++ sed 's/,/\t/g;s/"//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/2026-03-18-total_RNAseq_SLX-19644_GEO/,FOLDER_NAME=total_RNAseq_SLX-19644_GEO,RUNname=2026-03-18-total_RNAseq_SLX-19644_GEO,TMPdir=/faststorage/project/PAN_illumina/tmp//thomasgrnbk/dm6/RNAseq/2026-03-18-total_RNAseq_SLX-19644_GEO/,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=,DEMUXonly=N,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/2026-03-18-total_RNAseq_SLX-19644_GEO/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=6,FILE_CONTAINING_LIBRARIES=/faststorage/project/PAN_illumina/tmp//thomasgrnbk/dm6/RNAseq/2026-03-18-total_RNAseq_SLX-19644_GEO/files.txt,FOLDER_NAME=total_RNAseq_SLX-19644_GEO,GENOME_VERSION=dm6,subCOLOR=0~128~0,FORCE=,SYSTEM=EXTERN,LOGs=/faststorage/project/PAN_illumina/results//thomasgrnbk/dm6/RNAseq/2026-03-18-total_RNAseq_SLX-19644_GEO/LOGs/,prepareREF=no,nSPLITS=1000000,SE=N,SE2nd=,maxCOUNT=1000000,demuxFASTA=N,autoViewLimits=,only5end=,PingPong=,DGE=Y,GEO=,noSTRANDED=,FORCEimport=,exportBAM=N,exportBAMuncollapsed=N,exportSalmon=N,RATIOtracks=N,GENOMEdir=/faststorage/project/PAN_illumina/results//thomasgrnbk/dm6/,newCOLLECTION=N,prepANNOTATIONgff=,prepGENOMEfasta=,prepTRANSCRIPTOMEfasta=,prepCDSfasta=,prepNCRNAfasta=,extraSEQ=,FORCEquant_unstranded=N,refGENO=rhi_00h,GENO=white_00h~piwi_00h~rhi_00h,Nexec=1 + VARI='USER_NAME=thomasgrnbk TYPE=RNAseq SLAM=N BASE_FOLDER=/faststorage/project/PAN_illumina/results/ FOLDER=/faststorage/project/PAN_illumina/results//thomasgrnbk/dm6/RNAseq/2026-03-18-total_RNAseq_SLX-19644_GEO/ FOLDER_NAME=total_RNAseq_SLX-19644_GEO RUNname=2026-03-18-total_RNAseq_SLX-19644_GEO TMPdir=/faststorage/project/PAN_illumina/tmp//thomasgrnbk/dm6/RNAseq/2026-03-18-total_RNAseq_SLX-19644_GEO/ 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= DEMUXonly=N 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/2026-03-18-total_RNAseq_SLX-19644_GEO/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=6 FILE_CONTAINING_LIBRARIES=/faststorage/project/PAN_illumina/tmp//thomasgrnbk/dm6/RNAseq/2026-03-18-total_RNAseq_SLX-19644_GEO/files.txt FOLDER_NAME=total_RNAseq_SLX-19644_GEO GENOME_VERSION=dm6 subCOLOR=0~128~0 FORCE= SYSTEM=EXTERN LOGs=/faststorage/project/PAN_illumina/results//thomasgrnbk/dm6/RNAseq/2026-03-18-total_RNAseq_SLX-19644_GEO/LOGs/ prepareREF=no nSPLITS=1000000 SE=N SE2nd= maxCOUNT=1000000 demuxFASTA=N autoViewLimits= only5end= PingPong= DGE=Y GEO= noSTRANDED= FORCEimport= exportBAM=N exportBAMuncollapsed=N exportSalmon=N RATIOtracks=N GENOMEdir=/faststorage/project/PAN_illumina/results//thomasgrnbk/dm6/ newCOLLECTION=N prepANNOTATIONgff= prepGENOMEfasta= prepTRANSCRIPTOMEfasta= prepCDSfasta= prepNCRNAfasta= extraSEQ= FORCEquant_unstranded=N refGENO=rhi_00h GENO=white_00h~piwi_00h~rhi_00h 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/2026-03-18-total_RNAseq_SLX-19644_GEO/ FOLDER_NAME=total_RNAseq_SLX-19644_GEO RUNname=2026-03-18-total_RNAseq_SLX-19644_GEO TMPdir=/faststorage/project/PAN_illumina/tmp//thomasgrnbk/dm6/RNAseq/2026-03-18-total_RNAseq_SLX-19644_GEO/ 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= DEMUXonly=N 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/2026-03-18-total_RNAseq_SLX-19644_GEO/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=6 FILE_CONTAINING_LIBRARIES=/faststorage/project/PAN_illumina/tmp//thomasgrnbk/dm6/RNAseq/2026-03-18-total_RNAseq_SLX-19644_GEO/files.txt FOLDER_NAME=total_RNAseq_SLX-19644_GEO GENOME_VERSION=dm6 subCOLOR=0~128~0 FORCE= SYSTEM=EXTERN LOGs=/faststorage/project/PAN_illumina/results//thomasgrnbk/dm6/RNAseq/2026-03-18-total_RNAseq_SLX-19644_GEO/LOGs/ prepareREF=no nSPLITS=1000000 SE=N SE2nd= maxCOUNT=1000000 demuxFASTA=N autoViewLimits= only5end= PingPong= DGE=Y GEO= noSTRANDED= FORCEimport= exportBAM=N exportBAMuncollapsed=N exportSalmon=N RATIOtracks=N GENOMEdir=/faststorage/project/PAN_illumina/results//thomasgrnbk/dm6/ newCOLLECTION=N prepANNOTATIONgff= prepGENOMEfasta= prepTRANSCRIPTOMEfasta= prepCDSfasta= prepNCRNAfasta= extraSEQ= FORCEquant_unstranded=N refGENO=rhi_00h GENO=white_00h~piwi_00h~rhi_00h 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/2026-03-18-total_RNAseq_SLX-19644_GEO/ ++ FOLDER_NAME=total_RNAseq_SLX-19644_GEO ++ RUNname=2026-03-18-total_RNAseq_SLX-19644_GEO ++ TMPdir=/faststorage/project/PAN_illumina/tmp//thomasgrnbk/dm6/RNAseq/2026-03-18-total_RNAseq_SLX-19644_GEO/ ++ 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= ++ DEMUXonly=N ++ 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/2026-03-18-total_RNAseq_SLX-19644_GEO/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=6 ++ FILE_CONTAINING_LIBRARIES=/faststorage/project/PAN_illumina/tmp//thomasgrnbk/dm6/RNAseq/2026-03-18-total_RNAseq_SLX-19644_GEO/files.txt ++ FOLDER_NAME=total_RNAseq_SLX-19644_GEO ++ GENOME_VERSION=dm6 ++ subCOLOR=0~128~0 ++ FORCE= ++ SYSTEM=EXTERN ++ LOGs=/faststorage/project/PAN_illumina/results//thomasgrnbk/dm6/RNAseq/2026-03-18-total_RNAseq_SLX-19644_GEO/LOGs/ ++ prepareREF=no ++ nSPLITS=1000000 ++ SE=N ++ SE2nd= ++ maxCOUNT=1000000 ++ demuxFASTA=N ++ autoViewLimits= ++ only5end= ++ PingPong= ++ DGE=Y ++ GEO= ++ noSTRANDED= ++ FORCEimport= ++ exportBAM=N ++ exportBAMuncollapsed=N ++ exportSalmon=N ++ RATIOtracks=N ++ GENOMEdir=/faststorage/project/PAN_illumina/results//thomasgrnbk/dm6/ ++ newCOLLECTION=N ++ prepANNOTATIONgff= ++ prepGENOMEfasta= ++ prepTRANSCRIPTOMEfasta= ++ prepCDSfasta= ++ prepNCRNAfasta= ++ extraSEQ= ++ FORCEquant_unstranded=N ++ refGENO=rhi_00h ++ GENO=white_00h~piwi_00h~rhi_00h ++ 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/2026-03-18-total_RNAseq_SLX-19644_GEO/,FOLDER_NAME=total_RNAseq_SLX-19644_GEO,RUNname=2026-03-18-total_RNAseq_SLX-19644_GEO,TMPdir=/faststorage/project/PAN_illumina/tmp//thomasgrnbk/dm6/RNAseq/2026-03-18-total_RNAseq_SLX-19644_GEO/,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=,DEMUXonly=N,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/2026-03-18-total_RNAseq_SLX-19644_GEO/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=6,FILE_CONTAINING_LIBRARIES=/faststorage/project/PAN_illumina/tmp//thomasgrnbk/dm6/RNAseq/2026-03-18-total_RNAseq_SLX-19644_GEO/files.txt,FOLDER_NAME=total_RNAseq_SLX-19644_GEO,GENOME_VERSION=dm6,subCOLOR=0~128~0,FORCE=,SYSTEM=EXTERN,LOGs=/faststorage/project/PAN_illumina/results//thomasgrnbk/dm6/RNAseq/2026-03-18-total_RNAseq_SLX-19644_GEO/LOGs/,prepareREF=no,nSPLITS=1000000,SE=N,SE2nd=,maxCOUNT=1000000,demuxFASTA=N,autoViewLimits=,only5end=,PingPong=,DGE=Y,GEO=,noSTRANDED=,FORCEimport=,exportBAM=N,exportBAMuncollapsed=N,exportSalmon=N,RATIOtracks=N,GENOMEdir=/faststorage/project/PAN_illumina/results//thomasgrnbk/dm6/,newCOLLECTION=N,prepANNOTATIONgff=,prepGENOMEfasta=,prepTRANSCRIPTOMEfasta=,prepCDSfasta=,prepNCRNAfasta=,extraSEQ=,FORCEquant_unstranded=N,refGENO=rhi_00h,GENO=white_00h~piwi_00h~rhi_00h,Nexec=1 ++ date +%s + TIME=1773841463 + TIMEx=1773841463 + [[ SLURM == SLURM ]] + CORES=2 + echo 2 + source /faststorage/project/PAN_illumina/tmp//thomasgrnbk/dm6/RNAseq/2026-03-18-total_RNAseq_SLX-19644_GEO/script-files/tools ++ set -a + Rscript /faststorage/project/PAN_illumina/tmp//thomasgrnbk/dm6/RNAseq/2026-03-18-total_RNAseq_SLX-19644_GEO/script-files/DGE.R TMP=/faststorage/project/PAN_illumina/tmp//thomasgrnbk/dm6/RNAseq/2026-03-18-total_RNAseq_SLX-19644_GEO/ refGENO=rhi_00h GENO=white_00h~piwi_00h~rhi_00h FOLDER=/faststorage/project/PAN_illumina/results//thomasgrnbk/dm6/RNAseq/2026-03-18-total_RNAseq_SLX-19644_GEO/ DGE=Y Nexec=1 + singularity exec --cleanenv -B /faststorage/project/PAN_illumina/tmp//thomasgrnbk/dm6/RNAseq/2026-03-18-total_RNAseq_SLX-19644_GEO/:/tmp /home/thomasgrnbk/AP_singu/R.simg Rscript /faststorage/project/PAN_illumina/tmp//thomasgrnbk/dm6/RNAseq/2026-03-18-total_RNAseq_SLX-19644_GEO/script-files/DGE.R TMP=/faststorage/project/PAN_illumina/tmp//thomasgrnbk/dm6/RNAseq/2026-03-18-total_RNAseq_SLX-19644_GEO/ refGENO=rhi_00h GENO=white_00h~piwi_00h~rhi_00h FOLDER=/faststorage/project/PAN_illumina/results//thomasgrnbk/dm6/RNAseq/2026-03-18-total_RNAseq_SLX-19644_GEO/ DGE=Y 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 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 43798 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 46176 rows containing non-finite values (`stat_boxplot()`). reading in files with read_tsv 1 2 3 4 5 6 summarizing abundance summarizing counts summarizing length summarizing inferential replicates using counts and average transcript lengths from tximport Warning message: In DESeqDataSet(se, design = design, ignoreRank) : some variables in design formula are characters, converting to factors estimating size factors using 'avgTxLength' from assays(dds), correcting for library size estimating dispersions gene-wise dispersion estimates mean-dispersion relationship final dispersion estimates fitting model and testing reading in files with read_tsv 1 2 3 4 summarizing abundance summarizing counts summarizing length summarizing inferential replicates using counts and average transcript lengths from tximport estimating size factors using 'avgTxLength' from assays(dds), correcting for library size estimating dispersions gene-wise dispersion estimates mean-dispersion relationship final dispersion estimates fitting model and testing using 'apeglm' for LFC shrinkage. If used in published research, please cite: Zhu, A., Ibrahim, J.G., Love, M.I. (2018) Heavy-tailed prior distributions for sequence count data: removing the noise and preserving large differences. Bioinformatics. https://doi.org/10.1093/bioinformatics/bty895 1413 of 10406 genes were filtered out in DESeq2 tests reading in files with read_tsv 1 2 3 4 summarizing abundance summarizing counts summarizing length summarizing inferential replicates using counts and average transcript lengths from tximport estimating size factors using 'avgTxLength' from assays(dds), correcting for library size estimating dispersions gene-wise dispersion estimates mean-dispersion relationship final dispersion estimates fitting model and testing using 'apeglm' for LFC shrinkage. If used in published research, please cite: Zhu, A., Ibrahim, J.G., Love, M.I. (2018) Heavy-tailed prior distributions for sequence count data: removing the noise and preserving large differences. Bioinformatics. https://doi.org/10.1093/bioinformatics/bty895 1421 of 10468 genes were filtered out in DESeq2 tests reading in files with read_tsv 1 2 3 4 summarizing abundance summarizing counts summarizing length summarizing inferential replicates using counts and average transcript lengths from tximport estimating size factors using 'avgTxLength' from assays(dds), correcting for library size estimating dispersions gene-wise dispersion estimates mean-dispersion relationship final dispersion estimates fitting model and testing using 'apeglm' for LFC shrinkage. If used in published research, please cite: Zhu, A., Ibrahim, J.G., Love, M.I. (2018) Heavy-tailed prior distributions for sequence count data: removing the noise and preserving large differences. Bioinformatics. https://doi.org/10.1093/bioinformatics/bty895 407 of 10494 genes were filtered out in DESeq2 tests Warning messages: 1: In DESeqDataSet(se, design = design, ignoreRank) : some variables in design formula are characters, converting to factors 2: In DESeqDataSet(se, design = design, ignoreRank) : some variables in design formula are characters, converting to factors 3: In DESeqDataSet(se, design = design, ignoreRank) : some variables in design formula are characters, converting to factors ++ mawk '{ print ($1-$2)/60 }' ++ singularity exec --cleanenv -B /faststorage/project/PAN_illumina/tmp//thomasgrnbk/dm6/RNAseq/2026-03-18-total_RNAseq_SLX-19644_GEO/:/tmp /home/thomasgrnbk/AP_singu/APmaster.simg mawk '{ print ($1-$2)/60 }' +++ date +%s ++ echo -e 1773841510 1773841463 + PROCESSED_TIME=0.783333 + echo 'DGE - processing_time=' 0.783333 + echo 0.783333 + exit