Re: mafft [was Re: VIP]
Hi Tony,
thanks for your trust and reaching out here. Since it seems to be a
complex problem its probably sensible to open a bug report also for the
Debian package (and please be so kind to refer with explicitly links to
the bug you was talking about).
I also think that the issue should be reported upstream since they
actually know the code and where to debug which is not the case for
random Debian / Ubuntu maintainers.
Thanks again,
Andreas.
On Mon, Sep 28, 2020 at 01:32:27PM +0100, Tony Travis wrote:
> 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.
>
> --
> Minke Informatics Limited, Registered in Scotland - Company No. SC419028
> Registered Office: 3 Donview, Bridge of Alford, AB33 8QJ, Scotland (UK)
> tel. +44(0)19755 63548 http://minke-informatics.co.uk
> mob. +44(0)7985 078324 mailto:tony.travis@minke-informatics.co.uk
>
>
--
http://fam-tille.de
Reply to: