/srv/GT/analysis/course_sushi/public/gstore/projects/p1001/NfCoreDemo_2026-03-26--14-24-55/scripts/demo_NextSeq500_20190507_NS278_o5638_subSampled_2185.sh_sushiID3622_2026-03-26--14-24-58_o.log -------------------------------------------------- Job runs on fgcz-h-155 at /scratch/NfCoreDemo_2026-03-26--14-24-55_temp1711581 sample 1 S1_undiff 2 S2_undiff 3 S3_undiff 4 S4_diff 5 S5_diff 6 S6_diff fastq_1 1 /srv/GT/analysis/course_sushi/public/gstore/projects/p1000/NextSeq500_20190507_NS278_o5638_subSampled/20190507.A-S1a_undiff_R1-subsample.fastq.gz 2 /srv/GT/analysis/course_sushi/public/gstore/projects/p1000/NextSeq500_20190507_NS278_o5638_subSampled/20190507.A-S2_undiff_R1-subsample.fastq.gz 3 /srv/GT/analysis/course_sushi/public/gstore/projects/p1000/NextSeq500_20190507_NS278_o5638_subSampled/20190507.A-S3_undiff_R1-subsample.fastq.gz 4 /srv/GT/analysis/course_sushi/public/gstore/projects/p1000/NextSeq500_20190507_NS278_o5638_subSampled/20190507.A-S4_diff_R1-subsample.fastq.gz 5 /srv/GT/analysis/course_sushi/public/gstore/projects/p1000/NextSeq500_20190507_NS278_o5638_subSampled/20190507.A-S5_diff_R1-subsample.fastq.gz 6 /srv/GT/analysis/course_sushi/public/gstore/projects/p1000/NextSeq500_20190507_NS278_o5638_subSampled/20190507.A-S6_diff_R1-subsample.fastq.gz N E X T F L O W ~ version 25.10.4 Pulling nf-core/demo ... downloaded from https://github.com/nf-core/demo.git Downloading plugin nf-schema@2.6.1 Launching `https://github.com/nf-core/demo` [elated_torvalds] DSL2 - revision: 45904cb9d1 [1.1.0] ------------------------------------------------------ ,--./,-. ___ __ __ __ ___ /,-._.--~' |\ | |__ __ / ` / \ |__) |__ } { | \| | \__, \__/ | \ |___ \`-._,-`-, `._,._,' nf-core/demo 1.1.0 ------------------------------------------------------ Input/output options input : samplesheet.csv outdir : _result Generic options trace_report_suffix: 2026-03-26_14-25-29 Core Nextflow options revision : 1.1.0 runName : elated_torvalds containerEngine : singularity launchDir : /scratch/NfCoreDemo_2026-03-26--14-24-55_temp1711581 workDir : /scratch/NfCoreDemo_2026-03-26--14-24-55_temp1711581/work projectDir : /home/trxcopy/.nextflow/assets/nf-core/demo userName : trxcopy profile : singularity configFiles : /home/trxcopy/.nextflow/assets/nf-core/demo/nextflow.config, /scratch/NfCoreDemo_2026-03-26--14-24-55_temp1711581/custom_resources.config !! Only displaying parameters that differ from the pipeline defaults !! ------------------------------------------------------ * The pipeline https://doi.org/10.5281/zenodo.12192442 * The nf-core framework https://doi.org/10.1038/s41587-020-0439-x * Software dependencies https://github.com/nf-core/demo/blob/master/CITATIONS.md Downloading plugin nf-amazon@3.4.4 [- ] NFCORE_DEMO:DEMO:FASTQC - [- ] NFCORE_DEMO:DEMO:SEQTK_TRIM - [- ] NFCORE_DEMO:DEMO:MULTIQC - [- ] NFCORE_DEMO:DEMO:FASTQC | 0 of 6 [- ] NFCORE_DEMO:DEMO:SEQTK_TRIM | 0 of 6 [- ] NFCORE_DEMO:DEMO:MULTIQC - executor > local (1) [04/c4eb00] NFC…DEMO:DEMO:FASTQC (S4_diff) | 0 of 6 [- ] NFCORE_DEMO:DEMO:SEQTK_TRIM | 0 of 6 [- ] NFCORE_DEMO:DEMO:MULTIQC - executor > local (2) [04/c4eb00] NFC…DEMO:DEMO:FASTQC (S4_diff) | 1 of 6 [- ] NFCORE_DEMO:DEMO:SEQTK_TRIM | 0 of 6 [- ] NFCORE_DEMO:DEMO:MULTIQC - executor > local (3) [ed/5a9cc8] NFC…MO:DEMO:FASTQC (S3_undiff) | 2 of 6 [- ] NFCORE_DEMO:DEMO:SEQTK_TRIM | 0 of 6 [- ] NFCORE_DEMO:DEMO:MULTIQC - executor > local (5) [ed/5a9cc8] NFC…MO:DEMO:FASTQC (S3_undiff) | 3 of 6 [48/4595bb] NFC…EMO:SEQTK_TRIM (S3_undiff) | 0 of 6 [- ] NFCORE_DEMO:DEMO:MULTIQC - executor > local (5) [ed/5a9cc8] NFC…MO:DEMO:FASTQC (S3_undiff) | 3 of 6 [48/4595bb] NFC…EMO:SEQTK_TRIM (S3_undiff) | 0 of 6 [- ] NFCORE_DEMO:DEMO:MULTIQC - executor > local (7) [ed/5a9cc8] NFC…MO:DEMO:FASTQC (S3_undiff) | 3 of 6 [91/74264d] NFC…:DEMO:SEQTK_TRIM (S5_diff) | 2 of 6 [- ] NFCORE_DEMO:DEMO:MULTIQC - executor > local (7) [ed/5a9cc8] NFC…MO:DEMO:FASTQC (S3_undiff) | 3 of 6 [91/74264d] NFC…:DEMO:SEQTK_TRIM (S5_diff) | 2 of 6 [- ] NFCORE_DEMO:DEMO:MULTIQC - executor > local (8) [ed/5a9cc8] NFC…MO:DEMO:FASTQC (S3_undiff) | 3 of 6 [2a/45b31e] NFC…:DEMO:SEQTK_TRIM (S6_diff) | 3 of 6 [- ] NFCORE_DEMO:DEMO:MULTIQC - executor > local (9) [ed/5a9cc8] NFC…MO:DEMO:FASTQC (S3_undiff) | 3 of 6 [35/984fc6] NFC…EMO:SEQTK_TRIM (S1_undiff) | 4 of 6 [- ] NFCORE_DEMO:DEMO:MULTIQC - executor > local (9) [ed/5a9cc8] NFC…MO:DEMO:FASTQC (S3_undiff) | 3 of 6 [35/984fc6] NFC…EMO:SEQTK_TRIM (S1_undiff) | 4 of 6 [- ] NFCORE_DEMO:DEMO:MULTIQC - executor > local (9) [ed/5a9cc8] NFC…MO:DEMO:FASTQC (S3_undiff) | 3 of 6 [2a/45b31e] NFC…:DEMO:SEQTK_TRIM (S6_diff) | 5 of 6 [- ] NFCORE_DEMO:DEMO:MULTIQC - executor > local (10) [6e/9fd9ad] NFC…MO:DEMO:FASTQC (S2_undiff) | 3 of 6 [35/984fc6] NFC…EMO:SEQTK_TRIM (S1_undiff) | 6 of 6 ✔ [- ] NFCORE_DEMO:DEMO:MULTIQC - executor > local (10) [6e/9fd9ad] NFC…MO:DEMO:FASTQC (S2_undiff) | 3 of 6 [35/984fc6] NFC…EMO:SEQTK_TRIM (S1_undiff) | 6 of 6 ✔ [- ] NFCORE_DEMO:DEMO:MULTIQC - executor > local (11) [ae/c0af8d] NFC…DEMO:DEMO:FASTQC (S5_diff) | 4 of 6 [35/984fc6] NFC…EMO:SEQTK_TRIM (S1_undiff) | 6 of 6 ✔ [- ] NFCORE_DEMO:DEMO:MULTIQC - executor > local (11) [ae/c0af8d] NFC…DEMO:DEMO:FASTQC (S5_diff) | 4 of 6 [35/984fc6] NFC…EMO:SEQTK_TRIM (S1_undiff) | 6 of 6 ✔ [- ] NFCORE_DEMO:DEMO:MULTIQC - executor > local (12) [f5/9a0f9c] NFC…MO:DEMO:FASTQC (S1_undiff) | 5 of 6 [35/984fc6] NFC…EMO:SEQTK_TRIM (S1_undiff) | 6 of 6 ✔ [- ] NFCORE_DEMO:DEMO:MULTIQC - executor > local (12) [f5/9a0f9c] NFC…MO:DEMO:FASTQC (S1_undiff) | 6 of 6 ✔ [35/984fc6] NFC…EMO:SEQTK_TRIM (S1_undiff) | 6 of 6 ✔ [- ] NFCORE_DEMO:DEMO:MULTIQC - executor > local (13) [f5/9a0f9c] NFC…MO:DEMO:FASTQC (S1_undiff) | 6 of 6 ✔ [35/984fc6] NFC…EMO:SEQTK_TRIM (S1_undiff) | 6 of 6 ✔ [4e/783c46] NFCORE_DEMO:DEMO:MULTIQC | 0 of 1 executor > local (13) [f5/9a0f9c] NFC…MO:DEMO:FASTQC (S1_undiff) | 6 of 6 ✔ [35/984fc6] NFC…EMO:SEQTK_TRIM (S1_undiff) | 6 of 6 ✔ [4e/783c46] NFCORE_DEMO:DEMO:MULTIQC | 1 of 1 ✔ executor > local (13) [f5/9a0f9c] NFC…MO:DEMO:FASTQC (S1_undiff) | 6 of 6 ✔ [35/984fc6] NFC…EMO:SEQTK_TRIM (S1_undiff) | 6 of 6 ✔ [4e/783c46] NFCORE_DEMO:DEMO:MULTIQC | 1 of 1 ✔ -[nf-core/demo] Pipeline completed successfully- Completed at: 26-Mar-2026 14:26:47 Duration : 1m 13s CPU hours : 0.1 Succeeded : 13 [1] 0 ___STDOUT_END___ /srv/GT/analysis/course_sushi/public/gstore/projects/p1001/NfCoreDemo_2026-03-26--14-24-55/scripts/demo_NextSeq500_20190507_NS278_o5638_subSampled_2185.sh_sushiID3622_2026-03-26--14-24-58_e.log -------------------------------------------------- + set -o pipefail + umask 0002 + SCRATCH_DIR=/scratch/NfCoreDemo_2026-03-26--14-24-55_temp1711581 + GSTORE_DIR=/srv/GT/analysis/course_sushi/public/gstore/projects + INPUT_DATASET=/srv/GT/analysis/course_sushi/public/gstore/projects/p1001/NfCoreDemo_2026-03-26--14-24-55/input_dataset.tsv + LAST_JOB=TRUE ++ hostname + echo 'Job runs on fgcz-h-155' + echo 'at /scratch/NfCoreDemo_2026-03-26--14-24-55_temp1711581' + mkdir /scratch/NfCoreDemo_2026-03-26--14-24-55_temp1711581 + cd /scratch/NfCoreDemo_2026-03-26--14-24-55_temp1711581 + 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/1711581/exe ']' ++++ /bin/readlink /proc/1711581/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' + export NXF_SINGULARITY_CACHEDIR=/misc/fgcz01/nextflow_apptainer_cache/ + NXF_SINGULARITY_CACHEDIR=/misc/fgcz01/nextflow_apptainer_cache/ + export SINGULARITY_CACHEDIR=/misc/fgcz01/nextflow_apptainer_cache/ + SINGULARITY_CACHEDIR=/misc/fgcz01/nextflow_apptainer_cache/ + 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 1.6.0 ✔ ggplot2 4.0.1 ✔ tibble 3.3.1 ✔ lubridate 1.9.4 ✔ tidyr 1.3.2 ✔ 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() ✖ lubridate::isoyear() masks data.table::isoyear() ✖ 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 Loading required package: logger Sample sheet written to: samplesheet.csv Sample sheet contents: Custom config written: custom_resources.config // Executor: total available resources for this job executor { name = 'local' cpus = 8 memory = '30.GB' } // Cap all process labels to fit within executor limits process { resourceLimits = [ cpus: 8, memory: '30.GB' ] } Loading module: nextflow/25.10 Loading Nextflow 25.10.4 Running command: nextflow run nf-core/demo -r 1.1.0 --input samplesheet.csv --outdir _result -profile singularity -c custom_resources.config --skip_trim 'false' INFO (ezRun) [2026-03-26 14:25:05] EXECUTED CMD: nextflow run nf-core/demo -r 1.1.0 --input samplesheet.csv --outdir _result -profile singularity -c custom_resources.config --skip_trim 'false' + rsync -r _result /srv/GT/analysis/course_sushi/public/gstore/projects/p1001/NfCoreDemo_2026-03-26--14-24-55/ + cd /scratch + rm -rf /scratch/NfCoreDemo_2026-03-26--14-24-55_temp1711581 ___STDERR_END___