Tag: QIIME2

MarinaZ (Marina) February 8, 2024, 11:01am 1 Hello, I’ve been experiencing the following error: (1/1?) No such option: –imput-path (Possible options: –input-path, –output-path)I have single-end demultiplexed with quality data and I’m trying to import them in qiime in order to create .qza file. The command that I used and gives…

JThurston (Josh Thurston) January 19, 2024, 8:05pm 1 Hi all! I’m currently working through a Qiime2 pipeline analysing Illumina miseq paired-end amplicon data. I’ve successfully analysed bacterial (16s) amplicons from importing, filtering through to taxonomic assignment. However, I also have amplicon data for a functional gene (nifH; nitrogenase for N2…

komal (Komalk) January 19, 2024, 12:02pm 1 Hi this is regarding DESeq2. I first created a phyloseq object from qiime2 artifacts and then subjected it to Deseq2. At one step I got a errorError in estimateSizeFactorsForMatrix(counts(object), locfunc = locfunc, :every gene contains at least one zero, cannot compute log geometric…

President’s Report It has been an honor and privilege to serve as your president this past year, and I look forward to my second year in this … 2023 In Vitro Biology Meeting Update The Society for In Vitro Biology (SIVB) is excited to announce that its annual meeting is…

What are the challenges and opportunities in using phylogenomics to study spiders?5 answersPhylogenomics has provided valuable insights into the study of spiders, but it also presents challenges and opportunities. One challenge is the low capture efficiency of available UCE probe sets for spider phylogenomics, which are not optimized for certain…

Hi, I am running Qiime2-2023.7. I ran a mantel test for unweighted unifrac distance matrices between two groups to correlate their populations. Is there a way I can add a linear regression line or a line to show correlation as shown in references below. Almost all papers I see use…

Microbiomes contain diverse microbial communities whose interactions not only impact the system residents, but also have profound effects on the ecology, chemistry, and health of their shared host or environment. Capturing the interactions among microbes is essential as we expand our understanding of host-microbe dynamics, evaluate environmental degradation or remediation,…

ZhangSR (June) December 7, 2023, 6:36am 1 Hi~ When I updated the ITSxpress within QIIME2-202309 following the updated tutorial here github.com/USDA-ARS-GBRU/itsxpress-tutorial/blob/master/ITSxpress-tutorial.md, there were some confusions. I updated the itsxpress by conda install -c bioconda itsxpress and then qiime dev refresh-cache under the QIIME2 environment I failed to call itsxpress by…

Andrea_G (Andrea Gatti) November 28, 2023, 2:19pm 1 Hello, I have to start working on a cluster and I tired to install Qiime2 in a conda environment, but I was reported with an error during Qiime2 installation, specifying: Preparing transaction: done Verifying transaction: – SafetyError: The package for r-base located…

Informal elements in English academic writing: threats or opportunities for advanced non-native speakers? 5 answers in the context of programming, what is system? 4 answers How can the deconstruction of labelling in a poster be used to create a more effective poster? 4 answers How does using ChatGPT to enhance…

qiime2 paired end fastqs import 1 Hi all, I’m trying to import data into Qiime2. This process seems convoluted and complicated. i’ve tried importing in several ways but the software does not play nice with paried end reads. therefore i have followed their instructions for creating a manifest file, to…

Dereplication of nanopore sequences using q2ONT workflow 0 Dear, I i am using q2ONT workflow for the Nanopore seq data. I am also using it for my 16srRNA gene seq data. I am facing a problem with dereplication of the sequences. When i see my 5-derep-table.qzv, i get all the…

Hello everyone, I am struggling with a problem I would like to solve inside the qiime2 eviroment. I am running an experiment in which I have two groups that have different alpha diversity for the observed features metric. I would like to visualize (maybe a qzv) what are the taxon…

Has anyone had any luck importing a braken database? Managed to get kraken2 to work by downloading a one of the tar.gz files, extracting and only keeping the ‘k2d’ files and running: qiime tools import \ –type ‘Kraken2DB’ \ –input-path k2_pluspfp_16gb_20231009_q2 \ –output-path k2_pluspf.qza But trying something similar with –type…

Large qiime2 table (107 gb) to phyloseq 0 Hello, I’m currently engaged in a microbiome meta-analysis and have combined a dada2 table involving data from 83 different studies. The file size of this merged table is 107GB. However, I’m encountering difficulties reading this file in R to conduct statistical analyses….

Using data generated from QIIME2 jupyter notebookLinks to an external site., generate a 1 page report. Include in your report the following: Project description Hypothesis statement Figure of analysis pipeline and brief description of steps (may be bullet points) Figure of DNA sequence quality Figure of alpha diversity, scaled appropriately…

A flow diagram of the study is shown in Fig. 3. Figure 3 Flow diagram of the study. Ethical approval and consent to participant This study was approved by the Institutional Review Board of the Nagoya University Graduate School of Medicine (approval number 2022-0084; approval date, June 3, 2022). Written informed…

News:Course -Metabarcoding in Microbial Ecology 0 Dear all, Registrations are now open for the next edition of theonline course, “METABARCODING IN MICROBIAL ECOLOGY,” scheduled for February 5th to February 9th, 2024. This course offers an immersive journey into the realm of metabarcoding techniques in microbial ecology. We will delve into…

I read that I might need to rename the files and reinstall with manifest or perform deblur outside qiime2. I would happy to get a detailed step on how to rectify this error as I am new to qiime. QIIME 2 Version: qiime2-2023.7 in conda environment Command ran:qiime deblur denoise-16S…

I have experienced installation issue with qiime2-shotgun-2023.9please help me to resolve this issue.Collecting package metadata (repodata.json): doneSolving environment: failed ResolvePackageNotFound: gxx_impl_linux-64=13.2.0 libgomp=13.2.0 bracken=2.9 xcb-util-image=0.4.0 keyutils=1.6.1 xkeyboard-config=2.38 jack=1.9.22 libcups=2.3.3 alsa-lib=1.2.8 libsanitizer=13.2.0 libgcc-devel_linux-64=13.2.0 gfortran_impl_linux-64=13.2.0 attr=2.5.1 libstdcxx-ng=13.2.0 xcb-util=0.4.0 gcc_impl_linux-64=13.2.0 libnsl=2.0.0 libstdcxx-devel_linux-64=13.2.0 xcb-util-wm=0.4.1 libcap=2.66 xcb-util-keysyms=0.4.0 pulseaudio=16.1 libsystemd0=252 xcb-util-renderutil=0.3.9 libxkbcommon=1.5.0 _openmp_mutex=4.5 libgfortran-ng=13.2.0 libgcc-ng=13.2.0 libudev1=253 gridss=2.13.2…

Hi there! Trying to run my samples using QIIME2 2023.7. As a novice, cutadapt has never been an issue before. However, while running my samples today I encountered the following error: The command used was: qiime cutadapt trim-paired –i-demultiplexed-sequences paired-end-demux.qza –o-trimmed-sequences paired-end-trimmed.qza Where could I have gone wrong? Quick help…

Hello there!I am typing because I was trying to retrieve the new Qiime2 version but brutally failed I don’t have Docker on my device, but I have singularity, therefore I go with: singularity build qiime2_2023.2 It worked with 2023.2, but here instead it retrieves the following: INFO: Starting build…FATAL: While…

komal (komalk) October 11, 2023, 4:12am 1 Can anyone confirm if my pipeline mentioned below is right for qiime2 analysis so we first import the data in form of manifest file 2)I now will trucate my forward and reverse reads from where the quality of bases fall below Q20 or…

I am trying to install an updated version of QIIME2 on a departmental computer. I first ran into some problems with permissions, but once an override code was identified I am now getting an unfamiliar error response during the final stage of installation. Wget is working find from what I…

Hello fellow qiime2 users,I’ve been trying to figure out differentially abundant microbial population in diabetic patients but facing so many obstacles that I can’t figure out alone as a novice metagenomic analyst, so I need your help and I’m attaching all the files I used and errors I got below….

Hello, I have a problem with the feature classifier.So I tried this on multiple computers (with intel and AMD chips) and with multiple versions of QIIME2 (QIIME2 2023.5 and 2023.7)So I have a dual boot on my computer with Windows and Linux Ubuntu, newest release. It has 16 GB of…

Hello,I’ve previously used fragment-insertion plugin without any issues. However, recently as I’m trying generate the tree using rep_seq file generated from vsearch open-reference clustering. I’m getting the following error from the this plugin. And the log file says- Removing /tmp/tmp.etXzw1y7jQ/sepp-tmp-CaHDDnOVOTTraceback (most recent call last):File “/home/turtle/miniconda3/envs/qiime2-2023.2/lib/python3.8/site-packages/q2cli/commands.py”, line 352, in callresults =…

Eman (Eman Khalaf) October 8, 2023, 4:50pm 1 Hi, I have many samples (~650) sequenced by PacBio platform. RStudio can not process dada function due to the memory limit of the software. The total size of the samples is 30 GB and I need to use pool=TRUE parameter. So, I…

kulandai1 (Balamurugan) October 5, 2023, 9:21am 1 HiI am running qiime in hpc with pbs script, I got error as Traceback (most recent call last):File “/home/dell_emc/easybuild/software/QIIME2/2023.5/lib/python3.8/site-packages/q2cli/commands.py”, line 473, in callresults = action(**arguments)File “”, line 2, in align_to_tree_mafft_fasttreeFile “/home/dell_emc/easybuild/software/QIIME2/2023.5/lib/python3.8/site-packages/qiime2/sdk/action.py”, line 411, in parsl_wrappersetup_parallel()File “/home/dell_emc/easybuild/software/QIIME2/2023.5/lib/python3.8/site-packages/qiime2/sdk/parallel_config.py”, line 69, in setup_parallelconfig_fp = _get_vendored_config()File “/home/dell_emc/easybuild/software/QIIME2/2023.5/lib/python3.8/site-packages/qiime2/sdk/parallel_config.py”,…

Hi all, I am trying to incorporate some complete/near complete 16s rRNA sequences that I have extracted from annotated genomes following some PacBio HiFi metagenomic sequencing I have done. The aim here is to compare these sequences against a V1-V2 16s rRNA sequencing dataset, generating a phylogenetic tree to see…

The Rank of the website you are interested in is: 39.4 Controversial. Risky. Red Flags. The rank is based on a 1-100 scale, with 100 being the most reputable. Is view.qiime2.org legit? Is it secure or possibly risky? According to our analysis, the website has a medium-low trusting rank so…

Soil incubation and cell extraction Approximately 3 kg of unmanaged marginal soil (pH 8) was collected from the Pacific Northwest National Laboratory field site in Prosser, Washington (46° 15′ 04″ N and 119° 43′ 43″ W) [23], homogenized, sieved (4 mm mesh size), and stored at 4 °C until further processing. Probe specific…

I am currently running 2023.7 and am getting a non-zero exit status I don’t understand. I had run core metrics on this same dataset in 2020.11 and didn’t have an issue. qiime diversity core-metrics-phylogenetic –i-table removed_samples/1_filtered_table.qza –i-phylogeny removed_samples/fastree/rooted_tree.qza –p-sampling-depth 5200 –m-metadata-file new_newt_metadata.tsv –output-dir removed_samples/core_metrics/alpha_5200/ –verbose Running external command line application….

Hello, I am attempting to use the DEICODE plugin, but I am getting what appears to be an incompatibility error. I am running the qiime2-2023.7 version that was installed in a conda environment for the new (M2) mac. I haven’t had any issues running this version of QIIME2 for other…

Leran (Leran) September 25, 2023, 8:02pm 1 Hi, I’m running qiime2 to demultiplex data. I have a forward.fastq.gz file, a reverse.fastq.gz and a barcode.fastq.gz file. So the syntax I used is as below: qiime tools import –type EMPPairedEndSequences –input-path emp-paired-end-sequences –output-path emp-paired-end-sequences.qza then: qiime demux emp-paired –i-seqs emp-paired-end-sequences.qza –m-barcodes-file sample-metadata.tsv…

nur (Nur Anwar) September 25, 2023, 4:08pm 1 Update: I successfully installed it when i deleted the line bioconductor-genomeinfodb line from the .yml file and installed it separately. With me bioconductor-genomeinfodbdata wasn’t causing any conflicts but bioconductor-genomeinfodb. I had to check. Thank you. qiime2 is now installed. Hello, glad it…

Rubin, S., Parr, T., Da Costa, L. & Friston, K. Future climates: Markov blankets and active inference in the biosphere. J. R. Soc. Interface 17, 20200503 (2020). Article  CAS  PubMed  PubMed Central  Google Scholar  Cantonati, M. et al. Characteristics, main impacts, and stewardship of natural and artificial freshwater environments: Consequences…

Hello! I’m trying to classify some sequences of fungal ITS2, following this tutorial: Fungal ITS analysis tutorial. I’m running Qiime2-2023.7 on a server through my university. I’m very new to using servers so I’ll try to answer questions about it as best as I can. And using the UNITE database,…

shibayu (Miao Li) September 22, 2023, 8:01am 1 Hello, everyone! Some of the species in my study area do not have corresponding reference sequences on NCBI, and I now want to amplify those reference sequences that are not available on NCBI myself, how should I organize these sequences into a…

To Whom it May Concern: Hello. I am trying to run a few practice trials on getting sequences from NCBI via q2-fondue prior to a larger scale analysis. The code was working just fine up until dada2 where I encountered a common error that the forum believes is a storage…

KBauer (Kylynda) September 21, 2023, 9:17pm 1 Continuing the discussion from PCoA plots with confidence ellipsoids: Hello, I’ve tried to use stat_ellipse () in my R graphs, integrating from QIIME2(Tutorial: Integrating QIIME2 and R for data visualization and analysis using qiime2R – #21) Here is my code:IJ$data$Vectors %>%dplyr::select(SampleID, PC1, PC2)…

I was originally running qiime2-2023.2 but had to install qiime2-2023.5 to go along with the 2023.5 version of q2-fmt-alpha. I tried to generate a raincloud plot and it gave me an error qiime stats plot-rainclouds \ –i-data timepoint-dists.qza \ –i-stats stats_baseline0.qza \ –o-visualization raincloud-baseline0.qzv Based on previous posts on the…

Hi,I have 24 clean CCS read datasets and i want to get amplicon sequence variants by running dada2.I got one issue when running dada2 denoise-ccs with QIIME2. When i am running dada2 in qiime2 with all 24 samples:The command I used was: qiime dada2 denoise-ccs –i-demultiplexed-seqs reads_qza/ccs_reads.qza –p-min-len 1200 –p-max-len…

debug.txt (182.2 KB)The attachment appears when I run the conda env create -n qiime2-2023.7 –file qiime2-2023.7-py38-linux-conda.yml command in Ubuntu 22.04.3 LTS (GNU/Linux 6.2.0-32-generic x86_64) I don’t know how to solve the error. Can anyone help me? My anaconda version is conda 22.9.0 Hello @a17370910195, Welcome to the forums! In that…

HiI am running the Parkison mice sample data, and I have updated the Qiime2, and my computer have enough capacity. But I still met this problem. Could you please help me deal with it? Plugin error from fragment-insertion: Command ‘[‘run-sepp.sh’, ‘/tmp/qiime2-archive-6m4if51o/a3c55eab-dffc-426e-8521-3d193cab2fc0/data/dna-sequences.fasta’, ‘q2-fragment-insertion’, ‘-x’, ‘1’, ‘-A’, ‘1000’, ‘-P’, ‘5000’, ‘-a’, ‘/tmp/qiime2-archive-0s212g0k/a14c6180-506b-4ecb-bacb-9cb30bc3044b/data/aligned-dna-sequences.fasta’,…

Introduction Endophthalmitis is a severe infection in the eye that can occur as a consequence of intraocular surgery, intraocular injections, trauma, the presence of a central venous catheter and systemic infectious diseases such as sepsis, abscesses or urinary tract infection.1 2 Acute bacterial endophthalmitis represents a significant ocular pathology that…

Hi!I am facing a problem in alpha rarefaction curve plotting. In this study my samples were sequenced in two different runs “under same conditions” using Illumina Platform- MiSeq. For that reason I have merged the data from both the runs using same filtering parameters and following DADA2. Till “phylogeny align-to-tree-mafft-fasttree”…

Warning: [blastn] Examining 5 or more matches is recommended/home/lucy2/anaconda3/envs/qiime2-2023.7/lib/python3.8/site-packages/q2_feature_classifier/_blast.py:80: FutureWarning: The frame.append method is deprecated and will be removed from pandas in a future version. Use pandas.concat instead.missed = missed.append(/home/lucy2/anaconda3/envs/qiime2-2023.7/lib/python3.8/site-packages/q2_feature_classifier/_blast.py:84: FutureWarning: The frame.append method is deprecated and will be removed from pandas in a future version. Use pandas.concat instead.result =…

cjj102664 (俊杰 陈) September 10, 2023, 3:52pm 1 Does anyone know,it is necessary to run qiime cutadapt trim-paired before run dada2. Hello @cjj102664. Welcome to the forums! cjj102664: it is necessary to run qiime cutadapt trim-paired before run dada2. Not necessarily! cutadapt will ‘cut adapters’ from your input reads. Some…

Yiggrite (Yiggrite Wu) September 7, 2023, 6:53pm 1 Hi, please look at my problem. I totally followed the steps on the tutorial page. I think i am in the working directory. What is the problem? and What should I do? manifest.tsv 100%[=================================================>] 4.53K –.-KB/s in 0s 2023-09-07 14:02:42 (198 MB/s)…

rjay428 (Rylee Jensen) September 5, 2023, 10:34pm 1 Hi all! Brand new to QIIME2 and with the Python environment as well. I’m running into an issue during the installation process that is close to what is posted on here, but I haven’t been able to figure out this exact problem….

Location and sample collection Samples were taken from 10 composting piles (between May and August 2020) at a food waste (FW) composting facility (Zhejiang, China; 30°52′51.50″N; 119°46′12.87″E). A consistent pre-treatment method was used for each pile. Specifically, about 8 tons of FW was collected every 3 days and subsequently crushed into…

I have QIIME2 outputs (feature table, tree, taxonomy, and metadata) that I’ve imported into R using qiime2R (v. 0.99.6) ‘qza_to_phyloseq’ to create a phyloseq object. My QIIME feature table shows reasonable values for ASV abundance across all samples (n=16; feature table available upon request). Problem: The otu_table the ASV values…

This workshop will give you an introduction to metabar coding analysis using the QIIME2 analysis platform. About this Event QIIME2 analysis of bacterial 16s rRNALead trainer: Laura Geissler (School of Biosciences, The University of Melbourne) Workshop Description: This workshop will give you an introduction to the QIIME2 analysis platform using…

Did not find the exact answer to this on the forum; new to QIIME2, apologies. QIIME2-2023.5, running in Conda through university’s central Linux-based system Apply DADA2 denoising qiime dada2 denoise-paired –i-demultiplexed-seqs paired-end-demux.qza –p-trunc-len-f 280 –p-trunc-len-r 220 –p-n-threads 24 –o-representative-sequences rep-seqs-dada.qza –o-table table-dada2.qza –o-denoising-stats dada-stats.qza –verbose R version 4.2.3 (2023-03-15)Loading required…

Siyu_Song (Siyu Song) August 22, 2023, 8:19pm 1 Hi everyone, I am new to qiime and I am struggling so much on how to upload my sequences to qiime2. So I have generated a manifest file as below, and I tried to import my sequence with the code: qiime tools…

Hi all, I am trying to generate an unweighted unifrac with the qiime2 python API and get the following output and error: from qiime2 import Artifact from qiime2.plugins import diversity_lib tab1N=(‘/home/sdegregori/TOL/GMTOLsubsample/GMTOLsong_tablef_V4_N1_pythontest.qza’) phyf=(‘/home/sdegregori/TOL/GMTOLsubsample/GMTOLsong_rooted_treef.qza’) table1N = Artifact.load(tab1N) phylogenyf = Artifact.load(phyf) distance_matrix_result = diversity_lib.methods.unweighted_unifrac(table=table1N,phylogeny=phylogenyf) distance_matrix = distance_matrix_result.distance_matrix distance_matrix.save(‘/home/sdegregori/TOL/GMTOLsubsample/adonis/UW1N.qza’) Running external command line application….

HI,I’m trying to install QIIME2 using miniconda3 using the exact command provided in the website using Linux systemdocs.qiime2.org/2023.5/install/native/using these provided steps : Updating Miniconda After installing Miniconda and opening a new terminal, make sure you’re running the latest version of conda: conda update conda Installing wget conda install wget Install…

When counting ASVs in DADA2, does a hit/count only occur at 100% alignment percent identity? 0 I was asked to identify which ASVs came from which samples. My understanding is that an ASV can be present in multiple samples but then that led me to the question of whether or…

QIIME2 analysis pipeline 0. activate conda environment conda activate qiime2-2019.10 1. flip sequences to the same direction mkdir raw_data_rc/ mkdir raw_data_cat/ parallel -j 8 ‘seqtk seq -r {} > raw_data_rc/{/.}_rc.fastq’ ::: rawdata/*.fastq parallel -j 8 –link ‘cat {1} {2} > raw_data_cat/{1/.}_cat.fastq’ ::: rawdata/*.fastq ::: raw_data_rc/*_rc.fastq 2. trim primers mkdir trimmed_reads/…

sgalera (Sergio Galera) August 8, 2023, 10:40am 1 Hi guys! I wanted to create a 16S rRNA library of the V1 to the V9 regions. However, I wasn’t completely sure that I could classify taxonomically those sequences after the library preparation. I have seen different questions about sequencing V1-V9 so…

Kaza, S., Yao, L. C., Bhada-Tata, P. & Van Woerden, F. What a Waste 20: A Global Snapshot of Solid Waste Management to 2050 (World Bank, 2018). doi.org/10.1596/978-1-4648-1329-0. Book  Google Scholar  Lim, S. L., Lee, L. H. & Wu, T. Y. Sustainability of using composting and vermicomposting technologies for organic…

D_S (Dharmesh Singh) July 31, 2023, 10:25am 1 sample_id.csv (575 Bytes) cutadapt_trimming.log.txt (809 Bytes) env_log.txt (3.1 KB) list_log.txt (48.3 KB) qiime_info_log.txt (782 Bytes) Hello Forum, I am running qiime2 on a virtual machine (Hyper V manager, Windows 10 professional) and I am stuck at the step where I am trying…

Study populations Between 2015 and 2019, stool samples and data were collected from 219 IBD subjects (CD or UC) attending the Internal Medicine Clinics, King Fahd Hospital of the University, Al-Khobar and King Fahad Hospital, Alhafof, Saudi Arabia. Diagnosis of IBD was based on endoscopy (for CD) or colonoscopy (for…

mavino (Mariano Avino) July 25, 2023, 1:11pm 1 Hi there,I am a new qiime2 user and I need help with qiime view.My volatility plot file is not showing, page is white.My command was: qiime longitudinal volatility –i-table genus-rf-table_3xTg.qza –p-state-column time.on.diet –m-metadata-file sample-metadata_3xTg.txt diversity-core-metrics-phylogenetic_3xTg/jaccard_pcoa_results.qza –p-individual-id-column fastqfile –p-default-group-column diet –o-visualization volatility-plot-1_3xTg_genus_jaccard.qzv here…

Hello Everyone! I’m extremely new to bioinformatics, so please understand my complete ignorance to this process. My lab use to utilize Michigan States Ribosomal Database Project (RDP), but it recently stopped being supported and is no longer available. We are attempting to pivot to QIIME 2 to clean up and…

Field site Akagera National Park (ANP; 1°52’S, 30°42E) lies in eastern Rwanda, along the border with Tanzania. It is roughly 250,000 ha in size and is characterized by woodland, swamps, low mountains and savannah. At least one quarter of the park contains the swamps and lakes of the Kagera River system,…

Hello, I am experiencing the following error (below) when running the following command (below). I tried this command on multiple cloud instances with high specs, and I have tried running the artifact on the latest version of QIIME 2 after initially trying this on version QIIME2_2019.10. I even tried filtering…

Hello everyone!I am new to qiime2 and at the moment I have problems importing the Taxonomy.txt file.Maybe it helps to solve the problem if I explain that I transferred the taxonomy manually into a text document (TextEdit). I copied from Geneious Prime “Name” and “Taxonomy” (tab separated). Since it was…

Hi I tried to install q2-ancombc as described here GitHub – mortonjt/q2-ancombc: qiime2 plugin for ANCOMBC.R version 4.0.5 (2021-03-31) if (!requireNamespace(“BiocManager”, quietly=TRUE))install.packages(“BiocManager”)BiocManager::install(“ANCOMBC”)install.packages(‘tidyverse’) I noticed following errors ERROR: dependency ‘nloptr’ is not available for package ‘ANCOMBC’ERROR: dependency ‘ragg’ is not available for package ‘tidyverse’ I would appreciate if you could help…

Hi allI am trying to import dataset in qiime2 using the command:qiime tools import –type ‘SequenceData[PairedEndSequenceWithQuality]’ –input-path /home/qiime2/metadata/manifest.tsv.txt –output-path /home/qiime2/metadata/manifest.qza –input-format PairedEndFastqManifestPhred64Traceback (most recent call last):File “/home/qiime2/miniconda/envs/qiime2-2022.2/lib/python3.8/site-packages/q2cli/builtin/tools.py”, line 157, in import_dataartifact = qiime2.sdk.Artifact.import_data(type, input_path,File “/home/qiime2/miniconda/envs/qiime2-2022.2/lib/python3.8/site-packages/qiime2/sdk/result.py”, line 277, in import_datareturn cls.from_view(type, view, view_type, provenance_capture,File “/home/qiime2/miniconda/envs/qiime2-2022.2/lib/python3.8/site-packages/qiime2/sdk/result.py”, line 293, in _from_viewoutput_dir_fmt = pm.get_directory_format(type)File…

I received paired end amplicon sequence from a LAB with different lengths for R1 (320) and R2(280). Should I trust this lab to sequence other samples? Also, I had to do a trimming over the R2 at 220(because Phred score was below 30) in the qiime2/DADA2 pipeline. Do you think…

Hello, I have recently been having errors with viewing new dropbox links via qiime2 view. Interestingly, I am getting the error – Error: Network error, recieved 503 from server. on chrome and firefox, and the error – TypeError: Load failed on safari. I am getting this error for all possible…

The Environmental Protection Agency (EPA) reports a significant number of heavy metal-contaminated sites across the United States. To address this public health concern, rhizoremediation using microbes has emerged as a promising solution, considering the limitations and inefficiencies of current approaches. We hypothesized that if Pseudomonas fluorescens, Burkholderia vietnamiensis, and Rhizobium…

Hi everyone, I am using qiime2 for analyzing the microbiome data. I am stuck at the step of using dada2 denoise-paired for quality control processing. For this step I am using the command:qiime dada2 denoise-paired –i-demultiplexed-seqs demux-paired-end.qza –p-trunc-len-f 150 –p-trunc-len-r 150 –o-representative-sequences rep-seqs-dada2.qza –o-table table-dada2.qza –o-denoising-stats stats-dada2.qza –p-n-threads 10 –verbose…

Subject: Need help with Qiime2 installation: ResolvePackageNotFound error Dear Qiime2 Community, I hope this message finds you well. I am currently facing an issue during the installation of Qiime2 and would greatly appreciate your assistance in resolving it. During the installation process, after following the Qiime2 instructions, I encountered the…

Hello, I am new to this forum. I am using qiime on Debian 8 machine and when  run summarize_taxa_through_plots.py I take an error. The command is:  summarize_taxa_through_plots.py -i /…/observation_table_sorted.biom -o …/ko_summary_plots/ -f -s and the output is:  *** ERROR RAISED DURING STEP: Plot Taxonomy SummaryCommand run was: plot_taxa_summary.py -i Scrivania/Salvo/shotgun/pear_assembly/reverse_blat_mapped/ko_summary_plots/observation_table_sorted_sorted_L2.txt,Scrivania/Salvo/shotgun/pear_assembly/reverse_blat_mapped/ko_summary_plots/observation_table_sorted_sorted_L3.txt,Scrivania/Salvo/shotgun/pear_assembly/reverse_blat_mapped/ko_summary_plots/observation_table_sorted_sorted_L4.txt,Scrivania/Salvo/shotgun/pear_assembly/reverse_blat_mapped/ko_summary_plots/observation_table_sorted_sorted_L5.txt,Scrivania/Salvo/shotgun/pear_assembly/reverse_blat_mapped/ko_summary_plots/observation_table_sorted_sorted_L6.txt -o…

Hi!I`m having problems running qiime2 (version 2023.5).When I run:conda activate qiime2-2023.5 I receive the following message and cant use qiime:QIIME is caching your current deployment for improved performance. This may take a few moments and should only happen once per deployment. If anyone could help me. Thanks! That’s a normal…

hdeel (Heather Deel) July 7, 2023, 4:55pm 1 Hello Q2 folks, Hope you all are well. I am having issues importing some demultiplexed 18S data into qiime2-2023.5, and after a good while searching on the forum and troubleshooting, I keep getting the same error. Here is the command:qiime tools import…

Mammalian host swab sample selection To investigate mammalian skin microbial communities using the cpn60 gene, 95 representative skin swab samples, already extracted for genomic DNA and sequenced from a previous project [8], were selected for additional amplification and sequencing of the cpn60 gene. This cpn60 gene amplicon dataset contained samples…

Nelly (Nelly) July 4, 2023, 12:27pm 1 Hi,I have a Phyloseq object and I am interested in exporting the Phyloseq tree to QIIME2. Since I created the Phyloseq object from WGS data, I wasn’t able to take the sequences and construct a phylogenetic tree based on the sequences. Instead, I…

Good morning! I recognize that QIIME1 is no longer supported, so if there is no answer to my question, I completely understand. I am attempting to download and run QIIME1 to analyze some 16S data because we are wondering whether or not the bacteria will be classified the same as…

Martyn July 3, 2023, 11:49am 1 Hi everyone, I am still having a problem creating a QIIME2 artefact in galaxy. I have my paired end sequences and i have my metadata loaded up. All i need to do is combine them in QIIME2. The tutorial on this page Importing demultiplexed…

Han_Do (Han Do) June 28, 2023, 7:43pm 1 Hi everyone, I wanted to make a 2D PCoA plots similar to the one below. I can’t find any other codes than these. So, I used it and it gave me error. (qiime2-2023.5) hando@Cinderellas-MacBook-Pro AlphaDiversity_FS % qiime tools export –output-dir exported unweighted_unifrac_pcoa_results.qzamake_2d_plots.py…

I wanted to see V3 and V4 regions as well as all other regions in the Classify taxonomy step, so I downloaded the latest version (138.1) of the data from the Download tab on the SILVA homepage and followed the steps below.However, I got an error message in the ‘qiime…

CHANG (CHANG) June 23, 2023, 4:47pm 1 Hello!I am using WSL on Windows 10 Enterprise, and have successfully installed miniconda3 (with python 3.10), but cannot install Qiime2 following the instructions here: Natively installing QIIME 2 — QIIME 2 2023.5.1 documentation Both commands conda update conda And conda install wget Give…

Hi,I got a problem in qiime2 install using conda. It seems the R package bioconductor-genomeinfodbdata cannot be installed. Previously somebody posted similar issues, but were not well solved. I also tried to install bioconductor-genomeinfodbdata indenpendently but also failed, so I guess it should be some problem in this R package….

Hi,I’m getting the error message: Viewing visualization failed while attempting to open /tmp/qiime2/ktaylo363/data/70617dfd-b77c-41f4-b136-0b23e6594c46/data/index.html when trying to run the command qiime tools view demux.qzv in the moving pictures tutorial Using qiime2 version 2023.5, using linux and conda in WSL I have searched for the problem on the forum and did find…

Hello there, I’m working with ITS sequences from 45 samples in total. They were sequenced through an Illumina Novaseq 6000 instrument. Using the last version of QIIME2 (2023.5), my problem occurs while I perform the denoising analysis through dada2 with the following command: qiime dada2 denoise-paired –i-demultiplexed-seqs paired-end-demux.qza –p-trunc-len-f 155…

Newt (Aly) June 19, 2023, 2:43pm 1 Hello, I am getting this error message when running qiime feature-classifier classify-consensus-blast. As of now, the command seems to running, but I am not sure what the future warning message means. I’m using qiime2-2023.5 using ubuntu. Command: blastn -query /tmp/qiime2/newt/data/70940ada-947d-4c21-af08-457d2fc6aed1/data/dna-sequences.fasta -evalue 0.001 -strand…

baehsung (HEE-SUNG BAE) June 19, 2023, 8:25pm 1 Hi, I’m struggling with qiime2 installing in university supper computer system (HPG).Initially, I had run qiime2 in /home/ directory. Since that dir has memory space not to enough, I got another bigger directory with a new path /blue/. Thus, I have tried…

I installed QIIME 2 2023.5 in a container (using singularity) as conda environment using the instructions posted for Linux: wget data.qiime2.org/distro/core/qiime2-2023.5-py38-linux-conda.yml conda env create -n qiime2-2023.5 –file qiime2-2023.5-py38-linux-conda.yml There were no errors with this installation. Previous container installations have worked seamlessly, last installation on cluster being 2-2022.11. However, running qiime…

baehsung (HEE-SUNG BAE) June 15, 2023, 12:40am 1 Hi, I’m installing qiime2-2023.5 in HPC serve. With command $ wget data.qiime2.org/distro/core/qiime2-2023.5-py38-linux-conda.yml,I downloaded “qiime2-2023.5-py38-linux-conda.yml” in a directory “/blue/hsbae“. But in the next step,command “$ conda env create -n qiime2-2023.5 –file qiime2-2023.5-py38-linux-conda.yml” generated following error. CondaValueError: prefix already exists: /home/hsbae/.conda/envs/qiime2-2023.5. It looks qiime2-2023.5…

This is a similar issue to this and this, but I have not been able to solve my case with the available information there. I am running qiime2 version 2023.2 in a conda environment. The problem was detected when I tried to run an analysis, but I could replicate the…

Hello, I have been having issues installing qiime2 on windows. I read through the instructions on the website that said that downloading Windows subsystem for linux would be necessary. I also checked the forums and Francisco Cardenas provided a good guide up to a point. So following the Windows (via…

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Hello everyone,I’m trying to run dada2 denoise-paired on already demultiplexed Novaseq 6000 150 PE 12s sequences (amplicon size 100 bp ca) of fishes. I have already seen some topics about this issue I think. From what I have understands there is something about the new binned quality scores of Novaseq…

Hi, everyone. I’m new to qiime2 and I have a technical issue. I have the same problem with forum.qiime2.org/t/plugin-error-from-dada2-an-error-was-encountered-while-running-dada2-in-r-return-code-255/21016 when I ran Parkinson’s Mouse Tutorial, but I noticed the problem didn’t solved in the website above.That’s my error info: Plugin error from dada2: An error was encountered while running DADA2…

I am trying to transform a distance matrix from the qiime2 pathway using a centred log ratio in R. I uploaded the matrix directly from a qiime2 output file, and have converted to a data matrix and have checked that it is symmetrical. structure(list(X1 = c(0, 0.2177609998, 0.2133361674, 0.1549136105, 0.1400395799),…

rgas20 (rgas20) June 10, 2023, 4:34am 1 Hello, We are experiencing this problem with qiime2-2023.5. We are attempting to install on a CentOS 7 machine using a Conda environment. We are using the instructions below: wget data.qiime2.org/distro/core/qiime2-2023.5-py38-linux-conda.ymlconda env create -n qiime2-2023.5 –file qiime2-2023.5-py38-linux-conda.yml When we follow these exact instructions, the…