Problem extending/scaffolding contigs with MiSeq 250bp reads?

[Genomics101]

Greetings. I have some denovo assembled contigs (Velvet 1.2.10) made from 250bp MiSeq (Illumina) reads. After I make the contigs, I normally extend and scaffold them using SSPACE v1.0. This usually goes off without a hitch with my old 100bp GAiix data, however it's not working with SSPACE apparently because it's not detecting that the reads are actually paired (" Unsatisfied pairing logic within contigs"):

READ PAIRS STATS:
Assembled pairs: 225450 (450900 sequences)
  Satisfied in distance/logic within contigs (i.e. -> <-, distance on target: 513 +/-20.52): 0
  Unsatisfied in distance within contigs (i.e. distance out-of-bounds): 0
  Unsatisfied pairing logic within contigs (i.e. illogical pairing ->->, <-<- or <-->): 225450
                ---
  Satisfied in distance/logic within a given contig pair (pre-scaffold): 0
  Unsatisfied in distance within a given contig pair (i.e. calculated distances out-of-bounds): 0
                ---
Total satisfied: 0      unsatisfied: 225450

Any ideas on how to fix this or just use a better extending and scaffolding program?

[flxlex]

I am not familiar with SSPACE, but could it be that your version does not understand the new sequence IDs? See both versions at http://en.wikipedia.org/wiki/FASTQ_f...ce_identifiers