Ok, sorry to bother you. I'll ask my cluster admin for an update.
On Tue Nov 26 17:24:34 2013, Wei Shi wrote:
Hi Ryan,
It seems you are using a quite old version of Subread. The latest version of
SourceForge Subread is 1.4.2 and the latest version of bioc Rsubread is 1.12.3.
These indexing building issues had already been fixed.
Cheers,
Wei
On Nov 27, 2013, at 12:12 PM, Ryan C. Thompson wrote:
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
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