Assistance with resolving Sub.sample tool output error

[Erica_Dasi]

Greetings,

I am currently using the Galaxy Europe platform to analyze 16S sequencing data, while using the 16S Microbial Analysis tutorial (https://galaxyproject.github.io/training-material/topics/metagenomics/tutorials/mothur-miseq-sop/tutorial.html#otu-clustering). I have reached the step where the data is normalized using the sub.sample tool. I have followed the procedure provided in the tutorial and used the following parameters within the sub.sample tool:

• “Select type of data to subsample”: OTU Shared
• “Shared”: The “shared” file from Make.shared tool
• “Size”: 3242

However, after running the tool several times I receive an empty list with an error indicator in red rather. As a result, I am unable to proceed with the analysis.

I have also received an error message from the Galaxy platform mentioning the following:

“An error occurred while updating information with the server. Please contact a Galaxy administrator if the problem persists.”

Is it possible that this error message is linked to the error that I am receiving when using the sub.sample tool?

I also tried contacting a Galaxy administrator on Friday, October 11, 2019 for assistance at contact@usegalaxy.eu, however I have not received a response. I was unable to locate contact information for a Galaxy administrator or for technical support.

I was wondering if there are additional recommendations on addressing this challenge or for contacting an Galaxy administrator for help.

Thank you for your time and I look forward to hearing from you.

Sincerely,
Erica

[Erica_Dasi]

Good Afternoon,

I wanted to follow up in regards to my previous message. I have been trying to continue with my 16S sequencing analysis in the Galaxy Platform. Unfortunately, I have not been able to complete my workfow. When I attempt to use a variety of tools, I receive an error message indicating the following:

Parent instance <ToolShedRepository at 0x7faa284037d0> is not bound to a Session; lazy load operation of attribute ‘tool_dependencies’ cannot proceed (Background on this error at: http://sqlalche.me/e/bhk3)

Has anyone had experience with resolving this error?

Sincerely,
Erica

[Erica_Dasi]

[jennaj]

Hi @Erica_Dasi

First, try a rerun as these look like server-side issues – the Galaxy EU https://usegalaxy.org server was undergoing an update Mon-Weds. The issue may be resolved by now.

If that fails again – or maybe they can help now – let’s ping the admin here: @bjoern.gruening. He is in Germany (probably! unless in travel, etc) so please be patient for a reply. Might not get back till Mon/Tues. You also might want to submit a bug report from the red error dataset directly, that way of reporting problems gives much more context. You can mention you wrote in directly and give the subject line/date of that email so they can link the two. Should also put a link to this post in the comments, to link everything together.

Let us know if the rerun worked or not, please

[bjoern.gruening]

@Erica_Dasi we hope that this bug is now fixed. Please let us know if you encounter it again.

Sorry for the trouble!
Bjoern

[Erica_Dasi]

Thank you for reaching out. Unfortunately, I have encountered the same problem again using the sub.sample tool. The output that I receive when using the tool is an error indicator in red. I have attached a screenshot of along with this message. When I click the sub.sample tool to retrieve the associated error dataset, I only find a message informing me that the list is empty. As a result, I am unable to provide additional context regarding this issue. I have tried ru-running the tool, however, I have received the same error.

[Erica_Dasi]

Good Afternoon,

Hope all is well. I wanted to follow up in regards to my previous message. I look forward to receiving your assistance.

Sincerely,
Erica

[jennaj]

ping @bjoern.gruening

He may request a bug report. If you haven’t sent one in already, be sure to put a link to this thread in the comments so the EU team has the full context and can link the reported issues.

Update/edit: Oh! Your input list is empty. That’s why tool this tool is failing

Check the upstream steps/inputs. Mothur outputs are very easy to mix up, especially in that particular longer tutorial. Even I rarely get it all steps right when testing/reviewing it So some detective work on your part is needed. Use the “rerun” (double circle) icon to view which inputs were originally used at any particular step and you’ll be able to find where things went wrong.

[Erica_Dasi]

Hi Jennifer,

I hope you are well. Thank you for your assistance and suggestions with addressing the challenge I am experiencing. I have carefully reviewed the previous steps to ensure that the correct outputs are being used. Unfortunately, I am still receiving the same error message. I have been following the 16S microbial analysis using Mothur quite carefully am able to proceed past the sub.sampling step in Galaxy Austrailia. Therefore, I don’t believe the challenge is associated with my workflow. Unfortunately, Galaxy Australia is limited to the number visualization tools available. As a result, I have been trying to continue troubleshooting with the Galaxy Europe platform.

I will ping @bjoern.gruening for further assistance and provide an update on the status of my analysis in the Galaxy Europe website.

Thank you for your time and have a wonderful day!

Sincerely,
Erica

[bjoern.gruening]

Hi @Erica_Dasi,

we can try to look into your history or at your bug report. For this please sent us a bug report by clicking on the bug-icon at the red-dataset or share us your history.

Thanks,
Bjoern

[Erica_Dasi]

Good Morning @bjoern.gruening,

Hope you are well. I wanted to follow up in regards to receiving assistance with the challenge I am experiencing with the subsample tool. I submitted an error report on Monday, Oct. 28, 2019 and awaiting a response from the Galaxy Europe Administrators. Thank you in advance and I look forward to your response.

Sincerely,
Erica