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artic-network / artic-ncov2019

ARTIC nanopore protocol for nCoV2019 novel coronavirus

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Scheme reference file not found: #40

Open AroobAlhumaidy opened 3 years ago

AroobAlhumaidy commented 3 years ago

when i run this code: (artic minion --normalise 200 --threads 4 --scheme-directory ~/artic-ncov2019/primer_schemes --read-file run_name_barcode03.fastq --fast5-directory path_to_fast5 --sequencing-summary path_to_sequencing_summary.txt nCoV-2019/V3 samplename):

I get this error: (Scheme reference file not found: /Users/aroobalhumaidy/artic-ncov2019/nCoV-2019/V3/nCoV-2019.reference.fasta)

will-rowe commented 3 years ago

Sorry for the slow reply @AroobAlhumaidy - did you manage to get this working?

If not, let me know the output of:

ls -R ~/artic-ncov2019/primer_schemes