skip to main content

SRA Toolkit Documentation

Back to List of the Tools

Tool: vdb-decrypt

vdb-decrypt - decrypt a file or all the files (recursively) in a directory
vdb-decrypt [options] <source-file>
vdb-decrypt [options] <source-file> <destination-file>
vdb-decrypt [options] <source-file> <destination-directory>
vdb-decrypt [options] <directory>
source-file - file to decrypt
destination-file - name of resulting file
destination-directory - directory of resulting file
directory - directory to decrypt
Decrypt a file or all the files (recursively) in a directory
-h | --help Output brief explanation for the program.
-f | --force force overwrite of existing files
--decrypt-sra-files decrypt sra archives [NOT RECOMMENDED]
-h | --help Output brief explanation of program usage
-V | --version Display the version of the program
-L | --log-level <level> Logging level as number or enum string One of (fatal|sys|int|err|warn|info) or (0-5). Current/default is warn
-v | --verbose Increase the verbosity level of the program. Use multiple times for more verbosity
--option-file Read file for more options and parameters
Use examples:
vdb-decrypt <file>
Will decrypt a single encrypted file that has been downloaded.
Possible errors and their solution:
File not readable after decryption.
Decryption seems to succeed typically with the message vdb-decrypt.2.5: exiting: success However the file is not readable or the content seems corrupted. This is caused by the toolkit being unable to locate the proper decryption key to use on the file. The most common causes are either that the repository key has not been installed or that the decryption process was being run outside of the project workspace.
vdb-decrypt.2.5 err: file exists while parsing argument list - can not over-write
There is already a file by the same name where vdb-decrypt is attempting to save the decrypted file. Either specify a new file name using vdb-decrypt [options] <source-file> <destination-file> or overwrite the exisitng file using the -f option.

With a single parameter, decryptions are in place, replacing files with new files that are decrypted.

With two parameters, decrypted copies of files are created, without changing the original files. If a file is already decrypted, it will only be copied.

Hidden files (that begin with a '.') having the extension .vdb-decrypt-tmp or .vdb-decrypt-tmp.lock are considered temporary files used by vdb-decrypt and are not decrypted. If encountered during in-place decryption, these files will be considered busy and skipped, unless the --force option was given.

In all other cases no file extensions are considered or changed.

Missing directories in the destination path will be created.