AlleleCall not detecting valid .fna input files (v2.8.5)

[EdDjonlagic2]

Hi,

I’m having trouble running chewBBACA.py AlleleCall (v2.8.5). I’ve tried providing a directory of valid .fna files as input using the -i flag, but I consistently get this error:

'Could not get input files. Please provide a directory with FASTA files or a file with the list of full paths to the FASTA files and ensure that filenames end with one of the following suffixes: ['.fasta', '.fna', '.ffn', '.fa'].'

All of the .fna files:
• Are standard multi-entry FASTA files (CDS predicted from Prokka)
• Are readable and non-empty
• Have correct extensions (.fna)
• Contain hundreds of CDS entries each

I also tried renaming them to .fasta, and using a text file (.txt) with full paths to the .fna files (one per line) and still the same result.

I noticed there were similar issues reported in earlier versions of chewBBACA but I haven’t seen anything specific to v2.8.5. Has something changed in how input files are validated?

Thanks in advance for your help!

—Ed

[rfm-targa]

Greetings @EdDjonlagic2,

If possible, I recommend upgrading to chewBBACA's latest version, v3.3.10. chewBBACA v2.8.5 is an outdated version with lower efficiency and accuracy. It also lacks features that help with data analysis.
The issue with chewBBACA v2.8.5 may be due to it not finding the schema files. The path to the schema must be the path to the directory containing the loci FASTA files (1 FASTA file per locus in the schema and a folder named 'short' containing 1 FASTA file with the representative alleles per locus); it cannot be a path to an upper directory.
Please let us know if this helped resolve the issue.

Cheers,

Rafael

[annanguyen32]

Hi, I've got the similar problem with version 3.3.10. I run AlleleCall with the command:
$ chewBBACA.py AlleleCall -i ~/Cgmlst/genomes/ -g ~/cgMLST_alleles/ --ptf ~/cgMLST_alleles/shema.ptf -o ~/results/ --cpu 8
Provided path does not include all the necessary schema files. Please verify that you have passed the correct path to the schema.

I have already check my ~/cgMLST_alleles/ that it only contains FASTA files and a .ptf file for running but the error was still occured. The schema data had downloaded from https://www.cgmlst.org/ and the .zip package had been already extracted before running.
Could you please help me?
Thanks in advance.

[rfm-targa]

Hey @annanguyen32,

In your case, chewBBACA is reporting that there is at least one file missing from the schema, not necessarily the FASTA files. Did you use the PrepExternalSchema module to adapt the schema downloaded from https://www.cgmlst.org/ before running the AlleleCall module? The schema may be missing the configuration files, such as the .schema_config or .genes_list files. If the schema includes a Prodigal training file you also do not need to pass --ptf ~/cgMLST_alleles/shema.ptf to the AlleleCall module.
Let us know if using the PrepExternalSchema solves the issue.

Cheers,

Rafael