vgteam
vg autoindex --workflow mpmap
I executed the command vg autoindex --workflow mpmap, but it consumed a large amount of memory and resources. I would like to know if it's possible to construct the index by species chromosome separately and then merge them together. How should I proceed with this?
If you are starting from VCF and a reference FASTA, then vg autoindex is already doing that internally. With GFA input, that's not currently implemented, and my understanding is that it wouldn't significantly reduce the peak resource use. You could try to encourage more memory thrift using the -M argument, although it's best to consider it an "approximate memory limit", since it's hard to predict future memory use at run time. I also might able to give more guidance if you provide the stderr log, which should tell you which stage of the indexing pipeline is hitting your resource limits.
