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='GM19191_VDR_ChIP-exo_VD_stimulated-GSM1889572/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='GM19191_VDR_ChIP-exo_VD_stimulated-GSM1889572/', 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 GM19191_VDR_ChIP-exo_VD_stimulated-GSM1889572/aligned.36mers.unique.bam
Reading in data... Reading data took 6.14884591103 s
Creating peak regions... Creating peak regions took 78.1261770725 s
Estimating background... Estimating background took 21.2905771732 s


Processing GM19191_VDR_ChIP-exo_VD_stimulated-GSM1889572/aligned.36mers.unique.bam
Reading in data... Reading data took 6.90092182159 s
Creating peak regions... Creating peak regions took 79.9921929836 s
Estimating background... Estimating background took 22.3661839962 s


Processing GM19191_VDR_ChIP-exo_VD_stimulated-GSM1889572/aligned.36mers.unique.bam
Reading in data... Reading data took 5.57508778572 s
Creating peak regions... Creating peak regions took 61.1345870495 s
Estimating background... Estimating background took 19.0237560272 s


Processing GM19191_VDR_ChIP-exo_VD_stimulated-GSM1889572/aligned.36mers.unique.bam
Reading in data... Reading data took 5.53283405304 s
Creating peak regions... Creating peak regions took 62.8910958767 s
Estimating background... Estimating background took 18.7401828766 s


Processing GM19191_VDR_ChIP-exo_VD_stimulated-GSM1889572/aligned.36mers.unique.bam
Reading in data... Reading data took 5.4909799099 s
Creating peak regions... Creating peak regions took 65.7065019608 s
Estimating background... Estimating background took 17.2547011375 s


Processing GM19191_VDR_ChIP-exo_VD_stimulated-GSM1889572/aligned.36mers.unique.bam
Reading in data... Reading data took 5.26736903191 s
Creating peak regions... Creating peak regions took 56.1689012051 s
Estimating background... Estimating background took 16.9820959568 s


Processing GM19191_VDR_ChIP-exo_VD_stimulated-GSM1889572/aligned.36mers.unique.bam
Reading in data... Reading data took 5.11990499496 s
Creating peak regions... Creating peak regions took 52.4905498028 s
Estimating background... Estimating background took 13.9980208874 s


Processing GM19191_VDR_ChIP-exo_VD_stimulated-GSM1889572/aligned.36mers.unique.bam
Reading in data... Reading data took 4.06236290932 s
Creating peak regions... Creating peak regions took 48.0243990421 s
Estimating background... Estimating background took 13.4251101017 s


Processing GM19191_VDR_ChIP-exo_VD_stimulated-GSM1889572/aligned.36mers.unique.bam
Reading in data... Reading data took 3.36213088036 s
Creating peak regions... Creating peak regions took 42.8130691051 s
Estimating background... Estimating background took 10.9716639519 s


Processing GM19191_VDR_ChIP-exo_VD_stimulated-GSM1889572/aligned.36mers.unique.bam
Reading in data... Reading data took 3.70047092438 s
Creating peak regions... Creating peak regions took 43.5347239971 s
Estimating background... Estimating background took 12.4144778252 s


Processing GM19191_VDR_ChIP-exo_VD_stimulated-GSM1889572/aligned.36mers.unique.bam
Reading in data... Reading data took 4.10679316521 s
Creating peak regions... Creating peak regions took 44.7878749371 s
Estimating background... Estimating background took 12.8836839199 s


Processing GM19191_VDR_ChIP-exo_VD_stimulated-GSM1889572/aligned.36mers.unique.bam
Reading in data... Reading data took 3.82355809212 s
Creating peak regions... Creating peak regions took 48.1506049633 s
Estimating background... Estimating background took 13.134955883 s


Processing GM19191_VDR_ChIP-exo_VD_stimulated-GSM1889572/aligned.36mers.unique.bam
Reading in data... Reading data took 2.79746103287 s
Creating peak regions... Creating peak regions took 35.4354500771 s
Estimating background... Estimating background took 9.44687700272 s


Processing GM19191_VDR_ChIP-exo_VD_stimulated-GSM1889572/aligned.36mers.unique.bam
Reading in data... Reading data took 2.87693190575 s
Creating peak regions... Creating peak regions took 39.4220819473 s
Estimating background... Estimating background took 8.91454291344 s


Processing GM19191_VDR_ChIP-exo_VD_stimulated-GSM1889572/aligned.36mers.unique.bam
Reading in data... Reading data took 2.27104711533 s
Creating peak regions... Creating peak regions took 33.1329960823 s
Estimating background... Estimating background took 8.08825206757 s


Processing GM19191_VDR_ChIP-exo_VD_stimulated-GSM1889572/aligned.36mers.unique.bam
Reading in data... Reading data took 2.19237780571 s
Creating peak regions... Creating peak regions took 28.7911159992 s
Estimating background... Estimating background took 7.49635386467 s


Processing GM19191_VDR_ChIP-exo_VD_stimulated-GSM1889572/aligned.36mers.unique.bam
Reading in data... Reading data took 2.09732198715 s
Creating peak regions... Creating peak regions took 26.7035501003 s
Estimating background... Estimating background took 7.82814192772 s


Processing GM19191_VDR_ChIP-exo_VD_stimulated-GSM1889572/aligned.36mers.unique.bam
Reading in data... Reading data took 2.21678090096 s
Creating peak regions... Creating peak regions took 25.8269422054 s
Estimating background... Estimating background took 7.42370986938 s


Processing GM19191_VDR_ChIP-exo_VD_stimulated-GSM1889572/aligned.36mers.unique.bam
Reading in data... Reading data took 1.525578022 s
Creating peak regions... Creating peak regions took 19.2887628078 s
Estimating background... Estimating background took 5.16294407845 s


Processing GM19191_VDR_ChIP-exo_VD_stimulated-GSM1889572/aligned.36mers.unique.bam
Reading in data... Reading data took 1.7037050724 s
Creating peak regions... Creating peak regions took 20.5018239021 s
Estimating background... Estimating background took 5.61801409721 s


Processing GM19191_VDR_ChIP-exo_VD_stimulated-GSM1889572/aligned.36mers.unique.bam
Reading in data... Reading data took 1.02960205078 s
Creating peak regions... Creating peak regions took 15.2017831802 s
Estimating background... Estimating background took 4.16078996658 s


Processing GM19191_VDR_ChIP-exo_VD_stimulated-GSM1889572/aligned.36mers.unique.bam
Reading in data... Reading data took 0.913558959961 s
Creating peak regions... Creating peak regions took 15.7120940685 s
Estimating background... Estimating background took 3.64010691643 s


Processing GM19191_VDR_ChIP-exo_VD_stimulated-GSM1889572/aligned.36mers.unique.bam
Reading in data... Reading data took 2.25290083885 s
Creating peak regions... Creating peak regions took 49.9193580151 s
Estimating background... Estimating background took 6.67802596092 s


Processing GM19191_VDR_ChIP-exo_VD_stimulated-GSM1889572/aligned.36mers.unique.bam
Reading in data... Reading data took 1.19309616089 s
Creating peak regions... Creating peak regions took 0.256279945374 s
Estimating background... Estimating background took 1.72883582115 s