Demovir produces an empty output

Question

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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Quoting the GitHub repository:

"Democratic taxonomic classification of viral contigs to Order and Family level

When performing metagenomic sequencing of Viral-Like Particle (VLP), the majority of returned sequences often bare little to no homology to reference sequences - Viral Dark Matter. Frequently it may be useful to know which viral taxonomic group these novel viruses are likely to belong to as this will give information about nucleic acid type, size and behaviour."

Answer 1

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