ItokawaK
commented
2 years ago 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
https://github.com/artic-network/fieldbioinformatics/blob/23a8460f5b881c5b2712c0381e0ec4dc84d38359/artic/minion.py#L61 https://github.com/artic-network/fieldbioinformatics/blob/23a8460f5b881c5b2712c0381e0ec4dc84d38359/artic/minion.py#L62+
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