I’m currently using this script to run nf-core/rnasplice:

# Run Nextflow with your local rnasplice pipeline and include the mouse liver data
echo "Starting Nextflow pipeline..."
./nextflow run nf-core/rnasplice -resume -profile singularity \
   --input /home/tud03125/pipeline/mouse_liver_utf8.csv \
   --fasta /home/tud03125/pipeline/Mus_musculus.GRCm39.dna_sm.primary_assembly.fa \
   --gtf /home/tud03125/pipeline/Mus_musculus.GRCm39.112.gtf \
   --save_reference \
   --outdir /home/tud03125/pipeline/mouse_liver_rnasplice \
   --star_index /home/tud03125/STAR_index_mouse \
   --salmon_index /home/tud03125/salmon_index_mouse \
   --rmats \
   --rmats_novel_splice_site \
   --suppa \
   --contrasts /home/tud03125/pipeline/contrast_mouse_liver.csv

Currently, I’m facing this problem:

Error executing process > 'NFCORE_RNASPLICE:RNASPLICE:TX2GENE_TXIMPORT_SALMON:TXIMPORT (Mus_musculus.GRCm39.112.tx2gene.tsv)'

Caused by:
 Process `NFCORE_RNASPLICE:RNASPLICE:TX2GENE_TXIMPORT_SALMON:TXIMPORT (Mus_musculus.GRCm39.112.tx2gene.tsv)` terminated with an error exit status (1)


Command executed:

 tximport.R Mus_musculus.GRCm39.112.tx2gene.tsv salmon salmon.merged
 
 cat <<-END_VERSIONS > versions.yml
 "NFCORE_RNASPLICE:RNASPLICE:TX2GENE_TXIMPORT_SALMON:TXIMPORT":
     r-base: $(echo $(R --version 2>&1) | sed 's/^.*R version //; s/ .*$//')
     bioconductor-tximeta: $(Rscript -e "library(tximeta); cat(as.character(packageVersion('tximeta')))")
 END_VERSIONS

Command exit status:
 1

Command output:
 (empty)

Command error:
 WARNING: Skipping mount /var/singularity/mnt/session/etc/resolv.conf [files]: /etc/resolv.conf doesn't exist in container
 reading in files with read.delim (install 'readr' package for speed up)
 1 2 3 4 5 6 7 8 9 10 11 
 reading in files with read.delim (install 'readr' package for speed up)
 1 2 3 4 5 6 7 8 9 10 11 
 reading in files with read.delim (install 'readr' package for speed up)
 1 2 3 4 5 6 7 8 9 10 11 
 Error in .local(object, ...) : 
   None of the transcripts in the quantification files are present
   in the first column of tx2gene. Check to see that you are using
   the same annotation for both.
 
 Example IDs (file): [ENSMUST00000196221.2, ENSMUST00000179664.2, ENSMUST00000177564.2, ...]
 
 Example IDs (tx2gene): [ENSMUST00000000001, ENSMUST00000000003, ENSMUST00000000010, ...]
 
   This can sometimes (not always) be fixed using 'ignoreTxVersion' or 'ignoreAfterBar'.
 
 Calls: -> -> .local
 Execution halted

Work dir:
 /home/tud03125/pipeline/mouse_liver_rnasplice/work/fc/a46fdde8958b3a66e12a0343d87431

Tip: when you have fixed the problem you can continue the execution adding the option `-resume` to the run command line

When I first ran nf-core/rnasplice with Homo Sapiens, this

TXIMPORT

error never happened, particularly with version IDs. That happened with me in

MISO_SASHIMI

, but later. But, one thing that caught my eye is this suggestion of theirs:

This can sometimes (not always) be fixed using 'ignoreTxVersion' or 'ignoreAfterBar'.

Inside nf-core/rnasplice parameters link: https://nf-co.re/rnasplice/1.0.4/parameters/,

ignoreTxVersion

or

ignoreAfterBar

is nowhere to be find in their list of parameters. So, how do I address that?

You are using two references that are not compatible, because one uses transcript IDs with versions, and the other without. My best guess is that these references are the GTF and the Salmon index (presumably made with a different GTF). You could of course try ignoring the version suffix, but that is not a good idea in my opinion, because if the GTFs differ in that, they may have other differences as well (e.g. new or removed or changed transcripts or genes) that will come back to bite you later. I see two solutions (provided my guess is correct): • Use the same GTF that was used to create the Salmon index, or • don't specify a Salmon index, so a new one will be built using the GTF (plus the genome FASTA) you provided.