Documentation on CLI function 'clock' is wrong. Date has to be date format not year decimal.

[m-d-grunnill]

Documentation on CLI function 'clock' is wrong. Date has to be date format not year decimal see below:

I could not get the function to work unless I used date format.

[rneher]

One the example data, the function works as specified.

treetime clock --tree data/ebola/ebola.nwk --dates data/ebola/ebola.metadata.csv --sequence-length 20000

and the metadata there specifies dates as

name, date
EM_COY_2015_015982, 2015.30
G3676, 2014.40
EM_COY_2015_015980, 2015.30
G3670, 2014.40
CON-10590, 2015.61
NM042, 2014.42
EM_079497, 2014.26

But it is true that the TreeTime will also attempt to parse dates in ISO-format if they can't parsed as a float.

What exact command are you running?

[liamxg]

Dear @rneher,

My date.csv file has the first column that contains 'name', but still reports error:

ttempting to parse dates...
Traceback (most recent call last):
  File "/Users/liam/opt/miniconda3/bin/treetime", line 8, in <module>
  sys.exit(main())
File "/Users/liam/opt/miniconda3/lib/python3.9/site-packages/treetime/__main__.py", line 21, in main
return_code = params.func(params)
File "/Users/liam/opt/miniconda3/lib/python3.9/site-packages/treetime/argument_parser.py", line 238, in toplevel
timetree(params)
File "/Users/liam/opt/miniconda3/lib/python3.9/site-packages/treetime/wrappers.py", line 306, in timetree
dates = utils.parse_dates(params.dates, date_col=params.date_column, name_col=params.name_column)
File "/Users/liam/opt/miniconda3/lib/python3.9/site-packages/treetime/utils.py", line 336, in parse_dates
raise err
File "/Users/liam/opt/miniconda3/lib/python3.9/site-packages/treetime/utils.py", line 285, in parse_dates
raise MissingDataError("ERROR: Cannot read metadata: need at least one column that contains the taxon labels."
                       treetime.MissingDataError: ERROR: Cannot read metadata: need at least one column that contains the taxon labels. Looking for the first column that contains 'name', 'strain', or 'accession' in the header.

Best,
Liam

[rneher]

@liamxg , could you share a bit more info about the file you are using?