soap2 segmentation fault when loading index table

[[email protected]]

Hi all,

I try to use soap2 to align PE reads from HiSeq2000. Each read file is about 25GB. I have had very little luck with soap aligner.

I used 2twt-builder to build the index files first on hg19.fa, which took quote a while, then called:

soap -a s_5_1_testN.fq -b s_5_2_testN.fq -D /genomes/human/hg19/soap/hg19.fa.index -o mapped.soap -2 se.soap -m 140 -x 400 -p 2


Begin Program SOAPaligner/soap2
Fri Feb 25 16:30:06 2011
Reference: /genomes/human/hg19/soap/hg19.fa.index
Query File a: s_5_1_testN.fq
Query File b: s_5_2_testN.fq
Output File: mapped.soap
se.soap
Load Index Table ...
Segmentation fault

The machine has sufficient available memory. Did I build the index files incorrectly? Anyone had the same kind of problem? Thanks a lot for any insight on this.

[jiyan]

Just a few minutes ago, I was puzzled by the same question. One probable reason is that the '2twt-builder' and the 'soap' are not from the same verion of soap package. Maybe you need check their paths using 'which 2twt-builder' and 'which soap'.