I am de novo assembling a plant transcriptome from 430M quality-trimmed 2x100 Illumina reads on a 24 CPU 156 GB RAM machine using velvet. Everything was fine until this velvetg step:
..... [16974.644928] Threading through reads 179000000 / 430800790 [17586.290922] === Threaded in 9824.522651 s
Here I expect the assembly o proceed to the next step, but it does not. I waited for many hours but nothing happens. The process is still running, but does not use any CPU. However, memory is 100% in use and 48G in swap. Disk is at 250 k/s reading from swap.
What should I do? Shall I stop the assembly? Computer time is expensive so I don't want to wait for something that will not happen.
Thanks in advance!