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/female.mm10.chrom.sizes', e4='PeakXus', fastq='TAL1_G1E-ER4_0h_Rep3-GSM1689026/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='TAL1_G1E-ER4_0h_Rep3-GSM1689026/', 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='TAL1_G1E-ER4_0h_Rep3-GSM1689026/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='TAL1_G1E-ER4_0h_Rep3-GSM1689026/', 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 TAL1_G1E-ER4_0h_Rep3-GSM1689026/aligned.36mers.unique.bam Reading in data... Reading data took 0.257122993469 s Creating peak regions... Creating peak regions took 27.91527915 s Estimating background... Estimating background took 0.238194942474 s Processing TAL1_G1E-ER4_0h_Rep3-GSM1689026/aligned.36mers.unique.bam Reading in data... Reading data took 0.328768014908 s Creating peak regions... Creating peak regions took 26.7711801529 s Estimating background... Estimating background took 0.227128982544 s Processing TAL1_G1E-ER4_0h_Rep3-GSM1689026/aligned.36mers.unique.bam Reading in data... Reading data took 0.333498001099 s Creating peak regions... Creating peak regions took 24.8550040722 s Estimating background... Estimating background took 0.226830005646 s Processing TAL1_G1E-ER4_0h_Rep3-GSM1689026/aligned.36mers.unique.bam Reading in data... Reading data took 0.396862030029 s Creating peak regions... Creating peak regions took 25.359719038 s Estimating background... Estimating background took 0.216956138611 s Processing TAL1_G1E-ER4_0h_Rep3-GSM1689026/aligned.36mers.unique.bam Reading in data... Reading data took 0.373118877411 s Creating peak regions... Creating peak regions took 26.6657090187 s Estimating background... Estimating background took 0.225522994995 s Processing TAL1_G1E-ER4_0h_Rep3-GSM1689026/aligned.36mers.unique.bam Reading in data... Reading data took 0.295754909515 s Creating peak regions... Creating peak regions took 22.3910980225 s Estimating background... Estimating background took 0.215760946274 s Processing TAL1_G1E-ER4_0h_Rep3-GSM1689026/aligned.36mers.unique.bam Reading in data... Reading data took 0.324258804321 s Creating peak regions... Creating peak regions took 19.9558119774 s Estimating background... Estimating background took 0.209553956985 s Processing TAL1_G1E-ER4_0h_Rep3-GSM1689026/aligned.36mers.unique.bam Reading in data... Reading data took 0.282360076904 s Creating peak regions... Creating peak regions took 22.1947000027 s Estimating background... Estimating background took 0.246004104614 s Processing TAL1_G1E-ER4_0h_Rep3-GSM1689026/aligned.36mers.unique.bam Reading in data... Reading data took 0.254323959351 s Creating peak regions... Creating peak regions took 18.5413479805 s Estimating background... Estimating background took 0.23695898056 s Processing TAL1_G1E-ER4_0h_Rep3-GSM1689026/aligned.36mers.unique.bam Reading in data... Reading data took 0.167431116104 s Creating peak regions... Creating peak regions took 13.0140769482 s Estimating background... Estimating background took 0.226119995117 s Processing TAL1_G1E-ER4_0h_Rep3-GSM1689026/aligned.36mers.unique.bam Reading in data... Reading data took 0.59077501297 s Creating peak regions... Creating peak regions took 41.9435100555 s Estimating background... Estimating background took 0.269423007965 s Processing TAL1_G1E-ER4_0h_Rep3-GSM1689026/aligned.36mers.unique.bam Reading in data... Reading data took 0.0565900802612 s Creating peak regions... Creating peak regions took 0.155516147614 s Estimating background... Estimating background took 0.275469064713 s Processing TAL1_G1E-ER4_0h_Rep3-GSM1689026/aligned.36mers.unique.bam Reading in data... Reading data took 0.0380570888519 s Creating peak regions... Creating peak regions took 0.169009923935 s Estimating background... Estimating background took 0.281491994858 s Processing TAL1_G1E-ER4_0h_Rep3-GSM1689026/aligned.36mers.unique.bam Reading in data... Reading data took 0.0403220653534 s Creating peak regions... Creating peak regions took 0.159820079803 s Estimating background... Estimating background took 0.276895999908 s Processing TAL1_G1E-ER4_0h_Rep3-GSM1689026/aligned.36mers.unique.bam Reading in data... Processing TAL1_G1E-ER4_0h_Rep3-GSM1689026/aligned.36mers.unique.bam Reading in data... Reading data took 0.0185489654541 s Creating peak regions... Creating peak regions took 0.15217590332 s Estimating background... Estimating background took 0.279119968414 s Processing TAL1_G1E-ER4_0h_Rep3-GSM1689026/aligned.36mers.unique.bam Reading in data... Reading data took 0.5843770504 s Creating peak regions... Creating peak regions took 37.8546791077 s Estimating background... Estimating background took 0.243186950684 s Processing TAL1_G1E-ER4_0h_Rep3-GSM1689026/aligned.36mers.unique.bam Reading in data... Reading data took 0.456166028976 s Creating peak regions... Creating peak regions took 34.8352401257 s Estimating background... Estimating background took 0.247330904007 s Processing TAL1_G1E-ER4_0h_Rep3-GSM1689026/aligned.36mers.unique.bam Reading in data... Reading data took 0.399343013763 s Creating peak regions... Creating peak regions took 32.0397520065 s Estimating background... Estimating background took 0.261689901352 s Processing TAL1_G1E-ER4_0h_Rep3-GSM1689026/aligned.36mers.unique.bam Reading in data... Reading data took 0.0507500171661 s Creating peak regions... Creating peak regions took 0.0792288780212 s Estimating background... Estimating background took 0.251320123672 s Processing TAL1_G1E-ER4_0h_Rep3-GSM1689026/aligned.36mers.unique.bam Reading in data... Processing TAL1_G1E-ER4_0h_Rep3-GSM1689026/aligned.36mers.unique.bam Reading in data... Processing TAL1_G1E-ER4_0h_Rep3-GSM1689026/aligned.36mers.unique.bam Reading in data... Processing TAL1_G1E-ER4_0h_Rep3-GSM1689026/aligned.36mers.unique.bam Reading in data... Processing TAL1_G1E-ER4_0h_Rep3-GSM1689026/aligned.36mers.unique.bam Reading in data... Processing TAL1_G1E-ER4_0h_Rep3-GSM1689026/aligned.36mers.unique.bam Reading in data... Reading data took 0.431495904922 s Creating peak regions... Creating peak regions took 31.9752020836 s Estimating background... Estimating background took 0.275677204132 s Processing TAL1_G1E-ER4_0h_Rep3-GSM1689026/aligned.36mers.unique.bam Reading in data... Processing TAL1_G1E-ER4_0h_Rep3-GSM1689026/aligned.36mers.unique.bam Reading in data... Processing TAL1_G1E-ER4_0h_Rep3-GSM1689026/aligned.36mers.unique.bam Reading in data... Processing TAL1_G1E-ER4_0h_Rep3-GSM1689026/aligned.36mers.unique.bam Reading in data... Processing TAL1_G1E-ER4_0h_Rep3-GSM1689026/aligned.36mers.unique.bam Reading in data... Processing TAL1_G1E-ER4_0h_Rep3-GSM1689026/aligned.36mers.unique.bam Reading in data... Reading data took 0.318427801132 s Creating peak regions... Creating peak regions took 31.4921009541 s Estimating background... Estimating background took 0.264460086823 s Processing TAL1_G1E-ER4_0h_Rep3-GSM1689026/aligned.36mers.unique.bam Reading in data... Reading data took 0.608122110367 s Creating peak regions... Creating peak regions took 29.8217940331 s Estimating background... Estimating background took 0.261835098267 s Processing TAL1_G1E-ER4_0h_Rep3-GSM1689026/aligned.36mers.unique.bam Reading in data... Processing TAL1_G1E-ER4_0h_Rep3-GSM1689026/aligned.36mers.unique.bam Reading in data... Reading data took 0.416887998581 s Creating peak regions... Creating peak regions took 28.1847710609 s Estimating background... Estimating background took 0.260521888733 s Processing TAL1_G1E-ER4_0h_Rep3-GSM1689026/aligned.36mers.unique.bam Reading in data... Reading data took 0.410284996033 s Creating peak regions... Creating peak regions took 25.7024168968 s Estimating background... Estimating background took 0.226982116699 s Processing TAL1_G1E-ER4_0h_Rep3-GSM1689026/aligned.36mers.unique.bam Reading in data... Reading data took 0.0579710006714 s Creating peak regions... Creating peak regions took 0.0245039463043 s Estimating background... Estimating background took 0.258060932159 s Processing TAL1_G1E-ER4_0h_Rep3-GSM1689026/aligned.36mers.unique.bam Reading in data... Reading data took 0.0384819507599 s Creating peak regions... Creating peak regions took 0.0181441307068 s Estimating background... Estimating background took 0.266660928726 s Processing TAL1_G1E-ER4_0h_Rep3-GSM1689026/aligned.36mers.unique.bam Reading in data... Processing TAL1_G1E-ER4_0h_Rep3-GSM1689026/aligned.36mers.unique.bam Reading in data... Processing TAL1_G1E-ER4_0h_Rep3-GSM1689026/aligned.36mers.unique.bam Reading in data... Processing TAL1_G1E-ER4_0h_Rep3-GSM1689026/aligned.36mers.unique.bam Reading in data... Processing TAL1_G1E-ER4_0h_Rep3-GSM1689026/aligned.36mers.unique.bam Reading in data... Processing TAL1_G1E-ER4_0h_Rep3-GSM1689026/aligned.36mers.unique.bam Reading in data... Processing TAL1_G1E-ER4_0h_Rep3-GSM1689026/aligned.36mers.unique.bam Reading in data... Processing TAL1_G1E-ER4_0h_Rep3-GSM1689026/aligned.36mers.unique.bam Reading in data... Reading data took 0.0176680088043 s Creating peak regions... Creating peak regions took 0.0260829925537 s Estimating background... Estimating background took 0.269758224487 s Processing TAL1_G1E-ER4_0h_Rep3-GSM1689026/aligned.36mers.unique.bam Reading in data... Processing TAL1_G1E-ER4_0h_Rep3-GSM1689026/aligned.36mers.unique.bam Reading in data... Processing TAL1_G1E-ER4_0h_Rep3-GSM1689026/aligned.36mers.unique.bam Reading in data... Processing TAL1_G1E-ER4_0h_Rep3-GSM1689026/aligned.36mers.unique.bam Reading in data... Reading data took 0.0235447883606 s Creating peak regions... Creating peak regions took 0.0443630218506 s Estimating background... Estimating background took 0.264930009842 s Processing TAL1_G1E-ER4_0h_Rep3-GSM1689026/aligned.36mers.unique.bam Reading in data... Processing TAL1_G1E-ER4_0h_Rep3-GSM1689026/aligned.36mers.unique.bam Reading in data... Processing TAL1_G1E-ER4_0h_Rep3-GSM1689026/aligned.36mers.unique.bam Reading in data... Reading data took 0.0428669452667 s Creating peak regions... Creating peak regions took 0.0323700904846 s Estimating background... Estimating background took 0.238481044769 s Processing TAL1_G1E-ER4_0h_Rep3-GSM1689026/aligned.36mers.unique.bam Reading in data... Reading data took 0.0254671573639 s Creating peak regions... Creating peak regions took 0.0290141105652 s Estimating background... Estimating background took 0.270651817322 s Processing TAL1_G1E-ER4_0h_Rep3-GSM1689026/aligned.36mers.unique.bam Reading in data... Reading data took 0.0458710193634 s Creating peak regions... Creating peak regions took 0.0414118766785 s Estimating background... Estimating background took 0.28064084053 s Processing TAL1_G1E-ER4_0h_Rep3-GSM1689026/aligned.36mers.unique.bam Reading in data... Reading data took 0.038318157196 s Creating peak regions... Creating peak regions took 0.0949029922485 s Estimating background... Estimating background took 0.24661898613 s Processing TAL1_G1E-ER4_0h_Rep3-GSM1689026/aligned.36mers.unique.bam Reading in data... Processing TAL1_G1E-ER4_0h_Rep3-GSM1689026/aligned.36mers.unique.bam Reading in data... Reading data took 0.0291378498077 s Creating peak regions... Creating peak regions took 0.0337429046631 s Estimating background... Estimating background took 0.248055934906 s Processing TAL1_G1E-ER4_0h_Rep3-GSM1689026/aligned.36mers.unique.bam Reading in data... Reading data took 0.0417160987854 s Creating peak regions... Creating peak regions took 0.137181043625 s Estimating background... Estimating background took 0.244612932205 s Processing TAL1_G1E-ER4_0h_Rep3-GSM1689026/aligned.36mers.unique.bam Reading in data... Reading data took 0.171435832977 s Creating peak regions... Creating peak regions took 37.6247770786 s Estimating background... Estimating background took 0.253332853317 s Processing TAL1_G1E-ER4_0h_Rep3-GSM1689026/aligned.36mers.unique.bam Reading in data... Reading data took 0.0263350009918 s Creating peak regions... Creating peak regions took 0.256098985672 s Estimating background... Estimating background took 0.272192955017 s Processing TAL1_G1E-ER4_0h_Rep3-GSM1689026/aligned.36mers.unique.bam Reading in data... Reading data took 0.0401790142059 s Creating peak regions... Creating peak regions took 19.4255099297 s Estimating background... Estimating background took 0.292186021805 s Processing TAL1_G1E-ER4_0h_Rep3-GSM1689026/aligned.36mers.unique.bam Reading in data... Processing TAL1_G1E-ER4_0h_Rep3-GSM1689026/aligned.36mers.unique.bam Reading in data... Processing TAL1_G1E-ER4_0h_Rep3-GSM1689026/aligned.36mers.unique.bam Reading in data... Processing TAL1_G1E-ER4_0h_Rep3-GSM1689026/aligned.36mers.unique.bam Reading in data...