/srv/GT/analysis/course_sushi/public/gstore/projects/p1001/NfCoreRnaseq_2026-02-26--16-15-22/scripts/Transcriptomics_NextSeq500_20190507_NS278_o5638_subSampled_2185.sh_sushiID3060_2026-02-26--16-28-44_o.log
--------------------------------------------------
Job runs on fgcz-h-156
at /scratch/NfCoreRnaseq_2026-02-26--16-15-22_temp1241139

___STDOUT_END___

/srv/GT/analysis/course_sushi/public/gstore/projects/p1001/NfCoreRnaseq_2026-02-26--16-15-22/scripts/Transcriptomics_NextSeq500_20190507_NS278_o5638_subSampled_2185.sh_sushiID3060_2026-02-26--16-28-44_e.log
--------------------------------------------------
+ set -o pipefail
+ umask 0002
+ SCRATCH_DIR=/scratch/NfCoreRnaseq_2026-02-26--16-15-22_temp1241139
+ GSTORE_DIR=/srv/GT/analysis/course_sushi/public/gstore/projects
+ INPUT_DATASET=/srv/GT/analysis/course_sushi/public/gstore/projects/p1001/NfCoreRnaseq_2026-02-26--16-15-22/input_dataset.tsv
+ LAST_JOB=TRUE
++ hostname
+ echo 'Job runs on fgcz-h-156'
+ echo 'at /scratch/NfCoreRnaseq_2026-02-26--16-15-22_temp1241139'
+ mkdir /scratch/NfCoreRnaseq_2026-02-26--16-15-22_temp1241139
+ cd /scratch/NfCoreRnaseq_2026-02-26--16-15-22_temp1241139
+ 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/1241139/exe ']'
++++ /bin/readlink /proc/1241139/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
/var/spool/slurmd/job131347/slurm_script: line 22: projectDir: unbound variable

___STDERR_END___