Bonjour @team.software ,
serait il possible d'installer panaroo sur le core cluster ?
merci beaucoup par avance !
Chloé
Pas de soucis.
Installation en cours :
Je ne vais peut-être pas être disponible dans les heures à venir pour donner le GO.
Dès que c'est vert ici, ça sera tout bon :
Cordialement
vert !
merci
@gildaslecorguille
j'ai fait un test avec panaroo et voici mon erreur.
Ce que je ne comprends pas c'est que mes annotations proviennent de prokka, des .gff et ils marchent très bien avec iqtree ou d'autres outils ...
est ce de mon côté que ça plante ou du côté de l'outil ?
Merci beaucoup Chloé
File "/shared/ifbstor1/software/miniconda/envs/panaroo-1.2.10/lib/python3.9/site-packages/joblib/_parallel_backends.py", line 595, in __call__
return self.func(*args, **kwargs)
File "/shared/ifbstor1/software/miniconda/envs/panaroo-1.2.10/lib/python3.9/site-packages/joblib/parallel.py", line 262, in __call__
return [func(*args, **kwargs)
File "/shared/ifbstor1/software/miniconda/envs/panaroo-1.2.10/lib/python3.9/site-packages/joblib/parallel.py", line 262, in <listcomp>
return [func(*args, **kwargs)
File "/shared/ifbstor1/software/miniconda/envs/panaroo-1.2.10/lib/python3.9/site-packages/panaroo/prokka.py", line 175, in get_gene_sequences
return sequence_dictionary, translate_sequences(sequence_dictionary, table)
File "/shared/ifbstor1/software/miniconda/envs/panaroo-1.2.10/lib/python3.9/site-packages/panaroo/prokka.py", line 192, in translate_sequences
raise ValueError("Premature stop codon in a gene!")
ValueError: Premature stop codon in a gene!
"""
The above exception was the direct cause of the following exception:
Traceback (most recent call last):
File "/shared/ifbstor1/software/miniconda/envs/panaroo-1.2.10/lib/python3.9/site-packages/panaroo/prokka.py", line 245, in process_prokka_input
gene_sequence_list = Parallel(n_jobs=n_cpu)(
File "/shared/ifbstor1/software/miniconda/envs/panaroo-1.2.10/lib/python3.9/site-packages/joblib/parallel.py", line 1056, in __call__
self.retrieve()
File "/shared/ifbstor1/software/miniconda/envs/panaroo-1.2.10/lib/python3.9/site-packages/joblib/parallel.py", line 935, in retrieve
self._output.extend(job.get(timeout=self.timeout))
File "/shared/ifbstor1/software/miniconda/envs/panaroo-1.2.10/lib/python3.9/site-packages/joblib/_parallel_backends.py", line 542, in wrap_future_result
return future.result(timeout=timeout)
File "/shared/ifbstor1/software/miniconda/envs/panaroo-1.2.10/lib/python3.9/concurrent/futures/_base.py", line 439, in result
return self.__get_result()
File "/shared/ifbstor1/software/miniconda/envs/panaroo-1.2.10/lib/python3.9/concurrent/futures/_base.py", line 391, in __get_result
raise self._exception
ValueError: Premature stop codon in a gene!
During handling of the above exception, another exception occurred:
Traceback (most recent call last):
File "/shared/ifbstor1/software/miniconda/envs/panaroo-1.2.10/bin/panaroo", line 10, in <module>
sys.exit(main())
File "/shared/ifbstor1/software/miniconda/envs/panaroo-1.2.10/lib/python3.9/site-packages/panaroo/__main__.py", line 286, in main
process_prokka_input(args.input_files, args.output_dir,
File "/shared/ifbstor1/software/miniconda/envs/panaroo-1.2.10/lib/python3.9/site-packages/panaroo/prokka.py", line 257, in process_prokka_input
raise RuntimeError("Error reading prokka input!")
RuntimeError: Error reading prokka input!
A priori, cela ne semble pas lié à l'installation.
Je ne suis pas utilisateur de panaroo. As-tu regardé dans les issues déjà résolu sur leur GitHub:
Issues · gtonkinhill/panaroo · GitHub ?