Unable to run the example usage

[AnoshMostaghimi]

I have created a docker container of this pipeline. Upon trying to run one of the Example Usages from the container's shell as noted in the documentation:

root@84aa2191e3f7:/app/ChroQueTas# bin/ChroQueTas.sh -g test_dataset/Calbicans_SRR13587609.fasta.gz -s Candida_albicans -o Calbicans_SRR13587609_ChroQueTas

I see the following output:

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

By way of further context, I have expanded the database file db-v20250811.tgz listed under the FungAMR_db and see the following:

root@84aa2191e3f7:/app/ChroQueTas/FungAMR_db/db-v0.6.0# ls
Arthroderma_vanbreuseghemii Candida_parapsilosis Fusarium_graminearum Pyrenopeziza_brassicae
Aspergillus_awamori Candida_tropicalis Fusarium_incarnatum Saccharomyces_cerevisiae
Aspergillus_fumigatus Candidozyma_auris Fusarium_pseudograminearum Saccharomyces_paradoxus
Aspergillus_niger Cercospora_beticola Histoplasma_capsulatum Tapesia_acuformis
Aspergillus_terreus Clavispora_lusitaniae Kluyveromyces_marxianus Tapesia_yallundae
Aspergillus_tubingensis Colletotrichum_acutatum Magnaporthe_grisea Trichophyton_indotineae
Beauveria_bassiana Colletotrichum_fructicola Monilinia_fructicola Trichophyton_interdigitale
Blumeria_graminis Colletotrichum_gloeosporioides Mycosphaerella_fijiensis Trichophyton_mentagrophytes
Blumeria_graminis_hordei Colletotrichum_graminicola Nakaseomyces_glabratus Trichophyton_rubrum
Blumeria_graminis_tritici Colletotrichum_siamense Passalora_fulva Ustilaginoidea_virens
Botrytis_cinerea Corynespora_cassiicola Phaeosphaeria_nodorum Venturia_inaequalis
Candida_albicans Cryptococcus_deuterogattii Phakopsora_pachyrhizi Zymoseptoria_tritici
Candida_dubliniensis Cryptococcus_neoformans Pichia_kudriavzevii
Candida_metapsilosis Erysiphe_necator Pneumocystis_jirovecii
Candida_orthopsilosis Fusarium_fujikuroi Puccinia_triticina

Lastly, the version of the tool is

root@2c0b31798a0a:/app/ChroQueTas# bin/ChroQueTas.sh --version
ChroQueTas (Chromosome Query Targets) version 1.0.0

Can you please let me know what I am doing wrong?

Thank you,
Anosh

[Luke-ebbis]

Hey Anosh, I am now working on another Dockerfile where your command has the following output

docker run --rm -it your-image-name  -g test_dataset/Calbicans_SRR13587609.fasta.gz -s Candida_albicans -o Calbicans_SRR13587609_ChroQueTas

Put some...

   ____ _                ___            _____          
  / ___| |__  _ __ ___  / _ \ _   _  __|_   _|_ _ ___  
 | |   | '_ \| '__/ _ \| | | | | | |/ _ \| |/ _` / __| 
 | |___| | | | | | (_) | |_| | |_| |  __/| | (_| \__ \ 
  \____|_| |_|_|  \___/ \__\__\__,_|\___||_|\__,_|___/   v1.0.0


                                                            ...IN YOUR LIFE!

Four steps and you are there!

The species Candida_albicans has 11 proteins associated with AMR

PLEASE NOTE: as -c/--trans_code has not been specified and Candida_albicans belongs to CTG clade, genetic code has been automatically set to alternative yeast code (12)

Running protein prediction and extraction (step 1/4)
Done! (step 1/4)
Calculating protein similarity with reference (step 2/4)
Done! (step 2/4)
Performing alignment with reference (step 3/4)
Done! (step 3/4)
Inspecting mutations potentially causing AMR (step 4/4)
Done! (step 4/4)

 -FungAMR mutations found: 2
 -New mutations found: 0

Thanks for using ChroQueTas!


PLEASE NOTE: the mutations reported by ChroQueTas must be considered according their confidence scores, where different combinations might exist.

See the main repositories for further details:
 -https://github.com/nmquijada/ChroQueTas
 -https://card.mcmaster.ca/fungamrhome

Please stay tuned for the pull request and docker image.

[AnoshMostaghimi]

Thank you. Looking forward to it.