soapaligner error

[[email protected]]

Hi,

Has anyone had problem with SOAPaligner? I make an index then start align below

./2bwt-builder ${adiref_file}
./soap -a s_1_sequence.txt.trimmed.single -D adiref.fa.index -o soapTestOut.txt -p 8 -u unmap.fq

Then I got this error.

Begin Program SOAPaligner/soap2
Mon May 23 17:05:43 2011
Reference: adiref.fa.index
Query File a: s_1_sequence.txt.trimmed.single
Output File: soapTestOut.txt
unmap.fq
Load Index Table ...
Load Index Table OK
Begin Alignment ...
File Error: unrecognized file

I have no idea which file that is the unrecognized file. One thing that is strange is .index.amb file is empty. Is it normal?

Any suggestion will be great.

Thanks,
Sutada

[Lucas_USP]

Input file

Is your input file .fasta or fastq?