problems downloading Pedicularis example data

dereneaton / ipyrad

Interactive assembly and analysis of RAD-seq data sets

http://ipyrad.readthedocs.io

GNU General Public License v3.0

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problems downloading Pedicularis example data #552

Open jesus-mavarez opened 3 months ago

jesus-mavarez commented 3 months ago

Hi After typing this code: micromamba$ ipyrad --download SRP021469 example_empirical_data/

I receive this message:

Encountered an Error. Message: 2024-03-22T14:14:50 fastq-dump.2.9.6 err: column not found while opening table within short read archive module - failed /home/mavarezj/micromamba/example_empirical_data/41478_cyathophylloides_SRR1754722.sra

Any idea about what's going on?

isaacovercast commented 3 months ago

Yes, the SRA download feature is currently broken. NCBI updates the sra-tools from time to time and this breaks our integration. I like this feature so I hope to fix it soon.