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='GM12264_VDR_ChIP-exo_VD_stimulated-GSM1889564/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='GM12264_VDR_ChIP-exo_VD_stimulated-GSM1889564/', 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 GM12264_VDR_ChIP-exo_VD_stimulated-GSM1889564/aligned.36mers.unique.bam
Reading in data... Reading data took 2.01489806175 s
Creating peak regions... Creating peak regions took 64.8397541046 s
Estimating background... Estimating background took 7.94450092316 s


Processing GM12264_VDR_ChIP-exo_VD_stimulated-GSM1889564/aligned.36mers.unique.bam
Reading in data... Reading data took 1.60247182846 s
Creating peak regions... Creating peak regions took 58.8975729942 s
Estimating background... Estimating background took 5.86700320244 s


Processing GM12264_VDR_ChIP-exo_VD_stimulated-GSM1889564/aligned.36mers.unique.bam
Reading in data... Reading data took 1.68203210831 s
Creating peak regions... Creating peak regions took 49.5055251122 s
Estimating background... Estimating background took 5.44117903709 s


Processing GM12264_VDR_ChIP-exo_VD_stimulated-GSM1889564/aligned.36mers.unique.bam
Reading in data... Reading data took 1.0337600708 s
Creating peak regions... Creating peak regions took 48.0561959743 s
Estimating background... Estimating background took 4.97176003456 s


Processing GM12264_VDR_ChIP-exo_VD_stimulated-GSM1889564/aligned.36mers.unique.bam
Reading in data... Reading data took 1.43854999542 s
Creating peak regions... Creating peak regions took 41.8017289639 s
Estimating background... Estimating background took 0.991928100586 s


Processing GM12264_VDR_ChIP-exo_VD_stimulated-GSM1889564/aligned.36mers.unique.bam
Reading in data... Reading data took 1.48735713959 s
Creating peak regions... Creating peak regions took 38.4307088852 s
Estimating background... Estimating background took 4.58375287056 s


Processing GM12264_VDR_ChIP-exo_VD_stimulated-GSM1889564/aligned.36mers.unique.bam
Reading in data... Reading data took 1.14588999748 s
Creating peak regions... Creating peak regions took 42.5246529579 s
Estimating background... Estimating background took 0.954375982285 s


Processing GM12264_VDR_ChIP-exo_VD_stimulated-GSM1889564/aligned.36mers.unique.bam
Reading in data... Reading data took 1.16997098923 s
Creating peak regions... Creating peak regions took 34.5061991215 s
Estimating background... Estimating background took 0.958503961563 s


Processing GM12264_VDR_ChIP-exo_VD_stimulated-GSM1889564/aligned.36mers.unique.bam
Reading in data... Reading data took 1.25760602951 s
Creating peak regions... Creating peak regions took 31.9300031662 s
Estimating background... Estimating background took 3.80571198463 s


Processing GM12264_VDR_ChIP-exo_VD_stimulated-GSM1889564/aligned.36mers.unique.bam
Reading in data... Reading data took 0.905559062958 s
Creating peak regions... Creating peak regions took 30.3351581097 s
Estimating background... Estimating background took 0.865588903427 s


Processing GM12264_VDR_ChIP-exo_VD_stimulated-GSM1889564/aligned.36mers.unique.bam
Reading in data... Reading data took 1.23858690262 s
Creating peak regions... Creating peak regions took 30.0178639889 s
Estimating background... Estimating background took 3.62147903442 s


Processing GM12264_VDR_ChIP-exo_VD_stimulated-GSM1889564/aligned.36mers.unique.bam
Reading in data... Reading data took 1.18198180199 s
Creating peak regions... Creating peak regions took 29.9420289993 s
Estimating background... Estimating background took 0.755439996719 s


Processing GM12264_VDR_ChIP-exo_VD_stimulated-GSM1889564/aligned.36mers.unique.bam
Reading in data... Reading data took 0.60769200325 s
Creating peak regions... Creating peak regions took 26.1246888638 s
Estimating background... Estimating background took 0.692212104797 s


Processing GM12264_VDR_ChIP-exo_VD_stimulated-GSM1889564/aligned.36mers.unique.bam
Reading in data... Reading data took 0.812597990036 s
Creating peak regions... Creating peak regions took 25.6521449089 s
Estimating background... Estimating background took 3.5380179882 s


Processing GM12264_VDR_ChIP-exo_VD_stimulated-GSM1889564/aligned.36mers.unique.bam
Reading in data... Reading data took 0.491302967072 s
Creating peak regions... Creating peak regions took 23.0442669392 s
Estimating background... Estimating background took 0.649479866028 s


Processing GM12264_VDR_ChIP-exo_VD_stimulated-GSM1889564/aligned.36mers.unique.bam
Reading in data... Reading data took 0.632911920547 s
Creating peak regions... Creating peak regions took 20.6718931198 s
Estimating background... Estimating background took 0.640195846558 s


Processing GM12264_VDR_ChIP-exo_VD_stimulated-GSM1889564/aligned.36mers.unique.bam
Reading in data... Reading data took 0.667392015457 s
Creating peak regions... Creating peak regions took 17.8678028584 s
Estimating background... Estimating background took 0.742941141129 s


Processing GM12264_VDR_ChIP-exo_VD_stimulated-GSM1889564/aligned.36mers.unique.bam
Reading in data... Reading data took 0.613268852234 s
Creating peak regions... Creating peak regions took 17.0114700794 s
Estimating background... Estimating background took 0.658890962601 s


Processing GM12264_VDR_ChIP-exo_VD_stimulated-GSM1889564/aligned.36mers.unique.bam
Reading in data... Reading data took 0.361544132233 s
Creating peak regions... Creating peak regions took 13.5306558609 s
Estimating background... Estimating background took 2.56779789925 s


Processing GM12264_VDR_ChIP-exo_VD_stimulated-GSM1889564/aligned.36mers.unique.bam
Reading in data... Reading data took 0.366291046143 s
Creating peak regions... Creating peak regions took 14.4345321655 s
Estimating background... Estimating background took 0.664987802505 s


Processing GM12264_VDR_ChIP-exo_VD_stimulated-GSM1889564/aligned.36mers.unique.bam
Reading in data... Reading data took 0.424762010574 s
Creating peak regions... Creating peak regions took 12.9916138649 s
Estimating background... Estimating background took 0.599597930908 s


Processing GM12264_VDR_ChIP-exo_VD_stimulated-GSM1889564/aligned.36mers.unique.bam
Reading in data... Reading data took 0.304263114929 s
Creating peak regions... Creating peak regions took 12.6478869915 s
Estimating background... Estimating background took 0.516253948212 s


Processing GM12264_VDR_ChIP-exo_VD_stimulated-GSM1889564/aligned.36mers.unique.bam
Reading in data... Reading data took 0.684621095657 s
Creating peak regions... Creating peak regions took 39.7985498905 s
Estimating background... Estimating background took 3.84865808487 s


Processing GM12264_VDR_ChIP-exo_VD_stimulated-GSM1889564/aligned.36mers.unique.bam
Reading in data... Reading data took 0.329499006271 s
Creating peak regions... Creating peak regions took 0.126645088196 s
Estimating background... Estimating background took 1.21494793892 s