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='MEF2A_ChIP-exo-GSM1499534/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='MEF2A_ChIP-exo-GSM1499534/', 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 MEF2A_ChIP-exo-GSM1499534/alignments.36mers.unique.bam Reading in data... Reading data took 7.28654408455 s Creating peak regions... Creating peak regions took 40.7242019176 s Estimating background... Estimating background took 14.5907509327 s Processing MEF2A_ChIP-exo-GSM1499534/alignments.36mers.unique.bam Reading in data... Reading data took 9.40338897705 s Creating peak regions... Creating peak regions took 42.8080132008 s Estimating background... Estimating background took 20.9338610172 s Processing MEF2A_ChIP-exo-GSM1499534/alignments.36mers.unique.bam Reading in data... Reading data took 6.44415903091 s Creating peak regions... Creating peak regions took 37.2447390556 s Estimating background... Estimating background took 12.5497860909 s Processing MEF2A_ChIP-exo-GSM1499534/alignments.36mers.unique.bam Reading in data... Reading data took 7.12909007072 s Creating peak regions... Creating peak regions took 39.2497420311 s Estimating background... Estimating background took 14.2934908867 s Processing MEF2A_ChIP-exo-GSM1499534/alignments.36mers.unique.bam Reading in data... Reading data took 7.46676301956 s Creating peak regions... Creating peak regions took 41.1463680267 s Estimating background... Estimating background took 13.6291220188 s Processing MEF2A_ChIP-exo-GSM1499534/alignments.36mers.unique.bam Reading in data... Reading data took 8.66746306419 s Creating peak regions... Creating peak regions took 37.3832690716 s Estimating background... Estimating background took 21.8934140205 s Processing MEF2A_ChIP-exo-GSM1499534/alignments.36mers.unique.bam Reading in data... Reading data took 6.30901312828 s Creating peak regions... Creating peak regions took 34.850425005 s Estimating background... Estimating background took 11.9871730804 s Processing MEF2A_ChIP-exo-GSM1499534/alignments.36mers.unique.bam Reading in data... Reading data took 0.0899181365967 s Creating peak regions... Creating peak regions took 24.162981987 s Estimating background... Estimating background took 0.265249967575 s Processing MEF2A_ChIP-exo-GSM1499534/alignments.36mers.unique.bam Reading in data... Reading data took 0.0749089717865 s Creating peak regions... Creating peak regions took 22.9832530022 s Estimating background... Estimating background took 0.278596162796 s Processing MEF2A_ChIP-exo-GSM1499534/alignments.36mers.unique.bam Reading in data... Reading data took 0.0785989761353 s Creating peak regions... Creating peak regions took 16.5005609989 s Estimating background... Estimating background took 0.283559083939 s Processing MEF2A_ChIP-exo-GSM1499534/alignments.36mers.unique.bam Reading in data... Reading data took 14.5982179642 s Creating peak regions... Creating peak regions took 69.8056130409 s Estimating background... Estimating background took 32.8354380131 s Processing MEF2A_ChIP-exo-GSM1499534/alignments.36mers.unique.bam Reading in data... Reading data took 0.642559051514 s Creating peak regions... Creating peak regions took 1.65074181557 s Estimating background... Estimating background took 0.365369081497 s Processing MEF2A_ChIP-exo-GSM1499534/alignments.36mers.unique.bam Reading in data... Reading data took 0.0580830574036 s Creating peak regions... Creating peak regions took 0.391700983047 s Estimating background... Estimating background took 0.361974000931 s Processing MEF2A_ChIP-exo-GSM1499534/alignments.36mers.unique.bam Reading in data... Reading data took 0.0540480613708 s Creating peak regions... Creating peak regions took 0.223831176758 s Estimating background... Estimating background took 0.361293077469 s Processing MEF2A_ChIP-exo-GSM1499534/alignments.36mers.unique.bam Reading in data... Processing MEF2A_ChIP-exo-GSM1499534/alignments.36mers.unique.bam Reading in data... Reading data took 0.053375005722 s Creating peak regions... Creating peak regions took 0.276798009872 s Estimating background... Estimating background took 0.360229969025 s Processing MEF2A_ChIP-exo-GSM1499534/alignments.36mers.unique.bam Reading in data... Reading data took 20.576723814 s Creating peak regions... Creating peak regions took 65.3270511627 s Estimating background... Estimating background took 32.743516922 s Processing MEF2A_ChIP-exo-GSM1499534/alignments.36mers.unique.bam Reading in data... Reading data took 13.2789609432 s Creating peak regions... Creating peak regions took 55.5819189548 s Estimating background... Estimating background took 28.7312369347 s Processing MEF2A_ChIP-exo-GSM1499534/alignments.36mers.unique.bam Reading in data... Reading data took 13.6175861359 s Creating peak regions... Creating peak regions took 68.5728189945 s Estimating background... Estimating background took 24.4969689846 s Processing MEF2A_ChIP-exo-GSM1499534/alignments.36mers.unique.bam Reading in data... Reading data took 0.415166854858 s Creating peak regions... Creating peak regions took 0.341307878494 s Estimating background... Estimating background took 0.319369077682 s Processing MEF2A_ChIP-exo-GSM1499534/alignments.36mers.unique.bam Reading in data... Processing MEF2A_ChIP-exo-GSM1499534/alignments.36mers.unique.bam Reading in data... Reading data took 0.0667569637299 s Creating peak regions... Creating peak regions took 0.0367970466614 s Estimating background... Estimating background took 0.365650892258 s Processing MEF2A_ChIP-exo-GSM1499534/alignments.36mers.unique.bam Reading in data... Processing MEF2A_ChIP-exo-GSM1499534/alignments.36mers.unique.bam Reading in data... Processing MEF2A_ChIP-exo-GSM1499534/alignments.36mers.unique.bam Reading in data... Processing MEF2A_ChIP-exo-GSM1499534/alignments.36mers.unique.bam Reading in data... Reading data took 10.7977859974 s Creating peak regions... Creating peak regions took 58.5230350494 s Estimating background... Estimating background took 17.9642970562 s Processing MEF2A_ChIP-exo-GSM1499534/alignments.36mers.unique.bam Reading in data... Processing MEF2A_ChIP-exo-GSM1499534/alignments.36mers.unique.bam Reading in data... Processing MEF2A_ChIP-exo-GSM1499534/alignments.36mers.unique.bam Reading in data... Reading data took 0.0403990745544 s Creating peak regions... Creating peak regions took 0.350583076477 s Estimating background... Estimating background took 0.349858045578 s Processing MEF2A_ChIP-exo-GSM1499534/alignments.36mers.unique.bam Reading in data... Processing MEF2A_ChIP-exo-GSM1499534/alignments.36mers.unique.bam Reading in data... Reading data took 0.0497980117798 s Creating peak regions... Creating peak regions took 1.06893491745 s Estimating background... Estimating background took 0.322629213333 s Processing MEF2A_ChIP-exo-GSM1499534/alignments.36mers.unique.bam Reading in data... Reading data took 10.9127600193 s Creating peak regions... Creating peak regions took 54.942497015 s Estimating background... Estimating background took 21.3655481339 s Processing MEF2A_ChIP-exo-GSM1499534/alignments.36mers.unique.bam Reading in data... Reading data took 8.77226400375 s Creating peak regions... Creating peak regions took 50.7855119705 s Estimating background... Estimating background took 14.9313309193 s Processing MEF2A_ChIP-exo-GSM1499534/alignments.36mers.unique.bam Reading in data... Processing MEF2A_ChIP-exo-GSM1499534/alignments.36mers.unique.bam Reading in data... Reading data took 9.6662311554 s Creating peak regions... Creating peak regions took 50.4810311794 s Estimating background... Estimating background took 22.841697216 s Processing MEF2A_ChIP-exo-GSM1499534/alignments.36mers.unique.bam Reading in data... Reading data took 10.8554692268 s Creating peak regions... Creating peak regions took 44.2821769714 s Estimating background... Estimating background took 14.5621061325 s Processing MEF2A_ChIP-exo-GSM1499534/alignments.36mers.unique.bam Reading in data... Reading data took 0.24133682251 s Creating peak regions... Creating peak regions took 0.184512138367 s Estimating background... Estimating background took 0.445162057877 s Processing MEF2A_ChIP-exo-GSM1499534/alignments.36mers.unique.bam Reading in data... Reading data took 0.0750110149384 s Creating peak regions... Creating peak regions took 0.0935230255127 s Estimating background... Estimating background took 0.359758138657 s Processing MEF2A_ChIP-exo-GSM1499534/alignments.36mers.unique.bam Reading in data... Reading data took 0.0572521686554 s Creating peak regions... Creating peak regions took 0.0408291816711 s Estimating background... Estimating background took 0.360721111298 s Processing MEF2A_ChIP-exo-GSM1499534/alignments.36mers.unique.bam Reading in data... Reading data took 0.0687339305878 s Creating peak regions... Creating peak regions took 0.0570931434631 s Estimating background... Estimating background took 0.340320825577 s Processing MEF2A_ChIP-exo-GSM1499534/alignments.36mers.unique.bam Reading in data... Reading data took 0.0510728359222 s Creating peak regions... Creating peak regions took 0.0845019817352 s Estimating background... Estimating background took 0.348704099655 s Processing MEF2A_ChIP-exo-GSM1499534/alignments.36mers.unique.bam Reading in data... Reading data took 0.0487160682678 s Creating peak regions... Creating peak regions took 0.0837550163269 s Estimating background... Estimating background took 0.319548130035 s Processing MEF2A_ChIP-exo-GSM1499534/alignments.36mers.unique.bam Reading in data... Reading data took 0.0451760292053 s Creating peak regions... Creating peak regions took 0.0346698760986 s Estimating background... Estimating background took 0.323299884796 s Processing MEF2A_ChIP-exo-GSM1499534/alignments.36mers.unique.bam Reading in data... Reading data took 0.0652320384979 s Creating peak regions... Creating peak regions took 0.0405149459839 s Estimating background... Estimating background took 0.334861040115 s Processing MEF2A_ChIP-exo-GSM1499534/alignments.36mers.unique.bam Reading in data... Reading data took 0.0719699859619 s Creating peak regions... Creating peak regions took 0.0501101016998 s Estimating background... Estimating background took 0.322537899017 s Processing MEF2A_ChIP-exo-GSM1499534/alignments.36mers.unique.bam Reading in data... Reading data took 0.0476279258728 s Creating peak regions... Creating peak regions took 0.0479321479797 s Estimating background... Estimating background took 0.32194519043 s Processing MEF2A_ChIP-exo-GSM1499534/alignments.36mers.unique.bam Reading in data... Reading data took 0.0485360622406 s Creating peak regions... Creating peak regions took 0.121431112289 s Estimating background... Estimating background took 0.322690010071 s Processing MEF2A_ChIP-exo-GSM1499534/alignments.36mers.unique.bam Reading in data... Reading data took 0.0455729961395 s Creating peak regions... Creating peak regions took 0.0305988788605 s Estimating background... Estimating background took 0.321633815765 s Processing MEF2A_ChIP-exo-GSM1499534/alignments.36mers.unique.bam Reading in data... Reading data took 0.0453190803528 s Creating peak regions... Creating peak regions took 0.0313799381256 s Estimating background... Estimating background took 0.353193044662 s Processing MEF2A_ChIP-exo-GSM1499534/alignments.36mers.unique.bam Reading in data... Reading data took 0.142146110535 s Creating peak regions... Creating peak regions took 0.0810668468475 s Estimating background... Estimating background took 0.362697124481 s Processing MEF2A_ChIP-exo-GSM1499534/alignments.36mers.unique.bam Reading in data... Reading data took 0.0504779815674 s Creating peak regions... Creating peak regions took 0.0581650733948 s Estimating background... Estimating background took 0.361531019211 s Processing MEF2A_ChIP-exo-GSM1499534/alignments.36mers.unique.bam Reading in data... Reading data took 0.0741360187531 s Creating peak regions... Creating peak regions took 0.0457010269165 s Estimating background... Estimating background took 0.322928905487 s Processing MEF2A_ChIP-exo-GSM1499534/alignments.36mers.unique.bam Reading in data... Reading data took 1.23273086548 s Creating peak regions... Creating peak regions took 0.0474631786346 s Estimating background... Estimating background took 0.762130022049 s Processing MEF2A_ChIP-exo-GSM1499534/alignments.36mers.unique.bam Reading in data... Reading data took 0.104052782059 s Creating peak regions... Creating peak regions took 0.0620701313019 s Estimating background... Estimating background took 0.353178024292 s Processing MEF2A_ChIP-exo-GSM1499534/alignments.36mers.unique.bam Reading in data... Reading data took 0.284645795822 s Creating peak regions... Creating peak regions took 0.0288438796997 s Estimating background... Estimating background took 0.428417921066 s Processing MEF2A_ChIP-exo-GSM1499534/alignments.36mers.unique.bam Reading in data... Reading data took 0.101066112518 s Creating peak regions... Creating peak regions took 0.0981509685516 s Estimating background... Estimating background took 0.321588993073 s Processing MEF2A_ChIP-exo-GSM1499534/alignments.36mers.unique.bam Reading in data... Reading data took 0.0494530200958 s Creating peak regions... Creating peak regions took 0.0380871295929 s Estimating background... Estimating background took 0.339865922928 s Processing MEF2A_ChIP-exo-GSM1499534/alignments.36mers.unique.bam Reading in data... Reading data took 0.0810379981995 s Creating peak regions... Creating peak regions took 0.0567870140076 s Estimating background... Estimating background took 0.350045919418 s Processing MEF2A_ChIP-exo-GSM1499534/alignments.36mers.unique.bam Reading in data... Reading data took 0.288498163223 s Creating peak regions... Creating peak regions took 0.196779966354 s Estimating background... Estimating background took 0.630077123642 s Processing MEF2A_ChIP-exo-GSM1499534/alignments.36mers.unique.bam Reading in data... Reading data took 0.0980579853058 s Creating peak regions... Creating peak regions took 48.8636381626 s Estimating background... Estimating background took 0.341029882431 s Processing MEF2A_ChIP-exo-GSM1499534/alignments.36mers.unique.bam Reading in data... Reading data took 0.0795681476593 s Creating peak regions... Creating peak regions took 0.467441082001 s Estimating background... Estimating background took 0.335704088211 s Processing MEF2A_ChIP-exo-GSM1499534/alignments.36mers.unique.bam Reading in data... Reading data took 0.0635361671448 s Creating peak regions... Creating peak regions took 25.2224609852 s Estimating background... Estimating background took 0.378089904785 s Processing MEF2A_ChIP-exo-GSM1499534/alignments.36mers.unique.bam Reading in data... Processing MEF2A_ChIP-exo-GSM1499534/alignments.36mers.unique.bam Reading in data... Processing MEF2A_ChIP-exo-GSM1499534/alignments.36mers.unique.bam Reading in data... Processing MEF2A_ChIP-exo-GSM1499534/alignments.36mers.unique.bam Reading in data...