Problem with lat/longs


I am successfully using Nextstrain to analyze Sars-Cov-2.
However, when I loaded the genome obtained from a division whose coordinates were not previously specified, specifying the coordinates in the defaults/lat_longs.tsv and this division in the color_ordering.tsv, I received the following error:

Traceback (most recent call last):
File “./scripts/”, line 149, in
update_latlongs (input_json [“meta”] [“geo_resolutions”], sampling_values, latlongs)
File “./scripts/”, line 94, in update_latlongs
trait = [x for x in geo_resolutions if x [“key”] == SAMPLING_TRAIT] [0]
IndexError: list index out of range

The following warnings were also indicated for all division (even those that were already in the file), an example for division ‘Omsk Region’:
WARNING: division-> Omsk Region did not have an associated lat / long value (matching performed in lower case). Auspice won’t be able to display this location.

The analysis was performed, but I could not find the display of divisions on the map. Nevertheless, the new division was highlighted in a separate color on the phylogenetic tree. I am using for visualization

Please help me solve this problem.

Hi @MariStar, thanks for reaching out! Hm, it seems like there’s a problem in reading in and assigning the lat-long which means the one you’ve added isn’t being read-in and thus can’t be used for the output. Can you double-check that you have put the new lat-long value in separated by tabs, rather than spaces or anything else? There should be a tab between each of the columns and between the two latitude and longitude values. Let us know if that helps!

1 Like

Hello, Emma!

Thanks a lot for your reply!

I checked the padding many times and reinstalled the pipeline several times and it worked. The problem was probably with the text editor I was using.

Best regards,

пт, 28 авг. 2020 г. в 16:44, Emma Hodcroft via Nextstrain Discussion <>:

Hi Maria,
Oh dear!! I am so sorry this took so much time on your part to get this working. I don’t really understand what the problem might have been. I’m glad you got it working, but sorry it caused so much frustration!
Best wishes,