Stopping In STEP4 -> 04.rundiamond.pl. Program Finished Abnormally

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Introduction

SqueezeMeta is a powerful tool for analyzing metagenomes, providing a comprehensive pipeline for processing and interpreting large datasets. However, like any complex software, it can encounter issues that hinder its performance. In this article, we will delve into a specific problem encountered by a user, where the pipeline stopped at STEP4 with an error message indicating that the program finished abnormally. We will explore the possible causes of this issue, discuss potential solutions, and provide guidance on troubleshooting similar problems.

Background

The user in question is utilizing SqueezeMeta version 1.6.5post1 to analyze 496 metagenomes. Initially, the pipeline completed half of the samples without any issues. However, a few days ago, the pipeline stopped at STEP4, resulting in the following error message:

Stopping in STEP4 -> 04.rundiamond.pl. Program finished abnormally

Error Message Analysis

The error message suggests that the program terminated abnormally, and the user is encouraged to search for similar issues on the SqueezeMeta GitHub page. If the solution is not found, the user is invited to open a new issue, providing a brief description of the problem and attaching the relevant log file, in this case, the /home/hongchang/Data/sequential/OER00128095/syslog file.

Upon further investigation, the user discovered that the diamond.nr.log file in the temp folder contained the following message:

terminate called after throwing an instance of 'std::runtime_error' what(): Format error: Invalid varint encoding.

This error message indicates that the Diamond program encountered a format error due to invalid varint encoding.

Similar Issues and Potential Solutions

The user found a similar issue on the SqueezeMeta GitHub forum (#672) and attempted to update the Diamond version to 2.1.1, as suggested in the issue #653 on the Diamond GitHub page. However, this solution did not resolve the problem.

Troubleshooting Steps

To troubleshoot this issue, we recommend the following steps:

  1. Check the Diamond version: Ensure that the Diamond version is up-to-date and compatible with the SqueezeMeta pipeline.
  2. Verify the input files: Inspect the input files for any formatting errors or inconsistencies that may be causing the Diamond program to fail.
  3. Analyze the log files: Examine the log files, including the diamond.nr.log file, to identify any specific error messages or patterns that may indicate the root cause of the issue.
  4. Search for similar issues: Consult the SqueezeMeta GitHub page and other relevant resources to see if similar issues have been reported and resolved.
  5. Open a new issue: If the solution is not found, create a new issue on the SqueezeMeta GitHub page, providing a brief description of the problem and attaching the relevant log files.

Conclusion

In conclusion, the error message "Stopping in STEP4 -> 04.rundiamond.pl. Program finished abnormally" indicates that the SqueezeMeta pipeline encountered an issue at STEP4, resulting in the termination of the. By analyzing the error message, searching for similar issues, and following the troubleshooting steps outlined above, users can identify the root cause of the problem and potentially resolve the issue.

Additional Resources

For further assistance, please refer to the following resources:

Q&A: Troubleshooting SqueezeMeta Pipeline Issues

Q: What is the cause of the "Stopping in STEP4 -> 04.rundiamond.pl. Program finished abnormally" error message?

A: The error message indicates that the SqueezeMeta pipeline encountered an issue at STEP4, resulting in the termination of the program. The specific cause of the issue is not immediately clear, but it is likely related to a problem with the Diamond program, which is used in STEP4.

Q: What is Diamond, and why is it used in STEP4?

A: Diamond is a protein sequence search tool that is used in STEP4 of the SqueezeMeta pipeline to search for protein sequences in the metagenome. It is used to identify protein sequences that are similar to known protein sequences in the database.

Q: What is the "Format error: Invalid varint encoding" error message, and how is it related to the issue?

A: The "Format error: Invalid varint encoding" error message indicates that the Diamond program encountered a problem with the format of the input data. Varint encoding is a way of encoding integers in a compact binary format, and the error message suggests that the Diamond program was unable to correctly decode the varint encoding in the input data.

Q: How can I troubleshoot the issue and resolve the problem?

A: To troubleshoot the issue, you can try the following steps:

  1. Check the Diamond version: Ensure that the Diamond version is up-to-date and compatible with the SqueezeMeta pipeline.
  2. Verify the input files: Inspect the input files for any formatting errors or inconsistencies that may be causing the Diamond program to fail.
  3. Analyze the log files: Examine the log files, including the diamond.nr.log file, to identify any specific error messages or patterns that may indicate the root cause of the issue.
  4. Search for similar issues: Consult the SqueezeMeta GitHub page and other relevant resources to see if similar issues have been reported and resolved.
  5. Open a new issue: If the solution is not found, create a new issue on the SqueezeMeta GitHub page, providing a brief description of the problem and attaching the relevant log files.

Q: What are some common causes of the "Stopping in STEP4 -> 04.rundiamond.pl. Program finished abnormally" error message?

A: Some common causes of the error message include:

  • Outdated Diamond version: Using an outdated version of Diamond that is not compatible with the SqueezeMeta pipeline.
  • Formatting errors in input files: Errors in the formatting of the input files that are causing the Diamond program to fail.
  • Varint encoding issues: Problems with the varint encoding in the input data that are causing the Diamond program to fail.
  • Memory or resource issues: Insufficient memory or resources to run the Diamond program.

Q: How can I prevent the "Stopping in STEP4 -> 04.rundiamond.pl Program finished abnormally" error message from occurring in the future?

A: To prevent the error message from occurring in the future, you can try the following:

  • Regularly update Diamond: Ensure that the Diamond version is up-to-date and compatible with the SqueezeMeta pipeline.
  • Verify input files: Inspect the input files for any formatting errors or inconsistencies that may be causing the Diamond program to fail.
  • Monitor log files: Regularly examine the log files to identify any specific error messages or patterns that may indicate the root cause of the issue.
  • Search for similar issues: Consult the SqueezeMeta GitHub page and other relevant resources to see if similar issues have been reported and resolved.

Conclusion

In conclusion, the "Stopping in STEP4 -> 04.rundiamond.pl. Program finished abnormally" error message is a common issue that can be caused by a variety of factors, including outdated Diamond versions, formatting errors in input files, varint encoding issues, and memory or resource issues. By following the troubleshooting steps outlined above and taking preventative measures, you can resolve the issue and prevent it from occurring in the future.