jiarong
jiarong
Hi, what operating system are you using? can you paste the whole message from virsorter2?
You can copy the messages that VirSorter2 prints to the screen, and paste them here.
Your sample is bulk metaG, not virome, right? More stringent score cutoff, 0.9 or even 0.95 is recommended.
CheckV is very conservative on calling viral genes. Manually check on those with 0 checkV viral genes are recommended.
Hi, thanks for the feedback. Can you paste the content of "log/iter-0/step2-extract-feature/extract-feature-from-hmmout-common.log" here?
Looks like there is an issue with hmmer output formatting. I need to see the input files to find the problem. Could you upload the following files: iter-0/all.pdg.Archaea.hmmtbl iter-0/all.pdg.Bacteria.hmmtbl iter-0/all.pdg.Eukaryota.hmmtbl...
Sorry for the delay. I found `all.pdg.Bacteria.txt` is corrupted, which might be caused by instability of hardware. Re-run the sample should resolve the problem.
Hi, the `trim_bp_start` and `trim_bp_end` are the boundaries used for final viral contigs. Be aware that host region trimming in VS2 is conservative, meaning there might be host region left....
Hi, some contigs in the boundary file are remove if viral gene % is less than cellular gene %. I do not recommend including them since they are more likely...
Good catch. This one is not easy to notice.. The bug is caused by inconsistency in treating numbers as number or string. Fixed.