I've been trying to run velvetg but everytime it returns 'Killed' after nearly getting through all of the 'nodes visted' part, for example:
[11019.929049] 11860000 / 11927480 nodes visted
I have sufficient hd space available and I don't know where to proceed because of vagueness (and frankly rudeness) of 'Killed'. Thanks in advanced.
edits: data is short paired illumina reads
minimum contig length=100
read trackage is on (data is a transcriptome that I want to run through Oases afterwards)
as far as memory goes, as I'm running velvetg again top is showing about 10% memory use
Edit 2: Thanks for all the advice! I think I just don't have enough memory to muscle through this with the current settings, I upped the kmer value and I've had much more success.
Programmers routinely (if rather insensitively) refer to terminating the action of a running process as "killing the process". "Killed" is not a helpful error message to the end user, but I wouldn't take it personally. Don't even get me started on "master and slave processes", though...
what is the length of your reads and the k value you're using?
The system will kill processes that consume too much memory. Have you monitored memory usage during the run (e.g. using top) ?
maybe you're using a k too small. It's recommended to set the k at least as the minimum of the read length