QMaker models?

[KyleTDavid]

Hello, I receive a Cannot read alignment file (file exists but is invalid) error whenever I try to use a "Q" model following RAXML syntax (Q.pfam, Q.insect, Q.yeast, etc.) is it possible these models have not yet been included? If not, are there any workarounds? I'm using the latest conda version (2.0.4) if that helps. Thank you!

[KyleTDavid]

UPDATE: I have tried to supply the Q matrix myself using the name of a file in PAML format (attached) ala RAXML-ng or IQTREE, but receive the same error. Q.yeast.paml.txt

[BenoitMorel]

Hello Kyle, Thanks for your mail. This should work. Just to be sure, have you tried to see if that works when replacing the Q model with any other model such as LG? Another explanation could be that the conda version is a bit outdated. Could you try to install generax from github to see if that works better? (it should be quite straightforward) Let me know if that helps Best, Benoit

Le jeu. 4 janv. 2024 à 19:08, Kyle David @.***> a écrit :

UPDATE: I have tried to supply the Q matrix myself using the name of a file in PAML format (attached) ala RAXML-ng or IQTREE, but receive the same error. Q.yeast.paml.txt https://github.com/BenoitMorel/GeneRax/files/13834045/Q.yeast.paml.txt

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[KyleTDavid]

Thanks for you reply. Correct, the conda install seems to run fine with LG and other models I've tried. Using the github installation, I receive a illegal instruction: illegal operand error I'm not really sure what to make sense of, regardless of which model I use. I'll attach the stdout and my working directory from that run if it helps, let me know what you think! stdout.txt generaxplay.tar.gz

[BenoitMorel]

Hi Kyle, This won't be easy to fix, because I can't reproduce on my machine (it works fine) :( Can you try the following: in the cloned GeneRax repository, open the file src/CMakeLists.txt and replace set(CMAKE_CXX_FLAGS "${CMAKE_CXX_FLAGS} -g -Wall -Wextra) with set(CMAKE_CXX_FLAGS "${CMAKE_CXX_FLAGS} -g -Wall -Wextra -march=native")

Recompile (./install.sh), and rerun. It will crash again, I just wonder where it will crash (send me again your stdout.txt) Thanks :-) Benoit

Le lun. 8 janv. 2024 à 13:10, Kyle David @.***> a écrit :

Thanks for you reply. Correct, the conda install seems to run fine with LG and other models I've tried. Using the github installation, I receive a illegal instruction: illegal operand error I'm not really sure what to make sense of, regardless of which model I use. I'll attach the stdout and my working directory from that run if it helps, let me know what you think! stdout.txt https://github.com/BenoitMorel/GeneRax/files/13859796/stdout.txt generaxplay.tar.gz https://github.com/BenoitMorel/GeneRax/files/13859797/generaxplay.tar.gz

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[KyleTDavid]

Unfortunately it doesn't look like there was much of a change. Would it be any easier to somehow stick the Q.yeast substitution matrix I need into my conda installation? stdout.txt

[BenoitMorel]

Hi Kyle, I'm updating the conda package with the newest release. It might take a few days before it gets available Benoit

Le mar. 9 janv. 2024 à 22:10, Kyle David @.***> a écrit :

Unfortunately it doesn't look like there was much of a change. Would it be any easier to somehow stick the Q.yeast substitution matrix I need into my conda installation? stdout.txt https://github.com/BenoitMorel/GeneRax/files/13879066/stdout.txt

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[KyleTDavid]

That would be awesome, thank you!

[KyleTDavid]

Sorry I just saw that conda had been updated. While I am able to run 2.0.4 without issue (as long as I use the LG substitution matrix), when I run 2.1.3 on the same data I receive a Illegal Instruction error during the filter ing step. I'll attach my input files, any idea what might be going on? test.zip

[BenoitMorel]

Hi Kyle, I really don't know... It looks like things don't work for you in the recent versions of GeneRax (I think you got the same error when installing from github), but your test example works fine for me. You could try to skip the filtering step (--skip-family-filtering) since that's where it crashes, but I don't know if that will really fix anything. Are you using any special environment (virtual machine etc.)? Best, Benoit

Le mar. 30 janv. 2024 à 17:25, Kyle David @.***> a écrit :

Sorry I just saw that conda had been updated. While I am able to run 2.0.4 without issue (as long as I use the LG substitution matrix), when I run 2.1.3 on the same data I receive a Illegal Instruction error during the filter ing step. I'll attach my input files, any idea what might be going on? test.zip https://github.com/BenoitMorel/GeneRax/files/14101370/test.zip

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