# User Support **URL:** https://forum.qiime2.org/c/user-support/6.md [Latest](https://forum.qiime2.org/latest.md) · [Categories](https://forum.qiime2.org/categories.md) · [Tags](https://forum.qiime2.org/tags.md) --- ## [About the User Support category](https://forum.qiime2.org/t/about-the-user-support-category/56)
**Author:** [@q2d2](https://forum.qiime2.org/u/q2d2)\ **Replies:** 0\ **Last updated:** [October 27, 2016, 6:08pm UTC](https://forum.qiime2.org/t/about-the-user-support-category/56 "2016-10-27T18:08:44Z")
Post to this category if you need help understanding output produced while running QIIME 2. Examples of this include help understanding plots labels, techniques that are used in QIIME 2, etc. Posts in this category will … --- ## [class-weight parameter for rescript-evaluate evaluate-fit-classifier function](https://forum.qiime2.org/t/class-weight-parameter-for-rescript-evaluate-evaluate-fit-classifier-function/34320)
**Author:** [@irvinng98](https://forum.qiime2.org/u/irvinng98)\ **Replies:** 3\ **Last updated:** [September 22, 2026, 9:00pm UTC](https://forum.qiime2.org/t/class-weight-parameter-for-rescript-evaluate-evaluate-fit-classifier-function/34320 "2026-09-22T21:00:32Z")
Hello, Previously I had used the qiime feature-classifier fit-classifier-naive-bayes function as the last step to create my classifier. This function allowed me to use --i-class-weight as an option for input. However, I… --- ## [import multiplexed miseq single-end, barcodes in mapping file](https://forum.qiime2.org/t/import-multiplexed-miseq-single-end-barcodes-in-mapping-file/34333)
**Author:** [@Scott\_Kelley1](https://forum.qiime2.org/u/Scott_Kelley1)\ **Replies:** 1\ **Last updated:** [September 22, 2026, 3:30am UTC](https://forum.qiime2.org/t/import-multiplexed-miseq-single-end-barcodes-in-mapping-file/34333 "2026-09-22T03:30:04Z")
Version: qiime2-amplicon-2024.10 I have an older Illumina miSeq single-end dataset with NO barcodes.fastq.gz file. The barcodes are in the mapping file (see below). I searched the forums and I found the cutadapt code th… --- ## [PacBio DADA2-ccs plugin is losing lots of data](https://forum.qiime2.org/t/pacbio-dada2-ccs-plugin-is-losing-lots-of-data/34299)
**Author:** [@Prajina-N](https://forum.qiime2.org/u/Prajina-N)\ **Replies:** 6\ **Last updated:** [September 22, 2026, 3:03am UTC](https://forum.qiime2.org/t/pacbio-dada2-ccs-plugin-is-losing-lots-of-data/34299 "2026-09-22T03:03:27Z")
Howdy, I ran DADA2-ccs plugin for PacBio sequences for Bac16S but I am losing a lot of reads in filtering step. Search: sample-id #q2:types input numeric primer-removed numeric percentage of input primer-removed nu… --- ## [High Read Loss Due to Poor Merging and Chimeras During DADA denoising](https://forum.qiime2.org/t/high-read-loss-due-to-poor-merging-and-chimeras-during-dada-denoising/34323)
**Author:** [@deClare125](https://forum.qiime2.org/u/deClare125)\ **Replies:** 9\ **Last updated:** [September 19, 2026, 2:54pm UTC](https://forum.qiime2.org/t/high-read-loss-due-to-poor-merging-and-chimeras-during-dada-denoising/34323 "2026-09-19T14:54:47Z")
Hi QIIME forum! I am currently stuck at the denoising phase, where my data has really low pair-end merging rates and lots of loss due to chimeras. I am a total newbie to metabarcoding so while I have read a lot of posts… --- ## [Dada2: Trimming 4 pe sequencing runs so they can merge (3 runs 150 pb pe, 1 run 100 pb pe)](https://forum.qiime2.org/t/dada2-trimming-4-pe-sequencing-runs-so-they-can-merge-3-runs-150-pb-pe-1-run-100-pb-pe/34322)
**Author:** [@baenal](https://forum.qiime2.org/u/baenal)\ **Replies:** 2\ **Last updated:** [September 11, 2026, 2:18pm UTC](https://forum.qiime2.org/t/dada2-trimming-4-pe-sequencing-runs-so-they-can-merge-3-runs-150-pb-pe-1-run-100-pb-pe/34322 "2026-09-11T14:18:12Z")
Hi all, I have found bits and pieces of my question answered across different discussions, but nothing that completes the picture. I have 4 different sequencing runs that I would like to merge later on. These are from d… --- ## [PacBio ITS workflow - some questions](https://forum.qiime2.org/t/pacbio-its-workflow-some-questions/34263)
**Author:** [@Rob\_DNA](https://forum.qiime2.org/u/Rob_DNA)\ **Replies:** 4\ **Last updated:** [September 9, 2026, 9:41am UTC](https://forum.qiime2.org/t/pacbio-its-workflow-some-questions/34263 "2026-09-09T09:41:44Z")
Hello, I've use QIIME2 quite a lot for Illumina paired end data, but now it is the first time I'll use it with PacBio full ITS data. The primers used are ITS9mun (GTACACACCGCCCGTCG) and ITS4ngsUni (CGCCTSCSCTTANTDATATGC… --- ## [AVITI vs. Illumina](https://forum.qiime2.org/t/aviti-vs-illumina/34303)
**Author:** [@szec](https://forum.qiime2.org/u/szec)\ **Replies:** 3\ **Last updated:** [September 1, 2026, 5:59pm UTC](https://forum.qiime2.org/t/aviti-vs-illumina/34303 "2026-09-01T17:59:47Z")
Hi all, I have 3 years of data; the first (2023) was sequenced using Illumina and the last two (2024 & 2025) were sequenced using AVITI. When processing them, everything runs smoothly, but when I try to combine them, th… --- ## [Is ANCOM-BC2 the best choice for my data?](https://forum.qiime2.org/t/is-ancom-bc2-the-best-choice-for-my-data/34294)
**Author:** [@kranderson](https://forum.qiime2.org/u/kranderson)\ **Replies:** 2\ **Last updated:** [September 1, 2026, 6:03am UTC](https://forum.qiime2.org/t/is-ancom-bc2-the-best-choice-for-my-data/34294 "2026-09-01T06:03:31Z")
My study is comparing the fungal diversity between soil that experienced a wildfire (NoRxF) between soil that was treated with prescribed fire prior to experiencing the wildfire (RxF). It's a paired study design where 6 … --- ## [Very low percentage of merged reads in DADA2 with 16S V4, 2×150 bp paired-end sequencing](https://forum.qiime2.org/t/very-low-percentage-of-merged-reads-in-dada2-with-16s-v4-2x150-bp-paired-end-sequencing/34302)
**Author:** [@Sergio](https://forum.qiime2.org/u/Sergio)\ **Replies:** 3\ **Last updated:** [August 28, 2026, 7:12pm UTC](https://forum.qiime2.org/t/very-low-percentage-of-merged-reads-in-dada2-with-16s-v4-2x150-bp-paired-end-sequencing/34302 "2026-08-28T19:12:58Z")
Question Hi, I am processing 16S rRNA amplicon sequencing data using QIIME 2 and DADA2. My samples were amplified targeting the V4 region of the 16S rRNA gene using the 515F and 806R primers. The libraries were sequenc… --- ## [Why are my reads filtered out (98%) when quality seems okay?](https://forum.qiime2.org/t/why-are-my-reads-filtered-out-98-when-quality-seems-okay/34292)
**Author:** [@lineroager](https://forum.qiime2.org/u/lineroager)\ **Replies:** 6\ **Last updated:** [August 20, 2026, 11:38am UTC](https://forum.qiime2.org/t/why-are-my-reads-filtered-out-98-when-quality-seems-okay/34292 "2026-08-20T11:38:51Z")
I am using qiime2 2026.7 on a WSL system in Ubuntu and working on paired-end 18S seq data (Illumina Miseq 2x300) from a mixed seawater community. My data is already imported and demultiplexed, but at the denoising step (… --- ## [extract-seq-segments: number of reads vs accuracy of reads.](https://forum.qiime2.org/t/extract-seq-segments-number-of-reads-vs-accuracy-of-reads/34293)
**Author:** [@deClare125](https://forum.qiime2.org/u/deClare125)\ **Replies:** 3\ **Last updated:** [August 19, 2026, 7:06pm UTC](https://forum.qiime2.org/t/extract-seq-segments-number-of-reads-vs-accuracy-of-reads/34293 "2026-08-19T19:06:13Z")
Hi Mike, I read this from your post: "But if you are hoping to strictly stay within the bounds of your expected amplicon length, then Id simply do more iterations, at a much higher similarity, say 90% then go up.", and … --- ## [q2 boots: should I use replacement or no-replacement with low-frequency samples?](https://forum.qiime2.org/t/q2-boots-should-i-use-replacement-or-no-replacement-with-low-frequency-samples/34279)
**Author:** [@Emma\_Gardner](https://forum.qiime2.org/u/Emma_Gardner)\ **Replies:** 3\ **Last updated:** [August 11, 2026, 12:31pm UTC](https://forum.qiime2.org/t/q2-boots-should-i-use-replacement-or-no-replacement-with-low-frequency-samples/34279 "2026-08-11T12:31:06Z")
Hi, I am on qiime2-2025.7, and I would like a little more clarification on how the rarefaction process works with low-frequency samples in boots. I am planning to run the following command: qiime boots core-metrics \\ -… --- ## [fastp --detect\_adapter\_for\_pe in qiime version of fastp?](https://forum.qiime2.org/t/fastp-detect-adapter-for-pe-in-qiime-version-of-fastp/34259)
**Author:** [@amp](https://forum.qiime2.org/u/amp)\ **Replies:** 2\ **Last updated:** [August 4, 2026, 7:11am UTC](https://forum.qiime2.org/t/fastp-detect-adapter-for-pe-in-qiime-version-of-fastp/34259 "2026-08-04T07:11:11Z")
Hi, I'm building a pipeline to process large-ish datasets pulled from the SRA database. I am using fondue to pull the data based on an SRA query. I found that fastp has an option for automatically detecting and removing… --- ## [Imported seq summary histograms not matching sequence counts](https://forum.qiime2.org/t/imported-seq-summary-histograms-not-matching-sequence-counts/34254)
**Author:** [@kranderson](https://forum.qiime2.org/u/kranderson)\ **Replies:** 6\ **Last updated:** [August 4, 2026, 6:43am UTC](https://forum.qiime2.org/t/imported-seq-summary-histograms-not-matching-sequence-counts/34254 "2026-08-04T06:43:29Z")
Hi! The forum has many post that look like they would share my concern, but they were mostly about specific error messages or about the quality plots. My confusion is why the forward and reverse reads frequency histogram… --- ## [Losing reads at DADA2 Merge step 30% of my samples lost over 50% - I have tried multiple steps to fix- please help](https://forum.qiime2.org/t/losing-reads-at-dada2-merge-step-30-of-my-samples-lost-over-50-i-have-tried-multiple-steps-to-fix-please-help/34253)
**Author:** [@rdkramp](https://forum.qiime2.org/u/rdkramp)\ **Replies:** 1\ **Last updated:** [July 21, 2026, 7:50am UTC](https://forum.qiime2.org/t/losing-reads-at-dada2-merge-step-30-of-my-samples-lost-over-50-i-have-tried-multiple-steps-to-fix-please-help/34253 "2026-07-21T07:50:37Z")
Hello, I am running fish skin swabs for 16s rRNA 515F/806R sequences using Illumina MiSeq, V2, 500 cycle kit (2x250). I am having an issue with the merging step in DADA2. Around 30% of my samples have 50% loss at the m… --- ## [Can DADA2 be used with nearly uniform Q38 quality scores?](https://forum.qiime2.org/t/can-dada2-be-used-with-nearly-uniform-q38-quality-scores/34252)
**Author:** [@Katerina\_Fialova](https://forum.qiime2.org/u/Katerina_Fialova)\ **Replies:** 2\ **Last updated:** [July 21, 2026, 7:36am UTC](https://forum.qiime2.org/t/can-dada2-be-used-with-nearly-uniform-q38-quality-scores/34252 "2026-07-21T07:36:47Z")
Hi, I am analysing paired-end 16S rRNA amplicon data in QIIME 2 and would like to use DADA2 because my previous datasets were processed with the same pipeline, and I need the results to remain as comparable as possible. … --- ## [Low Read Maps to Scaffolds using MEGAHIT](https://forum.qiime2.org/t/low-read-maps-to-scaffolds-using-megahit/34240)
**Author:** [@MasonDavis](https://forum.qiime2.org/u/MasonDavis)\ **Replies:** 2\ **Last updated:** [July 17, 2026, 4:30am UTC](https://forum.qiime2.org/t/low-read-maps-to-scaffolds-using-megahit/34240 "2026-07-17T04:30:54Z")
Hello, I am new to bioinformatics analysis, and I am currently running a set of complex soil samples via qiime2-moshpit-2025.7 installed via conda. I am posting to hopefully resolve an issue with my assembly generating a… --- ## [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… --- ## [q2 boots beta - reuse rarefaction tables](https://forum.qiime2.org/t/q2-boots-beta-reuse-rarefaction-tables/34241)
**Author:** [@arwqiime](https://forum.qiime2.org/u/arwqiime)\ **Replies:** 2\ **Last updated:** [July 14, 2026, 8:33am UTC](https://forum.qiime2.org/t/q2-boots-beta-reuse-rarefaction-tables/34241 "2026-07-14T08:33:46Z")
Hi, I would like to add another beta diversity metrics (aitchison) to rarefaction analyses by q2 boots beta and I am wondering whether I can reuse the previous rarefaction tables produced by q2 boots core-metrics. Ther… --- ## [adonis beta div statistics](https://forum.qiime2.org/t/adonis-beta-div-statistics/34216)
**Author:** [@Angeliki](https://forum.qiime2.org/u/Angeliki)\ **Replies:** 2\ **Last updated:** [June 17, 2026, 12:36am UTC](https://forum.qiime2.org/t/adonis-beta-div-statistics/34216 "2026-06-17T00:36:02Z")
Hi, i am using adonis on my beta diversity results so that i can find which of my metadata categories contributes the most to the results. Every time i run adonis i get different resuts regarding the significance if i c… --- ## [Heatmap generation with clustered groups](https://forum.qiime2.org/t/heatmap-generation-with-clustered-groups/34217)
**Author:** [@M\_F](https://forum.qiime2.org/u/M_F)\ **Replies:** 1\ **Last updated:** [June 16, 2026, 10:56pm UTC](https://forum.qiime2.org/t/heatmap-generation-with-clustered-groups/34217 "2026-06-16T22:56:56Z")
Hi, I would like to generate a heatmap showing the clustered groups (T2D, H, OB, and T2D\_CV). However, when I use the following command lines, the resulting heatmap is generated for individual participants rather than f… --- ## [export visualization as svg](https://forum.qiime2.org/t/export-visualization-as-svg/34211)
**Author:** [@Pan](https://forum.qiime2.org/u/Pan)\ **Replies:** 1\ **Last updated:** [June 8, 2026, 6:37pm UTC](https://forum.qiime2.org/t/export-visualization-as-svg/34211 "2026-06-08T18:37:03Z")
How to exported as svg from the figure? I can use "qiime tools view "to view the barplot in firefox brower, but there no option(button) to save the figure as svg. Help me --- ## [All reads removed after filtering, merging, and quimeras removal with DADA2](https://forum.qiime2.org/t/all-reads-removed-after-filtering-merging-and-quimeras-removal-with-dada2/34198)
**Author:** [@ines](https://forum.qiime2.org/u/ines)\ **Replies:** 5\ **Last updated:** [June 8, 2026, 6:31pm UTC](https://forum.qiime2.org/t/all-reads-removed-after-filtering-merging-and-quimeras-removal-with-dada2/34198 "2026-06-08T18:31:07Z")
Hi everyone! I'm using QIIME2 version 2018.2 to perform bacterial community analysis. All went well and I got the qzv file after denoising and QC filtering ( file attached). However, when i try to do the filtering, merg… --- ## [Qiime2 manifests and import methods](https://forum.qiime2.org/t/qiime2-manifests-and-import-methods/34206)
**Author:** [@wenzix](https://forum.qiime2.org/u/wenzix)\ **Replies:** 1\ **Last updated:** [June 6, 2026, 3:46pm UTC](https://forum.qiime2.org/t/qiime2-manifests-and-import-methods/34206 "2026-06-06T15:46:49Z")
Hello, everyone. I recently started working with microbiomes and am using Qiime2. I’d like to know if there are any other import methods besides generating a manifest. I tried creating one to import my sequences, but it … --- ## [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… --- ## [Importing fastq.gz files to qiime2.2026.4](https://forum.qiime2.org/t/importing-fastq-gz-files-to-qiime2-2026-4/34178)
**Author:** [@Francisco.Herrarte](https://forum.qiime2.org/u/Francisco.Herrarte)\ **Replies:** 2\ **Last updated:** [May 18, 2026, 7:28pm UTC](https://forum.qiime2.org/t/importing-fastq-gz-files-to-qiime2-2026-4/34178 "2026-05-18T19:28:09Z")
Hello, I´m new to QIIME2. I was trying to import some fastq.gz files to qiime using the guide in the How to Guide of Qiime2. After many trials and error i finally got a manifest that correctly separates de columns but it… --- ## [SEPP fragment insertion fails with exit status 1 under WSL2](https://forum.qiime2.org/t/sepp-fragment-insertion-fails-with-exit-status-1-under-wsl2/34165)
**Author:** [@Andrea\_Madrigal\_Juar](https://forum.qiime2.org/u/Andrea_Madrigal_Juar)\ **Replies:** 4\ **Last updated:** [May 7, 2026, 4:14pm UTC](https://forum.qiime2.org/t/sepp-fragment-insertion-fails-with-exit-status-1-under-wsl2/34165 "2026-05-07T16:14:19Z")
Hi everyone, I’m running into persistent issues when trying to execute fragment insertion using SEPP in QIIME 2, and I would really appreciate any guidance. Context: I am working on a microbiome dataset and attempting … --- ## [Qiime version and singletons](https://forum.qiime2.org/t/qiime-version-and-singletons/34151)
**Author:** [@Alessandro](https://forum.qiime2.org/u/Alessandro)\ **Replies:** 3\ **Last updated:** [April 27, 2026, 11:45pm UTC](https://forum.qiime2.org/t/qiime-version-and-singletons/34151 "2026-04-27T23:45:36Z")
Hello everyone, I’m running into a difference between QIIME 2 versions and I’d like to understand what’s going on. At the end of 2025, I performed 16S analyses using QIIME 2 version 2025.10.1. With that version, the fea… --- ## [UNITE database use for classification](https://forum.qiime2.org/t/unite-database-use-for-classification/34125)
**Author:** [@evepyrenees](https://forum.qiime2.org/u/evepyrenees)\ **Replies:** 1\ **Last updated:** [April 22, 2026, 4:15pm UTC](https://forum.qiime2.org/t/unite-database-use-for-classification/34125 "2026-04-22T16:15:19Z")
Hello! I am working with ITS1 data and have used a workflow borrowing heavily from the Langille lab’s microbiome helper, with a few fungal modifications including extracting the ITS1 region (Microbiome Helper 2 Marker ge… [Next page](https://forum.qiime2.org/c/user-support/6.md?page=1)