get-fastq-pe fails on some SRRs even though fasterq dump gets it

harvardinformatics / snpArcher

Snakemake workflow for highly parallel variant calling designed for ease-of-use in non-model organisms.

MIT License

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get-fastq-pe fails on some SRRs even though fasterq dump gets it #64

Closed cademirch closed 1 year ago

cademirch commented 1 year ago

For example SRR15284758 failed on the rule with a 404 not found, though fasterq-dump was able to download it. Might be an issue with the link structure?

tsackton commented 1 year ago

Is this failing on main or dev? I tested with ffq and it looks like the links work fine. The new get fastq rule is still only in dev for now -- I will merge next week.

cademirch commented 1 year ago

Ah I see. It failed on main.

tsackton commented 1 year ago

Closed by #65