How to download specific file types when downloading runs from BaseSpace using BaseSpace CLI

Downloading runs from BaseSpace using the BaseSpace Command Line Interface (CLI) will by default download all data stored under the run on BaseSpace. This will include thumbnail images, which are numerous and can often increase overall download times. If thumbnails are not required for any reason (they are not needed for FASTQ Generation) the methods below can greatly reduce run download times.

BaseSpace CLI can be downloaded from the BaseSpace Sequence Hub CLI page.

BaseSpace CLI To skip over thumbnail images (usually stored as .jpg files) when downloading runs from BaseSpace, the --extension option can be used to restrict the download to only those files needed for FASTQ Generation. Adding the option/argument combination shown below to a bs download command will accomplish this (all data needed to view run metrics in Sequencing Analysis Viewer (SAV) will also be included):

--extension=bcl.gz,bcl.bgzf,cbcl,bci,stats,locs,filter,bin,xml,csv  

The basecall file types will depend on the instrument (e.g. bcl.gz for MiSeq and cbcl NovaSeq, etc), however, including all possible (even if nonexistent) basecall file types (as shown below) will not affect the download. A complete example command for downloading a run with BaseSpace CLI and restricting to only the file types needed for FASTQ Generation (and viewing of SAV data) is shown below:

bs download run -i {RunID} -o {Destination} --extension=bcl.gz,bcl.bgzf,cbcl,bci,stats,locs,filter,bin,xml,csv  

Note: Adding the option --no-progress-bars to the command above may also speed things up as it will prevent printing the download progress of every file to the terminal.

For any feedback or questions regarding this article (Illumina Knowledge Article #3154), contact Illumina Technical Support [email protected].