Yes, the feature is removed now from feature table, but when I generate my working-file (export biom object), then run R script, I got an error when importing biom file:
Error in read_biom(biom_file = BIOMfilename) : Both attempts to read input file: feature-table-with-taxonomy-json.biom either as JSON (BIOM-v1) or HDF5 (BIOM-v2). Check file path, file name, file itself, then try again.
stop(“Both attempts to read input file:\n”, biom_file, “\n”, “either as JSON (BIOM-v1) or HDF5 (BIOM-v2).\n”, “Check file path, file name, file itself, then try again.”)
read_biom(biom_file = BIOMfilename)
import_biom(biomfile, treefile, fastafile, parseFunction = parse_taxonomy_default)
I guess because of the mismatch of featureID across feature table, rep_seq and taxonomy table. The feature was removed only from feature table artifact??
However, I think the feature table has the parent key for the analysis.
So, I removed the ambiguous feature from rep_seq using this code:
qiime taxa filter-seqs --i-sequences rep_seq.qza --i-taxonomy taxonomy.qza --p-include D_0__ --p-exclude Ambiguous_taxa --o-filtered-sequences sequences-no-ambiguous.qza
and generated a new tree, so the feature is now removed from all files except taxonomy file that based on it feature-table-with-taxonomy.biom file is generated??
However, I still could not import the files in R at this step:
featuretable <- import_biom(biomfile, treefile, fastafile, parseFunction=parse_taxonomy_default)
and got the same error
I am not sure if something else is missing or what I did was incorrect?
May you please help me to figure it out