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edgardomortiz / Captus

Assembly of Phylogenomic Datasets from High-Throughput Sequencing data
https://edgardomortiz.github.io/captus.docs/
GNU General Public License v3.0
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running Captus as an array #3

Open veronicamb opened 1 year ago

veronicamb commented 1 year ago

Hello,

I was wondering if there's a way to run Captus as array on a HPC. I tried a few different ways, but failed unfortunately. Do you have any suggestions?

thank you!

Veronica

edgardomortiz commented 1 year ago

I guess you want to run Captus across multiple nodes in your cluster. Unfortunately it is not able to do it. But you could do something similar, for example, let's imagine you have 600 sample, you could make 10 batches of 60 samples, and then run clean, assemble, and extract in 10 nodes. Then move all the sample assembly folders to a single location, and proceed with and align in a single node.

I hope it helps!

Edgardo

veronicamb commented 1 year ago

Hi Edgardo,

Thank you for your reply! I'll try your suggestion.

best,

Veronica

edgardomortiz commented 1 year ago

You should put all the sample extraction folders together prior to alignment (not sample assembly folders, as I said, sorry about that).

Edgardo