"summary.tax" returns "seqxxx is not in your name file"

Commands in mothur
1

I ran command:

summary.tax(taxonomy=…/…/…/Metagenomics/datasets/candidates/test/0426/taxAll.taxonomy,
name=…/…/…/Metagenomics/datasets/candidates/test/0426/seqAll.names,
group=…/…/…/Metagenomics/datasets/candidates/test/0426/groupAll.groups)

it returned “gnl|SRA|SRR095093.7.5 is not in your name file please correct.”

I checked, and the sequence is in both seqAll.names and groupAll.groups
what’s wrong?

2

Mothur expects every sequence in the taxonomy file to be a representative sequence, ie in the first column of the names file if you are using a names file. gnl|SRA|SRR095093.7.5 is represented by gnl|SRA|SRR095045.545.5 in your names file. Both are in your taxonomy file. Try running the following:

list.seqs(fasta=fastaFileAssociatedWithTheNamesFile) - to list all representative sequences
get.seqs(taxonomy=yourTaxonomyFile, accnos=current) - to select representative sequences from the taxonomy file