Could not find primer scheme

[amv33576]

Hello,

I am using my own scheme of primers, the directory looks like:
fieldbioinformatics/schemes
fieldbioinformatics/schemes/vc07
fieldbioinformatics/schemes/vc07/vc07.insert.bed
fieldbioinformatics/schemes/vc07/vc07.primer.bed
fieldbioinformatics/schemes/vc07/vc07.reference.fasta
fieldbioinformatics/schemes/vc07/vc07.reference.fasta.fai

the primer.bed file looks like:

contig 2905711 2905730 Vc07_LEFT 1 +
contig 2907061 2907080 Vc07_RIGHT 1 -

if I type: artic-tools validate_scheme schemes/vc07/vc07.scheme.bed
I get:
[01:19:09] [artic-tools::validate_scheme] starting primer scheme validator
[01:19:09] [artic-tools::validate_scheme] reading scheme
[01:19:09] [artic-tools::validate_scheme] collecting scheme stats
[01:19:09] [artic-tools::validate_scheme] primer scheme file: schemes/vc07/vc07.scheme.bed
[01:19:09] [artic-tools::validate_scheme] reference sequence: VCAR10162
[01:19:09] [artic-tools::validate_scheme] number of pools: 1
[01:19:09] [artic-tools::validate_scheme] number of primers: 2 (includes 0 alts)
[01:19:09] [artic-tools::validate_scheme] minimum primer size: 19
[01:19:09] [artic-tools::validate_scheme] maximum primer size: 19
[01:19:09] [artic-tools::validate_scheme] number of amplicons: 1
[01:19:09] [artic-tools::validate_scheme] mean amplicon size: 1331
[01:19:09] [artic-tools::validate_scheme] maximum amplicon size: 1331
[01:19:09] [artic-tools::validate_scheme] scheme ref. span: 2905711-2907080
[01:19:09] [artic-tools::validate_scheme] scheme overlaps: 0.0%

but when I run: artic minion --read-file 'barcode19.fastq' --scheme-directory schemes --skip-nanopolish --medaka --medaka-model r941_min_fast_g303 --scheme-version vc07 barcode19

I get:

could not find primer scheme and reference sequence, attempting to download
Running: artic-tools get_scheme vc07 --schemeVersion 1
[01:15:00] [artic-tools::get_scheme] starting primer scheme downloader
[01:15:00] [artic-tools::get_scheme] requested scheme: vc07
[01:15:00] [artic-tools::get_scheme] requested version: 1
[01:15:00] [artic-tools::get_scheme] fetching manifest file
[01:15:00] [artic-tools::get_scheme] ARTIC manifest URL: https://raw.githubusercontent.com/artic-network/primer-schemes/master/schemes_manifest.json
[01:15:00] [artic-tools::get_scheme] ARTIC repository DOI: 10.5281/zenodo.4004423
[01:15:00] [artic-tools::get_scheme] finding primer scheme
[01:15:00] [artic-tools::get_scheme] scheme not found: vc07
[01:15:00] [artic-tools::get_scheme] listing available scheme aliases (case insensitive)
[01:15:00] [artic-tools::get_scheme] - ebola
[01:15:00] [artic-tools::get_scheme] - ebov
[01:15:00] [artic-tools::get_scheme] - zaire
[01:15:00] [artic-tools::get_scheme] - nipah
[01:15:00] [artic-tools::get_scheme] - niv
[01:15:00] [artic-tools::get_scheme] - sars-cov-2
[01:15:00] [artic-tools::get_scheme] - scov2
[01:15:00] [artic-tools::get_scheme] - ncov
[01:15:00] [artic-tools::get_scheme] - ncov-2019
error--> no primer scheme available for vc07

Why is not finding the primer scheme? Running on conda environment, artic 1.2.1

Thanks,

Anyi

[ItokawaK]

Maybe, structure of scheme dilectry should be like below.

${scheme_dir}/${scheme_name}/V${scheme_version}/${scheme_name}.scheme.bed
${scheme_dir}/${scheme_name}/V${scheme_version}/${scheme_name}.reference.fasta

Then, your command should look like below.

artic minion --read-file 'barcode19.fastq' --scheme-directory ${scheme_dir} --skip-nanopolish --medaka --medaka-model r941_min_fast_g303 --scheme-version ${scheme_version} ${scheme_name} barcode19

fieldbioinformatics/artic/minion.py

Line 61 in 23a8460

bed = "%s/%s/V%s/%s.scheme.bed" % (scheme_directory, scheme_name, scheme_version, scheme_name)

https://github.com/artic-network/fieldbioinformatics/blob/23a8460f5b881c5b2712c0381e0ec4dc84d38359/artic/minion.py#L62+