strainphlan

[valei]

Hi, I'm running strainphlan on my Centos7 system. I accurately followed the guide I found here. I got this error message "No alignments found to concatenate" and "An error was ocurred executing a external tool, exiting..." I wonder, what means the message? And, what is the external tool returning an error? Please, help me. Valentina

strainphlan -s consensus_markers/*.pkl -m db_markers/s__Lactobacillus_fermentum.fna -o output -n 4 -c s__Lactobacillus_fermentum --mutation_rates Wed Dec 1 12:37:55 2021: Start StrainPhlAn 3.0 execution Wed Dec 1 12:37:55 2021: Creating temporary directory... Wed Dec 1 12:37:55 2021: Done. Wed Dec 1 12:37:55 2021: Getting markers from main sample files... Wed Dec 1 12:37:55 2021: Done. Wed Dec 1 12:37:55 2021: Getting markers from main reference files... Wed Dec 1 12:37:55 2021: Done. Wed Dec 1 12:37:55 2021: Removing bad markers / samples... Wed Dec 1 12:37:55 2021: Done. Wed Dec 1 12:37:55 2021: Writing samples as markers' FASTA files... Wed Dec 1 12:37:56 2021: Done. Wed Dec 1 12:37:56 2021: Writing filtered clade markers as FASTA file... Wed Dec 1 12:37:56 2021: Done. Wed Dec 1 12:37:56 2021: Calculating polymorphic rates... Wed Dec 1 12:37:56 2021: Done. Wed Dec 1 12:37:56 2021: Executing PhyloPhlAn 3.0... Wed Dec 1 12:37:56 2021: Creating PhyloPhlAn 3.0 database... Wed Dec 1 12:37:56 2021: Done. Wed Dec 1 12:37:56 2021: Generating PhyloPhlAn 3.0 configuration file... Wed Dec 1 12:37:56 2021: Done. Wed Dec 1 12:37:56 2021: Processing samples...[e] "/usr/local/lib/python3.7/site-packages/phylophlan/phylophlan_configs/" folder does not exists

[e] No alignments found to concatenate

[e] An error was ocurred executing a external tool, exiting... Wed Dec 1 12:37:58 2021: Stop StrainPhlAn 3.0 execution.

[fbeghini]

Can you check if you have the latest version of phylophlan installed? You can create that folder and then run from there phylophlan_write_default_configs.sh