Closed roey-angel closed 5 years ago
OK this is of course because outputBootstraps=TRUE
produces a list so addSpecies()
needs to be run on taxa[[1]]
rather than taxa
OK this is of course because
outputBootstraps=TRUE
produces a list soaddSpecies()
needs to be run ontaxa[[1]]
rather thantaxa
Hi @roey-angel & @benjjneb , I've hit the same problem described in issue #690 in a batch processing script where I'd like to run assignTaxonomy, then addSpecies and then write an output *.csv file. Would you mind explaining what taxa[[1]]
is? I cannot find any reference to this in the tutorial. I have used outputBootstraps = TRUE in my batch script and understand that it's probably causing the issue but the workaround is unclear. Thanks!
When outputBootstraps=TRUE
the return value of assignTaxonomy
is a two element list. The first element (taxa[[1]]
) is the usual taxonomy matrix, which is acceptable input to addSpecies
. The second element (taxa[[2]]
) is a numeric matrix of the bootstrap values at each taxonomic level.
So, if you want to run addSpecies
, you should run it on taxa[[1]]
, the normal taxonomy table. I'm not sure what you are wanting to do with the bootstrap value matrix, but remember that it won't have a species column, since addSpecies
doesn't use boostrapping.
This is because
getUniques()
fails to run and gives the following error:But running
assignTaxonomy()
withoutputBootstraps=FALSE
and thenaddSpecies()
works (eventhoughgetUniques()
would still fail)