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artic-network / artic-ncov2019

ARTIC nanopore protocol for nCoV2019 novel coronavirus
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multiple references in V4.1 refereces.fasta -> "FASTA has more than one sequence" #88

Open bwlang opened 2 years ago

bwlang commented 2 years ago

running artic like this:

artic minion --threads 16 --scheme-directory ~/src/artic-ncov2019/primer_schemes/ --scheme-version 4.1 SARS-CoV-2 test --skip-nanopolish --medaka --medaka-model r941_min_fast_g303 --read-file test.fastq.gz

produces this error: 'FASTA has more than one sequence'

Multiple fasta entries is disallowed by this code: https://github.com/artic-network/fieldbioinformatics/blob/7ba124971569f39487b098bf533299f8091eced4/artic/minion.py#L13

replacing SARS-CoV-2.reference.fasta with the the one in the V4 directory avoids the error.