[e] mapping file (--maas) not specified

[IRSINGH27]

[db_aa]
program_name = diamond
params = makedb
threads = --threads
input = --in
output = --db
version = version
command_line = #program_name# #params# #threads# #input# #output#

[map_dna]
program_name = diamond
params = blastx --quiet --threads 1 --outfmt 6 --more-sensitive --id 50 --max-hsps 35 -k 0 --query-gencode 11
input = --query
database = --db
output = --out
version = version
command_line = #program_name# #params# #input# #database# #output#

[map_aa]
program_name = 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 = muscle
params = -amino -refineiters 2
input = -super5
output = -output
version = -version
command_line = #program_name# #params# #input# #output#

[trim]
program_name = trimal
params = -gappyout
input = -in
output = -out
version = --version
command_line = #program_name# #params# #input# #output#

[gene_tree1]
program_name = iqtree
params =  -m LG
input = -s
output = -pre
version = -version
command_line = #program_name# #params# #input# #output#

[tree1]
program_name = java -jar astral-4.11.1/astral.4.11.1.jar
input = -i
output = -o
version = -i astral-4.11.1/test_data/song_mammals.424.gene.tre
command_line = #program_name# #input# #output#

This is my cfg file i have used the phylophlan_write_config_file to write this file and edited the msa params as muscle was showing errors,

But now its stopping at the error of mapping files not specified

[fasnicar]

Hi there! For the substitution models, you can have a look at this section in the wiki: https://github.com/biobakery/phylophlan/wiki#substitution-models The error about the --maas param is that PhyloPhlAn won't estimate the best substitution models for all genes but expect a mapping file that provides that info instead. The models in the phylophlan_substitution_models/phylophlan.tsv file are of the proteins in the phylophlan database. So, if you're using a different database, you should create a specific mapping file.

Let me know if something is not clear.

Many thanks, Francesco

[IRSINGH27]

thanks now it's working