# \#silva **URL:** https://forum.qiime2.org/tag/silva/70.md [Latest](https://forum.qiime2.org/latest.md) · [Categories](https://forum.qiime2.org/categories.md) · [Tags](https://forum.qiime2.org/tags.md) --- ## [Bug in new SILVA 144 taxmap file](https://forum.qiime2.org/t/bug-in-new-silva-144-taxmap-file/34308)
**Author:** [@hdeel](https://forum.qiime2.org/u/hdeel)\ **Replies:** 6\ **Last updated:** [September 3, 2026, 2:48pm UTC](https://forum.qiime2.org/t/bug-in-new-silva-144-taxmap-file/34308 "2026-09-03T14:48:51Z")
Hello Q2 folks, I was unable to find this reported on the forum anywhere, so I thought it would be good to make a quick post. I am working on creating a custom taxonomic classifier with the new SILVA 144 version (follow… --- ## [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… --- ## [Looking for pre-trained SILVA 138 V4 classifier for QIIME2 2024.10](https://forum.qiime2.org/t/looking-for-pre-trained-silva-138-v4-classifier-for-qiime2-2024-10/34190)
**Author:** [@Richa](https://forum.qiime2.org/u/Richa)\ **Replies:** 7\ **Last updated:** [June 16, 2026, 8:56am UTC](https://forum.qiime2.org/t/looking-for-pre-trained-silva-138-v4-classifier-for-qiime2-2024-10/34190 "2026-06-16T08:56:57Z")
Hi everyone, I am working on 16S rRNA gene V4 region analysis using QIIME2 2024.10 on a Windows machine with WSL (16GB RAM). I am looking for a pre-trained SILVA 138 99% OTU classifier for the V4 region with the followi… --- ## [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 … --- ## [Greengenes2 vs. SILVA](https://forum.qiime2.org/t/greengenes2-vs-silva/33393)
**Author:** [@Kcucumber](https://forum.qiime2.org/u/Kcucumber)\ **Replies:** 0\ **Last updated:** [July 3, 2025, 8:51pm UTC](https://forum.qiime2.org/t/greengenes2-vs-silva/33393 "2025-07-03T20:51:37Z")
I am preparing to perform an analysis, and I am currently building my roadmap for the process. I saw that Greengenes has recently updated to Greengenes2, where it appears that they have updated the nomenclature and integ… --- ## [Difficulty assigning taxonomy to cyanobacterial ASVs](https://forum.qiime2.org/t/difficulty-assigning-taxonomy-to-cyanobacterial-asvs/33226)
**Author:** [@Mahima\_y](https://forum.qiime2.org/u/Mahima_y)\ **Replies:** 2\ **Last updated:** [June 5, 2025, 5:48pm UTC](https://forum.qiime2.org/t/difficulty-assigning-taxonomy-to-cyanobacterial-asvs/33226 "2025-06-05T17:48:24Z")
Hello! I am trying to find the best method and database to assign taxonomy to my 1,107 ASVs. (For context, my samples were collected from seawater that was filtered and prepared for sequencing, bioinformatics, etc). Beca… --- ## [SILVA 138.2 classifier](https://forum.qiime2.org/t/silva-138-2-classifier/33209)
**Author:** [@mari\_lopes](https://forum.qiime2.org/u/mari_lopes)\ **Replies:** 2\ **Last updated:** [May 28, 2025, 1:46pm UTC](https://forum.qiime2.org/t/silva-138-2-classifier/33209 "2025-05-28T13:46:53Z")
Hello there! I wanted to ask if at any point there will be an upload of SILVA 138.2 classifiers (full-length, and/or for specific hypervariable regions) in the resources page (QIIME 2 Library). I'd prefer to train my ow… --- ## [SILVA vs PR2 database using qiime2](https://forum.qiime2.org/t/silva-vs-pr2-database-using-qiime2/32787)
**Author:** [@Adyasha\_Panda](https://forum.qiime2.org/u/Adyasha_Panda)\ **Replies:** 1\ **Last updated:** [March 19, 2025, 1:33pm UTC](https://forum.qiime2.org/t/silva-vs-pr2-database-using-qiime2/32787 "2025-03-19T13:33:55Z")
Hello everyone, I Have some 18S amplicon sequenced data from marine. I Have ran DADA2 For denoising after that I have done taxonomy classification using both silva-138-99-nb-classifier.qza and pr2-classifier.qza. It gav… --- ## [Comparison of OTU Identifications with Silva 138.1 and Greengenes 2022.10 databases](https://forum.qiime2.org/t/comparison-of-otu-identifications-with-silva-138-1-and-greengenes-2022-10-databases/32740)
**Author:** [@Bonita\_Mc](https://forum.qiime2.org/u/Bonita_Mc)\ **Replies:** 7\ **Last updated:** [March 16, 2025, 2:57pm UTC](https://forum.qiime2.org/t/comparison-of-otu-identifications-with-silva-138-1-and-greengenes-2022-10-databases/32740 "2025-03-16T14:57:47Z")
I have been using the bioinformatics services provided by Novogene. We use the most cost efficient option which still uses QIIME and the Silva 138.1 database. I have made my own classifier using the Greengenes 2022.10 b… --- ## [Is there an issue with the 2024.5 silva138-99-nb classifier?](https://forum.qiime2.org/t/is-there-an-issue-with-the-2024-5-silva138-99-nb-classifier/32247)
**Author:** [@anwesh](https://forum.qiime2.org/u/anwesh)\ **Replies:** 4\ **Last updated:** [January 6, 2025, 11:15pm UTC](https://forum.qiime2.org/t/is-there-an-issue-with-the-2024-5-silva138-99-nb-classifier/32247 "2025-01-06T23:15:44Z")
Hello QIIME team, Thanks for developing such a useful analysis package. I observed different classification outputs with the new silva-nb classifier when I was running the feature-classifier with different silva full-l… --- ## [Problem with vizualization of SSU in bar plot](https://forum.qiime2.org/t/problem-with-vizualization-of-ssu-in-bar-plot/32053)
**Author:** [@jko](https://forum.qiime2.org/u/jko)\ **Replies:** 7\ **Last updated:** [December 14, 2024, 5:20pm UTC](https://forum.qiime2.org/t/problem-with-vizualization-of-ssu-in-bar-plot/32053 "2024-12-14T17:20:44Z")
Hello, I have a problem with silva-138.1-ssu-nr99-classifier.qza Finally more RAM in machine let me install this silva, but I have new complications with them. I get data in tables and bar plots in only form: d\_Bacter… --- ## [Not able to find E. coli in my taxonomy file](https://forum.qiime2.org/t/not-able-to-find-e-coli-in-my-taxonomy-file/32050)
**Author:** [@NivedhithaU](https://forum.qiime2.org/u/NivedhithaU)\ **Replies:** 3\ **Last updated:** [December 5, 2024, 9:27am UTC](https://forum.qiime2.org/t/not-able-to-find-e-coli-in-my-taxonomy-file/32050 "2024-12-05T09:27:49Z")
Hello, I am analyzing mouse fecal samples. We have sequenced the V3-V4 region of the 16s rRNA and the taxonomic classification has been done based on silva-138-99-tax.qza. The code I used is given below. 1. Importing f… --- ## [feature-classifier stopped with "Killed"](https://forum.qiime2.org/t/feature-classifier-stopped-with-killed/31727)
**Author:** [@jko](https://forum.qiime2.org/u/jko)\ **Replies:** 1\ **Last updated:** [October 24, 2024, 12:45pm UTC](https://forum.qiime2.org/t/feature-classifier-stopped-with-killed/31727 "2024-10-24T12:45:41Z")
Hello everyone, I have a problem. I used tutorial by SoilRotifer to processing, filtering and evaluation the SILVA database with Rescript from this forum: https://forum.qiime2.org/t/processing-filtering-and-evaluating-… --- ## [Make OTU cluster from SILVAdatabase](https://forum.qiime2.org/t/make-otu-cluster-from-silvadatabase/31546)
**Author:** [@W.H](https://forum.qiime2.org/u/W.H)\ **Replies:** 2\ **Last updated:** [October 2, 2024, 2:39am UTC](https://forum.qiime2.org/t/make-otu-cluster-from-silvadatabase/31546 "2024-10-02T02:39:33Z")
Hi, Qiime Users. I'm student and using this tool for the first time. At first in case what I ask sounds strange and not reasonable, please don't be hesitate to point out, since I am totally beginner of bioinfomatics. M… --- ## [Interpreting Silva Bacterial Taxonomy (Incertae Sedis)](https://forum.qiime2.org/t/interpreting-silva-bacterial-taxonomy-incertae-sedis/31493)
**Author:** [@areaume](https://forum.qiime2.org/u/areaume)\ **Replies:** 2\ **Last updated:** [September 24, 2024, 3:20pm UTC](https://forum.qiime2.org/t/interpreting-silva-bacterial-taxonomy-incertae-sedis/31493 "2024-09-24T15:20:45Z")
Hi all, I'm new to bacterial communities and have been working with a 16S V3-V4 dataset classified with SILVA 138.1, which I downloaded using the RESCRIPt tutorial. I've been noticing that some of my taxonomy assignmen… --- ## [Reconciling 16s Databases in a Single Pipeline](https://forum.qiime2.org/t/reconciling-16s-databases-in-a-single-pipeline/31258)
**Author:** [@pone](https://forum.qiime2.org/u/pone)\ **Replies:** 5\ **Last updated:** [August 28, 2024, 3:36pm UTC](https://forum.qiime2.org/t/reconciling-16s-databases-in-a-single-pipeline/31258 "2024-08-28T15:36:18Z")
Is it possible to create a pipeline for 16s sequences that would try to reconcile sequence assignments across multiple databases? The point of this is to expose ambiguities and different assignments explicitly within … --- ## [Training Silva 138 data base to use in qiime1](https://forum.qiime2.org/t/training-silva-138-data-base-to-use-in-qiime1/30707)
**Author:** [@Rajendra\_Prasad\_Sahu](https://forum.qiime2.org/u/Rajendra_Prasad_Sahu)\ **Replies:** 1\ **Last updated:** [July 3, 2024, 9:28am UTC](https://forum.qiime2.org/t/training-silva-138-data-base-to-use-in-qiime1/30707 "2024-07-03T09:28:32Z")
Hi there I want to use the Silva 138 data base in QIIME1 for my analysis. I have done most of the statistical analysis of my manuscript by using data obtained from QIIME1. Considering the comment of the reviewer, I want… --- ## [Taxonomic Classification Issues in Meiofauna Analysis using QIIME2 and SILVA 138 and 138.1](https://forum.qiime2.org/t/taxonomic-classification-issues-in-meiofauna-analysis-using-qiime2-and-silva-138-and-138-1/30340)
**Author:** [@Pepe\_Calderon](https://forum.qiime2.org/u/Pepe_Calderon)\ **Replies:** 3\ **Last updated:** [May 30, 2024, 9:00am UTC](https://forum.qiime2.org/t/taxonomic-classification-issues-in-meiofauna-analysis-using-qiime2-and-silva-138-and-138-1/30340 "2024-05-30T09:00:43Z")
Hi, I am conducting a meiofauna analysis in beach sand. I have 192 samples. My samples were sequenced using the primers 18S F04mod: GCTTGWCTCAAAGATTAAGCC and R22mod: CCTGCTGCCTTCCTTDGA. I used the silva-138-99-nb-classif… --- ## [Train the Silva database (Qiime2) by extracting two types of primers: Region v3-v4 and v4 of the 16S rRNA](https://forum.qiime2.org/t/train-the-silva-database-qiime2-by-extracting-two-types-of-primers-region-v3-v4-and-v4-of-the-16s-rrna/30168)
**Author:** [@LisethBolCol](https://forum.qiime2.org/u/LisethBolCol)\ **Replies:** 2\ **Last updated:** [May 19, 2024, 2:22am UTC](https://forum.qiime2.org/t/train-the-silva-database-qiime2-by-extracting-two-types-of-primers-region-v3-v4-and-v4-of-the-16s-rrna/30168 "2024-05-19T02:22:21Z")
Hello, I am new to using Qiime 2. I have already done one of the tutorials and I am currently analyzing samples of the bacterial microbiome from pigeon fecal matter. For this, I am using the version of qiime2-amplicon-20… --- ## [How can I set the parameters of feature-classifier extract-reads ?](https://forum.qiime2.org/t/how-can-i-set-the-parameters-of-feature-classifier-extract-reads/29096)
**Author:** [@elifi](https://forum.qiime2.org/u/elifi)\ **Replies:** 1\ **Last updated:** [January 30, 2024, 3:52pm UTC](https://forum.qiime2.org/t/how-can-i-set-the-parameters-of-feature-classifier-extract-reads/29096 "2024-01-30T15:52:23Z")
Hi all, I set the denoise-paired parameters as follows according to qc plot. qiime dada2 denoise-paired --i-demultiplexed-seqs Sample1\_Results/Trimming/Sample1\_trimmed\_adapters.qza --p-trunc-len-f 290 --p-trun… --- ## [Greengenes assigning wrong family to genus level](https://forum.qiime2.org/t/greengenes-assigning-wrong-family-to-genus-level/29022)
**Author:** [@Liviacmg](https://forum.qiime2.org/u/Liviacmg)\ **Replies:** 8\ **Last updated:** [January 26, 2024, 2:51am UTC](https://forum.qiime2.org/t/greengenes-assigning-wrong-family-to-genus-level/29022 "2024-01-26T02:51:25Z")
Hey guys, I'm comparing outputs of taxonomic classification from kraken2, greengenes (gg-2022-10-nb-classifier.qza) and silva (silva-138-99-nb-classifier.qza). I'm using qiime2 version 2023.5. I runned them for the same… --- ## [Is there a pretrainer classifer for silva 138.1 specifically for 515-806 V4 sequences available on this website?](https://forum.qiime2.org/t/is-there-a-pretrainer-classifer-for-silva-138-1-specifically-for-515-806-v4-sequences-available-on-this-website/28617)
**Author:** [@Estewart](https://forum.qiime2.org/u/Estewart)\ **Replies:** 1\ **Last updated:** [December 15, 2023, 2:11pm UTC](https://forum.qiime2.org/t/is-there-a-pretrainer-classifer-for-silva-138-1-specifically-for-515-806-v4-sequences-available-on-this-website/28617 "2023-12-15T14:11:03Z")
I have been using the pretrained classifier available on this website called "silva-138-99-515-806-nb-classifier.qza" but noticed silva released a 138.1 version in 2020. Is there a pretrainer classifier available for thi… --- ## ["\[Errno 28\] No space left on device" during Silva-based taxonomy classification](https://forum.qiime2.org/t/errno-28-no-space-left-on-device-during-silva-based-taxonomy-classification/28515)
**Author:** [@microbiome\_25](https://forum.qiime2.org/u/microbiome_25)\ **Replies:** 10\ **Last updated:** [December 15, 2023, 6:03am UTC](https://forum.qiime2.org/t/errno-28-no-space-left-on-device-during-silva-based-taxonomy-classification/28515 "2023-12-15T06:03:55Z")
I've been trying to perform Silva-based taxonomy classification using V1-V2 16S rRNA sequencing data. I am using a Naive Bayes classifier trained on Silva 138 99% OTUs full-length sequences available on the QIIME2 offici… --- ## [Questions about SILVA classifier for v3v4](https://forum.qiime2.org/t/questions-about-silva-classifier-for-v3v4/28478)
**Author:** [@linki11](https://forum.qiime2.org/u/linki11)\ **Replies:** 1\ **Last updated:** [December 1, 2023, 2:17pm UTC](https://forum.qiime2.org/t/questions-about-silva-classifier-for-v3v4/28478 "2023-12-01T14:17:48Z")
Dear Mike, I am following this post trying to generate my own silva reference database. my sequencing data was v3-v4 region and wanna to do close-reference-like approaches. I tried to generate a trained classifier which… --- ## [fit classifier naives bayes Silva 138 database](https://forum.qiime2.org/t/fit-classifier-naives-bayes-silva-138-database/27934)
**Author:** [@JessG](https://forum.qiime2.org/u/JessG)\ **Replies:** 3\ **Last updated:** [October 23, 2023, 4:45pm UTC](https://forum.qiime2.org/t/fit-classifier-naives-bayes-silva-138-database/27934 "2023-10-23T16:45:56Z")
Hi, I am having problems running the below script: qiime feature-classifier fit-classifier-naive-bayes \\ --i-reference-reads silva-138-99-seqs.qza --i-reference-taxonomy silva-138-99-tax.qza --o-classifier Silva\_c… --- ## [how to compare SILVA 138 taxonomy and NCBI taxonomy](https://forum.qiime2.org/t/how-to-compare-silva-138-taxonomy-and-ncbi-taxonomy/27414)
**Author:** [@Wei\_Zhang](https://forum.qiime2.org/u/Wei_Zhang)\ **Replies:** 3\ **Last updated:** [August 22, 2023, 5:23pm UTC](https://forum.qiime2.org/t/how-to-compare-silva-138-taxonomy-and-ncbi-taxonomy/27414 "2023-08-22T17:23:20Z")
Hi there, I have two datasets, 16S rRNA data that was annotated with SILVA taxonomy, and shotgun data that was annotated with NCBI taxonomy. I want to compare the difference and find common taxa between the two datasets… --- ## [extracting amplicon region from alignment](https://forum.qiime2.org/t/extracting-amplicon-region-from-alignment/27276)
**Author:** [@leo\_gm](https://forum.qiime2.org/u/leo_gm)\ **Replies:** 2\ **Last updated:** [August 2, 2023, 3:39am UTC](https://forum.qiime2.org/t/extracting-amplicon-region-from-alignment/27276 "2023-08-02T03:39:02Z")
Hi i have a problem using the reverse-transcribe, i have an AllignedRNASequence that i want to pass to DNASequence to do: qiime feature-classifier extract-reads --i-sequences silva-138.1-fullaling.qza --p-f-primer CCTAC… --- ## [Update of Greengenes](https://forum.qiime2.org/t/update-of-greengenes/27014)
**Author:** [@JGarcia](https://forum.qiime2.org/u/JGarcia)\ **Replies:** 1\ **Last updated:** [July 10, 2023, 5:49pm UTC](https://forum.qiime2.org/t/update-of-greengenes/27014 "2023-07-10T17:49:29Z")
Hi! I do not now whether this has already been asked. I have searched for it but did not find anything. Until now, I have been using SILVA database for performing taxonomy classification. However, I just have seen that … --- ## [classify-sklearn not working without error message](https://forum.qiime2.org/t/classify-sklearn-not-working-without-error-message/26957)
**Author:** [@kestrelb](https://forum.qiime2.org/u/kestrelb)\ **Replies:** 2\ **Last updated:** [July 6, 2023, 5:20pm UTC](https://forum.qiime2.org/t/classify-sklearn-not-working-without-error-message/26957 "2023-07-06T17:20:40Z")
I am running Qiime2 with several sample sets with the pre-compiled Silva and Greengenes taxonomic classifiers (v2022.2). For one sample set, the Greengenes classifier is working but Silva is not. For the others sample se… --- ## [Understanding options for assigning taxonomy](https://forum.qiime2.org/t/understanding-options-for-assigning-taxonomy/26466)
**Author:** [@areaume](https://forum.qiime2.org/u/areaume)\ **Replies:** 2\ **Last updated:** [May 16, 2023, 7:23pm UTC](https://forum.qiime2.org/t/understanding-options-for-assigning-taxonomy/26466 "2023-05-16T19:23:57Z")
I have been using the classify-consensus-vsearch option recently with PR2 and SILVA, but I'm confused as to how it differs from some past work I have done in BLAST. In prior work (and in some other literature I have rea… [Next page](https://forum.qiime2.org/tag/silva/70.md?match_all_tags=true&page=1&tags%5B%5D=silva)