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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.

Many thanks.

Ernie

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maybe you can open the demovir.R file with Rstudio and execute line by line to check where the failure is. - @zorbax

Thanks for your suggestion. I eventually got a correct final output already.

The key issue was Prodigal would add extra strings after my original contig IDs, so it would cause R not recongnising my viral contigs. Therefore, I added a flag -trunclabels in Usearch (after e-value flag) to truncate my contig names. Finally, I re-ran the demovir.sh in ubuntu VM and it has worked well.

Ernie

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