Hi everyone,
I am trying to import a .biom file from metagenomeseq 1.16.0 to mothur (1.43.0), but it keeps giving me error message that
[ERROR]: you file does not have a type provided.
[ERROR]: you file does not have a matrix_type provided.
[ERROR]: you file does not have a matrix_element_type provided.
[ERROR]: you file does not have a rows provided.
[ERROR]: you file does not have a columns provided.
[ERROR]: you file does not have a shape provided.
[ERROR]: you file does not have a data provided.
The part of my biom file looks like this:
{
“id”: null,
format: “Biological Observation Matrix 1.0.0-dev”,
format_url: “http://biom-format.org/documentation/format_versions/biom-1.0.html”,
type: “OTU table”,
generated_by: “metagenomeSeq 1.16.0”,
date: “2018-05-24 07:37:51”,
matrix_type: “dense”,
matrix_element_type: “float”,
shape: [ 5030, 237 ],
rows: [
{
“id”: “OTU_88”,
metadata: {
“taxonomy”: [ “k__Bacteria”, “p__Proteobacteria”, “c__Betaproteobacteria”, “o__Burkholderiales”, “f__Comamonadaceae”, “g__Polaromonas”, “s__” ]
}
},
{
“id”: “OTU_53”,
metadata: {
“taxonomy”: [ “k__Bacteria”, “p__Bacteroidetes”, “c__Sphingobacteriia”, “o__Sphingobacteriales”, “f__”, “g__”, “s__” ]
}
},
{
“id”: “OTU_1”,
metadata: {
“taxonomy”: [ “k__Bacteria”, “p__Cyanobacteria”, “c__Nostocophycideae”, “o__Nostocales”, “f__Nostocaceae”, “g__Dolichospermum”, “s__” ]
}
},
Could anyone help with this? Thanks a lot!