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jiarong / VirSorter2

customizable pipeline to identify viral sequences from (meta)genomic data
GNU General Public License v2.0
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final-viral-boundary.tsv file missing #159

Open dnolin13 opened 1 year ago

dnolin13 commented 1 year ago

Hello, I am trying to import my VS2 results into anvio and it requires the final-viral-boundary tsv file, but the only outputs I got from my run were the final-viral-score.tsv and final-viral-combined.fa files. I know the boundary file is technically an intermediate file, is it output somewhere else? Or did I need to run a specific flag to have it output? If so, can I rerun via snakemake to just get that file? Any help is greatly appreciated, thanks!!

jiarong commented 1 year ago

It should be produced by default in the same directory as the other two. Yes, you can rename the score table and re-run the same command line to generate that file.

dnolin13 commented 1 year ago

Thanks! Unfortunately, this took several weeks to run, is there a way to speed up the run to just generate the boundary file? Or do I need to redo the whole pipeline? Thanks!!

dnolin13 commented 1 year ago

my original command for context was: virsorter run --prep-for-dramv -w ${VirSorter_RESULTS} -i ${FINAL_ASSEMBLY} -j 40 --provirus-off

run in the vs2 bioconda env

jiarong commented 1 year ago

Hi, it does not produce the boundary file with --provirus-off. You can remove that option and rerun. It will build the boundary file using existing intermediate files from previous run.

dnolin13 commented 1 year ago

ah gotcha, thanks so much!!