Wheat 17G genome build index Segmentation fault about bwa-mem2 HOT 9 CLOSED

We will look into this and get back to you.

from bwa-mem2.

@fei0810 Fixed the code to work with wheat genome. Now, it needs 28N space = 28*17 = 476 GB to build wheat genome.
Also, fixed the rest of the code so that wheat genome (and other larger genomes) can be mapped to correctly.

from bwa-mem2.

We will look into this and get back to you.

Hi, is there any progress on this issue?

from bwa-mem2.

We are working on it. We have reproduced the bug. Trying to fix it now.

from bwa-mem2.

Most likely, you are running out of memory. Creating the index using the current code needs maximum memory of 34N Bytes, where N is the size of the reference sequence. With the wheat genome, it would be 34*17 = 578 GB. We are trying to reduce the maximum memory required.

from bwa-mem2.

Hi, I'm getting same error when indexing hg19.fa with 32GB RAM:

bwa-mem2 index hg19.fa
[bwa_index] Pack FASTA... 7.61 sec
init ticks = 257657731164
ref seq len = 6274322528
binary seq ticks = 133066087488
Segmentation fault (core dumped)

from bwa-mem2.

Hi, that is because the indexing of human genome requires nearly 40 GB of memory.

from bwa-mem2.

Right, just tried in a 64GB machine and worked, thanks!

from bwa-mem2.

@fei0810 Fixed the code to work with wheat genome. Now, it needs 28N space = 28*17 = 476 GB to build wheat genome.
Also, fixed the rest of the code so that wheat genome (and other larger genomes) can be mapped to correctly.

Coooool!
Thank you so much.

from bwa-mem2.