sff_extract and ssaha2 problem facing

[edge]

I try to run : sff_extract -o EG -l linker.fasta -i "insert_size:3000,insert_stdev:900" 454_flx_reads.sff

And I got this:

Working on '454_flx_reads.sff:
Creating temporary sequences from reads in '454_flx_reads.sff' ... done.
Searching linker sequences with SSAHA2 (this may take a while) ...

An error occured during the SSAHA2 execution, aborting.

Can I know what is the problem causing it happend?
My ssaha2 version is 2.4.1
My sff_extract version is 0.2.6
Thanks a lot for all of your guide and suggestion.

[spenthil]

What are the contents of EG*?

[edge]

Hi, EG is the bacteria...
And I just named the output file as EG.
Do you have any suggestion to solve my trouble?
Thanks ya.

What are the contents of EG*?

[spenthil]

Sorry, should be more specific - were any files created when you ran it, and what are there contents?

If not, we could modify sff_extract pretty easily to give more information on why SSAHA2 is failing.

[edge]

Hi, my input file is bacillus .sff data that sequencing by 454FLX technique.
I just try to run the command refer the paper "Instructions for scaffolding MIRA 454 contigs & 25 KB paired-end data with BAMBUS"
Do you have any idea to solve my problem facing?
Thanks a lot.

Sorry, should be more specific - were any files created when you ran it, and what are there contents?

If not, we could modify sff_extract pretty easily to give more information on why SSAHA2 is failing.