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lh3 / miniprot

Align proteins to genomes with splicing and frameshift
https://lh3.github.io/miniprot/
MIT License
310 stars 16 forks source link

'Killed' message from index build #44

Closed crowja closed 1 year ago

crowja commented 1 year ago

Building a miniprot index for maize fails with a 'Killed' message:

$ miniprot -t 4 -d test.mpi ../test.fa
[M::mp_ntseq_read@13.628*0.51] read 2176935545 bases in 13 contigs
[M::mp_idx_build@13.628*0.51] 17007324 blocks
[M::mp_idx_build@50.757*2.97] collected syncmers
Killed
$ echo $?
137

Any thoughts on how to proceed? Possibly a tmp file thing?

lh3 commented 1 year ago

Probably insufficient memory

crowja commented 1 year ago

Yep, that was the issue. I doubled the memory and the indexing proceeds nicely. Thanks!

lh3 commented 1 year ago

Just FYI: indexing usually takes more memory than alignment