Medaka failed: Command failed:longshot -P 0 -F -A --no_haps

[gvaleman]

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]

I am receiving the same error. Any resolution here?