gsMapper error codes

[spacedninja]

Hi everyone, I was wondering if someone here could help me. I've already sent a few emails out to the people who gave me this software (after they got permission) so if they solve it first I'll come back and mark it as solved.
This is the first time I've had to compile everything for gsMapper myself, I'm using a .fasta as a reference, and .fna files formatted
>name
sequence
I finally got past my running out of memory issue by cutting the fna files in half but now I'm getting a terminating error that I have no idea how to fix. the error reads
"Error: An internal error (exit status 9) has occurred in the computation"
It always happens when the project is generating output and reading flowgrams.

any suggestions?

[DNAjunk]

I have got the same problem with newbler version 2.6
I am using sff files of genomic paired-end reads as input (original sff files and split into smaller files) mapping to mammalian genome.

[natstreet]

I also have the same issue with v2.6. I'm finding that many assemblies that worked using v2.3 no longer work using 2.6. This is the case for cDNA and genomic assemblies. I've tried on Ubuntu and RedHat machines, both with the same issue.