Execute ion hammer only

[joowkim]

Hello,

I would like to know if it is possible to only run ion-hammer. I have a single end fastq file from Ion torrent and I would like to process my fastq file with ion hammer. I tried it with --iontorrent --only-errorcorrection options but it didn't work for me. Please let me know if it is possible :-)

Command line: /home/jaykim/miniconda3/envs/ABL1/bin/spades.py	--iontorrent	--only-error-correction	-o	/home/jaykim/abl1/ion-hammer/out	-s	/home/jaykim/abl1/ion-hammer/ABL1.fq	

System information:
  SPAdes version: 3.13.0
  Python version: 3.10.4
  OS: Linux-4.15.0-142-generic-x86_64-with-glibc2.23

Output dir: /home/jaykim/abl1/ion-hammer/out
Mode: ONLY read error correction (without assembling)
Debug mode is turned OFF

Dataset parameters:
  IonTorrent data
  Multi-cell mode (you should set '--sc' flag if input data was obtained with MDA (single-cell) technology or --meta flag if processing metagenomic dataset)
  Reads:
Traceback (most recent call last):
  File "/home/jaykim/miniconda3/envs/ABL1/bin/spades.py", line 1093, in <module>
    main(sys.argv)
  File "/home/jaykim/miniconda3/envs/ABL1/bin/spades.py", line 714, in main
    print_used_values(cfg, log)
  File "/home/jaykim/miniconda3/envs/ABL1/bin/spades.py", line 110, in print_used_values
    dataset_data = pyyaml.load(open(cfg["dataset"].yaml_filename, 'r'))
  File "/home/jaykim/miniconda3/envs/ABL1/share/spades-3.13.0-0/share/spades/pyyaml3/__init__.py", line 72, in load
    return loader.get_single_data()
  File "/home/jaykim/miniconda3/envs/ABL1/share/spades-3.13.0-0/share/spades/pyyaml3/constructor.py", line 37, in get_single_data
    return self.construct_document(node)
  File "/home/jaykim/miniconda3/envs/ABL1/share/spades-3.13.0-0/share/spades/pyyaml3/constructor.py", line 46, in construct_document
    for dummy in generator:
  File "/home/jaykim/miniconda3/envs/ABL1/share/spades-3.13.0-0/share/spades/pyyaml3/constructor.py", line 398, in construct_yaml_map
    value = self.construct_mapping(node)
  File "/home/jaykim/miniconda3/envs/ABL1/share/spades-3.13.0-0/share/spades/pyyaml3/constructor.py", line 204, in construct_mapping
    return super().construct_mapping(node, deep=deep)
  File "/home/jaykim/miniconda3/envs/ABL1/share/spades-3.13.0-0/share/spades/pyyaml3/constructor.py", line 126, in construct_mapping
    if not isinstance(key, collections.Hashable):
AttributeError: module 'collections' has no attribute 'Hashable'

[asl]

This is a known issue with ancient SPAdes 3.13 you're using and latest Python. Consider upgrading to 3.15.5

[joowkim]

Thank you, it works very well now!