changes to error handling and SRA downloads #11
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…mmended in the docs. This should avoid large temporary sra files from being stored in the default chache location.
rpetit3
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Apr 19, 2023
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Hi @gtonkinhill
Thank you very much for the PR. Just some suggestions.
I'm going to do some testing on my end (I think I should be able to mimic ENA or SRA being down). I'll update soon, probably early next week.
Thanks again!
Robert
Co-authored-by: Robert A. Petit III <robbie.petit@gmail.com>
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Ignore the formatting the CI is complaining about, I'll get it fixed. I also repointed to a dev branch so I can test things out! Thanks again! |
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Hi,
Thanks very much for developing such a useful tool!
The ENA ftp server seemed to go down the other day and I noticed that
fastq-dlwas crashing rather than reverting to an SRA download. I've attempted to add a fix for this and have also added some other changes to the way SRA downloads are handled to avoid the temporary.srafiles from being stored in the default chache directory.In summary this pull request
prefetchfollowed byfasterq-dumpwhen downloading using the SRA--split-3 --mem 1Gparameters infasterq-dump. This should avoid cases of orphaned reads appearing in paired end files and hopefully increase the speed a bit (not tested).--forceoption that will overwrite files if they already exist and if the checksum does not match (in the case of ENA downloads).I have only done some fairly limited testing so it is probably worth double checking that I haven't broken anything. I'm also not 100% sure I have been running the tool correctly so apologies if any of these changes were not necessary.