Hello,
I am using function qza_to_phyloseq function in qiime2R to create a phyloseq object. When using read_qza individually on my qza files (feature table, taxonomy, and phylogenetic tree) and read.table on my metadata.txt everything appears okay. However, when I run qza_to_phyloseq function I get an error message: Error in validObject(.Object) : invalid class “phyloseq” object:
Component sample names do not match.
Try sample_names()
Initially, I used numbers for my sampleid column of my metadata file. Following recommendations in this post here and discussion here, I reindexed my samples in my feature table with qiime feature-table group from "#" to "Sample#" and changed my metadata file accordingly under column sampleid. I validated the new metadata file with keemei.
GreenOnly4660PhyloseqObj <- qza_to_phyloseq(
features = "qza_files/rarefied_table_4660_eelgrass_GreenOnly_reindexed.qza",
tree = "qza_files/2019_eelgrass_runs_1_3_16S_rep_sequences_deblur_aligned_masked_rooted_tree.qza",
taxonomy = "qza_files/2019_eelgrass_runs_1_3_16S_rep_sequences_deblur_sklearn_naive_bayes_taxonomy.qza",
metadata = "reindex_samplenumber/EelgrassMicrobiomeWaterSamples2019MetadataFullquotetrue_sampleid.txt"
)
Error in validObject(.Object) : invalid class “phyloseq” object:
Component sample names do not match.
Try sample_names()
sample_names(metadata.table.reindex)
NULL
gplots::venn(list(metadata=rownames(metadata.table.reindex),featuretable=colnames(GreenOnly_rarefied_table_4660_reindex)))
no common values for row names and column names
Any ideas what could be the source of this error? My metadata file was generated by write.table in R and validated with Keemei.
rarefied_table_4660_eelgrass_GreenOnly_reindexed.qza (1.7 MB)
EelgrassMicrobiomeWaterSamples2019MetadataFullquotetrue_sampleid.txt (294.5 KB)