Nextstrain error with multiple contigs

Error message:

Command error:
  Traceback (most recent call last):
    File "/usr/local/lib/python3.8/site-packages/augur/__init__.py", line 67, in run
      return args.__command__.run(args)
    File "/usr/local/lib/python3.8/site-packages/augur/tree.py", line 448, in run
      compress_seq = read_vcf(args.alignment, args.vcf_reference)
    File "/usr/local/lib/python3.8/site-packages/treetime/vcf_utils.py", line 267, in read_vcf
      refSeq = SeqIO.read(ref_file, format='fasta')
    File "/usr/local/lib/python3.8/site-packages/Bio/SeqIO/__init__.py", line 659, in read
      raise ValueError("More than one record found in handle")
  ValueError: More than one record found in handle

ParSNP VCF file also malformed?

Burk VCF only has CHROM 'NZ_CP008782.1' but POS re-starts at some point and this corrsponds to the second chromosome

SarahNadeau / burk-nextstrain

Nextstrain error with multiple contigs #3