Tutorial issues - De novo transcriptome assembly, annotation, and differential expression analysis.

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1

Hi all,

I am having some trouble with the following tutorial -

De novo transcriptome assembly, annotation, and differential expression analysis.

I am currently on the annotation step, working with the dummy dataset provided. I have completed the similarity search, and I an currently trying to perform the find signal peptides, find transmembrane domains, and search again profile database steps. The TMHMM tool works fine, however when I try to run the find signal peptides with SignalP 3.0, I receive the following error message -

“open: can’t stat file
apparent state: unit 8 named /usr/local/tools/signalp/signalp-3.0//syn/CS.euk.1.syn
lately writing sequential formatted external IO
One or more tasks failed, e.g. 1 from 'signalp -short -t euk /data/jwd02f/main/068/711/68711023/tmp/”

Here is the URL to the history -

Does anyone have any idea why this tool is failing?

Thanks!

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Hi @FireProofJames

This part looks like it was a transient server problem. Have you tried a rerun yet?

I am also testing with your history. Thanks for sharing it! More feedback soon.

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Hi @FireProofJames

Update: I can reproduce this with test data, and it seems to be a tool configuration issue impacting all versions. I’ve reported it to the EU server administrators using the :beetle: icon within the red error dataset and included the link back to this topic in the comments.

They are usually able to fix things quickly, and will likely post back here once ready to try again. Feel free to check back in a couple of days as needed.

Thanks for reporting the problem! :slight_smile:

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Thank you so much, JennaJ. Im glad that it wasn’t something silly that I did.

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