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phac-nml / mob-suite

MOB-suite: Software tools for clustering, reconstruction and typing of plasmids from draft assemblies
Apache License 2.0
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Database not installed properly #167

Open Santhi17 opened 5 months ago

Santhi17 commented 5 months ago

Screenshot from 2024-06-20 21-37-18

Kindly help me solve this error!!

Database is in the path as mentioned.

kbessonov1984 commented 1 month ago

Hello,

There seem to be an issue with the database initialization. Try to run again mob_init. If does not help, check that you have MASH installed and download databases manually. If you need to have database in a separate location different from the default, you can run mob_init -d <path2folder>. MOB-Suite 3.1.9 database is located at https://zenodo.org/records/10304948/files/data.tar.gz?download=1 but needs to be initialized that includes running MASH and ETE3 taxonomy initialization. The successful database initialization ends by writing status.txt file with the download date and time info

usage: mob_init [-h] [-d DATABASE_DIRECTORY] [-v] [-V]

MOB-INIT: initialize databases version: 3.1.9

optional arguments:
  -h, --help            show this help message and exit
  -d DATABASE_DIRECTORY, --database_directory DATABASE_DIRECTORY
                        Directory to download databases to. Defaults to /Users/kirill/opt/miniconda3/envs/mob_suite_dev/lib/python3.8/site-packages/mob_suite/databases
  -v, --verbose         Set the verbosity level. Can by used multiple times
  -V, --version         show program's version number and exit

You can also run MOB-Suite in a container with all versions available at https://biocontainers.pro/tools/mob_suite. You can copy database folder from the image to your install directory and initialize database in this simple way. E.g. in my case mob_init reports that all my databases are located in /Users/kirill/opt/miniconda3/envs/mob_suite_dev/lib/python3.8/site-packages/mob_suite/databases