***** Running produceGENEplots (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 14:13:45 2021 > 1. Request Memory to Operating System Loading the R color schema > 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/H3K27me3_mESC_GENEplot_5000 Filename for the GENE average profile ./catalina/results/H3K27me3_mESC_GENEplot_5000/GENEprofile_H3K27me3_mESC_5000.txt PDF file for the plot file ./catalina/results/H3K27me3_mESC_GENEplot_5000/PlotGENEprofile_H3K27me3_mESC_5000.pdf > 4. Reading Refgene file data/mm9/refGene.txt: 12.61 Mb 46881 transcripts of RefSeq were successfully acquired > 5. Processing the BAM/SAM file samples/mouse/H3K27me3_mESC.bam: 1694.38 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 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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] 33884649 reads of the SAM file processed 16940940 forward reads acquired 16943943 reverse reads acquired > 6. Processing the List of target genes List of non-available genes: 1700074H08Rik 2010315B03Rik 4930526I15Rik AF067063 Aida B020031M17Rik BC147527 Brox Ccdc82 Ccl28 Csprs Defb33 Dhrsx Disp1 Gm20736 Gm20738 Gm20747 Gm20806 Gm20809 Gm20815 Gm20816 Gm20819 Gm20822 Gm20823 Gm20824 Gm20826 Gm20831 Gm20852 Gm20854 Gm20857 Gm20858 Gm20865 Gm20867 Gm20868 Gm20871 Gm20877 Gm20879 Gm20901 Gm20909 Gm20917 Gm20924 Gm20931 Gm21064 Gm21242 Gm21258 Gm21292 Gm21302 Gm21308 Gm21316 Gm21330 Gm21379 Gm21394 Gm21440 Gm21454 Gm21469 Gm21679 Gm21724 Gm21745 Gm21751 Gm21753 Gm21763 Gm21783 Gm21805 Gm21810 Gm21818 Gm21828 Gm21838 Gm21843 Gm21908 Gm21918 Gm21943 Gm21944 Gm28093 Gm28371 Gm28459 Gm28840 Gm29317 Gm31186 Gm41077 Hhipl2 Hmgcs1 Jrkl LOC100041034 LOC100041877 LOC100861691 LOC102638047 LOC664787 Mia3 Mucl1 Mucl2 Nim1k Nlrp4g Orly Ppp2r3d Rbm31y Sly Spry3 Srsy Ssty1 Ssty2 Taf1a Tcstv1 Tcstv3 Tmlhe Ulbp1 Vamp7 Vmn2r123 Zf12 Zfp131 18446 target genes were successfully processed Normalization factor: 33.884647 > 7. Running R to produce the plots Preparing the Rscript file ./catalina/results/H3K27me3_mESC_GENEplot_5000/RscriptGENEprofile_H3K27me3_mESC_5000.txt R CMD BATCH ./catalina/results/H3K27me3_mESC_GENEplot_5000/RscriptGENEprofile_H3K27me3_mESC_5000.txt Removing the out R file rm -f *.Rout __________________________________________________________________________ Memory usage: 1061.85 Megabytes CPU time: 28.30 secs Total time: 45 secs (0.75 mins)