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

Wei Shi shi at wehi.EDU.AU
Wed Nov 27 02:24:34 CET 2013

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.


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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