Question: velvetg problem after Threading through reads
gravatar for avolkov
3.5 years ago by
avolkov10 wrote:

Hi all!

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.

enter image description here 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!

velvet rna-seq de novo • 789 views
ADD COMMENTlink modified 3.5 years ago by Antonio R. Franco4.2k • written 3.5 years ago by avolkov10
gravatar for Antonio R. Franco
3.5 years ago by
Spain. Universidad de Córdoba
Antonio R. Franco4.2k wrote:

Iy seems that you run out of memory ant the program is using a virtual disk. The whole population of der Bruijn nodes (kmers) are usually kept in memory

If so, you need to be alerted that memory works a lot much faster (in the order of nanoseconds) than when used a disk (sometimes in the order of milliseconds).

If you are aware of a very high activity of the disk, this should be the reason of your delay

ADD COMMENTlink written 3.5 years ago by Antonio R. Franco4.2k

Thanks for the answer. The problem is that there is barely any disk activity. But i also believe that this problem is memory-related. Still, it looks like the software is not doing anything, since the message about the next step is usually there instantly after threading. For now i stopped the assembly. Will have to retry with more memory and perhaps a fast ssd disk.

ADD REPLYlink written 3.5 years ago by avolkov10
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