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

Question

[Pratibha kadam]

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.

[ATpoint]

You should open an issue at the GitHub of the developer of this.