check_install

The check_install command is used to verify the integrity of the GTDB-Tk reference data.

If any inconsistencies are identified then the program will exit with code 1 and HASH MISMATCH will be displayed next to the inconsistent item.

Arguments

usage: gtdbtk check_install [--db_version DB_VERSION] [--debug] [-h]

Named Arguments

--db_version

GTDB-Tk version package to test for compatibility.

--debug

create intermediate files for debugging purposes

Example

Input

gtdbtk check_install

Output

[2025-08-05 17:02:59] INFO: GTDB-Tk v2.5.0
[2025-08-05 17:02:59] INFO: gtdbtk check_install
[2025-08-05 17:02:59] INFO: Using GTDB-Tk reference data version r226: /release226
[2025-08-05 17:02:59] INFO: Running install verification
[2025-08-05 17:02:59] INFO: Checking that all third-party software are on the system path:
[2025-08-05 17:02:59] INFO:          |-- FastTree         OK
[2025-08-05 17:02:59] INFO:          |-- FastTreeMP       OK
[2025-08-05 17:02:59] INFO:          |-- guppy            OK
[2025-08-05 17:02:59] INFO:          |-- hmmalign         OK
[2025-08-05 17:02:59] INFO:          |-- hmmsearch        OK
[2025-08-05 17:02:59] INFO:          |-- pplacer          OK
[2025-08-05 17:02:59] INFO:          |-- prodigal         OK
[2025-08-05 17:02:59] INFO:          |-- skani            OK
[2025-08-05 17:02:59] INFO: Checking integrity of reference package: /release226
[2025-08-05 17:02:59] INFO:          |-- pplacer          OK
[2025-08-05 17:02:59] INFO:          |-- masks            OK
[2025-08-05 17:03:00] INFO:          |-- markers          OK
[2025-08-05 17:03:00] INFO:          |-- radii            OK
[2025-08-05 17:03:05] INFO:          |-- msa              OK
[2025-08-05 17:03:05] INFO:          |-- metadata         OK
[2025-08-05 17:03:05] INFO:          |-- taxonomy         OK
[2025-08-05 17:06:35] INFO:          |-- skani            OK
[2025-08-05 17:06:35] INFO:          |-- mrca_red         OK
[2025-08-05 17:06:35] INFO: Done.