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/hg19/wgEncodeHg19ConsensusSignalArtifactRegions.bed', center6=0, chromnames='/oak/stanford/groups/akundaje/marinovg/genomes/hg19/female.hg19.chrom.sizes', e4='PeakXus', fastq='FoxA1_ChIP-exo_replicate_1-GSM2994890/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='FoxA1_ChIP-exo_replicate_1-GSM2994890/', 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 FoxA1_ChIP-exo_replicate_1-GSM2994890/aligned.36mers.unique.bam
Reading in data... Reading data took 6.00072193146 s
Creating peak regions... Creating peak regions took 66.6511421204 s
Estimating background... Estimating background took 44.0738039017 s


Processing FoxA1_ChIP-exo_replicate_1-GSM2994890/aligned.36mers.unique.bam
Reading in data... Reading data took 7.77335500717 s
Creating peak regions... Creating peak regions took 78.2636208534 s
Estimating background... Estimating background took 42.1978800297 s


Processing FoxA1_ChIP-exo_replicate_1-GSM2994890/aligned.36mers.unique.bam
Reading in data... Reading data took 6.67119479179 s
Creating peak regions... Creating peak regions took 60.6443419456 s
Estimating background... Estimating background took 46.2733271122 s


Processing FoxA1_ChIP-exo_replicate_1-GSM2994890/aligned.36mers.unique.bam
Reading in data... Reading data took 4.04904413223 s
Creating peak regions... Creating peak regions took 54.5307281017 s
Estimating background... Estimating background took 19.1244950294 s


Processing FoxA1_ChIP-exo_replicate_1-GSM2994890/aligned.36mers.unique.bam
Reading in data... Reading data took 5.24413514137 s
Creating peak regions... Creating peak regions took 50.8624868393 s
Estimating background... Estimating background took 32.7730228901 s


Processing FoxA1_ChIP-exo_replicate_1-GSM2994890/aligned.36mers.unique.bam
Reading in data... Reading data took 5.26703095436 s
Creating peak regions... Creating peak regions took 54.9350409508 s
Estimating background... Estimating background took 28.6293439865 s


Processing FoxA1_ChIP-exo_replicate_1-GSM2994890/aligned.36mers.unique.bam
Reading in data... Reading data took 5.27420401573 s
Creating peak regions... Creating peak regions took 49.6182348728 s
Estimating background... Estimating background took 30.0470252037 s


Processing FoxA1_ChIP-exo_replicate_1-GSM2994890/aligned.36mers.unique.bam
Reading in data... Reading data took 4.95408892632 s
Creating peak regions... Creating peak regions took 46.7516131401 s
Estimating background... Estimating background took 31.1828842163 s


Processing FoxA1_ChIP-exo_replicate_1-GSM2994890/aligned.36mers.unique.bam
Reading in data... Reading data took 3.67838406563 s
Creating peak regions... Creating peak regions took 40.6651000977 s
Estimating background... Estimating background took 20.0244848728 s


Processing FoxA1_ChIP-exo_replicate_1-GSM2994890/aligned.36mers.unique.bam
Reading in data... Reading data took 4.10771512985 s
Creating peak regions... Creating peak regions took 45.0551700592 s
Estimating background... Estimating background took 23.4738960266 s


Processing FoxA1_ChIP-exo_replicate_1-GSM2994890/aligned.36mers.unique.bam
Reading in data... Reading data took 4.29791307449 s
Creating peak regions... Creating peak regions took 43.2715480328 s
Estimating background... Estimating background took 20.226377964 s


Processing FoxA1_ChIP-exo_replicate_1-GSM2994890/aligned.36mers.unique.bam
Reading in data... Reading data took 4.6048719883 s
Creating peak regions... Creating peak regions took 37.890996933 s
Estimating background... Estimating background took 24.3133211136 s


Processing FoxA1_ChIP-exo_replicate_1-GSM2994890/aligned.36mers.unique.bam
Reading in data... Reading data took 2.17995405197 s
Creating peak regions... Creating peak regions took 32.1931760311 s
Estimating background... Estimating background took 11.010434866 s


Processing FoxA1_ChIP-exo_replicate_1-GSM2994890/aligned.36mers.unique.bam
Reading in data... Reading data took 3.43940091133 s
Creating peak regions... Creating peak regions took 32.580892086 s
Estimating background... Estimating background took 21.8317630291 s


Processing FoxA1_ChIP-exo_replicate_1-GSM2994890/aligned.36mers.unique.bam
Reading in data... Reading data took 2.88775110245 s
Creating peak regions... Creating peak regions took 30.8085210323 s
Estimating background... Estimating background took 18.4654650688 s


Processing FoxA1_ChIP-exo_replicate_1-GSM2994890/aligned.36mers.unique.bam
Reading in data... Reading data took 2.63626503944 s
Creating peak regions... Creating peak regions took 26.1520111561 s
Estimating background... Estimating background took 16.2696099281 s


Processing FoxA1_ChIP-exo_replicate_1-GSM2994890/aligned.36mers.unique.bam
Reading in data... Reading data took 4.33605885506 s
Creating peak regions... Creating peak regions took 31.2503159046 s
Estimating background... Estimating background took 39.8049030304 s


Processing FoxA1_ChIP-exo_replicate_1-GSM2994890/aligned.36mers.unique.bam
Reading in data... Reading data took 1.56383800507 s
Creating peak regions... Creating peak regions took 22.185323 s
Estimating background... Estimating background took 4.80924606323 s


Processing FoxA1_ChIP-exo_replicate_1-GSM2994890/aligned.36mers.unique.bam
Reading in data... Reading data took 2.18167304993 s
Creating peak regions... Creating peak regions took 16.802382946 s
Estimating background... Estimating background took 9.08283615112 s


Processing FoxA1_ChIP-exo_replicate_1-GSM2994890/aligned.36mers.unique.bam
Reading in data... Reading data took 4.51788496971 s
Creating peak regions... Creating peak regions took 22.4070441723 s
Estimating background... Estimating background took 43.5647330284 s


Processing FoxA1_ChIP-exo_replicate_1-GSM2994890/aligned.36mers.unique.bam
Reading in data... Reading data took 1.48824310303 s
Creating peak regions... Creating peak regions took 15.4933979511 s
Estimating background... Estimating background took 7.61617493629 s


Processing FoxA1_ChIP-exo_replicate_1-GSM2994890/aligned.36mers.unique.bam
Reading in data... Reading data took 1.00865101814 s
Creating peak regions... Creating peak regions took 15.0931830406 s
Estimating background... Estimating background took 4.40772914886 s


Processing FoxA1_ChIP-exo_replicate_1-GSM2994890/aligned.36mers.unique.bam
Reading in data... Reading data took 3.15012001991 s
Creating peak regions... Creating peak regions took 43.9801619053 s
Estimating background... Estimating background took 12.8241860867 s


Processing FoxA1_ChIP-exo_replicate_1-GSM2994890/aligned.36mers.unique.bam
Reading in data... Reading data took 0.112524032593 s
Creating peak regions... Creating peak regions took 0.242321968079 s
Estimating background... Estimating background took 0.611391067505 s