SOAP can't align read

[dhl]

HI everyone. I'm new here. I got a problem blocked me for days and plz help me.
I want to use SOAP to align my paired-end reads. command:

./SOAP -a /home/d-l/L008_R1_001.fastq -b /home/d-l/L008_R2_001.fastq -D /home/d-l/ref.fa.index -o /home/d-l/pairmapped.txt -2 /home/d-l/singlemapped.txt -u /home/d-l/unmapped.txt -m 500 -x 10000

But pairmapped.txt & singlemapped.txt are all size 0. unmapped.txt is large. No read mapped! Then I tried single read:

./SOAP -a /home/d-l/L008_R1_001.fastq -D /home/d-l/ref.fa.index -o /home/d-l/singletest.txt

But still singletest.txt is size 0.

I am going to be crazy. I can't explain to my supervisor. Any one who have succeed?

[oiiio]

Well... is there a reason you must use SOAP? Have you tried different programs like BWA?

[dhl]

Well... is there a reason you must use SOAP? Have you tried different programs like BWA?

Not must. Actually I want to use mapView to call SNPs(someone told me that it can). mapView only accept SOAP output for pair-end read.