Get bootstrap values on consensus tree

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Pailler Vincent

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Apr 2, 2024, 6:16:14 AMApr 2
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Dear Oleksiy, 

I work on a 16S sequencing project. I did first a DADA2 analysis to get my taxa. Now, I would like to get a tree on these data.

I did my sequences alignment with DECIPHER. Then I try to deal with raxml-ng. The computing time is very long when I try : 

./raxml-ng --msa ./output/alignement.fasta --model GTR+G --prefix test --threads 128

That's why I tried to get a consensus tree based on 100 starting trees (--start option) : 

./raxml-ng --msa ./output/alignement.fasta --model GTR+G --prefix starting --tree pars{50},rand{50} --start --threads 128

./raxml-ng --consense MRE --tree starting.raxml.startTree--prefix consensus.MRE --threads 128

Then, I tried to get the bootstrap values of that tree : 

./raxml-ng --bootstrap --msa ./output/alignement.fasta--prefix bootstrap --model GTR+G --seed 2 --threads 128

It is still running. I will finish by mapping these values on the consensus tree with : 

raxml-ng --support --tree consensus.MRE.consensusTreeMRE   --bs-trees allbootstraps --prefix bootstrap_tree --threads 32

Is that a correct way to do? Is there any parameter to trick with?

Best regards,
Paillou

Oleksiy Kozlov

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Apr 3, 2024, 4:55:22 AMApr 3
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Dear Paillou,

well, consensus of random starting trees is definitely not a good substitute for the ML tree.

To make ML tree inference faster, you can specify a (taxonomic) constraint tree, and/or use the
adaptive version of raxml-ng:

https://github.com/amkozlov/raxml-ng/wiki/Installation#building-adaptive-branch

Also, please have a look at this tutorial:
https://github.com/amkozlov/ng-tutorial/wiki/evomics2024

Best,
Oleksiy

On 02.04.24 10:55, Pailler Vincent wrote:
> Dear Oleksiy,
>
> I work on a 16S sequencing project. I did first a DADA2 analysis to get my taxa. Now, I would like
> to get a tree on these data.
>
> I did my sequences alignment with DECIPHER. Then I try to deal with raxml-ng. The computing time is
> very long when I try :
>
> ./raxml-ng --msa ./output/alignement.fasta--model GTR+G--prefix test --threads 128
>
> That's why I tried to get a consensus tree based on 100 starting trees (--start option) :
>
> ./raxml-ng --msa./output/alignement.fasta--model GTR+G--prefix starting --tree pars{50},rand{50}
> --start --threads 128
>
> ./raxml-ng --consense MRE --tree starting.raxml.startTree--prefix consensus.MRE --threads 128
>
> Then, I tried to get the bootstrap values of that tree :
>
> ./raxml-ng --bootstrap --msa ./output/alignement.fasta--prefix bootstrap --model GTR+G --seed 2
> --threads 128
>
> It is still running. I will finish by mapping these values on the consensus tree with :
>
> raxml-ng --support --tree consensus.MRE.consensusTreeMRE --bs-trees allbootstraps --prefix
> bootstrap_tree --threads 32
>
> Is that a correct way to do? Is there any parameter to trick with?
>
> Best regards,
> Paillou
>
> --
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Pailler Vincent

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Apr 16, 2024, 3:36:48 AMApr 16
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Dear Oleksiy, 

Thanks for your feedback. 

What I did is to reduce my dataset, from 19k ASV to 3.6k ASV. Also, I use the `--parse` option to optimize my number of CPUs. I used : 

`./raxml-ng --log progress --threads 9 --msa  ./output/alignement.fasta   --model GTR+G -prefix GTR -all --bs-metric fbp,tbe --force perf_threads --bs-trees 100` 

I had 20 starting trees and I also got my bootstrap values with `--all` , but with only 100 replicated. It ran well but I read a topic (https://stats.stackexchange.com/questions/86040/rule-of-thumb-for-number-of-bootstrap-samples#:~:text=Example%20(Table%20V%2C%20ibid.,95%25%20sure%2C%20850%20replications) when it  is advised to use many more replicated (over 700). 

It is to time-consuming if I leave the default `--bs-trees` (1000 replicates). Could I use these values on my ML tree even if my job crashes, at few hundreds of replicated?

Best,

Oleksiy Kozlov

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Apr 16, 2024, 6:26:40 AMApr 16
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Dear Paillou,

raxml-ng provides an integrated bootstrap convergence test, which can be applied during the tree
inference ("--bs-trees autoMRE"), or as a post-processing step:

Please see:

https://github.com/amkozlov/raxml-ng/wiki/Tutorial#bootstrapping

https://github.com/amkozlov/raxml-ng/wiki/Tuning-model-optimization-and-tree-search#bootstrapping

Best,
Oleksiy

On 16.04.24 09:36, Pailler Vincent wrote:
> Dear Oleksiy,
>
> <https://groups.google.com/d/msgid/raxml/b700f352-6b06-4095-8ccb-b29a1fe297b9n%40googlegroups.com?utm_medium=email&utm_source=footer <https://groups.google.com/d/msgid/raxml/b700f352-6b06-4095-8ccb-b29a1fe297b9n%40googlegroups.com?utm_medium=email&utm_source=footer>>.
>
> --
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Pailler Vincent

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Apr 16, 2024, 8:42:59 AMApr 16
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Thanks again for the help, I'll try your suggestion.

Best
Paillou

Pailler Vincent

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Apr 19, 2024, 9:29:45 AMApr 19
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Hi  Oleksiy,

I have a .bestTree obtained with --tree pars{50},rand{50} . Is there a way to run --bs-trees autoMRE on this tree rather than on the --msa file?

Best

Oleksiy Kozlov

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Apr 19, 2024, 10:40:05 AMApr 19
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autoMRE is a convergence test for bootstrap replicate trees, it does not require ML tree.

so you can use "--bootstrap --bs-trees autoMRE" (if you don't have bootstrap trees yet) or
"--bsconverge" (if you have them)

On 19.04.24 15:29, Pailler Vincent wrote:
> Hi Oleksiy,
>
> I have a .bestTree obtained with --tree pars{50},rand{50} . Is there a way to run --bs-trees autoMRE
> on this tree rather than on the --msa file?
>
> Best
>
> On Tuesday 16 April 2024 at 14:42:59 UTC+2 Pailler Vincent wrote:
>
> Thanks again for the help, I'll try your suggestion.
>
> Best
> Paillou
>
> On Tuesday 16 April 2024 at 12:26:40 UTC+2 Oleksiy Kozlov wrote:
>
> Dear Paillou,
>
> raxml-ng provides an integrated bootstrap convergence test, which can be applied during the
> tree
> inference ("--bs-trees autoMRE"), or as a post-processing step:
>
> Please see:
>
> https://github.com/amkozlov/raxml-ng/wiki/Tutorial#bootstrapping
> <https://github.com/amkozlov/raxml-ng/wiki/Tutorial#bootstrapping>
>
> https://github.com/amkozlov/raxml-ng/wiki/Tuning-model-optimization-and-tree-search#bootstrapping <https://github.com/amkozlov/raxml-ng/wiki/Tuning-model-optimization-and-tree-search#bootstrapping>
>
> Best,
> Oleksiy
>
> On 16.04.24 09:36, Pailler Vincent wrote:
> > Dear Oleksiy,
> >
> > Thanks for your feedback.
> >
> > What I did is to reduce my dataset, from 19k ASV to 3.6k ASV. Also, I use the `--parse`
> option to
> > optimize my number of CPUs. I used :
> >
> > `./raxml-ng --log progress --threads 9 --msa ./output/alignement.fasta   --model GTR+G
> -prefix GTR
> > -all --bs-metric fbp,tbe --force perf_threads --bs-trees 100`
> >
> > I had 20 starting trees and I also got my bootstrap values with `--all` , but with only 100
> > replicated. It ran well but I read a topic
> >
> (https://stats.stackexchange.com/questions/86040/rule-of-thumb-for-number-of-bootstrap-samples#:~:text=Example%20(Table%20V%2C%20ibid <https://stats.stackexchange.com/questions/86040/rule-of-thumb-for-number-of-bootstrap-samples#:~:text=Example%20(Table%20V%2C%20ibid>.,95%25%20sure%2C%20850%20replications) when it  is advised to use many more replicated (over 700).
> <https://groups.google.com/d/msgid/raxml/b700f352-6b06-4095-8ccb-b29a1fe297b9n%40googlegroups.com?utm_medium=email&utm_source=footer <https://groups.google.com/d/msgid/raxml/b700f352-6b06-4095-8ccb-b29a1fe297b9n%40googlegroups.com?utm_medium=email&utm_source=footer> <https://groups.google.com/d/msgid/raxml/b700f352-6b06-4095-8ccb-b29a1fe297b9n%40googlegroups.com?utm_medium=email&utm_source=footer <https://groups.google.com/d/msgid/raxml/b700f352-6b06-4095-8ccb-b29a1fe297b9n%40googlegroups.com?utm_medium=email&utm_source=footer>>>.
> >
> > --
> > You received this message because you are subscribed to the Google Groups "raxml" group.
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> >
> https://groups.google.com/d/msgid/raxml/1e79310e-8945-4907-b9ca-131f0b93ccc8n%40googlegroups.com <https://groups.google.com/d/msgid/raxml/1e79310e-8945-4907-b9ca-131f0b93ccc8n%40googlegroups.com>
> >
> <https://groups.google.com/d/msgid/raxml/1e79310e-8945-4907-b9ca-131f0b93ccc8n%40googlegroups.com?utm_medium=email&utm_source=footer <https://groups.google.com/d/msgid/raxml/1e79310e-8945-4907-b9ca-131f0b93ccc8n%40googlegroups.com?utm_medium=email&utm_source=footer>>.
>
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Pailler Vincent

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Apr 19, 2024, 10:48:30 AMApr 19
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Thanks
I run the MRE bootstrap with the msa file then. I will use --support to add the values on my best tree.
Best

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Pailler Vincent

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May 2, 2024, 11:40:15 AMMay 2
to raxml
Hi, my job crashed after 7 days with 270 replicates. Is it OK to run 4  jobs in parallel, on the same matrix, to get 270 replicates * 4 jobs and then, use --bsconverge to converge all of that? 
Best

Oleksiy Kozlov

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May 2, 2024, 2:25:32 PMMay 2
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yes it's OK, just make sure you specify distinct --seed for each job!
> https://github.com/amkozlov/raxml-ng/wiki/Tuning-model-optimization-and-tree-search#bootstrapping <https://github.com/amkozlov/raxml-ng/wiki/Tuning-model-optimization-and-tree-search#bootstrapping> <https://github.com/amkozlov/raxml-ng/wiki/Tuning-model-optimization-and-tree-search#bootstrapping <https://github.com/amkozlov/raxml-ng/wiki/Tuning-model-optimization-and-tree-search#bootstrapping>>
> >
> >         Best,
> >         Oleksiy
> >
> >         On 16.04.24 09:36, Pailler Vincent wrote:
> >          > Dear Oleksiy,
> >          >
> >          > Thanks for your feedback.
> >          >
> >          > What I did is to reduce my dataset, from 19k ASV to 3.6k ASV. Also, I use the
> `--parse`
> >         option to
> >          > optimize my number of CPUs. I used :
> >          >
> >          > `./raxml-ng --log progress --threads 9 --msa ./output/alignement.fasta
>  --model GTR+G
> >         -prefix GTR
> >          > -all --bs-metric fbp,tbe --force perf_threads --bs-trees 100`
> >          >
> >          > I had 20 starting trees and I also got my bootstrap values with `--all` , but
> with only 100
> >          > replicated. It ran well but I read a topic
> >          >
> >
>  (https://stats.stackexchange.com/questions/86040/rule-of-thumb-for-number-of-bootstrap-samples#:~:text=Example%20(Table%20V%2C%20ibid <https://stats.stackexchange.com/questions/86040/rule-of-thumb-for-number-of-bootstrap-samples#:~:text=Example%20(Table%20V%2C%20ibid> <https://stats.stackexchange.com/questions/86040/rule-of-thumb-for-number-of-bootstrap-samples#:~:text=Example%20(Table%20V%2C%20ibid <https://stats.stackexchange.com/questions/86040/rule-of-thumb-for-number-of-bootstrap-samples#:~:text=Example%20(Table%20V%2C%20ibid>>.,95%25%20sure%2C%20850%20replications) when it  is advised to use many more replicated (over 700).
>  <https://groups.google.com/d/msgid/raxml/b700f352-6b06-4095-8ccb-b29a1fe297b9n%40googlegroups.com?utm_medium=email&utm_source=footer <https://groups.google.com/d/msgid/raxml/b700f352-6b06-4095-8ccb-b29a1fe297b9n%40googlegroups.com?utm_medium=email&utm_source=footer> <https://groups.google.com/d/msgid/raxml/b700f352-6b06-4095-8ccb-b29a1fe297b9n%40googlegroups.com?utm_medium=email&utm_source=footer <https://groups.google.com/d/msgid/raxml/b700f352-6b06-4095-8ccb-b29a1fe297b9n%40googlegroups.com?utm_medium=email&utm_source=footer>> <https://groups.google.com/d/msgid/raxml/b700f352-6b06-4095-8ccb-b29a1fe297b9n%40googlegroups.com?utm_medium=email&utm_source=footer <https://groups.google.com/d/msgid/raxml/b700f352-6b06-4095-8ccb-b29a1fe297b9n%40googlegroups.com?utm_medium=email&utm_source=footer> <https://groups.google.com/d/msgid/raxml/b700f352-6b06-4095-8ccb-b29a1fe297b9n%40googlegroups.com?utm_medium=email&utm_source=footer <https://groups.google.com/d/msgid/raxml/b700f352-6b06-4095-8ccb-b29a1fe297b9n%40googlegroups.com?utm_medium=email&utm_source=footer>>>>.
> >          >
> >          > --
> >          > You received this message because you are subscribed to the Google Groups
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> >          >
> >
> https://groups.google.com/d/msgid/raxml/1e79310e-8945-4907-b9ca-131f0b93ccc8n%40googlegroups.com <https://groups.google.com/d/msgid/raxml/1e79310e-8945-4907-b9ca-131f0b93ccc8n%40googlegroups.com> <https://groups.google.com/d/msgid/raxml/1e79310e-8945-4907-b9ca-131f0b93ccc8n%40googlegroups.com <https://groups.google.com/d/msgid/raxml/1e79310e-8945-4907-b9ca-131f0b93ccc8n%40googlegroups.com>>
> >          >
> >
>  <https://groups.google.com/d/msgid/raxml/1e79310e-8945-4907-b9ca-131f0b93ccc8n%40googlegroups.com?utm_medium=email&utm_source=footer <https://groups.google.com/d/msgid/raxml/1e79310e-8945-4907-b9ca-131f0b93ccc8n%40googlegroups.com?utm_medium=email&utm_source=footer> <https://groups.google.com/d/msgid/raxml/1e79310e-8945-4907-b9ca-131f0b93ccc8n%40googlegroups.com?utm_medium=email&utm_source=footer <https://groups.google.com/d/msgid/raxml/1e79310e-8945-4907-b9ca-131f0b93ccc8n%40googlegroups.com?utm_medium=email&utm_source=footer>>>.
> >
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