Error: samtools sort: failed to read header from "-" ARTIC Pipeline for SAR-COV-2

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Hello,I have problem while running artic minion command
eating

  1. It could not recognize the pimer scheme which i have provided path of. so its creating new primer set folder.

  2. while running it throws error

samtools sort: failed to read header from "-"

the command is:

artic minion --minimap2 --medaka --medaka-model r941_min_fast_g303 --normalise 200 --threads 6 --scheme-directory /home/fmr/fieldbioinformatics-1.2.1/primer_scheme/ --read-file barcode3.fastq nCoV-2019/V3 barcode3

please let me know the solution.


NGS


pipeline


nanopore


bioinformatics


artic

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