Not recognized as an internal or external command, operable program, or batch file

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Aline Silva

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Jan 24, 2024, 12:01:58 PMJan 24
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Hello, I'm trying to run a Maximum Likelihood analysis with RAxML, but after providing the concatenated data file (.phy) and the partition file inferred by IQ-Tree in .txt format, I'm encountering an error. RAxML returns: "not recognized as an internal or external command, operable program, or batch file."

Here is my partition file:

DNA, 12S_16S_COI_codon1_RAG1_codon3 = 1-972, 973-3544, 3546-4203\3, 4206-4659\3

DNA, COI_codon2_RAG1_codon1_RAG1_codon2 = 3547-4203\3, 4204-4659\3, 4205-4659\3

DNA, COI_codon3 = 3545-4203\3

 

And this is the command I run in RAxML:

raxmlHPC -s Pseudopaludicola_Concat_RaxML.phy -p 1234 -m GTRGAMMA -q

Particoes_Pseudopaludicola_raxml.txt -n Pseudopaludicola_best -# 1000

Alexandros Stamatakis

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Jan 25, 2024, 4:18:10 AMJan 25
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The problem seems to be that raxmlHPC does not seem to be recognized as
an executable on your system, what happens if you type "raxmlHPC -h",
I'd assume that raxmlHPC is not in your $PATH.

Also please consider switching to the new version of RAxML called RAxML-NG:

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

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)

Aline Silva

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Jan 26, 2024, 3:51:32 AMJan 26
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Dear Alexandros Stamatakis,

When I type "raxmlHPC -h," I receive the following message: This application cannot be run on your computer - to find a version for your PC, please consult the software provider.

And I still haven't been able to run the analysis successfully.

Sincerely,
Aline Silva.

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--
Aline Nascimento da Silva
Pós-graduanda em Zoologia - PPGZOOL - UFPA / MPEG

Alexandros Stamatakis

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Jan 26, 2024, 4:25:31 AMJan 26
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It's not a RAxML issue but your computer can simply not find the RAxML
command in the first place. Are you using Windows or Linux?

Alexis

On 25.01.24 18:15, Aline Silva wrote:
> Dear Alexandros Stamatakis,
>
> When I type "raxmlHPC -h," I receive the following message: This
> application cannot be run on your computer - to find a version for your
> PC, please consult the software provider.
>
> And I still haven't been able to run the analysis successfully.
>
> Sincerely,
> Aline Silva.
>
> Em qui., 25 de jan. de 2024 às 06:18, Alexandros Stamatakis
> <alexandros...@gmail.com
> <mailto:alexandros...@gmail.com>> escreveu:
> <mailto:raxml%2Bunsu...@googlegroups.com>
> > <mailto:raxml+un...@googlegroups.com
> <mailto:raxml%2Bunsu...@googlegroups.com>>.
> > To view this discussion on the web visit
> >
> https://groups.google.com/d/msgid/raxml/37f20ff4-251f-4076-97f4-166ec772837fn%40googlegroups.com <https://groups.google.com/d/msgid/raxml/37f20ff4-251f-4076-97f4-166ec772837fn%40googlegroups.com> <https://groups.google.com/d/msgid/raxml/37f20ff4-251f-4076-97f4-166ec772837fn%40googlegroups.com?utm_medium=email&utm_source=footer <https://groups.google.com/d/msgid/raxml/37f20ff4-251f-4076-97f4-166ec772837fn%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)
>
> --
> You received this message because you are subscribed to the Google
> Groups "raxml" group.
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> send an email to raxml+un...@googlegroups.com
> <mailto:raxml%2Bunsu...@googlegroups.com>.
> To view this discussion on the web visit
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>
>
>
> --
> Aline Nascimento da Silva
> Pós-graduanda em Zoologia - PPGZOOL - UFPA / MPEG
> Currículo lattes: http://lattes.cnpq.br/4470607779706510
> <http://lattes.cnpq.br/4470607779706510>
>
> --
> 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
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> <mailto:raxml+un...@googlegroups.com>.
> To view this discussion on the web visit
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Aline Silva

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Jan 26, 2024, 8:37:06 AMJan 26
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Dear Alexis,

Thank you for your response. I am using Windows 11. I would be grateful if you could assist me with specific steps or recommended solutions to resolve the issue.

Best regards,
Aline.

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Brandon Stark

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Jan 27, 2024, 1:54:56 AMJan 27
to raxml
Dear Aline,
you can use raxml-ng as a choice.

Alexandros Stamatakis

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Jan 27, 2024, 2:52:29 AMJan 27
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Yes please try raxml-ng first, but as I said the problem is that your
computer does not find the raxml executable, so this is operating system
dependent. I have been using Linux only for the last 25 years, so I
won't be of great help here.

Alexis
> https://groups.google.com/d/msgid/raxml/37f20ff4-251f-4076-97f4-166ec772837fn%40googlegroups.com <https://groups.google.com/d/msgid/raxml/37f20ff4-251f-4076-97f4-166ec772837fn%40googlegroups.com> <https://groups.google.com/d/msgid/raxml/37f20ff4-251f-4076-97f4-166ec772837fn%40googlegroups.com <https://groups.google.com/d/msgid/raxml/37f20ff4-251f-4076-97f4-166ec772837fn%40googlegroups.com>> <https://groups.google.com/d/msgid/raxml/37f20ff4-251f-4076-97f4-166ec772837fn%40googlegroups.com?utm_medium=email&utm_source=footer <https://groups.google.com/d/msgid/raxml/37f20ff4-251f-4076-97f4-166ec772837fn%40googlegroups.com?utm_medium=email&utm_source=footer> <https://groups.google.com/d/msgid/raxml/37f20ff4-251f-4076-97f4-166ec772837fn%40googlegroups.com?utm_medium=email&utm_source=footer <https://groups.google.com/d/msgid/raxml/37f20ff4-251f-4076-97f4-166ec772837fn%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> <http://www.biocomp.gr
> <http://www.exelixis-lab.org <http://www.exelixis-lab.org>>
> (Heidelberg lab)
> >
> >     --
> >     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%2Bunsu...@googlegroups.com>.
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> >
> https://groups.google.com/d/msgid/raxml/e42ae678-857f-400c-b384-4ebdcef71d59%40gmail.com <https://groups.google.com/d/msgid/raxml/e42ae678-857f-400c-b384-4ebdcef71d59%40gmail.com> <https://groups.google.com/d/msgid/raxml/e42ae678-857f-400c-b384-4ebdcef71d59%40gmail.com <https://groups.google.com/d/msgid/raxml/e42ae678-857f-400c-b384-4ebdcef71d59%40gmail.com>>.
> >
> >
> >
> > --
> > Aline Nascimento da Silva
> > Pós-graduanda em Zoologia - PPGZOOL - UFPA / MPEG
> > Currículo lattes: http://lattes.cnpq.br/4470607779706510
> <http://lattes.cnpq.br/4470607779706510>
> > <http://lattes.cnpq.br/4470607779706510
> <http://lattes.cnpq.br/4470607779706510>>
> >
> > --
> > You received this message because you are subscribed to the
> Google
> > Groups "raxml" group.
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> it, send
> > an email to raxml+un...@googlegroups.com
> > <mailto:raxml+un...@googlegroups.com>.
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> >
> https://groups.google.com/d/msgid/raxml/CA%2BnCa8gfLOc%2B3NGxEzTg8u7Y2eT%3Dm_4xsy1uV0XYfVPBbEFKOw%40mail.gmail.com <https://groups.google.com/d/msgid/raxml/CA%2BnCa8gfLOc%2B3NGxEzTg8u7Y2eT%3Dm_4xsy1uV0XYfVPBbEFKOw%40mail.gmail.com> <https://groups.google.com/d/msgid/raxml/CA%2BnCa8gfLOc%2B3NGxEzTg8u7Y2eT%3Dm_4xsy1uV0XYfVPBbEFKOw%40mail.gmail.com?utm_medium=email&utm_source=footer <https://groups.google.com/d/msgid/raxml/CA%2BnCa8gfLOc%2B3NGxEzTg8u7Y2eT%3Dm_4xsy1uV0XYfVPBbEFKOw%40mail.gmail.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)
>
> --
> 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.
> To view this discussion on the web visit
> https://groups.google.com/d/msgid/raxml/51fe1f46-7982-496a-ba4d-e3f6b6c6bbd5%40gmail.com <https://groups.google.com/d/msgid/raxml/51fe1f46-7982-496a-ba4d-e3f6b6c6bbd5%40gmail.com>.
>
>
>
> --
> Aline Nascimento da Silva
> Pós-graduanda em Zoologia - PPGZOOL - UFPA / MPEG
> Currículo lattes: http://lattes.cnpq.br/4470607779706510
> <http://lattes.cnpq.br/4470607779706510>
>
> --
> You received this message because you are subscribed to the Google
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> To unsubscribe from this group and stop receiving emails from it, send
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