Segmentation fault with -x asm20 full options.

[theo-allnutt-bioinformatics]

Using the full options for preset -x asm20 causes segmentation fault.

minimap2 -x asm20 -t 48 brassica_chloroplast.fasta brassica_chloroplast.fasta > brassica.paf
[M::mm_idx_gen::0.0341.02] collected minimizers
[M::mm_idx_gen::0.0478.96] sorted minimizers
[M::main::0.0478.96] loaded/built the index for 3 target sequence(s)
[M::mm_mapopt_update::0.0498.63] mid_occ = 50
[M::mm_idx_stat] kmer size: 19; skip: 10; is_hpc: 0; #seq: 3
[M::mm_idx_stat::0.0508.40] distinct minimizers: 23298 (0.10% are singletons); average occurrences: 3.605; average spacing: 5.482; total length: 460460
[M::worker_pipeline::0.2054.28] mapped 3 sequences
[M::main] Version: 2.24-r1122
[M::main] CMD: minimap2 -x asm20 -t 48 brassica_chloroplast.fasta brassica_chloroplast.fasta
[M::main] Real time: 0.210 sec; CPU: 0.881 sec; Peak RSS: 0.030 GB

minimap2 -k19 -w10 -U50,500 --rmq -r100k -g10k -A1 -B4 -O6,26 -E2,1 -s200 -z200 -N50 -t 48 brassica_chloroplast.fasta brassica_chloroplast.fasta > brassica.paf
Segmentation fault

brassica_chloroplast.fasta.txt

[lh3]

minimap2 is done. The segfault is caused by other things.

[theo-allnutt-bioinformatics]

Are you saying minimap2 completes for you? I have tried on two different systems with the same segfault.

[lh3]

I see what you mean now. You can change "--rmq" to "--rmq=yes".