+ set -o pipefail + umask 0002 + SCRATCH_DIR=/scratch/CountQC_2025-11-25--16-09-00_temp317477 + GSTORE_DIR=/srv/GT/analysis/course_sushi/public/gstore/projects + INPUT_DATASET=/srv/GT/analysis/course_sushi/public/gstore/projects/p1001/CountQC_2025-11-25--16-09-00/input_dataset.tsv + LAST_JOB=TRUE ++ hostname + echo 'Job runs on fgcz-h-901' + echo 'at /scratch/CountQC_2025-11-25--16-09-00_temp317477' + mkdir /scratch/CountQC_2025-11-25--16-09-00_temp317477 + cd /scratch/CountQC_2025-11-25--16-09-00_temp317477 + source /usr/local/ngseq/etc/lmod_profile +++ eval 'echo /usr/local/ngseq/etc/modules:/etc/fgcz-envmods/lmod:/etc/lmod/modules:/usr/share/lmod/lmod/modulefiles' ++++ echo /usr/local/ngseq/etc/modules:/etc/fgcz-envmods/lmod:/etc/lmod/modules:/usr/share/lmod/lmod/modulefiles ++ export MODULEPATH=/usr/local/ngseq/etc/modules:/usr/local/ngseq/etc/modules:/etc/fgcz-envmods/lmod:/etc/lmod/modules:/usr/share/lmod/lmod/modulefiles ++ MODULEPATH=/usr/local/ngseq/etc/modules:/usr/local/ngseq/etc/modules:/etc/fgcz-envmods/lmod:/etc/lmod/modules:/usr/share/lmod/lmod/modulefiles ++ source /usr/share/lmod/lmod/init/profile +++ '[' -z '' ']' +++ LMOD_ALLOW_ROOT_USE=yes +++ '[' -n '' ']' +++ '[' yes '!=' yes ']' +++ '[' -z /usr/share/modulefiles ']' +++ findExec READLINK_CMD /bin/readlink readlink +++ Nm=READLINK_CMD +++ confPath=/bin/readlink +++ execNm=readlink +++ eval READLINK_CMD=/bin/readlink ++++ READLINK_CMD=/bin/readlink +++ '[' '!' -x /bin/readlink ']' +++ unset Nm confPath execNm +++ findExec PS_CMD /bin/ps ps +++ Nm=PS_CMD +++ confPath=/bin/ps +++ execNm=ps +++ eval PS_CMD=/bin/ps ++++ PS_CMD=/bin/ps +++ '[' '!' -x /bin/ps ']' +++ unset Nm confPath execNm +++ findExec EXPR_CMD /usr/bin/expr expr +++ Nm=EXPR_CMD +++ confPath=/usr/bin/expr +++ execNm=expr +++ eval EXPR_CMD=/usr/bin/expr ++++ EXPR_CMD=/usr/bin/expr +++ '[' '!' -x /usr/bin/expr ']' +++ unset Nm confPath execNm +++ findExec BASENAME_CMD /usr/bin/basename basename +++ Nm=BASENAME_CMD +++ confPath=/usr/bin/basename +++ execNm=basename +++ eval BASENAME_CMD=/usr/bin/basename ++++ BASENAME_CMD=/usr/bin/basename +++ '[' '!' -x /usr/bin/basename ']' +++ unset Nm confPath execNm +++ unset -f findExec +++ '[' -f /proc/317477/exe ']' ++++ /bin/readlink /proc/317477/exe +++ my_shell=/usr/bin/bash ++++ /usr/bin/expr /usr/bin/bash : '-*\(.*\)' +++ my_shell=/usr/bin/bash ++++ /usr/bin/basename /usr/bin/bash +++ my_shell=bash +++ case ${my_shell} in +++ '[' -f /usr/share/lmod/lmod/init/bash ']' +++ . /usr/share/lmod/lmod/init/bash ++++ '[' -z '' ']' ++++ case "$-" in ++++ __lmod_vx=x ++++ '[' -n x ']' ++++ set +x Shell debugging temporarily silenced: export LMOD_SH_DBG_ON=1 for this output (/usr/share/lmod/lmod/init/bash) Shell debugging restarted ++++ unset __lmod_vx +++ unset my_shell PS_CMD EXPR_CMD BASENAME_CMD MODULEPATH_INIT LMOD_ALLOW_ROOT_USE READLINK_CMD ++ export NGSEQ=/usr/local/ngseq ++ NGSEQ=/usr/local/ngseq ++ export ngsrc=/usr/local/ngseq/srcm ++ ngsrc=/usr/local/ngseq/srcm ++ export ngpkg=/usr/local/ngseq/packages ++ ngpkg=/usr/local/ngseq/packages ++ export ngmdf=/usr/local/ngseq/etc/modules ++ ngmdf=/usr/local/ngseq/etc/modules ++ '[' -d /usr/local/ngseq/. ']' ++ PATH=/usr/local/ngseq/bin:/home/trxcopy/.conda/envs/gi_sushi_jobmanager_2024/bin:/misc/ngseq12/miniforge3/condabin:/usr/local/ngseq/bin:/usr/local/bin:/usr/bin:/bin:/usr/local/games:/usr/games ++ export PATH ++ LD_LIBRARY_PATH=/usr/local/ngseq/lib:/usr/local/ngseq/lib ++ export LD_LIBRARY_PATH ++ alias 'lmodInit=. /usr/local/ngseq/etc/lmod_profile' + module add Dev/R/4.5.0 + local __lmod_my_status + local __lmod_sh_dbg + '[' -z '' ']' + case "$-" in + __lmod_sh_dbg=x + '[' -n x ']' + set +x Shell debugging temporarily silenced: export LMOD_SH_DBG_ON=1 for Lmod's output Shell debugging restarted + return 0 + R --vanilla --slave Loading required package: data.table Loading required package: Biostrings Loading required package: BiocGenerics Loading required package: generics Attaching package: ‘generics’ The following objects are masked from ‘package:base’: as.difftime, as.factor, as.ordered, intersect, is.element, setdiff, setequal, union Attaching package: ‘BiocGenerics’ 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, is.unsorted, lapply, Map, mapply, match, mget, order, paste, pmax, pmax.int, pmin, pmin.int, Position, rank, rbind, Reduce, rownames, sapply, saveRDS, table, tapply, unique, unsplit, which.max, which.min Loading required package: S4Vectors Loading required package: stats4 Attaching package: ‘S4Vectors’ The following objects are masked from ‘package:data.table’: first, second 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:data.table’: shift Loading required package: XVector Loading required package: GenomeInfoDb Attaching package: ‘Biostrings’ The following object is masked from ‘package:base’: strsplit Loading required package: GenomicRanges Loading required package: tidyverse ── Attaching core tidyverse packages ──────────────────────── tidyverse 2.0.0 ── ✔ dplyr 1.1.4 ✔ readr 2.1.5 ✔ forcats 1.0.1 ✔ stringr 1.5.2 ✔ ggplot2 4.0.0 ✔ tibble 3.3.0 ✔ lubridate 1.9.4 ✔ tidyr 1.3.1 ✔ purrr 1.1.0 ── Conflicts ────────────────────────────────────────── tidyverse_conflicts() ── ✖ lubridate::%within%() masks IRanges::%within%() ✖ dplyr::between() masks data.table::between() ✖ dplyr::collapse() masks Biostrings::collapse(), IRanges::collapse() ✖ dplyr::combine() masks BiocGenerics::combine() ✖ purrr::compact() masks XVector::compact() ✖ dplyr::desc() masks IRanges::desc() ✖ tidyr::expand() masks S4Vectors::expand() ✖ dplyr::filter() masks stats::filter() ✖ dplyr::first() masks S4Vectors::first(), data.table::first() ✖ lubridate::hour() masks data.table::hour() ✖ lubridate::isoweek() masks data.table::isoweek() ✖ dplyr::lag() masks stats::lag() ✖ dplyr::last() masks data.table::last() ✖ lubridate::mday() masks data.table::mday() ✖ lubridate::minute() masks data.table::minute() ✖ lubridate::month() masks data.table::month() ✖ ggplot2::Position() masks BiocGenerics::Position(), base::Position() ✖ lubridate::quarter() masks data.table::quarter() ✖ purrr::reduce() masks GenomicRanges::reduce(), IRanges::reduce() ✖ dplyr::rename() masks S4Vectors::rename() ✖ lubridate::second() masks S4Vectors::second(), data.table::second() ✖ lubridate::second<-() masks S4Vectors::second<-() ✖ dplyr::slice() masks XVector::slice(), IRanges::slice() ✖ purrr::transpose() masks data.table::transpose() ✖ lubridate::wday() masks data.table::wday() ✖ lubridate::week() masks data.table::week() ✖ lubridate::yday() masks data.table::yday() ✖ lubridate::year() masks data.table::year() ℹ Use the conflicted package () to force all conflicts to become errors unknown param: partition unknown param: sushi_app unknown param: isLastJob Loading required package: tools 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 file: /srv/GT/analysis/course_sushi/public/gstore/projects/p1001/FeatureCounts_2025-11-25--16-05-59/S1_undiff.txt loading file: /srv/GT/analysis/course_sushi/public/gstore/projects/p1001/FeatureCounts_2025-11-25--16-05-59/S2_undiff.txt loading file: /srv/GT/analysis/course_sushi/public/gstore/projects/p1001/FeatureCounts_2025-11-25--16-05-59/S3_undiff.txt loading file: /srv/GT/analysis/course_sushi/public/gstore/projects/p1001/FeatureCounts_2025-11-25--16-05-59/S4_diff.txt loading file: /srv/GT/analysis/course_sushi/public/gstore/projects/p1001/FeatureCounts_2025-11-25--16-05-59/S5_diff.txt loading file: /srv/GT/analysis/course_sushi/public/gstore/projects/p1001/FeatureCounts_2025-11-25--16-05-59/S6_diff.txt Loading required package: rtracklayer Using gene level annotation: /srv/GT/reference/Homo_sapiens/GENCODE/GRCh38.p14/Annotation/Release_48-2025-07-03/Genes/genes_annotation_byGene.txt Loading required package: qs2 qs2 0.1.5 + rsync -r Count_QC /srv/GT/analysis/course_sushi/public/gstore/projects/p1001/CountQC_2025-11-25--16-09-00/ + cd /scratch + rm -rf /scratch/CountQC_2025-11-25--16-09-00_temp317477