Error during running wf-bacterial-genome (nextflow run epi2me-labs/wf-bacterial-genomes).

Question

[Anurag]

ERROR ~ Error executing process > 'calling_pipeline:medakaInference_consensus (11)'

Caused by:
  Process `calling_pipeline:medakaInference_consensus (11)` terminated with an error exit status (1)


Command executed:

  medaka --version
      echo dna_r10.4.1_e8.2_400bps_fast@v4.3.0:consensus
      medaka inference align.bam "barcode91.consensus_probs.hdf"         --threads 2 --regions "contig_2:1998000-2998000
  " --model dna_r10.4.1_e8.2_400bps_fast@v4.3.0:consensus

Command exit status:
  1

Command output:
  medaka 2.0.0
  dna_r10.4.1_e8.2_400bps_fast@v4.3.0:consensus

Command error:
  Cannot import pyabpoa, some features may not be available.
  medaka 2.0.0
  dna_r10.4.1_e8.2_400bps_fast@v4.3.0:consensus
  Cannot import pyabpoa, some features may not be available.
  Failed to interpret 'dna_r10.4.1_e8.2_400bps_fast@v4.3.0:consensus' as a basecaller model.
  Traceback (most recent call last):
    File "/home/epi2melabs/conda/lib/python3.8/site-packages/medaka/medaka.py", line 35, in __call__
      model_fp = medaka.models.resolve_model(val)
    File "/home/epi2melabs/conda/lib/python3.8/site-packages/medaka/models.py", line 55, in resolve_model
      raise ValueError(
  ValueError: Model dna_r10.4.1_e8.2_400bps_fast@v4.3.0:consensus is not a known model or existant file.

  During handling of the above exception, another exception occurred:

  Traceback (most recent call last):
    File "/home/epi2melabs/conda/bin/medaka", line 8, in <module>
      sys.exit(main())
    File "/home/epi2melabs/conda/lib/python3.8/site-packages/medaka/medaka.py", line 822, in main
      args = parser.parse_args()
    File "/home/epi2melabs/conda/lib/python3.8/argparse.py", line 1768, in parse_args
      args, argv = self.parse_known_args(args, namespace)
    File "/home/epi2melabs/conda/lib/python3.8/argparse.py", line 1800, in parse_known_args
      namespace, args = self._parse_known_args(args, namespace)
    File "/home/epi2melabs/conda/lib/python3.8/argparse.py", line 1988, in _parse_known_args
      positionals_end_index = consume_positionals(start_index)
    File "/home/epi2melabs/conda/lib/python3.8/argparse.py", line 1965, in consume_positionals
      take_action(action, args)
    File "/home/epi2melabs/conda/lib/python3.8/argparse.py", line 1874, in take_action
      action(self, namespace, argument_values, option_string)
    File "/home/epi2melabs/conda/lib/python3.8/argparse.py", line 1159, in __call__
      subnamespace, arg_strings = parser.parse_known_args(arg_strings, None)
    File "/home/epi2melabs/conda/lib/python3.8/argparse.py", line 1800, in parse_known_args
      namespace, args = self._parse_known_args(args, namespace)
    File "/home/epi2melabs/conda/lib/python3.8/argparse.py", line 2006, in _parse_known_args
      start_index = consume_optional(start_index)
    File "/home/epi2melabs/conda/lib/python3.8/argparse.py", line 1946, in consume_optional
      take_action(action, args, option_string)
    File "/home/epi2melabs/conda/lib/python3.8/argparse.py", line 1874, in take_action
      action(self, namespace, argument_values, option_string)
    File "/home/epi2melabs/conda/lib/python3.8/site-packages/medaka/medaka.py", line 38, in __call__
      raise RuntimeError(msg.format(self.dest, str(e)))
  RuntimeError: Error validating model from '--model' argument: Model dna_r10.4.1_e8.2_400bps_fas

[GenoMax]

Please add some detail about the command you are running and what exactly you are trying to do. You may have put part of the command line in the title but that is not useful. Otherwise you appear to have simply posted the error message as is.

[Anurag]

hello I am very new to this field, I am trying to assemble genome using wf-bacterial-genome (nextflow run epi2me-labs/wf-bacterial-genomes) pipline by Nanopore (EPI2ME). MEDAKA_MODEL="r1041_e82_400bps_fast_g632" nextflow run epi2me-labs/wf-bacterial-genomes --fastq '/data/Sagar/AMR SB_Round 1 copy/' -profile standard -work-dir '/data/Anurag/Analysis/' -resume this is the command I wrote. the pipline runs for a while and the posted error pops up. thanks for you help.

[GenoMax]

If you have the run data folder available then you should go back and re-call the bases using either HAC (high accuracy) or preferably SUP (super accuracy) calls. This will preferably require a GPU but it the end result will be much better.

As an aside, get away from the habit of using spaces in file/directory names. With linux they can only cause headaches. Replace the space in names with a _.

[Anurag]

Thank you for replying and the tip! I tried HAC & SUP both did not work for me.

[GenoMax]

I tried HAC & SUP both did not work for me.

What did not work? You actually need to recall the bases using HAC/SUP models and dorado basecaller. You can't simply replace FAST model with HAC/SUP in your nextflow command line. As noted by colindaven , you appear to be using calls that were done using FAST (least accurate) model.

[Anurag]

I am using EPI2ME nextflow beacterial genome pipeline is it still necessary to use dorado basecaller first ?

[GenoMax]

If you currently have only FAST basecalls and would like to get the higher quality HAC/SUP calls then you have to use dorado.

It may be easier to ask whoever did the sequencing for you to do the higher quality calls, since they will likely have the expertise/necessary hardware and your original data folder.

Answer 1

[colindaven]

The specified model is wrong.

ValueError: Model dna_r10.4.1_e8.2_400bps_fast@v4.3.0:consensus is not a known model or existant file.

You can find your available models using the info here:

https://github.com/nanoporetech/medaka?tab=readme-ov-file#models

As an aside - if you used fast basecalling you'll get a very poor genome (fast makes the most errors in basecalling, hac is better, sup is best)

[Anurag]

hey, thank you for reply still i am getting same error.