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FE open/GenBank model failed due to lower sequence counts · Issue #119 · nextstrain/forecasts-ncov · GitHub
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open/GenBank model failed due to lower sequence counts #119

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joverlee521 opened this issue Jan 15, 2025 · 1 comment
Open

open/GenBank model failed due to lower sequence counts #119

joverlee521 opened this issue Jan 15, 2025 · 1 comment
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@joverlee521
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Latest open/GenBank model run failed due to lower sequence counts

[batch] [2025-01-15T01:01:02+00:00] Setting max date (inclusive) as '2025-01-14'.
[batch] [2025-01-15T01:01:02+00:00] Setting min date (inclusive) as '2024-08-18'.
[batch] [2025-01-15T01:01:02+00:00] Only including locations that have at least 150 sequence(s) in the last 30 days of the analysis date range.
[batch] [2025-01-15T01:01:02+00:00] Excluding the following requested locations: ['Austria', 'Czech Republic', 'Lithuania', 'Luxembourg', 'Slovakia'].
[batch] [2025-01-15T01:01:02+00:00] Locations that will be included: [].
[batch] [2025-01-15T01:01:02+00:00] Traceback (most recent call last):
[batch] [2025-01-15T01:01:02+00:00]   File "/nextstrain/build/./scripts/prepare-data.py", line 147, in <module>
[batch] [2025-01-15T01:01:02+00:00]     assert len(locations_to_include) > 0, \
[batch] [2025-01-15T01:01:02+00:00] AssertionError: All locations have been excluded. Try again with different options, e.g. lowering the `--location-min-seq` cutoff.
[batch] [2025-01-15T01:01:02+00:00] Here's a summary of available sequences per location:
[batch] [2025-01-15T01:01:02+00:00] [{'location': 'Germany', 'sequences': 65}, {'location': 'USA', 'sequences': 128}, {'location': 'United Kingdom', 'sequences': 8}]

Unlike #117, this is not due lack of updates from the API, but a legitimate decrease in sequence counts.

@joverlee521
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Discussed in Slack.

I'll stop the open/GenBank model runs for now since it is not visualized anywhere. We can revisit whether to restart it when we do a review of sequence count cutoffs.

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