Hi everyone!
I am a beginner in the single-cell RNA seq world, and I am trying to run nf-core/scrnaseq for some cattle samples using cell ranger. The pipeline I am running is:
GENOME=“/project/brucella/GENOME/GCF_002263795.3_ARS-UCD2.0_genomic.fna.gz”
GTF=“/project/brucella/GTF/GCF_002263795.3_ARS-UCD2.0_genomic.gtf.gz”
nextflow run nf-core/scrnaseq
-profile singularity
–input sample_sheet.csv
–outdir star_rsem_output
–fasta {GENOME} \
--gtf {GTF}
–protocol 10XV2
–aligner cellranger
–outdir single_cell
And I am getting this error related to the reference:
Running preflight checks (please wait)…
2025-05-01 15:46:10 [runtime] (ready) ID.mkref_cellranger_reference.MAKE_REFERENCE._MAKE_REFERENCE
2025-05-01 15:46:10 [runtime] (run:local) ID.mkref_cellranger_reference.MAKE_REFERENCE._MAKE_REFERENCE.fork0.split
2025-05-01 15:46:13 [runtime] (split_complete) ID.mkref_cellranger_reference.MAKE_REFERENCE._MAKE_REFERENCE
2025-05-01 15:46:13 [runtime] (run:local) ID.mkref_cellranger_reference.MAKE_REFERENCE._MAKE_REFERENCE.fork0.join
2025-05-01 15:48:35 [runtime] (failed) ID.mkref_cellranger_reference.MAKE_REFERENCE._MAKE_REFERENCE
[error] mkref has failed: error building reference package
Error detected in GTF file: Parsing GTF on line 68: source: cannot contain spaces
Line = ‘NC_037328.1 Curated Genomic gene 699142 700071 . + . gene_id “OR5L18P”; db_xref “GeneID:787710”; db_xref “VGNC:VGNC:101589”; description “olfactory receptor family 5 subfamil
y L member 18, pseudogene”; gbkey “Gene”; gene “OR5L18P”; gene_biotype “pseudogene”; pseudo “true”;’
Has anyone experienced the same issue or knows how I can fix it?
Thank you!