/srv/GT/analysis/course_sushi/public/gstore/projects/p1001/FeatureCounts_2025-11-25--16-05-59/scripts/Count_S5_diff_STAR_2315.sh_sushiID2491_2025-11-25--16-06-15_o.log -------------------------------------------------- Job runs on fgcz-h-905 at /scratch/FeatureCounts_2025-11-25--16-05-59_S5_diff_temp280178 Starting EzAppFeatureCounts FeatureCounts_2025-11-25--16-05-59_S5_diff_temp280178 2025-11-25 16:06:21 ========== _____ _ _ ____ _____ ______ _____ ===== / ____| | | | _ \| __ \| ____| /\ | __ \ ===== | (___ | | | | |_) | |__) | |__ / \ | | | | ==== \___ \| | | | _ <| _ /| __| / /\ \ | | | | ==== ____) | |__| | |_) | | \ \| |____ / ____ \| |__| | ========== |_____/ \____/|____/|_| \_\______/_/ \_\_____/ Rsubread 2.22.1 //========================== featureCounts setting ===========================\\ || || || Input files : 1 BAM file || || || || S5_diff.bam || || || || Paired-end : no || || Count read pairs : no || || Annotation : 280203-genes.gtf (GTF) || || Dir for temp files : . || || Threads : 8 || || Level : meta-feature level || || Multimapping reads : counted || || Multiple alignments : primary alignment only || || Multi-overlapping reads : counted || || Min overlapping bases : 10 || || || \\============================================================================// //================================= Running ==================================\\ || || || Load annotation file 280203-genes.gtf ... || || Features : 1400876 || || Meta-features : 21077 || || Chromosomes/contigs : 39 || || || || Process BAM file S5_diff.bam... || || Strand specific : reversely stranded || || Single-end reads are included. || || Total alignments : 86106 || || Successfully assigned alignments : 64015 (74.3%) || || Running time : 0.00 minutes || || || || Write the final count table. || || Write the read assignment summary. || || || \\============================================================================// ezRun tag: 28496712ee737d3a120e054f95c1bc9b6b30a722 ezRun github link: https://github.com/uzh/ezRun/tree/28496712ee737d3a120e054f95c1bc9b6b30a722 R version 4.5.0 (2025-04-11) Platform: x86_64-pc-linux-gnu Running under: Debian GNU/Linux 12 (bookworm) Matrix products: default BLAS: /usr/lib/x86_64-linux-gnu/blas/libblas.so.3.11.0 LAPACK: /usr/lib/x86_64-linux-gnu/lapack/liblapack.so.3.11.0 LAPACK version 3.11.0 locale: [1] LC_CTYPE=en_US.UTF-8 LC_NUMERIC=C [3] LC_TIME=en_US.UTF-8 LC_COLLATE=en_US.UTF-8 [5] LC_MONETARY=en_US.UTF-8 LC_MESSAGES=en_US.UTF-8 [7] LC_PAPER=en_US.UTF-8 LC_NAME=C [9] LC_ADDRESS=C LC_TELEPHONE=C [11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C time zone: Europe/Zurich tzcode source: system (glibc) attached base packages: [1] stats4 stats graphics grDevices utils datasets methods [8] base other attached packages: [1] rtracklayer_1.68.0 Rsubread_2.22.1 ezRun_3.21.1 [4] lubridate_1.9.4 forcats_1.0.1 stringr_1.5.2 [7] dplyr_1.1.4 purrr_1.1.0 readr_2.1.5 [10] tidyr_1.3.1 tibble_3.3.0 ggplot2_4.0.0 [13] tidyverse_2.0.0 GenomicRanges_1.60.0 Biostrings_2.76.0 [16] GenomeInfoDb_1.44.3 XVector_0.48.0 IRanges_2.42.0 [19] S4Vectors_0.46.0 BiocGenerics_0.54.1 generics_0.1.4 [22] data.table_1.17.8 loaded via a namespace (and not attached): [1] SummarizedExperiment_1.38.1 gtable_0.3.6 [3] rjson_0.2.23 Biobase_2.68.0 [5] lattice_0.22-7 tzdb_0.5.0 [7] vctrs_0.6.5 tools_4.5.0 [9] bitops_1.0-9 curl_6.2.3 [11] parallel_4.5.0 pkgconfig_2.0.3 [13] Matrix_1.7-3 RColorBrewer_1.1-3 [15] S7_0.2.0 lifecycle_1.0.4 [17] GenomeInfoDbData_1.2.14 compiler_4.5.0 [19] farver_2.1.2 Rsamtools_2.24.0 [21] codetools_0.2-20 RCurl_1.98-1.17 [23] yaml_2.3.10 pillar_1.11.1 [25] crayon_1.5.3 BiocParallel_1.42.2 [27] DelayedArray_0.34.1 abind_1.4-8 [29] tidyselect_1.2.1 stringi_1.8.7 [31] restfulr_0.0.15 grid_4.5.0 [33] SparseArray_1.8.1 cli_3.6.5 [35] magrittr_2.0.4 S4Arrays_1.8.1 [37] dichromat_2.0-0.1 XML_3.99-0.18 [39] withr_3.0.2 scales_1.4.0 [41] UCSC.utils_1.4.0 timechange_0.3.0 [43] httr_1.4.7 matrixStats_1.5.0 [45] hms_1.1.3 BiocIO_1.18.0 [47] rlang_1.1.6 glue_1.8.0 [49] jsonlite_2.0.0 R6_2.6.1 [51] MatrixGenerics_1.20.0 GenomicAlignments_1.44.0 Finished EzAppFeatureCounts FeatureCounts_2025-11-25--16-05-59_S5_diff_temp280178 2025-11-25 16:07:38 [1] "Success" ___STDOUT_END___ /srv/GT/analysis/course_sushi/public/gstore/projects/p1001/FeatureCounts_2025-11-25--16-05-59/scripts/Count_S5_diff_STAR_2315.sh_sushiID2491_2025-11-25--16-06-15_e.log -------------------------------------------------- + set -o pipefail + umask 0002 + SCRATCH_DIR=/scratch/FeatureCounts_2025-11-25--16-05-59_S5_diff_temp280178 + GSTORE_DIR=/srv/GT/analysis/course_sushi/public/gstore/projects + INPUT_DATASET=/srv/GT/analysis/course_sushi/public/gstore/projects/p1001/FeatureCounts_2025-11-25--16-05-59/input_dataset.tsv + LAST_JOB=FALSE ++ hostname + echo 'Job runs on fgcz-h-905' + echo 'at /scratch/FeatureCounts_2025-11-25--16-05-59_S5_diff_temp280178' + mkdir /scratch/FeatureCounts_2025-11-25--16-05-59_S5_diff_temp280178 + cd /scratch/FeatureCounts_2025-11-25--16-05-59_S5_diff_temp280178 + 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/280178/exe ']' ++++ /bin/readlink /proc/280178/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 Tools/samtools/1.20 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: secondRef unknown param: sushi_app unknown param: isLastJob Loading required package: Rsubread Loading required package: rtracklayer + rsync -r S5_diff.txt /srv/GT/analysis/course_sushi/public/gstore/projects/p1001/FeatureCounts_2025-11-25--16-05-59/ + rsync -r S5_diff-stats.txt /srv/GT/analysis/course_sushi/public/gstore/projects/p1001/FeatureCounts_2025-11-25--16-05-59/ + cd /scratch + rm -rf /scratch/FeatureCounts_2025-11-25--16-05-59_S5_diff_temp280178 ___STDERR_END___