SOAPAligner Segmentation fault while loading Index Table

[ganygan25]

I am trying to use soap2.21 release to build and align reads to Human genome(UCSC hg18).
I downloaded individual chromosomes FASTA files and cat them into a single Human Genome file. The final file size is around 3GB.

Soap index built is run using the command:
./2bwt-builder humanGenome.fa

The above command generated 13 files. Now, I tried aligning some reads using this index file..

./soap –D index/humanGenome.fa.index –a reads/reads1_human.fastq –o output/reads_aligned_soap

The above command resulted in the following error on the console:

Begin Program SOAPaligner/soap2
Mon Feb 13 23:09:37 2012
Reference: index/humanGenome.fa.index
Query File a: reads/reads1_human.fastq
Output File: output/reads_aligned_soap
Load Index Table ...
Segmentation fault

Could someone throw some light on what could be the possible issue here?

Thanks and Regards,
gany

[mitochy]

Try adding -2 output/reads_UNaligned_soap. -2 is the file where soap has unmapped (or you could send it to /dev/null). Otherwise, rebuild index.

./soap –D index/humanGenome.fa.index –a reads/reads1_human.fastq –o output/reads_aligned_soap -2 output/reads_UNaligned_soap

[ganygan25]

Many thanks for the reply, but adding -2 doesn't help..
I have seen successful soap runs and it Loads Index Table first and then begins the alignment.

Rebuilded the index a few times and every time the same issue occurs.
The input genome is from UCSC hg18 full dataset. Downloaded all the chromosomes and cat into a single genome.fa file.
However, when I build index and align reads using a single chromosome, say for only chr9.fa, it works fine.

Suspect some issues in the whole genome..
Any other source where I can directly download 3GB full human genome?

[ganygan25]

Its the main memory size that causes this issue..
My original server's main memory size is less than 8GB and it didn't meet the required size specified in SOAPAligner website.
Now, ran the same set of commands on a different server which has 24GB main memory and it runs smooth.