AliSim codon models

[thednainus]

Hello,

I am trying to simulate some sequence alignment using a codon model.
I have tried the following command:

iqtree2 --alisim alignment_codon -m MG2K{1.0,0.3,0.5} -t tree.nwk
tree.nwk is the same tree as the example in here http://www.iqtree.org/doc/AliSim

I get the following error message:

IQ-TREE multicore version 2.3.2 COVID-edition for Mac OS X 64-bit built Apr 9 2024
Developed by Bui Quang Minh, James Barbetti, Nguyen Lam Tung,
Olga Chernomor, Heiko Schmidt, Dominik Schrempf, Michael Woodhams, Ly Trong Nhan, Thomas Wong

Host: Fabricias-Air.home (SSE4.2, 16 GB RAM)
Command: iqtree2 --alisim alignment_codon -m MG2K1.0 MG2K0.3 MG2K0.5 -t tree.nwk
Seed: 942363 (Using SPRNG - Scalable Parallel Random Number Generator)
Time: Tue May 14 10:59:10 2024
OMP: Info #276: omp_set_nested routine deprecated, please use omp_set_max_active_levels instead.
Kernel: SSE2 - 1 threads (8 CPU cores detected)

[Alignment Simulator] Executing
ERROR: File not found or incorrect input, pls check it again.MG2K1.0

Do you know why this is happens?
I am just trying to understand how AliSim works for codon models.
I took this parameter value -m MG2K{1.0,0.3,0.5} from the example in here http://www.iqtree.org/doc/Substitution-Models
I use a Mac OS Sonoma M2 chip.

Also note that if I use this example here:
iqtree2 --alisim alignment_codon -m MG{2.0}+F1X4{0.2/0.3/0.4/0.1} -t tree.nwk
It works fine.

Thanks,
Fabricia.

[trongnhanuit]

Dear Fabricia, Thank you for using AliSim. Can you try with: iqtree2 --alisim alignment_codon -m "MG2K{1.0,0.3,0.5}" -t tree.nwk (with "" covers the model and its parameters). Cheers, Nhan

…

On Tue, 14 May 2024 at 8:04 PM, Fabricia Nascimento < ***@***.***> wrote: Hello, I am trying to simulate some sequence alignment using a codon model. I have tried the following command: iqtree2 --alisim alignment_codon -m MG2K{1.0,0.3,0.5} -t tree.nwk tree.nwk is the same tree as the example in here http://www.iqtree.org/doc/AliSim I get the following error message: _IQ-TREE multicore version 2.3.2 COVID-edition for Mac OS X 64-bit built Apr 9 2024 Developed by Bui Quang Minh, James Barbetti, Nguyen Lam Tung, Olga Chernomor, Heiko Schmidt, Dominik Schrempf, Michael Woodhams, Ly Trong Nhan, Thomas Wong Host: Fabricias-Air.home (SSE4.2, 16 GB RAM) Command: iqtree2 --alisim alignment_codon -m MG2K1.0 MG2K0.3 MG2K0.5 -t tree.nwk Seed: 942363 (Using SPRNG - Scalable Parallel Random Number Generator) Time: Tue May 14 10:59:10 2024 OMP: Info #276: omp_set_nested routine deprecated, please use omp_set_max_active_levels instead. Kernel: SSE2 - 1 threads (8 CPU cores detected) [Alignment Simulator] Executing ERROR: File not found or incorrect input, pls check it again.MG2K1.0_ Do you know why this is happens? I use a Mac OS Sonoma M2 chip. Thanks, Fabricia. — Reply to this email directly, view it on GitHub <#196>, or unsubscribe <https://github.com/notifications/unsubscribe-auth/ABZPMLCDDPX4TL2PJ7BOXJTZCHORJAVCNFSM6AAAAABHV3DRN6VHI2DSMVQWIX3LMV43ERDJONRXK43TNFXW4OZWGY3DKNRYGM> . You are receiving this because you are subscribed to this thread.Message ID: ***@***.***>

[thednainus]

Hello!
Thanks for the replay! It does work in this way.
I guess I got confused because in the example that the model works, the "" are not needed.

Cheers,
Fabricia.

[bqminh]

The command line parser in Linux/Mac is doing something funny when you have a comma-separated string enclosed by curly brackets. If you compare your original command -m MG2K{1.0,0.3,0.5} with what iqtree printed in the log file (See "Command:" line), it becomes -m MG2K1.0 MG2K0.3 MG2K0.5. That's the reason.

Apart from the solution using single-quote or double-quote around the string to avoid that as @trongnhanuit suggested, you can also use slash-separated string, e.g., -m MG2K{1.0/0.3/0.5}. Slash is introduced as an alternative separator for comma. Then you don't need to use quotes.