I am trying to run the ONT pipeline for generating fasta for covid and working on the HPC server.
while running a test set on my system, I was able to generate fasta files along with vcf and bam files using the minion protocol.
however, while running a larger set on HPC, I am only getting the vcf and bam files but no fasta files are generating.
I have tried to re-install the artic-ncov2019 environment in Anaconda.
When my base-called files are run on a DGX server, fasta files and all other files are formed.
However, in the HPC server, we have a GPU node but running minion on that doesn't generate fasta.
I am utterly confused as it's my first time working on the server. But so far as I know the type of server doesn't matter for generating fasta.
Can anyone suggest what I can do?