Estimating background... Estimating background took 0.476094961166 s Processing exo_BATF_rep4-GSM2259187/aligned.36mers.unique.bam Reading in data... Reading data took 0.060791015625 s Creating peak regions... Creating peak regions took 0.0736529827118 s Estimating background... Estimating background took 0.369252920151 s Processing exo_BATF_rep4-GSM2259187/aligned.36mers.unique.bam Reading in data... Reading data took 0.115844964981 s Creating peak regions... Creating peak regions took 0.0556361675262 s Estimating background... Estimating background took 0.366420984268 s Processing exo_BATF_rep4-GSM2259187/aligned.36mers.unique.bam Reading in data... Reading data took 0.0798990726471 s Creating peak regions... Creating peak regions took 0.146028995514 s Estimating background... Estimating background took 0.365078210831 s Processing exo_BATF_rep4-GSM2259187/aligned.36mers.unique.bam Reading in data... Reading data took 0.0531749725342 s Creating peak regions... Creating peak regions took 0.0349900722504 s Estimating background... Estimating background took 0.369301080704 s Processing exo_BATF_rep4-GSM2259187/aligned.36mers.unique.bam Reading in data... Reading data took 0.0821208953857 s Creating peak regions... Creating peak regions took 0.0686480998993 s Estimating background... Estimating background took 0.345649957657 s Processing exo_BATF_rep4-GSM2259187/aligned.36mers.unique.bam Reading in data... Reading data took 0.106056213379 s Creating peak regions... Creating peak regions took 0.187272071838 s Estimating background... Estimating background took 0.53281712532 s Processing exo_BATF_rep4-GSM2259187/aligned.36mers.unique.bam Reading in data... Reading data took 2.91763496399 s Creating peak regions... Creating peak regions took 46.5673079491 s Estimating background... Estimating background took 7.47302317619 s Processing exo_BATF_rep4-GSM2259187/aligned.36mers.unique.bam Reading in data... Reading data took 0.070063829422 s Creating peak regions... Creating peak regions took 0.360450029373 s Estimating background... Estimating background took 0.341074943542 s Processing exo_BATF_rep4-GSM2259187/aligned.36mers.unique.bam Reading in data... Reading data took 0.0807111263275 s Creating peak regions... Creating peak regions took 20.1025960445 s Estimating background... Estimating background took 0.351338863373 s Processing exo_BATF_rep4-GSM2259187/aligned.36mers.unique.bam Reading in data... Processing exo_BATF_rep4-GSM2259187/aligned.36mers.unique.bam Reading in data... Processing exo_BATF_rep4-GSM2259187/aligned.36mers.unique.bam Reading in data... Processing exo_BATF_rep4-GSM2259187/aligned.36mers.unique.bam Reading in data...