App startup loop

[Christian Jansen]

Hey everyone,

I have a problem with executing my native basespace app.
It works fine with the basespace example dataset (Project MiSeq v3: 16S Metagenomics (Human Saliva, Wastewater Sludge, Alum Rock Cave)) however when I try to use my companies own data from one of our projects (also sequenced on an Illumina MiSeq by our partner laboratory), the app hangs itself up.

When I start the app with the respective data It displays the message below several times in a row (8x in my current try) and then does not respond any more. I don't get any error message and I also don't see any reaction by my local development VM which should receive the job from Basespace/SpaceDock

>> 2022-11-18 10:41:02Z [INFO] - Resolving datasets of library prep Unknown from BioSample '12345678'
>> 2022-11-18 10:41:02Z [INFO] - Resolving Sample from 1 Fastq Datasets: 12345678_L001
>> 2022-11-18 10:41:03Z [INFO] - Found one existing matching sample '12345678'

Has anyone else experienced such an issue before or knows what might be causing it?

I'm grateful for any hints and suggestions.

Best regards,

Christian

[Christian Jansen]

Dear community,

Unfortunately the problem above ist still not solved, so I did some additional debugging and want to lay out the examples here to maybe make the problem reproducible or get some insights on what the issue might be.

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                        The Problem

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The core problem is still the same, the App starts up as expected with some datasets while for others including our company dataset it will display the following 3 Lines over and over again until it crashes.

>> 2022-11-18 10:41:02Z [INFO] - Resolving datasets of library prep Unknown from BioSample '12345678'
>> 2022-11-18 10:41:02Z [INFO] - Resolving Sample from 1 Fastq Datasets: 12345678_L001
>> 2022-11-18 10:41:03Z [INFO] - Found one existing matching sample '12345678'

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                    Broken dataset

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As I am not able to share the dataset of my company, I tried an additional example dataset and was able to reproduce the problem.

The dataset in question is the MiSeq: 16S Metagenomics 2x300 (ATCC Microbiome Standard MSA-1003)

https://basespace.illumina.com/s/ZwcORR23almq

When starting the app with this dataset by sending the job to my local virtual machine, the console log displays the above described 3 lines with the sample-id of the first selected samples.

I also monitored the docker containers being launched on the virtual machine, however nothing is started there so the problem can not be located in the docker container or the scripts of the pipeline.

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                   Working dataset

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In contrast du the example dataset above, the dataset 16S Metagenomics Demo (https://basespace.illumina.com/s/ZwcORR23almq) launches the app as expected.
The same three lines as above are displayed but only once per sample, and afterwards the docker image is downloaded and the script to start up the app is executed according to the console log.

When monitoring the docker containers in the local virtual machine, the correct container is launched with the correct script and I am able to log into the container and observer the running processes of the app.

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                         Question

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At this point me and my colleagues are quite sure that the problem is not situated within our app but rather in the underlying software on the illumina servers.

Our best guess is, that there is some kind of permission error due to different permissions/ownerships etc. of the datasets.

If anyone reading this has experienced similar issues, we would be very grateful if you could describe your problem as well so we might get an idea on what is going on.

If a member of the Illumina developer team reads this, can you please look into this!
I am happy to provide further details to you for debugging via e-mail (christia...@biome-dx.com).

Thank you to everyone reading this and happy holidays,

Christian Jansen

[Al Maynard]

Hi Christian,

It's tricky to diagnose this without going through tech support to share more information on the issue, and your email gets truncated so I can't reach out directly.

That said, it sounds like you are running in a VM in your own environment. Unfortunately, that method of debugging is not recommended and is not reliable. 

Can you please try running in the BaseSpace infrastructure instead of a local agent and reporting if you see the same issue? 

Thanks

Al

[Christian Jansen]

Hi Al,

Thank you for your reply and a happy new year.

I have run the test datasets again on the basespace infrastructure and unfortunately I have the same issues as with the local VM environment.

Yes sorry, the shortening of the e-mail is caused by google groups.
The e-mail is: christian[dot]jansen[at]biome-dx[dot]com

I am very much looking forward to your response!
Best regards,

Christian

[Al Maynard]

Hi Christian,

Unfortunately, your timing isn't great... This group has been shut down - please see the announcement above.

Either way, it would be best if you contacted tech support: https://www.illumina.com/company/contact-us.html

Al