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='STH-Sp1-ChIP-Exo-GSM2226564/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='STH-Sp1-ChIP-Exo-GSM2226564/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='STH-Sp1-ChIP-Exo-GSM2226564/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='STH-Sp1-ChIP-Exo-GSM2226564/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 STH-Sp1-ChIP-Exo-GSM2226564/aligned.36mers.unique.bam Reading in data... Reading data took 19.0004770756 s Creating peak regions... Creating peak regions took 43.6162919998 s Estimating background... Estimating background took 76.8472909927 s Processing STH-Sp1-ChIP-Exo-GSM2226564/aligned.36mers.unique.bam Reading in data... Reading data took 16.4741430283 s Creating peak regions... Creating peak regions took 38.9351961613 s Estimating background... Estimating background took 52.6793689728 s Processing STH-Sp1-ChIP-Exo-GSM2226564/aligned.36mers.unique.bam Reading in data... Reading data took 10.7415280342 s Creating peak regions... Creating peak regions took 37.0420331955 s Estimating background... Estimating background took 29.3031949997 s Processing STH-Sp1-ChIP-Exo-GSM2226564/aligned.36mers.unique.bam Reading in data... Reading data took 11.2300591469 s Creating peak regions... Creating peak regions took 35.185683012 s Estimating background... Estimating background took 32.3340659142 s Processing STH-Sp1-ChIP-Exo-GSM2226564/aligned.36mers.unique.bam Reading in data... Reading data took 9.43203806877 s Creating peak regions... Creating peak regions took 35.526018858 s Estimating background... Estimating background took 25.6468911171 s Processing STH-Sp1-ChIP-Exo-GSM2226564/aligned.36mers.unique.bam Reading in data... Reading data took 18.7469980717 s Creating peak regions... Creating peak regions took 38.8306040764 s Estimating background... Estimating background took 69.4128961563 s Processing STH-Sp1-ChIP-Exo-GSM2226564/aligned.36mers.unique.bam Reading in data... Reading data took 11.5605301857 s Creating peak regions... Creating peak regions took 30.9939029217 s Estimating background... Estimating background took 30.5176770687 s Processing STH-Sp1-ChIP-Exo-GSM2226564/aligned.36mers.unique.bam Reading in data... Reading data took 12.5936660767 s Creating peak regions... Creating peak regions took 32.3077938557 s Estimating background... Estimating background took 44.3353528976 s Processing STH-Sp1-ChIP-Exo-GSM2226564/aligned.36mers.unique.bam Reading in data... Reading data took 8.51850199699 s Creating peak regions... Creating peak regions took 25.7564878464 s Estimating background... Estimating background took 21.9373569489 s Processing STH-Sp1-ChIP-Exo-GSM2226564/aligned.36mers.unique.bam Reading in data... Reading data took 9.11642813683 s Creating peak regions... Creating peak regions took 20.082062006 s Estimating background... Estimating background took 33.0977020264 s Processing STH-Sp1-ChIP-Exo-GSM2226564/aligned.36mers.unique.bam Reading in data... Reading data took 18.8094630241 s Creating peak regions... Creating peak regions took 55.8528800011 s Estimating background... Estimating background took 58.4713680744 s Processing STH-Sp1-ChIP-Exo-GSM2226564/aligned.36mers.unique.bam Reading in data... Reading data took 0.802366018295 s Creating peak regions... Creating peak regions took 1.20745205879 s Estimating background... Estimating background took 0.362632989883 s Processing STH-Sp1-ChIP-Exo-GSM2226564/aligned.36mers.unique.bam Reading in data... Reading data took 0.0880799293518 s Creating peak regions... Creating peak regions took 0.384938955307 s Estimating background... Estimating background took 0.35976600647 s Processing STH-Sp1-ChIP-Exo-GSM2226564/aligned.36mers.unique.bam Reading in data... Reading data took 0.0878360271454 s Creating peak regions... Creating peak regions took 0.256947994232 s Estimating background... Estimating background took 0.362613916397 s Processing STH-Sp1-ChIP-Exo-GSM2226564/aligned.36mers.unique.bam Reading in data... Processing STH-Sp1-ChIP-Exo-GSM2226564/aligned.36mers.unique.bam Reading in data... Reading data took 0.0723481178284 s Creating peak regions... Creating peak regions took 0.321235895157 s Estimating background... Estimating background took 0.362925052643 s Processing STH-Sp1-ChIP-Exo-GSM2226564/aligned.36mers.unique.bam Reading in data... Reading data took 23.171943903 s Creating peak regions... Creating peak regions took 56.8487188816 s Estimating background... Estimating background took 60.3248920441 s Processing STH-Sp1-ChIP-Exo-GSM2226564/aligned.36mers.unique.bam Reading in data... Reading data took 18.749958992 s Creating peak regions... Creating peak regions took 53.0303359032 s Estimating background... Estimating background took 53.7136600018 s Processing STH-Sp1-ChIP-Exo-GSM2226564/aligned.36mers.unique.bam Reading in data... Reading data took 17.4232540131 s Creating peak regions... Creating peak regions took 49.0990080833 s Estimating background... Estimating background took 47.6101541519 s Processing STH-Sp1-ChIP-Exo-GSM2226564/aligned.36mers.unique.bam Reading in data... Reading data took 0.842538118362 s Creating peak regions... Creating peak regions took 0.580078125 s Estimating background... Estimating background took 0.411138057709 s Processing STH-Sp1-ChIP-Exo-GSM2226564/aligned.36mers.unique.bam Reading in data... Processing STH-Sp1-ChIP-Exo-GSM2226564/aligned.36mers.unique.bam Reading in data... Reading data took 0.0461819171906 s Creating peak regions... Creating peak regions took 0.0204708576202 s Estimating background... Estimating background took 0.402322053909 s Processing STH-Sp1-ChIP-Exo-GSM2226564/aligned.36mers.unique.bam Reading in data... Processing STH-Sp1-ChIP-Exo-GSM2226564/aligned.36mers.unique.bam Reading in data... Processing STH-Sp1-ChIP-Exo-GSM2226564/aligned.36mers.unique.bam Reading in data... Reading data took 0.0456428527832 s Creating peak regions... Creating peak regions took 0.00388789176941 s Estimating background... Estimating background took 0.404375076294 s Processing STH-Sp1-ChIP-Exo-GSM2226564/aligned.36mers.unique.bam Reading in data... Reading data took 19.1944870949 s Creating peak regions... Creating peak regions took 49.256788969 s Estimating background... Estimating background took 48.7556419373 s Processing STH-Sp1-ChIP-Exo-GSM2226564/aligned.36mers.unique.bam Reading in data... Reading data took 0.978453874588 s Creating peak regions... Creating peak regions took 0.580159902573 s Estimating background... Estimating background took 0.411790847778 s Processing STH-Sp1-ChIP-Exo-GSM2226564/aligned.36mers.unique.bam Reading in data... Processing STH-Sp1-ChIP-Exo-GSM2226564/aligned.36mers.unique.bam Reading in data... Processing STH-Sp1-ChIP-Exo-GSM2226564/aligned.36mers.unique.bam Reading in data... Processing STH-Sp1-ChIP-Exo-GSM2226564/aligned.36mers.unique.bam Reading in data... Reading data took 0.0825071334839 s Creating peak regions... Creating peak regions took 1.19407296181 s Estimating background... Estimating background took 0.349689006805 s Processing STH-Sp1-ChIP-Exo-GSM2226564/aligned.36mers.unique.bam Reading in data... Reading data took 17.0547180176 s Creating peak regions... Creating peak regions took 54.4993200302 s Estimating background... Estimating background took 46.7071378231 s Processing STH-Sp1-ChIP-Exo-GSM2226564/aligned.36mers.unique.bam Reading in data... Reading data took 17.5023899078 s Creating peak regions... Creating peak regions took 46.55189991 s Estimating background... Estimating background took 40.4410500526 s Processing STH-Sp1-ChIP-Exo-GSM2226564/aligned.36mers.unique.bam Reading in data... Processing STH-Sp1-ChIP-Exo-GSM2226564/aligned.36mers.unique.bam Reading in data... Reading data took 17.4147839546 s Creating peak regions... Creating peak regions took 42.5605518818 s Estimating background... Estimating background took 58.1267411709 s Processing STH-Sp1-ChIP-Exo-GSM2226564/aligned.36mers.unique.bam Reading in data... Reading data took 17.1259491444 s Creating peak regions... Creating peak regions took 42.0498418808 s Estimating background... Estimating background took 36.9719889164 s Processing STH-Sp1-ChIP-Exo-GSM2226564/aligned.36mers.unique.bam Reading in data... Reading data took 2.32269096375 s Creating peak regions... Creating peak regions took 0.256706953049 s Estimating background... Estimating background took 0.519073963165 s Processing STH-Sp1-ChIP-Exo-GSM2226564/aligned.36mers.unique.bam Reading in data... Reading data took 0.0922229290009 s Creating peak regions... Creating peak regions took 0.101777076721 s Estimating background... Estimating background took 0.400506973267 s Processing STH-Sp1-ChIP-Exo-GSM2226564/aligned.36mers.unique.bam Reading in data... Reading data took 0.0604958534241 s Creating peak regions... Creating peak regions took 0.0448079109192 s Estimating background... Estimating background took 0.400120019913 s Processing STH-Sp1-ChIP-Exo-GSM2226564/aligned.36mers.unique.bam Reading in data... Reading data took 0.0589258670807 s Creating peak regions... Creating peak regions took 0.080570936203 s Estimating background... Estimating background took 0.399239063263 s Processing STH-Sp1-ChIP-Exo-GSM2226564/aligned.36mers.unique.bam Reading in data... Reading data took 0.0617699623108 s Creating peak regions... Creating peak regions took 0.0962541103363 s Estimating background... Estimating background took 0.399894952774 s Processing STH-Sp1-ChIP-Exo-GSM2226564/aligned.36mers.unique.bam Reading in data... Reading data took 0.0604290962219 s Creating peak regions... Creating peak regions took 0.0932879447937 s Estimating background... Estimating background took 0.423191070557 s Processing STH-Sp1-ChIP-Exo-GSM2226564/aligned.36mers.unique.bam Reading in data... Reading data took 0.0599319934845 s Creating peak regions... Creating peak regions took 0.0485808849335 s Estimating background... Estimating background took 0.399282932281 s Processing STH-Sp1-ChIP-Exo-GSM2226564/aligned.36mers.unique.bam Reading in data... Reading data took 0.0829031467438 s Creating peak regions... Creating peak regions took 0.0460531711578 s Estimating background... Estimating background took 0.409375905991 s Processing STH-Sp1-ChIP-Exo-GSM2226564/aligned.36mers.unique.bam Reading in data... Reading data took 0.0603759288788 s Creating peak regions... Creating peak regions took 0.0477797985077 s Estimating background... Estimating background took 0.404581069946 s Processing STH-Sp1-ChIP-Exo-GSM2226564/aligned.36mers.unique.bam Reading in data... Reading data took 0.0614631175995 s Creating peak regions... Creating peak regions took 0.0745198726654 s Estimating background... Estimating background took 0.411371946335 s Processing STH-Sp1-ChIP-Exo-GSM2226564/aligned.36mers.unique.bam Reading in data... Reading data took 0.0892300605774 s Creating peak regions... Creating peak regions took 0.1468501091 s Estimating background... Estimating background took 0.399369955063 s Processing STH-Sp1-ChIP-Exo-GSM2226564/aligned.36mers.unique.bam Reading in data... Reading data took 0.104089975357 s Creating peak regions... Creating peak regions took 0.0829060077667 s Estimating background... Estimating background took 0.408596038818 s Processing STH-Sp1-ChIP-Exo-GSM2226564/aligned.36mers.unique.bam Reading in data... Reading data took 0.0593650341034 s Creating peak regions... Creating peak regions took 0.036456823349 s Estimating background... Estimating background took 0.396625995636 s Processing STH-Sp1-ChIP-Exo-GSM2226564/aligned.36mers.unique.bam Reading in data... Reading data took 0.118335008621 s Creating peak regions... Creating peak regions took 0.0737428665161 s Estimating background... Estimating background took 0.508296966553 s Processing STH-Sp1-ChIP-Exo-GSM2226564/aligned.36mers.unique.bam Reading in data... Reading data took 0.0611522197723 s Creating peak regions... Creating peak regions took 0.0520870685577 s Estimating background... Estimating background took 0.409346103668 s Processing STH-Sp1-ChIP-Exo-GSM2226564/aligned.36mers.unique.bam Reading in data... Reading data took 0.0695831775665 s Creating peak regions... Creating peak regions took 0.0736119747162 s Estimating background... Estimating background took 0.409441947937 s Processing STH-Sp1-ChIP-Exo-GSM2226564/aligned.36mers.unique.bam Reading in data... Reading data took 1.01519298553 s Creating peak regions... Creating peak regions took 0.0480501651764 s Estimating background... Estimating background took 0.942690849304 s Processing STH-Sp1-ChIP-Exo-GSM2226564/aligned.36mers.unique.bam Reading in data... Reading data took 0.103251934052 s Creating peak regions... Creating peak regions took 0.0536389350891 s Estimating background... Estimating background took 0.505962848663 s Processing STH-Sp1-ChIP-Exo-GSM2226564/aligned.36mers.unique.bam Reading in data... Reading data took 0.312506198883 s Creating peak regions... Creating peak regions took 0.0348269939423 s Estimating background... Estimating background took 0.512343168259 s Processing STH-Sp1-ChIP-Exo-GSM2226564/aligned.36mers.unique.bam Reading in data... Reading data took 0.104601860046 s Creating peak regions... Creating peak regions took 0.0968050956726 s Estimating background... Estimating background took 0.512126922607 s Processing STH-Sp1-ChIP-Exo-GSM2226564/aligned.36mers.unique.bam Reading in data... Reading data took 0.0662660598755 s Creating peak regions... Creating peak regions took 0.0701131820679 s Estimating background... Estimating background took 0.393981218338 s Processing STH-Sp1-ChIP-Exo-GSM2226564/aligned.36mers.unique.bam Reading in data... Reading data took 0.0807199478149 s Creating peak regions... Creating peak regions took 0.039167881012 s Estimating background... Estimating background took 0.506067037582 s Processing STH-Sp1-ChIP-Exo-GSM2226564/aligned.36mers.unique.bam Reading in data... Reading data took 0.437582015991 s Creating peak regions... Creating peak regions took 0.197225809097 s Estimating background... Estimating background took 1.17962002754 s Processing STH-Sp1-ChIP-Exo-GSM2226564/aligned.36mers.unique.bam Reading in data... Reading data took 15.6587150097 s Creating peak regions... Creating peak regions took 53.7940399647 s Estimating background... Estimating background took 39.4473869801 s Processing STH-Sp1-ChIP-Exo-GSM2226564/aligned.36mers.unique.bam Reading in data... Reading data took 0.908445835114 s Creating peak regions... Creating peak regions took 0.681049823761 s Estimating background... Estimating background took 0.409687042236 s Processing STH-Sp1-ChIP-Exo-GSM2226564/aligned.36mers.unique.bam Reading in data... Reading data took 0.136884212494 s Creating peak regions... Creating peak regions took 24.6346139908 s Estimating background... Estimating background took 0.512343883514 s Processing STH-Sp1-ChIP-Exo-GSM2226564/aligned.36mers.unique.bam Reading in data... Processing STH-Sp1-ChIP-Exo-GSM2226564/aligned.36mers.unique.bam Reading in data... Processing STH-Sp1-ChIP-Exo-GSM2226564/aligned.36mers.unique.bam Reading in data... Processing STH-Sp1-ChIP-Exo-GSM2226564/aligned.36mers.unique.bam Reading in data...