BWA aln segmentation fault

[dlquan]

I tried searching for the answer to my problem but could not find it. I am trying to align a fastq file to the hg19 reference genome. To build the reference I downloaded the 25 chromosome files and joined them together. BWA 'index' function works fine, but the 'aln' function results in a Segmentation fault. Thanks!

The output looks like this:

[bwa_aln] 17bp reads: max_diff = 2
[bwa_aln] 38bp reads: max_diff = 3
[bwa_aln] 64bp reads: max_diff = 4
[bwa_aln] 93bp reads: max_diff = 5
[bwa_aln] 124bp reads: max_diff = 6
[bwa_aln] 157bp reads: max_diff = 7
[bwa_aln] 190bp reads: max_diff = 8
[bwa_aln] 225bp reads: max_diff = 9
Segmentation fault

[GenoMax]

Did you compile bwa from source? How much RAM do you have?

[dlquan]

I used a built in BWA software version 0.5.9r16 that was provided by the computing server. I don't know how much RAM it has, but it seems like there should be plenty. When I joined together Chromosomes 1-12 into a 2.1 Gb reference, the alignment worked. However, the 3.2 Gb total reference does not align and results in a segmentation fault error.

[swbarnes2]

There are two different ways to index genomes with bwa index. Only one works once the genome gets to be over a certain size. So remake the index (try

bwa index -a bwtsw

and see if that fixes it.

[GenoMax]

If using half the genome worked and full genome is not working then I have a feeling that a) you either do not have enough RAM or b) your job is not allowed to use more than a certain amount of RAM. Administrators sometimes set this restriction on shared compute resources.

You should at least ask the people who administer your compute server and see if the above is true.