java -jar picard.jar CheckIlluminaDirectory BASECALLS_DIR=/BaseCalls/ READ_STRUCTURE=25T8B25T LANES=1 DATA_TYPES=BaseCalls
BASECALLS_DIR (File) The basecalls output directory. Required.
DATA_TYPES (IlluminaDataType) The data types that should be checked for each tile/cycle. If no values are provided then the data types checked are those required by IlluminaBaseCallsToSam (which is a superset of those used in ExtractIlluminaBarcodes). These data types vary slightly depending on whether or not the run is barcoded so READ_STRUCTURE should be the same as that which will be passed to IlluminaBasecallsToSam. If this option is left unspecified then both ExtractIlluminaBarcodes and IlluminaBaseCallsToSam should complete successfully UNLESS the individual records of the files themselves are spurious. Default value: null. Possible values: {Position, BaseCalls, QualityScores, PF, Barcodes} This option may be specified 0 or more times.
READ_STRUCTURE (String) A description of the logical structure of clusters in an Illumina Run, i.e. a description of the structure IlluminaBasecallsToSam assumes the data to be in. It should consist of integer/character pairs describing the number of cycles and the type of those cycles (B for Sample Barcode, M for molecular barcode, T for Template, and S for skip). E.g. If the input data consists of 80 base clusters and we provide a read structure of "28T8M8B8S28T" then the sequence may be split up into four reads:
* read one with 28 cycles (bases) of template
* read two with 8 cycles (bases) of molecular barcode (ex. unique molecular barcode)
* read three with 8 cycles (bases) of sample barcode
* 8 cycles (bases) skipped.
* read four with 28 cycles (bases) of template
The skipped cycles would NOT be included in an output SAM/BAM file or in read groups therein. Note: If you want to check whether or not a future IlluminaBasecallsToSam or ExtractIlluminaBarcodes run will fail then be sure to use the exact same READ_STRUCTURE that you would pass to these programs for this run. Required.
LANES (Integer) The number of the lane(s) to check. Default value: null. This option must be specified at least 1 times.
TILE_NUMBERS (Integer) The number(s) of the tile(s) to check. Default value: null. This option may be specified 0 or more times.
FAKE_FILES (Boolean) A flag to determine whether or not to create fake versions of the missing files. Default value: false. This option can be set to 'null' to clear the default value. Possible values: {true, false}
LINK_LOCS (Boolean) A flag to create symlinks to the loc file for the X Ten for each tile. Default value: false. This option can be set to 'null' to clear the default value. Possible values: {true, false}