Hi all,

I'm putting this here in hopes that someone will understand and solve this issue for future users. This is already a known and apparently unsolved issue per this thread: https://github.com/DerrickWood/kraken2/issues/291

I am simply documenting this in hopes someone will figure it out and put the answer here. The database which gave this issue was the bacteria database installed per the instructions here https://github.com/DerrickWood/kraken2/wiki/Manual#standard-kraken-2-database with these commands:

kraken2-build --download-taxonomy --db $DBNAME

kraken2-build --download-library bacteria --db $DBNAME

after which the build command, and command which drew the error was run:

kraken2-build --build --db $DBNAME

it is worth noting that the above command kraken2-build --download-library bacteria --db $DBNAME gave:

rsync error: some files/attrs were not transferred (see previous errors) (code 23) at main.c(1865) [generator=3.2.7] rsync_from_ncbi.pl: rsync error, exiting: 5888

which is likely at the source of the No preliminary seqid/taxid mapping files found, aborting. error.