I am working on basecalling ONT sequencing data using dorado.
This is the error message:
[error] toml::parse: file open error -> [email protected]_5mCG@v0/config.toml
I have verified the file path, and have been able to verify the computer can find and read the file by using 'head' command.
Any other suggestions to fixing this problem?
Dear Annaliese Chang
Other than checking file path and permissions, you can do the following.
Make sure that:
- The file content is valid and not corrupted. Make sure the file follows the TOML syntax and does not contain any unexpected characters or errors.
- The file encoding is supported by the parser. Make sure the file is encoded in UTF-8 or ASCII and does not contain any BOM (byte order mark) characters.
You can try to validate your TOML file using an online tool like https://toml-parser.com/ or https://www.toml-lint.com/ to check for any syntax errors or formatting issues.
You can also try to use a different parser library or package that supports TOML, such as tomllib for Python or Tomli-W for writing TOML files.
Annaliese Chang When encountering the "toml::parse: file open error" in the context of working with dorado for basecalling ONT sequencing data, there are a few potential solutions you can try:
1. File permissions: Double-check the file permissions of the "config.toml" file. Ensure that the file is not locked or read-only, and that you have the necessary permissions to access and read it. You can use the "ls -l" command to view the file permissions and make any necessary adjustments using the "chmod" command.
2. File location: Confirm that the file is in the correct location and that the file path provided is accurate. Sometimes, a small error in the file path can lead to a "file open error." Consider using the absolute file path instead of a relative path to eliminate any ambiguity.
3. File encoding: Check if the file is encoded properly. Some applications might require specific encoding formats (e.g., UTF-8). Use tools like "file" or text editors that can display encoding information to verify if the file is encoded correctly. If necessary, convert the file to the required encoding format.
4. File format and content: Ensure that the "config.toml" file follows the correct format expected by the dorado application. TOML files have a specific syntax, so make sure there are no syntax errors or formatting issues in the file. You can use online TOML syntax validators to verify the integrity of the file.
5. Dependencies and libraries: Check if you have all the necessary dependencies and libraries required by dorado and the toml parser. Ensure that you have installed the correct versions and that they are compatible with each other. Upgrading or reinstalling the toml parser library might also help resolve any issues.
6. Error logs: Look for any additional error messages or logs that might provide more specific information about the issue. These logs can help identify the root cause of the problem and guide you towards a solution.
7. Community support: Seek assistance from the dorado or toml library's community or forums. Other users who have encountered similar issues might be able to provide insights or solutions based on their experiences.
Remember to document any steps you take and the outcomes, as this information can be helpful for troubleshooting and future reference. Good luck in resolving the "toml::parse: file open error" and successfully basecalling your ONT sequencing data using dorado!
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