++ echo USER_NAME=thomasgrnbk,TYPE=RNAseq,SLAM=N,BASE_FOLDER=/faststorage/project/PAN_illumina/results/,FOLDER=/faststorage/project/PAN_illumina/results//thomasgrnbk/dm6/RNAseq/2025-10-28-MTD_vs_TOsK_dKD_RNAseq/,FOLDER_NAME=MTD_vs_TOsK_dKD_RNAseq,RUNname=2025-10-28-MTD_vs_TOsK_dKD_RNAseq,TMPdir=/faststorage/project/PAN_illumina/tmp//thomasgrnbk/dm6/RNAseq/2025-10-28-MTD_vs_TOsK_dKD_RNAseq/,LIB_STORAGE_FOLDER=/faststorage/project/PAN_illumina/data/libSTORAGE/,SINGULARITYdir=/home/thomasgrnbk/AP_singu/,downDIR=/faststorage/project/PAN_illumina/tmp//NGS_downloads/,DEBUG=N,VERSION=r6.63,asmHUBpath=,ASMdir=,ASMname=,BAM=N,fwADAPTOR=,rvADAPTOR=,N_TRIMM=,rawPAIRED=N,onlyPAIRED=N,FASTQout=N,FASTQoutRAW=N,SUBSAMPLE=,MIN_LENGTH=18,MAX_LENGTH=1000,RAW=,TRIMM=Y,FIRST=6,LAST=200,INVERT=N,Ychrom=N,RANDOMmulti=N,MM=2,FILTERING_INPUT=rRNA:tRNA:mito,WIG=Y,WIG_FASTA=,spikeINnorm=N,noNORM=,EXTEND=0,COMPUTING=C,GRIDsystem=SLURM,keepTMP=N,SCRIPT_DIR=/faststorage/project/PAN_illumina/tmp//thomasgrnbk/dm6/RNAseq/2025-10-28-MTD_vs_TOsK_dKD_RNAseq/script-files/,BASE_UTILITY_LOCATION=/faststorage/project/PAN_illumina/utilities/AnnotationPipeline/,UTILITY_LOCATION=/faststorage/project/PAN_illumina/utilities/AnnotationPipeline/dmel/dm6/,RELEASE=,VERSION=r6.63,UTILITY_DIR=/faststorage/project/PAN_illumina/backup/scripts/AnnotationPipeline/utility-files/,nFILES=15,FILE_CONTAINING_LIBRARIES=/faststorage/project/PAN_illumina/tmp//thomasgrnbk/dm6/RNAseq/2025-10-28-MTD_vs_TOsK_dKD_RNAseq/files.txt,FOLDER_NAME=MTD_vs_TOsK_dKD_RNAseq,GENOME_VERSION=dm6,subCOLOR=0~128~0,FORCE=,SYSTEM=EXTERN,LOGs=/faststorage/project/PAN_illumina/results//thomasgrnbk/dm6/RNAseq/2025-10-28-MTD_vs_TOsK_dKD_RNAseq/LOGs/,prepareREF=no,nSPLITS=1000000,SE=N,SE2nd=,maxCOUNT=1000000,demuxFASTA=N,autoViewLimits=,only5end=,PingPong=,DGE=N,GEO=,noSTRANDED=,FORCEimport=,exportBAM=N,exportBAMuncollapsed=N,RATIOtracks=N,GENOMEdir=/faststorage/project/PAN_illumina/results//thomasgrnbk/dm6/,newCOLLECTION=N,prepANNOTATIONgff=,prepGENOMEfasta=,prepTRANSCRIPTOMEfasta=,prepCDSfasta=,prepNCRNAfasta=,refGENO=none,GENO=none,Nexec=1 ++ sed 's/,/\t/g;s/"//g' + VARI='USER_NAME=thomasgrnbk TYPE=RNAseq SLAM=N BASE_FOLDER=/faststorage/project/PAN_illumina/results/ FOLDER=/faststorage/project/PAN_illumina/results//thomasgrnbk/dm6/RNAseq/2025-10-28-MTD_vs_TOsK_dKD_RNAseq/ FOLDER_NAME=MTD_vs_TOsK_dKD_RNAseq RUNname=2025-10-28-MTD_vs_TOsK_dKD_RNAseq TMPdir=/faststorage/project/PAN_illumina/tmp//thomasgrnbk/dm6/RNAseq/2025-10-28-MTD_vs_TOsK_dKD_RNAseq/ LIB_STORAGE_FOLDER=/faststorage/project/PAN_illumina/data/libSTORAGE/ SINGULARITYdir=/home/thomasgrnbk/AP_singu/ downDIR=/faststorage/project/PAN_illumina/tmp//NGS_downloads/ DEBUG=N VERSION=r6.63 asmHUBpath= ASMdir= ASMname= BAM=N fwADAPTOR= rvADAPTOR= N_TRIMM= rawPAIRED=N onlyPAIRED=N FASTQout=N FASTQoutRAW=N SUBSAMPLE= MIN_LENGTH=18 MAX_LENGTH=1000 RAW= TRIMM=Y FIRST=6 LAST=200 INVERT=N Ychrom=N RANDOMmulti=N MM=2 FILTERING_INPUT=rRNA:tRNA:mito WIG=Y WIG_FASTA= spikeINnorm=N noNORM= EXTEND=0 COMPUTING=C GRIDsystem=SLURM keepTMP=N SCRIPT_DIR=/faststorage/project/PAN_illumina/tmp//thomasgrnbk/dm6/RNAseq/2025-10-28-MTD_vs_TOsK_dKD_RNAseq/script-files/ BASE_UTILITY_LOCATION=/faststorage/project/PAN_illumina/utilities/AnnotationPipeline/ UTILITY_LOCATION=/faststorage/project/PAN_illumina/utilities/AnnotationPipeline/dmel/dm6/ RELEASE= VERSION=r6.63 UTILITY_DIR=/faststorage/project/PAN_illumina/backup/scripts/AnnotationPipeline/utility-files/ nFILES=15 FILE_CONTAINING_LIBRARIES=/faststorage/project/PAN_illumina/tmp//thomasgrnbk/dm6/RNAseq/2025-10-28-MTD_vs_TOsK_dKD_RNAseq/files.txt FOLDER_NAME=MTD_vs_TOsK_dKD_RNAseq GENOME_VERSION=dm6 subCOLOR=0~128~0 FORCE= SYSTEM=EXTERN LOGs=/faststorage/project/PAN_illumina/results//thomasgrnbk/dm6/RNAseq/2025-10-28-MTD_vs_TOsK_dKD_RNAseq/LOGs/ prepareREF=no nSPLITS=1000000 SE=N SE2nd= maxCOUNT=1000000 demuxFASTA=N autoViewLimits= only5end= PingPong= DGE=N GEO= noSTRANDED= FORCEimport= exportBAM=N exportBAMuncollapsed=N RATIOtracks=N GENOMEdir=/faststorage/project/PAN_illumina/results//thomasgrnbk/dm6/ newCOLLECTION=N prepANNOTATIONgff= prepGENOMEfasta= prepTRANSCRIPTOMEfasta= prepCDSfasta= prepNCRNAfasta= refGENO=none GENO=none Nexec=1' + eval 'USER_NAME=thomasgrnbk TYPE=RNAseq SLAM=N BASE_FOLDER=/faststorage/project/PAN_illumina/results/ FOLDER=/faststorage/project/PAN_illumina/results//thomasgrnbk/dm6/RNAseq/2025-10-28-MTD_vs_TOsK_dKD_RNAseq/ FOLDER_NAME=MTD_vs_TOsK_dKD_RNAseq RUNname=2025-10-28-MTD_vs_TOsK_dKD_RNAseq TMPdir=/faststorage/project/PAN_illumina/tmp//thomasgrnbk/dm6/RNAseq/2025-10-28-MTD_vs_TOsK_dKD_RNAseq/ LIB_STORAGE_FOLDER=/faststorage/project/PAN_illumina/data/libSTORAGE/ SINGULARITYdir=/home/thomasgrnbk/AP_singu/ downDIR=/faststorage/project/PAN_illumina/tmp//NGS_downloads/ DEBUG=N VERSION=r6.63 asmHUBpath= ASMdir= ASMname= BAM=N fwADAPTOR= rvADAPTOR= N_TRIMM= rawPAIRED=N onlyPAIRED=N FASTQout=N FASTQoutRAW=N SUBSAMPLE= MIN_LENGTH=18 MAX_LENGTH=1000 RAW= TRIMM=Y FIRST=6 LAST=200 INVERT=N Ychrom=N RANDOMmulti=N MM=2 FILTERING_INPUT=rRNA:tRNA:mito WIG=Y WIG_FASTA= spikeINnorm=N noNORM= EXTEND=0 COMPUTING=C GRIDsystem=SLURM keepTMP=N SCRIPT_DIR=/faststorage/project/PAN_illumina/tmp//thomasgrnbk/dm6/RNAseq/2025-10-28-MTD_vs_TOsK_dKD_RNAseq/script-files/ BASE_UTILITY_LOCATION=/faststorage/project/PAN_illumina/utilities/AnnotationPipeline/ UTILITY_LOCATION=/faststorage/project/PAN_illumina/utilities/AnnotationPipeline/dmel/dm6/ RELEASE= VERSION=r6.63 UTILITY_DIR=/faststorage/project/PAN_illumina/backup/scripts/AnnotationPipeline/utility-files/ nFILES=15 FILE_CONTAINING_LIBRARIES=/faststorage/project/PAN_illumina/tmp//thomasgrnbk/dm6/RNAseq/2025-10-28-MTD_vs_TOsK_dKD_RNAseq/files.txt FOLDER_NAME=MTD_vs_TOsK_dKD_RNAseq GENOME_VERSION=dm6 subCOLOR=0~128~0 FORCE= SYSTEM=EXTERN LOGs=/faststorage/project/PAN_illumina/results//thomasgrnbk/dm6/RNAseq/2025-10-28-MTD_vs_TOsK_dKD_RNAseq/LOGs/ prepareREF=no nSPLITS=1000000 SE=N SE2nd= maxCOUNT=1000000 demuxFASTA=N autoViewLimits= only5end= PingPong= DGE=N GEO= noSTRANDED= FORCEimport= exportBAM=N exportBAMuncollapsed=N RATIOtracks=N GENOMEdir=/faststorage/project/PAN_illumina/results//thomasgrnbk/dm6/ newCOLLECTION=N prepANNOTATIONgff= prepGENOMEfasta= prepTRANSCRIPTOMEfasta= prepCDSfasta= prepNCRNAfasta= refGENO=none GENO=none Nexec=1' ++ USER_NAME=thomasgrnbk ++ TYPE=RNAseq ++ SLAM=N ++ BASE_FOLDER=/faststorage/project/PAN_illumina/results/ ++ FOLDER=/faststorage/project/PAN_illumina/results//thomasgrnbk/dm6/RNAseq/2025-10-28-MTD_vs_TOsK_dKD_RNAseq/ ++ FOLDER_NAME=MTD_vs_TOsK_dKD_RNAseq ++ RUNname=2025-10-28-MTD_vs_TOsK_dKD_RNAseq ++ TMPdir=/faststorage/project/PAN_illumina/tmp//thomasgrnbk/dm6/RNAseq/2025-10-28-MTD_vs_TOsK_dKD_RNAseq/ ++ LIB_STORAGE_FOLDER=/faststorage/project/PAN_illumina/data/libSTORAGE/ ++ SINGULARITYdir=/home/thomasgrnbk/AP_singu/ ++ downDIR=/faststorage/project/PAN_illumina/tmp//NGS_downloads/ ++ DEBUG=N ++ VERSION=r6.63 ++ asmHUBpath= ++ ASMdir= ++ ASMname= ++ BAM=N ++ fwADAPTOR= ++ rvADAPTOR= ++ N_TRIMM= ++ rawPAIRED=N ++ onlyPAIRED=N ++ FASTQout=N ++ FASTQoutRAW=N ++ SUBSAMPLE= ++ MIN_LENGTH=18 ++ MAX_LENGTH=1000 ++ RAW= ++ TRIMM=Y ++ FIRST=6 ++ LAST=200 ++ INVERT=N ++ Ychrom=N ++ RANDOMmulti=N ++ MM=2 ++ FILTERING_INPUT=rRNA:tRNA:mito ++ WIG=Y ++ WIG_FASTA= ++ spikeINnorm=N ++ noNORM= ++ EXTEND=0 ++ COMPUTING=C ++ GRIDsystem=SLURM ++ keepTMP=N ++ SCRIPT_DIR=/faststorage/project/PAN_illumina/tmp//thomasgrnbk/dm6/RNAseq/2025-10-28-MTD_vs_TOsK_dKD_RNAseq/script-files/ ++ BASE_UTILITY_LOCATION=/faststorage/project/PAN_illumina/utilities/AnnotationPipeline/ ++ UTILITY_LOCATION=/faststorage/project/PAN_illumina/utilities/AnnotationPipeline/dmel/dm6/ ++ RELEASE= ++ VERSION=r6.63 ++ UTILITY_DIR=/faststorage/project/PAN_illumina/backup/scripts/AnnotationPipeline/utility-files/ ++ nFILES=15 ++ FILE_CONTAINING_LIBRARIES=/faststorage/project/PAN_illumina/tmp//thomasgrnbk/dm6/RNAseq/2025-10-28-MTD_vs_TOsK_dKD_RNAseq/files.txt ++ FOLDER_NAME=MTD_vs_TOsK_dKD_RNAseq ++ GENOME_VERSION=dm6 ++ subCOLOR=0~128~0 ++ FORCE= ++ SYSTEM=EXTERN ++ LOGs=/faststorage/project/PAN_illumina/results//thomasgrnbk/dm6/RNAseq/2025-10-28-MTD_vs_TOsK_dKD_RNAseq/LOGs/ ++ prepareREF=no ++ nSPLITS=1000000 ++ SE=N ++ SE2nd= ++ maxCOUNT=1000000 ++ demuxFASTA=N ++ autoViewLimits= ++ only5end= ++ PingPong= ++ DGE=N ++ GEO= ++ noSTRANDED= ++ FORCEimport= ++ exportBAM=N ++ exportBAMuncollapsed=N ++ RATIOtracks=N ++ GENOMEdir=/faststorage/project/PAN_illumina/results//thomasgrnbk/dm6/ ++ newCOLLECTION=N ++ prepANNOTATIONgff= ++ prepGENOMEfasta= ++ prepTRANSCRIPTOMEfasta= ++ prepCDSfasta= ++ prepNCRNAfasta= ++ refGENO=none ++ GENO=none ++ Nexec=1 + sed 's/,/\n/g' + echo USER_NAME=thomasgrnbk,TYPE=RNAseq,SLAM=N,BASE_FOLDER=/faststorage/project/PAN_illumina/results/,FOLDER=/faststorage/project/PAN_illumina/results//thomasgrnbk/dm6/RNAseq/2025-10-28-MTD_vs_TOsK_dKD_RNAseq/,FOLDER_NAME=MTD_vs_TOsK_dKD_RNAseq,RUNname=2025-10-28-MTD_vs_TOsK_dKD_RNAseq,TMPdir=/faststorage/project/PAN_illumina/tmp//thomasgrnbk/dm6/RNAseq/2025-10-28-MTD_vs_TOsK_dKD_RNAseq/,LIB_STORAGE_FOLDER=/faststorage/project/PAN_illumina/data/libSTORAGE/,SINGULARITYdir=/home/thomasgrnbk/AP_singu/,downDIR=/faststorage/project/PAN_illumina/tmp//NGS_downloads/,DEBUG=N,VERSION=r6.63,asmHUBpath=,ASMdir=,ASMname=,BAM=N,fwADAPTOR=,rvADAPTOR=,N_TRIMM=,rawPAIRED=N,onlyPAIRED=N,FASTQout=N,FASTQoutRAW=N,SUBSAMPLE=,MIN_LENGTH=18,MAX_LENGTH=1000,RAW=,TRIMM=Y,FIRST=6,LAST=200,INVERT=N,Ychrom=N,RANDOMmulti=N,MM=2,FILTERING_INPUT=rRNA:tRNA:mito,WIG=Y,WIG_FASTA=,spikeINnorm=N,noNORM=,EXTEND=0,COMPUTING=C,GRIDsystem=SLURM,keepTMP=N,SCRIPT_DIR=/faststorage/project/PAN_illumina/tmp//thomasgrnbk/dm6/RNAseq/2025-10-28-MTD_vs_TOsK_dKD_RNAseq/script-files/,BASE_UTILITY_LOCATION=/faststorage/project/PAN_illumina/utilities/AnnotationPipeline/,UTILITY_LOCATION=/faststorage/project/PAN_illumina/utilities/AnnotationPipeline/dmel/dm6/,RELEASE=,VERSION=r6.63,UTILITY_DIR=/faststorage/project/PAN_illumina/backup/scripts/AnnotationPipeline/utility-files/,nFILES=15,FILE_CONTAINING_LIBRARIES=/faststorage/project/PAN_illumina/tmp//thomasgrnbk/dm6/RNAseq/2025-10-28-MTD_vs_TOsK_dKD_RNAseq/files.txt,FOLDER_NAME=MTD_vs_TOsK_dKD_RNAseq,GENOME_VERSION=dm6,subCOLOR=0~128~0,FORCE=,SYSTEM=EXTERN,LOGs=/faststorage/project/PAN_illumina/results//thomasgrnbk/dm6/RNAseq/2025-10-28-MTD_vs_TOsK_dKD_RNAseq/LOGs/,prepareREF=no,nSPLITS=1000000,SE=N,SE2nd=,maxCOUNT=1000000,demuxFASTA=N,autoViewLimits=,only5end=,PingPong=,DGE=N,GEO=,noSTRANDED=,FORCEimport=,exportBAM=N,exportBAMuncollapsed=N,RATIOtracks=N,GENOMEdir=/faststorage/project/PAN_illumina/results//thomasgrnbk/dm6/,newCOLLECTION=N,prepANNOTATIONgff=,prepGENOMEfasta=,prepTRANSCRIPTOMEfasta=,prepCDSfasta=,prepNCRNAfasta=,refGENO=none,GENO=none,Nexec=1 ++ date +%s + TIME=1761657820 + TIMEx=1761657820 + [[ SLURM == SLURM ]] + CORES=2 + echo 2 + source /faststorage/project/PAN_illumina/tmp//thomasgrnbk/dm6/RNAseq/2025-10-28-MTD_vs_TOsK_dKD_RNAseq/script-files/tools ++ set -a + Rscript /faststorage/project/PAN_illumina/tmp//thomasgrnbk/dm6/RNAseq/2025-10-28-MTD_vs_TOsK_dKD_RNAseq/script-files/DGE.R TMP=/faststorage/project/PAN_illumina/tmp//thomasgrnbk/dm6/RNAseq/2025-10-28-MTD_vs_TOsK_dKD_RNAseq/ refGENO=none GENO=none FOLDER=/faststorage/project/PAN_illumina/results//thomasgrnbk/dm6/RNAseq/2025-10-28-MTD_vs_TOsK_dKD_RNAseq/ DGE=N Nexec=1 + singularity exec --cleanenv -B /faststorage/project/PAN_illumina/tmp//thomasgrnbk/dm6/RNAseq/2025-10-28-MTD_vs_TOsK_dKD_RNAseq/:/tmp /home/thomasgrnbk/AP_singu/R.simg Rscript /faststorage/project/PAN_illumina/tmp//thomasgrnbk/dm6/RNAseq/2025-10-28-MTD_vs_TOsK_dKD_RNAseq/script-files/DGE.R TMP=/faststorage/project/PAN_illumina/tmp//thomasgrnbk/dm6/RNAseq/2025-10-28-MTD_vs_TOsK_dKD_RNAseq/ refGENO=none GENO=none FOLDER=/faststorage/project/PAN_illumina/results//thomasgrnbk/dm6/RNAseq/2025-10-28-MTD_vs_TOsK_dKD_RNAseq/ DGE=N Nexec=1 ── Attaching core tidyverse packages ──────────────────────── tidyverse 2.0.0 ── ✔ dplyr 1.1.3 ✔ readr 2.1.4 ✔ forcats 1.0.0 ✔ stringr 1.5.0 ✔ ggplot2 3.4.4 ✔ tibble 3.2.1 ✔ lubridate 1.9.3 ✔ tidyr 1.3.0 ✔ purrr 1.0.2 ── Conflicts ────────────────────────────────────────── tidyverse_conflicts() ── ✖ dplyr::combine() masks gridExtra::combine() ✖ dplyr::filter() masks stats::filter() ✖ dplyr::lag() masks stats::lag() ℹ Use the conflicted package () to force all conflicts to become errors Attaching package: ‘reshape2’ The following object is masked from ‘package:tidyr’: smiths Attaching package: ‘cowplot’ The following object is masked from ‘package:lubridate’: stamp Attaching package: ‘plotly’ The following object is masked from ‘package:ggplot2’: last_plot The following object is masked from ‘package:stats’: filter The following object is masked from ‘package:graphics’: layout Loading required package: S4Vectors Loading required package: stats4 Loading required package: BiocGenerics Attaching package: ‘BiocGenerics’ The following objects are masked from ‘package:lubridate’: intersect, setdiff, union The following objects are masked from ‘package:dplyr’: combine, intersect, setdiff, union The following object is masked from ‘package:gridExtra’: combine The following objects are masked from ‘package:stats’: IQR, mad, sd, var, xtabs The following objects are masked from ‘package:base’: anyDuplicated, aperm, append, as.data.frame, basename, cbind, colnames, dirname, do.call, duplicated, eval, evalq, Filter, Find, get, grep, grepl, intersect, is.unsorted, lapply, Map, mapply, match, mget, order, paste, pmax, pmax.int, pmin, pmin.int, Position, rank, rbind, Reduce, rownames, sapply, setdiff, sort, table, tapply, union, unique, unsplit, which.max, which.min Attaching package: ‘S4Vectors’ The following object is masked from ‘package:plotly’: rename The following objects are masked from ‘package:lubridate’: second, second<- The following objects are masked from ‘package:dplyr’: first, rename The following object is masked from ‘package:tidyr’: expand The following object is masked from ‘package:utils’: findMatches The following objects are masked from ‘package:base’: expand.grid, I, unname Loading required package: IRanges Attaching package: ‘IRanges’ The following object is masked from ‘package:plotly’: slice The following object is masked from ‘package:lubridate’: %within% The following objects are masked from ‘package:dplyr’: collapse, desc, slice The following object is masked from ‘package:purrr’: reduce Loading required package: GenomicRanges Loading required package: GenomeInfoDb Loading required package: SummarizedExperiment Loading required package: MatrixGenerics Loading required package: matrixStats Attaching package: ‘matrixStats’ The following object is masked from ‘package:dplyr’: count Attaching package: ‘MatrixGenerics’ The following objects are masked from ‘package:matrixStats’: colAlls, colAnyNAs, colAnys, colAvgsPerRowSet, colCollapse, colCounts, colCummaxs, colCummins, colCumprods, colCumsums, colDiffs, colIQRDiffs, colIQRs, colLogSumExps, colMadDiffs, colMads, colMaxs, colMeans2, colMedians, colMins, colOrderStats, colProds, colQuantiles, colRanges, colRanks, colSdDiffs, colSds, colSums2, colTabulates, colVarDiffs, colVars, colWeightedMads, colWeightedMeans, colWeightedMedians, colWeightedSds, colWeightedVars, rowAlls, rowAnyNAs, rowAnys, rowAvgsPerColSet, rowCollapse, rowCounts, rowCummaxs, rowCummins, rowCumprods, rowCumsums, rowDiffs, rowIQRDiffs, rowIQRs, rowLogSumExps, rowMadDiffs, rowMads, rowMaxs, rowMeans2, rowMedians, rowMins, rowOrderStats, rowProds, rowQuantiles, rowRanges, rowRanks, rowSdDiffs, rowSds, rowSums2, rowTabulates, rowVarDiffs, rowVars, rowWeightedMads, rowWeightedMeans, rowWeightedMedians, rowWeightedSds, rowWeightedVars Loading required package: Biobase Welcome to Bioconductor Vignettes contain introductory material; view with 'browseVignettes()'. To cite Bioconductor, see 'citation("Biobase")', and for packages 'citation("pkgname")'. Attaching package: ‘Biobase’ The following object is masked from ‘package:MatrixGenerics’: rowMedians The following objects are masked from ‘package:matrixStats’: anyMissing, rowMedians Loading required package: limma Attaching package: ‘limma’ The following object is masked from ‘package:DESeq2’: plotMA The following object is masked from ‘package:BiocGenerics’: plotMA reading in files with read_tsv 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 summarizing abundance summarizing counts summarizing length summarizing inferential replicates Warning messages: 1: In self$trans$transform(x) : NaNs produced 2: Transformation introduced infinite values in continuous y-axis 3: Removed 129064 rows containing non-finite values (`stat_boxplot()`). 4: In self$trans$transform(x) : NaNs produced 5: Transformation introduced infinite values in continuous y-axis 6: Removed 132740 rows containing non-finite values (`stat_boxplot()`). ++ mawk '{ print ($1-$2)/60 }' ++ singularity exec --cleanenv -B /faststorage/project/PAN_illumina/tmp//thomasgrnbk/dm6/RNAseq/2025-10-28-MTD_vs_TOsK_dKD_RNAseq/:/tmp /home/thomasgrnbk/AP_singu/APmaster.simg mawk '{ print ($1-$2)/60 }' +++ date +%s ++ echo -e 1761657849 1761657820 + PROCESSED_TIME=0.483333 + echo 'DGE - processing_time=' 0.483333 + echo 0.483333 + exit