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fix: explicitly specify how the root and ambiguous states are handled… #3104

fix: explicitly specify how the root and ambiguous states are handled…

fix: explicitly specify how the root and ambiguous states are handled… #3104

Triggered via pull request December 18, 2024 00:37
Status Failure
Total duration 13m 20s
Artifacts 12

ci.yaml

on: pull_request
Matrix: pytest-cram
Matrix: pathogen-repo-ci-v0
Matrix: pathogen-repo-ci
rebuild-docker-image
0s
rebuild-docker-image
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24 errors and 32 warnings
pathogen-repo-ci (zika)
The process '/home/runner/micromamba-bin/micromamba' failed with exit code null
pathogen-repo-ci (zika)
Process completed with exit code 1.
pathogen-repo-ci (zika)
ENOENT: no such file or directory, lstat '/home/runner/work/_temp/setup-micromamba/micromamba-shell'
test (python=3.11 biopython=1.82)
Process completed with exit code 1.
test (python=3.10 biopython=latest)
The job was canceled because "_3_11_1_82" failed.
test (python=3.10 biopython=latest)
The operation was canceled.
test (python=3.10 biopython=1.80)
The job was canceled because "_3_11_1_82" failed.
test (python=3.10 biopython=1.80)
The operation was canceled.
test (python=3.12 biopython=latest)
The job was canceled because "_3_11_1_82" failed.
test (python=3.12 biopython=latest)
The operation was canceled.
test (python=3.10 biopython=1.82)
The job was canceled because "_3_11_1_82" failed.
test (python=3.10 biopython=1.82)
The operation was canceled.
test (python=3.9 biopython=1.80)
The job was canceled because "_3_11_1_82" failed.
test (python=3.9 biopython=1.82)
The job was canceled because "_3_11_1_82" failed.
test (python=3.9 biopython=1.80)
The operation was canceled.
test (python=3.9 biopython=1.82)
The operation was canceled.
test (python=3.11 biopython=1.80)
The job was canceled because "_3_11_1_82" failed.
test (python=3.11 biopython=1.80)
The operation was canceled.
test (python=3.9 biopython=latest)
The job was canceled because "_3_11_1_82" failed.
test (python=3.9 biopython=latest)
The operation was canceled.
test (python=3.12 biopython=1.82)
The job was canceled because "_3_11_1_82" failed.
test (python=3.12 biopython=1.82)
The operation was canceled.
test (python=3.11 biopython=latest)
The job was canceled because "_3_11_1_82" failed.
test (python=3.11 biopython=latest)
The operation was canceled.
pyright
ubuntu-latest pipelines will use ubuntu-24.04 soon. For more details, see https://github.com/actions/runner-images/issues/10636
pyright
The `python-version` input is not set. The version of Python currently in `PATH` will be used.
pathogen-repo-ci (zika)
ubuntu-latest pipelines will use ubuntu-24.04 soon. For more details, see https://github.com/actions/runner-images/issues/10636
check-docs
ubuntu-latest pipelines will use ubuntu-24.04 soon. For more details, see https://github.com/actions/runner-images/issues/10636
check-docs
The `python-version` input is not set. The version of Python currently in `PATH` will be used.
mypy
ubuntu-latest pipelines will use ubuntu-24.04 soon. For more details, see https://github.com/actions/runner-images/issues/10636
mypy
The `python-version` input is not set. The version of Python currently in `PATH` will be used.
pathogen-repo-ci-v0 (mumps)
ubuntu-latest pipelines will use ubuntu-24.04 soon. For more details, see https://github.com/actions/runner-images/issues/10636
pathogen-repo-ci-v0 (mumps)
Failed to save: Unable to reserve cache with key 2024-12-18-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/1690/merge, Key: 2024-12-18-linux-64-augur-args-30d39f4-root-dcc80ee-bin-[object Promise], Version: 939591c2ddcc5f42a9b516a21218e7dd0d7bd1f9aa6ec5a1403b6d9c076f80ee
pathogen-repo-ci-v0 (avian-flu)
ubuntu-latest pipelines will use ubuntu-24.04 soon. For more details, see https://github.com/actions/runner-images/issues/10636
pathogen-repo-ci-v0 (avian-flu)
Failed to save: Unable to reserve cache with key 2024-12-18-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/1690/merge, Key: 2024-12-18-linux-64-augur-args-30d39f4-root-dcc80ee-bin-[object Promise], Version: 939591c2ddcc5f42a9b516a21218e7dd0d7bd1f9aa6ec5a1403b6d9c076f80ee
pathogen-repo-ci-v0 (ebola)
ubuntu-latest pipelines will use ubuntu-24.04 soon. For more details, see https://github.com/actions/runner-images/issues/10636
pathogen-repo-ci-v0 (ebola)
Failed to save: Unable to reserve cache with key 2024-12-18-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/1690/merge, Key: 2024-12-18-linux-64-augur-args-30d39f4-root-dcc80ee-bin-[object Promise], Version: 939591c2ddcc5f42a9b516a21218e7dd0d7bd1f9aa6ec5a1403b6d9c076f80ee
pathogen-repo-ci-v0 (ncov)
ubuntu-latest pipelines will use ubuntu-24.04 soon. For more details, see https://github.com/actions/runner-images/issues/10636
pathogen-repo-ci-v0 (ncov)
Failed to save: Unable to reserve cache with key 2024-12-18-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/1690/merge, Key: 2024-12-18-linux-64-augur-args-30d39f4-root-dcc80ee-bin-[object Promise], Version: 939591c2ddcc5f42a9b516a21218e7dd0d7bd1f9aa6ec5a1403b6d9c076f80ee
pathogen-repo-ci-v0 (seasonal-flu)
ubuntu-latest pipelines will use ubuntu-24.04 soon. For more details, see https://github.com/actions/runner-images/issues/10636
pathogen-repo-ci-v0 (seasonal-flu)
Failed to save: Unable to reserve cache with key 2024-12-18-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/1690/merge, Key: 2024-12-18-linux-64-augur-args-30d39f4-root-dcc80ee-bin-[object Promise], Version: 939591c2ddcc5f42a9b516a21218e7dd0d7bd1f9aa6ec5a1403b6d9c076f80ee
pathogen-repo-ci (mpox)
ubuntu-latest pipelines will use ubuntu-24.04 soon. For more details, see https://github.com/actions/runner-images/issues/10636
pathogen-repo-ci-v0 (tb)
ubuntu-latest pipelines will use ubuntu-24.04 soon. For more details, see https://github.com/actions/runner-images/issues/10636
pathogen-repo-ci-v0 (tb)
Failed to save: Unable to reserve cache with key 2024-12-18-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/1690/merge, Key: 2024-12-18-linux-64-augur-args-30d39f4-root-dcc80ee-bin-[object Promise], Version: 939591c2ddcc5f42a9b516a21218e7dd0d7bd1f9aa6ec5a1403b6d9c076f80ee
pathogen-repo-ci (measles)
ubuntu-latest pipelines will use ubuntu-24.04 soon. For more details, see https://github.com/actions/runner-images/issues/10636
pathogen-repo-ci (measles)
Failed to save: Unable to reserve cache with key 2024-12-18-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/1690/merge, Key: 2024-12-18-linux-64-augur-args-30d39f4-root-dcc80ee-bin-[object Promise], Version: 939591c2ddcc5f42a9b516a21218e7dd0d7bd1f9aa6ec5a1403b6d9c076f80ee
pathogen-repo-ci (seasonal-cov)
ubuntu-latest pipelines will use ubuntu-24.04 soon. For more details, see https://github.com/actions/runner-images/issues/10636
pathogen-repo-ci (seasonal-cov)
Failed to save: Unable to reserve cache with key 2024-12-18-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/1690/merge, Key: 2024-12-18-linux-64-augur-args-30d39f4-root-dcc80ee-bin-[object Promise], Version: 939591c2ddcc5f42a9b516a21218e7dd0d7bd1f9aa6ec5a1403b6d9c076f80ee
build-docs / build
ubuntu-latest pipelines will use ubuntu-24.04 soon. For more details, see https://github.com/actions/runner-images/issues/10636
pathogen-repo-ci (dengue)
ubuntu-latest pipelines will use ubuntu-24.04 soon. For more details, see https://github.com/actions/runner-images/issues/10636
pathogen-repo-ci (dengue)
Failed to save: Unable to reserve cache with key 2024-12-18-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/1690/merge, Key: 2024-12-18-linux-64-augur-args-30d39f4-root-dcc80ee-bin-[object Promise], Version: 939591c2ddcc5f42a9b516a21218e7dd0d7bd1f9aa6ec5a1403b6d9c076f80ee
pathogen-repo-ci (lassa)
ubuntu-latest pipelines will use ubuntu-24.04 soon. For more details, see https://github.com/actions/runner-images/issues/10636
pathogen-repo-ci (lassa)
Failed to save: Unable to reserve cache with key 2024-12-18-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/1690/merge, Key: 2024-12-18-linux-64-augur-args-30d39f4-root-dcc80ee-bin-[object Promise], Version: 939591c2ddcc5f42a9b516a21218e7dd0d7bd1f9aa6ec5a1403b6d9c076f80ee
pathogen-repo-ci-v0 (rsv)
ubuntu-latest pipelines will use ubuntu-24.04 soon. For more details, see https://github.com/actions/runner-images/issues/10636
pathogen-repo-ci-v0 (rsv)
Failed to save: Unable to reserve cache with key 2024-12-18-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/1690/merge, Key: 2024-12-18-linux-64-augur-args-30d39f4-root-dcc80ee-bin-[object Promise], Version: 939591c2ddcc5f42a9b516a21218e7dd0d7bd1f9aa6ec5a1403b6d9c076f80ee
test (python=3.11 biopython=1.82)
ubuntu-latest pipelines will use ubuntu-24.04 soon. For more details, see https://github.com/actions/runner-images/issues/10636

Artifacts

Produced during runtime
Name Size
output-avian-flu
96.5 KB
output-dengue
1.33 MB
output-ebola
112 KB
output-lassa
1.42 MB
output-measles
3.88 MB
output-mpox
12.8 MB
output-mumps
340 KB
output-ncov
709 KB
output-rsv
9.48 MB
output-seasonal-cov
1.58 MB
output-seasonal-flu
53.9 KB
output-tb
5.03 MB