Category
Fetch Data
Usage
vdb-validate [options] <path/file> [<path/file> ...]
Manual
Required arguments
- path(s): directories, files or VDB objects to be validated
Options
- -B, --BLOB-CRC : Check blobs CRC32 (default: yes)
- -I, --REFERENTIAL-INTEGRITY : Check data referential integrity for databases (default: yes)
- -C, --CONSISTENCY-CHECK : Deeply check data consistency for tables (default: no)
- -x, --exhaustive: Continue checking object for all possible errors (default: false)
- --sdc:rows : Specify maximum amount of secondary alignment table rows to look at before saying accession is good, default 100000. Specifying will iterate the whole table. Can be in percent (e.g. 5%)
- --sdc:seq-rows : Specify maximum amount of sequence table rows to look at before saying accession is good, default 100000. Specifying will iterate the whole table. Can be in percent (e.g. 5%)
- --sdc:plen_thold : Specify threshold for amount of secondary alignment which are shorter (hard-clipped) than corresponding primaries, default 1%.
- --ngc <path>: path to ngc file
- -h, --help: Output brief explanation for the program.
- -V, --version: Display the version of the program then quit.
- -L, --log-level <level>: Logging level as number or enum string. One of (fatal|sys|int|err|warn|info|debug) or (0-6) Current/default is warn.
- -v, --verbose: Increase the verbosity of the program status messages. Use multiple times for more verbosity. Negates quiet.
- -q, --quiet: Turn off all status messages for the program. Negated by verbose.
- --option-file <file>: Read more options and parameters from the file.
Example
First use prefecth to download the .sra and dependent files from NCBI SRA database:
prefetch -f yes SRR1552480
Then validate the downloaded file with vdb-validate:
vdb-validate SRR9045291/SRR9045291.sra
Finally, dump the .sra file to .fastq format with fastq-dump or fasterq-dump:
fastq-dump SRR1552480
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