MCMCTree error: raise NS?

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guo

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Mar 18, 2024, 9:38:09 AMMar 18
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Hello!
I had some problems using MCMCTree. The specific content of the error is as follows. I don't know what the problem is, and I really need your help.
Thank you!!mcmcerro.png
mcmctree.ctl
calibration.tree

Sandra AC

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Mar 18, 2024, 10:50:10 AMMar 18
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Hi there,

If you go to the `src` directory and open the `mcmctree.c` file with your favourite text editor, you need to modify the following line:

image.png

E.g., if you are analysing 1850 taxa, perhaps increase this variable to 2000. Once you have changed the line (e.g., #define NS      2000), you can save this file. To recompile the program, open your terminal from the `src` directory, type the command `make -f Makefile`, and you will see that all the PAML programs will have been recompiled and new binaries will appear. You can then remove the output files (i.e., `rm *o`) and the other compiled binaries except for the `mcmctree` binary -- this binary will allow MCMCtree to parse input files that have up to 2000 taxa. You may then export the PATH to this binary as you previously had in your system environment, which will hopefully allow you to run MCMCtree without problems. You may also want to check the PAML Wiki to make sure that your input files are in the correct format too.

Hope this helps!
S.

Sandra AC

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Mar 18, 2024, 10:52:34 AMMar 18
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P.S.: It seems that the image I attached in my previous message does not appear, here it goes again!raiseNS.png

guo

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Mar 18, 2024, 11:15:33 PMMar 18
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Hello!
Thank you very much for your reply! Previously I used the paml program installed by conda, this one does not have a src folder. Therefore, I re-downloaded the installation package of paml from the URL you gave me, and attempted to reinstall it. However, I am sorry that I have encountered trouble again in the step of "make -f Makefile", and the specific error is as follows. Is this a common question? How can I fix it? 
icc  -O3 -Wall -c baseml.c
make: icc: Command not found
make: *** [Makefile:30: baseml.o] Error 127

Many Thanks again!
Guo.

guo

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Mar 19, 2024, 1:52:01 AMMar 19
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Hello!
Sorry, I just downloaded the wrong installation package, now it is running successfully.
Thanks again for your help!
Guo.
在2024年3月18日星期一 UTC+8 22:50:10<sandr...@gmail.com> 写道:

Sandra AC

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Mar 19, 2024, 2:24:04 PMMar 19
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Glad that it worked in the end!

All the best,
S.

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