Issue while running teaser.py

[gupta-plantgenevo]

I am having issues like
self.config["cache_directory"] = os.path.abspath(self.config["cache_directory"])
KeyError: 'cache_directory'
and
abs_test_dirs = [os.path.abspath(dir) for dir in self.config["test_directories"]]
KeyError: 'test_directories'

I looked at the code and I don't understand how to resolve it. Any help will be much appreciated.

[fritzsedlazeck]

Hi,
can you forward the whole error msg plus your config file?
Thanks
Fritz

[gupta-plantgenevo]

Hi, The config file is attached and the error message is as follow: $ ./teaser.py trifida_test.yaml importing libraries... Loaded configuration /softwares/Teaser/setups/trifida_test.yaml [10:30:44] [Main ] Except, exception: Traceback (most recent call last): File "./teaser.py", line 950, in main self.initFromArgs() File "./teaser.py", line 710, in initFromArgs self.convertConfigPathsToAbs() File "./teaser.py", line 643, in convertConfigPathsToAbs self.config["cache_directory"] = os.path.abspath(self.config["cache_directory"]) KeyError: 'cache_directory' Traceback (most recent call last): File "./teaser.py", line 1091, in <module> mate.main() File "./teaser.py", line 1017, in main self.finalize() File "./teaser.py", line 1036, in finalize self.report.generate() AttributeError: 'bool' object has no attribute 'generate' I get the same error when I use the command as: "./teaser.py trifida_test.yaml -fc -fr -rn trifida_genome" Thanks! Sonal Gupta Graduate Student Ecology and Evolutionary Biology University of Michigan, Ann Arbor

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On Tue, Feb 20, 2018 at 10:22 AM, Fritz Sedlazeck ***@***.***> wrote: Hi, can you forward the whole error msg plus your config file? Thanks Fritz — You are receiving this because you authored the thread. Reply to this email directly, view it on GitHub <#12 (comment)>, or mute the thread <https://github.com/notifications/unsubscribe-auth/Ai9JTuSQAeKzZrjkI-MEIaHvYQtAKBrUks5tWuMagaJpZM4SLYOL> .

[smolkmo]

Hi Sonal,

first of all, thanks for your report and sorry for the delayed response!

Please make sure that your config file correctly imports the base configuration, by verifying that your config file starts with the following lines:

include:
  - base_teaser

Examples for some working configuration files can also be found in our wiki: https://github.com/Cibiv/Teaser/wiki/Command-Line-Configuration

If the problem persists, please attach the exact contents of your trifida_test.yaml file - so we can have a closer look.

Moritz