The running speed is too slow.

[guo23e]

Hello, I have a total of 20 samples. Each sample has nine chromosomes, and after partitioning, it should be around 2.6GB. The running is too slow, do you have any suggestions? Here are my commands and part of the log file. I used the following commands to run.

partition-before-pggb -i merged.fa -o out -n 20 -p 90 -s 5k -V '173_A#1#:1000'

pggb -i out/merged.fa.bf3285f.community.0.fa
-o out/merged.fa.bf3285f.community.0.fa.out
-s 5000 -l 25000 -p 90 -c 1 -K 19 -F 0.001 -g 30
-k 23 -f 0 -B 10M
-n 20 -j 0 -e 0 -G 700,900,1100 -P 1,19,39,3,81,1 -O 0.001 -d 100 -Q Consensus_
-Y "#" -V 173_A#1#:1000 --threads 80 --poa-threads 80

log file:
Starting pggb on 09-08-2025_163308

Command: pggb -i out/merged.fa.bf3285f.community.0.fa -o out/merged.fa.bf3285f.community.0.fa.out -s 5000 -l 25000 -p 90 -c 1 -K 19 -F 0.001 -g 30 -k 23 -f 0 -B 10M -n 20 -j 0 -e 0 -G 700,900,1100 -P 1,19,39,3,81,1 -O 0.001 -d 100 -Q Consensus_ -Y # -V 173_A#1#:1000 --threads 80 --poa-threads 80
.........
PARAMETERS
[smoothxg::(1-3)::smooth_and_lace] embedding 522119252 path fragments: 24.45% @ 2.10e+02 bp/s elapsed: 07:00:35:04 remain: 21:17:01:50