***** Running findPeaks (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 14:11:04 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/H3K27ac_mESC_findPeaks Filename for the Bed file ./catalina/results/H3K27ac_mESC_findPeaks/H3K27ac_mESC.bed > 4. Processing the BAM/SAM file samples/mouse/H3K27ac_mESC.bam: 1988.53 Mb Processing Single-end sequencing reads 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 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27700000 lines] [ 27800000 lines] [ 27900000 lines] [ 28000000 lines] [ 28100000 lines] [ 28200000 lines] [ 28300000 lines] [ 28400000 lines] [ 28500000 lines] [ 28600000 lines] [ 28700000 lines] [ 28800000 lines] [ 28900000 lines] [ 29000000 lines] [ 29100000 lines] [ 29200000 lines] [ 29300000 lines] [ 29400000 lines] [ 29500000 lines] [ 29600000 lines] [ 29700000 lines] [ 29800000 lines] [ 29900000 lines] [ 30000000 lines] [ 30100000 lines] [ 30200000 lines] [ 30300000 lines] [ 30400000 lines] [ 30500000 lines] [ 30600000 lines] [ 30700000 lines] [ 30800000 lines] [ 30900000 lines] [ 31000000 lines] [ 31100000 lines] [ 31200000 lines] [ 31300000 lines] [ 31400000 lines] [ 31500000 lines] [ 31600000 lines] [ 31700000 lines] [ 31800000 lines] [ 31900000 lines] [ 32000000 lines] [ 32100000 lines] [ 32200000 lines] [ 32300000 lines] [ 32400000 lines] [ 32500000 lines] [ 32600000 lines] [ 32700000 lines] [ 32800000 lines] [ 32900000 lines] [ 33000000 lines] [ 33100000 lines] [ 33200000 lines] [ 33300000 lines] [ 33400000 lines] [ 33500000 lines] [ 33600000 lines] [ 33700000 lines] [ 33800000 lines] [ 33900000 lines] [ 34000000 lines] 34078546 reads of the SAM file processed 17039279 forward reads acquired 17039401 reverse reads acquired > 5. Analyzing the reads to find peaks Processing chromosome chr8 (7) - 131738871 Processing chromosome chr9 (8) - 124076172 Processing chromosome chr10 (9) - 129993255 Processing chromosome chr11 (10) - 121843856 Processing chromosome chr12 (11) - 121257530 Processing chromosome chrX (20) - 166650296 Processing chromosome chr13 (12) - 120284312 Processing chromosome chrY (21) - 15902555 Processing chromosome chr14 (13) - 125194864 Processing chromosome chr15 (14) - 103494974 Processing chromosome chr16 (15) - 98319150 Processing chromosome chr17 (16) - 95272651 Processing chromosome chr18 (17) - 90772031 Processing chromosome chr19 (18) - 61342430 Processing chromosome chr1 (0) - 197195432 Processing chromosome chr2 (1) - 181748087 Processing chromosome chr3 (2) - 159599783 Processing chromosome chr4 (3) - 155630120 Processing chromosome chrM (19) - 16299 Processing chromosome chr5 (4) - 152537259 Processing chromosome chr6 (5) - 149517037 Processing chromosome chr7 (6) - 152524553 22 chromosomes sucessfully included into the peak calling Size of the resulting BED file (uncompressed): ./catalina/results/H3K27ac_mESC_findPeaks/H3K27ac_mESC.bed: 0.13 Mb Compressing the final BED profile gzip ./catalina/results/H3K27ac_mESC_findPeaks/H3K27ac_mESC.bed Size of the resulting BED file: ./catalina/results/H3K27ac_mESC_findPeaks/H3K27ac_mESC.bed.gz: 0.03 Mb __________________________________________________________________________ Memory usage: 109.67 Megabytes CPU time: 24.46 secs Total time: 44 secs (0.73 mins)