Seg fault with improper arguments

[twrightsman]

I accidentally used the -d option while attempting to do alignment and miniprot segfaulted instead of printing an error message.

$ miniprot --version
0.2-r116
$ miniprot -t8 -d genome.mpi query.faa.gz > aln.paf
[M::[email protected]*1.01] read 20843494 bases in 48265 contigs
[M::[email protected]*1.01] 210726 blocks
[M::[email protected]*3.88] collected syncmers
Segmentation fault

[lh3]

Thanks. Fully agree that miniprot should report an error rather than segfault. Will have a look.

[lh3]

Miniprot doesn't segfault now. However, it will parse proteins as if they are nucleotide sequences without outputting errors. Checking proteins vs nucleotides requires more work.

[silviaprietob]

Hello!
I think I might be having a similar issue to the one twrightsman had.
I accidentally used -gff instead of --gff when running miniprot, and now every time I try to run it with the correct option, miniprot returns a 'unrecogniszed option' and a Segmentation fault (core dumped) error.

`$ miniprot/miniprot -I --gff -outs=0.95 miniprot/genomicfastas/PHYGR.fa missingfastas/PHYGRmissing.fa > miniprotout/PHYGR.gff

[WARNING] unrecognized option: --gff
[M::[email protected]0.98] read 1373559025 bases in 460 contigs
[M::[email protected]0.98] 10731402 blocks
Segmentation fault (core dumped)`

I don't think it's the memory either as I have given it up to 50 G.

Any ideas as to why this might be, how to fix it?

Thank you very much!