search

epi2me-labs / wf-artic

ARTIC SARS-CoV-2 workflow and reporting
https://labs.epi2me.io/
Other
47 stars 34 forks source link

Medaka unable to download model #104

Closed ammaraziz closed 3 months ago

ammaraziz commented 8 months ago

Operating System

Ubuntu 22.04

Other Linux

No response

Workflow Version

v0.3.3

Workflow Execution

Command line

EPI2ME Version

No response

CLI command run

nextflow run epi2me-labs/wf-artic --fastq fastq_pass/ --sample_sheet samplesheet.csv --basecaller_cfg dna_r10.4.1_e8.2_400bps_hac --custom_scheme $PWD/custom_scheme/V1/ --max_len 1200 --min_len 150 --output_dir output/test1 --update_data --normalise 400

Running a slightly modified v0.3.33 which has || mock_artic removed for debugging purposes as it silences all errors making it impossible to debug.

Workflow Execution - CLI Execution Profile

None

What happened?

Medaka is unable to download the appropriate model.

Relevant log output

Relevant error:

Command error:
  [M::main] CMD: minimap2 -a -x map-ont -t 4 V1/./SARS-CoV-2.reference.fasta NEG_CON_01_NEG_CON_01.fastq
  [M::main] Real time: 0.026 sec; CPU: 0.066 sec; Peak RSS: 0.008 GB
  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 66, in resolve_model
      raise DownloadError(
  medaka.models.DownloadError: The model file for r1041_e82_400bps_hac_variant_g615 is not already installed and could not be downloaded. Check you are connected to the internet and try again.

Complete:

ERROR ~ Error executing process > 'pipeline:runArtic (1)'

Caused by:
  Process `pipeline:runArtic (1)` terminated with an error exit status (20)

Command executed:

  run_artic.sh         NEG_CON_01 seqs.fastq.gz 150 1200         r1041_e82_400bps_hac_variant_g615 SARS-CoV-2 V1         None 4 0 400
  bcftools stats NEG_CON_01.pass.named.vcf.gz > NEG_CON_01.pass.named.stats

Command exit status:
  20

Command output:
  Moving input: 'seqs.fastq.gz' to 'NEG_CON_01/NEG_CON_01.fastq.gz'
  NEG_CON_01_NEG_CON_01.fastq   1492
   - artic guppyplex finished
  Running hacked up minion.py

Command error:
  [M::main] CMD: minimap2 -a -x map-ont -t 4 V1/./SARS-CoV-2.reference.fasta NEG_CON_01_NEG_CON_01.fastq
  [M::main] Real time: 0.026 sec; CPU: 0.066 sec; Peak RSS: 0.008 GB
  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 66, in resolve_model
      raise DownloadError(
  medaka.models.DownloadError: The model file for r1041_e82_400bps_hac_variant_g615 is not already installed and could not be downloaded. Check you are connected to the internet and try again.

  During handling of the above exception, another exception occurred:

  Traceback (most recent call last):
    File "/home/epi2melabs/conda/bin/medaka", line 11, in <module>
      sys.exit(main())
    File "/home/epi2melabs/conda/lib/python3.8/site-packages/medaka/medaka.py", line 703, 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: The model file for r1041_e82_400bps_hac_variant_g615 is not already installed and could not be downloaded. Check you are connected to the internet and try again..
  Running hacked up minion.py
  /home/epi2melabs/conda/lib/python3.8/site-packages/clint/textui/prompt.py:68: SyntaxWarning: "is not" with a literal. Did you mean "!="?
    if prompt[-1] is not ' ':
  Running: minimap2 -a -x map-ont -t 4 V1/./SARS-CoV-2.reference.fasta NEG_CON_01_NEG_CON_01.fastq | samtools view -bS -F 4 - | samtools sort -o NEG_CON_01.sorted.bam -
  Running: samtools index NEG_CON_01.sorted.bam
  Running: align_trim NEG_CON_01.sorted.bam V1/./SARS-CoV-2.scheme.bed  --normalise 400 --start --report NEG_CON_01.alignreport.txt 2> NEG_CON_01.alignreport.er | samtools sort -T NEG_CON_01 - -o NEG_CON_01.trimmed.rg.sorted.bam
  Running: align_trim NEG_CON_01.sorted.bam V1/./SARS-CoV-2.scheme.bed  --normalise 400 --report NEG_CON_01.alignreport.txt 2> NEG_CON_01.alignreport.er | samtools sort -T NEG_CON_01 - -o NEG_CON_01.primertrimmed.rg.sorted.bam
  Running: samtools index NEG_CON_01.trimmed.rg.sorted.bam
  Running: samtools index NEG_CON_01.primertrimmed.rg.sorted.bam
  Running: medaka consensus --model r1041_e82_400bps_hac_variant_g615 --threads 4 --chunk_len 800 --chunk_ovlp 400 --RG 2 NEG_CON_01.trimmed.rg.sorted.bam NEG_CON_01.2.hdf
  Command failed:medaka consensus --model r1041_e82_400bps_hac_variant_g615 --threads 4 --chunk_len 800 --chunk_ovlp 400 --RG 2 NEG_CON_01.trimmed.rg.sorted.bam NEG_CON_01.2.hdf

Work dir:
  .../work/53/1cc9c73d23ab46429a724c3241849b

Tip: you can try to figure out what's wrong by changing to the process work dir and showing the script file named `.command.sh`

 -- Check '.nextflow.log' file for details

Related to https://github.com/nanoporetech/medaka/issues/414 ?

ammaraziz commented 7 months ago

I am closing this issue as I can not replicate it. It could have been an issue with the network or maybe an issue with the pipeline using the wrong docker containers.

Apologies for submitting a bug issue without testing on my end.

ammaraziz commented 4 months ago

Reopening this issue. I've identified the problem, will submit a pull request. Related to https://github.com/epi2me-labs/wf-artic/issues/95

ammaraziz commented 3 months ago

Closing, apologies for the back and forth.