How to deal with the .sra.vdbcache files after downloading a sra file?

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5.0 years ago

dz2353 ▴ 120

Hi, there

I have downloaded some .sra files by using prefetch command from GEO database. After that, I found some cache files in the same folder. The extension is .sra.vdbcache or .sra.vdbcache.cache. So I was wondering if I could delete them or how to deal with them? Does it mean that I do not download the complete .sra file? Thanks in advance.

RNA-Seq • 3.2k views

ADD COMMENT • link 5.0 years ago by dz2353 ▴ 120

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Did you solve the mystery? I have the same issue.

ADD REPLY • link 4.1 years ago by jlergajaso • 0

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I emailed to NLM-support and they replied to me as below:

The "vdbcache" files speed up the access to "sra" files that contain difficult or noisy data. Please note that the existence of these adjunct files does not mean that extraction to FASTQ will be fast; they are created only in cases where needed so that extraction isn't unbearably slow. If you keep the "sra" files around, you should also keep "vdbcache" files for them. If you are concerned about whether or not your .sra file is complete please use the SRA toolkit's vdb-validate (https://trace.ncbi.nlm.nih.gov/Traces/sra/sra.cgi?view=toolkit_doc&f=vdb-validate).

ADD REPLY • link 4.1 years ago by dz2353 ▴ 120

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