[protocols] velvet assembly after partitioning with khmer

[Stuart Jones]

Hello,
First, thanks so much for khmer and the protocols you have provided!  I am attempting to assemble the genome of a methanogen from paired-end MiSeq data generated from an enrichment culture.  I worked through the metagenome assembly protocol and was able to generate compressed PE and SE group files, but did not run the reinflating partitions steps.  After this, I attempted to assemble one of the PE and SE group files using Velvet and got an error I haven't seen from Velvet before:
">> Please re-order the filenames in yoru command line so as to have the reference sequence files before all the others"

Seen this before?

Thanks,
Stuart

Stuart E. Jones
Assistant Professor
University of Notre Dame
Dept. of Biological Sciences
264 Galvin Life Sciences
Notre Dame, IN 46556
sjones20 at nd.edu
(574) 631-5703