-f a -x bootstrapping prompted error

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Marco Mancuso

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Feb 5, 2024, 7:26:23 AMFeb 5
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Hello,
I'm trying to run a ML analysis on my MacBook Pro (MacOS Monterey 12.7.1. 2,7 GHz Dual-Core Intel Core i5) in RAxML on the latest version available at https://github.com/stamatak/standard-RAxML.

I was trying to run the following code: "/path/to/raxmlHPC-AVX2 -f a -x 482094802945 -# 10000 -J MR -m GTRGAMMAI -o outgroup_taxon -s data.fasta -n results_ML -p 482094802945 -q partitions.txt", but RAxML always prompts the error "The file  you want to open for reading does not exist, exiting ..." when the -f a - x 482094802945 option is specified. Otherwise, the program reads the rest of my data properly. What could the issue be? Otherwise it runs properly.

Best regards,
Marco.

Alexandros Stamatakis

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Feb 6, 2024, 6:16:46 AMFeb 6
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I think the problem might be an extra space or invalid character you
might have added somewhere, e.g.,

-f a - x 482094802945

the s[pace between - and x will cause an issue.

Also, please consider switching to the new version of RAxML:

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)
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