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lh3 / miniprot

Align proteins to genomes with splicing and frameshift
https://lh3.github.io/miniprot/
MIT License
323 stars 17 forks source link

out-of-memory error #25

Closed rwhetten closed 1 year ago

rwhetten commented 1 year ago

I pulled the latest version from the repository and compiled with gcc v10.2.0 on a node with 384 Gb RAM and SSE2 instruction set, but the program is killed by the oom-killer after less than 1 minute of run time trying to build an index of hg38. Monitoring the top command in an interactive session never shows >5 gb memory use. The command used was miniprot -t10 -d hg38.mpi hg38.fa and the command line output was

[M::mp_ntseq_read@9.319*1.00] read 3221011060 bases in 493 contigs
[M::mp_idx_build@9.319*1.00] 25164620 blocks
Killed

Is there some aspect of node architecture or configuration that could cause this?

lh3 commented 1 year ago

Cluster nodes typically cap the max memory unless you change it.