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VIP



Re: https://github.com/keylabivdc/VIP

Hi,

Does anyone have experience of running VIP?

I've been trying to get it working under Ubuntu 18.04/20.04 with Debian-Med installed in a Bioconda environment, but I've only managed to get it running in the author's Ubuntu 14.04 VIP Docker container...

It's running, but very slowly, and "mafft" is only running on one core even though there are 24 cores available and the "mafft" command-line specifies 12 cores. I think it might be caused by running it on an AMD Opteron 6000 that does not support SSE2 instructions, but any advice about VIP would be welcome - It's been running for a week now :-(

We're using the pipeline to check Tetse fly microbiota for viruses, but it may also be useful for Covid-19 work because the host databases are human by default.

Thanks,

  Tony.

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