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

[2020-11-04 09:35:16] INFO: GTDB-Tk v1.4.0
[2020-11-04 09:35:16] INFO: gtdbtk check_install
[2020-11-04 09:35:16] INFO: Using GTDB-Tk reference data version r95: /release95
[2020-11-04 09:35:16] INFO: Running install verification
[2020-11-04 09:35:16] INFO: Checking that all third-party software are on the system path:
[2020-11-04 09:35:16] INFO:          |-- FastTree         OK
[2020-11-04 09:35:16] INFO:          |-- FastTreeMP       OK
[2020-11-04 09:35:16] INFO:          |-- fastANI          OK
[2020-11-04 09:35:16] INFO:          |-- guppy            OK
[2020-11-04 09:35:16] INFO:          |-- hmmalign         OK
[2020-11-04 09:35:16] INFO:          |-- hmmsearch        OK
[2020-11-04 09:35:16] INFO:          |-- mash             OK
[2020-11-04 09:35:16] INFO:          |-- pplacer          OK
[2020-11-04 09:35:16] INFO:          |-- prodigal         OK
[2020-11-04 09:35:16] INFO: Checking /release95
[2020-11-04 09:35:16] INFO:          |-- pplacer          OK
[2020-11-04 09:35:16] INFO:          |-- masks            OK
[2020-11-04 09:35:17] INFO:          |-- markers          OK
[2020-11-04 09:35:17] INFO:          |-- radii            OK
[2020-11-04 09:35:20] INFO:          |-- msa              OK
[2020-11-04 09:35:20] INFO:          |-- metadata         OK
[2020-11-04 09:35:20] INFO:          |-- taxonomy         OK
[2020-11-04 09:47:36] INFO:          |-- fastani          OK
[2020-11-04 09:47:36] INFO:          |-- mrca_red         OK
[2020-11-04 09:47:36] INFO: Done.