CI #3996
corneliusroemerci.yaml
on: schedule
Matrix: pytest-cram
mypy
52s
pyright
34s
build-docs
/
build
1m 40s
check-docs
43s
check-subsample-config-schema
43s
Matrix: pathogen-repo-ci-v0
Matrix: pathogen-repo-ci
rebuild-docker-image
0s
Annotations
41 errors and 17 warnings
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test (python=3.10 biopython=latest numpy=latest)
ENOENT: no such file or directory, lstat '/home/runner/work/_temp/setup-micromamba/micromamba-shell'
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test (python=3.10 biopython=latest numpy=latest)
The process '/home/runner/micromamba-bin/micromamba' failed with exit code 1
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pathogen-repo-ci-v0 (ncov)
ENOENT: no such file or directory, lstat '/home/runner/work/_temp/setup-micromamba/micromamba-shell'
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pathogen-repo-ci-v0 (ncov)
The process '/home/runner/micromamba-bin/micromamba' failed with exit code 1
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pathogen-repo-ci (lassa)
ENOENT: no such file or directory, lstat '/home/runner/work/_temp/setup-micromamba/micromamba-shell'
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pathogen-repo-ci (lassa)
Process completed with exit code 1.
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pathogen-repo-ci (lassa)
The process '/home/runner/micromamba-bin/micromamba' failed with exit code 1
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test (python=3.10 biopython=1.80 numpy=latest)
The strategy configuration was canceled because "pytest-cram._3_10" failed
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test (python=3.10 biopython=1.80 numpy=latest)
The operation was canceled.
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test (python=3.9 biopython=1.80 numpy=latest)
The strategy configuration was canceled because "pytest-cram._3_10" failed
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test (python=3.10 biopython=1.85 numpy=latest)
The strategy configuration was canceled because "pytest-cram._3_10" failed
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test (python=3.9 biopython=1.80 numpy=latest)
The operation was canceled.
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test (python=3.10 biopython=1.85 numpy=latest)
The operation was canceled.
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test (python=3.11 biopython=1.80 numpy=latest)
The strategy configuration was canceled because "pytest-cram._3_10" failed
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test (python=3.11 biopython=1.80 numpy=latest)
The operation was canceled.
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test (python=3.9 biopython=1.85 numpy=latest)
The strategy configuration was canceled because "pytest-cram._3_10" failed
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test (python=3.11 biopython=1.85 numpy=latest)
The strategy configuration was canceled because "pytest-cram._3_10" failed
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test (python=3.9 biopython=1.85 numpy=latest)
The operation was canceled.
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test (python=3.11 biopython=1.85 numpy=latest)
The operation was canceled.
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test (python=3.9 biopython=1.82 numpy=latest)
The strategy configuration was canceled because "pytest-cram._3_10" failed
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test (python=3.9 biopython=1.82 numpy=latest)
The operation was canceled.
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test (python=3.12 biopython=1.85 numpy=latest)
The strategy configuration was canceled because "pytest-cram._3_10" failed
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test (python=3.12 biopython=1.85 numpy=latest)
The operation was canceled.
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test (python=3.12 biopython=1.82 numpy=latest)
The strategy configuration was canceled because "pytest-cram._3_10" failed
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test (python=3.12 biopython=1.82 numpy=latest)
The operation was canceled.
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test (python=3.11 biopython=1.82 numpy=latest)
The strategy configuration was canceled because "pytest-cram._3_10" failed
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test (python=3.11 biopython=1.82 numpy=latest)
The operation was canceled.
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test (python=3.10 biopython=1.82 numpy=latest)
The strategy configuration was canceled because "pytest-cram._3_10" failed
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test (python=3.10 biopython=1.82 numpy=latest)
The operation was canceled.
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test (python=3.13 biopython=1.85 numpy=latest)
The strategy configuration was canceled because "pytest-cram._3_10" failed
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test (python=3.13 biopython=1.85 numpy=latest)
The operation was canceled.
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test (python=3.11 biopython=latest numpy=latest)
The strategy configuration was canceled because "pytest-cram._3_10" failed
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test (python=3.11 biopython=latest numpy=latest)
The operation was canceled.
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test (python=3.13 biopython=latest numpy=latest)
The strategy configuration was canceled because "pytest-cram._3_10" failed
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test (python=3.13 biopython=latest numpy=latest)
The operation was canceled.
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test (python=3.10 biopython=1.80 numpy=1.26.4)
The strategy configuration was canceled because "pytest-cram._3_10" failed
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test (python=3.10 biopython=1.80 numpy=1.26.4)
The operation was canceled.
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test (python=3.12 biopython=latest numpy=1.26.4)
The strategy configuration was canceled because "pytest-cram._3_10" failed
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test (python=3.12 biopython=latest numpy=1.26.4)
The operation was canceled.
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test (python=3.12 biopython=latest numpy=latest)
The strategy configuration was canceled because "pytest-cram._3_10" failed
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test (python=3.12 biopython=latest numpy=latest)
The operation was canceled.
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pyright
The `python-version` input is not set. The version of Python currently in `PATH` will be used.
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check-subsample-config-schema
The `python-version` input is not set. The version of Python currently in `PATH` will be used.
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mypy
The `python-version` input is not set. The version of Python currently in `PATH` will be used.
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pathogen-repo-ci-v0 (avian-flu)
Failed to save: Unable to reserve cache with key 2025-10-19-linux-64-augur-args-30d39f4-root-dcc80ee-bin-7f980036a54bf9b731e96423dab2167633dab2652673dc4fef598b730ac364cb, another job may be creating this cache.
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pathogen-repo-ci-v0 (seasonal-flu)
Failed to save: Unable to reserve cache with key 2025-10-19-linux-64-augur-args-30d39f4-root-dcc80ee-bin-7f980036a54bf9b731e96423dab2167633dab2652673dc4fef598b730ac364cb, another job may be creating this cache.
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pathogen-repo-ci (mumps)
Failed to save: Unable to reserve cache with key 2025-10-19-linux-64-augur-args-30d39f4-root-dcc80ee-bin-7f980036a54bf9b731e96423dab2167633dab2652673dc4fef598b730ac364cb, another job may be creating this cache.
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pathogen-repo-ci-v0 (rsv)
Failed to save: Unable to reserve cache with key 2025-10-19-linux-64-augur-args-30d39f4-root-dcc80ee-bin-7f980036a54bf9b731e96423dab2167633dab2652673dc4fef598b730ac364cb, another job may be creating this cache.
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pathogen-repo-ci (dengue)
Failed to save: Unable to reserve cache with key 2025-10-19-linux-64-augur-args-30d39f4-root-dcc80ee-bin-7f980036a54bf9b731e96423dab2167633dab2652673dc4fef598b730ac364cb, another job may be creating this cache.
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pathogen-repo-ci-v0 (vcf-input-tutorial)
Failed to save: Unable to reserve cache with key 2025-10-19-linux-64-augur-args-30d39f4-root-dcc80ee-bin-7f980036a54bf9b731e96423dab2167633dab2652673dc4fef598b730ac364cb, another job may be creating this cache.
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pathogen-repo-ci (mpox)
Failed to save: Unable to reserve cache with key 2025-10-19-linux-64-augur-args-30d39f4-root-dcc80ee-bin-7f980036a54bf9b731e96423dab2167633dab2652673dc4fef598b730ac364cb, another job may be creating this cache.
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pathogen-repo-ci (zika)
Failed to save: Unable to reserve cache with key 2025-10-19-linux-64-augur-args-30d39f4-root-dcc80ee-bin-7f980036a54bf9b731e96423dab2167633dab2652673dc4fef598b730ac364cb, another job may be creating this cache.
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pathogen-repo-ci (oropouche)
Failed to save: Unable to reserve cache with key 2025-10-19-linux-64-augur-args-30d39f4-root-dcc80ee-bin-7f980036a54bf9b731e96423dab2167633dab2652673dc4fef598b730ac364cb, another job may be creating this cache.
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pathogen-repo-ci (measles)
Failed to save: Unable to reserve cache with key 2025-10-19-linux-64-augur-args-30d39f4-root-dcc80ee-bin-7f980036a54bf9b731e96423dab2167633dab2652673dc4fef598b730ac364cb, another job may be creating this cache.
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pathogen-repo-ci-v0 (ncov)
No files were found with the provided path: ./pathogen-repo/auspice/
./pathogen-repo/results/
./pathogen-repo/benchmarks/
./pathogen-repo/logs/
./pathogen-repo/.snakemake/log/. No artifacts will be uploaded.
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pathogen-repo-ci (seasonal-cov)
Failed to save: Unable to reserve cache with key 2025-10-19-linux-64-augur-args-30d39f4-root-dcc80ee-bin-7f980036a54bf9b731e96423dab2167633dab2652673dc4fef598b730ac364cb, another job may be creating this cache.
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pathogen-repo-ci (yellow-fever)
Failed to save: Unable to reserve cache with key 2025-10-19-linux-64-augur-args-30d39f4-root-dcc80ee-bin-7f980036a54bf9b731e96423dab2167633dab2652673dc4fef598b730ac364cb, another job may be creating this cache.
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pathogen-repo-ci (rabies)
Failed to save: Unable to reserve cache with key 2025-10-19-linux-64-augur-args-30d39f4-root-dcc80ee-bin-7f980036a54bf9b731e96423dab2167633dab2652673dc4fef598b730ac364cb, another job may be creating this cache.
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Artifacts
Produced during runtime
| Name | Size | Digest | |
|---|---|---|---|
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output-avian-flu
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98.2 KB |
sha256:8f9e98629eb0eb8aa7a6d439a18840b0c39a11b2fbe8bb6c3723a549fe5e6081
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output-dengue
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436 KB |
sha256:75f06c4c0911e1c920c30291c2a0c79f4e94ed3bfd117f0d737710a2424005a3
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output-measles
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3.94 MB |
sha256:af9e3f6cb65a6776df7018c6139084ca3400918cf4ce69bcff1dc6799bd688a5
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output-mpox
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14.4 MB |
sha256:f5e9e9eb6bbc0a8e46ddd75e159a7e9f37c3ccf78d46331f6df7fba5c282818f
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output-mumps
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379 KB |
sha256:5803247d03e2e292c0bf10a12750bfe47af541ae40cde21ca1826d655f1ce242
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output-oropouche
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588 KB |
sha256:ab899dfea9abc37a46370159b89c9ddce2bdb73b7c581fdd258ca994688026eb
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output-rabies
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5.28 MB |
sha256:83c2a8d17b745c202ea6f437a0a16eafca8585c77c200275c186aa99da74f474
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output-rsv
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1.2 MB |
sha256:de639c8a11f2800cd93644eccc2d808c77b6c47b43c090705f8f686df035777c
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output-seasonal-cov
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2.47 MB |
sha256:b5cfad825be79e20718aeb6475b49acd856f059c0d98f6004ce6830434ccab78
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output-seasonal-flu
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60.3 KB |
sha256:b006623db98496b373d96c60e1d2749f70db7f5567b1461fc68daafc8a4f934a
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output-vcf-input-tutorial
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5.03 MB |
sha256:70c3749c12f622ab29a56d6314fa0f77ea8f3d4e773e24a5a82dc56e1c0ebb05
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output-wnv
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241 KB |
sha256:a39ee52a86264fedd78b2f89e11151f5f67dca302c6fa6d9fd3ae852b79e4e40
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output-yellow-fever
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2.12 MB |
sha256:7ba2827f5fd454454c26a41bdc564f7df697b821bcbec422d350346138650480
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output-zika
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807 KB |
sha256:3be1a53039e64f60b85fccc1eb1cb52147f5e1f1ebc7b55bb7b87e1d7af84567
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