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

Ryan C. Thompson rct at thompsonclan.org
Wed Nov 27 02:01:48 CET 2013


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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