No such file or directory errors

Hi, thanks for this.

I'm running this on a bunch of *.faa files using this command:

for input_file in "$input_directory"/*.faa; do
    if [[ -f "$input_file" ]]; then
        filename=$(basename "$input_file")
        run_title="${filename%.faa}"

        python "$script_path" \
            --input_type AA \
            --input_file "$input_file" \
            --run_title "$run_title" \
            --cpu 20 \
            --neighborhoods FALSE \
            --merge FALSE

        echo "Processed '$input_file' with run title '$run_title'"
    fi
done

But I can't seem to get it to work. I followed the installation instructions and everything seemed to be fine. Here's the log:

DNA Methylase Finder!
Version 1.0.1
A seemingly good .faa file found. Continuing
Step 1. Splitting AA file for parallelization -- 05-28-24---07:48:18
Step 2. Querying input AA seqs against DNA methylase HMMs -- 05-28-24---07:48:18
cat: 'SPLIT_INPUT_AA_*.hmmscan.out': No such file or directory
found some preimlinary hits
Preliminary_DNA_methylase_calls1.trimmed_to_hit.faa not found
Done finding DNA methylases.
Step 4. Looking for adjacent DNA methylase gene fragments to combine into 1 gene -- 05-28-24---07:48:18
You chose AA input, so fragments will not be joined
cp: cannot stat '1002319__maxbin2__High.005.DNA_methylases.final_prediction.faa': No such file or directory
Step 5.  Guessing (low confidence) motif specificity and subtype of putative methylases -- 05-28-24---07:48:18
Combined Predicted Methylase .faa file not found.
Step 6.  Making summary table -- 05-28-24---07:48:18
not all files required for summary table found.
##### Done with all tasks #####
See output at: 1002319__maxbin2__High.005
End time -- 05-28-24---07:48:18
/software/DNA_methylase_finder
bioawk found
hmmscan found
blastp found
prodigal found
Biopython found
BCBio found
numpy found
Processed '/prodigal_aa_newheader_noduplicates/1002319__maxbin2__High.005.faa' with run title '1002319__maxbin2__High.005'

Thanks for your help.

mtisza1 / DNA_methylase_finder

No such file or directory errors #1