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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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Importing QIIME script as module, error importing from skbio

I'm trying to import a QIIME script as a module. The script works when I call it through linux cmd, but when I import the QIIME script as a module, I get the error ~/VirtualENV/lib/python2.7/site-packages/skbio/alignment/_ssw_wrapper.so:undefined…
Tichigan
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Adding a list to an array from different file format in perl

open(IN_FILE, $id_file) or die "Cant open $id_file file"; while (my $id_list= ) { chomp $id_list; if ($id_list =~ m/^#|^$/g) { next; } # This Works WELL # if the file comes in QIIME format …
abraham
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eliminate redundant in a list with perl

Hi I made this script to extract all phylum from a OTUs file obtained from qiime using silva database, I added a subroutine to eliminate duplicate taxon and extract all no redundant (one of each taxon), my problem is that I just get the las line…
abraham
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calling Qiime with system call from R

Hej, When I try to call QIIME with a system call from R, i.e system2("macqiime") R stops responding. It's no problem with other command line programs though. can certain programs not be called from R via system2() ? MacQIIME version: MacQIIME…
Latrunculia
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QIIME 1.9: ImportError: cannot import name subsample_counts

Every time I try to run any qiime script I get the following error: File "/usr/local/bin/assign_taxonomy.py", line 14, in from qiime.util import (parse_command_line_parameters, get_options_lookup, File…
gloria
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append a code to every other line in a set of files

I am currently appending some sample codes to a set of files using the following code cd /path/to/your/files word='code' base=1 for file in *; do sed -i -e "s/^/$word$base/" "${file}"; base=$(( $base + 1 )); done This adds the term 'code1' in front…
colin
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How do you get a StarCluster AMI to work with IPython 0.13?

I tried upgrading IPython on two different StarCluster AMIs (their default 64-bit Ubuntu 11.10 and the QIIME 1.5 image). In either case, when I start up my cluster the initialization script hangs at 'Waiting for JSON connector file...'. I logged in…
Alex Rubinsteyn
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How to add and specify additional ranks to phyloseq taxonomy?

Is it possible to specify the number and names of taxonomic ranks when reading in data to a phyloseq object? When creating a phyloseq object from qiime output, e.g., ps=qza_to_phyloseq(features="features.qza", taxonomy="taxonomy.qza",…
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I am triying to install qiime2-2023.2 from Miniconda3, but i get this error

Downloading and Extracting Packages Preparing transaction: done Verifying transaction: failed File "/mnt/e/curso_qiime2/miniconda3/lib/python3.8/site-packages/conda/exception_handler.py", line 16, in __call__ | 23% …
Leo GM
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Why is the distance matrix I upload into R not symmetric?

I am trying to upload a distance matrix for a PCoA plot produced by the qiime2 pathway into R for data transformation. I can't seem to attach the file here, but here is an example of what the file looks like: The distance matrix is symmetrical in…
shannonevelyne
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How Can You Reformat an OTU Table from qiime2 pathway to Include Sequence IDs?

I am trying to run Tax4Fun in MicrobiomeAnalyst, but am running into trouble with my table formatting. From the qiime2 pathway, I have an OTU, metadata and taxonomic table formatted like so: OTU table metadata taxonomy table In order to use Tax4Fun,…
shannonevelyne
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dada2 denoise issues : qiime2-2019.4/lib/R/etc/ldpaths missing

dada2 denoise issues : qiime2-2019.4/lib/R/etc/ldpaths missing Hey guys, I have problem when using ‘qiime2-2019.4’. Command: qiime dada2 denoise-paired \ --i-demultiplexed-seqs 2_sequences/demux_no_primer_${libname}.qza \ …
seaweed
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TypeError: Parameter 'metadata' received Metadata as an argument, which is incompatible with parameter type: MetadataColumn[Categorical]

TypeError: Parameter 'metadata' received Metadata as an argument, which is incompatible with parameter type: MetadataColumn[Categorical] for the following code: uUniFrac_BodySite_significance =…
c.kristina
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SyntaxError in python script that creates a qiime2 manifest file

My script creates a manifest document that contains the filepaths of my fastq data for upload into qiime2. The input is a text file of the sample names and a directory that contains the fastq files. I then run the shell file using python…
Geomicro
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Input distance matrix from QIIME2 to R

I am trying to coerce a distance matrix from QIIME2 to class dist in R. Upstream processing up to the generation of the distance matrix was performed as described in the QIIME2 document "Moving Pictures". When I call as.dist, I get the following…
Zac_Nephron
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