IQ tree and FastTree issues

[NicolasLouw]

Dear David,

I am new to Phylogenomics and have to say that the Orthofinder program along with all the available online resources have been tremendously useful, so thank you for all of that. I am however currently experiencing some issues that is hindering my research progress and I would love to get your insight regarding these matters.

Previously, I used orthofinder on 8 of my study species to find single copy orthologous genes and gene trees. To do this, I used the default parameters and successfully got results back, which is great. However, now I want to generate a species tree using a maximum-likelihood based method like IQtree. But I first need to run a multiple sequence alignment on my species to do so. Since Orthofinder has worked well for me already, I opted to include some additional parameters. Initially, I tried running the script with blast, msa and iqtree. However, when I tried running this script:

#!/bin/sh #SBATCH -J clean_aminos_April_weer #SBATCH --time=00-12:20:00 #SBATCH -p batch #SBATCH -N 1 #SBATCH -n 2 #SBATCH -c 1 #SBATCH --mem=50g #SBATCH --output=MyJob.%j.%N.out #SBATCH --error=MyJob.%j.%N.err #SBATCH --mail-type=ALL #SBATCH [email protected]

module load python/ module load orthofinder/2.5.4 module load mafft/7.481 module load iq-tree/2.1.3 module load blast/2.8.1 orthofinder -f /cluster/tufts/uricchiolab/nlouw01/post_gensas/april/peptides -S blast -M msa -T iqtree -A mafft

I received the following errors: ERROR: Cannot run user-configured tree method 'iqtree' Please check program is installed and that it is correctly configured in the orthofinder/config.json file

Dependencies have been met for inference of orthogroups but not for the subsequent orthologue inference. Either install the required dependencies or use the option '-og' to stop the analysis after the inference of orthogroups.

ERROR: An error occurred, please review the error messages they may contain useful information about the problem.

Some digging led me to this resolved issue: https://github.com/davidemms/OrthoFinder/issues/152 from another user, who experienced a similar issue. As you mentioned in that thread and by looking at the version of IQtree that I'm including here (2.1.3), is the problem that I'm using the multicore version instead of the single core version? If so, which version is the single core version? Also, in that resolved issue, you recommended that the user: "by putting the serial version of iqtree in your path instead (an alternative solution would be to edit the config.json file to add '-nt 1' to the iqtree arguments)." Where does one acquire this serial version number and what would that syntax look like?

I would dearly appreciate your insight regarding these matters.

Thanks in advance! Kind regards Nicolas

[davidemms]

Hi Nicolas

I'm the output I think OrthoFinder should have also printed out the iqtree command it was trying to run. I'd suggest just trying to run that in exactly the same way as you're trying to run OrthoFinder and see what happens with iqtree. Also, was there anything else in the output other than what you've posted?

I'm also working on something to make the check clearer still to reproduce, should be ready in a week or so if you're still having problems then.

[NicolasLouw]

Hi David,

Many thanks for getting back to me regarding this issue. When I ran exactly the same script, I get this error:

OrthoFinder version 2.5.4 Copyright (C) 2014 David Emms

2022-04-12 10:58:55 : Starting OrthoFinder 2.5.4 40 thread(s) for highly parallel tasks (BLAST searches etc.) 5 thread(s) for OrthoFinder algorithm

Checking required programs are installed

Test can run "makeblastdb -help" - ok Test can run "blastp -help" - ok Test can run "mcl -h" - ok Test can run "mafft /cluster/tufts/uricchiolab/nlouw01/post_gensas/april/peptides/OrthoFinder/Results_Apr12/WorkingDirectory//_dependencies_check/SimpleTest.fa" - ok Test can run "iqtree" - failed

/bin/sh: iqtree: command not found

ERROR: Cannot run user-configured tree method 'iqtree' Please check program is installed and that it is correctly configured in the orthofinder/config.json file

Dependencies have been met for inference of orthogroups but not for the subsequent orthologue inference. Either install the required dependencies or use the option '-og' to stop the analysis after the inference of orthogroups.

ERROR: An error occurred, please review the error messages they may contain useful information about the problem.

It looks like orthofinder is checking whether all the dependencies are installed and working properly and for iqtree it says "failed". Do you think if I request that the computing cluster at my university downloads the earlier version of iqtree (IQ-TREE/1.6.12-foss-2019b, version 1.6.12) would solve the issue?

Again, many thanks for your response. Best, Nicolas

[Xoey0314]

Hi,

Have you solved your problem ? I also meet this problem. And i can't find and modify the file "config.json" in ~/miniconda3/envs/orthogene/bin/.

And when i installed orthofinder, it gave me mention such as:

For Linux 64, Open MPI is built with CUDA awareness but this support is disabled by default. To enable it, please set the environment variable OMPI_MCA_opal_cuda_support=true before launching your MPI processes. Equivalently, you can set the MCA parameter in the command line: mpiexec --mca opal_cuda_support 1 ...

In addition, the UCX support is also built but disabled by default. To enable it, first install UCX (conda install -c conda-forge ucx). Then, set the environment variables OMPI_MCA_pml="ucx" OMPI_MCA_osc="ucx" before launching your MPI processes. Equivalently, you can set the MCA parameters in the command line: mpiexec --mca pml ucx --mca osc ucx ... Note that you might also need to set UCX_MEMTYPE_CACHE=n for CUDA awareness via UCX. Please consult UCX's documentation for detail.

Good luck with everyone's problems, and looking forward to reply. Best, Xin