PhyloseqR not showed up, not working

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Hii. I have used DADA2 for 16s metagenomics data analysis, it worked well till, but when I have tried to create PhyloseqR, it was not showed up in visualization tool and neither it came as error if not run properly in my history tab. How would I know where error occured. I have retried it using my metadata file which I have created using Notepad++. So, Can anyone tell me what to do and If its ok If I use other tools like kraken to prepare abundance and taxonomic profiling.
Thanks,
Shweta

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Welcome, @Shweta.203

Do you mean that you are getting an error with this tool?

  • Create phyloseq object from dada2 sequence and taxonomy tables
  • Links at the EU server and at the ORG server to help with confirming the tool. It may be hosted other places, too but the tool name at the top of the form would be the same.

If I guessed the correct tool, you can find an example of how to use it in the tutorials linked at the bottom of the tool form. This tool happens to have just one tutorial, I’ve pulled the link out to here. → Hands-on: Building an amplicon sequence variant (ASV) table from 16S data using DADA2 / Building an amplicon sequence variant (ASV) table from 16S data using DADA2 / Microbiome

To see how it works, try running the tutorial data through the tutorial workflow to create a sort of “answer key” example history. Then you can compare your custom inputs to the tutorial data, at all stages, and maybe find out where the problem was introduced.

And, you are welcome to share your work and we can try to help troubleshoot what else may be going wrong. How to do that is in the banner at this forum, and here directly. → How to get faster help with your question

If the job is not an error in the history (a red error dataset), you can try posting screenshots along with your history. Be sure to capture what the tool form looks like filled out. Those inputs will be in your shared history, and we can try to reproduce what you are doing to discover what may be going wrong.

Let’s start there! Sorry to hear you are having trouble but we can probably help to solve it. And if you are able to solve this on your own, please let us know! :slight_smile:

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As an example, this is my shared history using the tutorial data and workflow. This worked fine last week, and appears to be working again this week (so far!).

If new problems show up, we can sort out why that might be. :hammer_and_wrench:

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Hi Jenna, Thank you so much for your response.
I have shared my history, I am sharing my history:
Galaxy,
I am unable to use visualization tool of phyloseqR.
Could you please help me on this.
Thanks,
Shweta

1 Like
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Great, thank you for posting back your history, very helpful!

It turns out that the tool you are trying to use (the Phyloseq interactive environment) is a bit new, and the configuration currently has a problem at UseGalaxy.org.

Symptoms include the environment “never launching”, and it will eventually fail (turn “red” in the history).

Tracking ticket.

We expect to have that corrected some time next week. You don’t need to wait!

That ticket includes instructions for moving data around between Galaxy servers. UseGalaxy.eu is a good alternative. You can create and have an account at each of the servers to take advantage of the extra data storage space.

Thanks for reporting the problem with all the followup! :slight_smile:

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Thanks a lot Jenna for this solution, I hope it will work out. One thing I need to ask you that for metadata table, is it necessary to create metedata table on galaxy only or I can use my own metadata table (tabular form) created using notepad++.

Thanks a tonnes for your prompt response. Highly Appreciated.

1 Like
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So, the risks involved with creating tabular data inside of any text editing program (not just notepad++) is unintentionally introducing odd extra characters.

Sometimes these odd characters are “whitespace” characters: spaces, soft returns, extra returns (blank empty lines). Whitespace characters can all look the same when viewing the file’s text. But tools are very picky and will notice the difference, and then fail for odd reasons.

You can create simple text files with the Upload tool (that is the example in the tutorial you are following). Or, you can Upload a file you created on your computer, and double check the formatting in Galaxy, and even adjust it in Galaxy. Most of the command line utilities people commonly use are in Galaxy, plus there are environments where you can use those directly.

So, complicated answer! :slight_smile:

Yes. If you can ensure that the file is actually tabular – meaning, “tab separated values”, “tsv”, with no extra spaces, no extra blank lines at the top/end/internal – then, yes, you can load up any text file that you want to, and use it with tools (any tool, not just those in this tutorial). You can adjust the datatype to be “tabular” once in Galaxy.

More Tutorials!

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Hii Jenna,
It worked and thanks a lot for your suggestion, it really worked well. You saved my lots of time.

Many Thanks, you are doing great.

Thanks,
Shweta

1 Like
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Thanks, @Shweta.203 , I’m so glad this helped! You are doing great too! Learning how to move between servers is how to really get the most out of the public resources. :scientist:

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Hi Jenna,
Thanks for your response. Actually, I was able to create phyloseq for Dada2 in my previous query, it was resolved.
in my recent query, I am unable to make phyloseq for biom file. Hopefully your suggestion will work. I will try in Galaxy.eu.
Thanks,
Shweta

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Thanks @Shweta.203 that is interesting to know: one of the tools works but the other doesn’t. I’ll try to go through all of the options this week and follow up on any fixes needed. :hammer_and_wrench:

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Thanks Jenna,
I have tried in again to prepare Phyloseq for Biom file, but it didnot worked. the link for interactive tool was created but later on showed error. Only one time, it showed green and when I clicked on phyloseq link, it dispalyed 502 gateway error. Please suggest me what to do, I have the results but It cannot be visualized. I have barplots using Phinch and Krona chart for my data. But I am unable to use visualization tools for differential analysis and abundance plots. Please suggest me any alternative.

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Yes, the tool has not been corrected at UseGalaxy.org yet. You will need to try this at UseGalaxy.eu instead for now.

You can have an account at both (and any other Galaxy server!). Did you see how to move data between servers? This is very fast, and works with a URL so there is no download step. → FAQ: Transfer entire histories from one Galaxy server to another. You can copy just the files you want to move over into a new smaller history, then generate the history archive link, and move things over in a batch. I do this several times a day between servers and it works really well! :slight_smile:

Let’s close this ticket out and keep the conversation about the tool that has some issues in the original topic. PhyloseqR not showed up, not working