Why require delnodes.dmp and merged.dmp?

[nick-youngblut]

I created a tool for converting the Genomes Taxonomy DataBase (GTDB) taxonomy to nodes.dmp & names.dmp files. The tool is gtdb_to_taxdump. The output works with taxonkit<0.5.0, but fails for taxonkit>=0.5.0, since you now require delnodes.dmp and merged.dmp. Why do you require these files? Could an option be included to override that requirement or is it absolutely necessary for taxonkit 0.5 to work?

[shenwei356]

Because we'd like to detect merged or deleted taxids, see #19 .

I can make it optional. You can also try again by creating empty delnodes.dmp merged.dmp .

[nick-youngblut]

Thanks for the quick reply! I tried just creating empty delnodes.dmp and merged.dmp files, but I then get a "file empty" error.

[shenwei356]

try adding a line staring with #

[nick-youngblut]

That works as long as the file contains #\n. Thanks!

[shenwei356]

fixed:

• taxonkit_darwin_amd64.tar.gz
• taxonkit_linux_amd64.tar.gz
• taxonkit_windows_amd64.exe.tar.gz