The latest ProkaryoticViralRefSeq94-Merged database

[erchao]

I donnot know which one database is the latest, including the 94/97/88/85 (founded in the articles) and I couldnot find a useful help from the internet. maybe somewhere exists a instruction book, could you gays help me. thanks a lot

[Ben Bolduc]

Hello!

Thanks for your question. The most recent database is v201.

That said, the latest database is always the highest number. If you only have 97, 94, 88 and 85, then 97 is the latest.

Let me know if you have any further questions!

Cheers,

Ben

[HandymanAlan]

Hi Ben,

I used the RefSeq database v201 but it didn’t work. Below’s my command:

vcontact --raw-proteins 2013_VS2.part-1.faa --rel-mode 'Diamond' --proteins-fp 2013_VS2_001.csv --db ProkaryoticViralRefSeq201-Merged --pcs-mode MCL --vcs-mode ClusterONE --c1-bin /srv/scratch/z3336178/anaconda/envs/vContact2/bin/cluster_one-1.0.jar -t 8 --output-dir /srv/scratch/z3336178/NovaSeq/VirSorter2/vContact2/2013/VS2/Output_1_RefSeq_201

But the error indicates RefSeq V201 is not available in the command options:

vcontact: error: argument --db: invalid choice: 'ProkaryoticViralRefSeq201-Merged' (choose from 'None', 'ProkaryoticViralRefSeq85-ICTV', 'ProkaryoticViralRefSeq85-Merged', 'ProkaryoticViralRefSeq88-Merged', 'ProkaryoticViralRefSeq94-Merged', 'ProkaryoticViralRefSeq97-Merged', 'ArchaeaViralRefSeq85-Merged', 'ArchaeaViralRefSeq94-Merged', 'ArchaeaViralRefSeq97-Merged')

I have all the versions of RefSeq in the database folder. Is there some other way to use RefSeq v201 in vContact2?

Thank you!

Cheers

Alan

[HandymanAlan]

Hi Ben,

It worked after I change the name of RefSeq201 files to RefSeq97.

Cheers

Alan

[Ben Bolduc]

Should have been resolved several versions ago. Reopen if persists.