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Dear All,
I tried MetGEMs and got ec and ko terms. could you please tell which model can be used to get the predicted pathways?

Dear Author,
Sorry for the basic question. I did my taxonomic classification using silva database in DADA2 and tried to execute MetGem. But contionusly Iam getting the following error.

Traceback (most recent call last):
  File "/home/monica/.local/bin/metgem", line 7, in <module>
    exec(compile(f.read(), __file__, 'exec'))
  File "MetGEMs-master/MetGEM/scripts/metgem", line 39, in <module>
    retCode = main()
  File "MetGEMs-master/MetGEM/scripts/metgem", line 32, in main
    taskmodule.run()
  File MetGEMs-master/MetGEM/metgem/tasks/markp.py", line 53, in run
    taxtab = read_taxatable(args.taxtsv)
  File "MetGEMs-master/MetGEM/metgem/utils.py", line 103, in read_taxatable
    taxondf = pd.DataFrame.from_records(predf.Taxon.apply(gg_parse)).reindex(
  File "/home/.local/lib/python3.8/site-packages/pandas/core/series.py", line 4138, in apply
    mapped = lib.map_infer(values, f, convert=convert_dtype)
  File "pandas/_libs/lib.pyx", line 2467, in pandas._libs.lib.map_infer
  File "/MetGEMs-master/MetGEM/metgem/utils.py", line 191, in gg_parse
    abbrv, taxa = token.split("__")
ValueError: too many values to unpack (expected 2)

Kindly check the attached file. Every row has equal number of "__" and ";".
https://docs.google.com/spreadsheets/d/1dAIB3Do7IpHJmJ3ui4AN6NIziI2VZjFz8EQf4NceEp0/edit?usp=sharing

Any help would be appreciated

Hi!

I am not entirely sure whether 16S rRNA gene copy number corrections are performed automatically as part of the markp workflow. Looking at the code i get the idea that it probably is, however it would be great if you could comment on this.

Thank you!
Malte

After successfull installation of MetGEMs, running codes gives following errors. What will be the potential solutions.

metgem markp -i feature-table.tsv -t taxonomy_gg.tsv -m k_core -o output_ko.tsv
Traceback (most recent call last):
File "/home/X/anaconda3/envs/metgem_env/bin/metgem", line 7, in
exec(compile(f.read(), file, 'exec'))
File "/home/X/MetGEM/scripts/metgem", line 39, in
retCode = main()
File "/home/X/MetGEM/scripts/metgem", line 32, in main
taskmodule.run()
File "/home/X/MetGEM/metgem/tasks/markp.py", line 50, in run
modeltab = model.map2model(asvdata)
File "/home/ngc2/MetGEM/metgem/model.py", line 101, in map2model
log.info("Genus match to model {} - {}".format(gnuse))
IndexError: tuple index out of range