***** Running produceTSSplots (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 14:30:31 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/IgG_mESC_TSSplot_5000
	Filename for the TSS average profile ./catalina/results/IgG_mESC_TSSplot_5000/TSSprofile_IgG_mESC_5000.txt
	PDF file for the plot file ./catalina/results/IgG_mESC_TSSplot_5000/PlotTSSprofile_IgG_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/IgG_mESC.bam: 2301.85 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 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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]	[  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	20063131 forward reads acquired
	20056686 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
	Normalization factor: 40.119232
	26074 target genes were successfully processed
> 7. Running R to produce the plots
	Preparing the Rscript file ./catalina/results/IgG_mESC_TSSplot_5000/RscriptTSSprofile_IgG_mESC_5000.txt
	R CMD BATCH ./catalina/results/IgG_mESC_TSSplot_5000/RscriptTSSprofile_IgG_mESC_5000.txt
	Removing the out R file
	rm -f *.Rout
	__________________________________________________________________________

	Memory usage: 	1023.55 Megabytes
	CPU time: 	32.59 secs
	Total time: 	56 secs (0.93 mins)