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12 months ago
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Hi,
I have been trying to download data using the SRAtool kit. Most of the time, prefetch works well without having any issues. However, for a dataset I am trying to download recently, some of the accessions failed on downloading the vdbcache file, whereas the .sra is complete.
prefetch.3.0.7: HTTPS download failed
prefetch.3.0.7: 1) failed to download "SRRaccession.vdbcache': RC(rcNS,rcFile,rcValidating,rcNoObj,rcEmpty)
Can I remove the vdbcache which had failed to download and perform fastq-dump on the .sra from the same accession? Will this have any impact on the actual data itself? Thanks.
see: How to deal with the .sra.vdbcache files after downloading a sra file?
If those files are missing the conversion may be slow.
When possible you should try to get the direct fastq download links from
sra-explorer(LINK) or use software like https://github.com/rpetit3/fastq-dl.Hi GenoMax, thanks for the reply. I've also come across this post and my interpretation is that the conversion process is only going to be slower without the cache files. But I'm not too completely sure if this will affect the sequences stored in the fastq files in anyway with the incomplete cache file. I did notice that some accessions won't output the cache files at all.