[BUG] A YAML file argument cannot be used in combination with either the -s/--organism or -g/--genome arguments. The -s/--organism and the -g/--genome arguments replace the YAML file argument input.

[yulinpengcool]

The bug is: pgap.py: error: Invalid Command Line Argument Error: A YAML file argument cannot be used in combination with either the -s/--organism or -g/--genome arguments. The -s/--organism and the -g/--genome arguments replace the YAML file argument input.

Here is the command* I am running the python C:\Users\yulinpeng\miniconda3\envs\pgap_env\pgap\scripts\pgap.py -n -o D:\nda\new -g C:\Users\da\GCF.fasta -s 'Azotobacter vinelandii'

Expected behavior Results outputted to D:\bioconda\new subdirectory

Software versions (please complete the following information):

• OS: Windows 11
• pgap.py downloaded from https://github.com/ncbi/pgap.
• Docker (Docker Desktop, version 4.33.1]

Error I receive the error: error: Invalid Command Line Argument Error: A YAML file argument cannot be used in combination with either the -s/--organism or -g/--genome arguments. The -s/--organism and the -g/--genome arguments replace the YAML file argument input.

Log Files no log files are produced

[azat-badretdin]

Thank you for your report, user @yulinpengcool !

What did you see on your screen when you typed this command?

[yulinpengcool]

output: error: Invalid Command Line Argument Error: A YAML file argument cannot be used in combination with either the -s/--organism or -g/--genome arguments. The -s/--organism and the -g/--genome arguments replace the YAML file argument input.

[azat-badretdin]

Thank you! We will have a look at this in due order.

[yulinpengcool]

Thank you and Will

[george-coulouris]

@yulinpengcool, instead of apostrophes, please use quotation marks around the organism name:

pgap.py -n -o D:\nda\new -g C:\Users\da\GCF.fasta -s "Azotobacter vinelandii"