Having issues similar to #1003 "FASTQ_SUBSAMPLE_FQ_SALMON:SALMON_INDEX is launched multiple times and fails"

[Jgarlan1]

Description of the bug

Similar to what was already previously described #1003. I am receiving an error with Salmon generating the same command error as one of the other users in the thread.

This occurred both before and after installing the fix provided in the dev package using:
nextflow pull nf-core/rnaseq -r dev
nextflow run nf-core/rnaseq <OTHER_PARAMETERS> -r dev

Command used and terminal output

nextflow run nf-core/rnaseq  --input GraceCSV.csv     --outdir /home/jgarlan1/Grace/Results     --fasta /home/jgarlan1/ReferenceGenome/Homo_sapiens.GRCh38.dna.primary_assembly_HPVE7.fa --gtf /home/jgarlan1/ReferenceGenome/Homo_sapiens.GRCh38.111.filtered.HPVE7.gtf    -profile docker -r dev

Relevant files

GraceRNASeq.zip

System information

• Nexflow -v: 23.10.1.5891
• Hardware: HPC
• Container: Docker
• OS: Linux Ubuntu 22.04.3
• nf-core/rnaseq: 3.15.0dev

[Jgarlan1]

It was the same issue, went around the error by manually putting forward in strandedness instead of auto.

[drpatelh]

Hi @Jgarlan1 ! Unfortunately, I can't read the image you have uploaded in your initial comment to make any sense of what the issue might be here. Are you able to provide a redacted version of the .nextflow.log file here please? Also, given you used the dev version of the pipeline it will be quite tricky to reproduce without knowing the commit of the pipeline you ran at the time.

[pinin4fjords]

To be clear for anyone coming to this issue, this is unrelated to the OP in #1003 (multiple runs of Salmon index process), though it may have some overlap with a comment there.

@Jgarlan1 looking at your example, I think this will turn out to be something to do with the way you have constructed your custom reference files. I'm assuming the FASTA is a concatenation of the human genome and HPV virus? We'd need to have something reproducible, and ideally understand your FASTA and GTF to debug this - perhaps with @rob-p 's help.

That said, the pipeline has functionality for dealing with additional FASTA sequences (see additional_fasta), and you may want to see if supplying the HPV FASTA that way instead solves things for you.

[drpatelh]

I will close this for now as we are awaiting further information. Please feel free to re-open if and when you can provide more details. Please feel free to join the #rnaseq channel in the nf-core Slack Workspace for more real-time help.