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nf-core / smrnaseq

A small-RNA sequencing analysis pipeline
https://nf-co.re/smrnaseq
MIT License
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mirdeep2 output missing #330

Closed LucasMcNU closed 7 months ago

LucasMcNU commented 8 months ago

Description of the bug

Running the smRNAseq pipeline does not produce the output listed here. MirDeep2 output is missing. Everything else is there. Running this on the Northwestern University HPC using their configuration file. Used the following genome file:

projects/genomicsshare/AWS_iGenomes/references/Homo_sapiens/NCBI/GRCh38/Sequence/WholeGenomeFasta/genome.fa

Command I used is below:

Command used and terminal output

## Load modules
module purge

module load nextflow/23.04.3
module load singularity/latest
module load graphviz/2.40.1
module load java/jdk11.0.10

project_dir=/projects/b1042/BackmanLab/Lucas/101823_rnaseq/Backman19_10.18.2023/smallRNA/
cd $project_dir
OUTDIR=${project_dir}nextflow_results/
[ -d $OUTDIR ] || mkdir -p $OUTDIR

nextflow run nf-core/smrnaseq \
-profile nu_genomics \
--input $project_dir/samplesheet.csv \
--genome 'GRCh38' \
--mirtrace_species 'hsa' \
--protocol 'nextflex' \
--outdir $OUTDIR

Relevant files

nextflow.log

System information

No response

mazzalab commented 8 months ago

same here

apeltzer commented 7 months ago

https://github.com/nf-core/smrnaseq/pull/343 fixed