Issue with obtaining tomtom results from meme-chip

usegalaxy.eu support
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2

Hello @Orange_Pomeranian

Thanks for sharing the details! It sounds like you are simply not getting any hits from your query based on the current scientific parameters choices. A result of “no hits” is a valid result, so it won’t fail the tool (only actual errors e.g. seriously problematic inputs or some server issue will).

Some ideas of what to do to check the technical aspects, then to explore the scientific choices more.

  1. Do you see any messages from the tool in the job logs? Find these using the pencil icon → Details tab. The log boxes will expand. This is always the first place to check whenever you get an error – but also when you get unexpected results. These are the same messages you would get if the tool was run outside of Galaxy.

  2. Double check the format of the input query. You have set the options for DNA (nucleotide). Make sure the format is very simple. We can help with getting the technical details like this correct if you want to share your history back. See → How to get faster help with your question. You can unshare once we are done.

  3. Try running with the defaults. Then try running with a higher evalue (less significant). What happens? This is a way to see if “no hits” might be valid for this sample.

  4. Adjust other parameters to investigate. We have examples in our tutorials (also linked at the bottom of the tool form) and those link to the original author’s guide/publication, too.

  5. Subset your query into smaller chunks when running these parameter tests to help them to complete quicker. See the tool Split file to a dataset collection to do this. The elements will be under the Hidden tab in your history, and you can unhide one (or, a few) to use them as inputs.

  6. Finally, if you are not working at a UseGalaxy server, you could move your history over and see if that helps. See → FAQ: Transfer entire histories from one Galaxy server to another. UseGalaxy.org, UseGalaxy.eu. and UseGalaxy.org.au are the larger resourced choices.

Let’s start there! Hope this helps and if you do want to share the job logs or history back, we might be able to help with some of the above. :slight_smile: