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='GM11832_VDR_ChIP-exo_VD_stimulated-GSM1889561/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='GM11832_VDR_ChIP-exo_VD_stimulated-GSM1889561/', 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 GM11832_VDR_ChIP-exo_VD_stimulated-GSM1889561/aligned.36mers.unique.bam
Reading in data... Reading data took 3.01737809181 s
Creating peak regions... Creating peak regions took 61.9399402142 s
Estimating background... Estimating background took 7.84951090813 s


Processing GM11832_VDR_ChIP-exo_VD_stimulated-GSM1889561/aligned.36mers.unique.bam
Reading in data... Reading data took 3.54360485077 s
Creating peak regions... Creating peak regions took 73.0381190777 s
Estimating background... Estimating background took 8.02517104149 s


Processing GM11832_VDR_ChIP-exo_VD_stimulated-GSM1889561/aligned.36mers.unique.bam
Reading in data... Reading data took 2.36255192757 s
Creating peak regions... Creating peak regions took 52.7367589474 s
Estimating background... Estimating background took 6.64462304115 s


Processing GM11832_VDR_ChIP-exo_VD_stimulated-GSM1889561/aligned.36mers.unique.bam
Reading in data... Reading data took 2.52782392502 s
Creating peak regions... Creating peak regions took 57.3974280357 s
Estimating background... Estimating background took 6.16652107239 s


Processing GM11832_VDR_ChIP-exo_VD_stimulated-GSM1889561/aligned.36mers.unique.bam
Reading in data... Reading data took 2.27048206329 s
Creating peak regions... Creating peak regions took 50.3326900005 s
Estimating background... Estimating background took 5.87731003761 s


Processing GM11832_VDR_ChIP-exo_VD_stimulated-GSM1889561/aligned.36mers.unique.bam
Reading in data... Reading data took 2.23386001587 s
Creating peak regions... Creating peak regions took 44.5024840832 s
Estimating background... Estimating background took 5.86952114105 s


Processing GM11832_VDR_ChIP-exo_VD_stimulated-GSM1889561/aligned.36mers.unique.bam
Reading in data... Reading data took 1.6802239418 s
Creating peak regions... Creating peak regions took 41.8641700745 s
Estimating background... Estimating background took 5.43213105202 s


Processing GM11832_VDR_ChIP-exo_VD_stimulated-GSM1889561/aligned.36mers.unique.bam
Reading in data... Reading data took 1.98171210289 s
Creating peak regions... Creating peak regions took 38.1215009689 s
Estimating background... Estimating background took 5.02459096909 s


Processing GM11832_VDR_ChIP-exo_VD_stimulated-GSM1889561/aligned.36mers.unique.bam
Reading in data... Reading data took 1.25096797943 s
Creating peak regions... Creating peak regions took 36.6878008842 s
Estimating background... Estimating background took 4.77774500847 s


Processing GM11832_VDR_ChIP-exo_VD_stimulated-GSM1889561/aligned.36mers.unique.bam
Reading in data... Reading data took 1.76726412773 s
Creating peak regions... Creating peak regions took 34.7819259167 s
Estimating background... Estimating background took 4.92172813416 s


Processing GM11832_VDR_ChIP-exo_VD_stimulated-GSM1889561/aligned.36mers.unique.bam
Reading in data... Reading data took 1.64742588997 s
Creating peak regions... Creating peak regions took 39.9147469997 s
Estimating background... Estimating background took 5.27859807014 s


Processing GM11832_VDR_ChIP-exo_VD_stimulated-GSM1889561/aligned.36mers.unique.bam
Reading in data... Reading data took 1.64383387566 s
Creating peak regions... Creating peak regions took 34.8888838291 s
Estimating background... Estimating background took 4.75023508072 s


Processing GM11832_VDR_ChIP-exo_VD_stimulated-GSM1889561/aligned.36mers.unique.bam
Reading in data... Reading data took 1.4824950695 s
Creating peak regions... Creating peak regions took 29.5633170605 s
Estimating background... Estimating background took 3.75926399231 s


Processing GM11832_VDR_ChIP-exo_VD_stimulated-GSM1889561/aligned.36mers.unique.bam
Reading in data... Reading data took 1.4042289257 s
Creating peak regions... Creating peak regions took 27.9499258995 s
Estimating background... Estimating background took 3.82171416283 s


Processing GM11832_VDR_ChIP-exo_VD_stimulated-GSM1889561/aligned.36mers.unique.bam
Reading in data... Reading data took 0.908426046371 s
Creating peak regions... Creating peak regions took 24.5434701443 s
Estimating background... Estimating background took 3.56674599648 s


Processing GM11832_VDR_ChIP-exo_VD_stimulated-GSM1889561/aligned.36mers.unique.bam
Reading in data... Reading data took 0.989919900894 s
Creating peak regions... Creating peak regions took 23.4056508541 s
Estimating background... Estimating background took 1.508715868 s


Processing GM11832_VDR_ChIP-exo_VD_stimulated-GSM1889561/aligned.36mers.unique.bam
Reading in data... Reading data took 1.43476200104 s
Creating peak regions... Creating peak regions took 21.9743001461 s
Estimating background... Estimating background took 3.42136597633 s


Processing GM11832_VDR_ChIP-exo_VD_stimulated-GSM1889561/aligned.36mers.unique.bam
Reading in data... Reading data took 1.09598207474 s
Creating peak regions... Creating peak regions took 20.1267049313 s
Estimating background... Estimating background took 1.40323781967 s


Processing GM11832_VDR_ChIP-exo_VD_stimulated-GSM1889561/aligned.36mers.unique.bam
Reading in data... Reading data took 0.801148891449 s
Creating peak regions... Creating peak regions took 17.6359710693 s
Estimating background... Estimating background took 2.8128490448 s


Processing GM11832_VDR_ChIP-exo_VD_stimulated-GSM1889561/aligned.36mers.unique.bam
Reading in data... Reading data took 1.07162880898 s
Creating peak regions... Creating peak regions took 16.7752079964 s
Estimating background... Estimating background took 2.86723685265 s


Processing GM11832_VDR_ChIP-exo_VD_stimulated-GSM1889561/aligned.36mers.unique.bam
Reading in data... Reading data took 0.44082403183 s
Creating peak regions... Creating peak regions took 11.0243160725 s
Estimating background... Estimating background took 0.999947071075 s


Processing GM11832_VDR_ChIP-exo_VD_stimulated-GSM1889561/aligned.36mers.unique.bam
Reading in data... Reading data took 0.649415016174 s
Creating peak regions... Creating peak regions took 13.6505000591 s
Estimating background... Estimating background took 0.890357971191 s


Processing GM11832_VDR_ChIP-exo_VD_stimulated-GSM1889561/aligned.36mers.unique.bam
Reading in data... Reading data took 1.621778965 s
Creating peak regions... Creating peak regions took 38.1561689377 s
Estimating background... Estimating background took 4.76941204071 s


Processing GM11832_VDR_ChIP-exo_VD_stimulated-GSM1889561/aligned.36mers.unique.bam
Reading in data... Reading data took 0.350077867508 s
Creating peak regions... Creating peak regions took 0.178951978683 s
Estimating background... Estimating background took 1.31023907661 s