Creating a bacterial DB is taking more than 24 hours

[Nilay Lale]

Hello,

I have run the command "./set_target.sh DB_DIR bacteria" and i am aiming to use CLARK-l since I have very limited RAM (16Gb) but this DB creation is taking too long. It has been more than 30 hours and it is still running. Am I doing something wrong in here or its pretty normal to take this much of time. By the way my internet speed is over 50Mbps.

Thanks.

[Rachid]

Hi Nilay,

The command "set_targets.sh" does not build the databases but rather downloads all the genome files needed from NCBI (which are growing significantly years after years), decompresses them, then analyzes their taxonomy.

I do not know what is your installation/configuration so I can't tell if 30hours is a normal runtime for you. If you're using your laptop, I'd recommend you use an ethernet cable or any fast link to make sure you have best bandwidth you can get, and also check your laptop (and make sure it has a fast processor, 2.6GHz or more is preferable). You can monitor the scripts and make sure they are running, as well as the folder content inside the directory you set for the database.

I hope this helps!

Best,

Rachid