# \#rescript **URL:** https://forum.qiime2.org/tag/rescript/219.md [Latest](https://forum.qiime2.org/latest.md) · [Categories](https://forum.qiime2.org/categories.md) · [Tags](https://forum.qiime2.org/tags.md) --- ## [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 … --- ## [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… --- ## [RESCRIPt 'get-ncbi-genomes' and 'get-ncbi-data-protein' functions not supported?](https://forum.qiime2.org/t/rescript-get-ncbi-genomes-and-get-ncbi-data-protein-functions-not-supported/33995)
**Author:** [@Adam\_Cantor](https://forum.qiime2.org/u/Adam_Cantor)\ **Replies:** 2\ **Last updated:** [February 19, 2026, 4:47pm UTC](https://forum.qiime2.org/t/rescript-get-ncbi-genomes-and-get-ncbi-data-protein-functions-not-supported/33995 "2026-02-19T16:47:30Z")
Was trying the RESCRIPt ‘get-ncbi-genomes’ function in a q2 v2025.4 environment on my HPC. For context, just running Entrez queries works fine. My test command: qiime rescript get-ncbi-genomes --p-taxon "Bifidobacterium … --- ## ["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… --- ## [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… --- ## [Error when using qiime taxa barplot after fragment-insertion](https://forum.qiime2.org/t/error-when-using-qiime-taxa-barplot-after-fragment-insertion/33481)
**Author:** [@Julio](https://forum.qiime2.org/u/Julio)\ **Replies:** 8\ **Last updated:** [August 13, 2025, 9:43am UTC](https://forum.qiime2.org/t/error-when-using-qiime-taxa-barplot-after-fragment-insertion/33481 "2025-08-13T09:43:04Z")
Hi everyone, I used fragment-insertion sepp to insert some sequences to a reference tree. After that, I used fragment-insertion filter-features to filter my taxonomic table and used fragment-insertion classify-otus-expe… --- ## [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… --- ## [vsearch unrecognized option '--qseqout'](https://forum.qiime2.org/t/vsearch-unrecognized-option-qseqout/33381)
**Author:** [@alexkrohn](https://forum.qiime2.org/u/alexkrohn)\ **Replies:** 3\ **Last updated:** [July 1, 2025, 1:07pm UTC](https://forum.qiime2.org/t/vsearch-unrecognized-option-qseqout/33381 "2025-07-01T13:07:06Z")
Running qiime2 2022.2 (because of old processors that are not compatible with later versions). Running qiime rescript extract-seq-segments and I get an error with vsearch that the --qsegout parameter does not exist. Is t… --- ## [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… --- ## [mismatch between taxonomy and sequence data that download from NCBI using qiime rescript get-ncbi-data](https://forum.qiime2.org/t/mismatch-between-taxonomy-and-sequence-data-that-download-from-ncbi-using-qiime-rescript-get-ncbi-data/33130)
**Author:** [@Si\_Vivy](https://forum.qiime2.org/u/Si_Vivy)\ **Replies:** 3\ **Last updated:** [May 19, 2025, 7:58am UTC](https://forum.qiime2.org/t/mismatch-between-taxonomy-and-sequence-data-that-download-from-ncbi-using-qiime-rescript-get-ncbi-data/33130 "2025-05-19T07:58:44Z")
Hello ! I am trying to download COI data from NCBI with this code: qiime rescript get-ncbi-data \\ --p-query '(cytochrome c oxidase subunit I\[gene\] OR cytochrome oxidase subunit 1\[gene\] OR cytochrome oxidase subunit I\[… --- ## [RESCRIPt GTDB 226.0](https://forum.qiime2.org/t/rescript-gtdb-226-0/33085)
**Author:** [@microbialpeach](https://forum.qiime2.org/u/microbialpeach)\ **Replies:** 2\ **Last updated:** [May 5, 2025, 8:03pm UTC](https://forum.qiime2.org/t/rescript-gtdb-226-0/33085 "2025-05-05T20:03:03Z")
Hey team, the get gtdb data function of RESCRIPt only works for versions '202.0', '207.0', '214.0', '214.1', '220.0'. There's a new version, 226.0. What are the manual steps to download and import GTDB data ('SpeciesRep… --- ## [Almost all Reads are unclassified - custom 18S V4 classifier](https://forum.qiime2.org/t/almost-all-reads-are-unclassified-custom-18s-v4-classifier/33015)
**Author:** [@paperwolf](https://forum.qiime2.org/u/paperwolf)\ **Replies:** 12\ **Last updated:** [April 25, 2025, 5:42pm UTC](https://forum.qiime2.org/t/almost-all-reads-are-unclassified-custom-18s-v4-classifier/33015 "2025-04-25T17:42:57Z")
Hello! I am using qiime 2 (2024.5) on the university HPC and having some issues with my 18S classifier. It seems to be running as normal, but a majority of my reads are unclassified, which was odd cause if I blast them … --- ## [Contents of imported database](https://forum.qiime2.org/t/contents-of-imported-database/32736)
**Author:** [@klunn](https://forum.qiime2.org/u/klunn)\ **Replies:** 6\ **Last updated:** [March 18, 2025, 3:48pm UTC](https://forum.qiime2.org/t/contents-of-imported-database/32736 "2025-03-18T15:48:01Z")
Hello, I'm trying to assign taxonomy to my sequencing data for the ITS region using RESCRIPt. When I manually use ncbiBLAST to assign my ASVs, I often pick up a genus that does not appear when I assign taxonomy using RE… --- ## [Assigning Taxonomy with the Silva Classifier](https://forum.qiime2.org/t/assigning-taxonomy-with-the-silva-classifier/32682)
**Author:** [@jcunderwood](https://forum.qiime2.org/u/jcunderwood)\ **Replies:** 5\ **Last updated:** [March 5, 2025, 8:39pm UTC](https://forum.qiime2.org/t/assigning-taxonomy-with-the-silva-classifier/32682 "2025-03-05T20:39:30Z")
Hello, I'm trying to assign taxonomy using the Silva classifier files I obtained from the rescript command as well as other sources, however I get the following error : "Invalid value for '--i-classifier': Expected an a… --- ## [Filtering eukaryotes from SILVA database](https://forum.qiime2.org/t/filtering-eukaryotes-from-silva-database/32334)
**Author:** [@kevin\_SalOrt](https://forum.qiime2.org/u/kevin_SalOrt)\ **Replies:** 3\ **Last updated:** [January 17, 2025, 2:11pm UTC](https://forum.qiime2.org/t/filtering-eukaryotes-from-silva-database/32334 "2025-01-17T14:11:56Z")
I want to remove Eukaryota from SILVA 138, following these instructions i ran: qiime rescript filter-seqs-length-by-taxon \\ --i-sequences silva-138.1-ssu-nr99-seqs-cleaned.qza \\ --i-taxonomy silva-138.1-ssu-nr99… --- ## [RESCRIPT: species information in GTDB](https://forum.qiime2.org/t/rescript-species-information-in-gtdb/32287)
**Author:** [@GSH](https://forum.qiime2.org/u/GSH)\ **Replies:** 4\ **Last updated:** [January 13, 2025, 1:42pm UTC](https://forum.qiime2.org/t/rescript-species-information-in-gtdb/32287 "2025-01-13T13:42:46Z")
Hi @SoilRotifer, I noticed that when using "qiime rescript get-gtdb-data", the species-level info is incomplete. For example, "s\_\_Escherichia coli" only shows as "s\_\_Escherichia", missing everything after the space.This… --- ## [How to train a GTDB SSU classifier using RESCRIPt](https://forum.qiime2.org/t/how-to-train-a-gtdb-ssu-classifier-using-rescript/25725)
**Author:** [@SoilRotifer](https://forum.qiime2.org/u/SoilRotifer)\ **Replies:** 2\ **Last updated:** [July 23, 2024, 3:53pm UTC](https://forum.qiime2.org/t/how-to-train-a-gtdb-ssu-classifier-using-rescript/25725 "2024-07-23T15:53:56Z")
: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! H… --- ## [How to train a UNITE classifier using RESCRIPt](https://forum.qiime2.org/t/how-to-train-a-unite-classifier-using-rescript/28285)
**Author:** [@colinbrislawn](https://forum.qiime2.org/u/colinbrislawn)\ **Replies:** 8\ **Last updated:** [January 3, 2025, 2:37pm UTC](https://forum.qiime2.org/t/how-to-train-a-unite-classifier-using-rescript/28285 "2025-01-03T14:37:03Z")
:construction: This tutorial is a work in progress. Please leave us questions and comments so we can better help you use this database. All feedback is welcome. If you are looking for a pre-trained ITS classifier, you c… --- ## [Merging Custom Reference Sequences with rescript reference database](https://forum.qiime2.org/t/merging-custom-reference-sequences-with-rescript-reference-database/32115)
**Author:** [@alexkrohn](https://forum.qiime2.org/u/alexkrohn)\ **Replies:** 1\ **Last updated:** [December 11, 2024, 5:47pm UTC](https://forum.qiime2.org/t/merging-custom-reference-sequences-with-rescript-reference-database/32115 "2024-12-11T17:47:46Z")
I'm combining reference sequences generated with Sanger sequencing with those downloaded by rescript, and am getting the error that one of the sequences present in the reference sequences is not present in the taxonomy. … --- ## [...temporary files that no longer exist.](https://forum.qiime2.org/t/temporary-files-that-no-longer-exist/32013)
**Author:** [@ilasadar](https://forum.qiime2.org/u/ilasadar)\ **Replies:** 2\ **Last updated:** [December 3, 2024, 5:54pm UTC](https://forum.qiime2.org/t/temporary-files-that-no-longer-exist/32013 "2024-12-03T17:54:22Z")
Hi, I am using: QIIME 2 Plugin 'rescript' version 2024.5.1 (from package 'rescript' version 2024.5.1). Cluster (--mem=200G, -c 12) - Partial Rescript Code: qiime rescript extract-seq-segments \\ --i-input-sequences … --- ## [Using RESCRIPt to compile sequence databases and taxonomy classifiers from NCBI Genbank](https://forum.qiime2.org/t/using-rescript-to-compile-sequence-databases-and-taxonomy-classifiers-from-ncbi-genbank/15947)
**Author:** [@Nicholas\_Bokulich](https://forum.qiime2.org/u/Nicholas_Bokulich)\ **Replies:** 0\ **Last updated:** [August 4, 2020, 3:38pm UTC](https://forum.qiime2.org/t/using-rescript-to-compile-sequence-databases-and-taxonomy-classifiers-from-ncbi-genbank/15947 "2020-08-04T15:38:16Z")
This tutorial will describe how to create custom reference databases from NCBI Genbank using RESCRIPt. Read more about RESCRIPt here: Processing, filtering, and evaluating the SILVA database (and other reference sequenc… --- ## [Training silva classifiers based on NCBI taxonomy](https://forum.qiime2.org/t/training-silva-classifiers-based-on-ncbi-taxonomy/31578)
**Author:** [@Chengzi](https://forum.qiime2.org/u/Chengzi)\ **Replies:** 1\ **Last updated:** [October 3, 2024, 2:47pm UTC](https://forum.qiime2.org/t/training-silva-classifiers-based-on-ncbi-taxonomy/31578 "2024-10-03T14:47:58Z")
I want to train my classifier using the SILVA database based on the NCBI taxonomy, I have tried a few times using RESCRIPt but come across many problems, so I think maybe the file I have chosen is wrong. I go to the SIL… --- ## [RESCRIPt issue for --p-query retriving data from NCBI: No sequences for given query](https://forum.qiime2.org/t/rescript-issue-for-p-query-retriving-data-from-ncbi-no-sequences-for-given-query/31560)
**Author:** [@Immanuelle\_Kezia](https://forum.qiime2.org/u/Immanuelle_Kezia)\ **Replies:** 4\ **Last updated:** [October 2, 2024, 5:06pm UTC](https://forum.qiime2.org/t/rescript-issue-for-p-query-retriving-data-from-ncbi-no-sequences-for-given-query/31560 "2024-10-02T17:06:19Z")
Hi there! I'm trying to download RefSeq database from 10th December 2008 until 31st May 2018. I tried using this command --p-query '33175\[BioProject\] OR 33317\[BioProject\] AND ("2008/12/10"\[PDAT\] : "2018/05/31"\[PDAT\])' bu… --- ## [Sequences not retrieved via Rescript](https://forum.qiime2.org/t/sequences-not-retrieved-via-rescript/31361)
**Author:** [@paperwolf](https://forum.qiime2.org/u/paperwolf)\ **Replies:** 2\ **Last updated:** [September 9, 2024, 2:44pm UTC](https://forum.qiime2.org/t/sequences-not-retrieved-via-rescript/31361 "2024-09-09T14:44:35Z")
Hi! I was downloading CO1 sequences from NCBI over the weekend and in my output, I got some messages that it didn't download some sequences. Warnings in Output File (was stated multiple time): WARNING:2024-09-07 13:45:… --- ## [Manually Adding Positive Controls to classifier or reference database](https://forum.qiime2.org/t/manually-adding-positive-controls-to-classifier-or-reference-database/28733)
**Author:** [@alexkrohn](https://forum.qiime2.org/u/alexkrohn)\ **Replies:** 4\ **Last updated:** [August 30, 2024, 6:30pm UTC](https://forum.qiime2.org/t/manually-adding-positive-controls-to-classifier-or-reference-database/28733 "2024-08-30T18:30:22Z")
I'm wondering if there is an easy way to add sequences/taxonomy to a reference database created with QIIME. I'm working on an eDNA metabarcoding project and want to detect species not present on NCBI's GenBank database.… --- ## [qiime feature-classifier classify-sklearn low confidence despite 100% identity](https://forum.qiime2.org/t/qiime-feature-classifier-classify-sklearn-low-confidence-despite-100-identity/31197)
**Author:** [@Oryx-scimitar](https://forum.qiime2.org/u/Oryx-scimitar)\ **Replies:** 1\ **Last updated:** [August 21, 2024, 6:26am UTC](https://forum.qiime2.org/t/qiime-feature-classifier-classify-sklearn-low-confidence-despite-100-identity/31197 "2024-08-21T06:26:22Z")
I'm baffled by low classification confidence levels assigned using qiime feature-classifier classify-sklearn for ASVs with 100% ID and cover. I'm doing targeted amplicon sequencing for piroplasmids so I've created a cla… [Next page](https://forum.qiime2.org/tag/rescript/219.md?match_all_tags=true&page=1&tags%5B%5D=rescript)