q2-fondue error: SRAMetadataFormat error

[meghna_swayambhu]

I wanted to download HMP data using the q2-fondue plugin. I have a list of SRR ids of the samples 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. However, I get the following error and am unable to find useful information for troubleshooting online.

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

Some samples are missing IDs in the following fields: Experiment ID, Sample Accession.
Plugin error from fondue:
/var/folders/46/37q2f70d54zd23k0kk17p3wc0000gn/T/q2-SRAMetadataFormat-qidzz4e_ is not a(n) SRAMetadataFormat file:
Some samples are missing IDs in the following fields: Experiment ID, Sample Accession.
See above for debug info.

[misialq (Michal Ziemski)]

Hey @meghna_swayambhu,

welcome to the forum and sorry to hear you're experiencing issues! Do you think you could provide the IDs of the samples you are trying to fetch? It would help us debug your issue - the NCBIAccessionIDs artifact would do. Feel free to reach out directly if you don't want to post those publicly on the forum.

Cheers,
Michal

[meghna_swayambhu]

Hi Michal,
Thank you very much for your repsose! Attached below is the .qza file and the corresponding error message for this particular object.
SRR_id_elbow.qza (5.0 KB)

Plugin error from fondue:

/var/folders/46/37q2f70d54zd23k0kk17p3wc0000gn/T/q2-SRAMetadataFormat-omt0qb26 is not a(n) SRAMetadataFormat file:

Some samples are missing IDs in the following fields: Experiment ID, Sample Accession.

See above for debug info.

[misialq (Michal Ziemski)]

Hi @meghna_swayambhu,

it turns out you uncovered a little bug ! All should be fixed now, so you could try re-installing q2-fondue and re-running the command you ran before. I would suggest using the command below to simply recreate the conda environment (you may need to remove the previous one) - note the conda channel change to 2022.11:

mamba create -y -n fondue \
   -c https://packages.qiime2.org/qiime2/2022.11/tested/ \
   -c conda-forge -c bioconda -c defaults \
   q2cli q2-fondue

After that, you can follow the usual installation/usage instructions. Please note that until Q2 2022.11 is officially released this will install the 2022.11 dev version of QIIME 2.

Hope this helps - please do let us know whether you managed to get your sequences!

Best,
Michal

[meghna_swayambhu]

Hi Michal,
Thank you very much for sorting this matter so promptly! I will try to download the data again in the next few days and get back to you.

Thank you again and happy weekend!
Meghna