how to obtain bootstrap alignments in parallel

[lei chen]

Hi all,

   I am trying to generate 100 bootstrap alignments using commands:

   raxmlHPC-AVX -N 100 -b 271828 -f j -m GTRGAMMA -s merge.fa.phy -n REPS

  The size of my dataset is 25Gb. It takes too much time to get 100 bootstrap alignment files. I am wondering if there are some methods to speed up this process. Do you have some suggestions?

Best wishes,

Lei

[Alexey Kozlov]

Hi Lei,

so why don't you start multiple RAxML instances (preferably on different nodes due to memory constraints) generating
e.g. 10 replicates each?

Best,
Alexey

On 05.07.2017 15:31, lei chen wrote:
> Hi all,
> I am trying to generate 100 bootstrap alignments using commands:
>

> * raxmlHPC-AVX -N 100 -b 271828 -f j -m GTRGAMMA -s merge.fa.phy -n REPS*
> *
> *

> The size of my dataset is 25Gb. It takes too much time to get 100 bootstrap alignment files. I am wondering if there
> are some methods to speed up this process. Do you have some suggestions?
>
> Best wishes,
> Lei
>

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[Alexandros Stamatakis]

so if I understand correctly your input alignment has 25GB is that
correct? In that case you should consider using ExaML which is more
scalable to such large datasets. Please let us know how many taxa and
sites your dataset contains.

Alexis

--
Alexandros (Alexis) Stamatakis

Research Group Leader, Heidelberg Institute for Theoretical Studies
Full Professor, Dept. of Informatics, Karlsruhe Institute of Technology

www.exelixis-lab.org

[lei chen]

Yes, I have a 60 taxa X 400 Mb sites dataset. I am indeed going to use ExaML. I used RaxML to generate bootstrap alignments for ExaML. If I set the parameter "-N 10", should I change a different seed number (-b ) to avoid totally duplicated bootstrap alignments when execute the same command 10 times?

Best wishes,

Lei 

在 2017年7月6日星期四 UTC+8下午2:33:23，Alexis写道：

[Alexey Kozlov]

yes, please use different random seeds

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> >
>
> --
> Alexandros (Alexis) Stamatakis
>
> Research Group Leader, Heidelberg Institute for Theoretical Studies
> Full Professor, Dept. of Informatics, Karlsruhe Institute of Technology
>

> www.exelixis-lab.org <http://www.exelixis-lab.org>

[Yibo Dong]

Hi, I am also using ExaML to get a big tree. How can I do a bootstrap for this ExaML tree?

[Alexey Kozlov]

Hi Yibo,

please refer to pp. 17-18 and p.20 of the ExaML manual:

https://github.com/stamatak/ExaML/blob/master/manual/ExaML.pdf

In short: you generate BS replicate alignments, you run ExaML for each of them, concatenate the resulting trees, and
finally you assess convergence with RAxML "-I autoMRE" option.

Best,
Alexey

On 27.07.2017 00:12, Yibo Dong wrote:
> Hi, I am also using ExaML to get a big tree. How can I do a bootstrap for this ExaML tree?
>
> On Wednesday, July 5, 2017 at 8:31:26 AM UTC-5, lei chen wrote:
>
> Hi all,
> I am trying to generate 100 bootstrap alignments using commands:
>

> * raxmlHPC-AVX -N 100 -b 271828 -f j -m GTRGAMMA -s merge.fa.phy -n REPS*
> *
> *

> The size of my dataset is 25Gb. It takes too much time to get 100 bootstrap alignment files. I am wondering if
> there are some methods to speed up this process. Do you have some suggestions?
>
> Best wishes,
> Lei
>

[Yibo Dong]

Hi Alexey,

I have got bootstrap trees by ExaML. But next, how can I get a tree including bootstrap value?

Yibo

[Alexey Kozlov]

Hi Yibo,

please concatenate all bootstrap trees into one file (bstrees.nw), and then use "-f b" option to plot support values on
the best tree, e.g.

raxmlHPC-SSE3 -z bs_trees.nw -f b -m GTRGAMMA -t best_tree.nw -n bs_support

Best,
Alexey

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