Test can run "iqtree" - failed

[WJT0925]

I can use iqtree directly with typing "iqtree", and:

$iqtree IQ-TREE multicore version 2.1.4-beta COVID-edition for Linux 64-bit built Jun 24 2021 Developed by Bui Quang Minh, James Barbetti, Nguyen Lam Tung, Olga Chernomor, Heiko Schmidt, Dominik Schrempf, Michael Woodhams.

Command-line examples (replace 'iqtree2 ...' by actual path to executable):

1. Infer maximum-likelihood tree from a sequence alignment (example.phy) with the best-fit model automatically selected by ModelFinder: iqtree2 -s example.phy

2. Perform ModelFinder without subsequent tree inference: iqtree2 -s example.phy -m MF (use '-m TEST' to resemble jModelTest/ProtTest)

3. Combine ModelFinder, tree search, ultrafast bootstrap and SH-aLRT test: iqtree2 -s example.phy --alrt 1000 -B 1000

4. Perform edge-linked proportional partition model (example.nex): iqtree2 -s example.phy -p example.nex (replace '-p' by '-Q' for edge-unlinked model)

5. Find best partition scheme by possibly merging partitions: iqtree2 -s example.phy -p example.nex -m MF+MERGE (use '-m TESTMERGEONLY' to resemble PartitionFinder)

6. Find best partition scheme followed by tree inference and bootstrap: iqtree2 -s example.phy -p example.nex -m MFP+MERGE -B 1000

7. Use 4 CPU cores to speed up computation: add '-T 4' option

8. Polymorphism-aware model with HKY nucleotide model and Gamma rate: iqtree2 -s counts_file.cf -m HKY+P+G

9. PoMo mixture with virtual popsize 5 and weighted binomial sampling: iqtree2 -s counts_file.cf -m "MIX{HKY+P{EMP},JC+P}+N5+WB"

To show all available options: run 'iqtree2 -h'

Have a look at the tutorial and manual for more information: http://www.iqtree.org

./orthofinder -M msa -T iqtree -f ExampleData/

This is log context： OrthoFinder version 2.5.4 Copyright (C) 2014 David Emms

2023-02-08 12:53:59 : Starting OrthoFinder 2.5.4 80 thread(s) for highly parallel tasks (BLAST searches etc.) 10 thread(s) for OrthoFinder algorithm

Checking required programs are installed

Test can run "mcl -h" - ok Test can run "mafft /home/jingtian/MY/software/OrthoFinder/ExampleData/OrthoFinder/Results_Feb08_2/WorkingDirectory//_dependencies_check/SimpleTest.fa" - ok Test can run "iqtree" - failed

Checkpoint (/tmp/test.ckp.gz) indicates that a previous run successfully finished Use -redo option if you really want to redo the analysis and overwrite all output files. Use --redo-tree option if you want to restore ModelFinder and only redo tree search. Use --undo option if you want to continue previous run when changing/adding options.

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.###

[WJT0925]

I also change de config.json like this: "iqtree":{ "program_type": "tree", "cmd_line": "/home/jingtian/miniconda3/envs/py3/bin/iqtree -s INPUT -pre PATH/IDENTIFIER > /dev/null", "ouput_filename": "PATH/IDENTIFIER.treefile" },

[WJT0925]

I found that test fasta have only two sequence, but: /home/jingtian/miniconda3/envs/py3/bin/iqtree -s /home/jingtian/MY/software/OrthoFinder/ExampleData/OrthoFinder/Results_test/WorkingDirectory//_dependencies_check/SimpleTest.fa IQ-TREE multicore version 2.1.4-beta COVID-edition for Linux 64-bit built Jun 24 2021 Developed by Bui Quang Minh, James Barbetti, Nguyen Lam Tung, Olga Chernomor, Heiko Schmidt, Dominik Schrempf, Michael Woodhams.

Host: MEG (SSE4.2, 440 GB RAM) Command: /home/jingtian/miniconda3/envs/py3/bin/iqtree -s /home/jingtian/MY/software/OrthoFinder/ExampleData/OrthoFinder/Results_test/WorkingDirectory//_dependencies_check/SimpleTest.fa Seed: 734355 (Using SPRNG - Scalable Parallel Random Number Generator) Time: Wed Feb 8 13:15:47 2023 Kernel: SSE2 - 1 threads (80 CPU cores detected)

HINT: Use -nt option to specify number of threads because your CPU has 80 cores! HINT: -nt AUTO will automatically determine the best number of threads to use.

Reading alignment file /home/jingtian/MY/software/OrthoFinder/ExampleData/OrthoFinder/Results_test/WorkingDirectory//_dependencies_check/SimpleTest.fa ... Fasta format detected Alignment most likely contains DNA/RNA sequences ERROR: Alignment must have at least 3 sequences

[WJT0925]

That is right,I also found the log from: SimpleTest.fa.log in WorkingDirectory/_dependencies_check

$cat SimpleTest.fa.log IQ-TREE multicore version 1.6.12 for Linux 64-bit built Aug 15 2019 Developed by Bui Quang Minh, Nguyen Lam Tung, Olga Chernomor, Heiko Schmidt, Dominik Schrempf, Michael Woodhams.

Host: MEG (SSE4.2, 440 GB RAM) Command: /home/jingtian/MY/software/iqtree-1.6.12-Linux/bin/iqtree -s /home/jingtian/MY/software/OrthoFinder/ExampleData/OrthoFinder/Results_test/WorkingDirectory//_dependencies_check/SimpleTest.fa Seed: 548967 (Using SPRNG - Scalable Parallel Random Number Generator) Time: Wed Feb 8 13:23:34 2023 Kernel: SSE2 - 1 threads (80 CPU cores detected)

HINT: Use -nt option to specify number of threads because your CPU has 80 cores! HINT: -nt AUTO will automatically determine the best number of threads to use.

Reading alignment file /home/jingtian/MY/software/OrthoFinder/ExampleData/OrthoFinder/Results_test/WorkingDirectory//_dependencies_check/SimpleTest.fa ... Fasta format detected Alignment most likely contains DNA/RNA sequences ERROR: Alignment must have at least 3 sequences

[WJT0925]

How can I fix this error, or jump this check, or edit the SimpleTest.fa to three sequences?