Bonjour,
Désolée de vous déranger.
Je voudrais demander s'il serait possible de update SPAdes à version 3.15.4 ou 3.15.5 (le plus récent) et python 3.10 sur le serveur, s'il vous plait.
Je suis en train de développer un pipeline en utilisant le SPAdes, mais il y a des bug quand je le teste sur le serveur :
Command error:
--metaviral
Command line: /shared/ifbstor1/software/miniconda/envs/spades-3.15.2/bin/spades.py --metaviral -m 64 --threads 32 --pe1-1 D589_S1_L001_R1_001.host_removed.unmapped_1.fastq.gz --pe1-2 D589_S1_L001_R1_001.host_removed.unmapped_2.fastq.gz -k 35 -o spades
System information:
SPAdes version: 3.15.2
Python version: 3.10.9
OS: Linux-3.10.0-1160.6.1.el7.x86_64-x86_64-with-glibc2.17
Output dir: spades
Mode: read error correction and assembling
Debug mode is turned OFF
Dataset parameters:
Metagenomic mode
Reads:
Traceback (most recent call last):
File "/shared/ifbstor1/software/miniconda/envs/spades-3.15.2/bin/spades.py", line 651, in <module>
main(sys.argv)
File "/shared/ifbstor1/software/miniconda/envs/spades-3.15.2/bin/spades.py", line 591, in main
print_params(log, log_filename, command_line, args, cfg)
File "/shared/ifbstor1/software/miniconda/envs/spades-3.15.2/bin/spades.py", line 327, in print_params
print_used_values(cfg, log)
File "/shared/ifbstor1/software/miniconda/envs/spades-3.15.2/bin/spades.py", line 117, in print_used_values
dataset_data = pyyaml.load(open(cfg["dataset"].yaml_filename))
File "/shared/ifbstor1/software/miniconda/envs/spades-3.15.2/share/spades/pyyaml3/__init__.py", line 72, in load
return loader.get_single_data()
File "/shared/ifbstor1/software/miniconda/envs/spades-3.15.2/share/spades/pyyaml3/constructor.py", line 37, in get_single_data
return self.construct_document(node)
File "/shared/ifbstor1/software/miniconda/envs/spades-3.15.2/share/spades/pyyaml3/constructor.py", line 46, in construct_document
for dummy in generator:
File "/shared/ifbstor1/software/miniconda/envs/spades-3.15.2/share/spades/pyyaml3/constructor.py", line 398, in construct_yaml_map
value = self.construct_mapping(node)
File "/shared/ifbstor1/software/miniconda/envs/spades-3.15.2/share/spades/pyyaml3/constructor.py", line 204, in construct_mapping
return super().construct_mapping(node, deep=deep)
File "/shared/ifbstor1/software/miniconda/envs/spades-3.15.2/share/spades/pyyaml3/constructor.py", line 126, in construct_mapping
if not isinstance(key, collections.Hashable):
AttributeError: module 'collections' has no attribute 'Hashable'
Après avoir cherché dans les issus sur github de SPAdes,
j'ai trouvé que ce problème est réglé dans la version 3.15.4.
(Release SPAdes 3.15.4 · ablab/spades · GitHub)
Je testé mon pipeline sur local avec une version de 3.15.5 et python 3.10, il a bien marché.
Donc je suppose que la mise à jour de SPAdes pourrait peut-être résoudre mon problème...
Merci d'avance,
juejun