Kraken2-build hanging with --add-to-library

[joshielevy]

Hi -

I'm trying to add the RVDB viral database to my kraken 2 db

` kraken2-build --download-taxonomy --db data_input/my_kraken2_db/ kraken2-build --download-library viral --db data_input/my_kraken2_db/ --use-ftp

add rvdb

kraken2-build --add-to-library data_input/RVDB/U-RVDBv16.0.fasta --db data_input/my_kraken2_db/ `

but the final command is hanging above with no output. If I look at the library/added directory I can see:

ls -ltr data_input/my_kraken2_db/library/added total 4673762 -rwxrwxrwx 1 root root 75994222 Jul 19 12:27 prelim_map_Ck8W0Ku6ES.txt -rwxrwxrwx 1 root root 4709937207 Jul 19 12:30 IRMkdIWmVc.fna

...and the IRMkdIWmVc.fna file's timestamp was hours ago. I don't see any other files with the Jul 19 date. I'm running this in a docker container.

When I run ps, the process is:

/bin/bash /kraken2/add_to_library.sh data_input/RVDB/U-RVDBv16.0.fasta but in top it is consuming 0 memory and 0 cpu. Are there other processes I can look for? I don't see any child processes being called with the PID as parent.

Is there some way I can check progress - or whether something is holding the program up?

Thanks,

Josh

[joshielevy]

Ran a 2nd time and it finished - glitch?