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Old 02-09-2015, 03:49 AM   #1
Francy87
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Location: Italy

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Question bwa mem segmentation fault aligning 454 reads alignment to reference sequences

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?
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Old 02-09-2015, 04:03 AM   #2
GenoMax
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Are you using the newest bwa available?
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Old 02-09-2015, 04:03 AM   #3
TiborNagy
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Try to run using one thread. More threads uses more memory.
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Old 02-09-2015, 04:08 AM   #4
Francy87
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I'm using bwa-0.7.12.

The same error occurs also with -t 1.
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Old 03-21-2015, 04:33 AM   #5
salturki
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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.
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