Hi @ranocchia,
The problem appears to be an incomplete taxonomy.
We assume that every taxonomy is complete to the same level, but yours appears to have one that is specified as
k_Eukaryota; p_Parabasalia; c_Hypotrichomonadea; o_Hypotrichomonadida; f_Hypotrichomonadidae; g_Trichomitus sp.
without a species level classification. I can't check your taxonomy file directly, but that is what it looks like from the classifier.
So, you could either edit your taxonomy file to add a species for g_Trichomitus (I note that there is another entry for g_Trichomitus with s_unclassified, if that is helpful) or use the following command:
qiime feature-classifier classify-sklearn --i-reads rep-seqs.qza --i-classifier classifier.qza --o-classification result.qza --p-confidence -1 --p-read-orientation same
The second option skips the part where we need the species-level classification for g_Trichomitus, but forgoes confidence estimation and filtering.
Please don't hesitate to follow up if you have any more questions.