No inputs found error

Microbial community profiling PhyloPhlAn
1

PhyloPhlAn version 3.0.67 (24 August 2022)

Got this error:
[e] no inputs found, please check your params and inputs file extensions

Code:
phylophlan
-i input_isolates
-o output_isolates
-d s__Escherichia_coli
-f isolates_config.cfg
–diversity low

input_isolates is a directory with scaffolds.fasta files

Output:
[w] “/home/x/.conda/envs/phylophlan/lib/python3.10/site-packages/phylophlan/phylophlan_configs/” folder does not exists
Loading files from “/x/input_isolates”
Loading files from “/x/input_isolates”
Inputs already checked
[e] no inputs found, please check your params and inputs file extensions

2

Hi @kyannao, thanks for using PhyloPhlAn and reporting this and apologies for the late reply.

Your problem is that your input files ends with .fasta and PhyloPhlAn by default uses .fna. for representing genomes and .faafor representing proteomes. You can use the–genome_extensionparameter to set the input extension to.fasta`.

Many thanks,
Francesco