ExoGFF_threads.py script missing from ./src directory

[bheimbu]

Dear @cpouchon,

I'm trying to extract mitochondrial contigs using ORTHOSKIM (command ./orthoskim -m capture -t mitochondrion_CDS -c config_orthoskim.txt), however there is no python script called ExoGFF_threads.py in the ./src directory? Did you forget to include it?

Cheers Bastian

[cpouchon]

Dear Bastian,

ExoGFF_threads.py was an old function, I have modified the orthoskim executable, please to try with this new version of orthoskim (you just need to download the executable).

Let me know if it works

Cheers,

Charles

[bheimbu]

Now I get following error:

The above exception was the direct cause of the following exception:

Traceback (most recent call last):
  File "/home/uni08/bheimbu/bin/ORTHOSKIM/./src/ExoGFF_homolog.py", line 1621, in <module>
    x=Parallel(n_jobs=num_cores)(delayed(GeneExtraction)(i) for i in inputs)
  File "/usr/users/bheimbu/.conda/envs/orthoskim/lib/python3.9/site-packages/joblib/parallel.py", line 1054, in __call__
    self.retrieve()
  File "/usr/users/bheimbu/.conda/envs/orthoskim/lib/python3.9/site-packages/joblib/parallel.py", line 933, in retrieve
    self._output.extend(job.get(timeout=self.timeout))
  File "/usr/users/bheimbu/.conda/envs/orthoskim/lib/python3.9/site-packages/joblib/_parallel_backends.py", line 542, in wrap_future_result
    return future.result(timeout=timeout)
  File "/usr/users/bheimbu/.conda/envs/orthoskim/lib/python3.9/concurrent/futures/_base.py", line 445, in result
    return self.__get_result()
  File "/usr/users/bheimbu/.conda/envs/orthoskim/lib/python3.9/concurrent/futures/_base.py", line 390, in __get_result
    raise self._exception
KeyError: 'NODE_7684_length_9642_cov_6.475250'

Cheers Bastian

[bheimbu]

My fault,

had to change genetic code to 5 instead of 1.

Cheers Bastian

ps: I'm closing this issue.