Speeding up Vphaser2

[RG]

Hi, 

I wanted to know if there are any setting changes that can speed up vphaser 2. I am running a full plate of illumina with 96 samples of HIV sequences, with the OMP_NUM_THREADS=24 setting but its taking days. 

Thanks, 

Ron

[Xiao Yang]

what coverage of data you have? vphaser2 typically finishes within hours with coverage of 10,000x -- 100,000x. We have tried with 0.5million to 1 million coverage. Beyond that, I do not know how long it's going to take. 

The reason it takes long days might be too many artifacts in your alignment that could have variants in every single position in your sample (not sure if it is the case). But in case of extreme coverage, you could downsample the data.  

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- Xiao

[RG]

Hi, 

The sequences are dereplicated and artifacts removed with fastx. Coverage is about around 15,000 with 9000 bases, and i have 96 samples like this. The var.raw file output is SNPV: 1539; LPV: 995 , so definitely some mutations but doesnt seem so crazy (or is it?). 

Thanks, 

Ron

[Xiao Yang]

just want to clarify your meaning of taking days. 

Do you mean each sample takes days or total takes days ? 

If it is the former, then I'm not sure why it takes so long. 

But if it is the latter case, 96 x 1.5 (hr for instance) is > 3 days, which is not surprising. 

In this case, you can set each sample using 4 cores and run 6 samples at the same time,

which should be more efficient.  

[RG]

Yes, its 96x1.5 so I guess it makes sense. I can try the other way of splitting the core usage. 

Thanks, 

Ron