***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/Exp1/T.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/CHiCAGO/CHiCAGOinput/Exp1/PARCLymph1_2ndrun/PARCLymph1_2ndrun.chinput Read 0.0% of 142449945 rows Read 3.5% of 142449945 rows Read 7.1% of 142449945 rows Read 11.1% of 142449945 rows Read 15.1% of 142449945 rows Read 19.1% of 142449945 rows Read 23.1% of 142449945 rows Read 27.1% of 142449945 rows Read 31.1% of 142449945 rows Read 34.7% of 142449945 rows Read 38.2% of 142449945 rows Read 42.3% of 142449945 rows Read 46.3% of 142449945 rows Read 50.3% of 142449945 rows Read 53.9% of 142449945 rows Read 57.5% of 142449945 rows Read 61.5% of 142449945 rows Read 65.6% of 142449945 rows Read 69.7% of 142449945 rows Read 73.3% of 142449945 rows Read 76.9% of 142449945 rows Read 80.9% of 142449945 rows Read 85.0% of 142449945 rows Read 89.0% of 142449945 rows Read 92.6% of 142449945 rows Read 96.2% of 142449945 rows Read 142449945 rows and 5 (of 5) columns from 3.975 GB file in 00:00:37 Processing input... minFragLen = 150 maxFragLen = 40000 Filtered out 787901 interactions involving other ends < minFragLen or > maxFragLen. minNPerBait = 250 Filtered out 334 baits with < minNPerBait reads. Removed interactions with fragments adjacent to baits. Filtered out 1 baits without proximal non-Bait2bait interactions Reading /data/CHiCAGO/CHiCAGOinput/Exp1/PARCLymph2_2ndrun/PARCLymph2_2ndrun.chinput Read 0.0% of 220846294 rows Read 2.3% of 220846294 rows Read 4.6% of 220846294 rows Read 7.2% of 220846294 rows Read 9.8% of 220846294 rows Read 12.4% of 220846294 rows Read 15.0% of 220846294 rows Read 17.6% of 220846294 rows Read 20.2% of 220846294 rows Read 22.5% of 220846294 rows Read 24.8% of 220846294 rows Read 27.4% of 220846294 rows Read 30.0% of 220846294 rows Read 32.5% of 220846294 rows Read 34.8% of 220846294 rows Read 37.1% of 220846294 rows Read 39.4% of 220846294 rows Read 41.9% of 220846294 rows Read 44.5% of 220846294 rows Read 46.8% of 220846294 rows Read 49.1% of 220846294 rows Read 51.7% of 220846294 rows Read 54.4% of 220846294 rows Read 56.9% of 220846294 rows Read 59.2% of 220846294 rows Read 61.6% of 220846294 rows Read 64.2% of 220846294 rows Read 66.8% of 220846294 rows Read 69.5% of 220846294 rows Read 71.8% of 220846294 rows Read 74.1% of 220846294 rows Read 76.8% of 220846294 rows Read 79.4% of 220846294 rows Read 82.0% of 220846294 rows Read 84.3% of 220846294 rows Read 86.7% of 220846294 rows Read 89.3% of 220846294 rows Read 91.9% of 220846294 rows Read 94.5% of 220846294 rows Read 96.9% of 220846294 rows Read 99.2% of 220846294 rows Read 220846294 rows and 5 (of 5) columns from 6.017 GB file in 00:00:55 Processing input... minFragLen = 150 maxFragLen = 40000 Filtered out 1051658 interactions involving other ends < minFragLen or > maxFragLen. minNPerBait = 250 Filtered out 306 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 T 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 81.4% 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.....Error: cannot allocate vector of size 2.5 Gb Execution halted Warning message: system call failed: Cannot allocate memory