cov_cutoff option in velvet

[Brindha Lekshmisaran]

SOLVED:

I had got the same eror. I had followed a PDF instruction, copied the command onto the terminal and got a similar output with [0.000001] Unknown option: –cov_cutoff;

$ velvetg sample_51k –cov_cutoff 10 –ins_length 280 –ins_length_sd 80 –read_trkg no –min_contig_lgth 150 –exp_cov auto –scaffolding yes –min_pair_count 20 –unused_reads yes
[0.000001] Unknown option: –cov_cutoff;

It turns out the problem was the hyphen, copied from the possibly a windows generated file to Linux. When I manually typed out the hyphens in the terminal, the command worked fine.

$ velvetg sample_51k -cov_cutoff 10 -ins_length 280 -ins_length_sd 80 -read_trkg no -min_contig_lgth 150 -exp_cov auto -scaffolding yes -min_pair_count 20 -unused_reads yes
[0.000000] Reading roadmap file sample_51k/Roadmaps
[14.356802] 1796686 roadmaps read
[14.358097] Creating insertion markers
[14.853677] Ordering insertion markers

[pbm13]

Does anyone know why I might get this error from velvetg when I try to specify a coverage cutoff using: -cov_cutoff 4

[0.000000] Unknown option: –cov_cutoff;

But it says clearly in the usage that -cov_cutoff is a standard option. Any help is greatly appreciated!