q2-fondue error: Plugin error

Library Plugin Support
1

Hello,

I wanted to download seqeuncing data usinf the q2-fondue plugin. I have a list of SRR ids of the sample that I wish to download. I started by importing the SRR ids from a .txt file to a qiime2 object (.qza) and then used the $ qiime fondue get-all command. Howerver, I get the following error and am unable to find useful information for troubleshooting online.

Plugin error from fondue:
Neither single- nor paired-end sequences could be downloaded. Please check your accession IDs.
See above for debug info.

I have already checked the accession IDs on the NCBI database and I don't known why the IDs were not found by q2-fondue whereas I can find them online...

I would be very grateful for any help, thank you very much!

2

Hi @Cecile
Could you send me the .txt that contains the accession IDs so I can test this on my end?

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3

Hi @cherman2,

Yep of course, there it is !

Thanks!

SraAccList_PRJNA944200.txt (675 Bytes)

5

Hi @Cecile,
I am running this now locally. Having said that I already downloaded 2 sequences out of the 56 successfully.
I will get back to you once it finished.

6

Hi @Cecile,
I was able to successfully download these sequences.

here was my command:
qiime fondue get-sequences --i-accession-ids SraAccList_PRJNA944200.qza --p-email [my_email] --output-dir test --verbose

Could you try running this and let me know how it goes? Just make sure to replace [my_email] with your email!

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8

Hi @cherman2,

Thanks ! It seems to work !

I don't known why it doesn't work before with the command get-all that I have tried before ...

qiime fondue get-all --i-accession-ids SraAccList_PRJNA944200.qza --p-email [my_email] --p-retries 3 --verbose --output-dir fondue_V3V4_output

Whatever, thanks again !

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9

Hi @Cecile

sometimes there are transient errors, e.g., if the server is not responding. q2-fondue will attempt to download a few times, but if it is unable to find any sequences to download it can respond with an error like you saw. So in cases like this, when you know that you have a valid accession number and sequences are indeed available, it can be worth just waiting some time and trying again.

Good luck!

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