Database creation is taking more than 24 hours

[Nilay Lale]

Hello guys,

I have run the command "./set_target.sh DB_DIR bacteria" I am aiming to use Clark-l since my computer has only 16 GB RAM but this DB creation is taking too long. It has been more than 30 hours and the command is still running. Am I doing something wrong or its normal to take up this much time to create bacterial DB on CLARK?

Thanks.

[Rachid]

Hi Nilay,

Please be aware the long processing for "set_targets.sh" can be due by many different factors. 

Since you are using or want to use your laptop, please see the following questions:

- Do you have a fast internet connection? Indeed, your command " set_targets DB_DIR bacteria" will download all complete bacterial reference genomes from RefSeq, that a lot of data to download.

- Do you have a fast processor ? Is it more than 2.4 GHz ? set_targets.sh will decompress, and process a lot of data, so the processor speed is a factor.

- How busy is your laptop while downloading? If you are running other applications that are CPU-intensive, it will slow down "set_targets.sh" execution.

 

As you can see if you have a slow connection, or a slow laptop or using your laptop for other application, then I can see 30hours as an expected runtime.

Please let me know if this helps?

Thank you,

Best,

Rachid

[Rachid]

Hi Nilay,

I was wondering if you could provide some updates regarding the issue you encountered.

Were you able to download the database on your laptop?

Best,

Rachid