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/wgEncodeDacMapabilityConsensusExcludable.bed', center6=0, chromnames='/oak/stanford/groups/akundaje/marinovg/genomes/hg19/female.hg19.chrom.sizes', e4='PeakXus', fastq='CTCF_1-50bp_fragment.36mers.hg19-female.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='/oak/stanford/groups/akundaje/marinovg/various/2018-01-08-DamID-ChIPexo-ChEC/06-human-K562-CTCF-ChIP-exo/peakXus-CTCF_1-50bp_fragment/', 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_1-50bp_fragment.36mers.hg19-female.unique.bam
Reading in data... Reading data took 8.18650794029 s
Creating peak regions... Creating peak regions took 95.1067540646 s
Estimating background... Estimating background took 40.0313999653 s


Processing CTCF_1-50bp_fragment.36mers.hg19-female.unique.bam
Reading in data... Reading data took 4.73874020576 s
Creating peak regions... Creating peak regions took 89.2388529778 s
Estimating background... Estimating background took 25.4998509884 s


Processing CTCF_1-50bp_fragment.36mers.hg19-female.unique.bam
Reading in data... Reading data took 5.17051506042 s
Creating peak regions... Creating peak regions took 70.2182278633 s
Estimating background... Estimating background took 25.7251729965 s


Processing CTCF_1-50bp_fragment.36mers.hg19-female.unique.bam
Reading in data... Reading data took 3.06204199791 s
Creating peak regions... Creating peak regions took 70.0885081291 s
Estimating background... Estimating background took 15.3827738762 s


Processing CTCF_1-50bp_fragment.36mers.hg19-female.unique.bam
Reading in data... Reading data took 5.13246393204 s
Creating peak regions... Creating peak regions took 62.710078001 s
Estimating background... Estimating background took 25.0682530403 s


Processing CTCF_1-50bp_fragment.36mers.hg19-female.unique.bam
Reading in data... Reading data took 4.119576931 s
Creating peak regions... Creating peak regions took 60.7418930531 s
Estimating background... Estimating background took 20.7609350681 s


Processing CTCF_1-50bp_fragment.36mers.hg19-female.unique.bam
Reading in data... Reading data took 3.92948102951 s
Creating peak regions... Creating peak regions took 56.2316529751 s
Estimating background... Estimating background took 19.6285619736 s


Processing CTCF_1-50bp_fragment.36mers.hg19-female.unique.bam
Reading in data... Reading data took 3.79074501991 s
Creating peak regions... Creating peak regions took 51.9763269424 s
Estimating background... Estimating background took 18.7973980904 s


Processing CTCF_1-50bp_fragment.36mers.hg19-female.unique.bam
Reading in data... Reading data took 3.76622104645 s
Creating peak regions... Creating peak regions took 52.8990800381 s
Estimating background... Estimating background took 18.6157810688 s


Processing CTCF_1-50bp_fragment.36mers.hg19-female.unique.bam
Reading in data... Reading data took 3.30185580254 s
Creating peak regions... Creating peak regions took 46.557723999 s
Estimating background... Estimating background took 16.8597240448 s


Processing CTCF_1-50bp_fragment.36mers.hg19-female.unique.bam
Reading in data... Reading data took 4.34758019447 s
Creating peak regions... Creating peak regions took 50.714828968 s
Estimating background... Estimating background took 21.6805889606 s


Processing CTCF_1-50bp_fragment.36mers.hg19-female.unique.bam
Reading in data... Reading data took 4.36287093163 s
Creating peak regions... Creating peak regions took 47.7228951454 s
Estimating background... Estimating background took 20.9561288357 s


Processing CTCF_1-50bp_fragment.36mers.hg19-female.unique.bam
Reading in data... Reading data took 1.9969189167 s
Creating peak regions... Creating peak regions took 40.0089919567 s
Estimating background... Estimating background took 9.95664381981 s


Processing CTCF_1-50bp_fragment.36mers.hg19-female.unique.bam
Reading in data... Reading data took 2.3887898922 s
Creating peak regions... Creating peak regions took 37.3672959805 s
Estimating background... Estimating background took 13.1817259789 s


Processing CTCF_1-50bp_fragment.36mers.hg19-female.unique.bam
Reading in data... Reading data took 3.3237118721 s
Creating peak regions... Creating peak regions took 38.0633840561 s
Estimating background... Estimating background took 15.6498310566 s


Processing CTCF_1-50bp_fragment.36mers.hg19-female.unique.bam
Reading in data... Reading data took 2.58286690712 s
Creating peak regions... Creating peak regions took 31.5490128994 s
Estimating background... Estimating background took 12.4268550873 s


Processing CTCF_1-50bp_fragment.36mers.hg19-female.unique.bam
Reading in data... Reading data took 3.04445886612 s
Creating peak regions... Creating peak regions took 29.0880668163 s
Estimating background... Estimating background took 15.0194380283 s


Processing CTCF_1-50bp_fragment.36mers.hg19-female.unique.bam
Reading in data... Reading data took 1.95868706703 s
Creating peak regions... Creating peak regions took 28.6055169106 s
Estimating background... Estimating background took 9.22917103767 s


Processing CTCF_1-50bp_fragment.36mers.hg19-female.unique.bam
Reading in data... Reading data took 2.21610879898 s
Creating peak regions... Creating peak regions took 20.70134902 s
Estimating background... Estimating background took 12.1233870983 s


Processing CTCF_1-50bp_fragment.36mers.hg19-female.unique.bam
Reading in data... Reading data took 2.02825808525 s
Creating peak regions... Creating peak regions took 22.2336881161 s
Estimating background... Estimating background took 10.779695034 s


Processing CTCF_1-50bp_fragment.36mers.hg19-female.unique.bam
Reading in data... Reading data took 0.982616901398 s
Creating peak regions... Creating peak regions took 15.9988059998 s
Estimating background... Estimating background took 5.21509194374 s


Processing CTCF_1-50bp_fragment.36mers.hg19-female.unique.bam
Reading in data... Reading data took 0.868983030319 s
Creating peak regions... Creating peak regions took 18.1270508766 s
Estimating background... Estimating background took 4.06323194504 s


Processing CTCF_1-50bp_fragment.36mers.hg19-female.unique.bam
Reading in data... Reading data took 3.24626493454 s
Creating peak regions... Creating peak regions took 58.2633221149 s
Estimating background... Estimating background took 14.333053112 s


Processing CTCF_1-50bp_fragment.36mers.hg19-female.unique.bam
Reading in data... Reading data took 0.132868051529 s
Creating peak regions... Creating peak regions took 0.202564954758 s
Estimating background... Estimating background took 0.909596920013 s