***** Running recoverChIPLevels (SeqCode_v1.0) by Enrique Blanco (2020) ***** ***** GitHub source code: https://github.com/eblancoga/seqcode ***** ***** SeqCode homepage at: http://ldicrocelab.crg.es ***** > 0. Running on Wed Jun 9 14:39:50 2021 > 1. Request Memory to Operating System > 2. Reading Chromosome Sizes Dictionary (hash): chr8 | 7 chr9 | 8 chr10 | 9 chr11 | 10 chr12 | 11 chrX | 20 chr13 | 12 chrY | 21 chr14 | 13 chr15 | 14 chr16 | 15 chr17 | 16 chr18 | 17 chr19 | 18 chr1 | 0 chr2 | 1 chr3 | 2 chr4 | 3 chrM | 19 chr5 | 4 chr6 | 5 chr7 | 6 Chromosome sizes: 0 | 197195432 1 | 181748087 2 | 159599783 3 | 155630120 4 | 152537259 5 | 149517037 6 | 152524553 7 | 131738871 8 | 124076172 9 | 129993255 10 | 121843856 11 | 121257530 12 | 120284312 13 | 125194864 14 | 103494974 15 | 98319150 16 | 95272651 17 | 90772031 18 | 61342430 19 | 16299 20 | 166650296 21 | 15902555 Size was successfully acquired for 22 chromosomes > 3. Prepare the Output Folder The prefix folder ./ exists The prefix folder ./catalina/ exists The prefix folder ./catalina/results/ exists Creating the output folder ./catalina/results/Jarid2_mESC_recoverChIPlevels Filename for the PEAK ChIP levels file ./catalina/results/Jarid2_mESC_recoverChIPlevels/PEAKsignal_Jarid2_mESC.bed > 4. Processing the BAM/SAM file samples/mouse/Jarid2_mESC.bam: 1486.65 Mb Reading:  [ 0 lines] [ 100000 lines] [ 200000 lines] [ 300000 lines] [ 400000 lines] [ 500000 lines] [ 600000 lines] [ 700000 lines] [ 800000 lines] [ 900000 lines] [ 1000000 lines] [ 1100000 lines] [ 1200000 lines] [ 1300000 lines] [ 1400000 lines] [ 1500000 lines] [ 1600000 lines] [ 1700000 lines] [ 1800000 lines] [ 1900000 lines] [ 2000000 lines] [ 2100000 lines] [ 2200000 lines] [ 2300000 lines] [ 2400000 lines] [ 2500000 lines] [ 2600000 lines] [ 2700000 lines] [ 2800000 lines] [ 2900000 lines] [ 3000000 lines] [ 3100000 lines] [ 3200000 lines] [ 3300000 lines] [ 3400000 lines] [ 3500000 lines] [ 3600000 lines] [ 3700000 lines] [ 3800000 lines] [ 3900000 lines] [ 4000000 lines] [ 4100000 lines] [ 4200000 lines] [ 4300000 lines] [ 4400000 lines] [ 4500000 lines] [ 4600000 lines] [ 4700000 lines] [ 4800000 lines] [ 4900000 lines] [ 5000000 lines] [ 5100000 lines] [ 5200000 lines] [ 5300000 lines] [ 5400000 lines] [ 5500000 lines] [ 5600000 lines] [ 5700000 lines] [ 5800000 lines] [ 5900000 lines] [ 6000000 lines] [ 6100000 lines] [ 6200000 lines] [ 6300000 lines] [ 6400000 lines] [ 6500000 lines] [ 6600000 lines] [ 6700000 lines] [ 6800000 lines] [ 6900000 lines] [ 7000000 lines] [ 7100000 lines] [ 7200000 lines] [ 7300000 lines] [ 7400000 lines] [ 7500000 lines] [ 7600000 lines] [ 7700000 lines] [ 7800000 lines] [ 7900000 lines] [ 8000000 lines] [ 8100000 lines] [ 8200000 lines] [ 8300000 lines] [ 8400000 lines] [ 8500000 lines] [ 8600000 lines] [ 8700000 lines] [ 8800000 lines] [ 8900000 lines] [ 9000000 lines] [ 9100000 lines] [ 9200000 lines] [ 9300000 lines] [ 9400000 lines] [ 9500000 lines] [ 9600000 lines] [ 9700000 lines] [ 9800000 lines] [ 9900000 lines] [ 10000000 lines] [ 10100000 lines] [ 10200000 lines] [ 10300000 lines] [ 10400000 lines] [ 10500000 lines] [ 10600000 lines] [ 10700000 lines] [ 10800000 lines] [ 10900000 lines] [ 11000000 lines] [ 11100000 lines] [ 11200000 lines] [ 11300000 lines] [ 11400000 lines] [ 11500000 lines] [ 11600000 lines] [ 11700000 lines] [ 11800000 lines] [ 11900000 lines] [ 12000000 lines] [ 12100000 lines] [ 12200000 lines] [ 12300000 lines] [ 12400000 lines] [ 12500000 lines] [ 12600000 lines] [ 12700000 lines] [ 12800000 lines] [ 12900000 lines] [ 13000000 lines] [ 13100000 lines] [ 13200000 lines] [ 13300000 lines] [ 13400000 lines] [ 13500000 lines] [ 13600000 lines] [ 13700000 lines] [ 13800000 lines] [ 13900000 lines] [ 14000000 lines] [ 14100000 lines] [ 14200000 lines] [ 14300000 lines] [ 14400000 lines] [ 14500000 lines] [ 14600000 lines] [ 14700000 lines] [ 14800000 lines] [ 14900000 lines] [ 15000000 lines] [ 15100000 lines] [ 15200000 lines] [ 15300000 lines] [ 15400000 lines] [ 15500000 lines] [ 15600000 lines] [ 15700000 lines] [ 15800000 lines] [ 15900000 lines] [ 16000000 lines] [ 16100000 lines] [ 16200000 lines] [ 16300000 lines] [ 16400000 lines] [ 16500000 lines] [ 16600000 lines] [ 16700000 lines] [ 16800000 lines] [ 16900000 lines] [ 17000000 lines] [ 17100000 lines] [ 17200000 lines] [ 17300000 lines] [ 17400000 lines] [ 17500000 lines] [ 17600000 lines] [ 17700000 lines] [ 17800000 lines] [ 17900000 lines] [ 18000000 lines] [ 18100000 lines] [ 18200000 lines] [ 18300000 lines] [ 18400000 lines] [ 18500000 lines] [ 18600000 lines] [ 18700000 lines] [ 18800000 lines] [ 18900000 lines] [ 19000000 lines] [ 19100000 lines] [ 19200000 lines] [ 19300000 lines] [ 19400000 lines] [ 19500000 lines] [ 19600000 lines] [ 19700000 lines] [ 19800000 lines] [ 19900000 lines] [ 20000000 lines] [ 20100000 lines] [ 20200000 lines] [ 20300000 lines] [ 20400000 lines] [ 20500000 lines] [ 20600000 lines] [ 20700000 lines] [ 20800000 lines] [ 20900000 lines] [ 21000000 lines] [ 21100000 lines] [ 21200000 lines] [ 21300000 lines] [ 21400000 lines] [ 21500000 lines] [ 21600000 lines] [ 21700000 lines] [ 21800000 lines] [ 21900000 lines] [ 22000000 lines] [ 22100000 lines] [ 22200000 lines] [ 22300000 lines] [ 22400000 lines] [ 22500000 lines] [ 22600000 lines] [ 22700000 lines] [ 22800000 lines] [ 22900000 lines] [ 23000000 lines] [ 23100000 lines] [ 23200000 lines] [ 23300000 lines] [ 23400000 lines] [ 23500000 lines] [ 23600000 lines] [ 23700000 lines] [ 23800000 lines] [ 23900000 lines] [ 24000000 lines] [ 24100000 lines] [ 24200000 lines] [ 24300000 lines] [ 24400000 lines] [ 24500000 lines] [ 24600000 lines] [ 24700000 lines] [ 24800000 lines] [ 24900000 lines] [ 25000000 lines] [ 25100000 lines] [ 25200000 lines] [ 25300000 lines] [ 25400000 lines] [ 25500000 lines] [ 25600000 lines] [ 25700000 lines] [ 25800000 lines] [ 25900000 lines] [ 26000000 lines] [ 26100000 lines] [ 26200000 lines] [ 26300000 lines] [ 26400000 lines] 26404588 reads of the SAM file processed 13194537 forward reads acquired 13210224 reverse reads acquired > 5. Processing the List of peaks Reading:  [ 0 lines] [ 1000 lines] [ 2000 lines] [ 3000 lines] [ 4000 lines] [ 5000 lines] [ 6000 lines] [ 7000 lines] [ 8000 lines] [ 9000 lines] [ 10000 lines] [ 11000 lines] [ 12000 lines] [ 13000 lines] [ 14000 lines] [ 15000 lines] [ 16000 lines] [ 17000 lines] [ 18000 lines] [ 19000 lines] [ 20000 lines] [ 21000 lines] [ 22000 lines] [ 23000 lines] [ 24000 lines] [ 25000 lines] [ 26000 lines] [ 27000 lines] [ 28000 lines] [ 29000 lines] [ 30000 lines] [ 31000 lines] [ 32000 lines] [ 33000 lines] [ 34000 lines] [ 35000 lines] [ 36000 lines] [ 37000 lines] [ 38000 lines] [ 39000 lines] [ 40000 lines] [ 41000 lines] [ 42000 lines] [ 43000 lines] [ 44000 lines] [ 45000 lines] [ 46000 lines] 46881 peaks were successfully processed __________________________________________________________________________ Memory usage: 1021.16 Megabytes CPU time: 19.56 secs Total time: 35 secs (0.58 mins)