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¶
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.