training a classifier using HOMD database

[Ruby_Shi]

Hello
I would like to use HOMD database as reference database http://www.homd.org/ I download the Taxon Table and 16s rRNA gene reference sequences. my code is

qiime tools import
–type ‘FeatureData[Sequence]’
–input-path HOMD_16S_rRNA_RefSeq_V15.2.p9.fasta
–output-path homd-ref.qza

qiime tools import
–type ‘FeatureData[Taxonomy]’
–input-format HeaderlessTSVTaxonomyFormat
–input-path homd_taxonomy.txt
–output-path homd-ref-taxonomy.qza

qiime feature-classifier extract-reads
–i-sequences homd-ref.qza
–p-f-primer CCTACGGGNGGCWGCAG
–p-r-primer GACTACHVGGGTATCTAATCC
–p-trunc-len 200
–p-min-length 100
–p-max-length 400
–o-reads homd-ref-seqs.qza

qiime feature-classifier fit-classifier-naive-bayes
–i-reference-reads homd-ref-seqs.qza
–i-reference-taxonomy homd-ref-taxonomy.qza
–o-classifier classifier.qza

But got an error : Plugin error from feature-classifier:

not enough values to unpack (expected 2, got 0)

Debug info has been saved to /vol/tmp/qiime2-q2cli-err-ur9njsb0.log
Thank you in advance!

[Nicholas_Bokulich]

@Ruby_Shi

not enough values to unpack (expected 2, got 0)

This indicates that the taxonomy file is not formatted correctly. The classifier is expecting that all taxonomies contain the same number of ranks; you probably either have one or more seqs that are missing in the taxonomy, or have incomplete taxonomic info.

See here for an example of this error:

Feature Classifier - Not enough values to unpack

Hi again, I figured out what the problem was. The imported taxonomy file is not correct and does not contain the taxonomy strings. I previously had issues importing the taxonomy using the following command: qiime tools import --type ‘FeatureData[Taxonomy]’ --source-format HeaderlessTSVTaxonomyFormat --input-path /shared/c3/bio_db/Phytoref/qiime2.tax.txt --output-path phytoref_taxonomy.qza I got an error saying that the file I am trying to import is not headerless, even though it clearly didn’…

Please let us know what you find! This will be useful for others who are trying to use the HOMD database.