hisat2-build segmentation fault

[estolle]

Hi

Trying to index my genome (download from NCBI, GCF_910591885.1) and i am getting segfaults

This is my command:
mkdir hisat2_idx
hisat2-build -p 172 GCF_910591885.1_iyBomTerr1.2_genomic.formatted.fa hisat2_idx/genome

This is my output, tried on Ubuntu 24, fresh install, python3.12, HISAT2 version 2.2.1
Settings:
Output files: "hisat2_idx/genome..ht2"
Line rate: 6 (line is 64 bytes)
Lines per side: 1 (side is 64 bytes)
Offset rate: 4 (one in 16)
FTable chars: 10
Strings: unpacked
Local offset rate: 3 (one in 8)
Local fTable chars: 6
Local sequence length: 57344
Local sequence overlap between two consecutive indexes: 1024
Endianness: little
Actual local endianness: little
Sanity checking: disabled
Assertions: disabled
Random seed: 0
Sizeofs: void:8, int:4, long:8, size_t:8
Input files DNA, FASTA:
GCF_910591885.1_iyBomTerr1.2_genomic.formatted.fa
Reading reference sizes
Time reading reference sizes: 00:00:01
Calculating joined length
Writing header
Reserving space for joined string
Joining reference sequences
Time to join reference sequences: 00:00:01
Time to read SNPs and splice sites: 00:00:00
Using parameters --bmax 428359 --dcv 1024
Doing ahead-of-time memory usage test
Passed! Constructing with these parameters: --bmax 428359 --dcv 1024
Constructing suffix-array element generator
Building DifferenceCoverSample
Building sPrime
Building sPrimeOrder
V-Sorting samples
Segmentation fault (core dumped)

light formatting changes (seqtk seq -C -U -L 60) did not make a difference. same in python3.9

Do you have any idea how to work around this?

thanks

[estolle]

ah, seems I found the issue: I wanted it to run with 172 threads (which I do have in this machine). running it with 20 threads works.
hisat2-build -p 20 GCF_910591885.1_iyBomTerr1.2_genomic.formatted.fa hisat2_idx/genome