q2-fondue 'get-all' error for sequences

Community Plugin Support
1

I am attempting to use the 'get-all' command to and continue to get the following message:

Plugin error from fondue:

** Neither single- nor paired-end sequences could be downloaded. Please check your accession IDs.**

Debug info has been saved to /tmp/qiime2-q2cli-err-im4c2f82.log

Any thoughts?

2

Hi @Ms-Tai ,
Welcome to the forum!

Assuming that you have valid accession IDs (e.g., check the SRA website to confirm), the problem is most likely a transient connection or server-side issue. You can try again later to see if you have success.

I think you are maybe working with @SoilRotifer (I assume so because he reported the same error message in a direct message). In that case, we confirmed that was a transient issue and I think he got it working in the end.

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3

Thank you for your response! Yes, Dr. Robeson successfully assisted me in diagnosing and correcting the issue.

4

Hi @Nicholas_Bokulich and @SoilRotifer, was this really a transient issue?

I've been trying a download for a few days now, and I always end up with

q2_fondue.utils.DownloadError: Neither single- nor paired-end sequences could be downloaded. Please check your accession IDs.

The command I've been running is

qiime fondue get-all --i-accession-ids study-accession.qza --p-email my-unsw@email-address --p-retries 0 --verbose --output-dir fondue-output

Usually it gets as far as

2023-07-31 07:12:38,000 [MainThread] [INFO] [q2_fondue.metadata]: Fetching metadata for 481 run IDs.
2023-07-31 07:13:11,496 [MainThread] [INFO] [q2_fondue.sequences]: Downloading sequences for 481 accession IDs...

before it fails to download the sequences.

This is the single study accession I'm trying to download:

study-accession.qza (6.1 KB)

Thanks very much!

5

Hi @BenKaehler, other than 12 samples failing to download, I got it to run to completion.

6

Hi @BenKaehler,
Thanks for using q2-fondue :partying_face:

My guess is that your error appears because q2-fondue was not set up fully. Did you follow all the steps from the mandatory configuration instructions (especially vdb-config -i)?

After following the described steps, the download should run smoothly (it did in my case). Let me know if this helps!

3 Likes
7

Thanks @adamova! That was exactly it. I had not followed the mandatory configuration instructions. I should not have tried to play Zelda and install q2-fondue at the same time.

I apologise @adamova and @SoilRotifer for the user error.

Thanks,
Ben

1 Like
8

:smile: no worries, I'm glad it works now.

1 Like