search

gjeunen / reference_database_creator

creating reference databases for amplicon sequencing
MIT License
25 stars 8 forks source link

Download BOLD database with --marker #70

Closed domivika closed 1 hour ago

domivika commented 2 hours ago

Hi!

Is it possible to download the BOLD database while filtering only by the marker (e.g. COI)? I tried to include only the --marker argument: crabs --download-{wildcards.database} --marker {wildcards.marker} --output {wildcard.output}

but I got the following error:

> /// CRABS | v1.0.1

|            Function | Download BOLD database
|               ERROR | "--taxon" not provided, aborting analysis...

Thanks!

gjeunen commented 1 hour ago

Hello @domivika,

Thank you for using CRABS.

The reason why the --taxon parameter is required is that the BOLD servers will interrupt the download of the full database in a single transfer. I recommend making a list of taxonomic groups that cover the taxa of interest (can be at any level, but the more specific the better, as the amount to download in one go is limited) and loop over the list using the --taxon marker.

Apologies for this inconvenience, but this functionality is due to limitations on the BOLD server side.

I hope this helps :)

Best wishes, Gert-Jan

domivika commented 1 hour ago

Hello @gjeunen,

I understand, thanks for the quick answer!

Best, Dominika