Entering edit mode
7.4 years ago
StarCute
▴
110
Hey,
I'm using abyss version 2.0.2 and am unable to run an assembly to completion. I am running on a Ubuntu 16.10 server with a small (~1 GB dataset) with a small k (<=96). I have tried the solutions suggested in this and this post, but the assembly continues to hang during the Finding adjacent kmer .. step. Any suggestions?
How much RAM have you got - and what K size are you using?
512GB RAM and kmer 96
Have you tried running it with a lot smaller ksize - say 41/51 - to see if abyss works and that the issue is related to large ksize which those posts seem to suggest
Yeah. For some reason the assembler works fine if I just set the variable j (number of threads), but when I include the np (number of MPI processes) as well, it fails.
I have faced this problem for an earlier version of abyss, I think it is to do with the MPI configuration on the system.