Abyss assembler hangs
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?
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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.