Assistance Needed: Unexpected Error and Output Truncation During geNomad Tool Execution about genomad

[apcamargo]

Hi @david1ibarra

Can you try to run this before executing geNomad?

PYTHONIOENCODING="utf-8"
LANG="en_US.UTF-8"

Also, what do you mean by truncated output? Can you provide an example?

[david1ibarra]

I tried running what you provided before executing geNomad but it did not work. By truncated output I refer to something like this:
Traceback (most recent call last):
File "", line 198, in _run_module_as_main
...
UnicodeEncodeError: 'charmap' codec can't encode characters in position 423-624: character maps to
*** You may need to add PYTHONIOENCODING=utf-8 to your environment ***

[apcamargo]

If you rename the input to remove spaces and parenthesis, does it work?

[david1ibarra]

I tried this:

import subprocess

Specify the correct paths

input_file_path = "C:\Users\DavidIbarra\OneDrive - Cemvita Factory Inc\Desktop\E. coli K12 MG1655 (NC_000913).fasta.gz"
output_directory = "genomad_output"
database_path = "C:\Users\DavidIbarra\Downloads\genomad_db_v1.2.tar.gz"

Remove spaces and parentheses from the input file name

input_file_name = os.path.basename(input_file_path)
input_file_name_without_spaces_parentheses = input_file_name.replace(" ", "_").replace("(", "").replace(")", "")

Construct the new input file path with the modified filename

new_input_file_path = os.path.join(os.path.dirname(input_file_path), input_file_name_without_spaces_parentheses)

Rename the input file

os.rename(input_file_path, new_input_file_path)

Create the output directory if it doesn't exist

if not os.path.exists(output_directory):
... os.makedirs(output_directory)
...

Construct the command with the updated input file path

command = f'set PYTHONIOENCODING=utf-8 && genomad end-to-end --cleanup --splits 8 "{new_input_file_path}" {output_directory} {database_path}'

Run the command in the shell

subprocess.run(command, shell=True)
╭──────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────╮
│ Executing geNomad annotate (v1.7.0). This will perform gene calling in the input sequences and annotate the predicted │
│ proteins with geNomad's markers. │
│ ────────────────────────────────────────────────────────────────────────────────────────────────────────────────────── │
│ Outputs: │
│ genomad_output\E._coli_K12_MG1655_NC_000913_annotate │
│ ├── E._coli_K12_MG1655_NC_000913_annotate.json (execution parameters) │
│ ├── E._coli_K12_MG1655_NC_000913_genes.tsv (gene annotation data) │
│ ├── E._coli_K12_MG1655_NC_000913_taxonomy.tsv (taxonomic assignment) │
│ ├── E._coli_K12_MG1655_NC_000913_mmseqs2.tsv (MMseqs2 output file) │
│ └── E._coli_K12_MG1655_NC_000913_proteins.faa (protein FASTA file) │
╰──────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────╯
Traceback (most recent call last):
File "", line 198, in _run_module_as_main
File "", line 88, in run_code
File "C:\Users\DavidIbarra\AppData\Local\Programs\Python\Python311\Scripts\genomad.exe_main.py", line 7, in
File "C:\Users\DavidIbarra\AppData\Local\Programs\Python\Python311\Lib\site-packages\click\core.py", line 1157, in call
return self.main(*args, **kwargs)
^^^^^^^^^^^^^^^^^^^^^^^^^^
File "C:\Users\DavidIbarra\AppData\Local\Programs\Python\Python311\Lib\site-packages\rich_click\rich_group.py", line 21, in main
rv = super().main(*args, standalone_mode=False, **kwargs)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "C:\Users\DavidIbarra\AppData\Local\Programs\Python\Python311\Lib\site-packages\click\core.py", line 1078, in main
rv = self.invoke(ctx)
^^^^^^^^^^^^^^^^
File "C:\Users\DavidIbarra\AppData\Local\Programs\Python\Python311\Lib\site-packages\click\core.py", line 1688, in invoke
return _process_result(sub_ctx.command.invoke(sub_ctx))
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "C:\Users\DavidIbarra\AppData\Local\Programs\Python\Python311\Lib\site-packages\click\core.py", line 1434, in invoke
return ctx.invoke(self.callback, **ctx.params)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "C:\Users\DavidIbarra\AppData\Local\Programs\Python\Python311\Lib\site-packages\click\core.py", line 783, in invoke
return __callback(*args, **kwargs)
^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "C:\Users\DavidIbarra\AppData\Local\Programs\Python\Python311\Lib\site-packages\click\decorators.py", line 33, in new_func
return f(get_current_context(), *args, **kwargs)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "C:\Users\DavidIbarra\AppData\Local\Programs\Python\Python311\Lib\site-packages\genomad\cli.py", line 1240, in end_to_end
ctx.invoke(
File "C:\Users\DavidIbarra\AppData\Local\Programs\Python\Python311\Lib\site-packages\click\core.py", line 783, in invoke
return __callback(*args, **kwargs)
^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "C:\Users\DavidIbarra\AppData\Local\Programs\Python\Python311\Lib\site-packages\genomad\cli.py", line 441, in annotate
genomad.annotate.main(
File "C:\Users\DavidIbarra\AppData\Local\Programs\Python\Python311\Lib\site-packages\genomad\modules\annotate.py", line 82, in main
utils.display_header(
File "C:\Users\DavidIbarra\AppData\Local\Programs\Python\Python311\Lib\site-packages\genomad\utils.py", line 286, in display_header
console.print(
File "C:\Users\DavidIbarra\AppData\Local\Programs\Python\Python311\Lib\site-packages\genomad\utils.py", line 96, in print
self.write_print(*args, **kwargs)
File "C:\Users\DavidIbarra\AppData\Local\Programs\Python\Python311\Lib\site-packages\genomad\utils.py", line 80, in write_print
self.writer_console.print(*args, **kwargs)
File "C:\Users\DavidIbarra\AppData\Local\Programs\Python\Python311\Lib\site-packages\rich\console.py", line 1673, in print
with self:
File "C:\Users\DavidIbarra\AppData\Local\Programs\Python\Python311\Lib\site-packages\rich\console.py", line 865, in exit
self._exit_buffer()
File "C:\Users\DavidIbarra\AppData\Local\Programs\Python\Python311\Lib\site-packages\rich\console.py", line 823, in _exit_buffer
self._check_buffer()
File "C:\Users\DavidIbarra\AppData\Local\Programs\Python\Python311\Lib\site-packages\rich\console.py", line 2039, in _check_buffer
write(text)
File "C:\Users\DavidIbarra\AppData\Local\Programs\Python\Python311\Lib\encodings\cp1252.py", line 19, in encode
return codecs.charmap_encode(input,self.errors,encoding_table)[0]
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
UnicodeEncodeError: 'charmap' codec can't encode characters in position 381-498: character maps to
*** You may need to add PYTHONIOENCODING=utf-8 to your environment ***
CompletedProcess(args='set PYTHONIOENCODING=utf-8 && genomad end-to-end --cleanup --splits 8 "C:\Users\DavidIbarra\OneDrive - Cemvita Factory Inc\Desktop\E._coli_K12_MG1655_NC_000913.fasta.gz" genomad_output C:\Users\DavidIbarra\Downloads\genomad_db_v1.2.tar.gz', returncode=1)