Bootstrap problem

[Edson Alexandre]

Hello, everyone.

I would like to know if I can join multiple bootstrap trees from different jobs to get the support. I know that in raxml-ng is possible, but in raxml v. 8, is it possible? I only need to change the seed number?

[Alexandros Stamatakis]

Yes that's possible, you just need to concatenate the files with the
bootstrap trees from different runs into one large file, but as you
note, make asbolutely sure that each independent bootstrap job is run
with a distinct seed,

Alexis

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Alexandros (Alexis) Stamatakis

ERA Chair, Institute of Computer Science, Foundation for Research and
Technology - Hellas
Research Group Leader, Heidelberg Institute for Theoretical Studies
Full Professor, Dept. of Informatics, Karlsruhe Institute of Technology

www.biocomp.gr (Crete lab)
www.exelixis-lab.org (Heidelberg lab)

[Alexandros Stamatakis]

You should re-infer the best ML tree on the reduced alignment that you
used as input for bootstrapping.

Also please consider switching to RAxML-NG:

https://github.com/amkozlov/raxml-ng

Alexis

On 11.07.24 16:20, Edson Alexandre wrote:
> Hello! I am using the bootstrap result with reduced alignment file and
> the best tree file. I got this error below. I saw that in the bootstrap
> tree doesn't has the GCA_003354705.1_ASM335470v1_genomic, but in the
> best tree has it. Should I try to use the other alignment file which is
> not refined for generate the bootstrap values?
>
> Found a total of 1521 taxa in first tree of tree collection joined_boot.tree
> Expecting all remaining trees in collection to have the same taxon set
> add [GCA_903932605.1_HU-14_genomic]
> add [GCA_000967325.1_ASM96732v1_genomic]
> add [GCA_000967385.1_ASM96738v1_genomic]
> add [GCA_000967365.1_ASM96736v1_genomic]
> ...
>
> WARNING: RAxML is not checking sequences for duplicate seqs and sites
> with missing data!
>
>
> This is the RAxML Master Pthread
>
> This is RAxML Worker Pthread Number: 4
>
> This is RAxML Worker Pthread Number: 1
>
> This is RAxML Worker Pthread Number: 3
>
> This is RAxML Worker Pthread Number: 2
>
> This is RAxML Worker Pthread Number: 5
>
> This is RAxML Worker Pthread Number: 6
>
> This is RAxML Worker Pthread Number: 9
>
> This is RAxML Worker Pthread Number: 7
>
> This is RAxML Worker Pthread Number: 8
>
> This is RAxML Worker Pthread Number: 10
>
> This is RAxML Worker Pthread Number: 11
>
> This is RAxML Worker Pthread Number: 13
>
> This is RAxML Worker Pthread Number: 15
>
> This is RAxML Worker Pthread Number: 19
>
> This is RAxML Worker Pthread Number: 14
>
> This is RAxML Worker Pthread Number: 12
>
> This is RAxML Worker Pthread Number: 16
>
> This is RAxML Worker Pthread Number: 17
>
> This is RAxML Worker Pthread Number: 18
>
>
> This is RAxML version 8.2.12 released by Alexandros Stamatakis on May 2018.
>
> With greatly appreciated code contributions by:
> Andre Aberer      (HITS)
> Simon Berger      (HITS)
> Alexey Kozlov     (HITS)
> Kassian Kobert    (HITS)
> David Dao         (KIT and HITS)
> Sarah Lutteropp   (KIT and HITS)
> Nick Pattengale   (Sandia)
> Wayne Pfeiffer    (SDSC)
> Akifumi S. Tanabe (NRIFS)
> Charlie Taylor    (UF)
>
>
> RAxML Bipartition Computation: Drawing support values from trees in file
> joined_boot.tree onto tree in file
> RAxML_bestTree.QC_filtered_genome_files_refined.tre
>
>
> RAxML was called as follows:
>
> ./standard-RAxML/raxmlHPC-PTHREADS-SSE3 -m GTRCAT -f b -t
> RAxML_bestTree.QC_filtered_genome_files_refined.tre -z joined_boot.tree
> -n consensus -T 20
>
>
>
>
> Found 1 tree in File RAxML_bestTree.QC_filtered_genome_files_refined.tre
>
> ERROR: Cannot find tree species: GCA_003354705.1_ASM335470v1_genomic
> The species names in the input tree and alignment file may not match,
> please check!
> raxmlHPC-PTHREADS-SSE3: treeIO.c:1413: treeReadLen: Assertion `0' failed.
> Aborted
>
>
> Em segunda-feira, 8 de julho de 2024 às 03:42:45 UTC-3, Alexandros
> Stamatakis escreveu:

>
> Yes that's possible, you just need to concatenate the files with the
> bootstrap trees from different runs into one large file, but as you
> note, make asbolutely sure that each independent bootstrap job is run
> with a distinct seed,
>
> Alexis
>
> On 08.07.24 03:01, Edson Alexandre wrote:
> > Hello, everyone.
> >
> > I would like to know if I can join multiple bootstrap trees from
> > different jobs to get the support. I know that in raxml-ng is
> possible,
> > but in raxml v. 8, is it possible? I only need to change the seed
> number?
> >
> >
> > --
> > You received this message because you are subscribed to the Google
> > Groups "raxml" group.
> > To unsubscribe from this group and stop receiving emails from it,
> send
> > an email to raxml+un...@googlegroups.com
> > <mailto:raxml+un...@googlegroups.com>.
> > To view this discussion on the web visit
> >

> https://groups.google.com/d/msgid/raxml/cc47de42-44a5-4579-9cd4-733ba6189ad0n%40googlegroups.com <https://groups.google.com/d/msgid/raxml/cc47de42-44a5-4579-9cd4-733ba6189ad0n%40googlegroups.com> <https://groups.google.com/d/msgid/raxml/cc47de42-44a5-4579-9cd4-733ba6189ad0n%40googlegroups.com?utm_medium=email&utm_source=footer <https://groups.google.com/d/msgid/raxml/cc47de42-44a5-4579-9cd4-733ba6189ad0n%40googlegroups.com?utm_medium=email&utm_source=footer>>.

>
> --
> Alexandros (Alexis) Stamatakis
>
> ERA Chair, Institute of Computer Science, Foundation for Research and
> Technology - Hellas
> Research Group Leader, Heidelberg Institute for Theoretical Studies
> Full Professor, Dept. of Informatics, Karlsruhe Institute of Technology
>

> www.biocomp.gr <http://www.biocomp.gr> (Crete lab)
> www.exelixis-lab.org <http://www.exelixis-lab.org> (Heidelberg lab)

>
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