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='CTCF_ChIP-exo_replicate_1-GSM2994892/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='CTCF_ChIP-exo_replicate_1-GSM2994892/', 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 CTCF_ChIP-exo_replicate_1-GSM2994892/aligned.36mers.unique.bam
Reading in data... Reading data took 8.57017207146 s
Creating peak regions... Creating peak regions took 79.3806068897 s
Estimating background... Estimating background took 46.5591259003 s


Processing CTCF_ChIP-exo_replicate_1-GSM2994892/aligned.36mers.unique.bam
Reading in data... Reading data took 6.85529088974 s
Creating peak regions... Creating peak regions took 66.7326459885 s
Estimating background... Estimating background took 39.9182391167 s


Processing CTCF_ChIP-exo_replicate_1-GSM2994892/aligned.36mers.unique.bam
Reading in data... Reading data took 6.76496291161 s
Creating peak regions... Creating peak regions took 68.6409981251 s
Estimating background... Estimating background took 48.6513571739 s


Processing CTCF_ChIP-exo_replicate_1-GSM2994892/aligned.36mers.unique.bam
Reading in data... Reading data took 3.99340200424 s
Creating peak regions... Creating peak regions took 54.7612438202 s
Estimating background... Estimating background took 24.1771268845 s


Processing CTCF_ChIP-exo_replicate_1-GSM2994892/aligned.36mers.unique.bam
Reading in data... Reading data took 6.31762909889 s
Creating peak regions... Creating peak regions took 57.0990028381 s
Estimating background... Estimating background took 31.0269091129 s


Processing CTCF_ChIP-exo_replicate_1-GSM2994892/aligned.36mers.unique.bam
Reading in data... Reading data took 4.36886000633 s
Creating peak regions... Creating peak regions took 48.409129858 s
Estimating background... Estimating background took 27.9299020767 s


Processing CTCF_ChIP-exo_replicate_1-GSM2994892/aligned.36mers.unique.bam
Reading in data... Reading data took 4.75208497047 s
Creating peak regions... Creating peak regions took 44.256218195 s
Estimating background... Estimating background took 30.2869989872 s


Processing CTCF_ChIP-exo_replicate_1-GSM2994892/aligned.36mers.unique.bam
Reading in data... Reading data took 4.38933587074 s
Creating peak regions... Creating peak regions took 41.3507390022 s
Estimating background... Estimating background took 30.0581800938 s


Processing CTCF_ChIP-exo_replicate_1-GSM2994892/aligned.36mers.unique.bam
Reading in data... Reading data took 4.65575814247 s
Creating peak regions... Creating peak regions took 44.499019146 s
Estimating background... Estimating background took 21.9014370441 s


Processing CTCF_ChIP-exo_replicate_1-GSM2994892/aligned.36mers.unique.bam
Reading in data... Reading data took 4.44023799896 s
Creating peak regions... Creating peak regions took 37.6786358356 s
Estimating background... Estimating background took 22.587528944 s


Processing CTCF_ChIP-exo_replicate_1-GSM2994892/aligned.36mers.unique.bam
Reading in data... Reading data took 4.01034402847 s
Creating peak regions... Creating peak regions took 39.5938138962 s
Estimating background... Estimating background took 24.3481650352 s


Processing CTCF_ChIP-exo_replicate_1-GSM2994892/aligned.36mers.unique.bam
Reading in data... Reading data took 4.52649688721 s
Creating peak regions... Creating peak regions took 48.2471539974 s
Estimating background... Estimating background took 26.4825069904 s


Processing CTCF_ChIP-exo_replicate_1-GSM2994892/aligned.36mers.unique.bam
Reading in data... Reading data took 2.10290288925 s
Creating peak regions... Creating peak regions took 31.4897539616 s
Estimating background... Estimating background took 11.3695859909 s


Processing CTCF_ChIP-exo_replicate_1-GSM2994892/aligned.36mers.unique.bam
Reading in data... Reading data took 3.74478888512 s
Creating peak regions... Creating peak regions took 31.7215058804 s
Estimating background... Estimating background took 22.2341418266 s


Processing CTCF_ChIP-exo_replicate_1-GSM2994892/aligned.36mers.unique.bam
Reading in data... Reading data took 3.05716276169 s
Creating peak regions... Creating peak regions took 34.20839715 s
Estimating background... Estimating background took 21.2468690872 s


Processing CTCF_ChIP-exo_replicate_1-GSM2994892/aligned.36mers.unique.bam
Reading in data... Reading data took 2.98970913887 s
Creating peak regions... Creating peak regions took 26.9162638187 s
Estimating background... Estimating background took 17.8645119667 s


Processing CTCF_ChIP-exo_replicate_1-GSM2994892/aligned.36mers.unique.bam
Reading in data... Reading data took 4.64651298523 s
Creating peak regions... Creating peak regions took 25.4588091373 s
Estimating background... Estimating background took 39.3767058849 s


Processing CTCF_ChIP-exo_replicate_1-GSM2994892/aligned.36mers.unique.bam
Reading in data... Reading data took 1.44409799576 s
Creating peak regions... Creating peak regions took 21.3778860569 s
Estimating background... Estimating background took 5.22838306427 s


Processing CTCF_ChIP-exo_replicate_1-GSM2994892/aligned.36mers.unique.bam
Reading in data... Reading data took 2.36943793297 s
Creating peak regions... Creating peak regions took 16.5331940651 s
Estimating background... Estimating background took 12.4753661156 s


Processing CTCF_ChIP-exo_replicate_1-GSM2994892/aligned.36mers.unique.bam
Reading in data... Reading data took 5.0103199482 s
Creating peak regions... Creating peak regions took 20.3712439537 s
Estimating background... Estimating background took 40.6563231945 s


Processing CTCF_ChIP-exo_replicate_1-GSM2994892/aligned.36mers.unique.bam
Reading in data... Reading data took 1.23712205887 s
Creating peak regions... Creating peak regions took 13.3086988926 s
Estimating background... Estimating background took 7.85866880417 s


Processing CTCF_ChIP-exo_replicate_1-GSM2994892/aligned.36mers.unique.bam
Reading in data... Reading data took 0.737004995346 s
Creating peak regions... Creating peak regions took 12.8391129971 s
Estimating background... Estimating background took 5.69650602341 s


Processing CTCF_ChIP-exo_replicate_1-GSM2994892/aligned.36mers.unique.bam
Reading in data... Reading data took 2.92531991005 s
Creating peak regions... Creating peak regions took 43.4179840088 s
Estimating background... Estimating background took 15.819737196 s


Processing CTCF_ChIP-exo_replicate_1-GSM2994892/aligned.36mers.unique.bam
Reading in data... Reading data took 0.0964319705963 s
Creating peak regions... Creating peak regions took 0.231302022934 s
Estimating background... Estimating background took 0.837331056595 s