LINE search takes much longer compared to other steps about edta

[oushujun]

RM2 is described here: https://www.pnas.org/doi/10.1073/pnas.1921046117. Fig 1 shows the workflow. Currently, the whole RM2 workflow is executed, and SINE/LINE elements are harvested at the end output of RM2. If a particular module can be separated, or RM2 being further acclerated, it would be great!

Shujun

[oushujun]

Hi Artem,

Unfortunately, this is the case. The LINE search function is carried out by RepeatModeler which is slow on even small genomes. Because RepeatModeler's search is based on copy number and multiple alignments, splitting the genome into small subsets may lose families that are already low copy. You can run EDTA on SSD, which will significantly improve your RepeatModeler/RepeatMasker runs because they are I/O intense.

Shujun

[foriin]

Thanks, Shujun,
The cluster I ran EDTA on has only SSD, I think :) I see the problem now: we need to parallelize RM, but it has to establish communication between all the jobs in parallel. Could you please tell me what specific part of RM is assigned for LINE search?