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

[Ryan]

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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