No such file or directory errors

[marshomics]

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]

Hey Jim,

Thanks for opening the issue.

I haven't put as much care into this tool as it deserves. Looks like there is some faulty logic in cases when no preliminary hits are found. It should exit, but it doesn't. So, I imagine there are no hits in your .faa files that return this error.

I just uploaded a small test file to: https://github.com/mtisza1/DNA_methylase_finder/blob/main/test_seqs/mtases_GCA_016889925.1.faa

Can you confirm that the tool runs on the test data and generates the expected *DNA_methylases.combined.summary.tsv and *DNA_methylases.final_prediction.faa

[c-ruprecht]

Hi,
I am having the same issue. I ran the test and get the following output
`ruprec01@constantins-mbp Documents % python /Users/ruprec01/Documents/Apps/DNA_methylase_finder/run_DNA_methylase_finder.py
-it AA -f /Users/ruprec01/Documents/Apps/DNA_methylase_finder/test_seqs/mtases_GCA_016889925.1.faa -r TEST_AAs

/Users/ruprec01/Documents/Apps/DNA_methylase_finder
/Users/ruprec01/Documents/Apps/DNA_methylase_finder/run_DNA_methylase_finder.py:56: DeprecationWarning: Use shutil.which instead of find_executable
return find_executable(name) is not None
bioawk found
hmmscan found
blastp found
prodigal found
Biopython found
BCBio found
numpy found
DNA Methylase Finder!
Version 1.0.1
A seemingly good .faa file found. Continuing
Step 1. Splitting AA file for parallelization -- 09-30-24---11:55:40
Step 2. Querying input AA seqs against DNA methylase HMMs -- 09-30-24---11:55:40
found some preimlinary hits
/Users/ruprec01/Documents/Apps/DNA_methylase_finder/DNA_methylase_finder_v1.0.sh: line 109: SPLIT_INPUT_AA_0.hmmscan.out:mjt_mtase_bacteroides_model5a - 315 QRP88808.1__ - 1562 3.7e-213 698.6 3.9 1 1 9.4e-214 5.8e-213 698.0 3.9 1 315 667 981 667 981 1.00 --SPLIT_INPUT_AA_0.hmmscan.out:mjt_mtase_bacteroides_model5a - 315 QRP88808.1__ - 1562 3.7e-213 698.6 3.9 1 1 9.4e-214 5.8e-213 698.0 3.9 1 315 667 981 667 981 1.00 - : syntax error: invalid arithmetic operator (error token is ".hmmscan.out:mjt_mtase_bacteroides_model5a - 315 QRP88808.1__ - 1562 3.7e-213 698.6 3.9 1 1 9.4e-214 5.8e-213 698.0 3.9 1 315 667 981 667 981 1.00 --SPLIT_INPUT_AA_0.hmmscan.out:mjt_mtase_bacteroides_model5a - 315 QRP88808.1__ - 1562 3.7e-213 698.6 3.9 1 1 9.4e-214 5.8e-213 698.0 3.9 1 315 667 981 667 981 1.00 - ")
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 -- 09-30-24---11:55:41
You chose AA input, so fragments will not be joined
cp: mtases_GCA_016889925.1.DNA_methylases.final_prediction.faa: No such file or directory
Step 5. Guessing (low confidence) motif specificity and subtype of putative methylases -- 09-30-24---11:55:41
Combined Predicted Methylase .faa file not found.
Step 6. Making summary table -- 09-30-24---11:55:41
not all files required for summary table found.
Step 7. Annotating DNA methylase gene neighborhoods -- 09-30-24---11:55:41
input type was not nucleotide sequence, so neighborhoods were not determined

Done with all tasks

See output at: TEST_AAs
End time -- 09-30-24---11:55:41`