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feat(ancestral): Add optional Nextclade GFF3 compatibility mode #2971

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feat(ancestral): Add optional Nextclade GFF3 compatibility mode

feat(ancestral): Add optional Nextclade GFF3 compatibility mode #2971

Triggered via pull request November 9, 2024 02:45
@corneliusroemercorneliusroemer
opened #1664
nextclade-compat
Status Failure
Total duration 12m 29s
Artifacts 13

ci.yaml

on: pull_request
Matrix: pytest-cram
mypy
51s
mypy
pyright
31s
pyright
build-docs  /  build
2m 15s
build-docs / build
check-docs
34s
check-docs
Matrix: pathogen-repo-ci-v0
Matrix: pathogen-repo-ci
release
0s
release
codecov
0s
codecov
rebuild-docker-image
0s
rebuild-docker-image
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14 errors and 15 warnings
test (python=3.8 biopython=1.80)
Process completed with exit code 1.
test (python=3.8 biopython=latest)
Process completed with exit code 1.
test (python=3.10 biopython=1.80)
The job was canceled because "_3_8_1_80" failed.
test (python=3.10 biopython=1.80)
The operation was canceled.
test (python=3.11 biopython=latest)
The job was canceled because "_3_8_1_80" failed.
test (python=3.11 biopython=latest)
The operation was canceled.
test (python=3.10 biopython=latest)
The job was canceled because "_3_8_1_80" failed.
test (python=3.10 biopython=latest)
The operation was canceled.
test (python=3.9 biopython=1.80)
The job was canceled because "_3_8_1_80" failed.
test (python=3.9 biopython=1.80)
The operation was canceled.
test (python=3.11 biopython=1.80)
The job was canceled because "_3_8_1_80" failed.
test (python=3.11 biopython=1.80)
The operation was canceled.
test (python=3.9 biopython=latest)
The job was canceled because "_3_8_1_80" failed.
test (python=3.9 biopython=latest)
The operation was canceled.
pyright
The `python-version` input is not set. The version of Python currently in `PATH` will be used.
check-docs
The `python-version` input is not set. The version of Python currently in `PATH` will be used.
mypy
The `python-version` input is not set. The version of Python currently in `PATH` will be used.
pathogen-repo-ci-v0 (avian-flu)
Failed to save: Unable to reserve cache with key 2024-11-09-linux-64-augur-args-30d39f4-root-dcc80ee-bin-[object Promise], another job may be creating this cache. More details: Cache already exists. Scope: refs/pull/1664/merge, Key: 2024-11-09-linux-64-augur-args-30d39f4-root-dcc80ee-bin-[object Promise], Version: 939591c2ddcc5f42a9b516a21218e7dd0d7bd1f9aa6ec5a1403b6d9c076f80ee
pathogen-repo-ci-v0 (ebola)
Failed to save: Unable to reserve cache with key 2024-11-09-linux-64-augur-args-30d39f4-root-dcc80ee-bin-[object Promise], another job may be creating this cache. More details: Cache already exists. Scope: refs/pull/1664/merge, Key: 2024-11-09-linux-64-augur-args-30d39f4-root-dcc80ee-bin-[object Promise], Version: 939591c2ddcc5f42a9b516a21218e7dd0d7bd1f9aa6ec5a1403b6d9c076f80ee
pathogen-repo-ci-v0 (mumps)
Failed to save: Unable to reserve cache with key 2024-11-09-linux-64-augur-args-30d39f4-root-dcc80ee-bin-[object Promise], another job may be creating this cache. More details: Cache already exists. Scope: refs/pull/1664/merge, Key: 2024-11-09-linux-64-augur-args-30d39f4-root-dcc80ee-bin-[object Promise], Version: 939591c2ddcc5f42a9b516a21218e7dd0d7bd1f9aa6ec5a1403b6d9c076f80ee
pathogen-repo-ci-v0 (ncov)
Failed to save: Unable to reserve cache with key 2024-11-09-linux-64-augur-args-30d39f4-root-dcc80ee-bin-[object Promise], another job may be creating this cache. More details: Cache already exists. Scope: refs/pull/1664/merge, Key: 2024-11-09-linux-64-augur-args-30d39f4-root-dcc80ee-bin-[object Promise], Version: 939591c2ddcc5f42a9b516a21218e7dd0d7bd1f9aa6ec5a1403b6d9c076f80ee
pathogen-repo-ci (zika)
Failed to save: Unable to reserve cache with key 2024-11-09-linux-64-augur-args-30d39f4-root-dcc80ee-bin-[object Promise], another job may be creating this cache. More details: Cache already exists. Scope: refs/pull/1664/merge, Key: 2024-11-09-linux-64-augur-args-30d39f4-root-dcc80ee-bin-[object Promise], Version: 939591c2ddcc5f42a9b516a21218e7dd0d7bd1f9aa6ec5a1403b6d9c076f80ee
pathogen-repo-ci (mpox)
Failed to save: Unable to reserve cache with key 2024-11-09-linux-64-augur-args-30d39f4-root-dcc80ee-bin-[object Promise], another job may be creating this cache. More details: Cache already exists. Scope: refs/pull/1664/merge, Key: 2024-11-09-linux-64-augur-args-30d39f4-root-dcc80ee-bin-[object Promise], Version: 939591c2ddcc5f42a9b516a21218e7dd0d7bd1f9aa6ec5a1403b6d9c076f80ee
pathogen-repo-ci-v0 (seasonal-flu)
Failed to save: Unable to reserve cache with key 2024-11-09-linux-64-augur-args-30d39f4-root-dcc80ee-bin-[object Promise], another job may be creating this cache. More details: Cache already exists. Scope: refs/pull/1664/merge, Key: 2024-11-09-linux-64-augur-args-30d39f4-root-dcc80ee-bin-[object Promise], Version: 939591c2ddcc5f42a9b516a21218e7dd0d7bd1f9aa6ec5a1403b6d9c076f80ee
pathogen-repo-ci (measles)
Failed to save: Unable to reserve cache with key 2024-11-09-linux-64-augur-args-30d39f4-root-dcc80ee-bin-[object Promise], another job may be creating this cache. More details: Cache already exists. Scope: refs/pull/1664/merge, Key: 2024-11-09-linux-64-augur-args-30d39f4-root-dcc80ee-bin-[object Promise], Version: 939591c2ddcc5f42a9b516a21218e7dd0d7bd1f9aa6ec5a1403b6d9c076f80ee
pathogen-repo-ci-v0 (tb)
Failed to save: Unable to reserve cache with key 2024-11-09-linux-64-augur-args-30d39f4-root-dcc80ee-bin-[object Promise], another job may be creating this cache. More details: Cache already exists. Scope: refs/pull/1664/merge, Key: 2024-11-09-linux-64-augur-args-30d39f4-root-dcc80ee-bin-[object Promise], Version: 939591c2ddcc5f42a9b516a21218e7dd0d7bd1f9aa6ec5a1403b6d9c076f80ee
pathogen-repo-ci (seasonal-cov)
Failed to save: Unable to reserve cache with key 2024-11-09-linux-64-augur-args-30d39f4-root-dcc80ee-bin-[object Promise], another job may be creating this cache. More details: Cache already exists. Scope: refs/pull/1664/merge, Key: 2024-11-09-linux-64-augur-args-30d39f4-root-dcc80ee-bin-[object Promise], Version: 939591c2ddcc5f42a9b516a21218e7dd0d7bd1f9aa6ec5a1403b6d9c076f80ee
pathogen-repo-ci (dengue)
Failed to save: Unable to reserve cache with key 2024-11-09-linux-64-augur-args-30d39f4-root-dcc80ee-bin-[object Promise], another job may be creating this cache. More details: Cache already exists. Scope: refs/pull/1664/merge, Key: 2024-11-09-linux-64-augur-args-30d39f4-root-dcc80ee-bin-[object Promise], Version: 939591c2ddcc5f42a9b516a21218e7dd0d7bd1f9aa6ec5a1403b6d9c076f80ee
pathogen-repo-ci-v0 (rsv)
Failed to save: Unable to reserve cache with key 2024-11-09-linux-64-augur-args-30d39f4-root-dcc80ee-bin-[object Promise], another job may be creating this cache. More details: Cache already exists. Scope: refs/pull/1664/merge, Key: 2024-11-09-linux-64-augur-args-30d39f4-root-dcc80ee-bin-[object Promise], Version: 939591c2ddcc5f42a9b516a21218e7dd0d7bd1f9aa6ec5a1403b6d9c076f80ee

Artifacts

Produced during runtime
Name Size
output-avian-flu
96.8 KB
output-dengue
1.31 MB
output-ebola
112 KB
output-lassa
322 KB
output-measles
3.87 MB
output-mpox
12.7 MB
output-mumps
339 KB
output-ncov
707 KB
output-rsv
9.44 MB
output-seasonal-cov
1.54 MB
output-seasonal-flu
51.5 KB
output-tb
5.02 MB
output-zika
749 KB