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Questions tagged [qiime]

QIIME is an open source software package for comparison and analysis of microbial communities.

QIIME (pronounced "chime") stands for Quantitative Insights Into Microbial Ecology. QIIME is an open source software package for comparison and analysis of microbial communities, primarily based on high-throughput amplicon sequencing data (such as SSU rRNA) generated on a variety of platforms, but also supporting analysis of other types of data (such as shotgun metagenomic data). QIIME takes users from their raw sequencing output through initial analyses such as OTU picking, taxonomic assignment, and construction of phylogenetic trees from representative sequences of OTUs, and through downstream statistical analysis, visualization, and production of publication-quality graphics. QIIME has been applied to single studies based on billions of sequences from thousands of samples.

QIIME allows analysis of high-throughput community sequencing data.

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Trying to install qiime2 on anaconda

I'm very new to all of this. Im currently trying to install qiime2 into my anaconda environment. I've installed and activated anaconda3. conda version 4.9.2, python version 3.9.1. PLatform is linux 64. Ive been following various installation…
sophscutt
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How can I combine legends in GGPlot?

I am using the following code: all_bray_curtis_pcoa$data$Vectors %>% select(SampleID, PC1, PC2) %>% left_join(all_metadata) %>% ggplot(aes(x = PC1, y = PC2, color = Txt)) + geom_point(aes(shape = Sex), alpha = 0.8, size = 3) + …
Hannah Harder
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Installing Qiime2 with docker

I used docker to install Qiime2: However when I used the qiime command line, I get the message bash:qiime:command not found This is the message I get on bash Can someone please help me with this problem? I'm kinda new to programming
Howida Samir
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I am using ALDEx package for analysis of PICRUST2 output and gave me an error

I am following the tutorial below in the link: https://ycl6.github.io/16S-Demo/4_picrust2_tutorial.html after copying this code : # EC set.seed(12345) system.time({ aldex2_EC1 = aldex(p2EC1, sample_data(ps1a)$Group, mc.samples = 500, test =…
Abdelrhman Nabil
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QIIME2 error when running diversity analyses

I am running qiime2-2022.8, on my Linux laptop (Ubuntu 22.04.1 LTS x86_64). Installed via conda. I went through entire moving pictures tutorial, everything seemed to run fine. Now I tried my own data (and I also had this same error when trying to…
Mike Davis
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Qiime2 installation from pre built yaml file into conda environment doesnt work because of genomeinfodbdata package, how to fix?

When installing the newest qiime2 version (2022.8) into a conda environment with the given yaml file on the official qiime2 website. The installation gives an error which has something to do with the genomeinfodbdata package. I tried updating my…
Jippe
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loading a pandas table from a weird txt file

I'm working with a package called qiime2, that generates me a txt file I want to load to pandas as a table. An exapmle for the txt format is the following: The format is quite quacky. I want to load as a pandas table the part from line 10 downward…
Luis_12345
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Error : loadNamespace(x) there is no package called ‘devtools’

I was trying to install Github library using devtools. if (!requireNamespace("devtools", quietly = TRUE)){install.packages("devtools")} devtools::install_github("jbisanz/qiime2R") Therefore, I installed devtools with the code below, and when I…
yhlee
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Unsatisfiable error installing QIIME in conda environment glibc==2.31=0

I've been trying to install QIIME2 on Linux with the command conda install -c qiime2 qiime2 and get this error message: Collecting package metadata (current_repodata.json): done Solving environment: failed with initial frozen solve. Retrying with…
Lucca Mancilio
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How do I import my .qz files from illumina sequencing into qiime2 via a manifest file?

My data is from 16S gene sequencing that went through illumina and it is paired-end, demultiplexed, and does NOT have barcodes. I went through the qiime2 importing guide and it looks like I have to make a manifest file and I am not sure how to do…
Caroline Gonzalez
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How to extract the same data from different files

In order to extract a frecuency table from a qiime2 artifact and write It to a tsv output you have to: rel_freq_table <- read_qza("05.TaxonomyClassification/rel_freq/1_rel_freq_table.qza") rel_freq_table <-…
Jose Gracia Rodriguez
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Rename header in R with extracted information from the header

How can I rename the header in R, based on information from the current header? My df look likes: header: (index; d__Bacteria.p__Actinobacteriota.c__Actinobacteria ; d__Bacteria.p__Bacteroidota.c__Bacteroidia ) Row 1: (BF13A; 0; 14572) Row 2:…
jonsor
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Error when installing qiimer package for R

I tried to install qiimer package for R (3.6.2) from CRAN under Win10, but I failed. Then I tried to install it locally from ‘qiimer_0.9.4.tar.gz’, and failed, neither. I do not understand why CRAN does not afford this package anymore. I wonder how…
Zhang
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Illumina Overview Tutorial validate_mapping_file.py not found

I am new to QIIME. By following the Illumina overview tutorial, I ran: !validate_mapping_file.py -o vmf-map/ -m map.tsv and then I got an error message: /bin/sh: validate_mapping_file.py: command not found I also try to run command !qiime,…
user2829551
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Error during qiime1 installation on MacOS Mojave

I am trying to install qiime1 environment using terminal on Mac. Currently getting an error saying packages not found for matplotlib 1.4.3.
Adwaita Parab
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