Hi all,
I am working with a challenging genome (22 Gb haploid DNA content per nucleus, 18 Gb first-draft assembly in 31 million contigs), and using BWA 0.6.1 because it is the only short-read aligner I have found that can index a genome > 4 Gb. I used an AWS EC2 Cloudbiolinux instance (June 2012 release) with 68 Gb RAM to build the index, then saved it to an S3 bucket and terminated the instance. The version of BWA I used is based on what is available as a Ubuntu package with apt-get install.
I downloaded the index (as a .tgz archive) to my local Ubuntu 12.04 box (16 Gb RAM), unpacked it, and tried to align a fasta file of sample sequences (158,000 sequences), but bwa crashes after the line
[bwa_aln] 225bp reads: max_diff = 9 with the error
Segmentation fault (core dumped)
My local box is running the same version of BWA on essentially the same OS, but presumably different hardware from the AWS EC2 instance. It does not seem to be a problem with the .tgz archive, because I can download that to another Cloudbiolinux instance, unpack it, and map the same set of sample sequences to the index without problems.
Any suggestions for how to solve this would be greatly appreciated.
I am working with a challenging genome (22 Gb haploid DNA content per nucleus, 18 Gb first-draft assembly in 31 million contigs), and using BWA 0.6.1 because it is the only short-read aligner I have found that can index a genome > 4 Gb. I used an AWS EC2 Cloudbiolinux instance (June 2012 release) with 68 Gb RAM to build the index, then saved it to an S3 bucket and terminated the instance. The version of BWA I used is based on what is available as a Ubuntu package with apt-get install.
I downloaded the index (as a .tgz archive) to my local Ubuntu 12.04 box (16 Gb RAM), unpacked it, and tried to align a fasta file of sample sequences (158,000 sequences), but bwa crashes after the line
[bwa_aln] 225bp reads: max_diff = 9 with the error
Segmentation fault (core dumped)
My local box is running the same version of BWA on essentially the same OS, but presumably different hardware from the AWS EC2 instance. It does not seem to be a problem with the .tgz archive, because I can download that to another Cloudbiolinux instance, unpack it, and map the same set of sample sequences to the index without problems.
Any suggestions for how to solve this would be greatly appreciated.
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