AliSim codon models #196
Answered
by
trongnhanuit
thednainus
asked this question in
Q&A
Replies: 1 comment 2 replies
-
|
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: ***@***.***>
|
Beta Was this translation helpful? Give feedback.
2 replies
Answer selected by
thednainus
Sign up for free
to join this conversation on GitHub.
Already have an account?
Sign in to comment
Uh oh!
There was an error while loading. Please reload this page.
Uh oh!
There was an error while loading. Please reload this page.
-
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.nwktree.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.nwkIt works fine.
Thanks,
Fabricia.
Beta Was this translation helpful? Give feedback.
All reactions