Hi! I’m using phylophlan version3.1.68 to construct a phylogenic tree from 68 MAGs files, but I got an error message: [e] No alignments found to concatenate
I use this command to set the configuration file:
phylophlan_write_config_file -d a -o 02_tol.cfg --db_aa diamond --map_dna diamond --map_aa diamond --msa mafft --trim trimal --tree1 iqtree --verbose 2>&1 | tee phylophlan_write_config_file.log
And I use this command to run phylophlan:
phylophlan -i test/ --genome_extension .fa -d phylophlan-database/phylophlan/ -f 02_tol.cfg --diversity high --fast -o test_0827 --nproc 50 --verbose 2>&1 | tee phylophlan_0827.log
The log is:
phylophlan_0827.log.txt (192.3 KB)
I wonder if there is anything wrong with my command? Cause I have read those who got the same error as this one, all of them got the error due to lack of construction files, and this is not the same situation. By the way, I have use 58 of these 68 MAGs to construct another tree, and found that in the previous tree files there lost the 58 MAGs, so I want to reconstruct with the 58 lost one and 10 pass MAGs files to test if there is anything wrong with the 58 MAGs files.
Thanks and looking forward to your reply!
Sushi