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='GM07045_VDR_ChIP-exo_VD_stimulated-GSM1889556/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='GM07045_VDR_ChIP-exo_VD_stimulated-GSM1889556/', 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 GM07045_VDR_ChIP-exo_VD_stimulated-GSM1889556/aligned.36mers.unique.bam
Reading in data... Reading data took 2.65108513832 s
Creating peak regions... Creating peak regions took 60.1379230022 s
Estimating background... Estimating background took 7.63431096077 s


Processing GM07045_VDR_ChIP-exo_VD_stimulated-GSM1889556/aligned.36mers.unique.bam
Reading in data... Reading data took 2.82118487358 s
Creating peak regions... Creating peak regions took 58.0463030338 s
Estimating background... Estimating background took 7.89980316162 s


Processing GM07045_VDR_ChIP-exo_VD_stimulated-GSM1889556/aligned.36mers.unique.bam
Reading in data... Reading data took 2.02897286415 s
Creating peak regions... Creating peak regions took 49.8040311337 s
Estimating background... Estimating background took 6.61905407906 s


Processing GM07045_VDR_ChIP-exo_VD_stimulated-GSM1889556/aligned.36mers.unique.bam
Reading in data... Reading data took 1.90785098076 s
Creating peak regions... Creating peak regions took 46.5797848701 s
Estimating background... Estimating background took 6.30709505081 s


Processing GM07045_VDR_ChIP-exo_VD_stimulated-GSM1889556/aligned.36mers.unique.bam
Reading in data... Reading data took 2.067497015 s
Creating peak regions... Creating peak regions took 44.8019618988 s
Estimating background... Estimating background took 5.84003400803 s


Processing GM07045_VDR_ChIP-exo_VD_stimulated-GSM1889556/aligned.36mers.unique.bam
Reading in data... Reading data took 2.02108693123 s
Creating peak regions... Creating peak regions took 43.0727620125 s
Estimating background... Estimating background took 6.09248495102 s


Processing GM07045_VDR_ChIP-exo_VD_stimulated-GSM1889556/aligned.36mers.unique.bam
Reading in data... Reading data took 1.94464492798 s
Creating peak regions... Creating peak regions took 46.1470739841 s
Estimating background... Estimating background took 5.76773691177 s


Processing GM07045_VDR_ChIP-exo_VD_stimulated-GSM1889556/aligned.36mers.unique.bam
Reading in data... Reading data took 1.81985092163 s
Creating peak regions... Creating peak regions took 41.8785150051 s
Estimating background... Estimating background took 5.29010105133 s


Processing GM07045_VDR_ChIP-exo_VD_stimulated-GSM1889556/aligned.36mers.unique.bam
Reading in data... Reading data took 1.2556707859 s
Creating peak regions... Creating peak regions took 35.4831750393 s
Estimating background... Estimating background took 4.69424581528 s


Processing GM07045_VDR_ChIP-exo_VD_stimulated-GSM1889556/aligned.36mers.unique.bam
Reading in data... Reading data took 1.50677704811 s
Creating peak regions... Creating peak regions took 37.6193649769 s
Estimating background... Estimating background took 4.85408496857 s


Processing GM07045_VDR_ChIP-exo_VD_stimulated-GSM1889556/aligned.36mers.unique.bam
Reading in data... Reading data took 1.38929796219 s
Creating peak regions... Creating peak regions took 33.9755790234 s
Estimating background... Estimating background took 4.67922711372 s


Processing GM07045_VDR_ChIP-exo_VD_stimulated-GSM1889556/aligned.36mers.unique.bam
Reading in data... Reading data took 1.42882204056 s
Creating peak regions... Creating peak regions took 37.9519178867 s
Estimating background... Estimating background took 5.09790706635 s


Processing GM07045_VDR_ChIP-exo_VD_stimulated-GSM1889556/aligned.36mers.unique.bam
Reading in data... Reading data took 1.23597717285 s
Creating peak regions... Creating peak regions took 29.3911828995 s
Estimating background... Estimating background took 3.72880887985 s


Processing GM07045_VDR_ChIP-exo_VD_stimulated-GSM1889556/aligned.36mers.unique.bam
Reading in data... Reading data took 1.07046890259 s
Creating peak regions... Creating peak regions took 27.2278130054 s
Estimating background... Estimating background took 4.0977499485 s


Processing GM07045_VDR_ChIP-exo_VD_stimulated-GSM1889556/aligned.36mers.unique.bam
Reading in data... Reading data took 1.04693198204 s
Creating peak regions... Creating peak regions took 25.227560997 s
Estimating background... Estimating background took 1.33927989006 s


Processing GM07045_VDR_ChIP-exo_VD_stimulated-GSM1889556/aligned.36mers.unique.bam
Reading in data... Reading data took 0.91625213623 s
Creating peak regions... Creating peak regions took 21.8191781044 s
Estimating background... Estimating background took 3.30937004089 s


Processing GM07045_VDR_ChIP-exo_VD_stimulated-GSM1889556/aligned.36mers.unique.bam
Reading in data... Reading data took 0.792721033096 s
Creating peak regions... Creating peak regions took 17.6208460331 s
Estimating background... Estimating background took 3.04276013374 s


Processing GM07045_VDR_ChIP-exo_VD_stimulated-GSM1889556/aligned.36mers.unique.bam
Reading in data... Reading data took 0.835860967636 s
Creating peak regions... Creating peak regions took 18.984637022 s
Estimating background... Estimating background took 1.2088701725 s


Processing GM07045_VDR_ChIP-exo_VD_stimulated-GSM1889556/aligned.36mers.unique.bam
Reading in data... Reading data took 0.68029499054 s
Creating peak regions... Creating peak regions took 15.0507700443 s
Estimating background... Estimating background took 1.19970488548 s


Processing GM07045_VDR_ChIP-exo_VD_stimulated-GSM1889556/aligned.36mers.unique.bam
Reading in data... Reading data took 0.84862780571 s
Creating peak regions... Creating peak regions took 16.4609258175 s
Estimating background... Estimating background took 2.51372694969 s


Processing GM07045_VDR_ChIP-exo_VD_stimulated-GSM1889556/aligned.36mers.unique.bam
Reading in data... Reading data took 0.600826978683 s
Creating peak regions... Creating peak regions took 12.3914020061 s
Estimating background... Estimating background took 0.909914970398 s


Processing GM07045_VDR_ChIP-exo_VD_stimulated-GSM1889556/aligned.36mers.unique.bam
Reading in data... Reading data took 0.484519958496 s
Creating peak regions... Creating peak regions took 13.4839498997 s
Estimating background... Estimating background took 2.03790092468 s


Processing GM07045_VDR_ChIP-exo_VD_stimulated-GSM1889556/aligned.36mers.unique.bam
Reading in data... Reading data took 1.28962087631 s
Creating peak regions... Creating peak regions took 39.2781529427 s
Estimating background... Estimating background took 4.79708194733 s


Processing GM07045_VDR_ChIP-exo_VD_stimulated-GSM1889556/aligned.36mers.unique.bam
Reading in data... Reading data took 0.252577066422 s
Creating peak regions... Creating peak regions took 0.160822868347 s
Estimating background... Estimating background took 1.23601317406 s