Hi, I am running the

smrnaseq

pipeline with sheep samples (Ovis aries) using the following command:

nextflow run nf-core/smrnaseq -r 2.3.1 --input samplesheet-smrna.csv --outdir smallRNA --fasta GCF_016772045.2_ARS-UI_Ramb_v3.0_genomic.fa --mirtrace_species oar  -profile docker --max_memory 360.GB --max_cpus 24

I encountered the following error:

ERROR ~ Error executing process > 'NFCORE_SMRNASEQ:MIRNA_QUANT:MIRTOP_QUANT'

Caused by: Can't stage file https://mirbase.org/download/CURRENT/genomes/oar.gff3 -- reason: Unable to access path: https://mirbase.org/download/CURRENT/genomes/oar.gff3 When I checked back on miRBase, the file was not available. I then tried using the

--mirna_gtf oar.gff3

option, but I got another error:

Not a valid path value: 'oar.gff3'

How to resolve this? TIA Slack conversation

Hi:

nextflow run nf-core/smrnaseq -r 2.3.1 --input samplesheet-smrna.csv --outdir smallRNA --fasta GCF_016772045.2_ARS-UI_Ramb_v3.0_genomic.fa --mirtrace_species oar  -profile docker --max_memory 360.GB --max_cpus 24

I do not see oar as a species in mirbase (https://mirbase.org/download/) You will need to obtain a gff from your species of interest from another source. There is a similar issue opened in GitHub. https://github.com/nf-core/smrnaseq/issues/329 but we haven't worked in it yet.