DESeq2 returns results as empty list.

usegalaxy.org support
1

This had been working fine 6 months ago. I am now analyzing a new data set and it looks like it is running fine. The plots come out and look just fine as well as normalized count files but the list for the results is empty. I have rerun it over the course of the last few days and each time the list is still empty.

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2

Hi @acrocker

Please double-check that you are using the most current version of the tool:

If this is the version you are using, please confirm that you are working at the public Galaxy Main server at https://usegalaxy.org.

Thanks!

3

Yes. I am using 2.11.40.6 and believe I am working at the public instance of galaxy at usegalaxy.org.

Also I tried on the european site usegalaxy.eu and worked fine with the same current version of the tool.

Thank you

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4

Thanks for the extra info @acrocker

I wasn’t able to reproduce this with a test yesterday at usegalaxy.org.

Perhaps there is something special about your run configuration that is hitting a novel corner-case problem. If you would like a review, sharing the history that demonstrates the problem is the quickest way to communicate.

I am an administrator at both usegalaxy.org and here at Galaxy Help, so there are a few ways you could do this:

  1. If your registered account at both places uses the same email address, post back publically and state so, and note the name of the history and the datasets (by number) involved.

  2. If your registered accounts use different email addresses, send me a private direct message here with the email address you use at usegalaxy.org. Note the name of the history and the datasets (by number) involved.

  3. If your registered accounts use different email addresses, send me a private direct message here with a share link to the history. Note the datasets (by number) involved. When generating the share link, be sure to also check the box to “also share objects” in the history to make this go quicker. If you are not sure if the objects are shared, toggle the history share link off/on to check or make changes.

You do not need to post email addresses publically and you never need to share your password with anyone, no matter who they say that are – an administrator doesn’t need it – admins just need to know what data to review.

You could decide to post your history share link publically. Many do and that is fine. It depends on how concerned you are about data privacy around your work.

To send a direct message here in Galaxy Help, click on the other person’s “@” and you’ll see an envelope icon to use. I’m @jennaj. When you do this from within a topic, the message is branched off privately from the topic (adding helpful context).

For any choice: the history should contain all input and output datasets in an undeleted state, or help will be limited.

I added a tag to your post for “share-or-publish” – click on it and review prior Q&A if you are not sure how to generate a history share link with datasets also shared. Or, review these FAQs:

Sorry you had problems but let’s try a review and find out if this is some usage problem (and explain how to avoid it) or a novel tool issue (and report it/get it fixed).

5

Thanks for the report, I can reproduce this and we will release a fix shortly.

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6

Thanks again for the report, this should be fixed with DESeq2 version 2.11.40.6+galaxy1 (https://usegalaxy.org/root?tool_id=toolshed.g2.bx.psu.edu/repos/iuc/deseq2/deseq2/2.11.40.6+galaxy1)

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7

Thank you for helping with this. Sorry about the slow response I have been away. I will try it again when I am back.

Thank you

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