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artic-network / artic-ncov2019

ARTIC nanopore protocol for nCoV2019 novel coronavirus
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Medaka failed: Command failed:longshot -P 0 -F -A --no_haps #87

Open gvaleman opened 2 years ago

gvaleman commented 2 years ago

Hi! I was trying to get a consensus sequence using artic network bioinformatic protocol, i used the nex comand lines:

artic minion --medaka --medaka-model r941_min_high_g360 --normalise 200 --threads 4 --scheme-directory '/home/pc/artic-ncov2019/primer_schemes' --read-file '/home/pc/Escritorio/Porechop/BC73.fastq' nCoV-2019/V3 samplename

I got the next output:

2022-01-08 17:22:38 Automatically determining max read coverage. 2022-01-08 17:22:38 Estimating mean read coverage... 2022-01-08 17:22:38 Total reference positions: 0 2022-01-08 17:22:38 Total bases in bam: 0 2022-01-08 17:22:38 Mean read coverage: NaN error: {} ERROR: Max read coverage set to 0. Command failed:longshot -P 0 -F -A --no_haps --bam samplename.primertrimmed.rg.sorted.bam --ref /home/pc/artic-ncov2019/primer_schemes/nCoV-2019/V3/nCoV-2019.reference.fasta --out samplename.merged.vcf --potential_variants samplename.merged.vcf.gz

how can i solve this issue?

laura-bankers commented 1 year ago

I am receiving the same error. Any resolution here?