Open
Description
Description of the bug
When running the pipeline with star_rsem alignment the rsem_reference directory isn't passed to rsem-calculate-expression and instead an empty argument is passed
rsem-calculate-expression \
--num-threads 12 \
--temporary-folder ./tmp/ \
\
--paired-end \
--star --star-output-genome-bam --star-gzipped-read-file --estimate-rspd --seed 1 \
A6_trimmed_1_val_1.fq.gz A6_trimmed_2_val_2.fq.gz \
$INDEX \
A6
Command used and terminal output
Command to launch pipeline:
./nextflow run \
nf-core/rnaseq \
-r 3.19.0 \
-profile apptainer \
-params-file rnaseq_params.json
Output:
ERROR ~ Error executing process > 'NFCORE_RNASEQ:RNASEQ:QUANTIFY_RSEM:RSEM_CALCULATEEXPRESSION (A6)'
Caused by:
Process `NFCORE_RNASEQ:RNASEQ:QUANTIFY_RSEM:RSEM_CALCULATEEXPRESSION (A6)` terminated with an error exit status (2)
Command executed:
INDEX=`find -L ./ -name "*.grp" | sed 's/\.grp$//'`
rsem-calculate-expression \
--num-threads 12 \
--temporary-folder ./tmp/ \
\
--paired-end \
--star --star-output-genome-bam --star-gzipped-read-file --estimate-rspd --seed 1 \
A6_trimmed_1_val_1.fq.gz A6_trimmed_2_val_2.fq.gz \
$INDEX \
A6
cat <<-END_VERSIONS > versions.yml
"NFCORE_RNASEQ:RNASEQ:QUANTIFY_RSEM:RSEM_CALCULATEEXPRESSION":
rsem: $(rsem-calculate-expression --version | sed -e "s/Current version: RSEM v//g")
star: $(STAR --version | sed -e "s/STAR_//g")
END_VERSIONS
Command exit status:
2Relevant files
System information
- Nextflow version: 24.20.5
- Hardware: HPC
- Executor: slurm
- Container engine: Apptainer
- OS: CentOS Linux
- Version of nf-core/rnaseq: 3.19.0