/srv/GT/analysis/course_sushi/public/gstore/projects/p1001/NfCoreChipseq_2026-02-26--13-55-19/scripts/Epigenetics_NextSeq500_20190507_NS278_o5638_subSampled_2185.sh_sushiID3059_2026-02-26--16-28-44_o.log -------------------------------------------------- Job runs on fgcz-h-155 at /scratch/NfCoreChipseq_2026-02-26--13-55-19_temp1378197 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 fastq_2 replicate antibody control 1 NA NA NA NA 2 NA NA NA NA 3 NA NA NA NA 4 NA NA NA NA 5 NA NA NA NA 6 NA NA NA NA N E X T F L O W ~ version 24.10.3 Pulling nf-core/chipseq ... downloaded from https://github.com/nf-core/chipseq.git Launching `https://github.com/nf-core/chipseq` [deadly_williams] DSL2 - revision: 76e2382b6d [2.1.0] WARN: Access to undefined parameter `monochromeLogs` -- Initialise it to a default value eg. `params.monochromeLogs = some_value` ------------------------------------------------------ ,--./,-. ___ __ __ __ ___ /,-._.--~' |\ | |__ __ / ` / \ |__) |__ } { | \| | \__, \__/ | \ |___ \`-._,-`-, `._,._,' nf-core/chipseq v2.1.0-g76e2382 ------------------------------------------------------ Core Nextflow options revision : 2.1.0 runName : deadly_williams containerEngine: singularity launchDir : /scratch/NfCoreChipseq_2026-02-26--13-55-19_temp1378197 workDir : /scratch/NfCoreChipseq_2026-02-26--13-55-19_temp1378197/work projectDir : /home/trxcopy/.nextflow/assets/nf-core/chipseq userName : trxcopy profile : singularity configFiles : Input/output options input : samplesheet.csv outdir : _result Reference genome options fasta : /srv/GT/reference/Homo_sapiens/GENCODE/GRCh38.p14/Sequence/WholeGenomeFasta/genome.fa gtf : /srv/GT/reference/Homo_sapiens/GENCODE/GRCh38.p14/Annotation/Genes/genes.gtf Max job request options max_cpus : 8 max_memory : 30.GB !! Only displaying parameters that differ from the pipeline defaults !! ------------------------------------------------------ If you use nf-core/chipseq for your analysis please cite: * The pipeline https://doi.org/10.5281/zenodo.3240506 * The nf-core framework https://doi.org/10.1038/s41587-020-0439-x * Software dependencies https://github.com/nf-core/chipseq/blob/master/CITATIONS.md ------------------------------------------------------ ERROR ~ ERROR: Validation of 'input' file failed! -- Check '.nextflow.log' file for details ___STDOUT_END___ /srv/GT/analysis/course_sushi/public/gstore/projects/p1001/NfCoreChipseq_2026-02-26--13-55-19/scripts/Epigenetics_NextSeq500_20190507_NS278_o5638_subSampled_2185.sh_sushiID3059_2026-02-26--16-28-44_e.log -------------------------------------------------- + set -o pipefail + umask 0002 + SCRATCH_DIR=/scratch/NfCoreChipseq_2026-02-26--13-55-19_temp1378197 + GSTORE_DIR=/srv/GT/analysis/course_sushi/public/gstore/projects + INPUT_DATASET=/srv/GT/analysis/course_sushi/public/gstore/projects/p1001/NfCoreChipseq_2026-02-26--13-55-19/input_dataset.tsv + LAST_JOB=TRUE ++ hostname + echo 'Job runs on fgcz-h-155' + echo 'at /scratch/NfCoreChipseq_2026-02-26--13-55-19_temp1378197' + mkdir /scratch/NfCoreChipseq_2026-02-26--13-55-19_temp1378197 + cd /scratch/NfCoreChipseq_2026-02-26--13-55-19_temp1378197 + 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/1378197/exe ']' ++++ /bin/readlink /proc/1378197/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 Pipeline: chipseq Version: 2.1.0 Input Type: samplesheet Building input file for type: samplesheet Warning: Column 'Read2 [File]' not found in dataset for nf-core column 'fastq_2' Warning: Column 'Replicate' not found in dataset for nf-core column 'replicate' Warning: Column 'Antibody' not found in dataset for nf-core column 'antibody' Warning: Column 'Control' not found in dataset for nf-core column 'control' Sample sheet written to: samplesheet.csv Contents: Custom config written: custom_resources.config Resolved GTF from refBuild: /srv/GT/reference/Homo_sapiens/GENCODE/GRCh38.p14/Annotation/Genes/genes.gtf Running command: nextflow run nf-core/chipseq -r 2.1.0 --input samplesheet.csv --outdir _result -profile singularity -c custom_resources.config --fasta /srv/GT/reference/Homo_sapiens/GENCODE/GRCh38.p14/Sequence/WholeGenomeFasta/genome.fa --gtf /srv/GT/reference/Homo_sapiens/GENCODE/GRCh38.p14/Annotation/Genes/genes.gtf --aligner bwa INFO (ezRun) [2026-02-26 16:28:51] EXECUTED CMD: nextflow run nf-core/chipseq -r 2.1.0 --input samplesheet.csv --outdir _result -profile singularity -c custom_resources.config --fasta /srv/GT/reference/Homo_sapiens/GENCODE/GRCh38.p14/Sequence/WholeGenomeFasta/genome.fa --gtf /srv/GT/reference/Homo_sapiens/GENCODE/GRCh38.p14/Annotation/Genes/genes.gtf --aligner bwa Nextflow 25.10.4 is available - Please consider updating your version to it(B The following errors have been detected: * -- Entry 1 - replicate: Replicate id not an integer! (NA) * -- Entry 1 - fastq_2: FastQ file for reads 2 cannot contain spaces and must have extension '.fq.gz' or '.fastq.gz' (NA) * -- Entry 2 - replicate: Replicate id not an integer! (NA) * -- Entry 2 - fastq_2: FastQ file for reads 2 cannot contain spaces and must have extension '.fq.gz' or '.fastq.gz' (NA) * -- Entry 3 - replicate: Replicate id not an integer! (NA) * -- Entry 3 - fastq_2: FastQ file for reads 2 cannot contain spaces and must have extension '.fq.gz' or '.fastq.gz' (NA) * -- Entry 4 - replicate: Replicate id not an integer! (NA) * -- Entry 4 - fastq_2: FastQ file for reads 2 cannot contain spaces and must have extension '.fq.gz' or '.fastq.gz' (NA) * -- Entry 5 - replicate: Replicate id not an integer! (NA) * -- Entry 5 - fastq_2: FastQ file for reads 2 cannot contain spaces and must have extension '.fq.gz' or '.fastq.gz' (NA) * -- Entry 6 - replicate: Replicate id not an integer! (NA) * -- Entry 6 - fastq_2: FastQ file for reads 2 cannot contain spaces and must have extension '.fq.gz' or '.fastq.gz' (NA) -- Check script '/home/trxcopy/.nextflow/assets/nf-core/chipseq/./workflows/../subworkflows/local/utils_nfcore_chipseq_pipeline/../../nf-core/utils_nfvalidation_plugin/main.nf' at line: 57 or see '.nextflow.log' file for more details Error in ezSystem(cmd) : nextflow run nf-core/chipseq -r 2.1.0 --input samplesheet.csv --outdir _result -profile singularity -c custom_resources.config --fasta /srv/GT/reference/Homo_sapiens/GENCODE/GRCh38.p14/Sequence/WholeGenomeFasta/genome.fa --gtf /srv/GT/reference/Homo_sapiens/GENCODE/GRCh38.p14/Annotation/Genes/genes.gtf --aligner bwa failed Calls: -> ezSystem Execution halted ___STDERR_END___