little problem

[davidmadariaga]

Description of the bug

hi!, hope you are doing great. Im a newbie so i dont understand a lot about how this can work, but could you please help me with this, i think it's just a little thing. this is what im getting:

so, how could i download the database into this directory /home/bioren/mdavid/mettaannotator/ ?????

if it's just too stupid of a question then dont bother an answer, i'll try to figure it out.

Thanks in advance,

Cheers from Chile, South America.

Command used and terminal output

(base) [mdavid@mapudungun-frontend ~]$ nextflow run ebi-metagenomics/mettannotator/main.nf -r main --dbs home/bioren/mdavid/mettaannotator
Nextflow 23.10.4 is available - Please consider updating your version to it

 N E X T F L O W   ~  version 24.04.4

Launching `https://github.com/ebi-metagenomics/mettannotator` [backstabbing_lalande] DSL2 - revision: 5fe9266f47 [main]

ERROR ~ ERROR: Validation of pipeline parameters failed!

 -- Check '.nextflow.log' file for details
The following invalid input values have been detected:

* Missing required parameter: --input
* Missing required parameter: --outdir

 -- Check script '.nextflow/assets/ebi-metagenomics/mettannotator/main.nf' at line: 31 or see '.nextflow.log' file for more details
(base) [mdavid@mapudungun-frontend ~]$ nextflow run ebi-metagenomics/mettannotator --dbs /home/bioren/mdavid/met
metagenomics_snakemake/ mettaannotator/         
(base) [mdavid@mapudungun-frontend ~]$ nextflow run ebi-metagenomics/mettannotator --dbs /home/bioren/mdavid/met
metagenomics_snakemake/ mettaannotator/         
(base) [mdavid@mapudungun-frontend ~]$ nextflow run ebi-metagenomics/mettannotator --dbs /home/bioren/mdavid/mettaannotator/
Nextflow 23.10.4 is available - Please consider updating your version to it

 N E X T F L O W   ~  version 24.04.4

Project `ebi-metagenomics/mettannotator` is currently stuck on revision: main -- you need to explicitly specify a revision with the option `-r` in order to use it
(base) [mdavid@mapudungun-frontend ~]$ nextflow run ebi-metagenomics/mettannotator/main.nf --dbs /home/bioren/mdavid/mettaannotator/
Nextflow 23.10.4 is available - Please consider updating your version to it

 N E X T F L O W   ~  version 24.04.4

Project `ebi-metagenomics/mettannotator` is currently stuck on revision: main -- you need to explicitly specify a revision with the option `-r` in order to use it
(base) [mdavid@mapudungun-frontend ~]$ nextflow run ebi-metagenomics/mettannotator/main.nf -r main --dbs /home/bioren/mdavid/mettaannotator/
Nextflow 23.10.4 is available - Please consider updating your version to it

 N E X T F L O W   ~  version 24.04.4

Launching `https://github.com/ebi-metagenomics/mettannotator` [prickly_gautier] DSL2 - revision: 5fe9266f47 [main]

ERROR ~ ERROR: Validation of pipeline parameters failed!

 -- Check '.nextflow.log' file for details
The following invalid input values have been detected:

* Missing required parameter: --input
* Missing required parameter: --outdir

 -- Check script '.nextflow/assets/ebi-metagenomics/mettannotator/main.nf' at line: 31 or see '.nextflow.log' file for more details
(base) [mdavid@mapudungun-frontend ~]$

Relevant files

No response

System information

The hardware is a linux server

[tgurbich]

Hi @davidmadariaga ,

There is currently no separate database download step. The databases will be downloaded automatically into the folder you specify in the --dbs parameter as long as the annotation command is correct and complete. Your execution failed because the input and the output folders were not specified. Instead, try running something like this:

nextflow run ebi-metagenomics/mettannotator -profile <docker/singularity/...> --input <path to input file> --outdir <folder to save results to> --dbs /home/bioren/mdavid/mettaannotator

The format of the input file is described here. You could also use our example if you don't yet have genomes to annotate.

Hope this helps.

Best wishes,
Tanya

[davidmadariaga]

thanks a lot!!!!