How to troubleshoot this type of problem in general
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Click on the link inside the dataset to re-detect metadata. In many cases, this will clear up the problem.
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Check if the results are empty. Example: BAM results that have no data lines, only header lines.
- Double check that the intended target genome was actually mapped against. Use the rerun or job details buttons to review the original genome selected, modify if incorrect, and rerun.
- If using a custom genome, is it formatted correctly?
- Review quality metrics for fastq inputs with the tool
FastQCand address content issues. - Review the tool settings and online manuals. Does your data meet the minimum mapping criteria set by the parameters used? Is the tool appropriate for your datatype (spliced versus unspliced)? Adjust as needed. Most tool form options for most Galaxy tools are the same as when using a tool line-command.
- Test for server-side problems.
- Try at least one re-run to see if that resolves the problem (transient server/cluster issues).
- Is the tool marked as deprecated (public Galaxy server)? If so, choose an alternative tool that is not. See the Galaxy Tutorials if you are not sure of alternatives.
- Low memory resources (server/cluster that runs the jobs, different from account quota disk space) and related technical issues are possible.
- When running your own Galaxy, review the admin logs, disk space where you write outputs, etc.
- When using a public Galaxy server, contact the admins by email or through a bug report. Contact information is usually on the home page of a public server and often also here: https://galaxyproject.org/use
- Problems at a usegalaxy.* server can be reported at this forum. Specify which server by URL with your question.
Full help: Troubleshooting resources for errors or unexpected results