Failed to read parameters in config file

[JamesSCLiu]

Hello.

I created a virtual environment for princess and did the setup as described in the README file. Here is my command for princess: ./princess all -d /path/to/output/ -r ccs -e False -a ngmlr -s /path/to/sample.fastq.gz -f hg38.fa -c chr22.

I got this error:
Invalid config definition: Config entries have to be defined as name=value pairs.

None of the parameters specified was modified in the config.yaml inside /path/to/output/. I tried editing the config file manually but still got the same error. Did I miss any step?

Thank you!
James

[MeHelmy]

Thank you,

The issue is -e is a flag. So, we need to change the command to:

./princess all -d /path/to/output/ -r ccs -e -a ngmlr -s /path/to/sample.fastq.gz -f hg38.fa -c chr22

Best,
Medhat