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='GM19215_VDR_ChIP-exo_VD_stimulated-GSM1889575/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='GM19215_VDR_ChIP-exo_VD_stimulated-GSM1889575/', 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 GM19215_VDR_ChIP-exo_VD_stimulated-GSM1889575/aligned.36mers.unique.bam
Reading in data... Reading data took 1.28206706047 s
Creating peak regions... Creating peak regions took 73.5057609081 s
Estimating background... Estimating background took 6.5401468277 s


Processing GM19215_VDR_ChIP-exo_VD_stimulated-GSM1889575/aligned.36mers.unique.bam
Reading in data... Reading data took 1.24429702759 s
Creating peak regions... Creating peak regions took 82.1263730526 s
Estimating background... Estimating background took 1.05141401291 s


Processing GM19215_VDR_ChIP-exo_VD_stimulated-GSM1889575/aligned.36mers.unique.bam
Reading in data... Reading data took 1.20601987839 s
Creating peak regions... Creating peak regions took 65.0036280155 s
Estimating background... Estimating background took 7.39824604988 s


Processing GM19215_VDR_ChIP-exo_VD_stimulated-GSM1889575/aligned.36mers.unique.bam
Reading in data... Reading data took 0.944226026535 s
Creating peak regions... Creating peak regions took 61.4209558964 s
Estimating background... Estimating background took 0.963576793671 s


Processing GM19215_VDR_ChIP-exo_VD_stimulated-GSM1889575/aligned.36mers.unique.bam
Reading in data... Reading data took 1.05667805672 s
Creating peak regions... Creating peak regions took 58.1096830368 s
Estimating background... Estimating background took 0.941796064377 s


Processing GM19215_VDR_ChIP-exo_VD_stimulated-GSM1889575/aligned.36mers.unique.bam
Reading in data... Reading data took 1.07120203972 s
Creating peak regions... Creating peak regions took 54.3658251762 s
Estimating background... Estimating background took 5.43784213066 s


Processing GM19215_VDR_ChIP-exo_VD_stimulated-GSM1889575/aligned.36mers.unique.bam
Reading in data... Reading data took 0.736174106598 s
Creating peak regions... Creating peak regions took 44.7096610069 s
Estimating background... Estimating background took 4.66188788414 s


Processing GM19215_VDR_ChIP-exo_VD_stimulated-GSM1889575/aligned.36mers.unique.bam
Reading in data... Reading data took 0.71915602684 s
Creating peak regions... Creating peak regions took 45.5799181461 s
Estimating background... Estimating background took 0.85254406929 s


Processing GM19215_VDR_ChIP-exo_VD_stimulated-GSM1889575/aligned.36mers.unique.bam
Reading in data... Reading data took 0.723072052002 s
Creating peak regions... Creating peak regions took 41.2881560326 s
Estimating background... Estimating background took 0.74184513092 s


Processing GM19215_VDR_ChIP-exo_VD_stimulated-GSM1889575/aligned.36mers.unique.bam
Reading in data... Reading data took 0.92219209671 s
Creating peak regions... Creating peak regions took 45.6480638981 s
Estimating background... Estimating background took 0.83460521698 s


Processing GM19215_VDR_ChIP-exo_VD_stimulated-GSM1889575/aligned.36mers.unique.bam
Reading in data... Reading data took 0.794327020645 s
Creating peak regions... Creating peak regions took 39.5317790508 s
Estimating background... Estimating background took 0.824171066284 s


Processing GM19215_VDR_ChIP-exo_VD_stimulated-GSM1889575/aligned.36mers.unique.bam
Reading in data... Reading data took 0.796810865402 s
Creating peak regions... Creating peak regions took 38.6253681183 s
Estimating background... Estimating background took 0.859547138214 s


Processing GM19215_VDR_ChIP-exo_VD_stimulated-GSM1889575/aligned.36mers.unique.bam
Reading in data... Reading data took 0.576214790344 s
Creating peak regions... Creating peak regions took 39.471626997 s
Estimating background... Estimating background took 4.15985298157 s


Processing GM19215_VDR_ChIP-exo_VD_stimulated-GSM1889575/aligned.36mers.unique.bam
Reading in data... Reading data took 0.476523160934 s
Creating peak regions... Creating peak regions took 34.0038590431 s
Estimating background... Estimating background took 0.655596971512 s


Processing GM19215_VDR_ChIP-exo_VD_stimulated-GSM1889575/aligned.36mers.unique.bam
Reading in data... Reading data took 0.508358001709 s
Creating peak regions... Creating peak regions took 32.859746933 s
Estimating background... Estimating background took 0.627253055573 s


Processing GM19215_VDR_ChIP-exo_VD_stimulated-GSM1889575/aligned.36mers.unique.bam
Reading in data... Reading data took 0.468909025192 s
Creating peak regions... Creating peak regions took 25.9363441467 s
Estimating background... Estimating background took 0.744141101837 s


Processing GM19215_VDR_ChIP-exo_VD_stimulated-GSM1889575/aligned.36mers.unique.bam
Reading in data... Reading data took 0.612473964691 s
Creating peak regions... Creating peak regions took 23.7065021992 s
Estimating background... Estimating background took 0.653089046478 s


Processing GM19215_VDR_ChIP-exo_VD_stimulated-GSM1889575/aligned.36mers.unique.bam
Reading in data... Reading data took 0.45671415329 s
Creating peak regions... Creating peak regions took 23.5285770893 s
Estimating background... Estimating background took 0.63990688324 s


Processing GM19215_VDR_ChIP-exo_VD_stimulated-GSM1889575/aligned.36mers.unique.bam
Reading in data... Reading data took 0.327212095261 s
Creating peak regions... Creating peak regions took 17.9892580509 s
Estimating background... Estimating background took 0.64431810379 s


Processing GM19215_VDR_ChIP-exo_VD_stimulated-GSM1889575/aligned.36mers.unique.bam
Reading in data... Reading data took 0.409046173096 s
Creating peak regions... Creating peak regions took 19.1513791084 s
Estimating background... Estimating background took 0.651440858841 s


Processing GM19215_VDR_ChIP-exo_VD_stimulated-GSM1889575/aligned.36mers.unique.bam
Reading in data... Reading data took 0.248471975327 s
Creating peak regions... Creating peak regions took 14.935147047 s
Estimating background... Estimating background took 0.638438940048 s


Processing GM19215_VDR_ChIP-exo_VD_stimulated-GSM1889575/aligned.36mers.unique.bam
Reading in data... Reading data took 0.241449117661 s
Creating peak regions... Creating peak regions took 15.963570118 s
Estimating background... Estimating background took 0.53906416893 s


Processing GM19215_VDR_ChIP-exo_VD_stimulated-GSM1889575/aligned.36mers.unique.bam
Reading in data... Reading data took 0.800733089447 s
Creating peak regions... Creating peak regions took 47.0876560211 s
Estimating background... Estimating background took 0.615792036057 s


Processing GM19215_VDR_ChIP-exo_VD_stimulated-GSM1889575/aligned.36mers.unique.bam
Reading in data... Reading data took 0.291234016418 s
Creating peak regions... Creating peak regions took 0.151739120483 s
Estimating background... Estimating background took 4.93310308456 s