Error with diagnostic.py

Help and Getting Started
1

I am setting up a local nextstrain augur pipeline and on introducing a diagnostics rule similar to what is on the ncov site i get this issue

Job 7: 
   Scanning aligned sequences results/aligned.fasta for problematic sequences
Traceback (most recent call last):
  File "scripts/diagnostic.py", line 135, in <module>
    flag.write(f"{s}\t{metadata[s]['date'] if s in metadata else 'XXXX-XX-XX'}\t{metadata[s]['date_submitted'] if s in metadata else 'XXXX-XX-XX'}\t{msg}\n")
KeyError: 'date_submitted'

Not sure what the real issue is since all the dates are formatted correctly.

2

fixed! problem was with a metadata column.

3

That’s great! I’m facing the same error. What was the specific metadata issue? I just downloaded nextmeta from GISAID but it still appears to be throwing an error. Should I just delete the entire date_submitted column? or is it a specific value error? Thanks!