I am new to bioinformatics and am working on viral metagenomic (virome) datasets and so would like to use Demovir for doing taxonomic annotations on my viral contigs.
First, I installed all prerequisites in my macOS but I found that Usearch 32-bit version could not run on macOS Big Sur, so I installed all and re-ran
demovir.sh my.viral.contig.fasta threads in ubuntu VM. I could therefore successfully obtained trembl_ublast.viral.u.contigID.txt as an input for R, but I would always get an empty output after performing the demovir.R command of demovir.sh in ubuntu VM.
Thus, I took these back to my macOS, used conda to create a virtual environment for R-3.5.1 and installed R using
conda install -c r r=3.5.1, then ran
Rscript demovir.R trembl_ublast.viral.u.contigID.txt. Again, I got an empty output with only showing the headers of five columns.
I also tried to modify the demovir.sh script by removing all previous parts I've completed and retaining the last command
Rscript $DIR/demovir.Rthen ran
modified.demvir.sh my.viral.contigs.fasta threadsagain, but still got the same result.
Hopefully anyone can do me a favour to check and resolve this issue.