Supermatrix alignment has varying length -> error in tree build

Microbial community profiling PhyloPhlAn
1

I’m attempting to use PhyloPhlan to build a tree from some MAGs, but obtaining an error in tree building (with IQTREE):
ERROR: Sequence Ppolionotus_5F_Bin_77_1 contains not enough characters (4869)
ERROR: Sequence Ppolionotus_3F_Bin_38_2 contains not enough characters (4520)
ERROR: Sequence Ppolionotus_3F_Bin_53_4 contains not enough characters (5539)

The alignments indeed all seem to be of varied length.

I’m using version 3.0.58, and running the following configuration:

[db_aa]
program_name = /home/jgs286/miniconda3/envs/phylophlan/bin/diamond
params = makedb
threads = --threads
input = --in
output = --db
version = version
command_line = #program_name# #params# #threads# #input# #output#

[map_dna]
program_name = /home/jgs286/miniconda3/envs/phylophlan/bin/diamond
params = blastx --quiet --threads 1 --outfmt 6 --more-sensitive --id 50 --max-hsps 35 -k 0
input = --query
database = --db
output = --out
version = version
command_line = #program_name# #params# #input# #database# #output#

[map_aa]
program_name = /home/jgs286/miniconda3/envs/phylophlan/bin/diamond
params = blastp --quiet --threads 1 --outfmt 6 --more-sensitive --id 50 --max-hsps 35 -k 0
input = --query
database = --db
output = --out
version = version
command_line = #program_name# #params# #input# #database# #output#

[msa]
program_name = /home/jgs286/miniconda3/envs/phylophlan/bin/mafft
params = --quiet --anysymbol --thread 1 --auto
version = --version
command_line = #program_name# #params# #input# > #output#
environment = TMPDIR=/tmp

[trim]
program_name = /home/jgs286/miniconda3/envs/phylophlan/bin/trimal
params = -gappyout
input = -in
output = -out
version = --version
command_line = #program_name# #params# #input# #output#

[tree1]
program_name = /home/jgs286/miniconda3/envs/phylophlan/bin/iqtree
params = -quiet -nt AUTO -m LG
input = -s
output = -pre
version = -version
command_line = #program_name# #params# #input# #output#

Any clues? I have also uploaded the complete output to Dropbox and could send a link if helpful.

Thanks!!!

2

…updating, I’ve retried with the Amphora marker set and it seems to be working. Problem seems constrained to Phylophlan markers…

3

Hi @tanaes thank you for reporting this.
Can you provide me with the Dropbox link and the command line so that I can test it?

Many thanks,
Francesco