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='Sox2-ChIP-exo-GSM1537541/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='Sox2-ChIP-exo-GSM1537541/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='Sox2-ChIP-exo-GSM1537541/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='Sox2-ChIP-exo-GSM1537541/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 Sox2-ChIP-exo-GSM1537541/aligned.36mers.unique.bam Reading in data... Reading data took 13.8242001534 s Creating peak regions... Creating peak regions took 38.7989971638 s Estimating background... Estimating background took 67.0124480724 s Processing Sox2-ChIP-exo-GSM1537541/aligned.36mers.unique.bam Reading in data... Reading data took 16.8119668961 s Creating peak regions... Creating peak regions took 42.8778369427 s Estimating background... Estimating background took 85.6992821693 s Processing Sox2-ChIP-exo-GSM1537541/aligned.36mers.unique.bam Reading in data... Reading data took 13.2495000362 s Creating peak regions... Creating peak regions took 41.0931918621 s Estimating background... Estimating background took 63.3441970348 s Processing Sox2-ChIP-exo-GSM1537541/aligned.36mers.unique.bam Reading in data... Reading data took 14.2300429344 s Creating peak regions... Creating peak regions took 41.1797299385 s Estimating background... Estimating background took 68.0523002148 s Processing Sox2-ChIP-exo-GSM1537541/aligned.36mers.unique.bam Reading in data... Reading data took 15.875592947 s Creating peak regions... Creating peak regions took 44.656801939 s Estimating background... Estimating background took 83.1826472282 s Processing Sox2-ChIP-exo-GSM1537541/aligned.36mers.unique.bam Reading in data... Reading data took 12.6044299603 s Creating peak regions... Creating peak regions took 37.5150940418 s Estimating background... Estimating background took 61.2860720158 s Processing Sox2-ChIP-exo-GSM1537541/aligned.36mers.unique.bam Reading in data... Reading data took 11.5950109959 s Creating peak regions... Creating peak regions took 33.26658988 s Estimating background... Estimating background took 53.8404710293 s Processing Sox2-ChIP-exo-GSM1537541/aligned.36mers.unique.bam Reading in data... Reading data took 11.9149959087 s Creating peak regions... Creating peak regions took 33.3691141605 s Estimating background... Estimating background took 61.31716609 s Processing Sox2-ChIP-exo-GSM1537541/aligned.36mers.unique.bam Reading in data... Reading data took 11.5076999664 s Creating peak regions... Creating peak regions took 32.9981739521 s Estimating background... Estimating background took 49.9889290333 s Processing Sox2-ChIP-exo-GSM1537541/aligned.36mers.unique.bam Reading in data... Reading data took 8.39356088638 s Creating peak regions... Creating peak regions took 21.4543111324 s Estimating background... Estimating background took 35.9615671635 s Processing Sox2-ChIP-exo-GSM1537541/aligned.36mers.unique.bam Reading in data... Reading data took 22.6071710587 s Creating peak regions... Creating peak regions took 66.7588829994 s Estimating background... Estimating background took 107.903915882 s Processing Sox2-ChIP-exo-GSM1537541/aligned.36mers.unique.bam Reading in data... Reading data took 0.522836208344 s Creating peak regions... Creating peak regions took 1.70983290672 s Estimating background... Estimating background took 0.416132926941 s Processing Sox2-ChIP-exo-GSM1537541/aligned.36mers.unique.bam Reading in data... Reading data took 0.0678188800812 s Creating peak regions... Creating peak regions took 0.348081111908 s Estimating background... Estimating background took 0.374679088593 s Processing Sox2-ChIP-exo-GSM1537541/aligned.36mers.unique.bam Reading in data... Reading data took 0.0883111953735 s Creating peak regions... Creating peak regions took 0.241725921631 s Estimating background... Estimating background took 0.396437883377 s Processing Sox2-ChIP-exo-GSM1537541/aligned.36mers.unique.bam Reading in data... Processing Sox2-ChIP-exo-GSM1537541/aligned.36mers.unique.bam Reading in data... Reading data took 0.0593039989471 s Creating peak regions... Creating peak regions took 0.282566785812 s Estimating background... Estimating background took 0.399624109268 s Processing Sox2-ChIP-exo-GSM1537541/aligned.36mers.unique.bam Reading in data... Reading data took 29.2575011253 s Creating peak regions... Creating peak regions took 63.5361690521 s Estimating background... Estimating background took 107.722284079 s Processing Sox2-ChIP-exo-GSM1537541/aligned.36mers.unique.bam Reading in data... Reading data took 22.0038630962 s Creating peak regions... Creating peak regions took 59.8135302067 s Estimating background... Estimating background took 98.186095953 s Processing Sox2-ChIP-exo-GSM1537541/aligned.36mers.unique.bam Reading in data... Reading data took 20.2467970848 s Creating peak regions... Creating peak regions took 55.6928420067 s Estimating background... Estimating background took 91.24852705 s Processing Sox2-ChIP-exo-GSM1537541/aligned.36mers.unique.bam Reading in data... Reading data took 0.630914926529 s Creating peak regions... Creating peak regions took 0.446563959122 s Estimating background... Estimating background took 0.379289865494 s Processing Sox2-ChIP-exo-GSM1537541/aligned.36mers.unique.bam Reading in data... Processing Sox2-ChIP-exo-GSM1537541/aligned.36mers.unique.bam Reading in data... Reading data took 0.0495262145996 s Creating peak regions... Creating peak regions took 0.0186471939087 s Estimating background... Estimating background took 0.354048013687 s Processing Sox2-ChIP-exo-GSM1537541/aligned.36mers.unique.bam Reading in data... Processing Sox2-ChIP-exo-GSM1537541/aligned.36mers.unique.bam Reading in data... Processing Sox2-ChIP-exo-GSM1537541/aligned.36mers.unique.bam Reading in data... Reading data took 0.0518598556519 s Creating peak regions... Creating peak regions took 0.00303411483765 s Estimating background... Estimating background took 0.387995004654 s Processing Sox2-ChIP-exo-GSM1537541/aligned.36mers.unique.bam Reading in data... Reading data took 23.8766391277 s Creating peak regions... Creating peak regions took 57.0948269367 s Estimating background... Estimating background took 90.9171750546 s Processing Sox2-ChIP-exo-GSM1537541/aligned.36mers.unique.bam Reading in data... Reading data took 3.11918306351 s Creating peak regions... Creating peak regions took 0.774791002274 s Estimating background... Estimating background took 0.3893430233 s Processing Sox2-ChIP-exo-GSM1537541/aligned.36mers.unique.bam Reading in data... Processing Sox2-ChIP-exo-GSM1537541/aligned.36mers.unique.bam Reading in data... Processing Sox2-ChIP-exo-GSM1537541/aligned.36mers.unique.bam Reading in data... Processing Sox2-ChIP-exo-GSM1537541/aligned.36mers.unique.bam Reading in data... Reading data took 0.060791015625 s Creating peak regions... Creating peak regions took 1.15943098068 s Estimating background... Estimating background took 0.399585008621 s Processing Sox2-ChIP-exo-GSM1537541/aligned.36mers.unique.bam Reading in data... Reading data took 19.9554359913 s Creating peak regions... Creating peak regions took 53.4340150356 s Estimating background... Estimating background took 97.5209109783 s Processing Sox2-ChIP-exo-GSM1537541/aligned.36mers.unique.bam Reading in data... Reading data took 18.4776082039 s Creating peak regions... Creating peak regions took 52.7847850323 s Estimating background... Estimating background took 85.1133890152 s Processing Sox2-ChIP-exo-GSM1537541/aligned.36mers.unique.bam Reading in data... Processing Sox2-ChIP-exo-GSM1537541/aligned.36mers.unique.bam Reading in data... Reading data took 17.0172631741 s Creating peak regions... Creating peak regions took 46.764318943 s Estimating background... Estimating background took 80.6411399841 s Processing Sox2-ChIP-exo-GSM1537541/aligned.36mers.unique.bam Reading in data... Reading data took 17.9618508816 s Creating peak regions... Creating peak regions took 45.4066739082 s Estimating background... Estimating background took 76.9086880684 s Processing Sox2-ChIP-exo-GSM1537541/aligned.36mers.unique.bam Reading in data... Reading data took 2.96158599854 s Creating peak regions... Creating peak regions took 0.47623705864 s Estimating background... Estimating background took 0.935234069824 s Processing Sox2-ChIP-exo-GSM1537541/aligned.36mers.unique.bam Reading in data... Reading data took 0.0832149982452 s Creating peak regions... Creating peak regions took 0.0763981342316 s Estimating background... Estimating background took 0.408992052078 s Processing Sox2-ChIP-exo-GSM1537541/aligned.36mers.unique.bam Reading in data... Reading data took 0.0808410644531 s Creating peak regions... Creating peak regions took 0.0462329387665 s Estimating background... Estimating background took 0.397531032562 s Processing Sox2-ChIP-exo-GSM1537541/aligned.36mers.unique.bam Reading in data... Reading data took 0.0834329128265 s Creating peak regions... Creating peak regions took 0.0942139625549 s Estimating background... Estimating background took 0.393095016479 s Processing Sox2-ChIP-exo-GSM1537541/aligned.36mers.unique.bam Reading in data... Reading data took 0.0957849025726 s Creating peak regions... Creating peak regions took 0.111799955368 s Estimating background... Estimating background took 0.395873785019 s Processing Sox2-ChIP-exo-GSM1537541/aligned.36mers.unique.bam Reading in data... Reading data took 0.0835709571838 s Creating peak regions... Creating peak regions took 0.100735902786 s Estimating background... Estimating background took 0.396382808685 s Processing Sox2-ChIP-exo-GSM1537541/aligned.36mers.unique.bam Reading in data... Reading data took 0.0903699398041 s Creating peak regions... Creating peak regions took 0.0632560253143 s Estimating background... Estimating background took 0.403177976608 s Processing Sox2-ChIP-exo-GSM1537541/aligned.36mers.unique.bam Reading in data... Reading data took 0.0841639041901 s Creating peak regions... Creating peak regions took 0.0520341396332 s Estimating background... Estimating background took 0.399302959442 s Processing Sox2-ChIP-exo-GSM1537541/aligned.36mers.unique.bam Reading in data... Reading data took 0.0848670005798 s Creating peak regions... Creating peak regions took 0.0503940582275 s Estimating background... Estimating background took 0.400182008743 s Processing Sox2-ChIP-exo-GSM1537541/aligned.36mers.unique.bam Reading in data... Reading data took 0.0912749767303 s Creating peak regions... Creating peak regions took 0.0768909454346 s Estimating background... Estimating background took 0.397102832794 s Processing Sox2-ChIP-exo-GSM1537541/aligned.36mers.unique.bam Reading in data... Reading data took 0.0857231616974 s Creating peak regions... Creating peak regions took 0.145735025406 s Estimating background... Estimating background took 0.392210006714 s Processing Sox2-ChIP-exo-GSM1537541/aligned.36mers.unique.bam Reading in data... Reading data took 0.0630638599396 s Creating peak regions... Creating peak regions took 0.0682711601257 s Estimating background... Estimating background took 0.398445129395 s Processing Sox2-ChIP-exo-GSM1537541/aligned.36mers.unique.bam Reading in data... Reading data took 0.083456993103 s Creating peak regions... Creating peak regions took 0.0572099685669 s Estimating background... Estimating background took 0.443114995956 s Processing Sox2-ChIP-exo-GSM1537541/aligned.36mers.unique.bam Reading in data... Reading data took 0.157084941864 s Creating peak regions... Creating peak regions took 0.0684502124786 s Estimating background... Estimating background took 0.512804031372 s Processing Sox2-ChIP-exo-GSM1537541/aligned.36mers.unique.bam Reading in data... Reading data took 0.0612750053406 s Creating peak regions... Creating peak regions took 0.0683441162109 s Estimating background... Estimating background took 0.407660007477 s Processing Sox2-ChIP-exo-GSM1537541/aligned.36mers.unique.bam Reading in data... Reading data took 0.099907875061 s Creating peak regions... Creating peak regions took 0.0900900363922 s Estimating background... Estimating background took 0.445468902588 s Processing Sox2-ChIP-exo-GSM1537541/aligned.36mers.unique.bam Reading in data... Reading data took 1.03904008865 s Creating peak regions... Creating peak regions took 0.0297698974609 s Estimating background... Estimating background took 0.830536842346 s Processing Sox2-ChIP-exo-GSM1537541/aligned.36mers.unique.bam Reading in data... Reading data took 0.152092933655 s Creating peak regions... Creating peak regions took 0.051472902298 s Estimating background... Estimating background took 0.509066104889 s Processing Sox2-ChIP-exo-GSM1537541/aligned.36mers.unique.bam Reading in data... Reading data took 0.263946056366 s Creating peak regions... Creating peak regions took 0.0314071178436 s Estimating background... Estimating background took 0.514750003815 s Processing Sox2-ChIP-exo-GSM1537541/aligned.36mers.unique.bam Reading in data... Reading data took 0.123672962189 s Creating peak regions... Creating peak regions took 0.0972180366516 s Estimating background... Estimating background took 0.512642860413 s Processing Sox2-ChIP-exo-GSM1537541/aligned.36mers.unique.bam Reading in data... Reading data took 0.0868320465088 s Creating peak regions... Creating peak regions took 0.0694577693939 s Estimating background... Estimating background took 0.416741847992 s Processing Sox2-ChIP-exo-GSM1537541/aligned.36mers.unique.bam Reading in data... Reading data took 0.0951099395752 s Creating peak regions... Creating peak regions took 0.0496380329132 s Estimating background... Estimating background took 0.511740922928 s Processing Sox2-ChIP-exo-GSM1537541/aligned.36mers.unique.bam Reading in data... Reading data took 0.393846035004 s Creating peak regions... Creating peak regions took 0.187613964081 s Estimating background... Estimating background took 1.34389996529 s Processing Sox2-ChIP-exo-GSM1537541/aligned.36mers.unique.bam Reading in data... Reading data took 12.2126951218 s Creating peak regions... Creating peak regions took 54.4519739151 s Estimating background... Estimating background took 24.8425199986 s Processing Sox2-ChIP-exo-GSM1537541/aligned.36mers.unique.bam Reading in data... Reading data took 0.693964958191 s Creating peak regions... Creating peak regions took 0.584461927414 s Estimating background... Estimating background took 0.369507074356 s Processing Sox2-ChIP-exo-GSM1537541/aligned.36mers.unique.bam Reading in data... Reading data took 0.461932897568 s Creating peak regions... Creating peak regions took 33.8667731285 s Estimating background... Estimating background took 0.956269979477 s Processing Sox2-ChIP-exo-GSM1537541/aligned.36mers.unique.bam Reading in data... Processing Sox2-ChIP-exo-GSM1537541/aligned.36mers.unique.bam Reading in data... Processing Sox2-ChIP-exo-GSM1537541/aligned.36mers.unique.bam Reading in data... Processing Sox2-ChIP-exo-GSM1537541/aligned.36mers.unique.bam Reading in data...