SOAP2 alignment problem

[logicthief]

Hello there,

I tried SOAP2 to do alignments on paired-end data from illumina but the output was obviously wrong. Can anybody tell me where the problem is? Thanks!

Command:
soap -D human_g1k_v37.fasta.index -a s4.1.fastq -b s4.2.fastq -o soap_test_soap.soapaln -2 soap_test_soap_unpaired.soapout -p 12

Version:
Program: SOAPaligner/soap2
Compile Date: Sun Aug 22 11:51:04 CST 2010
Author: BGI shenzhen
Version: 2.21
Contact: [email protected]

System:
Linux 2.6.18-164.el5 #1 SMP Thu Sep 3 03:28:30 EDT 2009 x86_64 x86_64 x86_64 GNU/Linux

STDERR:
Begin Program SOAPaligner/soap2
Tue Apr 16 11:13:43 2013
Reference: human_g1k_v37.fasta.index
Query File a: s4.1.fastq
Query File b: s4.2.fastq
Output File: soap_test_soap.soapaln
soap_test_soap_unpaired.soapout
Load Index Table ...
Load Index Table OK
Begin Alignment ...
131072 ok 26.06 sec
262144 ok 27.69 sec
...
76229342 ok 17.47 sec
Total Pairs: 38114671 PE
Paired: 491344 ( 1.29%) PE
Singled: 56747655 (74.44%) SE
Total Elapsed Time: 17743.43
- Load Index Table: 27.63
- Alignment: 17715.80

SOAPaligner/soap2 End
Tue Apr 16 16:09:27 2013