Preservation of valuable data

Oct 13, 2025 by wbrum.org 54 views

Preserving Incomplete Output and Overwritten Files in Snakemake

Problem Description

When working with Snakemake, a popular workflow management system, it's not uncommon to encounter issues that lead to the removal of incomplete output files and the deletion of shadow directories. This can be frustrating, especially when large files generated after intensive computation are lost without any backups. In most cases, rerunning the job or checking logs can help diagnose the issue, but sometimes mistakes can be costly, and valuable data may be lost.

The Frustration of Data Loss

Snakemake's default behavior of removing broken or incomplete output files and cleaning up shadow directories, regardless of job success, can be a double-edged sword. On one hand, it helps keep the workflow execution manageable by removing unnecessary files. On the other hand, it can lead to data loss, which can be a significant setback, especially when working on complex projects that require significant computational resources.

Proposed Solution

To mitigate the risk of data loss, a proposed solution is to modify Snakemake's behavior to preserve failed or overwritten files in a designated cache directory. This would provide a safeguard against accidental data loss while keeping workflow execution manageable.

Preserving Failed or Overwritten Files

Instead of discarding failed or overwritten files outright, Snakemake could move them to a subfolder within .snakemake/, preserving the original directory structure. This would allow users to recover the files if needed. The proposed behavior is to move these files to .snakemake/cache/1-recycle/, ensuring that the original directory structure is preserved.

Consistent Naming Scheme for Shadow Directories

Another aspect of the proposed solution is to introduce a consistent naming scheme for shadow directories. This would help ensure that shadow directories are not removed if the job fails. The proposed naming scheme is .snakemake/shadow/1-xxxx, where xxxx is a unique identifier.

Preserving Shadow Directories

By introducing a consistent naming scheme for shadow directories, Snakemake can preserve these directories even if the job fails. This would prevent the loss of valuable data and ensure that the workflow execution is not disrupted.

Automatic Removal of Cached Files

To ensure that the cached files are no longer needed, a new workflow can attempt to create .snakemake/lock/1.out. If this file is created, it can assume that the cached broken files are no longer needed and remove them before execution.

Benefits of the Proposed Solution

The proposed solution provides several benefits, including:

Preservation of valuable data: By moving failed or overwritten files to a designated cache directory, users can recover the files if needed.
Consistent naming scheme for shadow directories: The proposed naming scheme ensures that shadow directories are not removed if the job fails.
Manageable workflow execution: The proposed solution ensures that workflow execution is not disrupted, even if the job fails.

Conclusion

In conclusion, the proposed solution provides a safeguard against accidental data loss while keeping workflow execution manageable. By preserving failed or overwritten files and introducing a consistent naming scheme for shadow directories, Snakemake can provide a more robust and reliable workflow management system.

Future Work

Future work could involve implementing the proposed solution in Snakemake and testing its effectiveness. Additionally, further research could be conducted to explore other ways to improve workflow execution and data preservation in Snakemake.

References

Snakemake documentation: https://snakemake.readthedocs.io/en/stable/
Snakemake GitHub repository: https://github.com/snakemake/snakemake
Frequently Asked Questions (FAQs) about Preserving Incomplete Output and Overwritten Files in Snakemake

Q: What is the current behavior of Snakemake regarding incomplete output files and shadow directories?

A: Snakemake currently removes any broken or incomplete output files and cleans up shadow directories, regardless of job success. This can lead to data loss, especially when large files generated after intensive computation are lost without backups.

Q: Why is it necessary to preserve incomplete output files and shadow directories?

A: Preserving incomplete output files and shadow directories provides a safeguard against accidental data loss. This is especially important when working on complex projects that require significant computational resources.

Q: How does the proposed solution address the issue of data loss?

A: The proposed solution moves failed or overwritten files to a designated cache directory, preserving the original directory structure. This allows users to recover the files if needed.

Q: What is the proposed naming scheme for shadow directories?

A: The proposed naming scheme for shadow directories is .snakemake/shadow/1-xxxx, where xxxx is a unique identifier.

Q: How does the proposed solution ensure that workflow execution is not disrupted?

A: The proposed solution ensures that workflow execution is not disrupted by introducing a consistent naming scheme for shadow directories. This prevents the removal of shadow directories if the job fails.

Q: Can a new workflow assume that the cached broken files are no longer needed and remove them before execution?

A: Yes, a new workflow can attempt to create .snakemake/lock/1.out. If this file is created, it can assume that the cached broken files are no longer needed and remove them before execution.

Q: What are the benefits of the proposed solution?

A: The proposed solution provides several benefits, including:

Preservation of valuable data: By moving failed or overwritten files to a designated cache directory, users can recover the files if needed.
Consistent naming scheme for shadow directories: The proposed naming scheme ensures that shadow directories are not removed if the job fails.
Manageable workflow execution: The proposed solution ensures that workflow execution is not disrupted, even if the job fails.

Q: How can I implement the proposed solution in Snakemake?

A: To implement the proposed solution in Snakemake, you can modify the Snakemake configuration file to include the following settings:

cache_dir: Set this to the directory where you want to store the cached files.
shadow_dir: Set this to the directory where you want to store the shadow directories.
lock_file: Set this to the file that will be used to indicate that the cached broken files are no longer needed.

Q: What are the potential risks or limitations of the proposed solution?

A: The proposed solution may introduce additional complexity to the workflow execution process. Additionally, the use of a cache directory may lead to increased storage requirements.

Q: How can I test the proposed solution?

A: To test the proposed solution, you can create a test workflow that includes the modified Snakemake configuration file. You can then run the workflow and verify that the cached broken files are preserved and the shadow directories are not removed.

Q: What are the next steps for implementing the proposed solution?

A: The next steps for implementing the proposed solution include:

Testing the proposed solution: Test the proposed solution in a controlled environment to ensure that it works as expected.
Refining the proposed solution: Refine the proposed solution based on the results of the testing process.
Implementing the proposed solution in Snakemake: Implement the proposed solution in Snakemake and make it available to users.

Q: How can I provide feedback or suggestions for improving the proposed solution?

A: You can provide feedback or suggestions for improving the proposed solution by submitting a pull request to the Snakemake GitHub repository or by contacting the Snakemake development team directly.