[e] No alignments found to concatenate

[jwkkang]

Hello,

I have run my code as below.

phylophlan -i ./spades_output/final_contigs_test --genome_extension .fasta \
-d phylophlan --databases_folder ./phylophlan_databases \
--diversity low \
--fast \
--verbose \
-f ./phylophlan_configs/supermatrix_aa.cfg \
-o ./phylophlan_output/fasta_contigs_phylophlan_test_slurm

But I got an error message. [e] No alignments found to concatenate. Could you please let me know what is the issue here?

I have attached the log file.

Thank you,

slurm-894215.txt

[fasnicar]

Hello, from the log it seems you only provided 3 input files, while the minimum number for building a phylogenetic tree is 4. Hence all markers are discarded because only 3/4 genomes are found and hence there is nothing to concatenate.

Many thanks, Francesco