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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
313 stars 51 forks source link

[BUG] cannot download a single experiment from command line #201

Open marcomoretto opened 1 year ago

marcomoretto commented 1 year ago

Describe the bug Running pysradb from command line to download a single experiment SRX results into the program hanging forever.

To Reproduce Steps to reproduce the behavior: pip install git+https://github.com/saketkc/pysradb pysradb download -y -t 8 --out-dir ./pysradb_downloads -x SRX1254413

Additional context I used Google colab to reproduce the bug with the latest version of pysradb available in GitHub

saketkc commented 12 months ago

Thanks for catching this and apoligies for the delayed response. I think there is a bug in the download module. For now I would recommend saving the metadata in a csv using pysradb metadata --detailed <SRP> --saveto x.tsv and using a tool like curl/wget to download files from the *_url column