Segmentation fault

[ksahlin]

Hi!

I'm trying to run graphmap2 on a SIRV, drosophila, and human dataset using graphmap2. The SIRV and drosophila data are found here

I'm running the version below because I can't build a newer version if any (see my previous installation issue).

Version: v0.6.3
Build date: Nov 21 2019 at 04:42:57

All my runs fail with a segmentation fault, both supplying graphmap2 with and without a gtf file. I have 256Gb available and it looks like graphmap2 is only using about 50-100Gb MaxRSS at failure, so I don't think insufficient memory is the problem.

For example, I run for SIRV:

graphmap2 align --index index.gmidx  --threads 19 -x rnaseq -r SIRV_isoforms_multi-fasta_170612a.fasta -d sirv_reads.fq -o reads.sam

index built with

graphmap2 align --index-only --index index.gmidx  -x rnaseq -r SIRV_isoforms_multi-fasta_170612a.fasta -d sirv_reads.fq 

Any ideas?

Best,
Kristoffer