Job and Tool Error Help

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Job and Tool Error Help

So you started a job and it ended up failing. The result datasets are red in the history.

What to do? It depends on the failure type and where you are using Galaxy.

In a rush to solve the problem? The top reasons for failures are listed here. Also consider searching Known Issues and review the advanced troubleshooting help covered in Reporting Usage Issues or Software bugs (all linked above). Your problem may be something we are already working to correct or have existing prior Q and A, Galaxy help posts, documentation, and/or Galaxy tutorials that include a solution.

Query all Galaxy resources with the "Search Galaxy" box above


  1. The general troubleshooting help applies to most Galaxy servers/tools/functions.
  2. The cluster error help is server specific for Galaxy Main at
  3. If working at a different public Galaxy server, contacting the admins directly to address server-related problems is often necessary. Each Galaxy is independently administered.

Determining the job failure type

Did the job fail with some comments that are not descriptive of the problem? Are you sure?

Click on the bug icon within the error dataset to review details about the problem. This does not need to be submitted if you can figure out and correct the problem. There is a good chance you'll be able to link your issue to existing troubleshooting help, either here in the Galaxy hub or at Galaxy Help. Archived Q\&A may still be helpful, find it here: Galaxy Biostars.

Advanced troubleshooting help is covered at: Reporting Usage Issues or Software bugs

If you are still stuck after reviewing, please do send in the bug report and we can help.

  • Include a link to questions asked about the same problem that you may have posted online (example: at Galaxy Help)
  • Leave the input and output datasets undeleted
  • Do not delete the history immediately after submitting a bug report. Otherwise, there is a good chance we won't be able to help you.
  • Should you solve the problem before we reply, a follow-up email to let us know is appreciated.
  • The majority of submitted reports are not true software bugs. Usage problems involving incorrect input format or content cause most errors.
  • Confirming correct tool usage is where we start when diagnosing a problem, and is where you should start, too.. Sharing details about what you checked is always helpful.

Type: input problems

Type: cancelled by admin or a cluster failure

Type: exceeds memory allocation

Type: execution exceeds maximum allowed job run time (walltime)

Type: ValueError: invalid literal for int() with base 10

Type: Tool and software problems

Software or Tool Bug? Or a usage error? Sometimes it is hard to tell.

Examples - bugs

Usage error:

  • A mapping job runs out of memory resources. The input fastq was never verified to be in fastqsanger format. Rescaling the quality scores with the Fastq Groomer tool creates a job that uses far less memory, and it is successful.
  • The first time you use a new tool, there is a job error. Checking the inputs reveals that the BED dataset has columns in the wrong order. Fixing the BED dataset format allows the re-run job to be successful.

Software or Tool Bug:

  • A tool fails and produces an error message stating that a dependency was not found. The tool is not on the list of Known tool issues and a search against all issues does not locate a prior reported problem. You report the issue through a bug report, it is clarified and confirmed, the developers make a fix, and the updated tool is installed on the server. Future jobs are now successful.
  • When importing an older workflow, a pop-up notice informs that an upgraded tool is available. This tool is edited into the workflow. However, now the workflow fails - at that same tool that was updated. The issue is reported and fixed. Now your workflow runs without problems.

How to detect - bugs

  • The tool ended with what appears to be a tool problem message.
  • See examples above.
  • Search Galaxy Resources to see if the problem is a current known problem with a workaround.

How to resolve - bugs

  • If you are on the public Galaxy Main ( server, and ran a tool that produced a red error dataset, then you will probably want to start by reviewing the error reasons here first.
  • Fixing inputs first, as needed, and rerunning is recommended.
  • If you cannot determine the problem, report the error in a bug report. Add in comments about your reasons why this seems like a tool bug and not a usage/input problem if you can.

Special cases - bugs

  • Software can fail for many reasons. If you think there is a problem, please report it.
  • Send in a bug report or ask a question at Galaxy Biostars if you want the issue vetted first.
  • If you are reasonably certain the problem is with software or tools, and not usage, please report it directly to the Galaxy Issue Board.