[Bioc-devel] subread-buildindex fails on genome with many scaffolds?

[Ryan C. Thompson]

Actually, scratch that. I just tried running subread-buildindex on a 
file with only the 20-ish chromosome sequences, and it didn't give the 
message about 50000 sections, but it still crashed with "Killed" and 
exit code 137.

On Tue 26 Nov 2013 05:01:48 PM PST, Ryan C. Thompson wrote:
> Hello,
>
> I'm trying to test out subjunc for mapping my RNA-seq data to the
> cynomolgus monkey genome, but when I try to build the index with
> subread-buildindex, I get the error:
>
> "There are too many sections in the chromosome data files (more than
> 50000 sections)."
>
> and then after "Building the index...", it says "Killed", and exits
> with code 137.
>
> The genome is unfinished and contains over 90,000 small
> scaffolds/contigs. My Subread version is 1.3.3. Is it planned to
> remove this limitation in future versions?
>
> -Ryan Thompson