/srv/GT/analysis/course_sushi/public/gstore/projects/p1001/o35755_Fastqc_2025-08-22--10-06-39/scripts/QC_ventricles_100k_1.sh_sushiID1623_2025-08-22--10-07-06_o.log -------------------------------------------------- Job runs on fgcz-h-121 at /scratch/o35755_Fastqc_2025-08-22--10-06-39_temp3626751 Starting EzAppFastqc FastQC o35755_Fastqc_2025-08-22--10-06-39_temp3626751 2025-08-22 10:07:15 EXECUTED CMD: fastqc --extract -o . -t 1 -a /srv/GT/databases/adapter/adapter_list.txt --kmers 7 --dir . -q /srv/GT/analysis/course_sushi/public/gstore/projects/p1001/ventricles_100k/MutantSample_1_R1.fastq.gz /srv/GT/analysis/course_sushi/public/gstore/projects/p1001/ventricles_100k/MutantSample_1_R2.fastq.gz /srv/GT/analysis/course_sushi/public/gstore/projects/p1001/ventricles_100k/MutantSample_2_R1.fastq.gz /srv/GT/analysis/course_sushi/public/gstore/projects/p1001/ventricles_100k/MutantSample_2_R2.fastq.gz > fastqc.out 2> fastqc.err EXECUTED CMD: multiqc --outdir ../multi_FastQC . ezRun tag: 3da2a8532fe0f1a8aabaac01d497d2ad006e25e1 ezRun github link: https://github.com/uzh/ezRun/tree/3da2a8532fe0f1a8aabaac01d497d2ad006e25e1 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=C.UTF-8 LC_NUMERIC=C LC_TIME=C.UTF-8 [4] LC_COLLATE=C.UTF-8 LC_MONETARY=C.UTF-8 LC_MESSAGES=C.UTF-8 [7] LC_PAPER=C.UTF-8 LC_NAME=C LC_ADDRESS=C [10] LC_TELEPHONE=C LC_MEASUREMENT=C.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] ezRun_3.21.1 lubridate_1.9.4 forcats_1.0.0 [4] stringr_1.5.1 dplyr_1.1.4 purrr_1.0.4 [7] readr_2.1.5 tidyr_1.3.1 tibble_3.2.1 [10] ggplot2_3.5.2 tidyverse_2.0.0 GenomicRanges_1.60.0 [13] Biostrings_2.76.0 GenomeInfoDb_1.44.0 XVector_0.48.0 [16] IRanges_2.42.0 S4Vectors_0.46.0 BiocGenerics_0.54.0 [19] generics_0.1.4 data.table_1.17.4 loaded via a namespace (and not attached): [1] gtable_0.3.6 jsonlite_2.0.0 compiler_4.5.0 [4] crayon_1.5.3 tidyselect_1.2.1 dichromat_2.0-0.1 [7] scales_1.4.0 R6_2.6.1 GenomeInfoDbData_1.2.14 [10] pillar_1.10.2 RColorBrewer_1.1-3 tzdb_0.5.0 [13] rlang_1.1.6 stringi_1.8.7 timechange_0.3.0 [16] cli_3.6.5 withr_3.0.2 magrittr_2.0.3 [19] grid_4.5.0 hms_1.1.3 lifecycle_1.0.4 [22] vctrs_0.6.5 glue_1.8.0 farver_2.1.2 [25] httr_1.4.7 tools_4.5.0 pkgconfig_2.0.3 [28] UCSC.utils_1.4.0 Finished EzAppFastqc FastQC o35755_Fastqc_2025-08-22--10-06-39_temp3626751 2025-08-22 10:07:32 [1] "Success" ___STDOUT_END___ /srv/GT/analysis/course_sushi/public/gstore/projects/p1001/o35755_Fastqc_2025-08-22--10-06-39/scripts/QC_ventricles_100k_1.sh_sushiID1623_2025-08-22--10-07-06_e.log -------------------------------------------------- + set -o pipefail + umask 0002 + SCRATCH_DIR=/scratch/o35755_Fastqc_2025-08-22--10-06-39_temp3626751 + GSTORE_DIR=/srv/GT/analysis/course_sushi/public/gstore/projects + INPUT_DATASET=/srv/GT/analysis/course_sushi/public/gstore/projects/p1001/o35755_Fastqc_2025-08-22--10-06-39/input_dataset.tsv + LAST_JOB=TRUE ++ hostname + echo 'Job runs on fgcz-h-121' + echo 'at /scratch/o35755_Fastqc_2025-08-22--10-06-39_temp3626751' + mkdir /scratch/o35755_Fastqc_2025-08-22--10-06-39_temp3626751 + cd /scratch/o35755_Fastqc_2025-08-22--10-06-39_temp3626751 + 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/3626751/exe ']' ++++ /bin/readlink /proc/3626751/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/packages/Dev/Ruby/3.3.7/bin:/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:/usr/local/ngseq/lib ++ export LD_LIBRARY_PATH ++ alias 'lmodInit=. /usr/local/ngseq/etc/lmod_profile' + module add QC/FastQC/0.12.1 Dev/R/4.5.0 Tools/Picard/3.2.0 Tools/samtools/1.20 Dev/Python/3.12.8 QC/fastp/0.23.4 + 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 1.0.0 ✔ stringr 1.5.1 ✔ ggplot2 3.5.2 ✔ tibble 3.2.1 ✔ lubridate 1.9.4 ✔ tidyr 1.3.1 ✔ purrr 1.0.4 ── 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 /// MultiQC 🔍 v1.30 file_search | Search path: /scratch/o35755_Fastqc_2025-08-22--10-06-39_temp3626751/FastQC fastqc | Found 4 reports write_results | Data : /scratch/o35755_Fastqc_2025-08-22--10-06-39_temp3626751/multi_FastQC/multiqc_data write_results | Report : /scratch/o35755_Fastqc_2025-08-22--10-06-39_temp3626751/multi_FastQC/multiqc_report.html multiqc | MultiQC complete + rsync -r multi_FastQC /srv/GT/analysis/course_sushi/public/gstore/projects/p1001/o35755_Fastqc_2025-08-22--10-06-39/ + rsync -r FastQC /srv/GT/analysis/course_sushi/public/gstore/projects/p1001/o35755_Fastqc_2025-08-22--10-06-39/ + cd /scratch + rm -rf /scratch/o35755_Fastqc_2025-08-22--10-06-39_temp3626751 ___STDERR_END___