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ingest fails #4

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joverlee521 opened this issue Jul 25, 2024 · 2 comments · Fixed by #5
Closed

ingest fails #4

joverlee521 opened this issue Jul 25, 2024 · 2 comments · Fixed by #5
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@joverlee521
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joverlee521 commented Jul 25, 2024 •
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Blocked on #1

First reported in Nextstrain office hours

The ingest workflow on the default branch fails during the curate rule.
Looking into the logs at ingest/logs/curate.txt, there's a bunch of warnings, but the actual error is

ERROR: Records do not have the same fields! Please check your input data has the same fields.
@joverlee521 joverlee521 added the bug Something isn't working label Jul 25, 2024
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Error only shows up when using environment with Augur >= 25.0.0 because of added check in nextstrain/augur#1518.

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Ah, the error stems from upstream warning

`transform-genbank-location` requires a `location` field; this record does not have one.

The bug is fixed in augur curate parse-genbank-location, so the fix here is to actually work on #1.

This was referenced Jul 25, 2024
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@tsibley tsibley mentioned this issue Oct 30, 2024
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ingest: use new augur curate commands nextstrain/rabies
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