Meta-velvet only producing one file of small size

[thh32]

I have used metavelvet before and it produced output from velvetg velveth and metavelvetg, however with the script below it only produced the meta-velvetg.contigs.fa file

velveth out-dir 51 -fasta  NZ_bowtie_aligned.done
/cm/shared/apps/velvet/1.2.10/velvetg out-dir -exp_cov auto
/ibers/ernie/home/thh32/bin/meta-velvetg out-dir -amos_file yes | tee logfile

That was the first issue and secondly I used metavelvet to assemble part of a metagenomic dataset which had been aligned to a group of genomes. The reads that aligned were about 500Mb, however the assembly is only 35Mb. This seems far too small or is that acceptable?

Sorry if these are silly questions.

Thanks,

Tom

[thh32]

Just incase people ask why I haven't stated -shortPaired or a similar option, its because the reads are merged so cant provide R1 and R2 files.