***runChicago.R Loading required package: methods Loading the Chicago package and dependencies... Loading required package: data.table Welcome to CHiCAGO - version 1.1.8 If you are new to CHiCAGO, please consider reading the vignette through the command: vignette("Chicago"). NOTE: Default values of tlb.minProxOEPerBin and tlb.minProxB2BPerBin changed as of Version 1.1.5. No action is required unless you specified non-default values, or wish to re-run the pipeline on old chicagoData objects. See news(package="Chicago") Warning: neither --en-feat-files nor --en-feat-list provided. Feature enrichments will not be computed Setting the experiment... Reading custom experimental settings from /data/CHiCAGO/CHiCAGOsettings/Exp2/wt.settings... Read 4 items Locating .baitmap in /data/CHiCAGO/HindIIIDesignDir/... Found Bait.baitmap Locating .rmap in /data/CHiCAGO/HindIIIDesignDir/... Found RestrictionEnz.rmap Locating .npb in /data/CHiCAGO/HindIIIDesignDir/... Found RestrictionEnz.npb Locating .nbpb in /data/CHiCAGO/HindIIIDesignDir/... Found RestrictionEnz.nbpb Locating .poe in /data/CHiCAGO/HindIIIDesignDir/... Found RestrictionEnz.poe Checking the design files... Reading input files... Reading /data/CHiCAGOinput/Exp2/PARCWT44/PARCWT44.chinput Read 0.0% of 144658995 rows Read 3.8% of 144658995 rows Read 7.6% of 144658995 rows Read 11.5% of 144658995 rows Read 15.3% of 144658995 rows Read 19.1% of 144658995 rows Read 22.9% of 144658995 rows Read 26.7% of 144658995 rows Read 30.5% of 144658995 rows Read 34.3% of 144658995 rows Read 38.2% of 144658995 rows Read 42.0% of 144658995 rows Read 45.9% of 144658995 rows Read 49.7% of 144658995 rows Read 53.6% of 144658995 rows Read 57.4% of 144658995 rows Read 61.2% of 144658995 rows Read 65.1% of 144658995 rows Read 68.9% of 144658995 rows Read 72.8% of 144658995 rows Read 76.7% of 144658995 rows Read 80.5% of 144658995 rows Read 84.4% of 144658995 rows Read 88.3% of 144658995 rows Read 92.1% of 144658995 rows Read 96.0% of 144658995 rows Read 99.8% of 144658995 rows Read 144658995 rows and 5 (of 5) columns from 4.043 GB file in 00:00:37 Processing input... minFragLen = 150 maxFragLen = 40000 Filtered out 2407705 interactions involving other ends < minFragLen or > maxFragLen. minNPerBait = 250 Filtered out 144 baits with < minNPerBait reads. Removed interactions with fragments adjacent to baits. Filtered out 0 baits without proximal non-Bait2bait interactions Reading /data/CHiCAGOinput/Exp2/PARCWT46/PARCWT46.chinput Read 0.0% of 132380674 rows Read 4.2% of 132380674 rows Read 8.4% of 132380674 rows Read 12.7% of 132380674 rows Read 16.9% of 132380674 rows Read 21.1% of 132380674 rows Read 25.3% of 132380674 rows Read 29.4% of 132380674 rows Read 33.6% of 132380674 rows Read 37.8% of 132380674 rows Read 42.1% of 132380674 rows Read 46.3% of 132380674 rows Read 50.5% of 132380674 rows Read 54.7% of 132380674 rows Read 58.9% of 132380674 rows Read 63.1% of 132380674 rows Read 67.4% of 132380674 rows Read 71.6% of 132380674 rows Read 75.9% of 132380674 rows Read 80.1% of 132380674 rows Read 84.4% of 132380674 rows Read 88.6% of 132380674 rows Read 92.9% of 132380674 rows Read 97.1% of 132380674 rows Read 132380674 rows and 5 (of 5) columns from 3.714 GB file in 00:00:33 Processing input... minFragLen = 150 maxFragLen = 40000 Filtered out 2283282 interactions involving other ends < minFragLen or > maxFragLen. minNPerBait = 250 Filtered out 151 baits with < minNPerBait reads. Removed interactions with fragments adjacent to baits. Filtered out 0 baits without proximal non-Bait2bait interactions Merging samples... Computing merged scores... Computing sample scaling factors... Reading NPerBin file... Computing normalisation scores... Warning: directory wt exists and will be reused. Starting chicagoPipeline... *** Running normaliseBaits... Normalising baits... Reading NPerBin file... Computing binwise means... *** Running normaliseOtherEnds... Preprocessing input... Computing trans-counts... Filtering out 78 other ends with top 0.01% number of trans-interactions Binning... Computing total bait counts... Reading NBaitsPerBin file... Read 87.4% of 823377 rows Read 823377 rows and 76 (of 76) columns from 0.121 GB file in 00:00:03 Computing scaling factors... Computing binwise means... Computing normalised counts... Post-processing... *** Running estimateTechnicalNoise... Estimating technical noise based on trans-counts... Binning baits based on observed trans-counts... Defining interaction pools and gathering the observed numbers of trans-counts per pool... Computing the total number of possible interactions per pool... Preparing the data..... Processing fragment pools................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................ Plotting... Post-processing the results... *** Running estimateDistFun... libgomp: Thread creation failed: Resource temporarily unavailable