Trying to use circexplorer 2, job has been running for 8 days and still running. Why is it taking so long?
Welcome, @piglet22
That does seem odd!
We can help to check what is going on. We’ll need to know more details about where you are working, and the data that was input. You can do both by sharing your history here, or you can post screenshots of that same information. The first is better/faster but you decide. How to get faster help with your question
Screenshot, I left it a bit longer but it is still running since 18th July. I tried again using the untrimmed files, but that is doing the same thing.
@jennaj
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Great, thanks for following up @piglet22 !!
I’m staging a test run in this history. It will use tiny example data and should help us figure out what is going on. 
https://usegalaxy.eu/u/jenj/h/test-circexplorer-circexplorer2
XREF
CIRCexplorer2
- The Galaxy development repository has the implementation details (and is where I sourced the test data) → tools-iuc/tools/circexplorer2 at main · galaxyproject/tools-iuc · GitHub
- The author’s documentation what I’ll be comparing against → GitHub - YangLab/CIRCexplorer2: circular RNA analysis toolset and Pipeline - CIRCexplorer2
CIRCexplorer – as a comparison
- Galaxy → galaxytools/tools/circexplorer at master · bgruening/galaxytools · GitHub
- Author → GitHub - YangLab/CIRCexplorer: A combined strategy to identify circular RNAs (circRNAs and ciRNAs) (Zhang et al., Complementary Sequence-Mediated Exon Circularization, Cell (2014), 159:134-147) and GitHub - YangLab/CIRCexplorer: A combined strategy to identify circular RNAs (circRNAs and ciRNAs) (Zhang et al., Complementary Sequence-Mediated Exon Circularization, Cell (2014), 159:134-147)
More soon as I get that running plus review the input details. 
Hi all –
I’ve set up the same test as defined in the tool’s XML file, and with the same test data.
That content has links to data and examples you can test with.
- Tests are near the bottom of the XML file here tools-iuc/tools/circexplorer2/circexplorer2.xml at main · galaxyproject/tools-iuc · GitHub
- Test data is here tools-iuc/tools/circexplorer2/test-data at main · galaxyproject/tools-iuc · GitHub
Tip: how to get test data into Galaxy?
- Go to the tool’s
test-datafolder at Github - Click on the file you want to retrieve, then in the upper right you’ll see a button labeled raw. Capture that link (“right-click” under MacOS for “Copy Link Address”) and paste it into the Galaxy Upload tool using all default settings.
That is now running in here, and I loaded data for a few of the tests already. Tool tests 2 and 3 ran pretty quickly on this very small data.
What to do now:
Larger data will take longer, and the parameters choices will also matter. This tool has several modes, so … I would suggest reviewing the example data to compare to yours to see if you can notice anything different.
If you cannot figure out what is going on, you can share back a link to your history and we can try to help more. The details will matter for this one, so screenshots will probably not be enough unless you really capture all of the details: job logs with expanded sections + each input file with both the metadata and some of the data content lines + how the job was set up with the paramaters.
These guides explain what we will need →
- Troubleshooting resources for errors or unexpected results. The screenshots at the end show the application landmarks to pay attention to.
- How to get faster help with your question. Simple help about the same content, plus how to create a share link to the history.
Hope this helps, and this is for the other post here Circexplorer2 runtime - #4 by piglet22 that @piglet22 is asking about. Both of you can follow this help, and post your details for feedback. This tool is too complicated to troubleshoot without those gory details!