[BUG] Metadata download only for a few run accessions, not for all the run accessions of the study

saketkc / pysradb

Package for fetching metadata and downloading data from SRA/ENA/GEO

https://saketkc.github.io/pysradb

BSD 3-Clause "New" or "Revised" License

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Closed cpavloud closed 6 months ago

cpavloud commented 6 months ago

Hello,

I am trying to run pysradb to retrieve the metadata for the study PRJEB55296. As you can see, the study has 670 run accessions.

However, when I run the command pysradb metadata PRJEB55296 --detailed --saveto output_SNMMP.txt

it only downloads the metadata for 7 of the accessions output_SNMMP.txt

I have used the same command before for other studies and it worked just fine.

Do you have any idea why is this happening?

Desktop:

saketkc commented 6 months ago

In this case it is just mimicking what you see on the NCIB's SRA search page: https://www.ncbi.nlm.nih.gov/sra/?term=PRJEB55296. Not sure why SRA is not synced up with ENA

cpavloud commented 6 months ago

Oh that's unfortunate... I wonder why they are not synced... I e-mailed NCBI's helpdesk. I hope they will reply!

cpavloud commented 6 months ago

Just to comment, NCBI corrected the study entry and now it has all the 670 accessions!

saketkc commented 6 months ago

Awsome, thanks for the update! And please feel free to reopen if you notice any other issues with pysradb