search

artic-network / primer-schemes

Primer schemes for real-time genome epidemiology
https://artic.network/
Creative Commons Attribution 4.0 International
27 stars 41 forks source link

'Scheme download failed' V4.1 primer scheme help #15

Closed CGB858 closed 1 year ago

CGB858 commented 2 years ago

Hello,

I have been trying to download the latest primer scheme (V4.1), i have tried using the command: artic-tools get_scheme nCoV-2019 But am presented with the error below:

[11:39:19] [artic-tools::get_scheme] starting primer scheme downloader [11:39:19] [artic-tools::get_scheme] requested scheme: nCoV-2019 [11:39:19] [artic-tools::get_scheme] requested version: latest [11:39:19] [artic-tools::get_scheme] fetching manifest file [11:39:19] [artic-tools::get_scheme] ARTIC manifest URL: https://raw.githubusercontent.com/artic-network/primer- schemes/master/schemes_manifest.json [11:39:20] [artic-tools::get_scheme] ARTIC repository DOI: 10.5281/zenodo.4004423 [11:39:20] [artic-tools::get_scheme] finding primer scheme [11:39:20] [artic-tools::get_scheme] found requested scheme: sars-cov-2 (using alias nCoV-2019) error--> conversion of data to type "j" failed

I have also tried downloading the primer schemes directly from GitHub but when running the Artic pipeline I get the following error:

'could not find primer scheme and reference sequence, attempting to download Running: artic-tools get_scheme nCoV-2019 --schemeVersion 4.1 Could not convert: --schemeVersion = 4.1 Run with --help for more information. scheme download failed'

I am very new to linux so I am at a bit of a loss of what else to try, and would appreciate any advice. Thank you :)

EDIT I have also tried using version 3 which has worked for me in the past and I am getting the same error

BioWilko commented 1 year ago

Apologies for the extremely late response but, this was due to using an out of date version of fieldbioinformatics which failed due to the scheme minor version number causing the scheme number type to no longer by an integer. This issue was fixed in artic version 1.2.2 (Feb 22 2022).