ERROR: unknown option for '-s/--scheme'

[Shaedeycool]

Good afternoon,

I tried to run the example code and received this error

ERROR: unknown option for '-s/--scheme'
Available schemes: Calbicans, Ztritici
Argument parsed: Zymoseptoria_tritici

However, when I change -s to Calbicans or Ztritici, I receive the following error

ls: cannot access 'FungAMR_db/db-v0.6.0/Ztritici/*faa': No such file or directory

The scheme Ztritici has 0 proteins associated with AMR

There seems to be a disconnect with the scheme name not matching the name in the database.

Kind regards,
S

[nmquijada]

Hi @Shaedeycool

Are you using the latest version of ChroQueTas? (v0.6.0 as in https://github.com/nmquijada/ChroQueTas/releases/tag/v0.6.0)
Type ChroQueTas.sh -v if you are not sure.

-s/--scheme option is deprecated and no longer functional.

Let me know!
N

[Shaedeycool]

Good day,

I'm still getting this same error

ChroQueTas-0.6.0/bin/ChroQueTas.sh -g ChroQueTas-0.6.0/test_dataset
/Calbicans_SRR13587609.fasta.gz -s Candida_albicans --min_id 75 --min_cov 75 -t 2 -o Calbicans_SRR13587609_ChroQueTas

ERROR: unknown option for '-s/--species'
Argument parsed: Candida_albicans
To inspect the species available use the '--list_species' flag

ChroQueTas-0.6.0/bin/ChroQueTas.sh -g ChroQueTas-0.6.0/test_dataset/Calbicans_SRR13587609.fasta.gz -s Calbicans --min_id 75 --min_cov 75 -t 2 -o Calbicans_SRR13587609_ChroQueTas

ERROR: unknown option for '-s/--species'
Argument parsed: Calbicans
To inspect the species available use the '--list_species' flag

Kind regards,
S

[nmquijada]

Hi @Shaedeycool

Sorry for the late reply. I am afraid we cannot reproduce your error with this information.
Have you tried to specify the path to the database with the -f/--fungamr?
How did you install ChroQueTas (conda or source)?
What is your operating systems?

We will make it work ;)
N