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_2-GSM2994891/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_2-GSM2994891/', 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_2-GSM2994891/aligned.36mers.unique.bam
Reading in data... Reading data took 5.23987102509 s
Creating peak regions... Creating peak regions took 62.1366579533 s
Estimating background... Estimating background took 31.4301640987 s


Processing FoxA1_ChIP-exo_replicate_2-GSM2994891/aligned.36mers.unique.bam
Reading in data... Reading data took 5.76143503189 s
Creating peak regions... Creating peak regions took 63.5421760082 s
Estimating background... Estimating background took 26.0238649845 s


Processing FoxA1_ChIP-exo_replicate_2-GSM2994891/aligned.36mers.unique.bam
Reading in data... Reading data took 5.88037109375 s
Creating peak regions... Creating peak regions took 65.7317121029 s
Estimating background... Estimating background took 32.2690029144 s


Processing FoxA1_ChIP-exo_replicate_2-GSM2994891/aligned.36mers.unique.bam
Reading in data... Reading data took 3.97773599625 s
Creating peak regions... Creating peak regions took 55.9084758759 s
Estimating background... Estimating background took 14.963835001 s


Processing FoxA1_ChIP-exo_replicate_2-GSM2994891/aligned.36mers.unique.bam
Reading in data... Reading data took 4.43557810783 s
Creating peak regions... Creating peak regions took 56.7604620457 s
Estimating background... Estimating background took 22.1864528656 s


Processing FoxA1_ChIP-exo_replicate_2-GSM2994891/aligned.36mers.unique.bam
Reading in data... Reading data took 3.90874481201 s
Creating peak regions... Creating peak regions took 51.765971899 s
Estimating background... Estimating background took 20.0765590668 s


Processing FoxA1_ChIP-exo_replicate_2-GSM2994891/aligned.36mers.unique.bam
Reading in data... Reading data took 4.04183888435 s
Creating peak regions... Creating peak regions took 44.606235981 s
Estimating background... Estimating background took 19.399960041 s


Processing FoxA1_ChIP-exo_replicate_2-GSM2994891/aligned.36mers.unique.bam
Reading in data... Reading data took 4.28915905952 s
Creating peak regions... Creating peak regions took 42.4647648335 s
Estimating background... Estimating background took 19.1769859791 s


Processing FoxA1_ChIP-exo_replicate_2-GSM2994891/aligned.36mers.unique.bam
Reading in data... Reading data took 3.25793600082 s
Creating peak regions... Creating peak regions took 40.8039391041 s
Estimating background... Estimating background took 13.7989239693 s


Processing FoxA1_ChIP-exo_replicate_2-GSM2994891/aligned.36mers.unique.bam
Reading in data... Reading data took 2.952876091 s
Creating peak regions... Creating peak regions took 38.3326079845 s
Estimating background... Estimating background took 15.422850132 s


Processing FoxA1_ChIP-exo_replicate_2-GSM2994891/aligned.36mers.unique.bam
Reading in data... Reading data took 3.09470105171 s
Creating peak regions... Creating peak regions took 34.7352759838 s
Estimating background... Estimating background took 12.1148569584 s


Processing FoxA1_ChIP-exo_replicate_2-GSM2994891/aligned.36mers.unique.bam
Reading in data... Reading data took 3.63366794586 s
Creating peak regions... Creating peak regions took 38.7904520035 s
Estimating background... Estimating background took 15.6105601788 s


Processing FoxA1_ChIP-exo_replicate_2-GSM2994891/aligned.36mers.unique.bam
Reading in data... Reading data took 1.92098903656 s
Creating peak regions... Creating peak regions took 33.9254591465 s
Estimating background... Estimating background took 7.87486505508 s


Processing FoxA1_ChIP-exo_replicate_2-GSM2994891/aligned.36mers.unique.bam
Reading in data... Reading data took 2.86297392845 s
Creating peak regions... Creating peak regions took 30.5526521206 s
Estimating background... Estimating background took 15.2573750019 s


Processing FoxA1_ChIP-exo_replicate_2-GSM2994891/aligned.36mers.unique.bam
Reading in data... Reading data took 2.67147183418 s
Creating peak regions... Creating peak regions took 27.4773728848 s
Estimating background... Estimating background took 12.780591011 s


Processing FoxA1_ChIP-exo_replicate_2-GSM2994891/aligned.36mers.unique.bam
Reading in data... Reading data took 2.34471297264 s
Creating peak regions... Creating peak regions took 30.3401780128 s
Estimating background... Estimating background took 11.4306671619 s


Processing FoxA1_ChIP-exo_replicate_2-GSM2994891/aligned.36mers.unique.bam
Reading in data... Reading data took 3.44410610199 s
Creating peak regions... Creating peak regions took 24.4112999439 s
Estimating background... Estimating background took 26.8802449703 s


Processing FoxA1_ChIP-exo_replicate_2-GSM2994891/aligned.36mers.unique.bam
Reading in data... Reading data took 1.21612286568 s
Creating peak regions... Creating peak regions took 22.8851211071 s
Estimating background... Estimating background took 5.35504484177 s


Processing FoxA1_ChIP-exo_replicate_2-GSM2994891/aligned.36mers.unique.bam
Reading in data... Reading data took 1.61218595505 s
Creating peak regions... Creating peak regions took 19.3908109665 s
Estimating background... Estimating background took 5.92491316795 s


Processing FoxA1_ChIP-exo_replicate_2-GSM2994891/aligned.36mers.unique.bam
Reading in data... Reading data took 3.45185399055 s
Creating peak regions... Creating peak regions took 20.3798611164 s
Estimating background... Estimating background took 31.5770039558 s


Processing FoxA1_ChIP-exo_replicate_2-GSM2994891/aligned.36mers.unique.bam
Reading in data... Reading data took 1.08467507362 s
Creating peak regions... Creating peak regions took 14.3279709816 s
Estimating background... Estimating background took 5.13606095314 s


Processing FoxA1_ChIP-exo_replicate_2-GSM2994891/aligned.36mers.unique.bam
Reading in data... Reading data took 0.71836400032 s
Creating peak regions... Creating peak regions took 15.215734005 s
Estimating background... Estimating background took 3.18455386162 s


Processing FoxA1_ChIP-exo_replicate_2-GSM2994891/aligned.36mers.unique.bam
Reading in data... Reading data took 2.54994106293 s
Creating peak regions... Creating peak regions took 44.1302418709 s
Estimating background... Estimating background took 9.76222896576 s


Processing FoxA1_ChIP-exo_replicate_2-GSM2994891/aligned.36mers.unique.bam
Reading in data... Reading data took 0.0924258232117 s
Creating peak regions... Creating peak regions took 0.209510087967 s
Estimating background... Estimating background took 0.692137002945 s