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lh3 / miniprot

Align proteins to genomes with splicing and frameshift
https://lh3.github.io/miniprot/
MIT License
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Segmentation fault #38

Closed KatharinaHoff closed 1 year ago

KatharinaHoff commented 1 year ago

Dear Heng,

I found a segmentation fault of miniprot 0.9-r223 on Tetraodon nigroviridis. I provide the genome and the naughty (hypothetical protein) at https://nextcloud.uni-greifswald.de/index.php/s/4dW9eSHrr8opTwZ

This is what I did:

miniprot -t48 -d genome.mpi genome.fa
miniprot -I -ut48 --outn=1 --aln genome.mpi cand2.fa >> protein_alignment_miniprot.aln

This is my output:

[M::mp_idx_restore@0.601*1.00] loaded the index
[M::mp_mapopt_set_max_intron] set max intron size to 68173
[M::mp_idx_print_stat] 2364577 distinct k-mers; mean occ of infrequent k-mers: 68.91; 5 frequent k-mers accounting for 212749 occurrences
Segmentation fault (core dumped)

I hope you can trace the problem and solve it :-)

Best wishes from Greifswald,

Katharina