Error using DNAbin for tree construction

[Victoria Glynn]

Hello RAxML group,

I hope this finds everyone well. 

I am attempting to build a RAxML tree using ITS2 sequences that have been run via a DADA2 pipeline to identify ASVs. From reading online, I have understood that I need to convert my ASV file as a DNAbin file for RAxML. 

In doing so, I keep receiving the following error that I am unsure how to troubleshoot/resolve:

Error in `[.default`(x, 1, 1, drop = FALSE) : 

  incorrect number of dimensions

Calls: raxml -> write.phy -> ifelse -> [ -> [.DNAbin -> NextMethod

My R Script looks as follows: 

aln.bin = as.DNAbin(alignment)

alignment.rax.gtr <- raxml(aln.bin,

                           m="GTRGAMMA", # model

                           f="a", # best tree and bootstrap

                           p=1234, # random number seed

                           x=2345, # random seed for rapid bootstrapping

                           N=500, # number of bootstrap replicates

                           file="RAxML_alignment", # name of output files

                           exec="/cvmfs/soft.computecanada.ca/easybuild/software/2020/avx2/MPI/intel2020/openmpi4/raxml/8.2.12/bin", # name of executable

                           threads=20)

alignment.rax.gtr

detach("package:phangorn", unload=TRUE)

Any insights would be greatly appreciated. Thank you in advance! 

- Victoria

[Alexandros Stamatakis]

This looks like an error from the script not from RAxML.

Alexis

On 13.05.21 06:29, Victoria Glynn wrote:
> Hello RAxML group,
>
> I hope this finds everyone well.
>
> I am attempting to build a RAxML tree using ITS2 sequences that have
> been run via a DADA2 pipeline to identify ASVs. From reading online, I
> have understood that I need to convert my ASV file as a DNAbin file for
> RAxML.
>

> *In doing so, I keep receiving the following error that I am unsure how
> to troubleshoot/resolve:*

>
> Error in `[.default`(x, 1, 1, drop = FALSE) :
>
>   incorrect number of dimensions
>
> Calls: raxml -> write.phy -> ifelse -> [ -> [.DNAbin -> NextMethod
>

> *My R Script looks as follows: *

>
> aln.bin = as.DNAbin(alignment)
>
> alignment.rax.gtr <- raxml(aln.bin,
>
>                            m="GTRGAMMA", # model
>
>                            f="a", # best tree and bootstrap
>
>                            p=1234, # random number seed
>
>                            x=2345, # random seed for rapid bootstrapping
>
>                            N=500, # number of bootstrap replicates
>
>                            file="RAxML_alignment", # name of output files
>
>
>  exec="/cvmfs/soft.computecanada.ca/easybuild/software/2020/avx2/MPI/intel2020/openmpi4/raxml/8.2.12/bin", # name of executable
>
>                            threads=20)
>
> alignment.rax.gtr
>
>
> detach("package:phangorn", unload=TRUE)
>
>
> Any insights would be greatly appreciated. Thank you in advance!
>
> - Victoria
>

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--
Alexandros (Alexis) Stamatakis

Research Group Leader, Heidelberg Institute for Theoretical Studies
Full Professor, Dept. of Informatics, Karlsruhe Institute of Technology
Affiliated Scientist, Evolutionary Genetics and Paleogenomics (EGP) lab,
Institute of Molecular Biology and Biotechnology, Foundation for
Research and Technology Hellas

www.exelixis-lab.org