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='GM19249_VDR_ChIP-exo_VD_stimulated-GSM1889581/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='GM19249_VDR_ChIP-exo_VD_stimulated-GSM1889581/', 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 GM19249_VDR_ChIP-exo_VD_stimulated-GSM1889581/aligned.36mers.unique.bam
Reading in data... Reading data took 8.51170492172 s
Creating peak regions... Creating peak regions took 67.4883658886 s
Estimating background... Estimating background took 44.9895379543 s


Processing GM19249_VDR_ChIP-exo_VD_stimulated-GSM1889581/aligned.36mers.unique.bam
Reading in data... Reading data took 8.90092015266 s
Creating peak regions... Creating peak regions took 71.3159370422 s
Estimating background... Estimating background took 46.4437301159 s


Processing GM19249_VDR_ChIP-exo_VD_stimulated-GSM1889581/aligned.36mers.unique.bam
Reading in data... Reading data took 8.28727984428 s
Creating peak regions... Creating peak regions took 61.8343629837 s
Estimating background... Estimating background took 37.5948870182 s


Processing GM19249_VDR_ChIP-exo_VD_stimulated-GSM1889581/aligned.36mers.unique.bam
Reading in data... Reading data took 7.15041518211 s
Creating peak regions... Creating peak regions took 57.7090761662 s
Estimating background... Estimating background took 32.2711429596 s


Processing GM19249_VDR_ChIP-exo_VD_stimulated-GSM1889581/aligned.36mers.unique.bam
Reading in data... Reading data took 7.45473885536 s
Creating peak regions... Creating peak regions took 59.8258881569 s
Estimating background... Estimating background took 34.493429184 s


Processing GM19249_VDR_ChIP-exo_VD_stimulated-GSM1889581/aligned.36mers.unique.bam
Reading in data... Reading data took 7.20603704453 s
Creating peak regions... Creating peak regions took 54.1517848969 s
Estimating background... Estimating background took 34.0010719299 s


Processing GM19249_VDR_ChIP-exo_VD_stimulated-GSM1889581/aligned.36mers.unique.bam
Reading in data... Reading data took 5.97864198685 s
Creating peak regions... Creating peak regions took 44.7741401196 s
Estimating background... Estimating background took 30.7174367905 s


Processing GM19249_VDR_ChIP-exo_VD_stimulated-GSM1889581/aligned.36mers.unique.bam
Reading in data... Reading data took 7.24410390854 s
Creating peak regions... Creating peak regions took 47.8132548332 s
Estimating background... Estimating background took 27.2431459427 s


Processing GM19249_VDR_ChIP-exo_VD_stimulated-GSM1889581/aligned.36mers.unique.bam
Reading in data... Reading data took 4.69326305389 s
Creating peak regions... Creating peak regions took 39.4385969639 s
Estimating background... Estimating background took 22.7181620598 s


Processing GM19249_VDR_ChIP-exo_VD_stimulated-GSM1889581/aligned.36mers.unique.bam
Reading in data... Reading data took 5.36619710922 s
Creating peak regions... Creating peak regions took 44.5877959728 s
Estimating background... Estimating background took 27.1869029999 s


Processing GM19249_VDR_ChIP-exo_VD_stimulated-GSM1889581/aligned.36mers.unique.bam
Reading in data... Reading data took 5.60038304329 s
Creating peak regions... Creating peak regions took 40.3443880081 s
Estimating background... Estimating background took 26.9776959419 s


Processing GM19249_VDR_ChIP-exo_VD_stimulated-GSM1889581/aligned.36mers.unique.bam
Reading in data... Reading data took 5.27116799355 s
Creating peak regions... Creating peak regions took 36.4109539986 s
Estimating background... Estimating background took 27.3788490295 s


Processing GM19249_VDR_ChIP-exo_VD_stimulated-GSM1889581/aligned.36mers.unique.bam
Reading in data... Reading data took 3.38127994537 s
Creating peak regions... Creating peak regions took 29.277271986 s
Estimating background... Estimating background took 16.9894990921 s


Processing GM19249_VDR_ChIP-exo_VD_stimulated-GSM1889581/aligned.36mers.unique.bam
Reading in data... Reading data took 3.71039605141 s
Creating peak regions... Creating peak regions took 28.4619679451 s
Estimating background... Estimating background took 18.8803741932 s


Processing GM19249_VDR_ChIP-exo_VD_stimulated-GSM1889581/aligned.36mers.unique.bam
Reading in data... Reading data took 3.22954392433 s
Creating peak regions... Creating peak regions took 29.6819930077 s
Estimating background... Estimating background took 16.5127570629 s


Processing GM19249_VDR_ChIP-exo_VD_stimulated-GSM1889581/aligned.36mers.unique.bam
Reading in data... Reading data took 3.77372503281 s
Creating peak regions... Creating peak regions took 26.6241161823 s
Estimating background... Estimating background took 17.65528512 s


Processing GM19249_VDR_ChIP-exo_VD_stimulated-GSM1889581/aligned.36mers.unique.bam
Reading in data... Reading data took 3.04361796379 s
Creating peak regions... Creating peak regions took 25.6594970226 s
Estimating background... Estimating background took 20.8901288509 s


Processing GM19249_VDR_ChIP-exo_VD_stimulated-GSM1889581/aligned.36mers.unique.bam
Reading in data... Reading data took 3.55687308311 s
Creating peak regions... Creating peak regions took 26.4762761593 s
Estimating background... Estimating background took 15.3164160252 s


Processing GM19249_VDR_ChIP-exo_VD_stimulated-GSM1889581/aligned.36mers.unique.bam
Reading in data... Reading data took 2.93426799774 s
Creating peak regions... Creating peak regions took 18.2486269474 s
Estimating background... Estimating background took 14.9097259045 s


Processing GM19249_VDR_ChIP-exo_VD_stimulated-GSM1889581/aligned.36mers.unique.bam
Reading in data... Reading data took 2.83066511154 s
Creating peak regions... Creating peak regions took 18.9419929981 s
Estimating background... Estimating background took 13.0235598087 s


Processing GM19249_VDR_ChIP-exo_VD_stimulated-GSM1889581/aligned.36mers.unique.bam
Reading in data... Reading data took 2.01894497871 s
Creating peak regions... Creating peak regions took 16.1427111626 s
Estimating background... Estimating background took 8.03068304062 s


Processing GM19249_VDR_ChIP-exo_VD_stimulated-GSM1889581/aligned.36mers.unique.bam
Reading in data... Reading data took 1.71667909622 s
Creating peak regions... Creating peak regions took 16.6956310272 s
Estimating background... Estimating background took 8.81967997551 s


Processing GM19249_VDR_ChIP-exo_VD_stimulated-GSM1889581/aligned.36mers.unique.bam
Reading in data... Reading data took 2.99345111847 s
Creating peak regions... Creating peak regions took 44.9452440739 s
Estimating background... Estimating background took 10.2033009529 s


Processing GM19249_VDR_ChIP-exo_VD_stimulated-GSM1889581/aligned.36mers.unique.bam
Reading in data... Reading data took 0.886627912521 s
Creating peak regions... Creating peak regions took 0.454316139221 s
Estimating background... Estimating background took 1.76289606094 s