Closed simon-l3 closed 6 years ago
This is because 1+(61+3)*2>127
, which triggers integer overflow in Smith-Waterman alignment. This is a bug, but a fix will be complicated and might be even impossible. I will have a look at later time. For now, make sure A+(O+E)*2<=127
.
Looking at the code, I realize this issue is an intrinsic limitation of the Smith-Waterman algorithm minimap2 is using. It is not resolvable. I will let minimap2 throw an error when the scoring system breaks the algorithm.
ab345e6 throws an error for impropriate scoring. Sorry that I am unable to fix the issue, only letting minimap2 abort. Thanks for your report anyway.
I was trying to locate relatively unique regions from two very close bacterial genomes and needed to set a divergence less than -x asm5. Then, I encountered a segmentation fault when I set gap open penalty to either -O60 -E4 or -O61 -E3
The commands that generated segmentation fault: ./minimap2 -c -A1 -B29 -O61 -E3 GCF_000195955.2_ASM19595v2_genomic.fna.gz GCF_000758245.1_ASM75824v1_genomic.fna.gz ./minimap2 -c -A1 -B29 -O60 -E4 GCF_000195955.2_ASM19595v2_genomic.fna.gz GCF_000758245.1_ASM75824v1_genomic.fna.gz
While this is ok: ./minimap2 -c -A1 -B29 -O60 -E3 GCF_000195955.2_ASM19595v2_genomic.fna.gz GCF_000758245.1_ASM75824v1_genomic.fna.gz
minimap2 version: 2.5 and 2.6