***** 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 15:40:14 2021 > 1. Request Memory to Operating System > 2. Reading Chromosome Sizes Dictionary (hash): chr8 | 7 chr9 | 8 chr10 | 9 chr20 | 19 chr11 | 10 chr21 | 20 chr12 | 11 chrX | 23 chr22 | 21 chr13 | 12 chrY | 24 chr14 | 13 chr15 | 14 chr16 | 15 chr17 | 16 chr18 | 17 chr19 | 18 chr1 | 0 chr2 | 1 chr3 | 2 chr4 | 3 chrM | 22 chr5 | 4 chr6 | 5 chr7 | 6 Chromosome sizes: 0 | 249250621 1 | 243199373 2 | 198022430 3 | 191154276 4 | 180915260 5 | 171115067 6 | 159138663 7 | 146364022 8 | 141213431 9 | 135534747 10 | 135006516 11 | 133851895 12 | 115169878 13 | 107349540 14 | 102531392 15 | 90354753 16 | 81195210 17 | 78077248 18 | 59128983 19 | 63025520 20 | 48129895 21 | 51304566 22 | 16571 23 | 155270560 24 | 59373566 Size was successfully acquired for 25 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/MTF2_DU145_findPeaks Filename for the Bed file ./catalina/results/MTF2_DU145_findPeaks/MTF2_DU145.bed > 4. Processing the BAM/SAM file samples/human/MTF2_DU145.bam: 1844.42 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 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Analyzing the reads to find peaks Processing chromosome chr8 (7) - 146364022 Processing chromosome chr9 (8) - 141213431 Processing chromosome chr10 (9) - 135534747 Processing chromosome chr20 (19) - 63025520 Processing chromosome chr11 (10) - 135006516 Processing chromosome chr21 (20) - 48129895 Processing chromosome chr12 (11) - 133851895 Processing chromosome chrX (23) - 155270560 Processing chromosome chr22 (21) - 51304566 Processing chromosome chr13 (12) - 115169878 Processing chromosome chrY (24) - 59373566 Processing chromosome chr14 (13) - 107349540 Processing chromosome chr15 (14) - 102531392 Processing chromosome chr16 (15) - 90354753 Processing chromosome chr17 (16) - 81195210 Processing chromosome chr18 (17) - 78077248 Processing chromosome chr19 (18) - 59128983 Processing chromosome chr1 (0) - 249250621 Processing chromosome chr2 (1) - 243199373 Processing chromosome chr3 (2) - 198022430 Processing chromosome chr4 (3) - 191154276 Processing chromosome chrM (22) - 16571 Processing chromosome chr5 (4) - 180915260 Processing chromosome chr6 (5) - 171115067 Processing chromosome chr7 (6) - 159138663 25 chromosomes sucessfully included into the peak calling Size of the resulting BED file (uncompressed): ./catalina/results/MTF2_DU145_findPeaks/MTF2_DU145.bed: 0.02 Mb Compressing the final BED profile gzip ./catalina/results/MTF2_DU145_findPeaks/MTF2_DU145.bed Size of the resulting BED file: ./catalina/results/MTF2_DU145_findPeaks/MTF2_DU145.bed.gz: 0.00 Mb __________________________________________________________________________ Memory usage: 127.63 Megabytes CPU time: 23.22 secs Total time: 40 secs (0.67 mins)