error when executing

[Pinolinoo]

Hi, I have issues running the pigx-rnaseq -s command.

it tells me:

Traceback (most recent call last):
  File "/home/proth/.guix-profile/bin/pigx-rnaseq", line 486, in <module>
    generate_config(args.configfile,
  File "/home/proth/.guix-profile/bin/pigx-rnaseq", line 236, in generate_config
    update_config(settings,yaml.safe_load(open(settingsfile, 'r')))
  File "/gnu/store/8kha44h8bvx8y8a2aphl0mygwflmqa51-snakemake-5.32.2/lib/python3.9/site-packages/snakemake/utils.py", line 480, in update_config
    _update(config, overwrite_config)
  File "/gnu/store/8kha44h8bvx8y8a2aphl0mygwflmqa51-snakemake-5.32.2/lib/python3.9/site-packages/snakemake/utils.py", line 473, in _update
    for (key, value) in u.items():

best
philipp

[Bora Uyar]

Hi Philipp,
Looks like something is wrong with the content of the settings file.
Did you modify the content of the settings file that is generated with --init?

Can you please provide a settings.yaml file that we can use to test if we can reproduce the error?

[Pinolinoo]

Ok solved it, I didn't know I had to delete the # in the init settings files but found out after comparing to the test_data settings file! :)
Kinda stupid of me :D but thanks!

[Bora Uyar]

Okay great!
That is a common mistake, I guess we should improve our documentation :)