mafft [was Re: VIP]
On 08/07/2020 14:56, Michael Crusoe wrote:
[...]
Could be that mafft has reached a point in the computation that is still
single threaded.
Their script specifies 8 threads:
https://github.com/keylabivdc/VIP/blob/d69b5e7615d8da76ef0dd66e51867c8ec42588d4/MSA.sh#L28
Though that is a different script than in the container, where it
references `--thread $total_cores` where `total_cores` appears to be set
to half of your available cores. Which matches your 12 of 24 cores report.
You could replace that `--threads $total_cores` with `--threads -1` to
see if that helps.
Hi, Michael.
I've been struggling to find out what the problem is for some time now
and I've tried the version of "mafft" packaged by you for Debian-Med.
The problem is not with "mafft", which is a shell script, but with the
"disttbfast" program spawned by "mafft", which hangs at 100% CPU on one
thread for more than seven days without completing and returning control
back to "mafft" regardless of how many threads are actually specified.
This only seems to happen with certain viral sequences and might be
because "disttbfast gets stuck in a local minimum and never converges?
I've just posted a bug-report including a 'problem' sequence to the
Ubuntu bug-tracker that should, presumably, find its way to you as the
Debian "mafft" package maintainer.
Thanks for looking into my VIP "mafft" problem,
Tony.
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