Hi @luweidong
The screenshot you posted is from the bug icon, not the job information icon. The latter has many more details that help with solving problems, and is what @igor was asking for to help more.
How/where to find job logs: Troubleshooting errors
When you get a red dataset in your history, it means something went wrong. But how can you find out what it was? And how can you report errors?
When something goes wrong in Galaxy, there are a number of things you can do to find out what it was. Error messages can help you figure out whether it was a problem with one of the settings of the tool, or with the input data, or maybe there is a bug in the tool itself and the problem should be reported. Below are the steps you can follow to troubleshoot your Galaxy errors.
- Expand the red history dataset by clicking on it.
- Sometimes you can already see an error message here
- View the error message by clicking on the bug icon
- Check the logs. Output (stdout) and error logs (stderr) of the tool are available:
- Expand the history item
- Click on the details icon
- Scroll down to the Job Information section to view the 2 logs:
- Tool Standard Output
- Tool Standard Error
- For more information about specific tool errors, please see the Troubleshooting section
What to do next
- Please post back what is in the stderr logs.
- You could also copy/paste back that entire page, with each of the sections fully expanded. This will speed up getting help, since any of those details could be the clue to solving the input problem.
Next time, for the fastest help, go ahead and post back that entire job information page content when asking a question. Don’t worry about it being long. You’ll get faster and better help from many more people. If you decide not to post the full content for some reason, then feedback is mostly an educated guess or just more requests for that same information.
When working in Galaxy, most of the technical details are in that view, instead of having to list things out. Meaning, most of these questions are answered in a single view: What information should I include when reporting a problem?
Writing bug reports is a good skill to have as bioinformaticians, and a key point is that you should include enough information from the first message to help the process of resolving your issue more efficient and a better experience for everyone.
What to include
- Which commands did you run, precisely, we want details. Which flags did you set?
- Which server(s) did you run those commands on?
- What account/username did you use?
- Where did it go wrong?
- What were the stdout/stderr of the tool that failed? Include the text.
- Did you try any workarounds? What results did those produce?
- (If relevant) screenshot(s) that show exactly the problem, if it cannot be described in text. Is there a details panel you could include too?
- If there are job IDs, please include them as text so administrators don’t have to manually transcribe the job ID in your picture.
It makes the process of answering ‘bug reports’ much smoother for us, as we will have to ask you these questions anyway. If you provide this information from the start, we can get straight to answering your question!
Please post back the content, and we can try to help solve the problem 