%%%% Starting SeqCode test for the produceTSSmaps tool by Enrique Blanco (mié 23 jun 2021 17:12:34 CEST) %%%% Stage 0. Reading options [DONE] %%%% Stage 1. Running the test for H3K4me3 --chr10:5,774,999-6,225,000 (mm9)-- in mESC (default plot) %%%% bin/produceTSSmaps -vd tests/inputs/ChromInfo.txt tests/inputs/refGene_sample.txt tests/inputs/H3K4me3_sample.bam tests/inputs/genes_sample.txt test_1 5000> produceTSSmaps > 0. Running on Wed Jun 23 17:12:34 2021 > 1. Request Memory to Operating System Loading the R color schema > 2. Reading Chromosome Sizes Dictionary (hash): chr8 | 17 chr9 | 18 chr10 | 1 chr11 | 2 chr12 | 3 chrX | 20 chr13 | 4 chrY | 21 chr14 | 5 chr15 | 6 chr16 | 7 chr17 | 8 chr18 | 9 chr19 | 10 chr1 | 0 chr2 | 11 chr3 | 12 chr4 | 13 chrM | 19 chr5 | 14 chr6 | 15 chr7 | 16 Chromosome sizes: 0 | 197195432 1 | 129993255 2 | 121843856 3 | 121257530 4 | 120284312 5 | 125194864 6 | 103494974 7 | 98319150 8 | 95272651 9 | 90772031 10 | 61342430 11 | 181748087 12 | 159599783 13 | 155630120 14 | 152537259 15 | 149517037 16 | 152524553 17 | 131738871 18 | 124076172 19 | 16299 20 | 166650296 21 | 15902555 Size was successfully acquired for 22 chromosomes > 3. Prepare the Output Folder The prefix folder ./ exists Creating the output folder ./test_1_TSSmap_5000 Filename for the HEAT matrix ./test_1_TSSmap_5000/HEATmatrix_test_1_5000.txt Filename for the processed HEAT matrix ./test_1_TSSmap_5000/HEATmatrix_test_1_5000_processed.txt Filename for the HEAT gene rank ./test_1_TSSmap_5000/HEATmatrix_test_1_5000_genes.txt PDF file for the HEAT plot file ./test_1_TSSmap_5000/PlotHEATmap_test_1_5000.pdf > 4. Reading Refgene file tests/inputs/refGene_sample.txt: 0.00 Mb 6 transcripts of RefSeq were successfully acquired > 5. Processing the BAM/SAM file tests/inputs/H3K4me3_sample.bam: 1.21 Mb Reading:  [ 0 lines] 21482 reads of the SAM file processed 10886 forward reads acquired 10596 reverse reads acquired > 6. Processing the List of target genes List of non-available genes: 6 target genes were successfully processed Extracting gene avg. values in ./test_1_TSSmap_5000/HEATmatrix_test_1_5000_genes.txt cut -f 1,102 ./test_1_TSSmap_5000/HEATmatrix_test_1_5000.txt | sort -nrk 2 > ./test_1_TSSmap_5000/HEATmatrix_test_1_5000_genes.txt Ranking the heat file: ./test_1_TSSmap_5000/HEATmatrix_test_1_5000_processed.txt sort -nk 102 ./test_1_TSSmap_5000/HEATmatrix_test_1_5000.txt | cut -f 2-101 > ./test_1_TSSmap_5000/HEATmatrix_test_1_5000_processed.txt > 7. Running R to produce the plots > Preparing the Rscript file ./test_1_TSSmap_5000/RscriptTSSmap_test_1_5000.txt R CMD BATCH ./test_1_TSSmap_5000/RscriptTSSmap_test_1_5000.txt Removing the out R file rm -f *.Rout __________________________________________________________________________ Memory usage: 111.98 Megabytes CPU time: 0.08 secs Total time: 1 secs (0.02 mins)  [DONE] %%%% Stage 2. Running the test for H3K4me3 --chr10:5,774,999-6,225,000 (mm9)-- in mESC (lower resolution) %%%% bin/produceTSSmaps -vd -w 1000 tests/inputs/ChromInfo.txt tests/inputs/refGene_sample.txt tests/inputs/H3K4me3_sample.bam tests/inputs/genes_sample.txt test_2 5000> produceTSSmaps > 0. Running on Wed Jun 23 17:12:35 2021 > 1. Request Memory to Operating System Loading the R color schema > 2. Reading Chromosome Sizes Dictionary (hash): chr8 | 17 chr9 | 18 chr10 | 1 chr11 | 2 chr12 | 3 chrX | 20 chr13 | 4 chrY | 21 chr14 | 5 chr15 | 6 chr16 | 7 chr17 | 8 chr18 | 9 chr19 | 10 chr1 | 0 chr2 | 11 chr3 | 12 chr4 | 13 chrM | 19 chr5 | 14 chr6 | 15 chr7 | 16 Chromosome sizes: 0 | 197195432 1 | 129993255 2 | 121843856 3 | 121257530 4 | 120284312 5 | 125194864 6 | 103494974 7 | 98319150 8 | 95272651 9 | 90772031 10 | 61342430 11 | 181748087 12 | 159599783 13 | 155630120 14 | 152537259 15 | 149517037 16 | 152524553 17 | 131738871 18 | 124076172 19 | 16299 20 | 166650296 21 | 15902555 Size was successfully acquired for 22 chromosomes > 3. Prepare the Output Folder The prefix folder ./ exists Creating the output folder ./test_2_TSSmap_5000 Filename for the HEAT matrix ./test_2_TSSmap_5000/HEATmatrix_test_2_5000.txt Filename for the processed HEAT matrix ./test_2_TSSmap_5000/HEATmatrix_test_2_5000_processed.txt Filename for the HEAT gene rank ./test_2_TSSmap_5000/HEATmatrix_test_2_5000_genes.txt PDF file for the HEAT plot file ./test_2_TSSmap_5000/PlotHEATmap_test_2_5000.pdf > 4. Reading Refgene file tests/inputs/refGene_sample.txt: 0.00 Mb 6 transcripts of RefSeq were successfully acquired > 5. Processing the BAM/SAM file tests/inputs/H3K4me3_sample.bam: 1.21 Mb Reading:  [ 0 lines] 21482 reads of the SAM file processed 10886 forward reads acquired 10596 reverse reads acquired > 6. Processing the List of target genes List of non-available genes: 6 target genes were successfully processed Extracting gene avg. values in ./test_2_TSSmap_5000/HEATmatrix_test_2_5000_genes.txt cut -f 1,12 ./test_2_TSSmap_5000/HEATmatrix_test_2_5000.txt | sort -nrk 2 > ./test_2_TSSmap_5000/HEATmatrix_test_2_5000_genes.txt Ranking the heat file: ./test_2_TSSmap_5000/HEATmatrix_test_2_5000_processed.txt sort -nk 12 ./test_2_TSSmap_5000/HEATmatrix_test_2_5000.txt | cut -f 2-11 > ./test_2_TSSmap_5000/HEATmatrix_test_2_5000_processed.txt > 7. Running R to produce the plots > Preparing the Rscript file ./test_2_TSSmap_5000/RscriptTSSmap_test_2_5000.txt R CMD BATCH ./test_2_TSSmap_5000/RscriptTSSmap_test_2_5000.txt Removing the out R file rm -f *.Rout __________________________________________________________________________ Memory usage: 20.83 Megabytes CPU time: 0.07 secs Total time: 1 secs (0.02 mins)  [DONE] %%%% Stage 3. Running the test for H3K4me3 --chr10:5,774,999-6,225,000 (mm9)-- in mESC (one gene, default plot) %%%% bin/produceTSSmaps -vd tests/inputs/ChromInfo.txt tests/inputs/refGene_sample.txt tests/inputs/H3K4me3_sample.bam tests/inputs/onegene.txt test_3 5000> produceTSSmaps > 0. Running on Wed Jun 23 17:12:36 2021 > 1. Request Memory to Operating System Loading the R color schema > 2. Reading Chromosome Sizes Dictionary (hash): chr8 | 17 chr9 | 18 chr10 | 1 chr11 | 2 chr12 | 3 chrX | 20 chr13 | 4 chrY | 21 chr14 | 5 chr15 | 6 chr16 | 7 chr17 | 8 chr18 | 9 chr19 | 10 chr1 | 0 chr2 | 11 chr3 | 12 chr4 | 13 chrM | 19 chr5 | 14 chr6 | 15 chr7 | 16 Chromosome sizes: 0 | 197195432 1 | 129993255 2 | 121843856 3 | 121257530 4 | 120284312 5 | 125194864 6 | 103494974 7 | 98319150 8 | 95272651 9 | 90772031 10 | 61342430 11 | 181748087 12 | 159599783 13 | 155630120 14 | 152537259 15 | 149517037 16 | 152524553 17 | 131738871 18 | 124076172 19 | 16299 20 | 166650296 21 | 15902555 Size was successfully acquired for 22 chromosomes > 3. Prepare the Output Folder The prefix folder ./ exists Creating the output folder ./test_3_TSSmap_5000 Filename for the HEAT matrix ./test_3_TSSmap_5000/HEATmatrix_test_3_5000.txt Filename for the processed HEAT matrix ./test_3_TSSmap_5000/HEATmatrix_test_3_5000_processed.txt Filename for the HEAT gene rank ./test_3_TSSmap_5000/HEATmatrix_test_3_5000_genes.txt PDF file for the HEAT plot file ./test_3_TSSmap_5000/PlotHEATmap_test_3_5000.pdf > 4. Reading Refgene file tests/inputs/refGene_sample.txt: 0.00 Mb 6 transcripts of RefSeq were successfully acquired > 5. Processing the BAM/SAM file tests/inputs/H3K4me3_sample.bam: 1.21 Mb Reading:  [ 0 lines] 21482 reads of the SAM file processed 10886 forward reads acquired 10596 reverse reads acquired > 6. Processing the List of target genes List of non-available genes: 1 target genes were successfully processed Extracting gene avg. values in ./test_3_TSSmap_5000/HEATmatrix_test_3_5000_genes.txt cut -f 1,102 ./test_3_TSSmap_5000/HEATmatrix_test_3_5000.txt | sort -nrk 2 > ./test_3_TSSmap_5000/HEATmatrix_test_3_5000_genes.txt Ranking the heat file: ./test_3_TSSmap_5000/HEATmatrix_test_3_5000_processed.txt sort -nk 102 ./test_3_TSSmap_5000/HEATmatrix_test_3_5000.txt | cut -f 2-101 > ./test_3_TSSmap_5000/HEATmatrix_test_3_5000_processed.txt > 7. Running R to produce the plots > Preparing the Rscript file ./test_3_TSSmap_5000/RscriptTSSmap_test_3_5000.txt R CMD BATCH ./test_3_TSSmap_5000/RscriptTSSmap_test_3_5000.txt Removing the out R file rm -f *.Rout __________________________________________________________________________ Memory usage: 111.98 Megabytes CPU time: 0.07 secs Total time: 1 secs (0.02 mins)  [DONE] %%%% Stage 4. Running the test for H3K4me3 --chr10:5,774,999-6,225,000 (mm9)-- in mESC (another color scheme) %%%% bin/produceTSSmaps -vd -b black -B black -H black -f darkgoldenrod1 -F darkgoldenrod1 tests/inputs/ChromInfo.txt tests/inputs/refGene_sample.txt tests/inputs/H3K4me3_sample.bam tests/inputs/genes_sample.txt test_4 5000> produceTSSmaps > 0. Running on Wed Jun 23 17:12:37 2021 > 1. Request Memory to Operating System Loading the R color schema > 2. Reading Chromosome Sizes Dictionary (hash): chr8 | 17 chr9 | 18 chr10 | 1 chr11 | 2 chr12 | 3 chrX | 20 chr13 | 4 chrY | 21 chr14 | 5 chr15 | 6 chr16 | 7 chr17 | 8 chr18 | 9 chr19 | 10 chr1 | 0 chr2 | 11 chr3 | 12 chr4 | 13 chrM | 19 chr5 | 14 chr6 | 15 chr7 | 16 Chromosome sizes: 0 | 197195432 1 | 129993255 2 | 121843856 3 | 121257530 4 | 120284312 5 | 125194864 6 | 103494974 7 | 98319150 8 | 95272651 9 | 90772031 10 | 61342430 11 | 181748087 12 | 159599783 13 | 155630120 14 | 152537259 15 | 149517037 16 | 152524553 17 | 131738871 18 | 124076172 19 | 16299 20 | 166650296 21 | 15902555 Size was successfully acquired for 22 chromosomes > 3. Prepare the Output Folder The prefix folder ./ exists Creating the output folder ./test_4_TSSmap_5000 Filename for the HEAT matrix ./test_4_TSSmap_5000/HEATmatrix_test_4_5000.txt Filename for the processed HEAT matrix ./test_4_TSSmap_5000/HEATmatrix_test_4_5000_processed.txt Filename for the HEAT gene rank ./test_4_TSSmap_5000/HEATmatrix_test_4_5000_genes.txt PDF file for the HEAT plot file ./test_4_TSSmap_5000/PlotHEATmap_test_4_5000.pdf > 4. Reading Refgene file tests/inputs/refGene_sample.txt: 0.00 Mb 6 transcripts of RefSeq were successfully acquired > 5. Processing the BAM/SAM file tests/inputs/H3K4me3_sample.bam: 1.21 Mb Reading:  [ 0 lines] 21482 reads of the SAM file processed 10886 forward reads acquired 10596 reverse reads acquired > 6. Processing the List of target genes List of non-available genes: 6 target genes were successfully processed Extracting gene avg. values in ./test_4_TSSmap_5000/HEATmatrix_test_4_5000_genes.txt cut -f 1,102 ./test_4_TSSmap_5000/HEATmatrix_test_4_5000.txt | sort -nrk 2 > ./test_4_TSSmap_5000/HEATmatrix_test_4_5000_genes.txt Ranking the heat file: ./test_4_TSSmap_5000/HEATmatrix_test_4_5000_processed.txt sort -nk 102 ./test_4_TSSmap_5000/HEATmatrix_test_4_5000.txt | cut -f 2-101 > ./test_4_TSSmap_5000/HEATmatrix_test_4_5000_processed.txt > 7. Running R to produce the plots > Preparing the Rscript file ./test_4_TSSmap_5000/RscriptTSSmap_test_4_5000.txt R CMD BATCH ./test_4_TSSmap_5000/RscriptTSSmap_test_4_5000.txt Removing the out R file rm -f *.Rout __________________________________________________________________________ Memory usage: 111.98 Megabytes CPU time: 0.08 secs Total time: 1 secs (0.02 mins)  [DONE] %%%% Stage 5. Running the test for H3K4me3 --chr10:5,774,999-6,225,000 (mm9)-- in mESC (noise reduction plot) %%%% bin/produceTSSmaps -vd -t 0 tests/inputs/ChromInfo.txt tests/inputs/refGene_sample.txt tests/inputs/H3K4me3_sample.bam tests/inputs/genes_sample.txt test_5 5000> produceTSSmaps > 0. Running on Wed Jun 23 17:12:37 2021 > 1. Request Memory to Operating System Loading the R color schema > 2. Reading Chromosome Sizes Dictionary (hash): chr8 | 17 chr9 | 18 chr10 | 1 chr11 | 2 chr12 | 3 chrX | 20 chr13 | 4 chrY | 21 chr14 | 5 chr15 | 6 chr16 | 7 chr17 | 8 chr18 | 9 chr19 | 10 chr1 | 0 chr2 | 11 chr3 | 12 chr4 | 13 chrM | 19 chr5 | 14 chr6 | 15 chr7 | 16 Chromosome sizes: 0 | 197195432 1 | 129993255 2 | 121843856 3 | 121257530 4 | 120284312 5 | 125194864 6 | 103494974 7 | 98319150 8 | 95272651 9 | 90772031 10 | 61342430 11 | 181748087 12 | 159599783 13 | 155630120 14 | 152537259 15 | 149517037 16 | 152524553 17 | 131738871 18 | 124076172 19 | 16299 20 | 166650296 21 | 15902555 Size was successfully acquired for 22 chromosomes > 3. Prepare the Output Folder The prefix folder ./ exists Creating the output folder ./test_5_TSSmap_5000 Filename for the HEAT matrix ./test_5_TSSmap_5000/HEATmatrix_test_5_5000.txt Filename for the processed HEAT matrix ./test_5_TSSmap_5000/HEATmatrix_test_5_5000_processed.txt Filename for the HEAT gene rank ./test_5_TSSmap_5000/HEATmatrix_test_5_5000_genes.txt PDF file for the HEAT plot file ./test_5_TSSmap_5000/PlotHEATmap_test_5_5000.pdf > 4. Reading Refgene file tests/inputs/refGene_sample.txt: 0.00 Mb 6 transcripts of RefSeq were successfully acquired > 5. Processing the BAM/SAM file tests/inputs/H3K4me3_sample.bam: 1.21 Mb Reading:  [ 0 lines] 21482 reads of the SAM file processed 10886 forward reads acquired 10596 reverse reads acquired > 6. Processing the List of target genes List of non-available genes: 6 target genes were successfully processed Extracting gene avg. values in ./test_5_TSSmap_5000/HEATmatrix_test_5_5000_genes.txt cut -f 1,102 ./test_5_TSSmap_5000/HEATmatrix_test_5_5000.txt | sort -nrk 2 > ./test_5_TSSmap_5000/HEATmatrix_test_5_5000_genes.txt Ranking the heat file: ./test_5_TSSmap_5000/HEATmatrix_test_5_5000_processed.txt sort -nk 102 ./test_5_TSSmap_5000/HEATmatrix_test_5_5000.txt | cut -f 2-101 > ./test_5_TSSmap_5000/HEATmatrix_test_5_5000_processed.txt > 7. Running R to produce the plots > Preparing the Rscript file ./test_5_TSSmap_5000/RscriptTSSmap_test_5_5000.txt R CMD BATCH ./test_5_TSSmap_5000/RscriptTSSmap_test_5_5000.txt Removing the out R file rm -f *.Rout __________________________________________________________________________ Memory usage: 111.98 Megabytes CPU time: 0.14 secs Total time: 1 secs (0.02 mins)  [DONE] %%%% Stage 6. Running the test for H3K4me3 --chr10:5,774,999-6,225,000 (mm9)-- in mESC (noise reduction plot 2) %%%% bin/produceTSSmaps -vd -t 2 tests/inputs/ChromInfo.txt tests/inputs/refGene_sample.txt tests/inputs/H3K4me3_sample.bam tests/inputs/genes_sample.txt test_6 5000> produceTSSmaps > 0. Running on Wed Jun 23 17:12:38 2021 > 1. Request Memory to Operating System Loading the R color schema > 2. Reading Chromosome Sizes Dictionary (hash): chr8 | 17 chr9 | 18 chr10 | 1 chr11 | 2 chr12 | 3 chrX | 20 chr13 | 4 chrY | 21 chr14 | 5 chr15 | 6 chr16 | 7 chr17 | 8 chr18 | 9 chr19 | 10 chr1 | 0 chr2 | 11 chr3 | 12 chr4 | 13 chrM | 19 chr5 | 14 chr6 | 15 chr7 | 16 Chromosome sizes: 0 | 197195432 1 | 129993255 2 | 121843856 3 | 121257530 4 | 120284312 5 | 125194864 6 | 103494974 7 | 98319150 8 | 95272651 9 | 90772031 10 | 61342430 11 | 181748087 12 | 159599783 13 | 155630120 14 | 152537259 15 | 149517037 16 | 152524553 17 | 131738871 18 | 124076172 19 | 16299 20 | 166650296 21 | 15902555 Size was successfully acquired for 22 chromosomes > 3. Prepare the Output Folder The prefix folder ./ exists Creating the output folder ./test_6_TSSmap_5000 Filename for the HEAT matrix ./test_6_TSSmap_5000/HEATmatrix_test_6_5000.txt Filename for the processed HEAT matrix ./test_6_TSSmap_5000/HEATmatrix_test_6_5000_processed.txt Filename for the HEAT gene rank ./test_6_TSSmap_5000/HEATmatrix_test_6_5000_genes.txt PDF file for the HEAT plot file ./test_6_TSSmap_5000/PlotHEATmap_test_6_5000.pdf > 4. Reading Refgene file tests/inputs/refGene_sample.txt: 0.00 Mb 6 transcripts of RefSeq were successfully acquired > 5. Processing the BAM/SAM file tests/inputs/H3K4me3_sample.bam: 1.21 Mb Reading:  [ 0 lines] 21482 reads of the SAM file processed 10886 forward reads acquired 10596 reverse reads acquired > 6. Processing the List of target genes List of non-available genes: 6 target genes were successfully processed Extracting gene avg. values in ./test_6_TSSmap_5000/HEATmatrix_test_6_5000_genes.txt cut -f 1,102 ./test_6_TSSmap_5000/HEATmatrix_test_6_5000.txt | sort -nrk 2 > ./test_6_TSSmap_5000/HEATmatrix_test_6_5000_genes.txt Ranking the heat file: ./test_6_TSSmap_5000/HEATmatrix_test_6_5000_processed.txt sort -nk 102 ./test_6_TSSmap_5000/HEATmatrix_test_6_5000.txt | cut -f 2-101 > ./test_6_TSSmap_5000/HEATmatrix_test_6_5000_processed.txt > 7. Running R to produce the plots > Preparing the Rscript file ./test_6_TSSmap_5000/RscriptTSSmap_test_6_5000.txt R CMD BATCH ./test_6_TSSmap_5000/RscriptTSSmap_test_6_5000.txt Removing the out R file rm -f *.Rout __________________________________________________________________________ Memory usage: 111.98 Megabytes CPU time: 0.08 secs Total time: 1 secs (0.02 mins)  [DONE] %%%% Stage 7. Running the test for H3 --chr10:5,774,999-6,225,000 (mm9)-- in mESC (default plot) %%%% bin/produceTSSmaps -vd tests/inputs/ChromInfo.txt tests/inputs/refGene_sample.txt tests/inputs/H3_sample.bam tests/inputs/genes_sample.txt test_7 5000> produceTSSmaps > 0. Running on Wed Jun 23 17:12:39 2021 > 1. Request Memory to Operating System Loading the R color schema > 2. Reading Chromosome Sizes Dictionary (hash): chr8 | 17 chr9 | 18 chr10 | 1 chr11 | 2 chr12 | 3 chrX | 20 chr13 | 4 chrY | 21 chr14 | 5 chr15 | 6 chr16 | 7 chr17 | 8 chr18 | 9 chr19 | 10 chr1 | 0 chr2 | 11 chr3 | 12 chr4 | 13 chrM | 19 chr5 | 14 chr6 | 15 chr7 | 16 Chromosome sizes: 0 | 197195432 1 | 129993255 2 | 121843856 3 | 121257530 4 | 120284312 5 | 125194864 6 | 103494974 7 | 98319150 8 | 95272651 9 | 90772031 10 | 61342430 11 | 181748087 12 | 159599783 13 | 155630120 14 | 152537259 15 | 149517037 16 | 152524553 17 | 131738871 18 | 124076172 19 | 16299 20 | 166650296 21 | 15902555 Size was successfully acquired for 22 chromosomes > 3. Prepare the Output Folder The prefix folder ./ exists Creating the output folder ./test_7_TSSmap_5000 Filename for the HEAT matrix ./test_7_TSSmap_5000/HEATmatrix_test_7_5000.txt Filename for the processed HEAT matrix ./test_7_TSSmap_5000/HEATmatrix_test_7_5000_processed.txt Filename for the HEAT gene rank ./test_7_TSSmap_5000/HEATmatrix_test_7_5000_genes.txt PDF file for the HEAT plot file ./test_7_TSSmap_5000/PlotHEATmap_test_7_5000.pdf > 4. Reading Refgene file tests/inputs/refGene_sample.txt: 0.00 Mb 6 transcripts of RefSeq were successfully acquired > 5. Processing the BAM/SAM file tests/inputs/H3_sample.bam: 0.27 Mb Reading:  [ 0 lines] 4640 reads of the SAM file processed 2362 forward reads acquired 2278 reverse reads acquired > 6. Processing the List of target genes List of non-available genes: 6 target genes were successfully processed Extracting gene avg. values in ./test_7_TSSmap_5000/HEATmatrix_test_7_5000_genes.txt cut -f 1,102 ./test_7_TSSmap_5000/HEATmatrix_test_7_5000.txt | sort -nrk 2 > ./test_7_TSSmap_5000/HEATmatrix_test_7_5000_genes.txt Ranking the heat file: ./test_7_TSSmap_5000/HEATmatrix_test_7_5000_processed.txt sort -nk 102 ./test_7_TSSmap_5000/HEATmatrix_test_7_5000.txt | cut -f 2-101 > ./test_7_TSSmap_5000/HEATmatrix_test_7_5000_processed.txt > 7. Running R to produce the plots > Preparing the Rscript file ./test_7_TSSmap_5000/RscriptTSSmap_test_7_5000.txt R CMD BATCH ./test_7_TSSmap_5000/RscriptTSSmap_test_7_5000.txt Removing the out R file rm -f *.Rout __________________________________________________________________________ Memory usage: 111.98 Megabytes CPU time: 0.04 secs Total time: 1 secs (0.02 mins)  [DONE] %%%% R CMD BATCH tests/inputs/Rscript_produceTSSmaps.txt [DONE] %%%% Stage 7. Finishing the test (produceTSSmaps) %%%% Checking output file 1: tests/outputs/produceTSSmaps/test_1_TSSmap_5000/PlotHEATmap_test_1_5000.pdf [OK] %%%% Checking output file 2: tests/outputs/produceTSSmaps/test_2_TSSmap_5000/PlotHEATmap_test_2_5000.pdf [OK] %%%% Checking output file 3: tests/outputs/produceTSSmaps/test_3_TSSmap_5000/PlotHEATmap_test_3_5000.pdf [OK] %%%% Checking output file 4: tests/outputs/produceTSSmaps/test_4_TSSmap_5000/PlotHEATmap_test_4_5000.pdf [OK] %%%% Checking output file 5: tests/outputs/produceTSSmaps/test_5_TSSmap_5000/PlotHEATmap_test_5_5000.pdf [OK] %%%% Checking output file 6: tests/outputs/produceTSSmaps/test_6_TSSmap_5000/PlotHEATmap_test_6_5000.pdf [OK] %%%% Checking output file 7: tests/outputs/produceTSSmaps/test_7_TSSmap_5000/PlotHEATmap_test_7_5000.pdf [OK] %%%% Checking output file 7 (2): tests/outputs/produceTSSmaps/produceTSS2maps.pdf [DONE] %%%% Total running time (hours): 0.001 hours %%%% Total running time (minutes): 0.116 mins %%%% Total running time (seconds): 7 secs %%%% Successful termination: [DONE]