[Bioperl-l] weird behavior with bulk_load_gff

[Michael Eisen]

I am having a very frustrating time loading a gff database and 
associated fasta files. This is something I've done thousands of times 
before, but for some reason, it's choking on my latest set of files, and 
I can't figure out why.

The files are contigs and scaffolds from an assembly of a fly genome. 
I've got a fasta file with the scaffolds (17 of them), and an associated 
gff file.

bulk_load_gff runs fine, all of the gff records are loaded into the 
fdata, but only loading 6 of the 17 sequences are loaded

when I try to run it splitting the scaffolds into individual files, it 
again only loads 6 of them, but this time a different 6 (in each case it 
only loads the first 6 - from a file the first six in the file, from a 
directory the first six in lexigraphic order)

Any thoughts on what's going wrong?


-- 
Michael B. Eisen, Ph.D. (MBEISEN at LBL.GOV)

Genome Sciences Division, Lawrence Berkeley Natl Lab
Dept. of Molecular and Cell Biology, UC Berkeley

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