***** Running produceGENEmaps (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 15:53:15 2021 > 1. Request Memory to Operating System Loading the R color schema > 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/SUZ12_DU145_GENEmap_5000 Filename for the HEAT matrix ./catalina/results/SUZ12_DU145_GENEmap_5000/HEATmatrix_SUZ12_DU145_5000.txt Filename for the processed HEAT matrix ./catalina/results/SUZ12_DU145_GENEmap_5000/HEATmatrix_SUZ12_DU145_5000_processed.txt Filename for the HEAT gene rank ./catalina/results/SUZ12_DU145_GENEmap_5000/HEATmatrix_SUZ12_DU145_5000_genes.txt PDF file for the HEAT plot file ./catalina/results/SUZ12_DU145_GENEmap_5000/PlotHEATmap_SUZ12_DU145_5000.pdf > 4. Reading Refgene file data/hg19/refGene.txt: 22.94 Mb 78106 transcripts of RefSeq were successfully acquired > 5. Processing the BAM/SAM file samples/human/SUZ12_DU145.bam: 1199.06 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] 23899291 reads of the SAM file processed 11949593 forward reads acquired 11950195 reverse reads acquired > 6. Processing the List of target genes List of non-available genes: DUX4 FAM230C FLJ43315 FRG1CP FRG1EP FRG1FP HLA-DRB3 HLA-DRB4 HYDIN2 KIR2DL2 KIR2DL5A KIR2DL5B KIR2DS1 KIR2DS2 KIR2DS3 KIR2DS5 KIR3DS1 LINC01667 LOC100233156 LOC100288966 LOC100505874 LOC100507412 LOC102723360 LOC102724219 LOC102724843 LOC102724951 LOC102725023 LOC105379477 LOC112268355 LOC283788 LOC389831 LOC389834 MAFIP MGC70870 MIR6724-1 MIR6724-2 MIR6724-3 MIR6724-4 RNA18SN1 RNA18SN2 RNA18SN3 RNA18SN4 RNA18SN5 RNA28SN1 RNA28SN2 RNA28SN3 RNA28SN4 RNA28SN5 RNA45SN1 RNA45SN2 RNA45SN3 RNA45SN4 RNA45SN5 RNA5-8SN1 RNA5-8SN2 RNA5-8SN3 RNA5-8SN4 RNA5-8SN5 20248 target genes were successfully processed Extracting gene avg. values in ./catalina/results/SUZ12_DU145_GENEmap_5000/HEATmatrix_SUZ12_DU145_5000_genes.txt cut -f 1,202 ./catalina/results/SUZ12_DU145_GENEmap_5000/HEATmatrix_SUZ12_DU145_5000.txt | sort -nrk 2 > ./catalina/results/SUZ12_DU145_GENEmap_5000/HEATmatrix_SUZ12_DU145_5000_genes.txt Ranking the heat file: ./catalina/results/SUZ12_DU145_GENEmap_5000/HEATmatrix_SUZ12_DU145_5000_processed.txt sort -nk 202 ./catalina/results/SUZ12_DU145_GENEmap_5000/HEATmatrix_SUZ12_DU145_5000.txt | cut -f 2-201 > ./catalina/results/SUZ12_DU145_GENEmap_5000/HEATmatrix_SUZ12_DU145_5000_processed.txt > 7. Running R to produce the plots > Preparing the Rscript file ./catalina/results/SUZ12_DU145_GENEmap_5000/RscriptGENEmap_SUZ12_DU145_5000.txt R CMD BATCH ./catalina/results/SUZ12_DU145_GENEmap_5000/RscriptGENEmap_SUZ12_DU145_5000.txt Removing the out R file rm -f *.Rout __________________________________________________________________________ Memory usage: 130.33 Megabytes CPU time: 19.68 secs Total time: 39 secs (0.65 mins)