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I've run into the error when using the -c option (to avoid running the setup script):
$ phigaro -c config.yml -f $FNA -o out/${SLURM_ARRAY_TASK_ID} --not-open -t 4 -e tsv Traceback (most recent call last): File "/global/home/users/snayfach/.conda/envs/phigaro_env/bin/phigaro", line 8, in <module> sys.exit(main()) File "/global/home/users/snayfach/.conda/envs/phigaro_env/lib/python3.7/site-packages/phigaro/cli/batch.py", line 206, in main hmmer_task=hmmer_task, File "/global/home/users/snayfach/.conda/envs/phigaro_env/lib/python3.7/site-packages/phigaro/cli/batch.py", line 35, in create_task task = task_class(*args, **kwargs) File "/global/home/users/snayfach/.conda/envs/phigaro_env/lib/python3.7/site-packages/phigaro/batch/task/run_phigaro.py", line 35, in __init__ super().__init__() File "/global/home/users/snayfach/.conda/envs/phigaro_env/lib/python3.7/site-packages/phigaro/batch/task/base.py", line 25, in __init__ self._prepare() File "/global/home/users/snayfach/.conda/envs/phigaro_env/lib/python3.7/site-packages/phigaro/batch/task/run_phigaro.py", line 44, in _prepare 'threshold_min_%s' % self.mode KeyError: 'threshold_min_basic'
My config file looks like:
hmmer: bin: /global/home/users/snayfach/.conda/envs/phigaro_env/bin/hmmsearch e_value_threshold: 0.00445 pvog_path: /global/scratch/snayfach/projects/checkv/4_imgvr_dtrs/2_run_tools/phigaro/phigaro-db/allpvoghmms phigaro: penalty_black: 2.2 penalty_white: 0.7 threshold_max: 46.0 threshold_min: 45.39 window_len: 32 prodigal: bin: /global/home/users/snayfach/.conda/envs/phigaro_env/bin/prodigal
Is there an easy fix to this?
The text was updated successfully, but these errors were encountered:
Hello, this problem will be solved if you use the given file: https://github.com/bobeobibo/phigaro/blob/master/config.yml
I am sorry, I forgot to update this part of READ.me while updating Phigaro up to 2.x.x version, I correct it now.
And thank you for the interest in our tool!)
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I've run into the error when using the -c option (to avoid running the setup script):
My config file looks like:
Is there an easy fix to this?
The text was updated successfully, but these errors were encountered: