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pachterlab / ffq

A tool to find sequencing data and metadata from public databases.
MIT License
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ffq not working anymore (ffq: error) #67

Closed rderelle closed 7 months ago

rderelle commented 7 months ago

Hi,

thanks for developing ffq. It has been really helpful so far!

However, it doesn't seem to work anymore. The following command line used to output something and I'm now getting an error message:

ffq SRR6046717 [2024-03-01 22:19:28,054] INFO Parsing run SRR6046717 [2024-03-01 22:19:28,192] ERROR 404 Client Error: for url: https://www.ebi.ac.uk/ena/browser/api/xml/SRR6046717/ [2024-03-01 22:19:28,192] ERROR Provided accession is invalid usage: ffq [-h] [-o OUT] [-l LEVEL] [--ftp] [--aws] [--gcp] [--ncbi] [--split] [--verbose] [--version] IDs [IDs ...] ffq: error: For possible failure modes, please see https://github.com/pachterlab/ffq#failure-modes

Does it have to do with ncbi depreciating the SRA IDs? Is there a work around?

Thanks in advance if you could help me.

sbooeshaghi commented 7 months ago

Please upgrade to v0.3.1 and this example will work. A change to the ENA database caused an error with ffq which has now been resolved.

https://pypi.org/project/ffq/0.3.1/

rderelle commented 7 months ago

Many thanks, it works!