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