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genomesDB STEP_4: add per-species sequence-table TSVs + fix manifest #129

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genomesDB STEP_4: add per-species sequence-table TSVs + fix manifest

genomesDB STEP_4: add per-species sequence-table TSVs + fix manifest #129

Triggered via push June 28, 2026 07:23
@000specific000specific
pushed 9c9f79c
main
Status Failure
Total duration 30s
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ci.yml

on: push
Validate YAML files
15s
Validate YAML files
Validate Python syntax
26s
Validate Python syntax
Validate shell scripts
21s
Validate shell scripts
Check project structure
4s
Check project structure
Check documentation
3s
Check documentation
Test demo (placeholder)
3s
Test demo (placeholder)
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2 errors and 16 warnings
Check project structure
Process completed with exit code 1.
Validate YAML files: ./gigantic_project-COPYME/subprojects/orthogroups/BLOCK_orthofinder/workflow-COPYME-run_orthofinder/START_HERE-user_config.yaml#L49
49:1 [key-duplicates] duplication of key "cpus" in mapping
Check documentation
Node.js 20 is deprecated. The following actions target Node.js 20 but are being forced to run on Node.js 24: actions/checkout@v4. For more information see: https://github.blog/changelog/2025-09-19-deprecation-of-node-20-on-github-actions-runners/
Test demo (placeholder)
Node.js 20 is deprecated. The following actions target Node.js 20 but are being forced to run on Node.js 24: actions/checkout@v4. For more information see: https://github.blog/changelog/2025-09-19-deprecation-of-node-20-on-github-actions-runners/
Check project structure
Node.js 20 is deprecated. The following actions target Node.js 20 but are being forced to run on Node.js 24: actions/checkout@v4. For more information see: https://github.blog/changelog/2025-09-19-deprecation-of-node-20-on-github-actions-runners/
Validate YAML files
Node.js 20 is deprecated. The following actions target Node.js 20 but are being forced to run on Node.js 24: actions/checkout@v4. For more information see: https://github.blog/changelog/2025-09-19-deprecation-of-node-20-on-github-actions-runners/
Validate YAML files: ./gigantic_project-COPYME/subprojects/trees_gene_groups/gene_groups_hgnc-COPYME/STEP_3-tree_visualization/workflow-COPYME-tree_visualization/ai/conda_environment.yml#L41
41:5 [indentation] wrong indentation: expected 6 but found 4
Validate YAML files: ./gigantic_project-COPYME/subprojects/trees_gene_groups/gene_groups-COPYME/STEP_3-tree_visualization/workflow-COPYME-tree_visualization/ai/conda_environment.yml#L41
41:5 [indentation] wrong indentation: expected 6 but found 4
Validate YAML files: ./gigantic_project-COPYME/subprojects/annotations_hmms/BLOCK_metapredict/workflow-COPYME-run_metapredict/ai/conda_environment.yml#L43
43:5 [indentation] wrong indentation: expected 6 but found 4
Validate YAML files: ./gigantic_project-COPYME/subprojects/annotations_hmms/BLOCK_tmbed/workflow-COPYME-run_tmbed/ai/conda_environment.yml#L57
57:5 [indentation] wrong indentation: expected 6 but found 4
Validate YAML files: ./gigantic_project-COPYME/subprojects/trees_gene_families/gene_family_COPYME/STEP_3-tree_visualization/workflow-COPYME-tree_visualization/ai/conda_environment.yml#L41
41:5 [indentation] wrong indentation: expected 6 but found 4
Validate YAML files: ./gigantic_project-COPYME/subprojects/annogroups/BLOCK_build_annogroups/workflow-COPYME-build_annogroups/START_HERE-user_config.yaml#L78
78:28 [commas] too many spaces after comma
Validate YAML files: ./gigantic_project-COPYME/subprojects/annogroups/BLOCK_build_annogroups/workflow-COPYME-build_annogroups/START_HERE-user_config.yaml#L77
77:28 [commas] too many spaces after comma
Validate YAML files: ./gigantic_project-COPYME/subprojects/annogroups/BLOCK_build_annogroups/workflow-COPYME-build_annogroups/START_HERE-user_config.yaml#L76
76:28 [commas] too many spaces after comma
Validate YAML files: ./gigantic_project-COPYME/subprojects/annogroups/BLOCK_build_annogroups/workflow-COPYME-build_annogroups/START_HERE-user_config.yaml#L75
75:28 [commas] too many spaces after comma
Validate YAML files: ./gigantic_project-COPYME/research_notebook/research_ai/subproject-genomesDB/ncbi_genomes-gigantic_T1_toolkit/toolkit-COPYME-ncbi_genomes_T1/START_HERE-user_config.yaml#L72
72:15 [colons] too many spaces after colon
Validate shell scripts
Node.js 20 is deprecated. The following actions target Node.js 20 but are being forced to run on Node.js 24: actions/checkout@v4. For more information see: https://github.blog/changelog/2025-09-19-deprecation-of-node-20-on-github-actions-runners/
Validate Python syntax
Node.js 20 is deprecated. The following actions target Node.js 20 but are being forced to run on Node.js 24: actions/checkout@v4, actions/setup-python@v5. For more information see: https://github.blog/changelog/2025-09-19-deprecation-of-node-20-on-github-actions-runners/