I'm trying to use Salmon in the mapping-based mode, and I downloaded the full decoy salmon indices via refgenie list here using the refgenie command refgenie pull hg38/salmon_sa_index and it download the full folder locally.
Now I have this index folder and SRR21898893_1.fastq.gz and SRR21898893_2.fastq.gz in the same folder and when I run my command:
docker run -v "$(pwd):/data" --rm combinelab/salmon salmon quant -i data/2230c535660fb4774114bfa966a62f823fdb6d21acf138d4/salmon_sa_index/default -l A -1 SRR21898893_1.fastq.gz -2 SRR21898893_2.fastq.gz --validateMappings -o transcripts_quant
I have this output:
It would appear that the file versionInfo.json does not exist however in the index folder it is present: