Question: Parallel processing and EAGLE-RC

[kenji-yt]

Hi,

Is there is a possibility to run EAGLE-RC on multiple cores?

If not, does that mean it will use only a single core, or how many can we expect it to use?

Thank you in advance,

Kenji

[tony-kuo]

There are 2 workflows:

1. EAGLE is run first then EAGLE-RC parses the results. The EAGLE part is multi-threaded and can use multiple cores
2. The --ngi parameter is used in EAGLE-RC. This unfortunately is single threaded.

[kenji-yt]

Thanks a lot for your reply.

To confirm, this mean that if I run using the --ngi flag, only 1 thread will be used by the entire process?

[tony-kuo]

Correct. Hopefully it shouldn't be too slow as it calculates the likelihood of every read in the bam against the reference. IO should be the bottleneck in this case in my estimation.

[kenji-yt]

Great, thanks! I also have a question regarding the --ngi mode. If I understand correctly, with --ngi we can only sort reads between two genomes? I wanted to use it for any number of genomes but it seems not to work.

[tony-kuo]

Hello, in order to do more than two genomes, you need to do multiple pair-wise comparisons.
For example in hexaploids, you can run A vs B, A vs C, B vs C. Then use the outputs from that to build a consensus.

This is shown in the existing hexaploid script

If you need higher ploidy, you'll have to work out the combinations of pair-wise comparisons and calculate the probabilities using the current scripts as templates.