# \#feature-classifier **URL:** https://forum.qiime2.org/tag/feature-classifier/28.md [Latest](https://forum.qiime2.org/latest.md) · [Categories](https://forum.qiime2.org/categories.md) · [Tags](https://forum.qiime2.org/tags.md) --- ## [Advice on Conducting a Targeted Pathogenic Species Search using ITS1 data using QIIME2 feature-classifier plugin](https://forum.qiime2.org/t/advice-on-conducting-a-targeted-pathogenic-species-search-using-its1-data-using-qiime2-feature-classifier-plugin/34336)
**Author:** [@vic.everhart](https://forum.qiime2.org/u/vic.everhart)\ **Replies:** 3\ **Last updated:** [September 24, 2026, 9:09pm UTC](https://forum.qiime2.org/t/advice-on-conducting-a-targeted-pathogenic-species-search-using-its1-data-using-qiime2-feature-classifier-plugin/34336 "2026-09-24T21:09:46Z")
Hello. I am currently working with ITS1 amplicon data and am new to QIIME2. I am interested in cross referencing my ITS1 data with a specifically curated database with fungal pathogens of interest. I'm interested in pote… --- ## [16S Sequencing for Species-Level Resolution](https://forum.qiime2.org/t/16s-sequencing-for-species-level-resolution/34284)
**Author:** [@Jeremie\_Auger](https://forum.qiime2.org/u/Jeremie_Auger)\ **Replies:** 5\ **Last updated:** [September 8, 2026, 12:59pm UTC](https://forum.qiime2.org/t/16s-sequencing-for-species-level-resolution/34284 "2026-09-08T12:59:15Z")
Hi qiime2 community. (This post is long, but needs some context.) The short story is that I think that the qiime2 classification (or taxa collapse) step are stopping species-level classification for vaginal swab microbi… --- ## [pre-trained UNITE ITS classifiers for QIIME 2026.7 and scikit-learn=1.7.1](https://forum.qiime2.org/t/pre-trained-unite-its-classifiers-for-qiime-2026-7-and-scikit-learn-1-7-1/24140)
**Author:** [@colinbrislawn](https://forum.qiime2.org/u/colinbrislawn)\ **Replies:** 15\ **Last updated:** [August 31, 2026, 6:59pm UTC](https://forum.qiime2.org/t/pre-trained-unite-its-classifiers-for-qiime-2026-7-and-scikit-learn-1-7-1/24140 "2026-08-31T18:59:19Z")
UNITE version 10.0 was updated on 2025-02-19, and I've built classifiers for it compatible with the newest version of Qiime2: New in 2026 Updated to qiime2-amplicon-2026.7 that includes scikit-learn=1.7.1 I've rewrit… --- ## [Using RESCRIPt's 'extract-seq-segments' to extract reference sequences without PCR primer pairs.](https://forum.qiime2.org/t/using-rescripts-extract-seq-segments-to-extract-reference-sequences-without-pcr-primer-pairs/23618)
**Author:** [@SoilRotifer](https://forum.qiime2.org/u/SoilRotifer)\ **Replies:** 5\ **Last updated:** [November 14, 2023, 7:22pm UTC](https://forum.qiime2.org/t/using-rescripts-extract-seq-segments-to-extract-reference-sequences-without-pcr-primer-pairs/23618 "2023-11-14T19:22:00Z")
:construction: Please consider this tutorial a living document, which may change based upon community feedback and ongoing plugin development. Please feel free to ask questions and provide feedback. Happy :qiime2:ing! … --- ## [Train a taxonomy classifier by extracting an amplicon region from a curated sequence alignment (using SILVA as an example).](https://forum.qiime2.org/t/train-a-taxonomy-classifier-by-extracting-an-amplicon-region-from-a-curated-sequence-alignment-using-silva-as-an-example/34289)
**Author:** [@SoilRotifer](https://forum.qiime2.org/u/SoilRotifer)\ **Replies:** 0\ **Last updated:** [August 12, 2026, 5:46pm UTC](https://forum.qiime2.org/t/train-a-taxonomy-classifier-by-extracting-an-amplicon-region-from-a-curated-sequence-alignment-using-silva-as-an-example/34289 "2026-08-12T17:46:15Z")
:construction: Please consider this tutorial a living document , which may change based upon community feedback and ongoing plugin development. :construction: Overview: There are several approaches within QIIME 2, and… --- ## [RESCRIPt-evaluate](https://forum.qiime2.org/t/rescript-evaluate/34265)
**Author:** [@SoilRotifer](https://forum.qiime2.org/u/SoilRotifer)\ **Replies:** 0\ **Last updated:** [July 27, 2026, 7:34pm UTC](https://forum.qiime2.org/t/rescript-evaluate/34265 "2026-07-27T19:34:46Z")
RESCRIPt-evaluate History: Due to dependency conflicts with other branches of rachis (i.e. moshpit & pathogenome), the actions evaluate-cross-validate and evaluate-fit-classifier were removed from recent versions of RESC… --- ## [Naive Bayes classifier trained on a custom NCBI RefSeq V3-V4 database classifies almost all ASVs as same species](https://forum.qiime2.org/t/naive-bayes-classifier-trained-on-a-custom-ncbi-refseq-v3-v4-database-classifies-almost-all-asvs-as-same-species/34249)
**Author:** [@Kris\_P](https://forum.qiime2.org/u/Kris_P)\ **Replies:** 1\ **Last updated:** [July 15, 2026, 3:00pm UTC](https://forum.qiime2.org/t/naive-bayes-classifier-trained-on-a-custom-ncbi-refseq-v3-v4-database-classifies-almost-all-asvs-as-same-species/34249 "2026-07-15T15:00:35Z")
Hello, I am currently using QIIME 2 2026.1. Previously, I built a custom full-length NCBI RefSeq 16S classifier using rescript get-ncbi-data with BioProject 33175 (Bacteria). I first created this workflow in 2023 and ha… --- ## [ITS Classifier: Extract reference reads - HiSeq:](https://forum.qiime2.org/t/its-classifier-extract-reference-reads-hiseq/34164)
**Author:** [@fabipc](https://forum.qiime2.org/u/fabipc)\ **Replies:** 2\ **Last updated:** [May 31, 2026, 6:42am UTC](https://forum.qiime2.org/t/its-classifier-extract-reference-reads-hiseq/34164 "2026-05-31T06:42:14Z")
Hello, I have a quick question. Our lab decided to try and use HISeq to test if we get similar or better resolution (taxonomic resolution), for our samples as we do with ASVs.However, the DADA2 parameters that give me t… --- ## [ITS2 classification: identical sequences but different results (DADA2 vs merged)](https://forum.qiime2.org/t/its2-classification-identical-sequences-but-different-results-dada2-vs-merged/34107)
**Author:** [@sissiyun](https://forum.qiime2.org/u/sissiyun)\ **Replies:** 6\ **Last updated:** [April 7, 2026, 6:38am UTC](https://forum.qiime2.org/t/its2-classification-identical-sequences-but-different-results-dada2-vs-merged/34107 "2026-04-07T06:38:15Z")
Dear supporters, I’m relatively new to QIIME2, so apoplogies if I’m missing something obvious. I’m working with fungal ITS2 data and ran into an issue during taxonomic classification with feature-classifier classify-sk… --- ## [MIMt database for 16S, 18S, ITS, 23S and 28S new release available (March 26)](https://forum.qiime2.org/t/mimt-database-for-16s-18s-its-23s-and-28s-new-release-available-march-26/34069)
**Author:** [@A\_Munoz](https://forum.qiime2.org/u/A_Munoz)\ **Replies:** 0\ **Last updated:** [March 18, 2026, 7:20pm UTC](https://forum.qiime2.org/t/mimt-database-for-16s-18s-its-23s-and-28s-new-release-available-march-26/34069 "2026-03-18T19:20:10Z")
MIMt database new version has been released (March 26). Now every marker database contains thousands of new species well identified at every taxonomic level. Each database counts with two versions, one only containing se… --- ## [Annotation and Classifier question](https://forum.qiime2.org/t/annotation-and-classifier-question/34055)
**Author:** [@ankurnaqib](https://forum.qiime2.org/u/ankurnaqib)\ **Replies:** 17\ **Last updated:** [March 18, 2026, 2:52pm UTC](https://forum.qiime2.org/t/annotation-and-classifier-question/34055 "2026-03-18T14:52:28Z")
Hi, I am trying to understand something here. I have a sequence in the ref database that has this sequence:- Seq.txt (1.7 KB) In the taxonomy, its labeled as RS\_GCF\_041226625.1~NZ\_JBCLUQ010000046.1 d\_\_Bacteria;p\_\_Ver… --- ## [process killed qiime 2024.5 on Ubuntu 24.04.4 LTS when running on multicore](https://forum.qiime2.org/t/process-killed-qiime-2024-5-on-ubuntu-24-04-4-lts-when-running-on-multicore/34053)
**Author:** [@scilexenko](https://forum.qiime2.org/u/scilexenko)\ **Replies:** 1\ **Last updated:** [March 11, 2026, 6:16pm UTC](https://forum.qiime2.org/t/process-killed-qiime-2024-5-on-ubuntu-24-04-4-lts-when-running-on-multicore/34053 "2026-03-11T18:16:44Z")
Hello, My classify-sklearn run is being killed due to OOM (Out of Memory) despite having 192GB of RAM. The input rep-seqs file is small (8,331 sequences), but the system monitor shows 100% RAM and Swap usage before the … --- ## [Integrating V3-V4 and V4 16S datasets for large-scale meta-analysis: Is Greengenes2 the optimal choice for cross-region alignment?](https://forum.qiime2.org/t/integrating-v3-v4-and-v4-16s-datasets-for-large-scale-meta-analysis-is-greengenes2-the-optimal-choice-for-cross-region-alignment/33938)
**Author:** [@wh466689](https://forum.qiime2.org/u/wh466689)\ **Replies:** 1\ **Last updated:** [March 6, 2026, 4:44pm UTC](https://forum.qiime2.org/t/integrating-v3-v4-and-v4-16s-datasets-for-large-scale-meta-analysis-is-greengenes2-the-optimal-choice-for-cross-region-alignment/33938 "2026-03-06T16:44:00Z")
Context & Motivation I am currently working on a large-scale meta-analysis involving hundreds of projects and over 10,000 samples. My dataset is a mixture of: V3-V4 region (e.g., amplicons from 341F/805R) V4 region (… --- ## [QIIME2-amplicon-2025.7 16S PacBio classification issues/discussion](https://forum.qiime2.org/t/qiime2-amplicon-2025-7-16s-pacbio-classification-issues-discussion/33999)
**Author:** [@ankurnaqib](https://forum.qiime2.org/u/ankurnaqib)\ **Replies:** 6\ **Last updated:** [February 24, 2026, 9:48pm UTC](https://forum.qiime2.org/t/qiime2-amplicon-2025-7-16s-pacbio-classification-issues-discussion/33999 "2026-02-24T21:48:47Z")
Hi, Apologies in advance for the long post. So I recently tried the GTDB226 classifier for the PacBio 16S full-length data. I am using the qiime2-amplicon-2025.7 version. Based on this reference - How to train a GTDB SS… --- ## [The differences in taxonomy output by the feature-classifier trainer and the full-length trainer](https://forum.qiime2.org/t/the-differences-in-taxonomy-output-by-the-feature-classifier-trainer-and-the-full-length-trainer/33911)
**Author:** [@CWZ](https://forum.qiime2.org/u/CWZ)\ **Replies:** 6\ **Last updated:** [January 18, 2026, 9:13am UTC](https://forum.qiime2.org/t/the-differences-in-taxonomy-output-by-the-feature-classifier-trainer-and-the-full-length-trainer/33911 "2026-01-18T09:13:37Z")
Hi guys, When I used the unite database to annotate the ITS results, why did the taxonomy table annotated by the classifier trained with primer (ITS1F 5'-CTTGGTCATTTAGAGGAAGTAA-3' ITS2R 5'-GCTGCGTTCTTCATCGATGC-3') differ… --- ## ["over-classification" of ASV taxonomy?](https://forum.qiime2.org/t/over-classification-of-asv-taxonomy/33898)
**Author:** [@sibilant](https://forum.qiime2.org/u/sibilant)\ **Replies:** 2\ **Last updated:** [January 9, 2026, 6:14pm UTC](https://forum.qiime2.org/t/over-classification-of-asv-taxonomy/33898 "2026-01-09T18:14:26Z")
Happy New Year Qiime Community! :tada: I'm new to qiime2 and to DADA2 and to analyzing ITS data. :baby: I'm running qiime2-amplicon-2025.7 in a conda environment. Based on qiime2 forum recommendations, I'm using a UNIT… --- ## [How to perform SILVA V3 classifier training?](https://forum.qiime2.org/t/how-to-perform-silva-v3-classifier-training/33790)
**Author:** [@Qiime2\_user](https://forum.qiime2.org/u/Qiime2_user)\ **Replies:** 9\ **Last updated:** [November 17, 2025, 7:55pm UTC](https://forum.qiime2.org/t/how-to-perform-silva-v3-classifier-training/33790 "2025-11-17T19:55:51Z")
Hi everyone, I’m trying to run taxonomy classification using the SILVA V3 classifier (for forward read only analysis), but I keep running into a scikit-learn version mismatch error in QIIME2-amplicon-2025.7. Here is the … --- ## [Troubleshoot classification where all ASVs are unassigned?](https://forum.qiime2.org/t/troubleshoot-classification-where-all-asvs-are-unassigned/33831)
**Author:** [@sibilant](https://forum.qiime2.org/u/sibilant)\ **Replies:** 7\ **Last updated:** [December 2, 2025, 4:45pm UTC](https://forum.qiime2.org/t/troubleshoot-classification-where-all-asvs-are-unassigned/33831 "2025-12-02T16:45:40Z")
Hello Qiime Community, :seedling: I am running qiime2-amplicon-2025.7, using a mock library of fungi to benchmark my ITS amplicon analysis pipeline. This is my first time using Qiime2. I used RESCRIPt to curate a cu… --- ## [Evaluate custom taxonomic classifier with RESCRIPt?](https://forum.qiime2.org/t/evaluate-custom-taxonomic-classifier-with-rescript/33813)
**Author:** [@sibilant](https://forum.qiime2.org/u/sibilant)\ **Replies:** 5\ **Last updated:** [November 27, 2025, 5:41am UTC](https://forum.qiime2.org/t/evaluate-custom-taxonomic-classifier-with-rescript/33813 "2025-11-27T05:41:23Z")
Greetings Q2 and RESCRIPt community, :globe\_showing\_europe\_africa: I am using qiime2-amplicon-2025.7, and am new to qiime2. I am analyzing ITS1 amplicon metagenomic data from MiSeq Illumina runs. I am benchmarking my p… --- ## [MIMt database new release!!! QIIME2 classifiers for markers 16S, ITS, 18S, 23S and 28S](https://forum.qiime2.org/t/mimt-database-new-release-qiime2-classifiers-for-markers-16s-its-18s-23s-and-28s/33758)
**Author:** [@A\_Munoz](https://forum.qiime2.org/u/A_Munoz)\ **Replies:** 0\ **Last updated:** [November 3, 2025, 7:16am UTC](https://forum.qiime2.org/t/mimt-database-new-release-qiime2-classifiers-for-markers-16s-its-18s-23s-and-28s/33758 "2025-11-03T07:16:26Z")
A new version for MIMt database have been released. MIMt contains from 500 to 1500 new species in each of the ribosomal markers (for prokaryotes and eukaryotes). Every sequence in the database is full-length and redund… --- ## [Feature-clasifier V3-V4](https://forum.qiime2.org/t/feature-clasifier-v3-v4/33721)
**Author:** [@irenedecarlos](https://forum.qiime2.org/u/irenedecarlos)\ **Replies:** 6\ **Last updated:** [October 21, 2025, 2:35pm UTC](https://forum.qiime2.org/t/feature-clasifier-v3-v4/33721 "2025-10-21T14:35:08Z")
Classifier works without extract-reads, but collapses to one phylum after trimming (BEExact, V3–V4) Hello, I am analysisn some sequences of the V3-V4 16S region. I trained a clasifier and the classifier worked great with… --- ## [Trained classifier output not found](https://forum.qiime2.org/t/trained-classifier-output-not-found/33632)
**Author:** [@cielo](https://forum.qiime2.org/u/cielo)\ **Replies:** 6\ **Last updated:** [September 11, 2025, 11:09pm UTC](https://forum.qiime2.org/t/trained-classifier-output-not-found/33632 "2025-09-11T23:09:03Z")
I am training a V3/V4 classifier using SILVA 138 but there is no generated output. I am using qiime2.2024.10. I downloaded the reference sequences and taxonomy from here: Then, I extracted the reads for the V3/V4 cla… --- ## [Question about consensus taxonomy assignment in classify-consensus-vsearch](https://forum.qiime2.org/t/question-about-consensus-taxonomy-assignment-in-classify-consensus-vsearch/33574)
**Author:** [@lacerta](https://forum.qiime2.org/u/lacerta)\ **Replies:** 6\ **Last updated:** [August 21, 2025, 1:26pm UTC](https://forum.qiime2.org/t/question-about-consensus-taxonomy-assignment-in-classify-consensus-vsearch/33574 "2025-08-21T13:26:48Z")
How does classify-consensus-vsearch compute consensus taxonomy? Hi everyone, I am running qiime feature-classifier classify-consensus-vsearch in qiime2-amplicon-2025.4 (installed via Conda), with the following parameter… --- ## [Is there a pre-trained QIIME 2 classifier with full-length 16S (.qza)?](https://forum.qiime2.org/t/is-there-a-pre-trained-qiime-2-classifier-with-full-length-16s-qza/33564)
**Author:** [@Scarleth\_Bravo](https://forum.qiime2.org/u/Scarleth_Bravo)\ **Replies:** 10\ **Last updated:** [August 14, 2025, 8:27pm UTC](https://forum.qiime2.org/t/is-there-a-pre-trained-qiime-2-classifier-with-full-length-16s-qza/33564 "2025-08-14T20:27:09Z")
Hello community, I am working with a full-length 16S database (from Metasquare, which merges several collections) and I have already completed the import steps in QIIME 2. The problem is that training the classifier is … --- ## [16S SRNA](https://forum.qiime2.org/t/16s-srna/33536)
**Author:** [@yesiso](https://forum.qiime2.org/u/yesiso)\ **Replies:** 1\ **Last updated:** [August 2, 2025, 8:44am UTC](https://forum.qiime2.org/t/16s-srna/33536 "2025-08-02T08:44:56Z")
What I want to ask is that if I collect the 16S SRNA data from 200 samples on the NCBI website, and I have grouped the data by type, not by primer, but by process type, and now when I look at the statistics, I see that s… --- ## [Greengenes2 and RESCRIPt](https://forum.qiime2.org/t/greengenes2-and-rescript/33409)
**Author:** [@spolizzi](https://forum.qiime2.org/u/spolizzi)\ **Replies:** 2\ **Last updated:** [July 9, 2025, 8:13am UTC](https://forum.qiime2.org/t/greengenes2-and-rescript/33409 "2025-07-09T08:13:13Z")
Hi everyone! Has anyone here used RESCRIPt to build a classifier with the Greengenes2 database? If so, can you help me figuring out which data files (from the current repository) are better to use? I’m having trouble ma… --- ## [SILVA 138.1 classifier trained on version 2023.5 and used in 2024.5](https://forum.qiime2.org/t/silva-138-1-classifier-trained-on-version-2023-5-and-used-in-2024-5/33372)
**Author:** [@Harshita\_Sharma1](https://forum.qiime2.org/u/Harshita_Sharma1)\ **Replies:** 2\ **Last updated:** [July 3, 2025, 10:18am UTC](https://forum.qiime2.org/t/silva-138-1-classifier-trained-on-version-2023-5-and-used-in-2024-5/33372 "2025-07-03T10:18:30Z")
I am using qiime2-2024.5 version for my analysis containing V3-V4 region of 16S rRNA. i have generated taxonomic profile of my data in two ways: using a classifier for V3-V4 region which was previously trained using 20… --- ## [Dealing with Poor Taxonomic Assignments](https://forum.qiime2.org/t/dealing-with-poor-taxonomic-assignments/33334)
**Author:** [@alexkrohn](https://forum.qiime2.org/u/alexkrohn)\ **Replies:** 6\ **Last updated:** [June 24, 2025, 8:04pm UTC](https://forum.qiime2.org/t/dealing-with-poor-taxonomic-assignments/33334 "2025-06-24T20:04:40Z")
I've created a number of reference databases for eDNA metabarcoding datasets using Qiime. In general they do well, but for a number of sequences, they do really poorly. In general I download primer and taxon specific seq… --- ## [Processing, filtering, and evaluating the SILVA database (and other reference sequence data) with RESCRIPt](https://forum.qiime2.org/t/processing-filtering-and-evaluating-the-silva-database-and-other-reference-sequence-data-with-rescript/15494)
**Author:** [@SoilRotifer](https://forum.qiime2.org/u/SoilRotifer)\ **Replies:** 8\ **Last updated:** [February 17, 2023, 5:34pm UTC](https://forum.qiime2.org/t/processing-filtering-and-evaluating-the-silva-database-and-other-reference-sequence-data-with-rescript/15494 "2023-02-17T17:34:52Z")
:construction: Please consider this tutorial a living document, which may change based upon community feedback and ongoing plugin development. RESCRIPt RESCRIPt (REference Sequence annotation and CuRatIon Pipeline) is… --- ## [Request for Pre-trained SILVA V1–V3 Naive Bayes Classifier](https://forum.qiime2.org/t/request-for-pre-trained-silva-v1-v3-naive-bayes-classifier/33314)
**Author:** [@diksha\_klair](https://forum.qiime2.org/u/diksha_klair)\ **Replies:** 2\ **Last updated:** [June 18, 2025, 7:17pm UTC](https://forum.qiime2.org/t/request-for-pre-trained-silva-v1-v3-naive-bayes-classifier/33314 "2025-06-18T19:17:55Z")
Hi QIIME2 community, I’m working on 16S rRNA amplicon sequencing using the V1–V3 region with the following primer pair: Forward: AGAGTTTGATCMTGGCTCAG Reverse: ATTACCGTGGCTGCTGG I'm using QIIME 2 version 2024.10 and w… [Next page](https://forum.qiime2.org/tag/feature-classifier/28.md?match_all_tags=true&page=1&tags%5B%5D=feature-classifier)