How to troubleshoot Galaxy job failures?

Check Job Outputs and Error Logs

• Locate the error logs under the "View Details" option for the failed job. These logs often provide valuable clues about the nature of the failure.

 

• Analyze the standard error and standard output sections in the logs to pinpoint any specific error messages or codes.

 

• Consult the "Galaxy History" panel for additional information on the job status and outputs that might provide insights.

Check Tool-Specific Issues

• Determine if the issues stem from specific tool errors by checking if the error replicates across various datasets with the same tool.

 

• Refer to the tool documentation or community forums for common issues associated with the particular version you're using.

 

• Verify if the tool requires specific parameters or input formatting that might not be met in the current configuration.

Resource Limitations

• Examine if the job's requirements exceed the available memory or time limits by reviewing the job configuration and cluster settings.

 

• Consider changing the destination for your jobs to a cluster with higher resource allocations if possible.

 

• Split large datasets into smaller chunks, if applicable, to decrease resource consumption.

Syntax and Input Format Errors

• Ensure that input files are in the correct format by cross-verifying with required formats listed in the Galaxy tool forms or documentation.

 

• Double-check for syntax errors or incorrect parameter settings which might be causing the job to fail.

 

• Test the tool with a known good dataset to differentiate between data-specific and tool-specific issues.

Galaxy Configuration Issues

• Review Galaxy instance settings and configurations to ensure there are no systemic issues affecting job performance.

 

• Update tools or Galaxy software to the latest stable versions, as bugs and fixes are often addressed in updates.

 

• Consult the Galaxy administrator for any relevant changes made at the system level that might impact job execution.

Seek Community Help

• Utilize community forums like Galaxy Biostar to post detailed descriptions of unresolvable issues. Include relevant logs or error messages for community insights.

 

• Look through archived discussions to see if a similar problem has been resolved in the past.