bgconfig ERROR -- Config error at mutability > format = Missing value or section.

[marianaurera]

Hi!

I tried to run oncodrivefml v1.24.0 with the docker using my own config file as I'm running it against hg38 and CADD v1.7. However, I get this error:
2024-11-27 08:00:46 bgconfig ERROR -- Config error at mutability > format = Missing value or section. 2024-11-27 08:00:46 oncodrivefml ERROR -- The config file '/input/my_oncodrivefml_config.txt' has errors.

My command is as follows:
docker run --rm -i \ -v ${BGDATA_LOCAL:-${HOME}/.bgdata}:/root/.bgdata \ -v /wes_scripts/mutation_selection:/mutation_selection \ -v /wes_scripts/mutation_selection/input:/input \ -v /wes_scripts/mutation_selection/oncodrive-fml:/oncodrive-fml \ --workdir /mutation_selection \ bbglab/oncodrivefml \ oncodrivefml -i /input/liver_variant_input.txt.gz -e /input/KEGG_Reactome_regions_input.tsv.gz \ -s wes -o /oncodrive-fml -c /input/my_oncodrivefml_config.txt

My config file looks like this:
`
[genome]
build = 'hg38'

[signature]
method = 'full'
normalize_by_sites = 'whole_exome'

[score]
file = '/input/whole_genome_SNVs.tsv.gz'
format = 'tabix'
chr = 0
chr_prefix = ''
pos = 1
ref = 2
alt = 3
score = 5

[statistic]
method = 'amean'
discard_mnp = True

sampling = 100000
sampling_max = 1000000
sampling_chunk = 100
sampling_min_obs = 10

  [[indels]]
      include = False
      max_size = 20
      method = 'max'
      max_consecutive = 0

      gene_exomic_frameshift_ratio = False
      stops_function = 'mean'
      minimum_number_of_stops = 1

[settings]
cores = 1
seed = 123
`

I checked the source code of this and BGConfig (thru bitbucket) and found that it should check my config file against oncodrivefml_v2.conf.template but I can't seem to find any field called 'mutability' there or in the documentation. Can you help me with this please?

thanks!