bwa mem segmentation fault aligning 454 reads alignment to reference sequences

[Francy87]

Hi!
I need to align 454 reads to a set of 17 reference sequences.
I thought to use bra with the men algorithm.

I built the index, then I tried:

bwa mem -t 5 -k 50 -r 1 -M poxE_bwa_db seqs.fna

It gave me this error:
[M::bwa_idx_load_from_disk] read 0 ALT contigs
[M:rocess] read 2805 sequences (1947633 bp)...
Segmentation fault: 11

However, I have only 2800 sees to map, so I don't think it could be a memory problem.

Any suggestions?

[GenoMax]

Are you using the newest bwa available?

[TiborNagy]

Try to run using one thread. More threads uses more memory.

[Francy87]

I'm using bwa-0.7.12.

The same error occurs also with -t 1.

[salturki]

I had the same error.

I used a newer version of BWA with a genome reference index created by an older version of BWA. I just had to re-index the genome again with current BWA (v0.7.12) and this fixed it.