dozob

ASP.NET Core 7 / Blazor Server App / Dockerfile

GitHub의 qiime2 아래 linux-worker-docker 프로젝트를 참고한다.

https://github.com/qiime2/linux-worker-docker

위 프로젝트의 Dockerfile 내용을 Blazor Server App의 Dockerfile 에 추가한다.

#See https://aka.ms/customizecontainer to learn how to customize your debug container
# and how Visual Studio uses this Dockerfile to build your images for faster debugging.
 
FROM mcr.microsoft.com/dotnet/aspnet:7.0 AS base
 
WORKDIR /app
EXPOSE 80
EXPOSE 443
 
# Locale for click
ENV LC_ALL C.UTF-8
ENV LANG C.UTF-8
 
# Utilities
RUN apt-get update -q
RUN apt-get install -yq wget unzip bzip2 git build-essential
 
# Install conda
RUN wget -q https://repo.continuum.io/miniconda/Miniconda3-latest-Linux-x86_64.sh -O /tmp/miniconda3.sh
RUN /bin/bash /tmp/miniconda3.sh -bp /opt/miniconda3
RUN rm /tmp/miniconda3.sh
 
# Update conda and install conda-build
RUN /opt/miniconda3/bin/conda update -yq conda
RUN /opt/miniconda3/bin/conda install -yq conda-build wget
 
RUN wget -q https://data.qiime2.org/distro/core/qiime2-2023.5-py38-linux-conda.yml
RUN /opt/miniconda3/bin/conda env create -yq -n qiime2-2023.5 --file qiime2-2023.5-py38-linux-conda.yml
 
# Install any other goodies
#RUN /opt/miniconda3/bin/conda run pip install -q https://github.com/qiime2/q2lint/archive/master.zip
#RUN /opt/miniconda3/bin/conda install -yq -c conda-forge nodejs
 
# Set conda environment
RUN echo "export PATH=/opt/miniconda3/bin:$PATH" > /etc/profile
ENV PATH /opt/miniconda3/bin:$PATH
 
 
FROM mcr.microsoft.com/dotnet/sdk:7.0 AS build
WORKDIR /src
COPY ["TestBlazorServerApp/TestBlazorServerApp.csproj", "TestBlazorServerApp/"]
RUN dotnet restore "TestBlazorServerApp/TestBlazorServerApp.csproj"
COPY . .
WORKDIR "/src/TestBlazorServerApp"
RUN dotnet build "TestBlazorServerApp.csproj" -c Release -o /app/build
 
FROM build AS publish
RUN dotnet publish "TestBlazorServerApp.csproj" -c Release -o /app/publish /p:UseAppHost=false
 
FROM base AS final
WORKDIR /app
COPY --from=publish /app/publish .
ENTRYPOINT ["dotnet", "TestBlazorServerApp.dll"]

Linux 상에서 bash 쉘 실행하기

public static class ShellHelper
{
    public static ShellOutput Bash(this string cmd, string sWorkingDir)
    {
        var sEscapedArgs = cmd.Replace("\"", "\\\"");
        var process = new Process
        {
            StartInfo = new ProcessStartInfo
            {
                FileName = "/bin/bash",
                Arguments = $"-c \"{sEscapedArgs}\"",
                RedirectStandardOutput = true,
                RedirectStandardError = true,
                UseShellExecute = false,
                CreateNoWindow = true,
                WorkingDirectory = sWorkingDir
            }
        };
 
        ShellOutput rv = null;
        try
        {
            process.Start();
            process.WaitForExit();
 
            rv = new ShellOutput(process);
        }
        catch (Exception ex)
        {
            rv = new ShellOutput(null, ex);
            LogEx.Logger.LogError(ex, nameof(ShellHelper));
        }
        return rv;
    }
}
 
public class ShellOutput
{
    public ShellOutput(Process process, Exception ex = null)
    {
        this.Process = process;
        m_sStdErr = ex?.Message;
    }
 
    #region Fields
 
    string m_sStdOut;
    string m_sStdErr;
 
    #endregion Fields
 
    public Process Process { get; }
 
    public bool IsSuccessful => this.Process?.ExitCode == 0;
 
    public string StdOutText => m_sStdOut ??= this.Process?.StandardOutput.ReadToEnd();
 
    public string StdErrText => m_sStdErr ??= this.Process?.StandardError.ReadToEnd();
}

qiime 2가 설치된 Python 가상환경에서 실행시키기 위한 스크립트 작성

#!/bin/bash
 
_CONDA_ROOT="/home/user/miniconda3"
 
export PATH=$_CONDA_ROOT/bin:$_CONDA_ROOT/condabin
 
source $_CONDA_ROOT/etc/profile.d/conda.sh
 
#echo conda activate qiime2-2023.5
conda activate qiime2-2023.5
 
if [ $# == 0 ]
then
    qiime info
then
    qiime $*
fi
 
#echo conda deactivate
conda deactivate

qiime 실행하고 결과 받기

string sResult = "Running...";
var rv = ShellHelper.Bash("~/qiime2/q2run.sh info", null);
//var rv = ShellHelper.Bash("~/qiime2/q2run.sh tools list-types", null);
//var rv = ShellHelper.Bash("~/qiime2/q2run.sh tools list-formats", null);
if (rv.IsSuccessful)
{
    sResult = rv.StdOutText;
}
else
{
    sResult = rv.StdErrText;
}

qiime 2가 설치된 Python 가상환경에서 여러 명령을 수행하는 스크립트

q2env.sh

#!/bin/bash
 
_CONDA_ROOT="/home/user/miniconda3"
 
export PATH=$_CONDA_ROOT/bin:$_CONDA_ROOT/condabin:$PATH
 
source $_CONDA_ROOT/etc/profile.d/conda.sh
 
#echo conda activate qiime2-2023.5
conda activate qiime2-2023.5
 
if [ $# == 0 ]
then
    qiime info
else
    tid=1
    for i
    do
        echo "### q2-task-$tid"
        echo "$i"
        echo ">>>"
        $i
        echo "<<<"
        tid=`expr $tid + 1`
    done
fi
 
#echo conda deactivate
conda deactivate

Example:

$ ./q2env.sh "qiime info" "qiime tools list-types"
### q2-task-1
qiime info
>>>
System versions
:
<<<
### q2-task-2
qiime tools list-types
>>>
Bowtie2Index
        No description
:
<<<
$

qiime tools

(qiime2-2023.5) user@user-DT:~/qiime2$ qiime tools --help
Usage: qiime tools [OPTIONS] COMMAND [ARGS]...
 
  Tools for working with QIIME 2 files.
 
Options:
  --help      Show this message and exit.
 
Commands:
  cache-create              Create an empty cache at the given location.
  cache-fetch               Fetches an artifact out of a cache into a .qza.
  cache-garbage-collection  Runs garbage collection on the cache at the
                            specified location.
  cache-remove              Removes a given key from a cache.
  cache-status              Checks the status of the cache.
  cache-store               Stores a .qza in the cache under a key.
  cast-metadata             Designate metadata column types.
  citations                 Print citations for a QIIME 2 result.
  export                    Export data from a QIIME 2 Artifact or a
                            Visualization
  extract                   Extract a QIIME 2 Artifact or Visualization
                            archive.
  import                    Import data into a new QIIME 2 Artifact.
  inspect-metadata          Inspect columns available in metadata.
  list-formats              List the available formats.
  list-types                List the available semantic types.
  peek                      Take a peek at a QIIME 2 Artifact or
                            Visualization.
  validate                  Validate data in a QIIME 2 Artifact.
  view                      View a QIIME 2 Visualization.

• export
• import
• list-formats
• list-types

qiime tools list-types

(qiime2-2023.5) user@user-DT:~/qiime2$ qiime tools list-types
Bowtie2Index
        No description
 
DeblurStats
        No description
 
DistanceMatrix
        A symmetric matrix representing distances between entities.
 
EMPPairedEndSequences
        No description
 
EMPSingleEndSequences
        No description
 
ErrorCorrectionDetails
        No description
 
FeatureData[AlignedProteinSequence]
        Aligned protein sequences associated with a set of feature
        identifiers. Exactly one sequence is associated with each
        feature identfiier.
 
FeatureData[AlignedRNASequence]
        Aligned RNA sequences associated with a set of feature
        identifiers. Exactly one sequence is associated with each
        feature identfiier.
 
FeatureData[AlignedSequence]
        Aligned DNA sequences associated with a set of feature
        identifiers (e.g., aligned ASV sequences or OTU representative
        sequence). Exactly one sequence is associated with each feature
        identfiier.
 
FeatureData[BLAST6]
        BLAST results associated with a set of feature identifiers.
 
FeatureData[DecontamScore]
        No description
 
FeatureData[DifferentialAbundance]
        No description
 
FeatureData[Differential]
        No description
 
FeatureData[Importance]
        No description
 
FeatureData[PairedEndRNASequence]
        No description
 
FeatureData[PairedEndSequence]
        No description
 
FeatureData[ProteinSequence]
        Unaligned protein sequences associated with a set of feature
        identifiers. Exactly one sequence is associated with each
        feature identfiier.
 
FeatureData[RNASequence]
        Unaligned RNA sequences associated with a set of feature
        identifiers. Exactly one sequence is associated with each
        feature identfiier.
 
FeatureData[Sequence]
        Unaligned DNA sequences associated with a set of feature
        identifiers (e.g., ASV sequences or OTU representative
        sequence). Exactly one sequence is associated with each feature
        identfiier.
 
FeatureData[Taxonomy]
        Hierarchical metadata or annotations associated with a set of
        features. This can contain one or more hierarchical levels, and
        annotations can be anything (e.g., taxonomy of organisms,
        functional categorization of gene families, ...) as long as it
        is strictly hierarchical.
 
FeatureTable[Balance]
        No description
 
FeatureTable[Composition]
        A feature table (e.g., samples by ASVs) where each value in the
        matrix is a whole number greater than 0 representing the
        frequency or count of a feature in the corresponding sample.
        These data are typically not raw counts, having been
        transformed in some way to exclude zero counts.
 
FeatureTable[Design]
        No description
 
FeatureTable[Frequency]
        A feature table (e.g., samples by ASVs) where each value in the
        matrix is a whole number greater than or equal to 0
        representing the frequency or count of a feature in the
        corresponding sample. These data should be raw (not normalized)
        counts.
 
FeatureTable[PercentileNormalized]
        No description
 
FeatureTable[PresenceAbsence]
        A feature table (e.g., samples by ASVs) where each value
        indicates is a boolean indication of whether the feature is
        observed in the sample or not.
 
FeatureTable[RelativeFrequency]
        A feature table (e.g., samples by ASVs) where each value in the
        matrix is a real number greater than or equal to 0.0 and less
        than or equal to 1.0 representing the proportion of the sample
        that is composed of that feature. The feature values for each
        sample should sum to 1.0.
 
Hierarchy
        No description
 
ImmutableMetadata
        Immutable sample or feature metadata.
 
MultiplexedPairedEndBarcodeInSequence
        Multiplexed sequences (i.e., representing multiple difference
        samples), which are paired-end reads, and which contain the
        barcode (i.e., index) indicating the source sample as part of
        the sequence read.
 
MultiplexedSingleEndBarcodeInSequence
        Multiplexed sequences (i.e., representing multiple difference
        samples), which are single-end reads, and which contain the
        barcode (i.e., index) indicating the source sample as part of
        the sequence read.
 
PCoAResults
        The results of running principal coordinate analysis (PCoA).
 
Phylogeny[Rooted]
        A phylogenetic tree containing a defined root.
 
Phylogeny[Unrooted]
        A phylogenetic tree not containing a defined root.
 
Placements
        No description
 
ProcrustesStatistics
        The results of running Procrustes analysis.
 
QualityFilterStats
        No description
 
RawSequences
        No description
 
SampleData[AlphaDiversity]
        Alpha diversity values, each associated with a single sample
        identifier.
 
SampleData[ArtificialGrouping]
        No description
 
SampleData[BooleanSeries]
        No description
 
SampleData[ClassifierPredictions]
        No description
 
SampleData[DADA2Stats]
        No description
 
SampleData[FirstDifferences]
        No description
 
SampleData[JoinedSequencesWithQuality]
        Collections of joined paired-end sequences with quality scores
        associated with specified samples (i.e., demultiplexed
        sequences).
 
SampleData[PairedEndSequencesWithQuality]
        Collections of unjoined paired-end sequences with quality
        scores associated with specified samples (i.e., demultiplexed
        sequences).
 
SampleData[Probabilities]
        No description
 
SampleData[RegressorPredictions]
        No description
 
SampleData[SequencesWithQuality]
        Collections of sequences with quality scores associated with
        specified samples (i.e., demultiplexed sequences).
 
SampleData[Sequences]
        Collections of sequences associated with specified samples
        (i.e., demultiplexed sequences).
 
SampleData[TrueTargets]
        No description
 
SampleEstimator[Classifier]
        No description
 
SampleEstimator[Regressor]
        No description
 
SeppReferenceDatabase
        No description
 
TaxonomicClassifier
        No description
 
UchimeStats
        No description

• SampleData[PairedEndSequencesWithQuality]
  • Collections of unjoined paired-end sequences with quality scores
    associated with specified samples (i.e., demultiplexed sequences).

qiime tools list-formats --importable / --exportable

(qiime2-2023.5) user@user-DT:~/qiime2$ qiime tools list-formats --importable
AlignedDNAFASTAFormat
        No description
 
AlignedDNASequencesDirectoryFormat
        No description
 
AlignedProteinFASTAFormat
        No description
 
AlignedProteinSequencesDirectoryFormat
        No description
 
AlignedRNAFASTAFormat
        No description
 
AlignedRNASequencesDirectoryFormat
        No description
 
AlphaDiversityDirectoryFormat
        No description
 
AlphaDiversityFormat
        No description
 
ArtificialGroupingDirectoryFormat
        No description
 
ArtificialGroupingFormat
        No description
 
BIOMV100DirFmt
        No description
 
BIOMV100Format
        No description
 
BIOMV210DirFmt
        No description
 
BIOMV210Format
        No description
 
BLAST6DirectoryFormat
        No description
 
BLAST6Format
        No description
 
BooleanSeriesDirectoryFormat
        No description
 
BooleanSeriesFormat
        No description
 
Bowtie2IndexDirFmt
        No description
 
CasavaOneEightLanelessPerSampleDirFmt
        No description
 
CasavaOneEightSingleLanePerSampleDirFmt
        No description
 
DADA2StatsDirFmt
        No description
 
DADA2StatsFormat
        No description
 
DNAFASTAFormat
        No description
 
DNASequencesDirectoryFormat
        No description
 
DataLoafPackageDirFmt
        No description
 
DeblurStatsDirFmt
        No description
 
DeblurStatsFmt
        No description
 
DecontamScoreDirFmt
        No description
 
DecontamScoreFormat
        No description
 
DifferentialDirectoryFormat
        No description
 
DifferentialFormat
        No description
 
DistanceMatrixDirectoryFormat
        No description
 
EMPPairedEndCasavaDirFmt
        No description
 
EMPPairedEndDirFmt
        No description
 
EMPSingleEndCasavaDirFmt
        No description
 
EMPSingleEndDirFmt
        No description
 
ErrorCorrectionDetailsDirFmt
        No description
 
FastqGzFormat
        A gzipped fastq file.
 
FirstDifferencesDirectoryFormat
        No description
 
FirstDifferencesFormat
        No description
 
HeaderlessTSVTaxonomyDirectoryFormat
        No description
 
HeaderlessTSVTaxonomyFormat
        Format for a 2+ column TSV file without a header.
 
ImmutableMetadataDirectoryFormat
        No description
 
ImmutableMetadataFormat
        No description
 
ImportanceDirectoryFormat
        No description
 
ImportanceFormat
        No description
 
LSMatFormat
        No description
 
MixedCaseAlignedDNAFASTAFormat
        No description
 
MixedCaseAlignedDNASequencesDirectoryFormat
        No description
 
MixedCaseAlignedRNAFASTAFormat
        No description
 
MixedCaseAlignedRNASequencesDirectoryFormat
        No description
 
MixedCaseDNAFASTAFormat
        No description
 
MixedCaseDNASequencesDirectoryFormat
        No description
 
MixedCaseRNAFASTAFormat
        No description
 
MixedCaseRNASequencesDirectoryFormat
        No description
 
MultiplexedFastaQualDirFmt
        No description
 
MultiplexedPairedEndBarcodeInSequenceDirFmt
        No description
 
MultiplexedSingleEndBarcodeInSequenceDirFmt
        No description
 
NewickDirectoryFormat
        No description
 
NewickFormat
        No description
 
OrdinationDirectoryFormat
        No description
 
OrdinationFormat
        No description
 
PairedDNASequencesDirectoryFormat
        No description
 
PairedEndFastqManifestPhred33
        No description
 
PairedEndFastqManifestPhred33V2
        No description
 
PairedEndFastqManifestPhred64
        No description
 
PairedEndFastqManifestPhred64V2
        No description
 
PairedRNASequencesDirectoryFormat
        No description
 
PlacementsDirFmt
        No description
 
PlacementsFormat
        No description
 
PredictionsDirectoryFormat
        No description
 
PredictionsFormat
        No description
 
ProbabilitiesDirectoryFormat
        No description
 
ProbabilitiesFormat
        No description
 
ProcrustesStatisticsDirFmt
        No description
 
ProcrustesStatisticsFmt
        No description
 
ProteinFASTAFormat
        No description
 
ProteinSequencesDirectoryFormat
        No description
 
QIIME1DemuxDirFmt
        No description
 
QIIME1DemuxFormat
        QIIME 1 demultiplexed FASTA format.
 
QualityFilterStatsDirFmt
        No description
 
QualityFilterStatsFmt
        No description
 
RNAFASTAFormat
        No description
 
RNASequencesDirectoryFormat
        No description
 
SampleEstimatorDirFmt
        No description
 
SampleIdIndexedSingleEndPerSampleDirFmt
        Single-end reads in fastq.gz files where base filename is the
        sample id
 
SeppReferenceDirFmt
        No description
 
SingleEndFastqManifestPhred33
        No description
 
SingleEndFastqManifestPhred33V2
        No description
 
SingleEndFastqManifestPhred64
        No description
 
SingleEndFastqManifestPhred64V2
        No description
 
SingleLanePerSamplePairedEndFastqDirFmt
        No description
 
SingleLanePerSampleSingleEndFastqDirFmt
        No description
 
TSVTaxonomyDirectoryFormat
        No description
 
TSVTaxonomyFormat
        Format for a 2+ column TSV file with an expected minimal
        header.
 
TaxonomicClassiferTemporaryPickleDirFmt
        No description
 
TrueTargetsDirectoryFormat
        No description
 
UchimeStatsDirFmt
        No description
 
UchimeStatsFmt
        No description

• PairedEndFastqManifestPhred33V2

qiime tools import

(qiime2-2023.5) user@user-DT:~/qiime2$ qiime tools import --help
Usage: qiime tools import [OPTIONS]
 
  Import data to create a new QIIME 2 Artifact. See https://docs.qiime2.org/
  for usage examples and details on the file types and associated semantic
  types that can be imported.
 
Options:
  --type TEXT             The semantic type of the artifact that will be
                          created upon importing. Use --show-importable-types
                          to see what importable semantic types are available
                          in the current deployment.                [required]
  --input-path PATH       Path to file or directory that should be imported.
                                                                    [required]
  --output-path ARTIFACT  Path where output artifact should be written.
                                                                    [required]
  --input-format TEXT     The format of the data to be imported. If not
                          provided, data must be in the format expected by the
                          semantic type provided via --type.
  --show-importable-types Show the semantic types that can be supplied to
                          --type to import data into an artifact.
  --show-importable-formats
                          Show formats that can be supplied to --input-format
                          to import data into an artifact.
  --help                  Show this message and exit.

$ qiime tools import \
    --type 'SampleData[PairedEndSequencesWithQuality]' \
    --input-path sample-metadata.tsv \
    --input-format PairedEndFastqManifestPhred33V2 \
    --output-path demux-paired-end.qza

qiime demux summarize

(qiime2-2023.5) user@user-DT:~/qiime2$ qiime demux summarize --help
Usage: qiime demux summarize [OPTIONS]
 
  Summarize counts per sample for all samples, and generate interactive
  positional quality plots based on `n` randomly selected sequences.
 
Inputs:
  --i-data ARTIFACT SampleData[SequencesWithQuality |
    PairedEndSequencesWithQuality | JoinedSequencesWithQuality]
                       The demultiplexed sequences to be summarized.
                                                                    [required]
Parameters:
  --p-n INTEGER        The number of sequences that should be selected at
                       random for quality score plots. The quality plots will
                       present the average positional qualities across all of
                       the sequences selected. If input sequences are paired
                       end, plots will be generated for both forward and
                       reverse reads for the same `n` sequences.
                                                              [default: 10000]
Outputs:
  --o-visualization VISUALIZATION
                                                                    [required]
Miscellaneous:
  --output-dir PATH    Output unspecified results to a directory
  --verbose / --quiet  Display verbose output to stdout and/or stderr during
                       execution of this action. Or silence output if
                       execution is successful (silence is golden).
  --example-data PATH  Write example data and exit.
  --citations          Show citations and exit.
  --help               Show this message and exit.
 
Examples:
  # ### example: demux
  qiime demux summarize \
    --i-data demux.qza \
    --o-visualization visualization.qzv

$ qiime demux summarize \
    --i-data demux-paired-end.qza \
    --o-visualization demux-paried-end.qzv

qiime dada2 denoise-paired

(qiime2-2023.5) user@user-DT:~/qiime2$ qiime dada2 denoise-paired --help
Usage: qiime dada2 denoise-paired [OPTIONS]
 
  This method denoises paired-end sequences, dereplicates them, and filters
  chimeras.
 
Inputs:
  --i-demultiplexed-seqs ARTIFACT SampleData[PairedEndSequencesWithQuality]
                         The paired-end demultiplexed sequences to be
                         denoised.                                  [required]
Parameters:
  --p-trunc-len-f INTEGER
                         Position at which forward read sequences should be
                         truncated due to decrease in quality. This truncates
                         the 3' end of the of the input sequences, which will
                         be the bases that were sequenced in the last cycles.
                         Reads that are shorter than this value will be
                         discarded. After this parameter is applied there must
                         still be at least a 12 nucleotide overlap between the
                         forward and reverse reads. If 0 is provided, no
                         truncation or length filtering will be performed
                                                                    [required]
  --p-trunc-len-r INTEGER
                         Position at which reverse read sequences should be
                         truncated due to decrease in quality. This truncates
                         the 3' end of the of the input sequences, which will
                         be the bases that were sequenced in the last cycles.
                         Reads that are shorter than this value will be
                         discarded. After this parameter is applied there must
                         still be at least a 12 nucleotide overlap between the
                         forward and reverse reads. If 0 is provided, no
                         truncation or length filtering will be performed
                                                                    [required]
  --p-trim-left-f INTEGER
                         Position at which forward read sequences should be
                         trimmed due to low quality. This trims the 5' end of
                         the input sequences, which will be the bases that
                         were sequenced in the first cycles.      [default: 0]
  --p-trim-left-r INTEGER
                         Position at which reverse read sequences should be
                         trimmed due to low quality. This trims the 5' end of
                         the input sequences, which will be the bases that
                         were sequenced in the first cycles.      [default: 0]
  --p-max-ee-f NUMBER    Forward reads with number of expected errors higher
                         than this value will be discarded.     [default: 2.0]
  --p-max-ee-r NUMBER    Reverse reads with number of expected errors higher
                         than this value will be discarded.     [default: 2.0]
  --p-trunc-q INTEGER    Reads are truncated at the first instance of a
                         quality score less than or equal to this value. If
                         the resulting read is then shorter than `trunc-len-f`
                         or `trunc-len-r` (depending on the direction of the
                         read) it is discarded.                   [default: 2]
  --p-min-overlap INTEGER
    Range(4, None)       The minimum length of the overlap required for
                         merging the forward and reverse reads.  [default: 12]
  --p-pooling-method TEXT Choices('independent', 'pseudo')
                         The method used to pool samples for denoising.
                         "independent": Samples are denoised indpendently.
                         "pseudo": The pseudo-pooling method is used to
                         approximate pooling of samples. In short, samples are
                         denoised independently once, ASVs detected in at
                         least 2 samples are recorded, and samples are
                         denoised independently a second time, but this time
                         with prior knowledge of the recorded ASVs and thus
                         higher sensitivity to those ASVs.
                                                      [default: 'independent']
  --p-chimera-method TEXT Choices('consensus', 'none', 'pooled')
                         The method used to remove chimeras. "none": No
                         chimera removal is performed. "pooled": All reads are
                         pooled prior to chimera detection. "consensus":
                         Chimeras are detected in samples individually, and
                         sequences found chimeric in a sufficient fraction of
                         samples are removed.           [default: 'consensus']
  --p-min-fold-parent-over-abundance NUMBER
                         The minimum abundance of potential parents of a
                         sequence being tested as chimeric, expressed as a
                         fold-change versus the abundance of the sequence
                         being tested. Values should be greater than or equal
                         to 1 (i.e. parents should be more abundant than the
                         sequence being tested). This parameter has no effect
                         if chimera-method is "none".           [default: 1.0]
  --p-allow-one-off / --p-no-allow-one-off
                         Bimeras that are one-off from exact are also
                         identified if the `allow-one-off` argument is TrueIf
                         True, a sequence will be identified as bimera if it
                         is one mismatch or indel away from an exact bimera.
                                                              [default: False]
  --p-n-threads INTEGER  The number of threads to use for multithreaded
                         processing. If 0 is provided, all available cores
                         will be used.                            [default: 1]
  --p-n-reads-learn INTEGER
                         The number of reads to use when training the error
                         model. Smaller numbers will result in a shorter run
                         time but a less reliable error model.
                                                            [default: 1000000]
  --p-hashed-feature-ids / --p-no-hashed-feature-ids
                         If true, the feature ids in the resulting table will
                         be presented as hashes of the sequences defining each
                         feature. The hash will always be the same for the
                         same sequence so this allows feature tables to be
                         merged across runs of this method. You should only
                         merge tables if the exact same parameters are used
                         for each run.                         [default: True]
Outputs:
  --o-table ARTIFACT FeatureTable[Frequency]
                         The resulting feature table.               [required]
  --o-representative-sequences ARTIFACT FeatureData[Sequence]
                         The resulting feature sequences. Each feature in the
                         feature table will be represented by exactly one
                         sequence, and these sequences will be the joined
                         paired-end sequences.                      [required]
  --o-denoising-stats ARTIFACT SampleData[DADA2Stats]
                                                                    [required]
Miscellaneous:
  --output-dir PATH      Output unspecified results to a directory
  --verbose / --quiet    Display verbose output to stdout and/or stderr
                         during execution of this action. Or silence output if
                         execution is successful (silence is golden).
  --example-data PATH    Write example data and exit.
  --citations            Show citations and exit.
  --help                 Show this message and exit.
 
Examples:
  # ### example: denoise paired
  qiime dada2 denoise-paired \
    --i-demultiplexed-seqs demux-paired.qza \
    --p-trunc-len-f 150 \
    --p-trunc-len-r 140 \
    --o-representative-sequences representative-sequences.qza \
    --o-table table.qza \
    --o-denoising-stats denoising-stats.qza

$ qiime dada2 denoise-paired \
    --i-demultiplexed-seqs demux-paired-end.qza \
    --p-trim-left-f 23 \
    --p-trim-left-r 23 \
    --p-trunc-len-f 240 \
    --p-trunc-len-r 226 \
    --o-representative-sequences rep-seqs-dada2.qza \
    --o-table table-dada2.qza \
    --o-denoising-stats stats-dada2.qza

qiime metadata tabulate

(qiime2-2023.5) user@user-DT:~/qiime2$ qiime metadata tabulate --help
Usage: qiime metadata tabulate [OPTIONS]
 
  Generate a tabular view of Metadata. The output visualization supports
  interactive filtering, sorting, and exporting to common file formats.
 
Parameters:
  --m-input-file METADATA...
    (multiple            The metadata to tabulate.
     arguments will be
     merged)                                                        [required]
  --p-page-size INTEGER  The maximum number of Metadata records to display
                         per page                               [default: 100]
Outputs:
  --o-visualization VISUALIZATION
                                                                    [required]
Miscellaneous:
  --output-dir PATH      Output unspecified results to a directory
  --verbose / --quiet    Display verbose output to stdout and/or stderr
                         during execution of this action. Or silence output if
                         execution is successful (silence is golden).
  --example-data PATH    Write example data and exit.
  --citations            Show citations and exit.
  --help                 Show this message and exit.

$ qiime metadata tabulate \
    --m-input-file stats-dada2.qza \
    --o-visualization stats-dada2.qzv

qiime feature-table summarize

(qiime2-2023.5) user@user-DT:~/qiime2$ qiime feature-table summarize --help
Usage: qiime feature-table summarize [OPTIONS]
 
  Generate visual and tabular summaries of a feature table.
 
Inputs:
  --i-table ARTIFACT FeatureTable[Frequency | RelativeFrequency |
    PresenceAbsence]   The feature table to be summarized.          [required]
Parameters:
  --m-sample-metadata-file METADATA...
    (multiple          The sample metadata.
     arguments will
     be merged)                                                     [optional]
Outputs:
  --o-visualization VISUALIZATION
                                                                    [required]
Miscellaneous:
  --output-dir PATH    Output unspecified results to a directory
  --verbose / --quiet  Display verbose output to stdout and/or stderr during
                       execution of this action. Or silence output if
                       execution is successful (silence is golden).
  --example-data PATH  Write example data and exit.
  --citations          Show citations and exit.
  --help               Show this message and exit.
 
Examples:
  # ### example: feature table summarize
  qiime feature-table summarize \
    --i-table feature-table.qza \
    --o-visualization table.qzv

$ qiime feature-table summarize \
    --i-table table-dada2.qza \
    --o-visualization table.qzv \
    --m-sample-metadata-file sample-metadata.tsv

qiime feature-table tabulate-seqs

(qiime2-2023.5) user@user-DT:~/qiime2$ qiime feature-table tabulate-seqs --help
Usage: qiime feature-table tabulate-seqs [OPTIONS]
 
  Generate tabular view of feature identifier to sequence mapping, including
  links to BLAST each sequence against the NCBI nt database.
 
Inputs:
  --i-data ARTIFACT FeatureData[Sequence | AlignedSequence]
                       The feature sequences to be tabulated.       [required]
Outputs:
  --o-visualization VISUALIZATION
                                                                    [required]
Miscellaneous:
  --output-dir PATH    Output unspecified results to a directory
  --verbose / --quiet  Display verbose output to stdout and/or stderr during
                       execution of this action. Or silence output if
                       execution is successful (silence is golden).
  --example-data PATH  Write example data and exit.
  --citations          Show citations and exit.
  --help               Show this message and exit.
 
Examples:
  # ### example: feature table tabulate seqs
  qiime feature-table tabulate-seqs \
    --i-data rep-seqs.qza \
    --o-visualization rep-seqs.qzv

$ qiime feature-table tabulate-seqs \
    --i-data rep-seqs-dada2.qza \
    --o-visualization rep-seqs.qzv

qiime phylogeny align-to-tree-mafft-fasttree

(qiime2-2023.5) user@user-DT:~/qiime2$ qiime phylogeny align-to-tree-mafft-fasttree --help
Usage: qiime phylogeny align-to-tree-mafft-fasttree [OPTIONS]
 
  This pipeline will start by creating a sequence alignment using MAFFT, after
  which any alignment columns that are phylogenetically uninformative or
  ambiguously aligned will be removed (masked). The resulting masked alignment
  will be used to infer a phylogenetic tree and then subsequently rooted at
  its midpoint. Output files from each step of the pipeline will be saved.
  This includes both the unmasked and masked MAFFT alignment from q2-alignment
  methods, and both the rooted and unrooted phylogenies from q2-phylogeny
  methods.
 
Inputs:
  --i-sequences ARTIFACT FeatureData[Sequence]
                          The sequences to be used for creating a fasttree
                          based rooted phylogenetic tree.           [required]
Parameters:
  --p-n-threads VALUE Int % Range(1, None) | Str % Choices('auto')
                          The number of threads. (Use `auto` to automatically
                          use all available cores) This value is used when
                          aligning the sequences and creating the tree with
                          fasttree.                               [default: 1]
  --p-mask-max-gap-frequency PROPORTION Range(0, 1, inclusive_end=True)
                          The maximum relative frequency of gap characters in
                          a column for the column to be retained. This
                          relative frequency must be a number between 0.0 and
                          1.0 (inclusive), where 0.0 retains only those
                          columns without gap characters, and 1.0 retains all
                          columns  regardless of gap character frequency. This
                          value is used when masking the aligned sequences.
                                                                [default: 1.0]
  --p-mask-min-conservation PROPORTION Range(0, 1, inclusive_end=True)
                          The minimum relative frequency of at least one
                          non-gap character in a column for that column to be
                          retained. This relative frequency must be a number
                          between 0.0 and 1.0 (inclusive). For example, if a
                          value of  0.4 is provided, a column will only be
                          retained  if it contains at least one character that
                          is present in at least 40% of the sequences. This
                          value is used when masking the aligned sequences.
                                                                [default: 0.4]
  --p-parttree / --p-no-parttree
                          This flag is required if the number of sequences
                          being aligned are larger than 1000000. Disabled by
                          default.                            [default: False]
Outputs:
  --o-alignment ARTIFACT FeatureData[AlignedSequence]
                          The aligned sequences.                    [required]
  --o-masked-alignment ARTIFACT FeatureData[AlignedSequence]
                          The masked alignment.                     [required]
  --o-tree ARTIFACT       The unrooted phylogenetic tree.
    Phylogeny[Unrooted]                                             [required]
  --o-rooted-tree ARTIFACT
    Phylogeny[Rooted]     The rooted phylogenetic tree.             [required]
Miscellaneous:
  --output-dir PATH       Output unspecified results to a directory
  --verbose / --quiet     Display verbose output to stdout and/or stderr
                          during execution of this action. Or silence output
                          if execution is successful (silence is golden).
  --recycle-pool TEXT     Use a cache pool for pipeline resumption. QIIME 2
                          will cache your results in this pool for reuse by
                          future invocations. These pool are retained until
                          deleted by the user. If not provided, QIIME 2 will
                          create a pool which is automatically reused by
                          invocations of the same action and removed if the
                          action is successful. Note: these pools are local to
                          the cache you are using.
  --no-recycle            Do not recycle results from a previous failed
                          pipeline run or save the results from this run for
                          future recycling.
  --parallel              Execute your action in parallel. This flag will use
                          your default parallel config.
  --parallel-config FILE  Execute your action in parallel using a config at
                          the indicated path.
  --use-cache DIRECTORY   Specify the cache to be used for the intermediate
                          work of this pipeline. If not provided, the default
                          cache under $TMP/qiime2/<uname> will be used.
                          IMPORTANT FOR HPC USERS: If you are on an HPC system
                          and are using parallel execution it is important to
                          set this to a location that is globally accessible
                          to all nodes in the cluster.
  --example-data PATH     Write example data and exit.
  --citations             Show citations and exit.
  --help                  Show this message and exit.
 
Examples:
  # ### example: align to tree mafft fasttree
  qiime phylogeny align-to-tree-mafft-fasttree \
    --i-sequences rep-seqs.qza \
    --o-alignment aligned-rep-seqs.qza \
    --o-masked-alignment masked-aligned-rep-seqs.qza \
    --o-tree unrooted-tree.qza \
    --o-rooted-tree rooted-tree.qza

$ qiime phylogeny align-to-tree-mafft-fasttree \
    --i-sequences rep-seqs-dada2.qza \
    --o-alignment aligned-rep-seqs.qza \
    --o-masked-alignment masked-aligned-rep-seqs.qza \
    --o-tree unrooted-tree.qza \
    --o-rooted-tree rooted-tree.qza

qiime feature-classifier classify-sklearn

(qiime2-2023.5) user@user-DT:~/qiime2$ qiime feature-classifier classify-sklearn --help
Usage: qiime feature-classifier classify-sklearn [OPTIONS]
 
  Classify reads by taxon using a fitted classifier.
 
Inputs:
  --i-reads ARTIFACT FeatureData[Sequence]
                         The feature data to be classified.         [required]
  --i-classifier ARTIFACT
    TaxonomicClassifier  The taxonomic classifier for classifying the reads.
                                                                    [required]
Parameters:
  --p-reads-per-batch VALUE Int % Range(1, None) | Str % Choices('auto')
                         Number of reads to process in each batch. If "auto",
                         this parameter is autoscaled to min( number of query
                         sequences / n-jobs, 20000).         [default: 'auto']
  --p-n-jobs INTEGER     The maximum number of concurrently worker processes.
                         If -1 all CPUs are used. If 1 is given, no parallel
                         computing code is used at all, which is useful for
                         debugging. For n-jobs below -1, (n_cpus + 1 + n-jobs)
                         are used. Thus for n-jobs = -2, all CPUs but one are
                         used.                                    [default: 1]
  --p-pre-dispatch TEXT  "all" or expression, as in "3*n_jobs". The number of
                         batches (of tasks) to be pre-dispatched.
                                                         [default: '2*n_jobs']
  --p-confidence VALUE Float % Range(0, 1, inclusive_end=True) | Str %
    Choices('disable')   Confidence threshold for limiting taxonomic depth.
                         Set to "disable" to disable confidence calculation,
                         or 0 to calculate confidence but not apply it to
                         limit the taxonomic depth of the assignments.
                                                                [default: 0.7]
  --p-read-orientation TEXT Choices('same', 'reverse-complement', 'auto')
                         Direction of reads with respect to reference
                         sequences. same will cause reads to be classified
                         unchanged; reverse-complement will cause reads to be
                         reversed and complemented prior to classification.
                         "auto" will autodetect orientation based on the
                         confidence estimates for the first 100 reads.
                                                             [default: 'auto']
Outputs:
  --o-classification ARTIFACT FeatureData[Taxonomy]
                                                                    [required]
Miscellaneous:
  --output-dir PATH      Output unspecified results to a directory
  --verbose / --quiet    Display verbose output to stdout and/or stderr
                         during execution of this action. Or silence output if
                         execution is successful (silence is golden).
  --example-data PATH    Write example data and exit.
  --citations            Show citations and exit.
  --help                 Show this message and exit.

$ qiime feature-classifier classify-sklearn \
    --i-reads rep-seqs.qza \
    --i-classifier silva-138-99-515-806-nb-classifier.qza \
    --o-classification taxonomy.qza

qiime diversity core-metrics-phylogenetic

(qiime2-2023.5) user@user-DT:~/qiime2$ qiime diversity core-metrics-phylogenetic --help
Usage: qiime diversity core-metrics-phylogenetic [OPTIONS]
 
  Applies a collection of diversity metrics (both phylogenetic and non-
  phylogenetic) to a feature table.
 
Inputs:
  --i-table ARTIFACT FeatureTable[Frequency]
                          The feature table containing the samples over which
                          diversity metrics should be computed.     [required]
  --i-phylogeny ARTIFACT  Phylogenetic tree containing tip identifiers that
    Phylogeny[Rooted]     correspond to the feature identifiers in the table.
                          This tree can contain tip ids that are not present
                          in the table, but all feature ids in the table must
                          be present in this tree.                  [required]
Parameters:
  --p-sampling-depth INTEGER
    Range(1, None)        The total frequency that each sample should be
                          rarefied to prior to computing diversity metrics.
                                                                    [required]
  --m-metadata-file METADATA...
    (multiple arguments   The sample metadata to use in the emperor plots.
     will be merged)                                                [required]
  --p-with-replacement / --p-no-with-replacement
                          Rarefy with replacement by sampling from the
                          multinomial distribution instead of rarefying
                          without replacement.                [default: False]
  --p-n-jobs-or-threads VALUE Int % Range(1, None) | Str % Choices('auto')
                          [beta/beta-phylogenetic methods only] - The number
                          of concurrent jobs or CPU threads to use in
                          performing this calculation. Individual methods will
                          create jobs/threads as implemented in
                          q2-diversity-lib dependencies. May not exceed the
                          number of available physical cores. If
                          n-jobs-or-threads = 'auto', one thread/job will be
                          created for each identified CPU core on the host.
                                                                  [default: 1]
Outputs:
  --o-rarefied-table ARTIFACT FeatureTable[Frequency]
                          The resulting rarefied feature table.     [required]
  --o-faith-pd-vector ARTIFACT SampleData[AlphaDiversity]
                          Vector of Faith PD values by sample.      [required]
  --o-observed-features-vector ARTIFACT SampleData[AlphaDiversity]
                          Vector of Observed Features values by sample.
                                                                    [required]
  --o-shannon-vector ARTIFACT SampleData[AlphaDiversity]
                          Vector of Shannon diversity values by sample.
                                                                    [required]
  --o-evenness-vector ARTIFACT SampleData[AlphaDiversity]
                          Vector of Pielou's evenness values by sample.
                                                                    [required]
  --o-unweighted-unifrac-distance-matrix ARTIFACT
    DistanceMatrix        Matrix of unweighted UniFrac distances between
                          pairs of samples.                         [required]
  --o-weighted-unifrac-distance-matrix ARTIFACT
    DistanceMatrix        Matrix of weighted UniFrac distances between pairs
                          of samples.                               [required]
  --o-jaccard-distance-matrix ARTIFACT
    DistanceMatrix        Matrix of Jaccard distances between pairs of
                          samples.                                  [required]
  --o-bray-curtis-distance-matrix ARTIFACT
    DistanceMatrix        Matrix of Bray-Curtis distances between pairs of
                          samples.                                  [required]
  --o-unweighted-unifrac-pcoa-results ARTIFACT
    PCoAResults           PCoA matrix computed from unweighted UniFrac
                          distances between samples.                [required]
  --o-weighted-unifrac-pcoa-results ARTIFACT
    PCoAResults           PCoA matrix computed from weighted UniFrac
                          distances between samples.                [required]
  --o-jaccard-pcoa-results ARTIFACT
    PCoAResults           PCoA matrix computed from Jaccard distances between
                          samples.                                  [required]
  --o-bray-curtis-pcoa-results ARTIFACT
    PCoAResults           PCoA matrix computed from Bray-Curtis distances
                          between samples.                          [required]
  --o-unweighted-unifrac-emperor VISUALIZATION
                          Emperor plot of the PCoA matrix computed from
                          unweighted UniFrac.                       [required]
  --o-weighted-unifrac-emperor VISUALIZATION
                          Emperor plot of the PCoA matrix computed from
                          weighted UniFrac.                         [required]
  --o-jaccard-emperor VISUALIZATION
                          Emperor plot of the PCoA matrix computed from
                          Jaccard.                                  [required]
  --o-bray-curtis-emperor VISUALIZATION
                          Emperor plot of the PCoA matrix computed from
                          Bray-Curtis.                              [required]
Miscellaneous:
  --output-dir PATH       Output unspecified results to a directory
  --verbose / --quiet     Display verbose output to stdout and/or stderr
                          during execution of this action. Or silence output
                          if execution is successful (silence is golden).
  --recycle-pool TEXT     Use a cache pool for pipeline resumption. QIIME 2
                          will cache your results in this pool for reuse by
                          future invocations. These pool are retained until
                          deleted by the user. If not provided, QIIME 2 will
                          create a pool which is automatically reused by
                          invocations of the same action and removed if the
                          action is successful. Note: these pools are local to
                          the cache you are using.
  --no-recycle            Do not recycle results from a previous failed
                          pipeline run or save the results from this run for
                          future recycling.
  --parallel              Execute your action in parallel. This flag will use
                          your default parallel config.
  --parallel-config FILE  Execute your action in parallel using a config at
                          the indicated path.
  --use-cache DIRECTORY   Specify the cache to be used for the intermediate
                          work of this pipeline. If not provided, the default
                          cache under $TMP/qiime2/<uname> will be used.
                          IMPORTANT FOR HPC USERS: If you are on an HPC system
                          and are using parallel execution it is important to
                          set this to a location that is globally accessible
                          to all nodes in the cluster.
  --example-data PATH     Write example data and exit.
  --citations             Show citations and exit.
  --help                  Show this message and exit.

$ qiime diversity core-metric-phylogenetic \
    --i-phylogeny rooted-tree.qza \
    --i-table table.qza \
    --p-sampling-depth 27,286.5 \
    --m-metadata-file sample-metadata.tsv \
    --output-dir core-metrics-results

qiime diversity alpha-group-significance

(qiime2-2023.5) user@user-DT:~/qiime2$ qiime diversity alpha-group-significance --help
Usage: qiime diversity alpha-group-significance [OPTIONS]
 
  Visually and statistically compare groups of alpha diversity values.
 
Inputs:
  --i-alpha-diversity ARTIFACT SampleData[AlphaDiversity]
                       Vector of alpha diversity values by sample.  [required]
Parameters:
  --m-metadata-file METADATA...
    (multiple          The sample metadata.
     arguments will
     be merged)                                                     [required]
Outputs:
  --o-visualization VISUALIZATION
                                                                    [required]
Miscellaneous:
  --output-dir PATH    Output unspecified results to a directory
  --verbose / --quiet  Display verbose output to stdout and/or stderr during
                       execution of this action. Or silence output if
                       execution is successful (silence is golden).
  --example-data PATH  Write example data and exit.
  --citations          Show citations and exit.
  --help               Show this message and exit.
 
Examples:
  # ### example: alpha group significance faith pd
  qiime diversity alpha-group-significance \
    --i-alpha-diversity alpha-div-faith-pd.qza \
    --m-metadata-file metadata.tsv \
    --o-visualization visualization.qzv

$ qiime diversity alpha-group-signifcance \
    --i-alpha-diversity core-metrics-results/faith_pd_vector.qza \
    --m-metadata-file sample-metadata.tsv \
    --o-visualization core-metrics-results/faith-pd-group-significance.qzv
 
$ qiime diversity alpha-group-signifcance \
    --i-alpha-diversity core-metrics-results/evenness_vector.qza \
    --m-metadata-file sample-metadata.tsv \
    --o-visualization core-metrics-results/evenness-group-significance.qzv

qiime diversity beta-group-significance

(qiime2-2023.5) user@user-DT:~/qiime2$ qiime diversity beta-group-significance --help
Usage: qiime diversity beta-group-significance [OPTIONS]
 
  Determine whether groups of samples are significantly different from one
  another using a permutation-based statistical test.
 
Inputs:
  --i-distance-matrix ARTIFACT
    DistanceMatrix     Matrix of distances between pairs of samples.
                                                                    [required]
Parameters:
  --m-metadata-file METADATA
  --m-metadata-column COLUMN  MetadataColumn[Categorical]
                       Categorical sample metadata column.          [required]
  --p-method TEXT Choices('permanova', 'anosim', 'permdisp')
                       The group significance test to be applied.
                                                        [default: 'permanova']
  --p-pairwise / --p-no-pairwise
                       Perform pairwise tests between all pairs of groups in
                       addition to the test across all groups. This can be
                       very slow if there are a lot of groups in the metadata
                       column.                                [default: False]
  --p-permutations INTEGER
                       The number of permutations to be run when computing
                       p-values.                                [default: 999]
Outputs:
  --o-visualization VISUALIZATION
                                                                    [required]
Miscellaneous:
  --output-dir PATH    Output unspecified results to a directory
  --verbose / --quiet  Display verbose output to stdout and/or stderr during
                       execution of this action. Or silence output if
                       execution is successful (silence is golden).
  --example-data PATH  Write example data and exit.
  --citations          Show citations and exit.
  --help               Show this message and exit.

$ qiime diversity beta-group-significance \
    --i-distance-matrix core-metrics-results/unweighted_unifrac_distance_matrix.qza \
    --m-metadata-file sample-metadata.tsv \
    --m-metadata-column Group \
    --o-visualization core-metrics-results/unweighted-unifrac-group-significance.qzv \
    --p-pairwise

qiime taxa filter-table

(qiime2-2023.5) user@user-DT:~/qiime2$ qiime taxa filter-table --help
Usage: qiime taxa filter-table [OPTIONS]
 
  This method filters features from a table based on their taxonomic
  annotations. Features can be retained in the resulting table by specifying
  one or more include search terms, and can be filtered out of the resulting
  table by specifying one or more exclude search terms. If both include and
  exclude are provided, the inclusion critera will be applied before the
  exclusion critera. Either include or exclude terms (or both) must be
  provided. Any samples that have a total frequency of zero after filtering
  will be removed from the resulting table.
 
Inputs:
  --i-table ARTIFACT FeatureTable[Frequency]
                         Feature table to be filtered.              [required]
  --i-taxonomy ARTIFACT FeatureData[Taxonomy]
                         Taxonomic annotations for features in the provided
                         feature table. All features in the feature table must
                         have a corresponding taxonomic annotation. Taxonomic
                         annotations for features that are not present in the
                         feature table will be ignored.             [required]
Parameters:
  --p-include TEXT       One or more search terms that indicate which taxa
                         should be included in the resulting table. If
                         providing more than one term, terms should be
                         delimited by the query-delimiter character. By
                         default, all taxa will be included.        [optional]
  --p-exclude TEXT       One or more search terms that indicate which taxa
                         should be excluded from the resulting table. If
                         providing more than one term, terms should be
                         delimited by the query-delimiter character. By
                         default, no taxa will be excluded.         [optional]
  --p-query-delimiter TEXT
                         The string used to delimit multiple search terms
                         provided to include or exclude. This parameter should
                         only need to be modified if the default delimiter (a
                         comma) is used in the provided taxonomic annotations.
                                                                [default: ',']
  --p-mode TEXT Choices('exact', 'contains')
                         Mode for determining if a search term matches a
                         taxonomic annotation. "contains" requires that the
                         annotation has the term as a substring; "exact"
                         requires that the annotation is a perfect match to a
                         search term.                    [default: 'contains']
Outputs:
  --o-filtered-table ARTIFACT FeatureTable[Frequency]
                         The taxonomy-filtered feature table.       [required]
Miscellaneous:
  --output-dir PATH      Output unspecified results to a directory
  --verbose / --quiet    Display verbose output to stdout and/or stderr
                         during execution of this action. Or silence output if
                         execution is successful (silence is golden).
  --example-data PATH    Write example data and exit.
  --citations            Show citations and exit.
  --help                 Show this message and exit.

$ qiime taxa filter-table \
    --i-table filtered-sequences/table-with-phyla-no-mitochondria-chloroplast.qza \
    --i-taxonomy taxonomy.qza \
    --p-exclude "k__Archaea" \
    --o-filtered-table filtered-sequences/table-with-phyla-no-mitochondria-chloroplasts-archaea.qza

qiime tools export

(qiime2-2023.5) user@user-DT:~/qiime2$ qiime tools export --help
Usage: qiime tools export [OPTIONS]
 
  Exporting extracts (and optionally transforms) data stored inside an
  Artifact or Visualization. Note that Visualizations cannot be transformed
  with --output-format
 
Options:
  --input-path ARTIFACT/VISUALIZATION
                        Path to file that should be exported        [required]
  --output-path PATH    Path to file or directory where data should be
                        exported to                                 [required]
  --output-format TEXT  Format which the data should be exported as. This
                        option cannot be used with Visualizations
  --help                Show this message and exit.

$ qiime tools export \
    --input-path rep-seqs.qza \
    --output-path rep-seqs.fna
 
$ qiime tools export \
    --input-path table.qza \
    --output-path feature-table.biom

Native conda installation

Installing Miniconda

https://docs.conda.io/en/latest/miniconda.html

Miniconda3 Linux 64-bit

$ wget https://repo.anaconda.com/miniconda/Miniconda3-latest-Linux-x86_64.sh
:
$ chmod +x Miniconda3-latest-Linux-x86_64.sh
$ ./Miniconda3-latest-Linux-x86_64.sh
:
Miniconda3 will now be installed into this location:
/home/jylee/miniconda3
 
  - Press ENTER to confirm the location
  - Press CTRL-C to abort the installation
  - Or specify a different location below
 
[/home/user/miniconda3] >>>
PREFIX=/home/user/miniconda3
Unpacking payload ...
 
Installing base environment...
 
Downloading and Extracting Packages
Downloading and Extracting Packages
 
Preparing transaction: done
Executing transaction: done
installation finished.
Do you wish the installer to initialize Miniconda3
by running conda init? [yes|no]
[no] >>> yes
no change     /home/user/miniconda3/condabin/conda
no change     /home/user/miniconda3/bin/conda
no change     /home/user/miniconda3/bin/conda-env
no change     /home/user/miniconda3/bin/activate
no change     /home/user/miniconda3/bin/deactivate
no change     /home/user/miniconda3/etc/profile.d/conda.sh
no change     /home/user/miniconda3/etc/fish/conf.d/conda.fish
no change     /home/user/miniconda3/shell/condabin/Conda.psm1
no change     /home/user/miniconda3/shell/condabin/conda-hook.ps1
no change     /home/user/miniconda3/lib/python3.11/site-packages/xontrib/conda.xsh
no change     /home/user/miniconda3/etc/profile.d/conda.csh
modified      /home/user/.bashrc
 
==> For changes to take effect, close and re-open your current shell. <==
 
If you'd prefer that conda's base environment not be activated on startup,
   set the auto_activate_base parameter to false:
 
conda config --set auto_activate_base false
 
Thank you for installing Miniconda3!

Updating Miniconda

$ conda update conda

Installing wget

$ conda install wget

Install QIIME 2 within a conda environment

These instructions are identical to the Linux instructions and are intended for users of the Windows Subsystem for Linux.

$ wget https://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

OPTIONAL CLEANUP

$ rm qiime2-2023.5-py38-linux-conda.yml

Activate the conda environment

$ conda activate qiime2-2023.5
:
$ conda deactivate

Test your installation

$ qiime --help

How do I update to the newest version of QIIME 2?

In order to update/upgrade to the newest release, you simply install the newest version in a new conda environment by following the instructions above. Then you will have two conda environments, one with the older version of QIIME 2 and one with the newer version.

※ 터미널을 다시 켤 때마다 base 가상 환경이 기본으로 실행되는 것 해제

$ conda config --set auto_activate_base false

https://docs.qiime2.org/2023.5/concepts/#

Data files: QIIME 2 artifacts

Data produced by QIMME 2 exist as QIIME 2 artifacts.

A QIIME 2 artifact contains data and metadata.

The metadata describes things about the data, such as its type, format and how it was generated (provenance).

A QIIME 2 artifact typically has the .qza file extension when stored in a file.

Since QIIME 2 works with artifacts instead of data files (e.g. FASTA files),

you must create a QIIME 2 artifact by importing data.

You can import data at any step in an analysis, though typically you will start by importing raw sequence data.

QIIME 2 also has tools to export data from an artifact.

By using QIIME 2 artifacts instead of simple data files, QIIME 2 can automatically track the type, format, and provenance of data for researchers. Using artifacts instead of data files enables researchers to focus on the analyses they want to perform, instead of the particular format the data needs to be in for an analysis.

Artifacts enable QIIME 2 to track, in addition to the data itself, the provenance of how the data came to be.

With an artifact's provenance, you can trace back to all previous analyses that were run to produce the artifact,
including the input data used at each step.

This automatic, integrated, and decentralized provenance tracking of data enables a researcher to archive artifacts, or for example, send an artifact to a collaborator, with the ability to understand exactly how the artifact was created.

This enables replicability(복제가능성) and reproducibility(재현성) of analyses, as well as generation of diagrams and text that can be used in the methods section of a paper.

Provenance also supports and encourages the paper attribution to underlying tools (e.g. FastTree to build a phylogenetic(계통 발생의) tree) used to generate the artifact.

Data files: Visualizations

Visualizations are another type of data generated by QIIME 2.

When written to disk, visualization files typically have the .qzv file extension.

Visualzations contain similar types of metadata as QIIME 2 artifacts, including provenance information.

Similar to QIIME 2 artifacts, visualizations are standalone information that can be archived or shared with collarborators.

In contrast to QIIME 2 artifacts, visualizations are terminal outputs of an analysis, and can represent, for example, a statistical results table, an interactive visualization, static images, or really any combination of visual data representations.

Since visualizations are terminal outputs, they cannot be used as input other analyses in QIIME 2.

Tip
Use https://view.qiime2.org to easily view QIIME 2 artifacts and visualizations files (generally .qza and .qzv files) without requiring a QIIME installation. This is helpful for sharing QIIME 2 data with collarborators who may not have QIIME 2 installed. https://view.qiime2.org also supports viewing data provenance.

Semantic types

Every artifact generated by QIIME 2 has a semantic type associated with it.

Semantic types enable QIIME 2 to identify artifacts that are suitable inputs to an analysis.

For example, if an analysis expects a distance matrix as input,
QIIME 2 can determine which artifacts have a distance matrix semantic type
and prevent incompatible artifacts from being used in the analysis
(e.g. an artifact representing a phylogenetic tree).

Semantic types also help users avoid semantically incorrect analyses.

For example, a feature table could contain presence/absence data
(i.e., a 1 to indicate that an OTU was observed at least one time in a given sample,
and a 0 to indicate that an OTU was not observed at least one time in a given sample).

However, if that feature table were provided to an analysis computing a quantitative diversity metric
where OTU abundances are included in the calculation (e.g., weighted UniFrac),
the analysis would complete successfully, but the result would not be meaningful.

Check out the semantic types page for more information about semantic types and what types are currently available.

Plugins

QIIME 2 microbiome(미생물) analyses are made available to users via plugins.

To perform analyses with QIIME 2, you will install one or more plugins
that provide the specific analyses you are interested in.

For example, if you want to demultiplex your raw sequence data, you might use the q2-demux QIIME 2 plugin,
or if you're wanting to perform alpha- or beta-deversity analyses, you could use the q2-diversity plugin.

Plugins are software packages that can be developed by anyone.

The QIIME 2 team has developed several plugins for an initial end-to-end microbiome analysis pipline,
but third-party developers are encouraged to create their own plugins to provide additional analyses.

Third-party developers will define these plugins in the same way that the QIIME 2 team has define the "official" plugins.

This decentralized development of microbiome analysis functionality means
that many more analyses and tools will be accessible to QIIME 2 users, including the latest techniques and protocols.

Plugins also allow users to choose and customize analysis pipeline for their specific needs.

Check out the plugin availability page to see what plugins are currently available
and the future plugins page for those that are being developed.

Methods and Visualizers

QIIME 2 plugins define methods and visualizers that are used to perform analyses.

A method accepts some combination of QIIME 2 artifacts and parameters as input,
and produces one or more QIIME 2 artifacts as output.

These output artifacts could subsequently be used as input to other QIIME 2 methods or visualizers.

Methods can produce intermediate or terminal outputs in a QIIME 2 analysis.

For example, the rarefy method defined in the q2-feature-table plugin
accepts a feature table artifact and sampling depth as input
and produces a rarefied feature table artifact as output.

This rarefied feature table artifact could then be used in another analysis,
such as alpha diversity calculations provided by the alpha method in q2-diversity.

A visualizer is similar to a mehtod in that it accepts some combination of QIIME 2 artifacts and parameters as input.

In contrast to a method, a visualizer produces exactly one visualization as output.

Visualizations, by definition, cannot be used as input to other QIIME 2 methods or visualizers.

Thus, visualizers can only produce terminal output in a QIIME 2 analysis.