I'm using 1st time unicycler and running hybrid assembly with this command,
unicycler -1 illumina_mtreads_R1mapped.fastq -2 illumina_mtreads_R2mapped.fastq -l Nanopore_mapped_longest_round2.fastq -o hybrid_mtreads_unicycler --threads 12
I have installed unicycler 0.5.0 using conda, its showing the below error :
Error: SPAdes encountered an error:
Traceback (most recent call last):
File "/root/anaconda3/envs/mitochondrial_genome_assembly/bin/spades.py", line 659, in <module>
main(sys.argv)
File "/root/anaconda3/envs/mitochondrial_genome_assembly/bin/spades.py", line 599, in main
print_params(log, log_filename, command_line, args, cfg)
File "/root/anaconda3/envs/mitochondrial_genome_assembly/bin/spades.py", line 327, in print_params
print_used_values(cfg, log)
File "/root/anaconda3/envs/mitochondrial_genome_assembly/bin/spades.py", line 117, in print_used_values
dataset_data = pyyaml.load(open(cfg["dataset"].yaml_filename))
File "/root/anaconda3/envs/mitochondrial_genome_assembly/share/spades/pyyaml3/__init__.py", line 72, in load
return loader.get_single_data()
File "/root/anaconda3/envs/mitochondrial_genome_assembly/share/spades/pyyaml3/constructor.py", line 37, in get_single_data
return self.construct_document(node)
File "/root/anaconda3/envs/mitochondrial_genome_assembly/share/spades/pyyaml3/constructor.py", line 46, in construct_document
for dummy in generator:
File "/root/anaconda3/envs/mitochondrial_genome_assembly/share/spades/pyyaml3/constructor.py", line 398, in construct_yaml_map
value = self.construct_mapping(node)
File "/root/anaconda3/envs/mitochondrial_genome_assembly/share/spades/pyyaml3/constructor.py", line 204, in construct_mapping
return super().construct_mapping(node, deep=deep)
File "/root/anaconda3/envs/mitochondrial_genome_assembly/share/spades/pyyaml3/constructor.py", line 126, in construct_mapping
if not isinstance(key, collections.Hashable):
AttributeError: module 'collections' has no attribute 'Hashable'
I'm using 1st time unicycler and running hybrid assembly with this command,
unicycler -1 illumina_mtreads_R1mapped.fastq -2 illumina_mtreads_R2mapped.fastq -l Nanopore_mapped_longest_round2.fastq -o hybrid_mtreads_unicycler --threads 12
I have installed unicycler 0.5.0 using conda, its showing the below error :