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endixk / ezaai

EzAAI - High Throughput Prokaryotic AAI Calculator
http://leb.snu.ac.kr/ezaai
GNU General Public License v3.0
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What would be the command needed to increase the number of CPU cores destinated to EzAAI execution? #5

Closed agg437 closed 2 years ago

agg437 commented 2 years ago

Hello EzAAI team,

In your publication you talk about how speed execution is increased when using 30 CPU cores, what would be the option to implement that CPU usage? PS: Great work with the pipeline, it is amazing! Best regards, Ana

endixk commented 2 years ago

Hello, Thank you for using our program!

The EzAAI calculate module can be boosted up using multiple cores by running it with -t option.

An example code would be: java -jar EzAAI.jar calculate -i db/ -j db/ -t 30 -o result.tsv

Unfortunately, extract module cannot be run with multiple cores, since the dependent program prodigal does not support multi-threading options. Nevertheless, you can still boost up your progress by running multiple extract module runs simultaneously cuz they only consume single thread resources.

Thanks!

agg437 commented 2 years ago

Perfect! that was what I was looking for! Thanks!