This uses the bascet integrated gecco command rather than the old mapcell system.
Usage
BascetMapCellGECCO(
bascetRoot,
inputName = "contigs",
outputName = "gecco",
numThreads = NULL,
dataDir = NULL,
threshold = 0.8,
cds = 3,
noMask = FALSE,
overwrite = FALSE,
runner = GetDefaultBascetRunner(),
bascetInstance = GetDefaultBascetInstance()
)Arguments
- bascetRoot
The root folder where all Bascets are stored
- inputName
Name of input shard
- outputName
Name of output shard
- numThreads
Total thread budget. Defaults to the runner CPU count
- dataDir
GECCO data directory containing HMM, CRF model, and InterPro files
- threshold
Minimum probability for cluster membership
- cds
Minimum number of annotated CDS in a cluster
- noMask
Do not mask ambiguous nucleotides during gene prediction
- overwrite
Force overwriting of existing files. The default is to do nothing files exist
- runner
The job manager, specifying how the command will be run (e.g. locally, or via SLURM)
- bascetInstance
A Bascet instance