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fastq-dump error code 3 with no cache and plenty of space? #878

Closed apredeus closed 10 months ago

apredeus commented 10 months ago

Dear SRA team,

I'm trying to use parallel-fastq-dump, which I'm sure as you know is a thin wrapper over fastq-dump. I keep getting error code 3 with at least one of the fastq-dump sub-processes, while I have plenty of lustre space (over 100 Tb), and has configured the tools to not use cache (and I indeed see that it's not used). The SRA files I'm processing are pre-downloaded, and they are quite large (20 Gb or more). Are there any parameters I can tune to avoid this error?

Thank you in advance!

apredeus commented 10 months ago

This has been resolved; I missed the warning that, when installed with conda, parallel-fastq-dump tends to install a really old version of sra-tools as a dependency. Forcing version 3.0.8 has solved the issue.