anvi-analyze-synteny [-h] -g GENOMES_STORAGE
                     [--ngram-window-range NGRAM_WINDOW_RANGE]
                     [-o FILE_PATH] [--annotation-source SOURCE NAME]
                     [-p PAN_DB] [-n NGRAM_SOURCE] [-l]
                     [--analyze-unknown-functions] [-G GENOME_NAMES]

  -g GENOMES_STORAGE, --genomes-storage GENOMES_STORAGE
                        Anvi'o genomes storage file
  --ngram-window-range NGRAM_WINDOW_RANGE
                        The range of window sizes of Ngrams to analyze for
                        synteny patterns.Please format the window-range as x:y
                        (e.g. Window sizes 2 to 4 would be denoted as: 2:4)
  -o FILE_PATH, --output-file FILE_PATH
                        File path to store results.

  --annotation-source SOURCE NAME
                        Get functional annotations for a specific annotation
                        source. You can use the flag '--list-annotation-
                        sources' to learn about what sources are available.
  -p PAN_DB, --pan-db PAN_DB
                        Anvi'o pan database
  -n NGRAM_SOURCE, --ngram-source NGRAM_SOURCE
                        If two annotation sources are provided, please choose
                        one annotation source that will be used to calcuate
                        Ngrams (e.g. gene_clusters, COG_FUNCTION)

  -l, --list-annotation-sources
                        List available functional annotation sources.
  --analyze-unknown-functions
                        Provide this flag if you want anvi-analyze-synteny to
                        report Ngrams that contain gene calls that have no
                        annotation.
  -G GENOME_NAMES, --genome-names GENOME_NAMES
                        Genome names to 'focus'. You can use this parameter to
                        limit the genomes included in your analysis. You can
                        provide these names as a comma-separated list of
                        names, or you can put them in a file, where you have a
                        single genome name in each line, and provide the file
                        path.

anvi-cluster-contigs [-h] -p PROFILE_DB -c CONTIGS_DB -C
                     COLLECTION_NAME --driver DRIVER [-T NUM_THREADS]
                     [--just-do-it]

  -p PROFILE_DB, --profile-db PROFILE_DB
                        Anvi'o profile database
  -c CONTIGS_DB, --contigs-db CONTIGS_DB
                        Anvi'o contigs database generated by 'anvi-gen-
                        contigs-database'
  -C COLLECTION_NAME, --collection-name COLLECTION_NAME
                        Collection name.
  --driver DRIVER       Automatic binning drivers. Available options 'concoct,
                        metabat2, maxbin2, dastool, binsanity'.
  -T NUM_THREADS, --num-threads NUM_THREADS
                        Maximum number of threads to use for multithreading
                        whenever possible. Very conservatively, the default is
                        1. It is a good idea to not exceed the number of CPUs
                        / cores on your system. Plus, please be careful with
                        this option if you are running your commands on a SGE
                        --if you are clusterizing your runs, and asking for
                        multiple threads to use, you may deplete your
                        resources very fast.
  --just-do-it          Don't bother me with questions or warnings, just do
                        it.
 
CONCOCT
::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::
  --clusters INT        specify maximal number of clusters for VGMM, default
                        400
  --kmer-length INT     pecify kmer length, default 4
  --length-threshold INT
                        specify the sequence length threshold, contigs shorter
                        than this value will not be included. Defaults to 1000
  --read-length INT     specify read length for coverage, default 100
  --no-cov-normalization
                        By default the coverage is normalized with regards to
                        samples, then normalized with regards of contigs and
                        finally log transformed. By setting this flag you skip
                        the normalization and only do log transorm of the
                        coverage.
  --total-percentage-pca INT
                        The percentage of variance explained by the principal
                        components for the combined data.
  --epsilon FLOAT       Specify the epsilon for VBGMM. Default value is 1.0e-6
  --iterations INT      Specify maximum number of iterations for the VBGMM.
                        Default value is 500
  --seed INT            Specify an integer to use as seed for clustering. 0
                        gives a random seed, 1 is the default seed and any
                        other positive integer can be used. Other values give
                        ArgumentTypeError.

MAXBIN2 [NOT FOUND]
 
DASTOOL
::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::
  -S COLLECTION_LIST, --source-collections COLLECTION_LIST
                        Comma-separated list of collections, case sensitive.
  --search-engine PROGRAM
                        Engine used for single copy gene identification
                        [blast/diamond/usearch]. (default: usearch)
  --score-threshold FLOAT
                        Score threshold until selection algorithm will keep
                        selecting bins [0..1]. (default: 0.5)
  --duplicate-penalty FLOAT
                        Penalty for duplicate single copy genes per bin
                        (weight b). Only change if you know what you're doing.
                        [0..3] (default: 0.6)
  --megabin-penalty FLOAT
                        Penalty for megabins (weight c). Only change if you
                        know what you're doing. [0..3] (default: 0.5)
  --db-directory PATH   Directory of single copy gene database. (default:
                        install_dir/db)
 
BINSANITY
::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::
  --preference INT  Specify a preference (default is -3) Note: decreasing the
                    preference leads to more lumping, increasing will lead to
                    more splitting. If your range of coverages are low you
                    will want to decrease the preference, if you have 10 or
                    less replicates increasing the preference could benefit
                    you.
  --maxiter INT     Specify a max number of iterations [default is 2000]
  --conviter INT    Specify the convergence iteration number (default is 200)
                    e.g Number of iterations with no change in the number of
                    estimated clusters that stops the convergence.
  --damp FLOAT      Specify a damping factor between 0.5 and 1, default is 0.9
  --contigsize INT  TNF probability cutoff for building TNF graph. Use it to
                    skip the preparation step. (0: auto).

anvi-compute-completeness [-h] [--splits-of-interest FILE] -c
                          CONTIGS_DB [-e E-VALUE]
                          [--list-completeness-sources]
                          [--completeness-source NAME]

  --splits-of-interest FILE
                        A file with split names. There should be only one
                        column in the file, and each line should correspond to
                        a unique split name.
  -c CONTIGS_DB, --contigs-db CONTIGS_DB
                        Anvi'o contigs database generated by 'anvi-gen-
                        contigs-database'
  -e E-VALUE, --min-e-value E-VALUE
                        Minimum significance score of an HMM find to be
                        considered as a valid hit. Default is 1e-15.
  --list-completeness-sources
                        Show available sources and exit.
  --completeness-source NAME
                        Single-copy gene source to use to estimate
                        completeness.

anvi-compute-gene-cluster-homogeneity [-h] -p PAN_DB
                                      [-g GENOMES_STORAGE]
                                      [-o FILE_PATH] [--store-in-db]
                                      [--gene-cluster-id GENE_CLUSTER_ID]
                                      [--gene-cluster-ids-file FILE_PATH]
                                      [-C COLLECTION_NAME]
                                      [-b BIN_NAME]
                                      [--quick-homogeneity]
                                      [-T NUM_THREADS] [--just-do-it]

  -p PAN_DB, --pan-db PAN_DB
                        Anvi'o pan database
  -g GENOMES_STORAGE, --genomes-storage GENOMES_STORAGE
                        Anvi'o genomes storage file

  -o FILE_PATH, --output-file FILE_PATH
                        File path to store results.
  --store-in-db         Store analysis results into the database directly.

  --gene-cluster-id GENE_CLUSTER_ID
                        Gene cluster ID you are interested in.
  --gene-cluster-ids-file FILE_PATH
                        Text file for gene clusters (each line should contain
                        be a unique gene cluster id).
  -C COLLECTION_NAME, --collection-name COLLECTION_NAME
                        Collection name.
  -b BIN_NAME, --bin-id BIN_NAME
                        Bin name you are interested in.

  --quick-homogeneity   By default, anvi'o will use a homogeneity algorithm
                        that checks for horizontal and vertical geometric
                        homogeneity (along with functional). With this flag,
                        you can tell anvi'o to skip horizontal geometric
                        homogeneity calculations. It will be less accurate but
                        quicker.
  -T NUM_THREADS, --num-threads NUM_THREADS
                        Maximum number of threads to use for multithreading
                        whenever possible. Very conservatively, the default is
                        1. It is a good idea to not exceed the number of CPUs
                        / cores on your system. Plus, please be careful with
                        this option if you are running your commands on a SGE
                        --if you are clusterizing your runs, and asking for
                        multiple threads to use, you may deplete your
                        resources very fast.
  --just-do-it          Don't bother me with questions or warnings, just do
                        it.

anvi-compute-genome-similarity [-h] [-i FILE_PATH] [-e FILE_PATH]
                               [-f FASTA_TEXT_FILE] -o DIR_PATH
                               [-p PAN_DB]
                               [--program {pyANI,fastANI,sourmash}]
                               [--fastani-kmer-size FASTANI_KMER_SIZE]
                               [--fragment-length FRAGMENT_LENGTH]
                               [--min-num-fragments MIN_NUM_FRAGMENTS]
                               [--method {ANIm,ANIb,ANIblastall,TETRA}]
                               [--min-alignment-fraction NUM]
                               [--significant-alignment-length INT]
                               [--min-full-percent-identity FULL_PERCENT_IDENTITY]
                               [--kmer-size INT] [--scale INT]
                               [--distance DISTANCE_METRIC]
                               [--linkage LINKAGE_METHOD]
                               [-T NUM_THREADS] [--just-do-it]
                               [--log-file FILE_PATH]

  -i FILE_PATH, --internal-genomes FILE_PATH
                        A five-column TAB-delimited flat text file. The header
                        line must contain these columns: 'name', 'bin_id',
                        'collection_id', 'profile_db_path', 'contigs_db_path'.
                        Each line should list a single entry, where 'name' can
                        be any name to describe the anvi'o bin identified as
                        'bin_id' that is stored in a collection.
  -e FILE_PATH, --external-genomes FILE_PATH
                        A two-column TAB-delimited flat text file that lists
                        anvi'o contigs databases. The first item in the header
                        line should read 'name', and the second should read
                        'contigs_db_path'. Each line in the file should
                        describe a single entry, where the first column is the
                        name of the genome (or MAG), and the second column is
                        the anvi'o contigs database generated for this genome.
  -f FASTA_TEXT_FILE, --fasta-text-file FASTA_TEXT_FILE
                        A two-column TAB-delimited file that lists multiple
                        FASTA files to import for analysis. If using for
                        `anvi-dereplicate-genomes` or `anvi-compute-distance`,
                        each FASTA is assumed to be a genome. The first item
                        in the header line should read 'name', and the second
                        item should read 'path'. Each line in the field should
                        describe a single entry, where the first column is the
                        name of the FASTA file or corresponding sequence, and
                        the second column is the path to the FASTA file
                        itself.

  -o DIR_PATH, --output-dir DIR_PATH
                        Directory path for output files
  -p PAN_DB, --pan-db PAN_DB
                        This is totally optional, but very useful when
                        applicable. If you are running this for genomes for
                        which you already have an anvi'o pangeome, then you
                        can show where the pan database is and anvi'o would
                        automatically add the results into the misc data
                        tables of your pangenome. Those data can then be shown
                        as heatmaps on the pan interactive interface through
                        the 'layers' tab.

  --program {pyANI,fastANI,sourmash}
                        Tell anvi'o which program to run to process genome
                        similarity. For ANI, you should either use pyANI or
                        fastANI. If accuracy is paramount (for example,
                        distinguishing things less than 1 percent different),
                        or for dealing with genomes < 80 percent similar,
                        pyANI is what we recommend. However, fastANI is much
                        faster. If you for some reason want to use mash
                        similarity, you can use sourmash, but its really not
                        intended for genome comparisons. If you don't choose
                        anything here, anvi'o will reluctantly set the program
                        to pyANI, but you really should be the one who is on
                        top of these things.

  --fastani-kmer-size FASTANI_KMER_SIZE
                        Choose a kmer. The default is 16.
  --fragment-length FRAGMENT_LENGTH
                        Choose a fragment length. The default is 3000.
  --min-num-fragments MIN_NUM_FRAGMENTS
                        Choose the minimum number of fragment lengths to that
                        can can be trusted. The default is 50.

  --method {ANIm,ANIb,ANIblastall,TETRA}
                        Method for pyANI. The default is ANIb. You must have
                        the necessary binary in path for whichever method you
                        choose. According to the pyANI help for v0.2.7 at
                        https://github.com/widdowquinn/pyani, the method
                        'ANIm' uses MUMmer (NUCmer) to align the input
                        sequences. 'ANIb' uses BLASTN+ to align 1020nt
                        fragments of the input sequences. 'ANIblastall': uses
                        the legacy BLASTN to align 1020nt fragments Finally,
                        'TETRA': calculates tetranucleotide frequencies of
                        each input sequence
  --min-alignment-fraction NUM
                        In some cases you may get high raw ANI estimates
                        (percent identity scores) between two genomes that
                        have little to do with each other simply because only
                        a small fraction of their content may be aligned. This
                        filter will set all ANI scores between two genomes to
                        0 if the alignment fraction is less than you deem
                        trustable. When you set a value, anvi'o will go
                        through the ANI results, and set percent identity
                        scores between two genomes to 0 if the alignment
                        fraction *between either of them* is less than the
                        parameter described here. The default is 0.
  --significant-alignment-length INT
                        So --min-alignment-fraction discards any hit that is
                        coming from alignments that represent shorter
                        fractions of genomes, but what if you still don't want
                        to miss an alignment that is longer than an X number
                        of nucleotides regardless of what fraction of the
                        genome it represents? Well, this parameter is to
                        recover things that may be lost due to --min-
                        alignment-fraction parameter. Let's say, if you set
                        --min-alignment-fraction to '0.05', and this parameter
                        to '5000', anvi'o will keep hits from alignments that
                        are longer than 5000 nts, EVEN IF THEY REPRESENT less
                        than 5 percent of a given genome pair. Basically if
                        --min-alignment-fraction is your shield to protect
                        yourself from incoming garbage, --significant-
                        alignment-length is your chopstick to pick out those
                        that may be interesting, and you are a true warrior
                        here.
  --min-full-percent-identity FULL_PERCENT_IDENTITY
                        In some cases you may get high raw ANI estimates
                        (percent identity scores) between two genomes that
                        have little to do with each other simply because only
                        a small fraction of their content may be aligned. This
                        can be partly alleviated by considering the *full*
                        percent identity, which includes in its calculation
                        regions that did not align. For example, if the
                        alignment is a whopping 97 percent identity but only 8
                        percent of the genome aligned, the *full* percent
                        identity is 0.970 * 0.080 = 0.078 OR 7.8 percent.
                        *full* percent identity is always included in the
                        report, but you can also use it as a filter for other
                        metrics, such as percent identity. This filter will
                        set all ANI measures between two genomes to 0 if the
                        *full* percent identity is less than you deem
                        trustable. When you set a value, anvi'o will go
                        through the ANI results, and set all ANI measures
                        between two genomes to 0 if the *full* percent
                        identity *between either of them* is less than the
                        parameter described here. The default is 0.

  --kmer-size INT       Set the k-mer size for mash similarity checks. We
                        found 13 in almost all cases correlates best with
                        alignment-based ANI.
  --scale INT           Set the compression ratio for fasta signature file
                        computations. The default is 1000. Smaller ratios
                        decrease sensitivity, while larger ratios will lead to
                        large fasta signatures.

  --distance DISTANCE_METRIC
                        The distance metric for the hierarchical clustering.
                        The default is "euclidean".
  --linkage LINKAGE_METHOD
                        The linkage method for the hierarchical clustering.
                        The default is "ward".

  -T NUM_THREADS, --num-threads NUM_THREADS
                        Maximum number of threads to use for multithreading
                        whenever possible. Very conservatively, the default is
                        1. It is a good idea to not exceed the number of CPUs
                        / cores on your system. Plus, please be careful with
                        this option if you are running your commands on a SGE
                        --if you are clusterizing your runs, and asking for
                        multiple threads to use, you may deplete your
                        resources very fast.
  --just-do-it          Don't bother me with questions or warnings, just do
                        it.
  --log-file FILE_PATH  File path to store debug/output messages.

anvi-db-info [-h] [--self-key SELF_KEY] [--self-value SELF_VALUE]
             [--just-do-it]
             DATABASE_PATH

  DATABASE_PATH         An anvi'o database for pan, profile, contigs, or
                        auxiliary data

  --self-key SELF_KEY   The key you wish to set or change.
  --self-value SELF_VALUE
                        The value you wish to set for the self key.
  --just-do-it          Don't bother me with questions or warnings, just do
                        it.

anvi-delete-collection [-h] -p PROFILE_DB [-C COLLECTION_NAME]
                       [--list-collections]

  -p PROFILE_DB, --profile-db PROFILE_DB
                        Anvi'o profile database
  -C COLLECTION_NAME, --collection-name COLLECTION_NAME
                        Collection name.
  --list-collections    Show available collections and exit.

anvi-delete-hmms [-h] -c CONTIGS_DB [--hmm-source SOURCE NAME] [-l]
                 [--just-do-it]

  -c CONTIGS_DB, --contigs-db CONTIGS_DB
                        Anvi'o contigs database generated by 'anvi-gen-
                        contigs-database'
  --hmm-source SOURCE NAME
                        Use a specific HMM source. You can use '--list-hmm-
                        sources' flag to see a list of available resources.
                        The default is 'None'.
  -l, --list-hmm-sources
                        List available HMM sources in the contigs database and
                        quit.
  --just-do-it          Don't bother me with questions or warnings, just do
                        it.

anvi-delete-misc-data [-h] [-p PAN_OR_PROFILE_DB] [-c CONTIGS_DB] -t
                      NAME [--keys-to-remove KEYS_TO_REMOVE]
                      [--groups-to-remove GROUPS_TO_REMOVE]
                      [--list-available-keys] [--just-do-it]

  -p PAN_OR_PROFILE_DB, --pan-or-profile-db PAN_OR_PROFILE_DB
                        Anvi'o pan or profile database (and even genes
                        database in appropriate contexts).
  -c CONTIGS_DB, --contigs-db CONTIGS_DB
                        Anvi'o contigs database generated by 'anvi-gen-
                        contigs-database'

  -t NAME, --target-data-table NAME
                        The target table is the table you are interested in
                        accessing. Currently it can be 'items','layers', or
                        'layer_orders'. Please see most up-to-date online
                        documentation for more information.
  --keys-to-remove KEYS_TO_REMOVE
                        A comma-separated list of data keys to remove from the
                        database. If you do not use this parameter, anvi'o
                        will simply remove everything from the target data
                        table immediately. Please note that you should not use
                        this parameter together with `--groups-to-remove` in a
                        single command.
  --groups-to-remove GROUPS_TO_REMOVE
                        A comma-separated list of data groups to remove from
                        the database. If you do not use this parameter, anvi'o
                        will simply remove everything from the target data
                        table immediately. Please note that you should not use
                        this parameter together with `--keys-to-remove` in a
                        single command.
  --list-available-keys
                        Using this flag will list available data keys in the
                        target data table and quit without doing anything
                        else.
  --just-do-it          Don't bother me with questions or warnings, just do
                        it.

anvi-delete-state [-h] -p PAN_OR_PROFILE_DB [-s STATE_NAME]
                  [--list-states]

  -p PAN_OR_PROFILE_DB, --pan-or-profile-db PAN_OR_PROFILE_DB
                        Anvi'o pan or profile database (and even genes
                        database in appropriate contexts).
  -s STATE_NAME, --state STATE_NAME
                        The state name to ... delete :(
  --list-states         Show available states and exit.

anvi-dereplicate-genomes [-h] [-i FILE_PATH] [-e FILE_PATH]
                         [-f FASTA_TEXT_FILE] [--ani-dir PATH]
                         [--mash-dir PATH] -o DIR_PATH
                         [--skip-fasta-report] [--report-all]
                         [--program {pyANI,fastANI,sourmash}]
                         [--fastani-kmer-size FASTANI_KMER_SIZE]
                         [--fragment-length FRAGMENT_LENGTH]
                         [--min-fraction MIN_FRACTION]
                         [--method {ANIm,ANIb,ANIblastall,TETRA}]
                         [--min-alignment-fraction NUM]
                         [--significant-alignment-length INT]
                         [--use-full-percent-identity]
                         [--min-full-percent-identity FULL_PERCENT_IDENTITY]
                         [--kmer-size INT] [--scale INT]
                         --similarity-threshold SIMILARITY_THRESHOLD
                         [--cluster-method {simple_greedy}]
                         [--representative-method {Qscore,length,centrality}]
                         [-T NUM_THREADS] [--just-do-it]
                         [--skip-checking-genome-hashes]
                         [--log-file FILE_PATH]

  -i FILE_PATH, --internal-genomes FILE_PATH
                        A five-column TAB-delimited flat text file. The header
                        line must contain these columns: 'name', 'bin_id',
                        'collection_id', 'profile_db_path', 'contigs_db_path'.
                        Each line should list a single entry, where 'name' can
                        be any name to describe the anvi'o bin identified as
                        'bin_id' that is stored in a collection.
  -e FILE_PATH, --external-genomes FILE_PATH
                        A two-column TAB-delimited flat text file that lists
                        anvi'o contigs databases. The first item in the header
                        line should read 'name', and the second should read
                        'contigs_db_path'. Each line in the file should
                        describe a single entry, where the first column is the
                        name of the genome (or MAG), and the second column is
                        the anvi'o contigs database generated for this genome.
  -f FASTA_TEXT_FILE, --fasta-text-file FASTA_TEXT_FILE
                        A two-column TAB-delimited file that lists multiple
                        FASTA files to import for analysis. If using for
                        `anvi-dereplicate-genomes` or `anvi-compute-distance`,
                        each FASTA is assumed to be a genome. The first item
                        in the header line should read 'name', and the second
                        item should read 'path'. Each line in the field should
                        describe a single entry, where the first column is the
                        name of the FASTA file or corresponding sequence, and
                        the second column is the path to the FASTA file
                        itself.

  --ani-dir PATH        You can import the directory created by `anvi-compute-
                        genome-similarity` if `--program` parameter was set to
                        `fastANI` or `pyANI` and use it for dereplication
  --mash-dir PATH       You can import the directory created by `anvi-compute-
                        genome-similarity` if `--program` parameter was set to
                        `sourmash` and use it for dereplication

  -o DIR_PATH, --output-dir DIR_PATH
                        Directory path for output files
  --skip-fasta-report   By default, if any sequence source is provided, FASTA
                        files of non-redundant genomes are reported. With this
                        flag, no FASTA files are reported.
  --report-all          By default, only FASTA files of non-redundant genomes
                        are reported, i.e. single representatives from each
                        cluster. With this flag, all genome FASTAS will be
                        reported.

  --program {pyANI,fastANI,sourmash}
                        Tell anvi'o which program to run to process genome
                        similarity. For ANI, you can either use pyANI or
                        fastANI. If accuracy is paramount (for example,
                        distinguishing things less than 1 percent different),
                        or for dealing with genomes < 80 percent similar,
                        pyANI is what we recommend. However, fastANI is much
                        faster. If you for some reason want to use mash
                        similarity, you can use sourmash, but its really not
                        intended for genome comparisons.

  --fastani-kmer-size FASTANI_KMER_SIZE
                        Choose a kmer. The default is 16.
  --fragment-length FRAGMENT_LENGTH
                        Choose a fragment length. The default is 3000.
  --min-fraction MIN_FRACTION
                        Minimum fraction of alignment to be shared between
                        genome pairs to calculate ANI. If reference and query
                        genome size differ, smaller one among the two is
                        considered. The default is 0.25.

  --method {ANIm,ANIb,ANIblastall,TETRA}
                        Method for pyANI. The default is ANIb. You must have
                        the necessary binary in path for whichever method you
                        choose. According to the pyANI help for v0.2.7 at
                        https://github.com/widdowquinn/pyani, the method
                        'ANIm' uses MUMmer (NUCmer) to align the input
                        sequences. 'ANIb' uses BLASTN+ to align 1020nt
                        fragments of the input sequences. 'ANIblastall': uses
                        the legacy BLASTN to align 1020nt fragments Finally,
                        'TETRA': calculates tetranucleotide frequencies of
                        each input sequence
  --min-alignment-fraction NUM
                        In some cases you may get high raw ANI estimates
                        (percent identity scores) between two genomes that
                        have little to do with each other simply because only
                        a small fraction of their content may be aligned. This
                        filter will set all ANI scores between two genomes to
                        0 if the alignment fraction is less than you deem
                        trustable. When you set a value, anvi'o will go
                        through the ANI results, and set percent identity
                        scores between two genomes to 0 if the alignment
                        fraction *between either of them* is less than the
                        parameter described here. The default is 0.25.
  --significant-alignment-length INT
                        So --min-alignment-fraction discards any hit that is
                        coming from alignments that represent shorter
                        fractions of genomes, but what if you still don't want
                        to miss an alignment that is longer than an X number
                        of nucleotides regardless of what fraction of the
                        genome it represents? Well, this parameter is to
                        recover things that may be lost due to --min-
                        alignment-fraction parameter. Let's say, if you set
                        --min-alignment-fraction to '0.05', and this parameter
                        to '5000', anvi'o will keep hits from alignments that
                        are longer than 5000 nts, EVEN IF THEY REPRESENT less
                        than 5 percent of a given genome pair. Basically if
                        --min-alignment-fraction is your shield to protect
                        yourself from incoming garbage, --significant-
                        alignment-length is your chopstick to pick out those
                        that may be interesting, and you are a true warrior
                        here.
  --use-full-percent-identity
                        Usually, percent identity is calculated only over
                        aligned regions, and this is what is used as a
                        distance metric by default. But with this flag, you
                        can instead use the *full* percent identity as the
                        distance metric. It is the same as percent identity,
                        except that regions that did not align are included in
                        the calculation. This means *full* percent identity
                        will always be less than or equal to percent identity.
                        How is it calculated? Well if P is the percentage
                        identity calculated in aligned regions, L is the
                        length of the genome, and A is the fraction of the
                        genome that aligned to a compared genome, the full
                        percent identity is P * (A/L). In other words, it is
                        the percent identity multiplied by the alignment
                        coverage. For example, if the alignment is a whopping
                        97 percent identity but only 8 percent of the genome
                        aligned, the *full* percent identity is 0.970 * 0.080
                        = 0.078, which is just 7.8 percent.
  --min-full-percent-identity FULL_PERCENT_IDENTITY
                        In some cases you may get high raw ANI estimates
                        (percent identity scores) between two genomes that
                        have little to do with each other simply because only
                        a small fraction of their content may be aligned. This
                        can be partly alleviated by considering the *full*
                        percent identity, which includes in its calculation
                        regions that did not align. For example, if the
                        alignment is a whopping 97 percent identity but only 8
                        percent of the genome aligned, the *full* percent
                        identity is 0.970 * 0.080 = 0.078 OR 7.8 percent.
                        *full* percent identity is always included in the
                        report, but you can also use it as a filter for other
                        metrics, such as percent identity. This filter will
                        set all ANI measures between two genomes to 0 if the
                        *full* percent identity is less than you deem
                        trustable. When you set a value, anvi'o will go
                        through the ANI results, and set all ANI measures
                        between two genomes to 0 if the *full* percent
                        identity *between either of them* is less than the
                        parameter described here. The default is 20.

  --kmer-size INT       Set the k-mer size for mash similarity checks. The
                        default is 13.
  --scale INT           Set the compression ratio for fasta signature file
                        computations. The default is 1000. Smaller ratios
                        decrease sensitivity, while larger ratios will lead to
                        large fasta signatures.

  --similarity-threshold SIMILARITY_THRESHOLD
                        If two genomes have a similarity greater than or equal
                        to this threshold, they will belong to the same
                        cluster. Since measures of 'similarity' depend
                        strongly on what method is used for calculation, and
                        since the threshold at which two genomes should be
                        considered 'similar enough' to be considered redundant
                        will depend on the application, anvi'o refuses to
                        provide a default parameter. If you're using pyANI,
                        maybe 0.90 is what you're after. If you're using
                        sourmash, maybe 0.25 is what you're after. Or maybe
                        not? Anvi'o is feeling nervous about this decision.
  --cluster-method {simple_greedy}
                        Currently, genomes are clustered based on a simple
                        greedy algorithm. Let's say your similarity threshold
                        is 0.90. If genome A is 0.95 similar to B, and B is
                        0.95 similar to C, and C is 0.95 similar to D, then
                        {A,B,C,D} will form a cluster. This is *even though* D
                        may share a similarity to A of merely 0.80, which is
                        below similarity threshold. You want better
                        alternatives? Contact the developers.
  --representative-method {Qscore,length,centrality}
                        After genomes are grouped into redundancy clusters,
                        you can define how anvi'o picks the representative
                        genome from the cluster. 'Qscore' computes the genome
                        with the highest completion and lowest redundancy as
                        the representative. 'length' returns the longest
                        genome. 'centrality' returns the genome with the
                        highest average similarity to everything in the
                        cluster, i.e. the most central. The default is
                        centrality

  -T NUM_THREADS, --num-threads NUM_THREADS
                        Maximum number of threads to use for multithreading
                        whenever possible. Very conservatively, the default is
                        1. It is a good idea to not exceed the number of CPUs
                        / cores on your system. Plus, please be careful with
                        this option if you are running your commands on a SGE
                        --if you are clusterizing your runs, and asking for
                        multiple threads to use, you may deplete your
                        resources very fast.
  --just-do-it          Don't bother me with questions or warnings, just do
                        it.
  --skip-checking-genome-hashes
                        Use this flag if you would like anvi'o to skip
                        checking genome hashes. This is only relevant if you
                        may have genomes in your internal or external genomes
                        files that have identical sequences with different
                        names AND if you are OK with it. You may be OK with
                        it, for instance, if you are using `anvi-dereplicate-
                        genomes` program to dereplicate genomes desribed in
                        multiple collections in an anvi'o profile database
                        that may be describing the same genome multiple times
                        (see https://github.com/merenlab/anvio/issues/1397 for
                        a case).
  --log-file FILE_PATH  File path to store debug/output messages.

anvi-display-contigs-stats [-h] [--report-as-text] [-o FILE_PATH]
                           [-I IP_ADDR] [-P INT] [--browser-path PATH]
                           [--server-only] [--password-protected]
                           CONTIG DATABASES) [CONTIG DATABASE(S ...]

  CONTIG DATABASE(S)    Anvio'o Contig databases to display statistics, you
                        can give multiple databases by seperating them with
                        space.

  --report-as-text      If you give this flag, Anvi'o will not open new
                        browser to show Contigs database statistics and write
                        all stats to TAB separated file and you should also
                        give --output-file with this flag otherwise Anvi'o
                        will complain.
  -o FILE_PATH, --output-file FILE_PATH
                        File path to store results.

  -I IP_ADDR, --ip-address IP_ADDR
                        IP address for the HTTP server. The default ip address
                        (0.0.0.0) should work just fine for most.
  -P INT, --port-number INT
                        Port number to use for anvi'o services. If nothing is
                        declared, anvi'o will try to find a suitable port
                        number, starting from the default port number, 8080.
  --browser-path PATH   By default, anvi'o will use your default browser to
                        launch the interactive interface. If you would like to
                        use something else than your system default, you can
                        provide a full path for an alternative browser using
                        this parameter, and hope for the best. For instance we
                        are using this parameter to call Google's experimental
                        browser, Canary, which performs better with demanding
                        visualizations.
  --server-only         The default behavior is to start the local server, and
                        fire up a browser that connects to the server. If you
                        have other plans, and want to start the server without
                        calling the browser, this is the flag you need.
  --password-protected  If this flag is set, command line tool will ask you to
                        enter a password and interactive interface will be
                        only accessible after entering same password. This
                        option is recommended for shared machines like
                        clusters or shared networks where computers are not
                        isolated.

anvi-display-metabolism [-h] -c CONTIGS_DB [-m]
                        [--kegg-data-dir KEGG_DATA_DIR] [-p PROFILE_DB]
                        [-C COLLECTION_NAME] [-b BIN_NAME]
                        [-B FILE_PATH]
                        [--module-completion-threshold NUM]
                        [-I IP_ADDR] [-P INT] [--browser-path PATH]
                        [--server-only] [--password-protected]

  -c CONTIGS_DB, --contigs-db CONTIGS_DB
                        Anvi'o contigs database generated by 'anvi-gen-
                        contigs-database'
  -m, --metagenome-mode
                        Treat a given contigs database as a metagenome rather
                        than treating it as a single genome.
  --kegg-data-dir KEGG_DATA_DIR
                        The directory path for your KEGG setup, which will
                        include things like KOfam profiles and KEGG MODULE
                        data. Anvi'o will try to use the default path if you
                        do not specify anything.

  -p PROFILE_DB, --profile-db PROFILE_DB
                        Anvi'o profile database
  -C COLLECTION_NAME, --collection-name COLLECTION_NAME
                        Collection name.
  -b BIN_NAME, --bin-id BIN_NAME
                        Bin name you are interested in.
  -B FILE_PATH, --bin-ids-file FILE_PATH
                        Text file for bins (each line should be a unique bin
                        id).

  --module-completion-threshold NUM
                        This threshold defines the point at which we consider
                        a KEGG module to be 'complete' or 'present' in a given
                        genome or bin. It is the fraction of steps that must
                        be complete in in order for the entire module to be
                        marked complete. The default is 0.75.

  -I IP_ADDR, --ip-address IP_ADDR
                        IP address for the HTTP server. The default ip address
                        (0.0.0.0) should work just fine for most.
  -P INT, --port-number INT
                        Port number to use for anvi'o services. If nothing is
                        declared, anvi'o will try to find a suitable port
                        number, starting from the default port number, 8080.
  --browser-path PATH   By default, anvi'o will use your default browser to
                        launch the interactive interface. If you would like to
                        use something else than your system default, you can
                        provide a full path for an alternative browser using
                        this parameter, and hope for the best. For instance we
                        are using this parameter to call Google's experimental
                        browser, Canary, which performs better with demanding
                        visualizations.
  --server-only         The default behavior is to start the local server, and
                        fire up a browser that connects to the server. If you
                        have other plans, and want to start the server without
                        calling the browser, this is the flag you need.
  --password-protected  If this flag is set, command line tool will ask you to
                        enter a password and interactive interface will be
                        only accessible after entering same password. This
                        option is recommended for shared machines like
                        clusters or shared networks where computers are not
                        isolated.

anvi-display-pan [-h] -p PAN_DB [-g GENOMES_STORAGE] [-d VIEW_DATA]
                 [-t NEWICK] [-V ADDITIONAL_VIEW]
                 [-A ADDITIONAL_LAYERS] [--view NAME] [--title NAME]
                 [--state-autoload NAME] [--collection-autoload NAME]
                 [--export-svg FILE_PATH] [--skip-init-functions]
                 [--dry-run] [--skip-auto-ordering] [-I IP_ADDR]
                 [-P INT] [--browser-path PATH] [--read-only]
                 [--server-only] [--password-protected]
                 [--user-server-shutdown]

  -p PAN_DB, --pan-db PAN_DB
                        Anvi'o pan database
  -g GENOMES_STORAGE, --genomes-storage GENOMES_STORAGE
                        Anvi'o genomes storage file

  -d VIEW_DATA, --view-data VIEW_DATA
                        A TAB-delimited file for view data
  -t NEWICK, --tree NEWICK
                        NEWICK formatted tree structure

  -V ADDITIONAL_VIEW, --additional-view ADDITIONAL_VIEW
                        A TAB-delimited file for an additional view to be used
                        in the interface. This file should contain all split
                        names, and values for each of them in all samples.
                        Each column in this file must correspond to a sample
                        name. Content of this file will be called 'user_view',
                        which will be available as a new item in the 'views'
                        combo box in the interface
  -A ADDITIONAL_LAYERS, --additional-layers ADDITIONAL_LAYERS
                        A TAB-delimited file for additional layers for splits.
                        The first column of this file must be split names, and
                        the remaining columns should be unique attributes. The
                        file does not need to contain all split names, or
                        values for each split in every column. Anvi'o will try
                        to deal with missing data nicely. Each column in this
                        file will be visualized as a new layer in the tree.

  --view NAME           Start the interface with a pre-selected view. To see a
                        list of available views, use --show-views flag.
  --title NAME          Title for the interface. If you are working with a
                        RUNINFO dict, the title will be determined based on
                        information stored in that file. Regardless, you can
                        override that value using this parameter.
  --state-autoload NAME
                        Automatically load previous saved state and draw tree.
                        To see a list of available states, use --show-states
                        flag.
  --collection-autoload NAME
                        Automatically load a collection and draw tree. To see
                        a list of available collections, use --list-
                        collections flag.
  --export-svg FILE_PATH
                        The SVG output file path.

  --skip-init-functions
                        When declared, function calls for genes will not be
                        initialized (therefore will be missing from all
                        relevant interfaces or output files). The use of this
                        flag may reduce the memory fingerprint and processing
                        time for large datasets.
  --dry-run             Don't do anything real. Test everything, and stop
                        right before wherever the developer said 'well, this
                        is enough testing', and decided to print out results.
  --skip-auto-ordering  When declared, the attempt to include automatically
                        generated orders of items based on additional data is
                        skipped. In case those buggers cause issues with your
                        data, and you still want to see your stuff and deal
                        with the other issue maybe later.

  -I IP_ADDR, --ip-address IP_ADDR
                        IP address for the HTTP server. The default ip address
                        (0.0.0.0) should work just fine for most.
  -P INT, --port-number INT
                        Port number to use for anvi'o services. If nothing is
                        declared, anvi'o will try to find a suitable port
                        number, starting from the default port number, 8080.
  --browser-path PATH   By default, anvi'o will use your default browser to
                        launch the interactive interface. If you would like to
                        use something else than your system default, you can
                        provide a full path for an alternative browser using
                        this parameter, and hope for the best. For instance we
                        are using this parameter to call Google's experimental
                        browser, Canary, which performs better with demanding
                        visualizations.
  --read-only           When the interactive interface is started with this
                        flag, all 'database write' operations will be
                        disabled.
  --server-only         The default behavior is to start the local server, and
                        fire up a browser that connects to the server. If you
                        have other plans, and want to start the server without
                        calling the browser, this is the flag you need.
  --password-protected  If this flag is set, command line tool will ask you to
                        enter a password and interactive interface will be
                        only accessible after entering same password. This
                        option is recommended for shared machines like
                        clusters or shared networks where computers are not
                        isolated.
  --user-server-shutdown
                        Allow users to shutdown an anvi'server via web
                        interface.

anvi-display-structure [-h] -s STRUCTURE_DB [-p PROFILE_DB]
                       [-c CONTIGS_DB] [-V VARIABILITY_TABLE]
                       [--splits-of-interest FILE] [-C COLLECTION_NAME]
                       [-b BIN_NAME] [--samples-of-interest FILE]
                       [--genes-of-interest FILE]
                       [--gene-caller-ids GENE_CALLER_IDS] [-j FLOAT]
                       [--SAAVs-only] [--SCVs-only] [-I IP_ADDR]
                       [-P INT] [--browser-path PATH] [--server-only]
                       [--password-protected]

  -s STRUCTURE_DB, --structure-db STRUCTURE_DB
                        Anvi'o structure database.

  -p PROFILE_DB, --profile-db PROFILE_DB
                        Anvi'o profile database
  -c CONTIGS_DB, --contigs-db CONTIGS_DB
                        Anvi'o contigs database generated by 'anvi-gen-
                        contigs-database'
  -V VARIABILITY_TABLE, --variability-profile VARIABILITY_TABLE
                        The output of anvi-gen-variability-profile, or a
                        different variant-calling output that has been
                        converted to the anvi'o format.

  --splits-of-interest FILE
                        A file with split names. There should be only one
                        column in the file, and each line should correspond to
                        a unique split name.
  -C COLLECTION_NAME, --collection-name COLLECTION_NAME
                        Collection name.
  -b BIN_NAME, --bin-id BIN_NAME
                        If provided, any genes found in both your bin and your
                        structure database will be available for display.
  --samples-of-interest FILE
                        A file with samples names. There should be only one
                        column in the file, and each line should correspond to
                        a unique sample name (without a column header).
  --genes-of-interest FILE
                        A file with anvi'o gene caller IDs. There should be
                        only one column in the file, and each line should
                        correspond to a unique gene caller id (without a
                        column header).
  --gene-caller-ids GENE_CALLER_IDS
                        Gene caller ids. Multiple of them can be declared
                        separated by a delimiter (the default is a comma). In
                        anvi-gen-variability-profile, if you declare nothing
                        you will get all genes matching your other filtering
                        criteria. In other programs, you may get everything,
                        nothing, or an error. It really depends on the
                        situation. Fortunately, mistakes are cheap, so it's
                        worth a try.
  -j FLOAT, --min-departure-from-consensus FLOAT
                        Takes a value between 0 and 1, where 1 is maximum
                        divergence from the consensus. it can be an expensive
                        operation to display every variable position, and so
                        the default is 0.05. To display every variable
                        position, set this parameter to 0
  --SAAVs-only          If provided, variability will be generated for single
                        amino acid variants (SAAVs) and not for single codon
                        variants (SCVs). This could save you some time if
                        you're only interested in SAAVs.
  --SCVs-only           If provided, variability will be generated for single
                        codon variants (SCVs) and not for single amino acid
                        variants (SAAVs). This could save you some time if
                        you're only interested in SCVs.

  -I IP_ADDR, --ip-address IP_ADDR
                        IP address for the HTTP server. The default ip address
                        (0.0.0.0) should work just fine for most.
  -P INT, --port-number INT
                        Port number to use for anvi'o services. If nothing is
                        declared, anvi'o will try to find a suitable port
                        number, starting from the default port number, 8080.
  --browser-path PATH   By default, anvi'o will use your default browser to
                        launch the interactive interface. If you would like to
                        use something else than your system default, you can
                        provide a full path for an alternative browser using
                        this parameter, and hope for the best. For instance we
                        are using this parameter to call Google's experimental
                        browser, Canary, which performs better with demanding
                        visualizations.
  --server-only         The default behavior is to start the local server, and
                        fire up a browser that connects to the server. If you
                        have other plans, and want to start the server without
                        calling the browser, this is the flag you need.
  --password-protected  If this flag is set, command line tool will ask you to
                        enter a password and interactive interface will be
                        only accessible after entering same password. This
                        option is recommended for shared machines like
                        clusters or shared networks where computers are not
                        isolated.

anvi-estimate-genome-completeness [-h] [-c CONTIGS_DB] [-e FILE_PATH]
                                  [-p PROFILE_DB] [-C COLLECTION_NAME]
                                  [--list-collections] [--just-do-it]
                                  [--concise] [-o FILE_PATH]

  -c CONTIGS_DB, --contigs-db CONTIGS_DB
                        Anvi'o contigs database generated by 'anvi-gen-
                        contigs-database'

  -e FILE_PATH, --external-genomes FILE_PATH
                        A two-column TAB-delimited flat text file that lists
                        anvi'o contigs databases. The first item in the header
                        line should read 'name', and the second should read
                        'contigs_db_path'. Each line in the file should
                        describe a single entry, where the first column is the
                        name of the genome (or MAG), and the second column is
                        the anvi'o contigs database generated for this genome.

  -p PROFILE_DB, --profile-db PROFILE_DB
                        Anvi'o profile database
  -C COLLECTION_NAME, --collection-name COLLECTION_NAME
                        Collection name.

  --list-collections    Show available collections and exit.
  --just-do-it          Don't bother me with questions or warnings, just do
                        it.
  --concise             Don't be verbose, print less messages whenever
                        possible.
  -o FILE_PATH, --output-file FILE_PATH
                        File path to store results.

anvi-estimate-metabolism [-h] [-c CONTIGS_DB] [-m]
                         [--kegg-data-dir KEGG_DATA_DIR]
                         [-p PROFILE_DB] [-C COLLECTION_NAME]
                         [-b BIN_NAME] [-B FILE_PATH] [-e FILE_PATH]
                         [-i FILE_PATH] [-M FILE_PATH]
                         [--module-completion-threshold NUM]
                         [-O FILENAME_PREFIX]
                         [--kegg-output-modes MODES]
                         [--list-available-modes]
                         [--custom-output-headers HEADERS]
                         [--list-available-output-headers]
                         [--matrix-format]
                         [--get-raw-data-as-json FILENAME_PREFIX]
                         [--store-json-without-estimation]
                         [--estimate-from-json FILE_PATH]

  -c CONTIGS_DB, --contigs-db CONTIGS_DB
                        Anvi'o contigs database generated by 'anvi-gen-
                        contigs-database'
  -m, --metagenome-mode
                        Treat a given contigs database as a metagenome rather
                        than treating it as a single genome.
  --kegg-data-dir KEGG_DATA_DIR
                        The directory path for your KEGG setup, which will
                        include things like KOfam profiles and KEGG MODULE
                        data. Anvi'o will try to use the default path if you
                        do not specify anything.

  -p PROFILE_DB, --profile-db PROFILE_DB
                        Anvi'o profile database
  -C COLLECTION_NAME, --collection-name COLLECTION_NAME
                        Collection name.
  -b BIN_NAME, --bin-id BIN_NAME
                        Bin name you are interested in.
  -B FILE_PATH, --bin-ids-file FILE_PATH
                        Text file for bins (each line should be a unique bin
                        id).

  -e FILE_PATH, --external-genomes FILE_PATH
                        A two-column TAB-delimited flat text file that lists
                        anvi'o contigs databases. The first item in the header
                        line should read 'name', and the second should read
                        'contigs_db_path'. Each line in the file should
                        describe a single entry, where the first column is the
                        name of the genome (or MAG), and the second column is
                        the anvi'o contigs database generated for this genome.
  -i FILE_PATH, --internal-genomes FILE_PATH
                        A five-column TAB-delimited flat text file. The header
                        line must contain these columns: 'name', 'bin_id',
                        'collection_id', 'profile_db_path', 'contigs_db_path'.
                        Each line should list a single entry, where 'name' can
                        be any name to describe the anvi'o bin identified as
                        'bin_id' that is stored in a collection.
  -M FILE_PATH, --metagenomes FILE_PATH
                        A two-column TAB-delimited flat text file. The header
                        line must contain these columns: 'name',
                        'contigs_db_path', and 'profile_db_path'. Each line
                        should list a single entry, where 'name' can be any
                        name to describe the metagenome stored in the anvi'o
                        contigs database. In this context, the anvi'o profiles
                        associated with contigs database must be SINGLE
                        PROFILES, as in generated by the program `anvi-
                        profile` and not `anvi-merge`.

  --module-completion-threshold NUM
                        This threshold defines the point at which we consider
                        a KEGG module to be 'complete' or 'present' in a given
                        genome or bin. It is the fraction of steps that must
                        be complete in in order for the entire module to be
                        marked complete. The default is 0.75.
  -O FILENAME_PREFIX, --output-file-prefix FILENAME_PREFIX
                        A prefix to be used while naming the output files (no
                        file type extensions please; just a prefix).
  --kegg-output-modes MODES
                        Use this flag to indicate what information you want in
                        the kegg metabolism output files, by providing a
                        comma-separated list of output modes (each 'mode' you
                        provide will result in a different output file, all
                        with the same prefix). The default output modes are
                        'kofam_hits' and 'complete_modules'. To see a list of
                        available output modes, run this script with the flag
                        --list-available-modes.
  --list-available-modes
                        Use this flag to see the available output modes and
                        their descriptions.
  --custom-output-headers HEADERS
                        For use with the 'custom' output mode. Provide a
                        comma-separated list of headers to include in the
                        output matrix. To see a list of available headers, run
                        this script with the flag --list-available-output-
                        headers.
  --list-available-output-headers
                        Use this flag to see the available output headers.
  --matrix-format       If you want to generate the output in several sparse
                        matrices instead of one file, use this flag. In each
                        matrix, contigs DBs will be arranged in columns and
                        KEGG modules in rows. This output option is especially
                        appropriate for input option #3.

  --get-raw-data-as-json FILENAME_PREFIX
                        If you want the raw metabolism estimation data
                        dictionary in JSON-format, provide a filename prefix
                        to this argument.The program will then output a file
                        with the .json extension containing this data.
  --store-json-without-estimation
                        This flag is used to control what is stored in the
                        JSON-formatted metabolism data dictionary. When this
                        flag is provided alongside the --get-raw-data-as-json
                        flag, the JSON file will be created without running
                        metabolism estimation, and that file will consequently
                        include only information about KOfam hits and gene
                        calls. The idea is that you can then modify this file
                        as you like and re-run this program using the flag
                        --estimate-from-json.
  --estimate-from-json FILE_PATH
                        If you have a JSON file containing KOfam hits and gene
                        call information from your contigs database (such as a
                        file produced using the --get-raw-data-as-json flag),
                        you can provide that file to this flag and KEGG
                        metabolism estimates will be computed from the
                        information within instead of from a contigs database.

anvi-estimate-scg-taxonomy [-h] [-c CONTIGS_DB] [-m] [-p PROFILE_DB]
                           [-C COLLECTION_NAME] [-M FILE_PATH]
                           [-o FILE_PATH] [-O FILENAME_PREFIX]
                           [--taxonomic-level {t_domain,t_phylum,t_class,t_order,t_family,t_genus,t_species}]
                           [--matrix-format] [--raw-output]
                           [-T NUM_THREADS] [-S SCG_NAME]
                           [--report-scg-frequencies FILE_PATH]
                           [--just-do-it]
                           [--simplify-taxonomy-information]
                           [--compute-scg-coverages]
                           [--update-profile-db-with-taxonomy]
                           [-r PATH]

  -c CONTIGS_DB, --contigs-db CONTIGS_DB
                        Anvi'o contigs database generated by 'anvi-gen-
                        contigs-database'
  -m, --metagenome-mode
                        Treat a given contigs database as a metagenome rather
                        than treating it as a single genome.

  -p PROFILE_DB, --profile-db PROFILE_DB
                        Anvi'o profile database
  -C COLLECTION_NAME, --collection-name COLLECTION_NAME
                        Collection name.

  -M FILE_PATH, --metagenomes FILE_PATH
                        A two-column TAB-delimited flat text file. The header
                        line must contain these columns: 'name',
                        'contigs_db_path', and 'profile_db_path'. Each line
                        should list a single entry, where 'name' can be any
                        name to describe the metagenome stored in the anvi'o
                        contigs database. In this context, the anvi'o profiles
                        associated with contigs database must be SINGLE
                        PROFILES, as in generated by the program `anvi-
                        profile` and not `anvi-merge`.

  -o FILE_PATH, --output-file FILE_PATH
                        File path to store results.
  -O FILENAME_PREFIX, --output-file-prefix FILENAME_PREFIX
                        A prefix to be used while naming the output files (no
                        file type extensions please; just a prefix).
  --taxonomic-level {t_domain,t_phylum,t_class,t_order,t_family,t_genus,t_species}
                        The taxonomic level to use whenever relevant and/or
                        available. The default taxonomic level is None, but if
                        you choose something specific, anvi'o will focus on
                        that whenever possible.
  --matrix-format       If you want the reports to look like sparse matrices
                        whenever possible, declare this flag. Matrices are
                        especially good to use when you are working with
                        internal/external genomes since they can show you
                        quickly the distribution of each taxon across all
                        metagenomes in programs like EXCEL. WELL TRY IT AND
                        SEE.
  --raw-output          Just store the raw output without any processing of
                        the primary data structure.

  -T NUM_THREADS, --num-threads NUM_THREADS
                        Maximum number of threads to use for multithreading
                        whenever possible. Very conservatively, the default is
                        1. It is a good idea to not exceed the number of CPUs
                        / cores on your system. Plus, please be careful with
                        this option if you are running your commands on a SGE
                        --if you are clusterizing your runs, and asking for
                        multiple threads to use, you may deplete your
                        resources very fast.

  -S SCG_NAME, --scg-name-for-metagenome-mode SCG_NAME
                        When running in metagenome mode, anvi'o automatically
                        chooses the most frequent single-copy core gene to
                        estimate the taxonomic composition within a contigs
                        database. If you have a different preference you can
                        use this parameter to communicate that.
  --report-scg-frequencies FILE_PATH
                        Report SCG frequencies in a TAB-delimited file and
                        quit. This is a great way to decide which SCG name to
                        use in metagenome mode (we often wish to use the most
                        frequent SCG to increase the detection of taxa).
  --just-do-it          Don't bother me with questions or warnings, just do
                        it.

  --simplify-taxonomy-information
                        The taxonomy output may include a large number of
                        names that contain clade-specific code for not-yet-
                        characterized taxa. With this flag you can simplify
                        taxon names. This will influence all output files and
                        displays as the use of this flag will on-the-fly trim
                        taxonomic levels with clade-specific code names.
  --compute-scg-coverages
                        When this flag is declared, anvi'o will go back to the
                        profile database to learn coverage statistics of
                        single-copy core genes for which we have taxonomy
                        information.
  --update-profile-db-with-taxonomy
                        When anvi'o knows all both taxonomic affiliations and
                        coverages across samples for single-copy core genes,
                        it can, in theory add this information to the profile
                        database. With this flag you can instruct anvi'o to do
                        that and find information on taxonomy in the `layers`
                        tab of your interactive interface.

  -r PATH, --taxonomy-database PATH
                        Path to the directory that contains the BLAST
                        databases for single-copy core genes. You will almost
                        never need to use this parameter unless you are trying
                        something very fancy. But when you do, you can tell
                        anvi'o where to look for database files through this
                        parameter.

anvi-experimental-organization [-h] [-p PROFILE_DB] -c CONTIGS_DB
                               [-i DIR_PATH] [-N NAME]
                               [--distance DISTANCE_METRIC]
                               [--linkage LINKAGE_METHOD]
                               [--skip-store-in-db] [-o FILE_PATH]
                               [--dry-run]
                               FILE

  FILE                  Config file for clustering of contigs. See
                        documentation for help.

  -p PROFILE_DB, --profile-db PROFILE_DB
                        Anvi'o profile database
  -c CONTIGS_DB, --contigs-db CONTIGS_DB
                        Anvi'o contigs database generated by 'anvi-gen-
                        contigs-database'
  -i DIR_PATH, --input-directory DIR_PATH
                        Input directory where the input files addressed from
                        the configuration file can be found (i.e., the profile
                        database, if PROFILE.db::TABLE notation is used in the
                        configuration file).
  -N NAME, --name NAME  The name to use when storing the resulting clustering
                        in the database. This name will appear in the
                        interactive interface and other relevant interfaces.
                        Please consider using a short and descriptive single-
                        word (if you do not do that you will make anvi'o
                        complain).
  --distance DISTANCE_METRIC
                        The distance metric for the hierarchical clustering.
                        If you do not use this flag, the distance metric you
                        defined in your clustering config file will be used.
                        If you have not defined one in your config file, then
                        the system default will be used, which is "euclidean".
  --linkage LINKAGE_METHOD
                        Same story with the `--distance`, except, the system
                        default for this one is ward.
  --skip-store-in-db    By default, analysis results are stored in the profile
                        database. The use of this flag will let you skip that
  -o FILE_PATH, --output-file FILE_PATH
                        File path to store results.
  --dry-run             Don't do anything real. Test everything, and stop
                        right before wherever the developer said 'well, this
                        is enough testing', and decided to print out results.

anvi-export-collection [-h] -p PAN_OR_PROFILE_DB [-C COLLECTION_NAME]
                       [-O FILENAME_PREFIX] [--list-collections]
                       [--include-unbinned]

  -p PAN_OR_PROFILE_DB, --pan-or-profile-db PAN_OR_PROFILE_DB
                        Anvi'o pan or profile database (and even genes
                        database in appropriate contexts).
  -C COLLECTION_NAME, --collection-name COLLECTION_NAME
                        Collection name.
  -O FILENAME_PREFIX, --output-file-prefix FILENAME_PREFIX
                        A prefix to be used while naming the output files (no
                        file type extensions please; just a prefix).
  --list-collections    Show available collections and exit.
  --include-unbinned    When this flag is used, anvi'o will also store in the
                        output file the items that do not appear in any of
                        your bins. This new bin will be called
                        'UNBINNED_ITEMS_BIN'. Yes. The ugly name is
                        intentional.

anvi-export-contigs [-h] -c CONTIGS_DB [--contigs-of-interest FILE]
                    [--splits-mode] -o FILE_PATH [--just-do-it]

  -c CONTIGS_DB, --contigs-db CONTIGS_DB
                        Anvi'o contigs database generated by 'anvi-gen-
                        contigs-database'
  --contigs-of-interest FILE
                        It is possible to focus on only a set of contigs. If
                        you would like to do that and ignore the rest of the
                        contigs in your contigs database, use this parameter
                        with a flat file every line of which desribes a single
                        contig name.
  --splits-mode         Export split sequences instead.
  -o FILE_PATH, --output-file FILE_PATH
                        File path to store results.
  --just-do-it          Don't bother me with questions or warnings, just do
                        it.

anvi-export-functions [-h] -c CONTIGS_DB [-o FILE_PATH]
                      [--annotation-sources SOURCE NAME[S]] [-l]

  -c CONTIGS_DB, --contigs-db CONTIGS_DB
                        Anvi'o contigs database generated by 'anvi-gen-
                        contigs-database'
  -o FILE_PATH, --output-file FILE_PATH
                        File path to store results.
  --annotation-sources SOURCE NAME[S]
                        Get functional annotations for a specific list of
                        annotation sources. You can specify one or more
                        sources by separating them from each other with a
                        comma character (i.e., '--annotation-sources
                        source_1,source_2,source_3'). The default behavior is
                        to return everything
  -l, --list-annotation-sources
                        List available functional annotation sources.

anvi-export-gene-calls [-h] -c CONTIGS_DB [-o FILE_PATH]
                       [--gene-caller GENE-CALLER]
                       [--list-gene-callers]
                       [--skip-sequence-reporting]

  -c CONTIGS_DB, --contigs-db CONTIGS_DB
                        Anvi'o contigs database generated by 'anvi-gen-
                        contigs-database'
  -o FILE_PATH, --output-file FILE_PATH
                        File path to store results.
  --gene-caller GENE-CALLER
                        Which gene caller(s) would you like to export gene
                        calls for? If providing multiple they should be comma-
                        separated (no spaces). If you don't know, use --list-
                        gene-callers
  --list-gene-callers   List available gene callers in the contigs database
                        and quit.
  --skip-sequence-reporting
                        By default, exported gene calls have an amino acid
                        sequences column in the output. Turn this behavior off
                        with this flag

anvi-export-gene-coverage-and-detection [-h] -p PROFILE_DB -c
                                        CONTIGS_DB -O FILENAME_PREFIX

  -p PROFILE_DB, --profile-db PROFILE_DB
                        Anvi'o profile database
  -c CONTIGS_DB, --contigs-db CONTIGS_DB
                        Anvi'o contigs database generated by 'anvi-gen-
                        contigs-database'
  -O FILENAME_PREFIX, --output-file-prefix FILENAME_PREFIX
                        A prefix to be used while naming the output files (no
                        file type extensions please; just a prefix).

anvi-export-items-order [-h] [-p DB PATH] [--name ORDER NAME]
                        [-o FILE_PATH]

  -p DB PATH, --db-path DB PATH
                        An appropriate anvi'o database.
  --name ORDER NAME     The name of the order you want to export. If you don't
                        provide an order name, anvi'o will show you the names
                        of all available orders in the database.

  -o FILE_PATH, --output-file FILE_PATH
                        File path to store results.

anvi-export-locus [-h] -c CONTIGS_DB [-s SEARCH_TERM]
                  [--gene-caller-ids GENE_CALLER_IDS]
                  [--delimiter CHAR] [-o DIR_PATH] -O FILENAME_PREFIX
                  [--flank-mode] [-n NUM_GENES] [--use-hmm]
                  [--hmm-sources SOURCE NAME] [-l]
                  [--annotation-sources SOURCE NAME[S]] [-W]
                  [--remove-partial-hits] [--never-reverse-complement]

  -c CONTIGS_DB, --contigs-db CONTIGS_DB
                        Anvi'o contigs database generated by 'anvi-gen-
                        contigs-database'

  -s SEARCH_TERM, --search-term SEARCH_TERM
                        search term.
  --gene-caller-ids GENE_CALLER_IDS
                        Gene caller ids. Multiple of them can be declared
                        separated by a delimiter (the default is a comma). In
                        anvi-gen-variability-profile, if you declare nothing
                        you will get all genes matching your other filtering
                        criteria. In other programs, you may get everything,
                        nothing, or an error. It really depends on the
                        situation. Fortunately, mistakes are cheap, so it's
                        worth a try.
  --delimiter CHAR      The delimiter to parse multiple input terms. The
                        default is ','.

  -o DIR_PATH, --output-dir DIR_PATH
                        Directory path for output files
  -O FILENAME_PREFIX, --output-file-prefix FILENAME_PREFIX
                        A prefix to be used while naming the output files (no
                        file type extensions please; just a prefix).

  --flank-mode          If in --flank-mode, anvi-export-locus will extract a
                        locus based on the coordinates of flanking genes. You
                        MUST provide 2 flanking genes in the form of TWO
                        --search-term, --gene-caller-ids, or --hmm-sources.
                        The --flank-mode option is appropriate for extracting
                        loci of variable gene number lengths, but are
                        consistently located between the same flanking genes
                        in the genome(s) of interest.
  -n NUM_GENES, --num-genes NUM_GENES
                        Required for DEFAULT mode. For each match (to the
                        function, or HMM that was searched) a sequence which
                        includes a block of genes will be saved. The block
                        could include either genes only in the forward
                        direction of the gene (defined according to the
                        direction of transcription of the gene) or reverse or
                        both. If you wish to get both direction use a comma
                        (no spaces) to define the block For example, '-n 4,5'
                        will give you four genes before and five genes after.
                        Whereas, '-n 5' will give you five genes after (in
                        addition to the gene that matched). To get only genes
                        preceding the match use '-n 5,0'. If the number of
                        genes requested exceeds the length of the contig, then
                        the output will include the sequence until the end of
                        the contig.
  --use-hmm             Use HMM hits instead of functional annotations. In
                        other words, --search-term will be queried against HMM
                        source annotations, NOT functional annotations. If you
                        choose this option, you must also say which HMM source
                        to use.
  --hmm-sources SOURCE NAME
                        Get sequences for a specific list of HMM sources. You
                        can list one or more sources by separating them from
                        each other with a comma character (i.e., '--hmm-
                        sources source_1,source_2,source_3'). If you would
                        like to see a list of available sources in the contigs
                        database, run this program with '--list-hmm-sources'
                        flag.
  -l, --list-hmm-sources
                        List available HMM sources in the contigs database and
                        quit.
  --annotation-sources SOURCE NAME[S]
                        Get functional annotations for a specific list of
                        annotation sources. You can specify one or more
                        sources by separating them from each other with a
                        comma character (i.e., '--annotation-sources
                        source_1,source_2,source_3'). The default behavior is
                        to return everything
  -W, --overwrite-output-destinations
                        Overwrite if the output files and/or directories
                        exist.
  --remove-partial-hits
                        By default anvi'o will return hits even if they are
                        partial. Declaring this flag will make anvi'o filter
                        all hits that are partial. Partial hits are hits in
                        which you asked for n1 genes before and n2 genes after
                        the gene that matched the search criteria but the
                        search hits the end of the contig before finding the
                        number of genes that you asked.
  --never-reverse-complement
                        By default, if a gene that is found by the search
                        criteria is reverse in it's direction, then the
                        sequence of the entire locus is reversed before it is
                        saved to the output. If you wish to prevent this
                        behavior then use the flag --never-reverse-complement.

anvi-export-misc-data [-h] [-p PAN_OR_PROFILE_DB] [-c CONTIGS_DB] -t
                      NAME [-D NAME] [-o FILE_PATH]

  -p PAN_OR_PROFILE_DB, --pan-or-profile-db PAN_OR_PROFILE_DB
                        Anvi'o pan or profile database (and even genes
                        database in appropriate contexts).
  -c CONTIGS_DB, --contigs-db CONTIGS_DB
                        Anvi'o contigs database generated by 'anvi-gen-
                        contigs-database'

  -t NAME, --target-data-table NAME
                        The target table is the table you are interested in
                        accessing. Currently it can be 'items','layers', or
                        'layer_orders'. Please see most up-to-date online
                        documentation for more information.
  -D NAME, --target-data-group NAME
                        Data group to focus. Anvi'o misc data tables support
                        associating a set of data keys with a data group. If
                        you have no idea what this is, then probably you don't
                        need it, and anvi'o will take care of you. Note: this
                        flag is IRRELEVANT if you are working with additional
                        order data tables.
  -o FILE_PATH, --output-file FILE_PATH
                        File path to store results.

anvi-export-splits-and-coverages [-h] -p PROFILE_DB -c CONTIGS_DB
                                 [-o DIR_PATH] [-O FILENAME_PREFIX]
                                 [--splits-mode] [--report-contigs]
                                 [--use-Q2Q3-coverages]

  -p PROFILE_DB, --profile-db PROFILE_DB
                        Anvi'o profile database
  -c CONTIGS_DB, --contigs-db CONTIGS_DB
                        Anvi'o contigs database generated by 'anvi-gen-
                        contigs-database'
  -o DIR_PATH, --output-dir DIR_PATH
                        Directory path for output files
  -O FILENAME_PREFIX, --output-file-prefix FILENAME_PREFIX
                        A prefix to be used while naming the output files (no
                        file type extensions please; just a prefix).
  --splits-mode         Specify this flag if you would like to output
                        coverages of individual 'splits', rather than their
                        'parent' contig coverages.
  --report-contigs      By default this program reports sequences and their
                        coverages for 'splits'. By using this flag, you can
                        report contig sequences and coverages instead. For
                        obvious reasons, you can't use this flag with
                        `--splits-mode` flag.
  --use-Q2Q3-coverages  By default this program reports the mean coverage of a
                        split (or contig, see --report-contigs) for each
                        sample. By using this flag, you can report the mean
                        Q2Q3 coverage by excluding 25 percent of the
                        nucleotide positions with the smallest coverage
                        values, and 25 percent of the nucleotide positions
                        with the largest coverage values. The hope is that
                        this removes 'outlier' positions resulting from non-
                        specific mapping, etc. that skew the mean coverage
                        estimate.

anvi-export-splits-taxonomy [-h] -c CONTIGS_DB -o FILE_PATH

  -c CONTIGS_DB, --contigs-db CONTIGS_DB
                        Anvi'o contigs database generated by 'anvi-gen-
                        contigs-database'
  -o FILE_PATH, --output-file FILE_PATH
                        File path to store results.

anvi-export-state [-h] -p PAN_OR_PROFILE_DB [-o FILE_PATH]
                  [-s STATE_NAME] [--list-states]

  -p PAN_OR_PROFILE_DB, --pan-or-profile-db PAN_OR_PROFILE_DB
                        Anvi'o pan or profile database (and even genes
                        database in appropriate contexts).
  -o FILE_PATH, --output-file FILE_PATH
                        File path to store results.
  -s STATE_NAME, --state STATE_NAME
                        The state name to export.
  --list-states         Show available states and exit.

anvi-export-structures [-h] -s STRUCTURE_DB [-o DIR_PATH]
                       [--gene-caller-ids GENE_CALLER_IDS]
                       [--genes-of-interest FILE]

  -s STRUCTURE_DB, --structure-db STRUCTURE_DB
                        Anvi'o structure database.
  -o DIR_PATH, --output-dir DIR_PATH
                        Directory path for output files
  --gene-caller-ids GENE_CALLER_IDS
                        Gene caller ids. Multiple of them can be declared
                        separated by a delimiter (the default is a comma). In
                        anvi-gen-variability-profile, if you declare nothing
                        you will get all genes matching your other filtering
                        criteria. In other programs, you may get everything,
                        nothing, or an error. It really depends on the
                        situation. Fortunately, mistakes are cheap, so it's
                        worth a try.
  --genes-of-interest FILE
                        A file with anvi'o gene caller IDs. There should be
                        only one column in the file, and each line should
                        correspond to a unique gene caller id (without a
                        column header).

anvi-export-table [-h] [--table TABLE_NAME] [-l] [-f FIELDS]
                  [-o FILE_PATH]
                  DB

  DB                    Anvi'o database to read from.

  --table TABLE_NAME    Table name to export.
  -l, --list            Gives a list of tables in a database and quits. If a
                        table is already declared this time it lists all the
                        fields in a given table, in case you would to export
                        only a specific list of fields from the table using
                        --fields parameter.
  -f FIELD(S), --fields FIELD(S)
                        Fields to report. Use --list-tables parameter with a
                        table name to see available fields You can list fields
                        using this notation: --fields 'field_1, field_2, ...
                        field_N'.
  -o FILE_PATH, --output-file FILE_PATH
                        File path to store results.

anvi-gen-contigs-database [-h] -f FASTA [-n PROJECT_NAME]
                          [-o DB_FILE_PATH] [--description TEXT_FILE]
                          [-L INT] [-K INT] [--skip-gene-calling]
                          [--prodigal-translation-table INT]
                          [--external-gene-calls GENE-CALLS]
                          [--ignore-internal-stop-codons]
                          [--skip-predict-frame]
                          [--skip-mindful-splitting]

  -f FASTA, --contigs-fasta FASTA
                        The FASTA file that contains reference sequences you
                        mapped your samples against. This could be a reference
                        genome, or contigs from your assembler. Contig names
                        in this file must match to those in other input files.
                        If there is a problem anvi'o will gracefully complain
                        about it.
  -n PROJECT_NAME, --project-name PROJECT_NAME
                        Name of the project. Please choose a short but
                        descriptive name (so anvi'o can use it whenever she
                        needs to name an output file, or add a new table in a
                        database, or name her first born).

  -o DB_FILE_PATH, --output-db-path DB_FILE_PATH
                        Output file path for the new database.
  --description TEXT_FILE
                        A plain text file that contains some description about
                        the project. You can use Markdwon syntax. The
                        description text will be rendered and shown in all
                        relevant interfaces, including the anvi'o interactive
                        interface, or anvi'o summary outputs.
  -L INT, --split-length INT
                        Anvi'o splits very long contigs into smaller pieces,
                        without actually splitting them for real. These
                        'virtual' splits improve the efficacy of the
                        visualization step, and changing the split size gives
                        freedom to the user to adjust the resolution of their
                        display when necessary. The default value is (20000).
                        If you are planning to use your contigs database for
                        metagenomic binning, we advise you to not go below
                        10,000 (since the lower the split size is, the more
                        items to show in the display, and decreasing the split
                        size does not really help much to binning). But if you
                        are thinking about using this parameter for ad hoc
                        investigations other than binning, you should ignore
                        our advice, and set the split size as low as you want.
                        If you do not want your contigs to be split, you can
                        set the split size to '0' or any other negative
                        integer (lots of unnecessary freedom here, enjoy!).
  -K INT, --kmer-size INT
                        K-mer size for k-mer frequency calculations. The
                        default k-mer size for composition-based analyses is
                        4, historically. Although tetra-nucleotide frequencies
                        seem to offer the the sweet spot of sensitivity,
                        information density, and manageable number of
                        dimensions for clustering approaches, you are welcome
                        to experiment (but maybe you should leave it as is for
                        your first set of analyses).
  --skip-mindful-splitting
                        By default, anvi'o attempts to prevent soft-splitting
                        large contigs by cutting proper gene calls to make
                        sure a single gene is not broken into multiple splits.
                        This requires a careful examination of where genes
                        start and end, and to find best locations to split
                        contigs with respect to this information. So, when the
                        user asks for a split size of, say, 1,000, it serves
                        as a mere suggestion. When this flag is used, anvi'o
                        does what the user wants and creates splits at desired
                        lengths (although some functionality may become
                        unavailable for the projects that rely on a contigs
                        database that is initiated this way).

  --skip-gene-calling   By default, generating an anvi'o contigs database
                        includes the identification of open reading frames in
                        contigs by running a bacterial gene caller. Declaring
                        this flag will by-pass that process. If you prefer,
                        you can later import your own gene calling results
                        into the database.
  --prodigal-translation-table INT
                        This is a parameter to pass to the Prodigal for a
                        specific translation table. This parameter corresponds
                        to the parameter `-g` in Prodigal, the default value
                        of which is 11 (so if you do not set anything, it will
                        be set to 11 in Prodigal runtime. Please refer to the
                        Prodigal documentation to determine what is the right
                        translation table for you if you think you need it.)
  --external-gene-calls GENE-CALLS
                        A TAB-delimited file to define external gene calls.
                        The file must have these columns: 'gene_callers_id' (a
                        unique integer number for each gene call, start from
                        1), 'contig' (the contig name the gene call is found),
                        'start' (start position, integer), 'stop' (stop
                        position, integer), 'direction' (the direction of the
                        gene open reading frame; can be 'f' or 'r'), 'partial'
                        (whether it is a complete gene call, or a partial one;
                        must be 1 for partial calls, and 0 for complete
                        calls), 'call_type' (1 if it is coding, 2 if it is
                        noncoding, or 3 if it is unknown (only gene calls with
                        call_type = 1 will have amino acid sequences
                        translated)), 'source' (the gene caller), and
                        'version' (the version of the gene caller, i.e.,
                        v2.6.7 or v1.0). An additional 'optional' column is
                        'aa_sequence' to explicitly define the amino acid
                        seqeuence of a gene call so anvi'o does not attempt to
                        translate the DNA sequence itself. An EXAMPLE FILE
                        (with the optional 'aa_sequence' column (so feel free
                        to take it out for your own case)) can be found at the
                        URL https://bit.ly/2qEEHuQ. If you are providing
                        external gene calls, please also see the flag `--skip-
                        predict-frame`.
  --ignore-internal-stop-codons
                        This is only relevant when you have an external gene
                        calls file. If anvi'o figures out that your custom
                        gene calls result in amino acid sequences with stop
                        codons in the middle, it will complain about it. You
                        can use this flag to tell anvi'o to don't check for
                        internal stop codons, Even though this shouldn't
                        happen in theory, we understand that it almost always
                        does. In these cases, anvi'o understands that
                        sometimes we don't want to care, and will not judge
                        you. Instead, it will replace every stop codon residue
                        in the amino acid sequence with an 'X' character.
                        Please let us know if you used this and things failed,
                        so we can tell you that you shouldn't have really used
                        it if you didn't like failures at the first place
                        (smiley).
  --skip-predict-frame  When you have provide an external gene calls file,
                        anvi'o will predict the correct frame for gene calls
                        as best as it can by using a previously-generated
                        Markov model that is trained using the uniprot50
                        database (see this for details:
                        https://github.com/merenlab/anvio/pull/1428), UNLESS
                        there is an `aa_sequence` entry for a given gene call
                        in the external gene calls file. Please note that
                        PREDICTING FRAMES MAY CHANGE START/STOP POSITIONS OF
                        YOUR GENE CALLS SLIGHTLY, if those that are in the
                        external gene calls file are not describing proper
                        gene calls according to the model. If you use this
                        flag, anvi'o will not rely on any model and will
                        attempt to translate your DNA sequences by solely
                        relying upon start/stop positions in the file, but it
                        will complain about sequences start/stop positions of
                        which are not divisible by 3.

anvi-gen-fixation-index-matrix [-h] [-p PROFILE_DB] [-c CONTIGS_DB]
                               [-s STRUCTURE_DB] [-V VARIABILITY_TABLE]
                               [-C COLLECTION_NAME] [-b BIN_NAME]
                               [--splits-of-interest FILE]
                               [--genes-of-interest FILE]
                               [--gene-caller-ids GENE_CALLER_IDS]
                               [--only-if-structure]
                               [--samples-of-interest FILE]
                               [--engine ENGINE]
                               [--min-coverage-in-each-sample INT]
                               [-o FIXATION_INDICES] [--keep-negatives]

  -p PROFILE_DB, --profile-db PROFILE_DB
                        Anvi'o profile database
  -c CONTIGS_DB, --contigs-db CONTIGS_DB
                        Anvi'o contigs database generated by 'anvi-gen-
                        contigs-database'
  -s STRUCTURE_DB, --structure-db STRUCTURE_DB
                        Anvi'o structure database.
  -V VARIABILITY_TABLE, --variability-profile VARIABILITY_TABLE
                        The output of anvi-gen-variability-profile, or a
                        different variant-calling output that has been
                        converted to the anvi'o format.

  -C COLLECTION_NAME, --collection-name COLLECTION_NAME
                        Collection name.
  -b BIN_NAME, --bin-id BIN_NAME
                        Bin name you are interested in.

  --splits-of-interest FILE
                        A file with split names. There should be only one
                        column in the file, and each line should correspond to
                        a unique split name.

  --genes-of-interest FILE
                        A file with anvi'o gene caller IDs. There should be
                        only one column in the file, and each line should
                        correspond to a unique gene caller id (without a
                        column header).
  --gene-caller-ids GENE_CALLER_IDS
                        Gene caller ids. Multiple of them can be declared
                        separated by a delimiter (the default is a comma). In
                        anvi-gen-variability-profile, if you declare nothing
                        you will get all genes matching your other filtering
                        criteria. In other programs, you may get everything,
                        nothing, or an error. It really depends on the
                        situation. Fortunately, mistakes are cheap, so it's
                        worth a try.
  --only-if-structure   If provided, your genes of interest will be further
                        subset to only include genes with structures in your
                        structure database, and therefore must be supplied in
                        conjunction with a structure database, i.e. `-s
                        <your_structure_database>`. If you did not specify
                        genes of interest, ALL genes will be subset to those
                        that have structures.

  --samples-of-interest FILE
                        A file with samples names. There should be only one
                        column in the file, and each line should correspond to
                        a unique sample name (without a column header).

  --engine ENGINE       Variability engine. The default is 'NT'.

  --min-coverage-in-each-sample INT
                        Minimum coverage of a given variable nucleotide
                        position in all samples. If a nucleotide position is
                        covered less than this value even in one sample, it
                        will be removed from the analysis. Default is 0.

  -o FIXATION_INDICES, --output-file FIXATION_INDICES
                        File path to store results.

  --keep-negatives      Negative numbers are theoretically possible, and are
                        sometimes interpreted as out-breeding. By default, we
                        set negative numbers to 0 so the results are
                        reflective of a standard distance metric. Provide this
                        flag if you would prefer otherwise.

anvi-gen-gene-consensus-sequences [-h] -p PROFILE_DB -c CONTIGS_DB
                                  [--gene-caller-ids GENE_CALLER_IDS]
                                  [--genes-of-interest FILE]
                                  [--samples-of-interest FILE]
                                  [-o FILE_PATH] [--tab-delimited]
                                  [--engine ENGINE] [--contigs-mode]
                                  [--quince-mode] [--compress-samples]

  --compress-samples    Normally all samples with variation will have their
                        own consensus sequence. If this flag is provided, the
                        coverages from each sample of interest will be summed
                        and only a single consenus sequence for each
                        gene/contig will be output.

  -p PROFILE_DB, --profile-db PROFILE_DB
                        Anvi'o profile database
  -c CONTIGS_DB, --contigs-db CONTIGS_DB
                        Anvi'o contigs database generated by 'anvi-gen-
                        contigs-database'

  --gene-caller-ids GENE_CALLER_IDS
                        Gene caller ids. Multiple of them can be declared
                        separated by a delimiter (the default is a comma). In
                        anvi-gen-variability-profile, if you declare nothing
                        you will get all genes matching your other filtering
                        criteria. In other programs, you may get everything,
                        nothing, or an error. It really depends on the
                        situation. Fortunately, mistakes are cheap, so it's
                        worth a try.
  --genes-of-interest FILE
                        A file with anvi'o gene caller IDs. There should be
                        only one column in the file, and each line should
                        correspond to a unique gene caller id (without a
                        column header).
  --samples-of-interest FILE
                        A file with samples names. There should be only one
                        column in the file, and each line should correspond to
                        a unique sample name (without a column header).

  -o FILE_PATH, --output-file FILE_PATH
                        The output file name. The boring default is
                        "genes.fa". You can change the output file format to a
                        TAB-delimited file using teh flag `--tab-delimited`,
                        in which case please do not forget to change the file
                        name, too.
  --tab-delimited       Use the TAB-delimited format for the output file.

  --engine ENGINE       Variability engine. The default is 'NT'.
  --contigs-mode        Use this flag to output consensus sequences of
                        contigs, instead of the default, which is genes
  --quince-mode         Use this flag to output consensus sequences for cases
                        even where there is no variability

anvi-gen-gene-level-stats-databases [-h] -c CONTIGS_DB -p PROFILE_DB
                                    [-C COLLECTION_NAME] [-b BIN_NAME]
                                    [-B FILE_PATH]
                                    [--zeros-are-outliers]
                                    [--outliers-threshold NUM]
                                    [--just-do-it] [--inseq-stats]

  -c CONTIGS_DB, --contigs-db CONTIGS_DB
                        Anvi'o contigs database generated by 'anvi-gen-
                        contigs-database'
  -p PROFILE_DB, --profile-db PROFILE_DB
                        Anvi'o profile database

  -C COLLECTION_NAME, --collection-name COLLECTION_NAME
                        Collection name.
  -b BIN_NAME, --bin-id BIN_NAME
                        Bin name you are interested in.
  -B FILE_PATH, --bin-ids-file FILE_PATH
                        Text file for bins (each line should be a unique bin
                        id).

  --zeros-are-outliers  If you want all zero coverage positions to be treated
                        like outliers then use this flag. The reason to treat
                        zero coverage as outliers is because when mapping
                        reads to a reference we could get many zero positions
                        due to accessory genes. These positions then skew the
                        average values that we compute.
  --outliers-threshold NUM
                        Threshold to use for the outlier detection. The
                        default value is '1.5'. Absolute deviation around the
                        median is used. To read more about the method please
                        refer to: 'How to Detect and Handle Outliers' by Boris
                        Iglewicz and David Hoaglin
                        (doi:10.1016/j.jesp.2013.03.013).

  --just-do-it          Don't bother me with questions or warnings, just do
                        it.

  --inseq-stats         Provide if working with INSeq/Tn-Seq genomic data.
                        With this, all gene level coverage stats will be
                        calculated using INSeq/Tn-Seq statistical methods.

anvi-gen-genomes-storage [-h] [-e FILE_PATH] [-i FILE_PATH]
                         [--gene-caller GENE-CALLER] -o GENOMES_STORAGE

  -e FILE_PATH, --external-genomes FILE_PATH
                        A two-column TAB-delimited flat text file that lists
                        anvi'o contigs databases. The first item in the header
                        line should read 'name', and the second should read
                        'contigs_db_path'. Each line in the file should
                        describe a single entry, where the first column is the
                        name of the genome (or MAG), and the second column is
                        the anvi'o contigs database generated for this genome.

  -i FILE_PATH, --internal-genomes FILE_PATH
                        A five-column TAB-delimited flat text file. The header
                        line must contain these columns: 'name', 'bin_id',
                        'collection_id', 'profile_db_path', 'contigs_db_path'.
                        Each line should list a single entry, where 'name' can
                        be any name to describe the anvi'o bin identified as
                        'bin_id' that is stored in a collection.

  --gene-caller GENE-CALLER
                        The gene caller to utilize. Anvi'o supports multiple
                        gene callers, and some operations (including this one)
                        requires an explicit mentioning of which one to use.
                        The default is 'prodigal', but it will not be enough
                        if you if you were a rebel and have used `--external-
                        gene-callers` or something.

  -o GENOMES_STORAGE, --output-file GENOMES_STORAGE
                        File path to store results.

anvi-gen-network [-h] -p PROFILE_DB -c CONTIGS_DB
                 [--annotation-source SOURCE NAME] [-l]

  -p PROFILE_DB, --profile-db PROFILE_DB
                        Anvi'o profile database
  -c CONTIGS_DB, --contigs-db CONTIGS_DB
                        Anvi'o contigs database generated by 'anvi-gen-
                        contigs-database'
  --annotation-source SOURCE NAME
                        Get functional annotations for a specific annotation
                        source. You can use the flag '--list-annotation-
                        sources' to learn about what sources are available.
  -l, --list-annotation-sources
                        List available functional annotation sources.

anvi-gen-phylogenomic-tree [-h] -f FASTA -o FILE_PATH
                           [--program PROGRAM_NAME]

  -f FASTA, --fasta-file FASTA
                        A FASTA-formatted input file

  -o FILE_PATH, --output-file FILE_PATH
                        File path to store results.

  --program PROGRAM_NAME
                        Program name.

anvi-gen-structure-database [-h] -c CONTIGS_DB [--pdb-db PDB_DB]
                            [--genes-of-interest FILE]
                            [--gene-caller-ids GENE_CALLER_IDS]
                            [-o DB_FILE_PATH] [--dump-dir DUMP_DIR]
                            [--num-models NUM_MODELS]
                            [--deviation DEVIATION]
                            [--modeller-database MODELLER_DATABASE]
                            [--scoring-method SCORING_METHOD]
                            [--very-fast]
                            [--percent-identical-cutoff PERCENT_IDENTICAL_CUTOFF]
                            [--max-number-templates MAX_NUMBER_TEMPLATES]
                            [--skip-DSSP]
                            [--modeller-executable MODELLER_EXECUTABLE]
                            [--offline-mode] [-T NUM_THREADS]
                            [--write-buffer-size-per-thread INT]

  -c CONTIGS_DB, --contigs-db CONTIGS_DB
                        Anvi'o contigs database generated by 'anvi-gen-
                        contigs-database'
  --pdb-db PDB_DB       By default, this program accesses the structure files
                        it needs from an internal anvi'o database that can be
                        set up with anvi-setup-pdb-database. If a required
                        structure is not in this database, it will instead be
                        downloaded from the RCSB PDB server. This parameter
                        exists only if a) you created a database and b) it
                        exists in a custom location. In this case, please
                        provide that path here. Otherwise we vibing.

  --genes-of-interest FILE
                        A file with anvi'o gene caller IDs. There should be
                        only one column in the file, and each line should
                        correspond to a unique gene caller id (without a
                        column header).
  --gene-caller-ids GENE_CALLER_IDS
                        Gene caller ids. Multiple of them can be declared
                        separated by a delimiter (the default is a comma). In
                        anvi-gen-variability-profile, if you declare nothing
                        you will get all genes matching your other filtering
                        criteria. In other programs, you may get everything,
                        nothing, or an error. It really depends on the
                        situation. Fortunately, mistakes are cheap, so it's
                        worth a try.

  -o DB_FILE_PATH, --output-db-path DB_FILE_PATH
                        Output file path for the new database.
  --dump-dir DUMP_DIR   Modeling and annotating structures requires a lot of
                        moving parts, each which have their own outputs. The
                        output of this program is a structure database
                        containing the pertinent results of this computation,
                        however a lot of stuff doesn't make the cut. By
                        providing a directory for this parameter you will get,
                        in addition to the structure database, a directory
                        containing the raw output for everything.

  --num-models NUM_MODELS, -N NUM_MODELS
                        This parameter determines the number of predicted
                        structures that are solved for a given protein. The
                        original atomic positions for each model are perturbed
                        by an amount defined by --deviation, which leads to
                        differences between each model. Therefore, whichever
                        of the N models is chosen to be the "best" model is
                        more likely to be accurate when --num-models is high,
                        since more of the solution space is searched. It
                        should be kept in mind that the largest determinant of
                        a model's accuracy is determined by the protein
                        templates used, so no need to go overboard with an
                        excessively large --num-models. The default is 1.
  --deviation DEVIATION, -d DEVIATION
                        Deviation (angstroms)
  --modeller-database MODELLER_DATABASE, -D MODELLER_DATABASE
                        Which database do you want to search the structures
                        of? Default is "pdb_95". If you have your own database
                        it must have either the extension .bin or .pir. If you
                        don't have a database or don't know what this means,
                        don't worry, we will both inform you and take care of
                        you.
  --scoring-method SCORING_METHOD, -b SCORING_METHOD
                        How should the best model be decided? The metric used
                        could be any of GA341_score, DOPE_score, and molpdf.
                        GA341 is an absolute measure, where a good model will
                        have a score near 1.0, whereas anything below 0.6 can
                        be considered bad. DOPE and molpdf scores are relative
                        energy measures, where lower scores are better. DOPE
                        has been generally shown to be a better distinguisher
                        between good and bad models than molpdf. By default,
                        DOPE is used. To learn more see the MODELLER tutorial:
                        https://salilab.org/modeller/tutorial/basic.html.
  --very-fast           If provided, a very fast optimization is done for each
                        model at the cost of accuracy. It is recommended to
                        use a --num-models of 1, since the optimization is so
                        crude that all models will likely converge to the same
                        solution.
  --percent-identical-cutoff PERCENT_IDENTICAL_CUTOFF, -p PERCENT_IDENTICAL_CUTOFF
                        If a protein in the database has a proper percent
                        identity to the gene of interest that is greater than
                        or equal to --percent-identical-cutoff, then it is
                        used as a template. Otherwise it is not. Here we
                        define proper percent identity as the percentage of
                        amino acids in the gene of interest that are identical
                        to an entry in the database given the sequence length
                        of the gene of interest. For example, if there is 100%
                        identity between the gene of interest and the template
                        over the length of the alignment, but the alignment
                        length is only half of the gene of interest sequence
                        length, then the proper percent identical is 50%.
                        (This helps us avoid the inflation of identity scores
                        due to only partially good matches). The default is
                        30.
  --max-number-templates MAX_NUMBER_TEMPLATES, -t MAX_NUMBER_TEMPLATES
                        Generally speaking it is best to use as many templates
                        as possible given that they have high proper percent
                        identity to the gene of interest. Taken from https://s
                        alilab.org/modeller/methenz/andras/node4.html: 'The
                        use of several templates generally increases the model
                        accuracy. One strength of MODELLER is that it can
                        combine information from multiple template structures,
                        in two ways. First, multiple template structures may
                        be aligned with different domains of the target, with
                        little overlap between them, in which case the
                        modeling procedure can construct a homology-based
                        model of the whole target sequence. Second, the
                        template structures may be aligned with the same part
                        of the target, in which case the modeling procedure is
                        likely to automatically build the model on the locally
                        best template [43,44]. In general, it is frequently
                        beneficial to include in the modeling process all the
                        templates that differ substantially from each other,
                        if they share approximately the same overall
                        similarity to the target sequence.' The default is 5.

  --skip-DSSP           Dictionary of Secondary Structure of Proteins (DSSP)
                        is a program that takes as its input a protein
                        structure file and outputs predicted secondary
                        structure (alpha helix, beta strand, etc.), measures
                        of solvent accessibility, and hydrogen bonds for each
                        residue in the protein. If for some reason you don't
                        want this, provide this flag.
  --modeller-executable MODELLER_EXECUTABLE
                        The MODELLER program to use. For example, `mod9.19`.
                        Anvi'o will try and find it if not provided
  --offline-mode        Anvi'o first tries to obtain template structures from
                        a database (see --pdb-db for details). If the
                        requested template does not exist in the database, its
                        structure will be downloaded from the RCSB PDB server.
                        However, if you don't have access to internet, or hate
                        the RCSB PDB, provide this flag so that all operations
                        of this program remain offline. If the template
                        structure is not in the database, then no template
                        structure for you.
  -T NUM_THREADS, --num-threads NUM_THREADS
                        Maximum number of threads to use for multithreading
                        whenever possible. Very conservatively, the default is
                        1. It is a good idea to not exceed the number of CPUs
                        / cores on your system. Plus, please be careful with
                        this option if you are running your commands on a SGE
                        --if you are clusterizing your runs, and asking for
                        multiple threads to use, you may deplete your
                        resources very fast.
  --write-buffer-size-per-thread INT
                        How many items should be kept in memory before they
                        are written do the disk. The default is 25 per thread.
                        So a single-threaded job would have a write buffer
                        size of 25, whereas a job with 4 threads would have a
                        write buffer size of 4*25. The larger the buffer size,
                        the less frequent the program will access to the disk,
                        yet the more memory will be consumed since the
                        processed items will be cleared off the memory only
                        after they are written to the disk. The default buffer
                        size will likely work for most cases. Please keep an
                        eye on the memory usage output to make sure the memory
                        use never exceeds the size of the physical memory. If
                        --num-threads is 1, this parameter is ignored because
                        the DB is written to after each gene

anvi-gen-variability-matrix [-h] -c CONTIGS_DB --splits-of-interest
                            FILE [--samples-of-interest FILE]
                            [--num-positions-from-each-split INT]
                            [-m INT] [-r RATIO] [-o FILE_PATH]
                            SUMMARY_DICT

  SUMMARY_DICT          Summary file

  -c CONTIGS_DB, --contigs-db CONTIGS_DB
                        Anvi'o contigs database generated by 'anvi-gen-
                        contigs-database'
  --splits-of-interest FILE
                        A file with split names. There should be only one
                        column in the file, and each line should correspond to
                        a unique split name.
  --samples-of-interest FILE
                        A file with samples names. There should be only one
                        column in the file, and each line should correspond to
                        a unique sample name (without a column header).
  --num-positions-from-each-split INT
                        Each split may have one or more variable positions. By
                        default, anvi'o will report every SNV position found
                        in a given split. This parameter will help you to
                        define a cutoff for the maximum number of SNVs to be
                        reported from a split (if the number of SNVs is more
                        than the number you declare using this parameter, the
                        positions will be randomly subsampled).
  -m INT, --min-scatter INT
                        This one is tricky. If you have N samples in your
                        dataset, a given variable position x in one of your
                        splits can split your N samples into `t` groups based
                        on the identity of the variation they harbor at
                        position x. For instance, `t` would have been 1, if
                        all samples had the same type of variation at position
                        x (which would not be very interesting, because in
                        this case position x would have zero contribution to a
                        deeper understanding of how these samples differ based
                        on variability. When `t` > 1, it would mean that
                        identities at position x across samples do differ. But
                        how much scattering occurs based on position x when t
                        > 1? If t=2, how many samples ended in each group?
                        Obviously, even distribution of samples across groups
                        may tell us something different than uneven
                        distribution of samples across groups. So, this
                        parameter filters out any x if 'the number of samples
                        in the second largest group' (=scatter) is less than
                        -m. Here is an example: let's assume you have 7
                        samples. While 5 of those have AG, 2 of them have TC
                        at position x. This would mean scatter of x is 2. If
                        you set -m to 2, this position would not be reported
                        in your output matrix. The default value for -m is 0,
                        which means every `x` found in the database and
                        survived previous filtering criteria will be reported.
                        Naturally, -m cannot be more than half of the number
                        of samples. Please refer to the user documentation if
                        this is confusing.
  -r RATIO, --min-ratio-of-competings-nts RATIO
                        Minimum ratio of the competing nucleotides at a given
                        position. Default is 0.
  -o FILE_PATH, --output-file FILE_PATH
                        File path to store results.

anvi-gen-variability-network [-h] -i VARIABILITY_PROFILE
                             [-n NUM_POSITIONS] [-o FILE_PATH]

  -i VARIABILITY_PROFILE, --input-file VARIABILITY_PROFILE
                        The anvi'o variability profile. Please see `anvi-gen-
                        variability-profile` to generate one.
  -n NUM_POSITIONS, --max-num-unique-positions NUM_POSITIONS
                        Maximum number of unique positions to be used in the
                        network. This may be one way to avoid extremely large
                        network descriptions that would defeat the purpose of
                        a quick visualization. If there are more unique
                        positions in the variability profile, the program will
                        randomly select a subset of them to match the `max-
                        num-unique-positions`. The default is 0, which means
                        all positions should be reported. Remember that the
                        number of nodes in the network will also depend on the
                        number of samples described in the variability
                        profile.
  -o FILE_PATH, --output-file FILE_PATH
                        File path to store results.

anvi-gen-variability-profile [-h] -p PROFILE_DB -c CONTIGS_DB
                             [-s STRUCTURE_DB] [-C COLLECTION_NAME]
                             [-b BIN_NAME] [--splits-of-interest FILE]
                             [--genes-of-interest FILE]
                             [--gene-caller-ids GENE_CALLER_IDS]
                             [--only-if-structure]
                             [--samples-of-interest FILE]
                             [--engine ENGINE] [--skip-synonymity]
                             [--num-positions-from-each-split INT]
                             [-r FLOAT] [-z FLOAT] [-j FLOAT]
                             [-a FLOAT] [-x NUM_SAMPLES]
                             [--min-coverage-in-each-sample INT]
                             [--quince-mode] [-o VARIABILITY_PROFILE]
                             [--include-contig-names]
                             [--include-split-names]
                             [--compute-gene-coverage-stats]

  -p PROFILE_DB, --profile-db PROFILE_DB
                        Anvi'o profile database
  -c CONTIGS_DB, --contigs-db CONTIGS_DB
                        Anvi'o contigs database generated by 'anvi-gen-
                        contigs-database'
  -s STRUCTURE_DB, --structure-db STRUCTURE_DB
                        Anvi'o structure database.

  -C COLLECTION_NAME, --collection-name COLLECTION_NAME
                        Collection name.
  -b BIN_NAME, --bin-id BIN_NAME
                        Bin name you are interested in.

  --splits-of-interest FILE
                        A file with split names. There should be only one
                        column in the file, and each line should correspond to
                        a unique split name.

  --genes-of-interest FILE
                        A file with anvi'o gene caller IDs. There should be
                        only one column in the file, and each line should
                        correspond to a unique gene caller id (without a
                        column header).
  --gene-caller-ids GENE_CALLER_IDS
                        Gene caller ids. Multiple of them can be declared
                        separated by a delimiter (the default is a comma). In
                        anvi-gen-variability-profile, if you declare nothing
                        you will get all genes matching your other filtering
                        criteria. In other programs, you may get everything,
                        nothing, or an error. It really depends on the
                        situation. Fortunately, mistakes are cheap, so it's
                        worth a try.
  --only-if-structure   If provided, your genes of interest will be further
                        subset to only include genes with structures in your
                        structure database, and therefore must be supplied in
                        conjunction with a structure database, i.e. `-s
                        <your_structure_database>`. If you did not specify
                        genes of interest, ALL genes will be subset to those
                        that have structures.

  --samples-of-interest FILE
                        A file with samples names. There should be only one
                        column in the file, and each line should correspond to
                        a unique sample name (without a column header).

  --engine ENGINE       Variability engine. The default is 'NT'.
  --skip-synonymity     Computing synonymity can be an expensive operation for
                        large data sets. Provide this flag to skip computing
                        synonymity. It only makes sense to provide this flag
                        when using --engine CDN.

  --num-positions-from-each-split INT
                        Each split may have one or more variable positions. By
                        default, anvi'o will report every SNV position found
                        in a given split. This parameter will help you to
                        define a cutoff for the maximum number of SNVs to be
                        reported from a split (if the number of SNVs is more
                        than the number you declare using this parameter, the
                        positions will be randomly subsampled).
  -r FLOAT, --min-departure-from-reference FLOAT
                        Takes a value between 0 and 1, where 1 is maximum
                        divergence from the reference. Default is 0.000000.
                        The reference here observation that corresponds to a
                        given position in the mapped context.
  -z FLOAT, --max-departure-from-reference FLOAT
                        Similar to '--min-departure-from-reference', but
                        defines an upper limit for divergence. The default is
                        1.000000.
  -j FLOAT, --min-departure-from-consensus FLOAT
                        Takes a value between 0 and 1, where 1 is maximum
                        divergence from the consensus for a given position.
                        The default is 0.000000. The consensus is the most
                        frequent observation at a given position.
  -a FLOAT, --max-departure-from-consensus FLOAT
                        Similar to '--min-departure-from-consensus', but
                        defines an upper limit for divergence. The default is
                        1.000000.
  -x NUM_SAMPLES, --min-occurrence NUM_SAMPLES
                        Minimum number of samples a nucleotide position should
                        be reported as variable. Default is 1. If you set it
                        to 2, for instance, each eligible variable position
                        will be expected to appear in at least two samples,
                        which will reduce the impact of stochastic, or
                        unintelligible variable positions.
  --min-coverage-in-each-sample INT
                        Minimum coverage of a given variable nucleotide
                        position in all samples. If a nucleotide position is
                        covered less than this value even in one sample, it
                        will be removed from the analysis. Default is 0.
  --quince-mode         The default behavior is to report base frequencies of
                        nucleotide positions only if there is any variation
                        reported during profiling (which by default uses some
                        heuristics to minimize the impact of error-driven
                        variation). So, if there are 10 samples, and a given
                        position has been reported as a variable site during
                        profiling in only one of those samples, there will be
                        no information will be stored in the database for the
                        remaining 9. When this flag is used, we go back to
                        each sample, and report base frequencies for each
                        sample at this position even if they do not vary. It
                        will take considerably longer to report when this flag
                        is on, and the use of it will increase the file size
                        dramatically, however it is inevitable for some
                        statistical approaches (as well as for some beautiful
                        visualizations).

  -o VARIABILITY_PROFILE, --output-file VARIABILITY_PROFILE
                        File path to store results.
  --include-contig-names
                        Use this flag if you would like contig names for each
                        variable position to be included in the output file as
                        a column. By default, we do not include contig names
                        since they can practically double the output file size
                        without any actual benefit in most cases.
  --include-split-names
                        Use this flag if you would like split names for each
                        variable position to be included in the output file as
                        a column.
  --compute-gene-coverage-stats
                        If provided, gene coverage statistics will be appended
                        for each entry in variability report. This is very
                        useful information, but will not be included by
                        default because it is an expensive operation, and may
                        take some additional time.

anvi-get-aa-counts [-h] -c CONTIGS_DB [-o FILE_PATH] [-p PROFILE_DB]
                   [-C COLLECTION_NAME] [-B FILE_PATH]
                   [--contigs-of-interest FILE]
                   [--gene-caller-ids GENE_CALLER_IDS]

  -c CONTIGS_DB, --contigs-db CONTIGS_DB
                        Anvi'o contigs database generated by 'anvi-gen-
                        contigs-database'
  -o FILE_PATH, --output-file FILE_PATH
                        File path to store results.

  -p PROFILE_DB, --profile-db PROFILE_DB
                        Anvi'o profile database
  -C COLLECTION_NAME, --collection-name COLLECTION_NAME
                        Collection name.
  -B FILE_PATH, --bin-ids-file FILE_PATH
                        Text file for bins (each line should be a unique bin
                        id).

  --contigs-of-interest FILE
                        A file with contig names. There should be only one
                        column in the file, and each line should correspond to
                        a unique split name.

  --gene-caller-ids GENE_CALLER_IDS
                        Gene caller ids. Multiple of them can be declared
                        separated by a delimiter (the default is a comma). In
                        anvi-gen-variability-profile, if you declare nothing
                        you will get all genes matching your other filtering
                        criteria. In other programs, you may get everything,
                        nothing, or an error. It really depends on the
                        situation. Fortunately, mistakes are cheap, so it's
                        worth a try.

anvi-get-codon-frequencies [-h] -c CONTIGS_DB
                           [--gene-caller-id GENE_CALLER_ID]
                           [--return-AA-frequencies-instead] -o
                           FILE_PATH [--percent-normalize]
                           [--merens-codon-normalization]

  -c CONTIGS_DB, --contigs-db CONTIGS_DB
                        Anvi'o contigs database generated by 'anvi-gen-
                        contigs-database'

  --gene-caller-id GENE_CALLER_ID
                        OK. You can declare a single gene caller ID if you
                        wish, in which case anvi'o would only return results
                        for a single gene call. If you don't declare anything,
                        well, you must be prepared to brace yourself if you
                        are working with a very large contigs database with
                        hundreds of thousands of genes.
  --return-AA-frequencies-instead
                        By default, anvi'o will return codon frequencies (as
                        the name suggests), but you can ask for amino acid
                        frequencies instead, simply because you always need
                        more data and more stuff. You're lucky this time, but
                        is there an end to this? Will you ever be satisfied
                        with what you have? Anvi'o needs answers.
  -o FILE_PATH, --output-file FILE_PATH
                        File path to store results.
  --percent-normalize   Instead of actual counts, report percent-normalized
                        frequencies per gene (because you are too lazy to do
                        things the proper way in R).
  --merens-codon-normalization
                        This is a flag to percent normalize codon frequenies
                        within those that encode for the same amino acid. It
                        is different from the flag --percent-normalize, since
                        it does not percent normalize frequencies of codons
                        within a gene based on all codon frequencies. Clearly
                        this flag is not applicable if you wish to work with
                        boring amino acids. WHO WORKS WITH AMINO ACIDS
                        ANYWAYS.

anvi-get-enriched-functions-per-pan-group [-h] -p PAN_DB
                                          [-g GENOMES_STORAGE]
                                          [--category-variable CATEGORY]
                                          [--annotation-source SOURCE NAME]
                                          [-l]
                                          [--include-gc-identity-as-function]
                                          -o FILE_PATH [-F FILE]
                                          [--exclude-ungrouped]
                                          [--just-do-it]

  -p PAN_DB, --pan-db PAN_DB
                        Anvi'o pan database
  -g GENOMES_STORAGE, --genomes-storage GENOMES_STORAGE
                        Anvi'o genomes storage file

  --category-variable CATEGORY
                        The additional layers data variable name that divides
                        layers into multiple categories.
  --annotation-source SOURCE NAME
                        Get functional annotations for a specific annotation
                        source. You can use the flag '--list-annotation-
                        sources' to learn about what sources are available.
  -l, --list-annotation-sources
                        List available functional annotation sources.
  --include-gc-identity-as-function
                        This is an option that asks anvi'o to treat gene
                        cluster names as functions. By doing so, you are in
                        fact creating an opportunity to study functional
                        enrichment statistics for each gene cluster
                        independently. For instance, multiple gene clusters
                        may have the same COG function. But if you wish to use
                        the same enrichment analysis in your pangenome without
                        collapsing multiple gene clusters into a single
                        function name, you can use this flag, and ask for
                        'IDENTITY' as the functional annotation source.

  -o FILE_PATH, --output-file FILE_PATH
                        File path to store results.
  -F FILE, --functional-occurrence-table-output FILE
                        Saves the occurrence frequency information for
                        functions in genomes in a TAB-delimited format. A file
                        name must be provided. To learn more about how the
                        functional occurrence is computed, please refer to the
                        tutorial.

  --exclude-ungrouped   Use this flag if you want anvi'o to ignore genomes
                        with no value set for the catergory variable (which
                        you specified using --category-variable). By default
                        all variables with no value will be considered as a
                        single group when preforming the statistical analysis.

  --just-do-it          Don't bother me with questions or warnings, just do
                        it.

anvi-get-sequences-for-gene-calls [-h] [-c CONTIGS_DB]
                                  [--gene-caller-ids GENE_CALLER_IDS]
                                  [--delimiter CHAR]
                                  [--report-extended-deflines]
                                  [--wrap WRAP] [--export-gff3]
                                  [--get-aa-sequences]
                                  [-g GENOMES_STORAGE]
                                  [-G GENOME_NAMES] -o FILE_PATH

  -c CONTIGS_DB, --contigs-db CONTIGS_DB
                        Anvi'o contigs database generated by 'anvi-gen-
                        contigs-database'
  --gene-caller-ids GENE_CALLER_IDS
                        Gene caller ids. Multiple of them can be declared
                        separated by a delimiter (the default is a comma). In
                        anvi-gen-variability-profile, if you declare nothing
                        you will get all genes matching your other filtering
                        criteria. In other programs, you may get everything,
                        nothing, or an error. It really depends on the
                        situation. Fortunately, mistakes are cheap, so it's
                        worth a try.
  --delimiter CHAR      The delimiter to parse multiple input terms. The
                        default is ','.
  --report-extended-deflines
                        When declared, the deflines in the resulting FASTA
                        file will contain more information.
  --wrap WRAP           When to wrap sequences when storing them in a FASTA
                        file. The default is '120'. A value of '0' would be
                        equivalent to 'do not wrap'.
  --export-gff3         If this is true, the output file will be in GFF3
                        format.
  --get-aa-sequences    Store amino acid sequences instead.

  -g GENOMES_STORAGE, --genomes-storage GENOMES_STORAGE
                        Anvi'o genomes storage file
  -G GENOME_NAMES, --genome-names GENOME_NAMES
                        Genome names to 'focus'. You can use this parameter to
                        limit the genomes included in your analysis. You can
                        provide these names as a comma-separated list of
                        names, or you can put them in a file, where you have a
                        single genome name in each line, and provide the file
                        path.

  -o FILE_PATH, --output-file FILE_PATH
                        File path to store results.

anvi-get-sequences-for-gene-clusters [-h] -p PAN_DB
                                     [-g GENOMES_STORAGE] [-o FASTA]
                                     [--report-DNA-sequences]
                                     [--gene-cluster-id GENE_CLUSTER_ID]
                                     [--gene-cluster-ids-file FILE_PATH]
                                     [-C COLLECTION_NAME] [-b BIN_NAME]
                                     [--min-num-genomes-gene-cluster-occurs INTEGER]
                                     [--max-num-genomes-gene-cluster-occurs INTEGER]
                                     [--min-num-genes-from-each-genome INTEGER]
                                     [--max-num-genes-from-each-genome INTEGER]
                                     [--max-num-gene-clusters-missing-from-genome INTEGER]
                                     [--min-functional-homogeneity-index FLOAT]
                                     [--max-functional-homogeneity-index FLOAT]
                                     [--min-geometric-homogeneity-index FLOAT]
                                     [--max-geometric-homogeneity-index FLOAT]
                                     [--min-combined-homogeneity-index FLOAT]
                                     [--max-combined-homogeneity-index FLOAT]
                                     [--add-into-items-additional-data-table NAME]
                                     [--list-collections] [--list-bins]
                                     [--concatenate-gene-clusters]
                                     [--partition-file FILE_PATH]
                                     [--separator STRING]
                                     [--align-with ALIGNER]
                                     [--list-aligners] [--just-do-it]
                                     [--dry-run]

  -p PAN_DB, --pan-db PAN_DB
                        Anvi'o pan database
  -g GENOMES_STORAGE, --genomes-storage GENOMES_STORAGE
                        Anvi'o genomes storage file

  -o FASTA, --output-file FASTA
                        File path to store results.
  --report-DNA-sequences
                        By default, this program reports amino acid sequences.
                        Use this flag to report DNA sequences instead.

  --gene-cluster-id GENE_CLUSTER_ID
                        Gene cluster ID you are interested in.
  --gene-cluster-ids-file FILE_PATH
                        Text file for gene clusters (each line should contain
                        be a unique gene cluster id).
  -C COLLECTION_NAME, --collection-name COLLECTION_NAME
                        Collection name.
  -b BIN_NAME, --bin-id BIN_NAME
                        Bin name you are interested in.

  --min-num-genomes-gene-cluster-occurs INTEGER
                        This filter will remove gene clusters from your
                        report. Let's assume you have 100 genomes in your pan
                        genome analysis. You can use this parameter if you
                        want to work only with gene clusters that occur in at
                        least X number of genomes. If you say '--min-num-
                        genomes-gene-cluster-occurs 90', each gene cluster in
                        the analysis will be required at least to appear in 90
                        genomes. If a gene occurs in less than that number of
                        genomes, it simply will not be reported. This is
                        especially useful for phylogenomic analyses, where you
                        may want to only focus on gene clusters that are
                        prevalent across the set of genomes you wish to
                        analyze.
  --max-num-genomes-gene-cluster-occurs INTEGER
                        This filter will remove gene clusters from your
                        report. Let's assume you have 100 genomes in your pan
                        genome analysis. You can use this parameter if you
                        want to work only with gene clusters that occur in at
                        most X number of genomes. If you say '--max-num-
                        genomes-gene-cluster-occurs 1', you will get gene
                        clusters that are singletons. Combining this parameter
                        with --min-num-genomes-gene-cluster-occurs can give
                        you a very precise way to filter your gene clusters.
  --min-num-genes-from-each-genome INTEGER
                        This filter will remove gene clusters from your
                        report. If you say '--min-num-genes-from-each-genome
                        2', this filter will remove every gene cluster, to
                        which every genome in your analysis contributed less
                        than 2 genes. This can be useful to find out gene
                        clusters with many genes from many genomes (such as
                        conserved multi-copy genes within a clade).
  --max-num-genes-from-each-genome INTEGER
                        This filter will remove gene clusters from your
                        report. If you say '--max-num-genes-from-each-genome
                        1', every gene cluster that has more than one gene
                        from any genome that contributes to it will be removed
                        from your analysis. This could be useful to remove
                        gene clusters with paralogs from your report for
                        appropriate phylogenomic analyses. For instance, using
                        '--max-num-genes-from-each-genome 1' and 'min-num-
                        genomes-gene-cluster-occurs X' where X is the total
                        number of your genomes, would give you the single-copy
                        gene clusters in your pan genome.
  --max-num-gene-clusters-missing-from-genome INTEGER
                        This filter will remove genomes from your report. If
                        you have a list of gene cluster names, you can use
                        this parameter to omit any genome from your report if
                        it is missing more than a number of genes you desire.
                        For instance, if you have 100 genomes in your pan
                        genome, and you are interested in working only with
                        genomes that have all 5 specific gene clusters of your
                        choice, you can use '--max-num-gene-clusters-missing-
                        from-genome 4' to remove remove the bins that are
                        missing more than 4 of those 5 genes. This is
                        especially useful for phylogenomic analyses. Parameter
                        0 will remove any genome that is missing any of the
                        genes.
  --min-functional-homogeneity-index FLOAT
                        This filter will remove gene clusters from your
                        report. If you say '--min-functional-homogeneity-index
                        0.3', every gene cluster with a functional homogeneity
                        index less than 0.3 will be removed from your
                        analysis. This can be useful if you only want to look
                        at gene clusters that are highly conserved in
                        resulting function
  --max-functional-homogeneity-index FLOAT
                        This filter will remove gene clusters from your
                        report. If you say '--max-functional-homogeneity-index
                        0.5', every gene cluster with a functional homogeneity
                        index greater than 0.5 will be removed from your
                        analysis. This can be useful if you only want to look
                        at gene clusters that don't seem to be functionally
                        conserved
  --min-geometric-homogeneity-index FLOAT
                        This filter will remove gene clusters from your
                        report. If you say '--min-geometric-homogeneity-index
                        0.3', every gene cluster with a geometric homogeneity
                        index less than 0.3 will be removed from your
                        analysis. This can be useful if you only want to look
                        at gene clusters that are highly conserved in
                        geometric configuration
  --max-geometric-homogeneity-index FLOAT
                        This filter will remove gene clusters from your
                        report. If you say '--max-geometric-homogeneity-index
                        0.5', every gene cluster with a geometric homogeneity
                        index greater than 0.5 will be removed from your
                        analysis. This can be useful if you only want to look
                        at gene clusters that have many not be as conserved as
                        others
  --min-combined-homogeneity-index FLOAT
                        This filter will remove gene clusters from your
                        report. If you say '--min-combined-homogeneity-index
                        0.3', every gene cluster with a combined homogeneity
                        index less than 0.3 will be removed from your
                        analysis. This can be useful if you only want to look
                        at gene clusters that are highly conserved overall
  --max-combined-homogeneity-index FLOAT
                        This filter will remove gene clusters from your
                        report. If you say '--max-combined-homogeneity-index
                        0.5', every gene cluster with a combined homogeneity
                        index greater than 0.5 will be removed from your
                        analysis. This can be useful if you only want to look
                        at gene clusters that have many not be as conserved
                        overall as others
  --add-into-items-additional-data-table NAME
                        If you use any of the filters, and would like to add
                        the resulting item names into the items additional
                        data table of your database, you can use this
                        parameter. You will need to give a name for these
                        results to be saved. If the given name is already in
                        the items additional data table, its contents will be
                        replaced with the new one. Then you can run anvi-
                        interactive or anvi-display-pan to 'see' the results
                        of your filters.

  --list-collections    Show available collections and exit.
  --list-bins           List available bins in a collection and exit.

  --concatenate-gene-clusters
                        Concatenate output gene clusters in the same order to
                        create a multi-gene alignment output that is suitable
                        for phylogenomic analyses.
  --partition-file FILE_PATH
                        Some commonly used software for phylogenetic analyses
                        (e.g., IQ-TREE, RAxML, etc) allow users to
                        specify/test different substitution models for each
                        gene of a concatenated multiple sequence alignments.
                        For this, they use a special file format called a
                        'partition file', which indicates the site for each
                        gene in the alignment. You can use this parameter to
                        declare an output path for anvi'o to report a NEXUS
                        format partition file in addition to your FASTA output
                        (requested by Massimiliano Molari in #1333).
  --separator STRING    Characters to separate things (the default is whatever
                        is most suitable).
  --align-with ALIGNER  The multiple sequence alignment program to use when
                        multiple sequence alignment is necessary. To see all
                        available options, use the flag `--list-aligners`.
  --list-aligners       Show available software for multiple sequence
                        alignment.

  --just-do-it          Don't bother me with questions or warnings, just do
                        it.
  --dry-run             Don't do anything real. Test everything, and stop
                        right before wherever the developer said 'well, this
                        is enough testing', and decided to print out results.

anvi-get-sequences-for-hmm-hits [-h] [-c CONTIGS_DB] [-p PROFILE_DB]
                                [-C COLLECTION_NAME] [-b BIN_NAME]
                                [-B FILE_PATH] [-e FILE_PATH]
                                [-i FILE_PATH]
                                [--hmm-sources SOURCE NAME]
                                [--gene-names HMM HIT NAME] [-l] [-L]
                                [-o FILE_PATH] [--no-wrap]
                                [--get-aa-sequences]
                                [--concatenate-genes]
                                [--partition-file FILE_PATH]
                                [--max-num-genes-missing-from-bin INTEGER]
                                [--min-num-bins-gene-occurs INTEGER]
                                [--align-with ALIGNER]
                                [--separator STRING]
                                [--return-best-hit] [--just-do-it]

  -c CONTIGS_DB, --contigs-db CONTIGS_DB
                        Anvi'o contigs database generated by 'anvi-gen-
                        contigs-database'

  -p PROFILE_DB, --profile-db PROFILE_DB
                        Anvi'o profile database
  -C COLLECTION_NAME, --collection-name COLLECTION_NAME
                        Collection name.
  -b BIN_NAME, --bin-id BIN_NAME
                        Bin name you are interested in.
  -B FILE_PATH, --bin-ids-file FILE_PATH
                        Text file for bins (each line should be a unique bin
                        id).

  -e FILE_PATH, --external-genomes FILE_PATH
                        A two-column TAB-delimited flat text file that lists
                        anvi'o contigs databases. The first item in the header
                        line should read 'name', and the second should read
                        'contigs_db_path'. Each line in the file should
                        describe a single entry, where the first column is the
                        name of the genome (or MAG), and the second column is
                        the anvi'o contigs database generated for this genome.
  -i FILE_PATH, --internal-genomes FILE_PATH
                        A five-column TAB-delimited flat text file. The header
                        line must contain these columns: 'name', 'bin_id',
                        'collection_id', 'profile_db_path', 'contigs_db_path'.
                        Each line should list a single entry, where 'name' can
                        be any name to describe the anvi'o bin identified as
                        'bin_id' that is stored in a collection.

  --hmm-sources SOURCE NAME
                        Get sequences for a specific list of HMM sources. You
                        can list one or more sources by separating them from
                        each other with a comma character (i.e., '--hmm-
                        sources source_1,source_2,source_3'). If you would
                        like to see a list of available sources in the contigs
                        database, run this program with '--list-hmm-sources'
                        flag.
  --gene-names HMM HIT NAME
                        Get sequences only for a specific gene name. Each name
                        should be separated from each other by a comma
                        character. For instance, if you want to get back only
                        RecA and Ribosomal_L27, you can type '--gene-names
                        RecA,Ribosomal_L27', and you will get any and every
                        hit that matches these names in any source. If you
                        would like to see a list of available gene names, you
                        can use '--list-available-gene-names' flag.
  -l, --list-hmm-sources
                        List available HMM sources in the contigs database and
                        quit.
  -L, --list-available-gene-names
                        List available gene names in HMM sources selection and
                        quit.

  -o FILE_PATH, --output-file FILE_PATH
                        File path to store results.
  --no-wrap             Do not be wrap sequences nicely in the output file.

  --get-aa-sequences    Store amino acid sequences instead.

  --concatenate-genes   Concatenate output genes in the same order to create a
                        multi-gene alignment output that is suitable for
                        phylogenomic analyses.
  --partition-file FILE_PATH
                        Some commonly used software for phylogenetic analyses
                        (e.g., IQ-TREE, RAxML, etc) allow users to
                        specify/test different substitution models for each
                        gene of a concatenated multiple sequence alignments.
                        For this, they use a special file format called a
                        'partition file', which indicates the site for each
                        gene in the alignment. You can use this parameter to
                        declare an output path for anvi'o to report a NEXUS
                        format partition file in addition to your FASTA output
                        (requested by Massimiliano Molari in #1333).
  --max-num-genes-missing-from-bin INTEGER
                        This filter removes bins (or genomes) from your
                        analysis. If you have a list of gene names, you can
                        use this parameter to omit any bin (or external
                        genome) that is missing more than a number of genes
                        you desire. For instance, if you have 100 genome bins,
                        and you are interested in working with 5 ribosomal
                        proteins, you can use '--max-num-genes-missing-from-
                        bin 4' to remove the bins that are missing more than 4
                        of those 5 genes. This is especially useful for
                        phylogenomic analyses. Parameter 0 will remove any bin
                        that is missing any of the genes.
  --min-num-bins-gene-occurs INTEGER
                        This filter removes genes from your analysis. Let's
                        assume you have 100 bins to get sequences for HMM
                        hits. If you want to work only with genes among all
                        the hits that occur in at least X number of bins, and
                        discard the rest of them, you can use this flag. If
                        you say '--min-num-bins-gene-occurs 90', each gene in
                        the analysis will be required at least to appear in 90
                        genomes. If a gene occurs in less than that number of
                        genomes, it simply will not be reported. This is
                        especially useful for phylogenomic analyses, where you
                        may want to only focus on genes that are prevalent
                        across the set of genomes you wish to analyze.
  --align-with ALIGNER  The multiple sequence alignment program to use when
                        multiple sequence alignment is necessary. To see all
                        available options, use the flag `--list-aligners`.
  --separator STRING    A word that will be used to sepaate concatenated gene
                        sequences from each other (IF you are using this
                        program with `--concatenate-genes` flag). The default
                        is "XXX" for amino acid sequences, and "NNN" for DNA
                        sequences

  --return-best-hit     A bin may contain more than one hit for a gene name in
                        a given HMM source. For instance, there may be
                        multiple RecA hits in a genome bin from Campbell et
                        al.. Using this flag, will go through all of the gene
                        names that appear multiple times, and remove all but
                        the one with the lowest e-value. Good for whenever you
                        really need to get only a single copy of single-copy
                        core genes from a genome bin.
  --just-do-it          Don't bother me with questions or warnings, just do
                        it.

anvi-get-short-reads-from-bam [-h] -p PROFILE_DB -c CONTIGS_DB
                              [-C COLLECTION_NAME] [-b BIN_NAME]
                              [-B FILE_PATH] [-o FILE_PATH]
                              [-O FILENAME_PREFIX] [-X] [-Q]
                              BAM FILE[S] [BAM FILE[S] ...]

  BAM FILE[S]           BAM file(s) to access to recover short reads

  -p PROFILE_DB, --profile-db PROFILE_DB
                        Anvi'o profile database
  -c CONTIGS_DB, --contigs-db CONTIGS_DB
                        Anvi'o contigs database generated by 'anvi-gen-
                        contigs-database'
  -C COLLECTION_NAME, --collection-name COLLECTION_NAME
                        Collection name.
  -b BIN_NAME, --bin-id BIN_NAME
                        Bin name you are interested in.
  -B FILE_PATH, --bin-ids-file FILE_PATH
                        Text file for bins (each line should be a unique bin
                        id).
  -o FILE_PATH, --output-file FILE_PATH
                        File path to store results.
  -O FILENAME_PREFIX, --output-file-prefix FILENAME_PREFIX
                        A prefix to be used while naming the output files (no
                        file type extensions please; just a prefix).
  -X, --gzip-output     When declared, output file(s) will be gzip compressed
                        and the extension `.gz` will be added.
  -Q, --split-R1-and-R2
                        When declared, this program outputs 3 FASTA files for
                        paired-end reads: one for R1, one for R2, and one for
                        unpaired reads.

anvi-get-short-reads-mapping-to-a-gene [-h] -c CONTIGS_DB -i
                                       INPUT_BAMS) [INPUT_BAM(S ...]
                                       [--gene-caller-id GENE_CALLER_ID]
                                       [--genes-of-interest FILE]
                                       [--leeway LEEWAY_NTs]
                                       [-O FILENAME_PREFIX]

  -c CONTIGS_DB, --contigs-db CONTIGS_DB
                        Anvi'o contigs database generated by 'anvi-gen-
                        contigs-database'
  -i INPUT_BAM(S) [INPUT_BAM(S) ...], --input-files INPUT_BAM(S) [INPUT_BAM(S) ...]
                        Sorted and indexed BAM files to analyze. It is
                        essential that all BAM files must be the result of
                        mappings against the same contigs.

  --gene-caller-id GENE_CALLER_ID
                        A single gene id.
  --genes-of-interest FILE
                        A file with anvi'o gene caller IDs. There should be
                        only one column in the file, and each line should
                        correspond to a unique gene caller id (without a
                        column header).
  --leeway LEEWAY_NTs   The minimum number of nucleotides for a given short
                        read mapping into the gene context for it to be
                        reported. You must consider the length of your short
                        reads, as well as the length of the gene you are
                        targeting. The default is 100 nts.

  -O FILENAME_PREFIX, --output-file-prefix FILENAME_PREFIX
                        A prefix to be used while naming the output files (no
                        file type extensions please; just a prefix).

anvi-get-split-coverages [-h] -p PROFILE_DB [--split-name SPLIT_NAME]
                         [-c CONTIGS_DB] [-C COLLECTION_NAME]
                         [-b BIN_NAME] [-o FILE_PATH] [--list-splits]
                         [--list-collections] [--list-bins]

  -p PROFILE_DB, --profile-db PROFILE_DB
                        Anvi'o profile database

  --split-name SPLIT_NAME
                        Split name.

  -c CONTIGS_DB, --contigs-db CONTIGS_DB
                        Anvi'o contigs database generated by 'anvi-gen-
                        contigs-database'
  -C COLLECTION_NAME, --collection-name COLLECTION_NAME
                        Collection name.
  -b BIN_NAME, --bin-id BIN_NAME
                        Bin name you are interested in.

  -o FILE_PATH, --output-file FILE_PATH
                        File path to store results.
  --list-splits         When declared, the program will list split names in
                        the profile database and quite
  --list-collections    Show available collections and exit.
  --list-bins           List available bins in a collection and exit.

anvi-help [-h] [--requires] [--provides] [--name] [--report REPORT]
          search-term

  search-term           Find programs associated with this search term. if you
                        want all programs, use 'ALL'

  --requires, -r        Restrict to programs that require this search term
  --provides, -p        Restrict to programs that provide this search term
  --name, -n            Restrict to programs that contain this search term in
                        their name
  --report REPORT, -R REPORT
                        Which information would you like to be in the report?
                        Mess with this if you are disappointed with the
                        default. Possibles are Description, Tags, Requires,
                        Provides, Status, and Resources. Add multiple of them
                        with commas (no whitespace). For example, if you
                        wanted Description and Resources, you would put here
                        Description,Resources

anvi-import-collection [-h] [-c CONTIGS_DB] [-p PAN_OR_PROFILE_DB] -C
                       COLLECTION_NAME [--bins-info BINS_INFO]
                       [--contigs-mode]
                       TAB DELIMITED FILE

  TAB DELIMITED FILE    The input file that describes bin IDs for each split
                        or contig.

  -c CONTIGS_DB, --contigs-db CONTIGS_DB
                        Anvi'o contigs database generated by 'anvi-gen-
                        contigs-database'
  -p PAN_OR_PROFILE_DB, --pan-or-profile-db PAN_OR_PROFILE_DB
                        Anvi'o pan or profile database (and even genes
                        database in appropriate contexts).
  -C COLLECTION_NAME, --collection-name COLLECTION_NAME
                        Collection name.
  --bins-info BINS_INFO
                        Additional information for bins. The file must contain
                        three TAB-delimited columns, where the first one must
                        be a unique bin name, the second should be a 'source',
                        and the last one should be a 7 character HTML color
                        code (i.e., '#424242'). Source column must contain
                        information about the origin of the bin. If these bins
                        are automatically identified by a program like
                        CONCOCT, this column could contain the program name
                        and version. The source information will be associated
                        with the bin in various interfaces so in a sense it is
                        not *that* critical what it says there, but on the
                        other hand it is, becuse we should also think about
                        people who may end up having to work with what we put
                        together later.
  --contigs-mode        Use this flag if your binning was done on contigs
                        instead of splits. Please refer to the documentation
                        for help.

anvi-import-functions [-h] -c CONTIGS_DB [-p PARSER] -i FILES)
                      [FILE(S ...] [--drop-previous-annotations]

  -c CONTIGS_DB, --contigs-db CONTIGS_DB
                        Anvi'o contigs database generated by 'anvi-gen-
                        contigs-database'
  -p PARSER, --parser PARSER
                        Parser to make sense of the input files (if you need
                        one). There are currently 1 parsers readily available:
                        ['interproscan']. IT IS OK if you do not select a
                        parser if you have a standard, TAB-delimited input
                        file for funcitonal annotation of genes. If this is
                        not like 2018 and everything is already outdated, you
                        should be able to go to this address and learn
                        everything you need like a boss:
                        http://merenlab.org/2016/06/18/importing-functions/
  -i FILE(S) [FILE(S) ...], --input-files FILE(S) [FILE(S) ...]
                        One or more input files should follow this parameter.
                        The way these files will be handled will depend on
                        which parser you selected (if you did select any).
  --drop-previous-annotations
                        Use this flag if you want anvi'o to remove ALL
                        previous functional annotations for your genes, and
                        then import the new data. The default behavior will
                        add any annotation source into the db incrementally
                        unless there are already annotations from this source.
                        In which case, it will first remove previous
                        annotations for that source only (i.e., if source X is
                        both in the db and in the incoming annotations data,
                        it will replace the content of source X in the db).

anvi-import-items-order [-h] [-i FILE] [-p DB PATH] [--name ORDER NAME]
                        [--make-default]

  -i FILE, --input-order FILE
                        One of the two important things you must provide: the
                        file that contains the items order. The format of this
                        file is important. It can either contain a proper
                        newick tree in it, or a complete list of 'items' in
                        the target database where every line of the file is
                        simply an item name. If you are providing a newick
                        tree, the entire file should be a single line. I know
                        it sounds hard, but you seriously can do this.
  -p DB PATH, --db-path DB PATH
                        An appropriate anvi'o database to import the items
                        order. Currently it can be a profile, pan, or genes
                        database. But you should try your chances with other
                        kinds of databases for fun and games. Basically, if
                        the database contains an items order table, then
                        things will work. Otherwise, you will probably get
                        angry errors back in the worst case scenario.

  --name ORDER NAME     What should we call this order? Give it a concise,
                        single-word name.
  --make-default        You have the option to make this order the default
                        order in the database. Which means, anvi'o will use
                        this one when someone runs the program anvi-
                        interactive and presses draw. Big responsibility. But
                        if you have a 'default' state, it will not work
                        because the default items order in the state file
                        overwrites the one that comes from the database. So
                        not that big of a responsibility.

anvi-import-misc-data [-h] [-p PAN_OR_PROFILE_DB] [-c CONTIGS_DB] -t
                      NAME [-D NAME] [--transpose] [--just-do-it]
                      TAB DELIMITED FILE

  TAB DELIMITED FILE    The input file that describes an additional data for
                        layers or items. The expected format of this file
                        depends on the data table you will target. This can
                        feel complicated, but we promise it is not (you
                        probably have a PhD or working on one, so trust us
                        when we say "it is not complicated"). You need to read
                        the online documentation if this is your first time
                        with this.

  -p PAN_OR_PROFILE_DB, --pan-or-profile-db PAN_OR_PROFILE_DB
                        Anvi'o pan or profile database (and even genes
                        database in appropriate contexts).
  -c CONTIGS_DB, --contigs-db CONTIGS_DB
                        Anvi'o contigs database generated by 'anvi-gen-
                        contigs-database'

  -t NAME, --target-data-table NAME
                        The target table is the table you are interested in
                        accessing. Currently it can be 'items','layers', or
                        'layer_orders'. Please see most up-to-date online
                        documentation for more information.
  -D NAME, --target-data-group NAME
                        Data group to focus. Anvi'o misc data tables support
                        associating a set of data keys with a data group. If
                        you have no idea what this is, then probably you don't
                        need it, and anvi'o will take care of you. Note: this
                        flag is IRRELEVANT if you are working with additional
                        order data tables.
  --transpose           Transpose the input matrix file before clustering.
  --just-do-it          Don't bother me with questions or warnings, just do
                        it.

anvi-import-state [-h] -p PAN_OR_PROFILE_DB -s STATE_FILE -n STATE_NAME

  -p PAN_OR_PROFILE_DB, --pan-or-profile-db PAN_OR_PROFILE_DB
                        Anvi'o pan or profile database (and even genes
                        database in appropriate contexts).
  -s STATE_FILE, --state STATE_FILE
                        JSON serializable anvi'o state file.
  -n STATE_NAME, --name STATE_NAME
                        State name.

anvi-import-taxonomy-for-genes [-h] -c CONTIGS_DB [-p PARSER] -i FILES)
                               [FILE(S ...] [--just-do-it]

  -c CONTIGS_DB, --contigs-db CONTIGS_DB
                        Anvi'o contigs database generated by 'anvi-gen-
                        contigs-database'
  -p PARSER, --parser PARSER
                        Parser to make sense of the input files. There are 3
                        parsers readily available: ['default_matrix',
                        'centrifuge', 'kaiju']. It is OK if you do not select
                        a parser, but in that case there will be no additional
                        contigs available except the identification of single-
                        copy genes in your contigs for later use. Using a
                        parser will not prevent the analysis of single-copy
                        genes, but make anvio more powerful to help you make
                        sense of your results. Please see the documentation,
                        or get in touch with the developers if you have any
                        questions regarding parsers.
  -i FILE(S) [FILE(S) ...], --input-files FILE(S) [FILE(S) ...]
                        Input file(s) for selected parser. Each parser (except
                        "blank") requires input files to process that you
                        generate before running anvio. Please see the
                        documentation for details.
  --just-do-it          Don't bother me with questions or warnings, just do
                        it.

anvi-import-taxonomy-for-layers [-h] -p PROFILE_DB [--parser PARSER] -i
                                FILES) [FILE(S ...]
                                [--min-abundance PERCENTAGE]

  -p PROFILE_DB, --profile-db PROFILE_DB
                        Anvi'o profile database
  --parser PARSER       Parser to make sense of the input files. There are 1
                        parsers readily available: ['krakenuniq'].
  -i FILE(S) [FILE(S) ...], --input-files FILE(S) [FILE(S) ...]
                        Input file(s) for selected parser. Each parser (except
                        "blank") requires input files to process that you
                        generate before running anvio. Please see the
                        documentation for details.
  --min-abundance PERCENTAGE
                        Short read-based taxonomy can be extremely noisy.
                        Therefore, here we have defeault minimum percentage
                        cutoff of 0.1% to eliminate any taxon that occurs less
                        than that in a given input file.

anvi-init-bam [-h] [-o FILE_PATH] [-T NUM_THREADS] BAM_FILE

  BAM_FILE              BAM file to analyze

  -o FILE_PATH, --output-file FILE_PATH
                        File path to store results.
  -T NUM_THREADS, --num-threads NUM_THREADS
                        Maximum number of threads to use for multithreading
                        whenever possible. Very conservatively, the default is
                        1. It is a good idea to not exceed the number of CPUs
                        / cores on your system. Plus, please be careful with
                        this option if you are running your commands on a SGE
                        --if you are clusterizing your runs, and asking for
                        multiple threads to use, you may deplete your
                        resources very fast.

anvi-inspect [-h] [-p PROFILE_DB] [-c CONTIGS_DB]
             [--split-name SPLIT_NAME] [--hide-outlier-SNVs]
             [-I IP_ADDR] [-P INT] [--server-only] [--just-do-it]

  -p PROFILE_DB, --profile-db PROFILE_DB
                        Anvi'o profile database
  -c CONTIGS_DB, --contigs-db CONTIGS_DB
                        Anvi'o contigs database generated by 'anvi-gen-
                        contigs-database'
  --split-name SPLIT_NAME
                        Split name.

  --hide-outlier-SNVs   During profiling, anvi'o marks positions of single-
                        nucleotide variations (SNVs) that originate from
                        places in contigs where coverage values are a bit
                        'sketchy'. If you would like to avoid SNVs in those
                        positions of splits in applicable projects you can use
                        this flag, and the interface would hide SNVs that are
                        marked as 'outlier' (although it is clearly the best
                        to see everything, no one will judge you if you end up
                        using this flag) (plus, there may or may not be some
                        historical data on this here:
                        https://github.com/meren/anvio/issues/309).

  -I IP_ADDR, --ip-address IP_ADDR
                        IP address for the HTTP server. The default ip address
                        (0.0.0.0) should work just fine for most.
  -P INT, --port-number INT
                        Port number to use for anvi'o services. If nothing is
                        declared, anvi'o will try to find a suitable port
                        number, starting from the default port number, 8080.
  --server-only         The default behavior is to start the local server, and
                        fire up a browser that connects to the server. If you
                        have other plans, and want to start the server without
                        calling the browser, this is the flag you need.

  --just-do-it          Don't bother me with questions or warnings, just do
                        it.

anvi-interactive [-h] [-p PROFILE_DB] [-c CONTIGS_DB]
                 [-C COLLECTION_NAME] [--manual-mode] [-f FASTA]
                 [-d VIEW_DATA] [-t NEWICK] [--items-order FLAT_FILE]
                 [-V ADDITIONAL_VIEW] [-A ADDITIONAL_LAYERS]
                 [--gene-mode] [--inseq-stats] [-b BIN_NAME]
                 [--view NAME] [--title NAME]
                 [--taxonomic-level {t_domain,t_phylum,t_class,t_order,t_family,t_genus,t_species}]
                 [--split-hmm-layers] [--hide-outlier-SNVs]
                 [--state-autoload NAME] [--collection-autoload NAME]
                 [--export-svg FILE_PATH] [--show-views]
                 [--skip-check-names] [-o DIR_PATH] [--dry-run]
                 [--show-states] [--list-collections]
                 [--skip-init-functions] [--skip-auto-ordering]
                 [--distance DISTANCE_METRIC]
                 [--linkage LINKAGE_METHOD] [-I IP_ADDR] [-P INT]
                 [--browser-path PATH] [--read-only] [--server-only]
                 [--password-protected] [--user-server-shutdown]

  -p PROFILE_DB, --profile-db PROFILE_DB
                        Anvi'o profile database
  -c CONTIGS_DB, --contigs-db CONTIGS_DB
                        Anvi'o contigs database generated by 'anvi-gen-
                        contigs-database'
  -C COLLECTION_NAME, --collection-name COLLECTION_NAME
                        If you have a collection in your profile database, you
                        can use this flag to start the interactive interface
                        with a tree showing your bins in your collection,
                        instead of each split. This is very useful when you
                        have imported your external binning results into
                        anvi'o, and want to see the distribution of your bins
                        across samples. In these cases anvi'o will cluster
                        your bins and based on multiple metrics. Because this
                        particular clustering will be done on the fly within
                        anvi'o interactive class, you get to define a
                        disntance metric and a linkage method using --linkage
                        and --distance parameters if you want!

  --manual-mode         Using this flag, you can run the interactive interface
                        in an ad hoc manner using input files you curated
                        instead of standard output files generated by an
                        anvi'o run. In the manual mode you will be asked to
                        provide a profile database. In this mode a profile
                        database is only used to store 'state' of the
                        interactive interface so you can reload your visual
                        settings when you re-analyze the same files again. If
                        the profile database you provide does not exist,
                        anvi'o will create an empty one for you.
  -f FASTA, --fasta-file FASTA
                        A FASTA-formatted input file
  -d VIEW_DATA, --view-data VIEW_DATA
                        A TAB-delimited file for view data
  -t NEWICK, --tree NEWICK
                        NEWICK formatted tree structure
  --items-order FLAT_FILE
                        A flat file that contains the order of items you wish
                        the display using the interactive interface. You may
                        want to use this if you have a specific order of items
                        in your mind, and do not want to display a tree in the
                        middle (or simply you don't have one). The file format
                        is simple: each line should have an item name, and
                        there should be no header.

  -V ADDITIONAL_VIEW, --additional-view ADDITIONAL_VIEW
                        A TAB-delimited file for an additional view to be used
                        in the interface. This file should contain all split
                        names, and values for each of them in all samples.
                        Each column in this file must correspond to a sample
                        name. Content of this file will be called 'user_view',
                        which will be available as a new item in the 'views'
                        combo box in the interface
  -A ADDITIONAL_LAYERS, --additional-layers ADDITIONAL_LAYERS
                        A TAB-delimited file for additional layers for splits.
                        The first column of this file must be split names, and
                        the remaining columns should be unique attributes. The
                        file does not need to contain all split names, or
                        values for each split in every column. Anvi'o will try
                        to deal with missing data nicely. Each column in this
                        file will be visualized as a new layer in the tree.

  --gene-mode           Initiate the interactive interface in 'gene mode'. In
                        this mode, the items are genes (instead of splits of
                        contigs). The following views are available: detection
                        (the detection value of each gene in each sample). The
                        mean_coverage (the mean coverage of genes). The
                        non_outlier_mean_coverage (the mean coverage of the
                        non-outlier nucleotide positions of each gene in each
                        sample (median absolute deviation is used to remove
                        outliers per gene per sample)). The
                        non_outlier_coverage_std view (standard deviation of
                        the coverage of non-outlier positions of genes in
                        samples). You can also choose to order items and
                        layers according to each one of the aforementioned
                        views. In addition, all layer ordering that are
                        available in the regular mode (i.e. the full mode
                        where you have contigs/splits) are also available in
                        'gene mode', so that, for example, you can choose to
                        order the layers according to 'detection', and that
                        would be the order according to the detection values
                        of splits, whereas if you choose 'genes_detections'
                        then the order of layers would be according to the
                        detection values of genes. Inspection and sequence
                        functionality are available (through the right-click
                        menu), except now sequences are of the specific gene.
                        Inspection has now two options available: 'Inspect
                        Context', which brings you to the inspection page of
                        the split to which the gene belongs where the
                        inspected gene will be highlighted in yellow in the
                        bottom, and 'Inspect Gene', which opens the inspection
                        page only for the gene and 100 nts around each side of
                        it (the purpose of this option is to make the
                        inspection page load faster if you only want to look
                        at the nucleotide coverage of a specific gene).
                        NOTICE: You can't store states or collections in 'gene
                        mode'. However, you still can make fake selections,
                        and create fake bins for your viewing convenience only
                        (smiley). Search options are available, and you can
                        even search for functions if you have them in your
                        contigs database. ANOTHER NOTICE: loading this mode
                        might take a while if your bin has many genes, and
                        your profile database has many samples, this is
                        because the gene coverages stats are computed in an
                        ad-hoc manner when you load this mode, we know this is
                        not ideal and we plan to improve that (along with
                        other things). If you have suggestions/complaints
                        regarding this mode please comment on this github
                        issue: https://goo.gl/yHhRei. Please refer to the
                        online tutorial for more information.
  --inseq-stats         Provide if working with INSeq/Tn-Seq genomic data.
                        With this, all gene level coverage stats will be
                        calculated using INSeq/Tn-Seq statistical methods.
  -b BIN_NAME, --bin-id BIN_NAME
                        Bin name you are interested in.

  --view NAME           Start the interface with a pre-selected view. To see a
                        list of available views, use --show-views flag.
  --title NAME          Title for the interface. If you are working with a
                        RUNINFO dict, the title will be determined based on
                        information stored in that file. Regardless, you can
                        override that value using this parameter.
  --taxonomic-level {t_domain,t_phylum,t_class,t_order,t_family,t_genus,t_species}
                        The taxonomic level to use whenever relevant and/or
                        available. The default taxonomic level is t_genus, but
                        if you choose something specific, anvi'o will focus on
                        that whenever possible.
  --split-hmm-layers    When declared, this flag tells the interface to split
                        every gene found in HMM searches that were performed
                        against non-singlecopy gene HMM profiles into their
                        own layer. Please see the documentation for details.
  --hide-outlier-SNVs   During profiling, anvi'o marks positions of single-
                        nucleotide variations (SNVs) that originate from
                        places in contigs where coverage values are a bit
                        'sketchy'. If you would like to avoid SNVs in those
                        positions of splits in applicable projects you can use
                        this flag, and the interface would hide SNVs that are
                        marked as 'outlier' (although it is clearly the best
                        to see everything, no one will judge you if you end up
                        using this flag) (plus, there may or may not be some
                        historical data on this here:
                        https://github.com/meren/anvio/issues/309).
  --state-autoload NAME
                        Automatically load previous saved state and draw tree.
                        To see a list of available states, use --show-states
                        flag.
  --collection-autoload NAME
                        Automatically load a collection and draw tree. To see
                        a list of available collections, use --list-
                        collections flag.
  --export-svg FILE_PATH
                        The SVG output file path.

  --show-views          When declared, the program will show a list of
                        available views, and exit.
  --skip-check-names    For debugging purposes. You should never really need
                        it.
  -o DIR_PATH, --output-dir DIR_PATH
                        Directory path for output files
  --dry-run             Don't do anything real. Test everything, and stop
                        right before wherever the developer said 'well, this
                        is enough testing', and decided to print out results.
  --show-states         When declared the program will print all available
                        states and exit.
  --list-collections    Show available collections and exit.
  --skip-init-functions
                        When declared, function calls for genes will not be
                        initialized (therefore will be missing from all
                        relevant interfaces or output files). The use of this
                        flag may reduce the memory fingerprint and processing
                        time for large datasets.
  --skip-auto-ordering  When declared, the attempt to include automatically
                        generated orders of items based on additional data is
                        skipped. In case those buggers cause issues with your
                        data, and you still want to see your stuff and deal
                        with the other issue maybe later.
  --distance DISTANCE_METRIC
                        The distance metric for the hierarchical clustering.
                        Only relevant if you are running the interactive
                        interface in "collection" mode. The default is
                        "euclidean".
  --linkage LINKAGE_METHOD
                        The linkage method for the hierarchical clustering.
                        Only relevant if you are running the interactive
                        interface in "collection" mode. The default is "ward".

  -I IP_ADDR, --ip-address IP_ADDR
                        IP address for the HTTP server. The default ip address
                        (0.0.0.0) should work just fine for most.
  -P INT, --port-number INT
                        Port number to use for anvi'o services. If nothing is
                        declared, anvi'o will try to find a suitable port
                        number, starting from the default port number, 8080.
  --browser-path PATH   By default, anvi'o will use your default browser to
                        launch the interactive interface. If you would like to
                        use something else than your system default, you can
                        provide a full path for an alternative browser using
                        this parameter, and hope for the best. For instance we
                        are using this parameter to call Google's experimental
                        browser, Canary, which performs better with demanding
                        visualizations.
  --read-only           When the interactive interface is started with this
                        flag, all 'database write' operations will be
                        disabled.
  --server-only         The default behavior is to start the local server, and
                        fire up a browser that connects to the server. If you
                        have other plans, and want to start the server without
                        calling the browser, this is the flag you need.
  --password-protected  If this flag is set, command line tool will ask you to
                        enter a password and interactive interface will be
                        only accessible after entering same password. This
                        option is recommended for shared machines like
                        clusters or shared networks where computers are not
                        isolated.
  --user-server-shutdown
                        Allow users to shutdown an anvi'server via web
                        interface.

anvi-matrix-to-newick [-h] [-o FILE_PATH]
                      [--items-order-file FILE PATH] [--transpose]
                      [--distance DISTANCE_METRIC]
                      [--linkage LINKAGE_METHOD]
                      PATH

  PATH                  Input matrix

  -o FILE_PATH, --output-file FILE_PATH
                        File path to store results.
  --items-order-file FILE PATH
                        In addition to a newick formatted output file, you can
                        ask anvi'o to report the order of items in the
                        resulting tree in a separate file. The content of this
                        file will be a single-column item names the way they
                        are ordered in the output newick dendrogram.

  --transpose           Transpose the input matrix file before clustering.
  --distance DISTANCE_METRIC
                        The distance metric for the hierarchical clustering.
                        The default distance metric is 'euclidean'. You can
                        find the full list of distance metrics either by
                        making a mistake (such as entering a non-existent
                        distance metric and making anvi'o upset), or by taking
                        a look at the help menu of the
                        hierarchy.distance.pdist function in the scipy.cluster
                        module.
  --linkage LINKAGE_METHOD
                        The linkage method for the hierarchical clustering.
                        The default linkage method is 'ward', because that is
                        the best one. It really is. We talked to a lot of
                        people and they were all like 'this is the best one
                        available' and it is just all out there. Honestly it
                        is so good that we will build a wall around it and
                        make other linkage methods pay for it. But if you want
                        to see a full list of available ones you can check the
                        hierarcy.linkage function in the scipy.cluster module.
                        Up to you really. But then you can't use ward anymore,
                        and you would have to leave anvi'o right now.

anvi-mcg-classifier [-h] -p PROFILE_DB -c CONTIGS_DB
                    [-O FILENAME_PREFIX] [-C COLLECTION_NAME]
                    [-b BIN_NAME] [-B FILE_PATH]
                    [--exclude-samples FILE] [--include-samples FILE]
                    [--gen-figures] [--get-samples-stats-only] [-W]
                    [--alpha NUM] [--outliers-threshold NUM]
                    [--zeros-are-outliers]

  -p PROFILE_DB, --profile-db PROFILE_DB
                        Anvi'o profile database
  -c CONTIGS_DB, --contigs-db CONTIGS_DB
                        Anvi'o contigs database generated by 'anvi-gen-
                        contigs-database'

  -O FILENAME_PREFIX, --output-file-prefix FILENAME_PREFIX
                        A prefix to be used while naming the output files (no
                        file type extensions please; just a prefix).
  -C COLLECTION_NAME, --collection-name COLLECTION_NAME
                        Collection name.

  -b BIN_NAME, --bin-id BIN_NAME
                        Bin name you are interested in.
  -B FILE_PATH, --bin-ids-file FILE_PATH
                        Text file for bins (each line should be a unique bin
                        id).
  --exclude-samples FILE
                        List of samples to exclude for the analysis.
  --include-samples FILE
                        List of samples to include for the analysis.
  --gen-figures         For those of you who wish to dig deeper, a collection
                        of figures could be created to allow you to get
                        insight into how the classification was generated.
                        This is especially useful to identify cases in which
                        you shouldn't trust the classification (for example
                        due to a large number of outliers). NOTICE: if you ask
                        anvi'o to generate these figures then it will
                        significantly extend the execution time. To learn
                        about which figures are created and what they mean,
                        contact your nearest anvi'o developer, because
                        currently it is a well-hidden secret.
  --get-samples-stats-only
                        If you only wish to get statistics regarding the
                        occurrence of bins in samples, then use this flag.
                        Especially when dealing with many samples or large
                        genomes, gene stats could be a long time to compute.
                        By using this flag you could save a lot of computation
                        time.
  -W, --overwrite-output-destinations
                        Overwrite if the output files and/or directories
                        exist.

  --alpha NUM, --genome-detection-uncertainty NUM
                        Determines the range of sample detection values that
                        are considered negative, ambiguous or positive. Min of
                        0 and smaller than 0.5, default of 0.25. For exmaple
                        for the default samples with detection below 0.5-0.25
                        = 0.25 will be considered negative (i.e. donot contain
                        the genome), samples with detection between 0.25 and
                        0.75 would be ambiguous (and hence would not be used
                        for the classification), and samples with detection
                        above 0.75 would be considered positive (i.e. contain
                        the genome).
  --outliers-threshold NUM
                        Threshold to use for the outlier detection. The
                        default value is '1.5'. Absolute deviation around the
                        median is used. To read more about the method please
                        refer to: 'How to Detect and Handle Outliers' by Boris
                        Iglewicz and David Hoaglin
                        (doi:10.1016/j.jesp.2013.03.013).
  --zeros-are-outliers  If you want all zero coverage positions to be treated
                        like outliers then use this flag. The reason to treat
                        zero coverage as outliers is because when mapping
                        reads to a reference we could get many zero positions
                        due to accessory genes. These positions then skew the
                        average values that we compute.

anvi-merge [-h] -c CONTIGS_DB [-o DIR_PATH] [-S NAME]
           [--description TEXT_FILE] [--skip-hierarchical-clustering]
           [--enforce-hierarchical-clustering]
           [--distance DISTANCE_METRIC] [--linkage LINKAGE_METHOD] [-W]
           SINGLE_PROFILES) [SINGLE_PROFILE(S ...]

  SINGLE_PROFILE(S)     Anvo'o single profiles to merge

  -c CONTIGS_DB, --contigs-db CONTIGS_DB
                        Anvi'o contigs database generated by 'anvi-gen-
                        contigs-database'
  -o DIR_PATH, --output-dir DIR_PATH
                        Directory path for output files
  -S NAME, --sample-name NAME
                        It is important to set a sample name (using only ASCII
                        letters and digits and without spaces) that is unique
                        (considering all others). If you do not provide one,
                        anvi'o will try to make up one for you based on other
                        information, although, you should never let the
                        software to decide these things).
  --description TEXT_FILE
                        A plain text file that contains some description about
                        the project. You can use Markdwon syntax. The
                        description text will be rendered and shown in all
                        relevant interfaces, including the anvi'o interactive
                        interface, or anvi'o summary outputs.
  --skip-hierarchical-clustering
                        If you are not planning to use the interactive
                        interface (or if you have other means to add a tree of
                        contigs in the database) you may skip the step where
                        hierarchical clustering of your items are preformed
                        based on default clustering recipes matching to your
                        database type.
  --enforce-hierarchical-clustering
                        If you have more than 25,000 splits in your merged
                        profile, anvi-merge will automatically skip the
                        hierarchical clustering of splits (by setting --skip-
                        hierarchical-clustering flag on). This is due to the
                        fact that computational time required for hierarchical
                        clustering increases exponentially with the number of
                        items being clustered. Based on our experience we
                        decided that 25,000 splits is about the maximum we
                        should try. However, this is not a theoretical limit,
                        and you can overwrite this heuristic by using this
                        flag, which would tell anvi'o to attempt to cluster
                        splits regardless.
  --distance DISTANCE_METRIC
                        The distance metric for the hierarchical clustering.
                        If you do not use this flag, the default distance
                        metric will be used for each clustering configuration
                        which is "euclidean".
  --linkage LINKAGE_METHOD
                        The same story with the `--distance`, except, the
                        system default for this one is ward.
  -W, --overwrite-output-destinations
                        Overwrite if the output files and/or directories
                        exist.

anvi-merge-bins [-h] -p PAN_OR_PROFILE_DB [-C COLLECTION_NAME]
                [-b BIN NAMES] [-B BIN NAME] [--list-collections]
                [--list-bins]

  -p PAN_OR_PROFILE_DB, --pan-or-profile-db PAN_OR_PROFILE_DB
                        Anvi'o pan or profile database (and even genes
                        database in appropriate contexts).
  -C COLLECTION_NAME, --collection-name COLLECTION_NAME
                        Collection name.

  -b BIN NAMES, --bin-names-list BIN NAMES
                        Comma-separated list of bin names.
  -B BIN NAME, --new-bin-name BIN NAME
                        The new bin name.

  --list-collections    Show available collections and exit.
  --list-bins           List available bins in a collection and exit.

anvi-meta-pan-genome [-h] -p PAN_DB [-g GENOMES_STORAGE] [-i FILE]
                     [--fraction-of-median-coverage FLOAT]
                     [--min-detection FLOAT]

  -p PAN_DB, --pan-db PAN_DB
                        Anvi'o pan database
  -g GENOMES_STORAGE, --genomes-storage GENOMES_STORAGE
                        Anvi'o genomes storage file

  -i FILE, --internal-genomes FILE
                        A four-column TAB-delimited flat text file. This file
                        should be identical to the internal genomes file you
                        used for your pangenomics analysis. Anvi'o will use
                        this file to find all profile and contigs databases
                        that contain the information for each gene and genome
                        across metagenomes.

  --fraction-of-median-coverage FLOAT
                        The value set here will be used to remove a gene if
                        its total coverage across environments is less than
                        the median coverage of all genes multiplied by this
                        value. The default is 0.25, which means, if the median
                        total coverage of all genes across all samples is
                        100X, then, a gene with a total coverage of less than
                        25X across all samples will be assumed not a part of
                        the 'environmental core'.
  --min-detection FLOAT
                        For this entire thing to work, the genome you are
                        focusing on should be detected in at least one
                        metagenome. If that is not the case, it would mean
                        that you do not have any sample that represents the
                        niche for this organism (or you do not have enough
                        depth of coverage) to investigate the detection of
                        genes in the environment. By default, this script
                        requires at least '0.5' of the genome to be detected
                        in at least one metagenome. This parameter allows you
                        to change that. 0 would mean no detection test
                        required, 1 would mean the entire genome must be
                        detected.

anvi-migrate [-h] [--migrate-dbs-safely] [--migrate-dbs-quickly]
             [--just-do-it] [-t VERSION]
             DATABASES) [DATABASE(S ...]

  DATABASE(S)           Anvi'o database or config file for migration. You can
                        give many of them all at once. Running `anvi-migrate
                        *.db` in a directory will migrate all databases in
                        that directory.

  --migrate-dbs-safely  If you chose this, anvi'o will first create a copy of
                        your original database. If something goes wrong, it
                        will restore the original. If everything works, it
                        will remove the old copy. IF YOU HAVE DATABASES THAT
                        ARE VERY LARGE OR IF YOU ARE MIGRATING MANY MANY OF
                        THEM THIS OPTION WILL ADD A HUGE I/O BURDEN ON YOUR
                        SYSTEM. But still. Safety is safe.
  --migrate-dbs-quickly
                        If you chose this, anvi'o will migrate your databases
                        in place. It will be much faster (and arguably more
                        fun) than the safe option, but if something goes
                        wrong, you will lose data. During the first five years
                        of anvi'o development not a single user lost data
                        using our migration scripts as far as we know. But
                        there is always a first, and today might be your lucky
                        day.

  --just-do-it          Don't bother me with questions or warnings, just do
                        it.
  -t VERSION, --target-version VERSION
                        Anvi'o will stop upgrading your database when it
                        reaches to this version.

anvi-oligotype-linkmers [-h] -i LINKMER_REPORT -o DIR_PATH

  -i LINKMER_REPORT, --input-file LINKMER_REPORT
                        Output file of `anvi-report-linkmers`.
  -o DIR_PATH, --output-dir DIR_PATH
                        Directory path for output files

anvi-pan-genome [-h] -g GENOMES_STORAGE [-G GENOME_NAMES]
                [--skip-alignments] [--skip-homogeneity]
                [--quick-homogeneity] [--align-with ALIGNER]
                [--exclude-partial-gene-calls] [--use-ncbi-blast]
                [--minbit MINBIT] [--mcl-inflation INFLATION]
                [--min-occurrence NUM_OCCURRENCE]
                [--min-percent-identity PERCENT] [--sensitive]
                [-n PROJECT_NAME] [--description TEXT_FILE]
                [-o PAN_DB_DIR] [-W] [-T NUM_THREADS]
                [--skip-hierarchical-clustering]
                [--enforce-hierarchical-clustering]
                [--distance DISTANCE_METRIC] [--linkage LINKAGE_METHOD]

  -g GENOMES_STORAGE, --genomes-storage GENOMES_STORAGE
                        Anvi'o genomes storage file
  -G GENOME_NAMES, --genome-names GENOME_NAMES
                        Genome names to 'focus'. You can use this parameter to
                        limit the genomes included in your analysis. You can
                        provide these names as a comma-separated list of
                        names, or you can put them in a file, where you have a
                        single genome name in each line, and provide the file
                        path.

  --skip-alignments     By default, anvi'o attempts to align amino acid
                        sequences in each gene cluster using multiple sequnce
                        alignment via muscle. You can use this flag to skip
                        that step and be upset later.
  --skip-homogeneity    By default, anvi'o attempts to calculate homogeneity
                        values for every gene cluster, given that they are
                        aligned. You can use this flag to have anvi'o skip
                        homogeneity calculations. Anvi'o will ignore this flag
                        if you decide to skip alignments
  --quick-homogeneity   By default, anvi'o will use a homogeneity algorithm
                        that checks for horizontal and vertical geometric
                        homogeneity (along with functional). With this flag,
                        you can tell anvi'o to skip horizontal geometric
                        homogeneity calculations. It will be less accurate but
                        quicker. Anvi'o will ignore this flag if you skip
                        homogeneity calculations or alignments all together.
  --align-with ALIGNER  The multiple sequence alignment program to use when
                        multiple sequence alignment is necessary. To see all
                        available options, use the flag `--list-aligners`.
  --exclude-partial-gene-calls
                        By default, anvi'o includes all partial gene calls
                        from the analysis, which, in some cases, may inflate
                        the number of gene clusters identified and introduce
                        extra heterogeneity within those gene clusters. Using
                        this flag, you can request anvi'o to exclude partial
                        gene calls from the analysis (whether a gene call is
                        partial or not is an information that comes directly
                        from the gene caller used to identify genes during the
                        generation of the contigs database).
  --use-ncbi-blast      This program uses DIAMOND by default, however, if you
                        like, you can use good ol' blastp from NCBI instead.
  --minbit MINBIT       The minimum minbit value. The minbit heuristic
                        provides a mean to set a to eliminate weak matches
                        between two amino acid sequences. We learned it from
                        ITEP (Benedict MN et al, doi:10.1186/1471-2164-15-8),
                        which is a comprehensive analysis workflow for
                        pangenomes, and decided to use it in the anvi'o
                        pangenomic workflow, as well. Briefly, If you have two
                        amino acid sequences, 'A' and 'B', the minbit is
                        defined as 'BITSCORE(A, B) / MIN(BITSCORE(A, A),
                        BITSCORE(B, B))'. So the minbit score between two
                        sequences goes to 1 if they are very similar over the
                        entire length of the 'shorter' amino acid sequence,
                        and goes to 0 if (1) they match over a very short
                        stretch compared even to the length of the shorter
                        amino acid sequence or (2) the match betwen sequence
                        identity is low. The default is 0.5.
  --mcl-inflation INFLATION
                        MCL inflation parameter, that defines the sensitivity
                        of the algorithm during the identification of the gene
                        clusters. More information on this parameter and it's
                        effect on cluster granularity is here:
                        (http://micans.org/mcl/man/mclfaq.html#faq7.2). The
                        default is 2.
  --min-occurrence NUM_OCCURRENCE
                        Do you not want singletons?\ You don't? Well, this
                        parameter will help you get rid of them (along with
                        doubletons, if you want). Anvi'o will remove gene
                        clusters that occur less than the number you set using
                        this parameter from the analysis. The default is 1,
                        which means everything will be kept. If you want to
                        remove singletons, set it to 2, if you want to remove
                        doubletons as well, set it to 3, and so on.
  --min-percent-identity PERCENT
                        Minimum percent identity between the two amino acid
                        sequences for them to have an edge for MCL analysis.
                        This value will be used to filter hits from Diamond
                        search results. Because percent identity is not a
                        predictor of a good match (since it does not
                        communicate many other important factors such as the
                        alignment length between the two sequences and its
                        proportion to the entire length of those involved), we
                        suggest you rely on 'minbit' parameter. But you know
                        what? Maybe you shouldn't listen to anyone, and
                        experiment on your own! The default is 0 percent.
  --sensitive           DIAMOND sensitivity. With this flag you can instruct
                        DIAMOND to be 'sensitive', rather than 'fast' during
                        the search. It is likely the search will take
                        remarkably longer. But, hey, if you are doing it for
                        your final analysis, maybe it should take longer and
                        be more accurate. This flag is only relevant if you
                        are running DIAMOND.

  -n PROJECT_NAME, --project-name PROJECT_NAME
                        Name of the project. Please choose a short but
                        descriptive name (so anvi'o can use it whenever she
                        needs to name an output file, or add a new table in a
                        database, or name her first born).
  --description TEXT_FILE
                        A plain text file that contains some description about
                        the project. You can use Markdwon syntax. The
                        description text will be rendered and shown in all
                        relevant interfaces, including the anvi'o interactive
                        interface, or anvi'o summary outputs.
  -o PAN_DB_DIR, --output-dir PAN_DB_DIR
                        Directory path for output files
  -W, --overwrite-output-destinations
                        Overwrite if the output files and/or directories
                        exist.
  -T NUM_THREADS, --num-threads NUM_THREADS
                        Maximum number of threads to use for multithreading
                        whenever possible. Very conservatively, the default is
                        1. It is a good idea to not exceed the number of CPUs
                        / cores on your system. Plus, please be careful with
                        this option if you are running your commands on a SGE
                        --if you are clusterizing your runs, and asking for
                        multiple threads to use, you may deplete your
                        resources very fast.

  --skip-hierarchical-clustering
                        Anvi'o attempts to generate a hierarchical clustering
                        of your gene clusters once it identifies them so you
                        can use `anvi-display-pan` to play with it. But if you
                        want to skip this step, this is your flag.
  --enforce-hierarchical-clustering
                        If you want anvi'o to try to generate a hierarchical
                        clustering of your gene clusters even if the number of
                        gene clusters exceeds its suggested limit for
                        hierarchical clustering, you can use this flag to
                        enforce it. Are you are a rebel of some sorts? Or did
                        computers made you upset? Express your anger towards
                        machine using this flag.
  --distance DISTANCE_METRIC
                        The distance metric for the clustering of gene
                        clusters. If you do not use this flag, the default
                        distance metric will be used for each clustering
                        configuration which is "euclidean".
  --linkage LINKAGE_METHOD
                        The same story with the `--distance`, except, the
                        system default for this one is ward.

anvi-profile [-h] [-i INPUT_BAM] [-c CONTIGS_DB] [--blank-profile]
             [-o DIR_PATH] [-W] [-S NAME] [--report-variability-full]
             [--skip-SNV-profiling] [--skip-INDEL-profiling]
             [--profile-SCVs] [--min-percent-identity PERCENT_IDENTITY]
             [--description TEXT_FILE] [--cluster-contigs]
             [--skip-hierarchical-clustering]
             [--distance DISTANCE_METRIC] [--linkage LINKAGE_METHOD]
             [-M INT] [--max-contig-length INT] [-X INT] [-V INT]
             [--list-contigs] [--contigs-of-interest FILE]
             [-T NUM_THREADS] [--queue-size INT]
             [--write-buffer-size-per-thread INT] [--force-multi]

  -i INPUT_BAM, --input-file INPUT_BAM
                        Sorted and indexed BAM file to analyze. Takes a long
                        time depending on the length of the file and
                        parameters used for profiling.
  -c CONTIGS_DB, --contigs-db CONTIGS_DB
                        Anvi'o contigs database generated by 'anvi-gen-
                        contigs-database'
  --blank-profile       If you only have contig sequences, but no mapping data
                        (i.e., you found a genome and would like to take a
                        look from it), this flag will become very hand. After
                        creating a contigs database for your contigs, you can
                        create a blank anvi'o profile database to use anvi'o
                        interactive interface with that contigs database
                        without any mapping data.

  -o DIR_PATH, --output-dir DIR_PATH
                        Directory path for output files
  -W, --overwrite-output-destinations
                        Overwrite if the output files and/or directories
                        exist.
  -S NAME, --sample-name NAME
                        It is important to set a sample name (using only ASCII
                        letters and digits and without spaces) that is unique
                        (considering all others). If you do not provide one,
                        anvi'o will try to make up one for you based on other
                        information, although, you should never let the
                        software to decide these things).
  --report-variability-full
                        One of the things anvi-profile does is to store
                        information about variable nucleotide positions.
                        Usually it does not report every variable position,
                        since not every variable position is genuine
                        variation. Say, if you have 1,000 coverage, and all
                        nucleotides at that position are Ts and only one of
                        them is a C, the confidence of that C being a real
                        variation is quite low. anvi'o has a simple algorithm
                        in place to reduce the impact of noise. However, using
                        this flag you can disable it and ask profiler to
                        report every single variation (which may result in
                        very large output files and millions of reports, but
                        you are the boss). Do not forget to take a look at '--
                        min-coverage-for-variability' parameter
  --skip-SNV-profiling  By default, anvi'o characterizes single-nucleotide
                        variation in each sample. The use of this flag will
                        instruct profiler to skip that step. Please remember
                        that parameters and flags must be identical between
                        different profiles using the same contigs database for
                        them to merge properly.
  --skip-INDEL-profiling
                        The alignment of a read to a reference genome/sequence
                        can be imperfect, such that the read exhibits
                        insertions or deletions relative to the reference.
                        Anvi'o normally stores this information in the profile
                        database since the time taken and extra storage do not
                        amount to much, but if insist on not having this
                        information, you can skip storing this information by
                        providing this flag. Note: If --skip-SNV-profiling is
                        provided, --skip-INDEL-profiling will automatically be
                        enforced.
  --profile-SCVs        Anvi'o can perform accurate characterization of codon
                        frequencies in genes during profiling. While having
                        codon frequencies opens doors to powerful evolutionary
                        insights in downstream analyses, due to its
                        computational complexity, this feature comes 'off' by
                        default. Using this flag you can rise against the
                        authority, as you always should, and make anvi'o
                        profile codons.
  --min-percent-identity PERCENT_IDENTITY
                        Ignore any reads with a percent identity to the
                        reference less than this number, e.g. 95. If not
                        provided, all reads in the BAM file will be used (and
                        things will run faster).
  --description TEXT_FILE
                        A plain text file that contains some description about
                        the project. You can use Markdwon syntax. The
                        description text will be rendered and shown in all
                        relevant interfaces, including the anvi'o interactive
                        interface, or anvi'o summary outputs.

  --cluster-contigs     Single profiles are rarely used for genome binning or
                        visualization, and since clustering step increases the
                        profiling runtime for no good reason, the default
                        behavior is to not cluster contigs for individual
                        runs. However, if you are planning to do binning on
                        one sample, you must use this flag to tell anvi'o to
                        run cluster configurations for single runs on your
                        sample.
  --skip-hierarchical-clustering
                        If you are not planning to use the interactive
                        interface (or if you have other means to add a tree of
                        contigs in the database) you may skip the step where
                        hierarchical clustering of your items are preformed
                        based on default clustering recipes matching to your
                        database type.
  --distance DISTANCE_METRIC
                        The distance metric for the hierarchical clustering.
                        Only relevant if you are using `--cluster-contigs`
                        flag. The default is "euclidean".
  --linkage LINKAGE_METHOD
                        The linkage method for the hierarchical clustering.
                        Just like the distance metric this is only relevant if
                        you are using it with `--cluster-contigs` flag. The
                        default is "ward".

  -M INT, --min-contig-length INT
                        Minimum length of contigs in a BAM file to analyze.
                        The minimum length should be long enough for tetra-
                        nucleotide frequency analysis to be meaningful. There
                        is no way to define a golden number of minimum length
                        that would be applicable to genomes found in all
                        environments, but we chose the default to be 1000, and
                        have been happy with it. You are welcome to
                        experiment, but we advise to never go below 1,000. You
                        also should remember that the lower you go, the more
                        time it will take to analyze all contigs. You can use
                        --list-contigs parameter to have an idea how many
                        contigs would be discarded for a given M.
  --max-contig-length INT
                        Just like the minimum contig length parameter, but to
                        set a maximum. Basically this will remove any contig
                        longer than a certain value. Why would anyone need
                        this? Who knows. But if you ever do, it is here.
  -X INT, --min-mean-coverage INT
                        Minimum mean coverage for contigs to be kept in the
                        analysis. The default value is 0, which is for your
                        best interest if you are going to profile multiple BAM
                        files which are then going to be merged for a cross-
                        sectional or time series analysis. Do not change it if
                        you are not sure this is what you want to do.
  -V INT, --min-coverage-for-variability INT
                        Minimum coverage of a nucleotide position to be
                        subjected to SNV profiling. By default, anvi'o will
                        not attempt to make sense of variation in a given
                        nucleotide position if it is covered less than 10X.
                        You can change that minimum using this parameter.

  --list-contigs        When declared, the program will list contigs in the
                        BAM file and exit gracefully without any further
                        analysis.
  --contigs-of-interest FILE
                        It is possible to focus on only a set of contigs. If
                        you would like to do that and ignore the rest of the
                        contigs in your contigs database, use this parameter
                        with a flat file every line of which desribes a single
                        contig name.

  -T NUM_THREADS, --num-threads NUM_THREADS
                        Maximum number of threads to use for multithreading
                        whenever possible. Very conservatively, the default is
                        1. It is a good idea to not exceed the number of CPUs
                        / cores on your system. Plus, please be careful with
                        this option if you are running your commands on a SGE
                        --if you are clusterizing your runs, and asking for
                        multiple threads to use, you may deplete your
                        resources very fast.
  --queue-size INT      The queue size for worker threads to store data to
                        communicate to the main thread. The default is set by
                        the class based on the number of threads. If you have
                        *any* hesitation about whether you know what you are
                        doing, you should not change this value.
  --write-buffer-size-per-thread INT
                        How many items should be kept in memory before they
                        are written do the disk. The default is 500 per
                        thread. So a single-threaded job would have a write
                        buffer size of 500, whereas a job with 4 threads would
                        have a write buffer size of 4*500. The larger the
                        buffer size, the less frequent the program will access
                        to the disk, yet the more memory will be consumed
                        since the processed items will be cleared off the
                        memory only after they are written to the disk. The
                        default buffer size will likely work for most cases.
                        Please keep an eye on the memory usage output to make
                        sure the memory use never exceeds the size of the
                        physical memory.
  --force-multi         This is not useful to non-developers. It forces the
                        multi-process routine even when 1 thread is chosen.

anvi-push [-h] --user USERNAME [--api-url API_URL] -n PROJECT_NAME
          [-t NEWICK] [--items-order FLAT_FILE] [-f FASTA]
          [-d VIEW_DATA] [-A ADDITIONAL_LAYERS] [-s STATE]
          [--description TEXT_FILE] [--bins BINS_DATA]
          [--bins-info BINS_INFO] [--delete-if-exists]

  --user USERNAME       The user for an anvi'server.
  --api-url API_URL     Anvi'server url

  -n PROJECT_NAME, --project-name PROJECT_NAME
                        Name of the project. Please choose a short but
                        descriptive name (so anvi'o can use it whenever she
                        needs to name an output file, or add a new table in a
                        database, or name her first born).
  -t NEWICK, --tree NEWICK
                        NEWICK formatted tree structure
  --items-order FLAT_FILE
                        A flat file that contains the order of items you wish
                        the display using the interactive interface. You may
                        want to use this if you have a specific order of items
                        in your mind, and do not want to display a tree in the
                        middle (or simply you don't have one). The file format
                        is simple: each line should have an item name, and
                        there should be no header.
  -f FASTA, --fasta-file FASTA
                        A FASTA-formatted input file
  -d VIEW_DATA, --view-data VIEW_DATA
                        A TAB-delimited file for view data
  -A ADDITIONAL_LAYERS, --additional-layers ADDITIONAL_LAYERS
                        A TAB-delimited file for additional layers for splits.
                        The first column of this file must be split names, and
                        the remaining columns should be unique attributes. The
                        file does not need to contain all split names, or
                        values for each split in every column. Anvi'o will try
                        to deal with missing data nicely. Each column in this
                        file will be visualized as a new layer in the tree.
  -s STATE, --state STATE
                        State file, you can export states from database using
                        anvi-export-state program
  --description TEXT_FILE
                        A plain text file that contains some description about
                        the project. You can use Markdwon syntax. The
                        description text will be rendered and shown in all
                        relevant interfaces, including the anvi'o interactive
                        interface, or anvi'o summary outputs.
  --bins BINS_DATA      Tab-delimited file, first column contains tree leaves
                        (gene clusters, splits, contigs etc.) and second
                        column contains which Bin they belong.
  --bins-info BINS_INFO
                        Additional information for bins. The file must contain
                        three TAB-delimited columns, where the first one must
                        be a unique bin name, the second should be a 'source',
                        and the last one should be a 7 character HTML color
                        code (i.e., '#424242'). Source column must contain
                        information about the origin of the bin. If these bins
                        are automatically identified by a program like
                        CONCOCT, this column could contain the program name
                        and version. The source information will be associated
                        with the bin in various interfaces so in a sense it is
                        not *that* critical what it says there, but on the
                        other hand it is, becuse we should also think about
                        people who may end up having to work with what we put
                        together later.

  --delete-if-exists    Be bold (at your own risk), and delete if exists.

anvi-refine [-h] -p PROFILE_DB -c CONTIGS_DB [-C COLLECTION_NAME]
            [-b BIN_NAME] [-B FILE_PATH]
            [--find-from-split-name SPLIT_NAME] [-t NEWICK]
            [--skip-hierarchical-clustering] [--load-full-state]
            [-V ADDITIONAL_VIEW] [-A ADDITIONAL_LAYERS]
            [--split-hmm-layers]
            [--taxonomic-level {t_domain,t_phylum,t_class,t_order,t_family,t_genus,t_species}]
            [--hide-outlier-SNVs] [--title NAME]
            [--export-svg FILE_PATH] [--dry-run]
            [--skip-init-functions] [--skip-auto-ordering] [-I IP_ADDR]
            [-P INT] [--browser-path PATH] [--read-only]
            [--server-only] [--password-protected]

  -p PROFILE_DB, --profile-db PROFILE_DB
                        Anvi'o profile database
  -c CONTIGS_DB, --contigs-db CONTIGS_DB
                        Anvi'o contigs database generated by 'anvi-gen-
                        contigs-database'

  -C COLLECTION_NAME, --collection-name COLLECTION_NAME
                        Collection name.
  -b BIN_NAME, --bin-id BIN_NAME
                        Bin name you are interested in.
  -B FILE_PATH, --bin-ids-file FILE_PATH
                        Text file for bins (each line should be a unique bin
                        id).
  --find-from-split-name SPLIT_NAME
                        If you don't know the bin name you want to work with
                        but if you know the split name it contains you can use
                        this parameter to tell anvi'o the split name, and so
                        it can find the bin for you automatically. This is
                        something extremely difficult for anvi'o to do, but it
                        does it anyway because you.

  -t NEWICK, --tree NEWICK
                        NEWICK formatted tree structure
  --skip-hierarchical-clustering
                        Skip hierarchical clustering for the splits in the
                        refined bin, if you skip clustering you need to
                        provide your own newick formatted tree using --tree
                        parameter.
  --load-full-state     Often the minimum and maximum values defined for the
                        an entire profile database that contains all contigs
                        do not scale well when you wish to work with a single
                        bin in the refine mode. For this reason, the default
                        behavior of anvi-refine is to ignore min/max values
                        set in the default state. This flag is your way of
                        telling anvi'o to not do that, and load the state
                        stored in the profile database as is.
  -V ADDITIONAL_VIEW, --additional-view ADDITIONAL_VIEW
                        A TAB-delimited file for an additional view to be used
                        in the interface. This file should contain all split
                        names, and values for each of them in all samples.
                        Each column in this file must correspond to a sample
                        name. Content of this file will be called 'user_view',
                        which will be available as a new item in the 'views'
                        combo box in the interface
  -A ADDITIONAL_LAYERS, --additional-layers ADDITIONAL_LAYERS
                        A TAB-delimited file for additional layers for splits.
                        The first column of this file must be split names, and
                        the remaining columns should be unique attributes. The
                        file does not need to contain all split names, or
                        values for each split in every column. Anvi'o will try
                        to deal with missing data nicely. Each column in this
                        file will be visualized as a new layer in the tree.

  --split-hmm-layers    When declared, this flag tells the interface to split
                        every gene found in HMM searches that were performed
                        against non-singlecopy gene HMM profiles into their
                        own layer. Please see the documentation for details.
  --taxonomic-level {t_domain,t_phylum,t_class,t_order,t_family,t_genus,t_species}
                        The taxonomic level to use whenever relevant and/or
                        available. The default taxonomic level is t_genus, but
                        if you choose something specific, anvi'o will focus on
                        that whenever possible.
  --hide-outlier-SNVs   During profiling, anvi'o marks positions of single-
                        nucleotide variations (SNVs) that originate from
                        places in contigs where coverage values are a bit
                        'sketchy'. If you would like to avoid SNVs in those
                        positions of splits in applicable projects you can use
                        this flag, and the interface would hide SNVs that are
                        marked as 'outlier' (although it is clearly the best
                        to see everything, no one will judge you if you end up
                        using this flag) (plus, there may or may not be some
                        historical data on this here:
                        https://github.com/meren/anvio/issues/309).
  --title NAME          Title for the interface. If you are working with a
                        RUNINFO dict, the title will be determined based on
                        information stored in that file. Regardless, you can
                        override that value using this parameter.
  --export-svg FILE_PATH
                        The SVG output file path.

  --dry-run             Don't do anything real. Test everything, and stop
                        right before wherever the developer said 'well, this
                        is enough testing', and decided to print out results.
  --skip-init-functions
                        When declared, function calls for genes will not be
                        initialized (therefore will be missing from all
                        relevant interfaces or output files). The use of this
                        flag may reduce the memory fingerprint and processing
                        time for large datasets.
  --skip-auto-ordering  When declared, the attempt to include automatically
                        generated orders of items based on additional data is
                        skipped. In case those buggers cause issues with your
                        data, and you still want to see your stuff and deal
                        with the other issue maybe later.

  -I IP_ADDR, --ip-address IP_ADDR
                        IP address for the HTTP server. The default ip address
                        (0.0.0.0) should work just fine for most.
  -P INT, --port-number INT
                        Port number to use for anvi'o services. If nothing is
                        declared, anvi'o will try to find a suitable port
                        number, starting from the default port number, 8080.
  --browser-path PATH   By default, anvi'o will use your default browser to
                        launch the interactive interface. If you would like to
                        use something else than your system default, you can
                        provide a full path for an alternative browser using
                        this parameter, and hope for the best. For instance we
                        are using this parameter to call Google's experimental
                        browser, Canary, which performs better with demanding
                        visualizations.
  --read-only           When the interactive interface is started with this
                        flag, all 'database write' operations will be
                        disabled.
  --server-only         The default behavior is to start the local server, and
                        fire up a browser that connects to the server. If you
                        have other plans, and want to start the server without
                        calling the browser, this is the flag you need.
  --password-protected  If this flag is set, command line tool will ask you to
                        enter a password and interactive interface will be
                        only accessible after entering same password. This
                        option is recommended for shared machines like
                        clusters or shared networks where computers are not
                        isolated.

anvi-rename-bins [-h] -c CONTIGS_DB -p PROFILE_DB
                 [--collection-to-read COLLECTION_TO_READ]
                 [--collection-to-write COLLECTION_TO_WRITE]
                 [--prefix PREFIX] [--report-file REPORT_FILE_PATH]
                 [--list-collections] [--dry-run] [--call-MAGs]
                 [--min-completion-for-MAG [0-100]]
                 [--max-redundancy-for-MAG [0-100]]
                 [--size-for-MAG MEGABASEPAIRS]

  -c CONTIGS_DB, --contigs-db CONTIGS_DB
                        Anvi'o contigs database generated by 'anvi-gen-
                        contigs-database'
  -p PROFILE_DB, --profile-db PROFILE_DB
                        Anvi'o profile database
  --collection-to-read COLLECTION_TO_READ
                        Collection name to read from. Anvi'o will not
                        overwrite an existing collection, instead, it will
                        create a copy of your collection with new bin names.
  --collection-to-write COLLECTION_TO_WRITE
                        The new collection name. Give it a nice, fancy name.

  --prefix PREFIX       Prefix for the bin names. Must be a single word,
                        composed of digits and numbers. The use of the
                        underscore character is OK, but that's about it (fine,
                        the use of the dash character is OK, too but no
                        more!). If the prefix is 'PREFIX', each bin will be
                        renamed as 'PREFIX_XXX_00001, PREFIX_XXX_00002', and
                        so on, in the order of percent completion minus
                        percent redundancy (what we call, 'substantive
                        completion'). The 'XXX' part will either be 'Bin', or
                        'MAG depending on other parameters you use. Keep
                        reading.
  --report-file REPORT_FILE_PATH
                        This file will report each name change event, so you
                        can trace back the original names of renamed bins
                        later.
  --list-collections    Show available collections and exit.
  --dry-run             When used does NOT update the profile database, just
                        creates the report file so you can view how things
                        will be renamed.

  --call-MAGs           This program by default rename your bins as
                        'PREFIX_Bin_00001', 'PREFIX_Bin_00002' and so on. If
                        you use this flag, it will name the ones that meet the
                        criteria described by MAG-related flags as
                        'PREFIX_MAG_00001', 'PREFIX_MAG_00002', and so on. The
                        ones that do not get to be named as MAGs will remain
                        as bins.
  --min-completion-for-MAG [0-100]
                        If --call-MAGs flag is used, call any bin a 'MAG' if
                        their completion estimate is above this (the default
                        is 70), and the redundancy estimate is less than
                        --max-redundancy-for-MAG.
  --max-redundancy-for-MAG [0-100]
                        If --call-MAGs flag is used, call any bin a 'MAG' if
                        their redundancy estimate is below this (the default
                        is 10) and the completion estimate is above --min-
                        completion-for-MAG.
  --size-for-MAG MEGABASEPAIRS
                        If --call-MAGs flag is used, call any bin a 'MAG' if
                        their redundancy estimate is less than --max-
                        redundancy-for-MAG, AND THEIR SIZE IS LARGER THAN THIS
                        VALUE REGARDLESS OF THE COMPLETION ESTIMATE. The
                        default behavior is to not care about this at all.

anvi-report-linkmers [-h] -i INPUT_BAMS) [INPUT_BAM(S ...]
                     --contigs-and-positions CONTIGS_AND_POS
                     [--only-complete-links] -o FILE_PATH
                     [--list-contigs]

  -i INPUT_BAM(S) [INPUT_BAM(S) ...], --input-files INPUT_BAM(S) [INPUT_BAM(S) ...]
                        Sorted and indexed BAM files to analyze. It is
                        essential that all BAM files must be the result of
                        mappings against the same contigs.
  --contigs-and-positions CONTIGS_AND_POS
                        This is the file where you list the contigs, and
                        nucleotide positions you are interested in. This is
                        supposed to be a TAB-delimited file with two columns.
                        In each line, the first column should be the contig
                        name, and the second column should be the comma-
                        separated list of integers for nucleotide positions.
  --only-complete-links
                        When declared, only reads that cover all positions
                        will be reported. It is necessary to use this flag if
                        you want to perform oligotyping-like analyses on
                        matching reads.
  -o FILE_PATH, --output-file FILE_PATH
                        File path to store results.
  --list-contigs        When declared, the program will list contigs in the
                        BAM file and exit gracefully without any further
                        analysis.

anvi-run-hmms [-h] -c CONTIGS_DB [-H HMM PROFILE PATH]
              [-I HMM PROFILE NAME] [--also-scan-trnas]
              [-T NUM_THREADS] [--hmmer-program HMMER_PROGRAM]
              [--just-do-it]

  -c CONTIGS_DB, --contigs-db CONTIGS_DB
                        Anvi'o contigs database generated by 'anvi-gen-
                        contigs-database'

  -H HMM PROFILE PATH, --hmm-profile-dir HMM PROFILE PATH
                        You can use this parameter you can specify a directory
                        path that contain an HMM profile. This way you can run
                        HMM profiles that are not included in anvi'o. See the
                        online to find out about the specifics of this
                        directory structure .
  -I HMM PROFILE NAME, --installed-hmm-profile HMM PROFILE NAME
                        When you run this program without any parameter, it
                        runs all 4 HMM profiles installed on your system. If
                        you want only a specific one to run, you can select it
                        by using this parameter. These are the currently
                        available ones: "Bacteria_71" (type: singlecopy),
                        "Archaea_76" (type: singlecopy), "Protista_83" (type:
                        singlecopy), "Ribosomal_RNAs" (type: Ribosomal_RNAs).

  --also-scan-trnas     Also scan tRNAs while you're at it.

  -T NUM_THREADS, --num-threads NUM_THREADS
                        Maximum number of threads to use for multithreading
                        whenever possible. Very conservatively, the default is
                        1. It is a good idea to not exceed the number of CPUs
                        / cores on your system. Plus, please be careful with
                        this option if you are running your commands on a SGE
                        --if you are clusterizing your runs, and asking for
                        multiple threads to use, you may deplete your
                        resources very fast.
  --hmmer-program HMMER_PROGRAM
                        Which of the HMMER programs to use to run HMMs
                        (hmmscan or hmmsearch). By default anvi'o will use
                        hmmscan for typical HMM operations like those in anvi-
                        run-hmms (as these tend to scan a very large number of
                        genes against a relatively small number of HMMs), but
                        if you are using this program to scan a very large
                        number of HMMs, hmmsearch might be a better choice for
                        performance. For this reason, hmmsearch is the default
                        in operations like anvi-run-pfams and anvi-run-kegg-
                        kofams. See this article for a discussion on the
                        performance of these two programs:
                        https://cryptogenomicon.org/2011/05/27/hmmscan-vs-
                        hmmsearch-speed-the-numerology/

  --just-do-it          Don't bother me with questions or warnings, just do
                        it.

anvi-run-kegg-kofams [-h] -c CONTIGS_DB [--kegg-data-dir KEGG_DATA_DIR]
                     [-T NUM_THREADS] [--hmmer-program HMMER_PROGRAM]
                     [--keep-all-hits] [--just-do-it]

  -c CONTIGS_DB, --contigs-db CONTIGS_DB
                        Anvi'o contigs database generated by 'anvi-gen-
                        contigs-database'

  --kegg-data-dir KEGG_DATA_DIR
                        The directory path for your KEGG setup, which will
                        include things like KOfam profiles and KEGG MODULE
                        data. Anvi'o will try to use the default path if you
                        do not specify anything.
  -T NUM_THREADS, --num-threads NUM_THREADS
                        Maximum number of threads to use for multithreading
                        whenever possible. Very conservatively, the default is
                        1. It is a good idea to not exceed the number of CPUs
                        / cores on your system. Plus, please be careful with
                        this option if you are running your commands on a SGE
                        --if you are clusterizing your runs, and asking for
                        multiple threads to use, you may deplete your
                        resources very fast.
  --hmmer-program HMMER_PROGRAM
                        Which of the HMMER programs to use to run HMMs
                        (hmmscan or hmmsearch). By default anvi'o will use
                        hmmscan for typical HMM operations like those in anvi-
                        run-hmms (as these tend to scan a very large number of
                        genes against a relatively small number of HMMs), but
                        if you are using this program to scan a very large
                        number of HMMs, hmmsearch might be a better choice for
                        performance. For this reason, hmmsearch is the default
                        in operations like anvi-run-pfams and anvi-run-kegg-
                        kofams. See this article for a discussion on the
                        performance of these two programs:
                        https://cryptogenomicon.org/2011/05/27/hmmscan-vs-
                        hmmsearch-speed-the-numerology/
  --keep-all-hits       If you use this flag, anvi'o will not get rid of any
                        raw HMM hits, even those that are below the score
                        threshold.
  --just-do-it          Don't bother me with questions or warnings, just do
                        it.

anvi-run-ncbi-cogs [-h] -c CONTIGS_DB [--cog-data-dir COG_DATA_DIR]
                   [-T NUM_THREADS] [--sensitive]
                   [--temporary-dir-path PATH]
                   [--search-with SEARCH_METHOD]

  -c CONTIGS_DB, --contigs-db CONTIGS_DB
                        Anvi'o contigs database generated by 'anvi-gen-
                        contigs-database'
  --cog-data-dir COG_DATA_DIR
                        The directory path for your COG setup. Anvi'o will try
                        to use the default path if you do not specify
                        anything.
  -T NUM_THREADS, --num-threads NUM_THREADS
                        Maximum number of threads to use for multithreading
                        whenever possible. Very conservatively, the default is
                        1. It is a good idea to not exceed the number of CPUs
                        / cores on your system. Plus, please be careful with
                        this option if you are running your commands on a SGE
                        --if you are clusterizing your runs, and asking for
                        multiple threads to use, you may deplete your
                        resources very fast.
  --sensitive           DIAMOND sensitivity. With this flag you can instruct
                        DIAMOND to be 'sensitive', rather than 'fast' during
                        the search. It is likely the search will take
                        remarkably longer. But, hey, if you are doing it for
                        your final analysis, maybe it should take longer and
                        be more accurate. This flag is only relevant if you
                        are running DIAMOND.
  --temporary-dir-path PATH
                        If you don't provide anything here, this program will
                        come up with a temporary directory path by itself to
                        store intermediate files, and clean it later. If you
                        want to have full control over this, you can use this
                        flag to define one..
  --search-with SEARCH_METHOD
                        What program to use for database searching. The
                        default search uses diamond. All available options
                        include: diamond, blastp.

anvi-run-pfams [-h] -c CONTIGS_DB [--pfam-data-dir PFAM_DATA_DIR]
               [-T NUM_THREADS] [--hmmer-program HMMER_PROGRAM]

  -c CONTIGS_DB, --contigs-db CONTIGS_DB
                        Anvi'o contigs database generated by 'anvi-gen-
                        contigs-database'
  --pfam-data-dir PFAM_DATA_DIR
                        The directory path for your Pfam setup. Anvi'o will
                        try to use the default path if you do not specify
                        anything.
  -T NUM_THREADS, --num-threads NUM_THREADS
                        Maximum number of threads to use for multithreading
                        whenever possible. Very conservatively, the default is
                        1. It is a good idea to not exceed the number of CPUs
                        / cores on your system. Plus, please be careful with
                        this option if you are running your commands on a SGE
                        --if you are clusterizing your runs, and asking for
                        multiple threads to use, you may deplete your
                        resources very fast.
  --hmmer-program HMMER_PROGRAM
                        Which of the HMMER programs to use to run HMMs
                        (hmmscan or hmmsearch). By default anvi'o will use
                        hmmscan for typical HMM operations like those in anvi-
                        run-hmms (as these tend to scan a very large number of
                        genes against a relatively small number of HMMs), but
                        if you are using this program to scan a very large
                        number of HMMs, hmmsearch might be a better choice for
                        performance. For this reason, hmmsearch is the default
                        in operations like anvi-run-pfams and anvi-run-kegg-
                        kofams. See this article for a discussion on the
                        performance of these two programs:
                        https://cryptogenomicon.org/2011/05/27/hmmscan-vs-
                        hmmsearch-speed-the-numerology/

anvi-run-scg-taxonomy [-h] -c CONTIGS_DB
                      [--scgs-taxonomy-data-dir PATH]
                      [--min-percent-identity PERCENT_IDENTITY]
                      [-P NUM_PROCESSES] [-T NUM_THREADS]
                      [--write-buffer-size INT]

  -c CONTIGS_DB, --contigs-db CONTIGS_DB
                        Anvi'o contigs database generated by 'anvi-gen-
                        contigs-database'

  --scgs-taxonomy-data-dir PATH
                        The directory for SCGs data to be stored (or read
                        from, depending on the context). If you leave it as is
                        without specifying anything, anvi'o will set up
                        everything in (or try to read things from) a pre-
                        defined default directory. The advantage of using the
                        default directory at the time of set up is that every
                        user of anvi'o on a computer system will be using a
                        single data directory, but then you may need to run
                        the setup program with superuser privileges. If you
                        don't have superuser privileges, then you can use this
                        parameter to tell anvi'o the location you wish to use
                        to setup your databases. If you are using a program
                        (such as `anvi-run-scg-taxonomy` or `anvi-estimate-
                        scg-taxonomy`) you will have to use this parameter to
                        tell those programs where your data are.
  --min-percent-identity PERCENT_IDENTITY
                        The defualt value for this is 90.0%, and in an ideal
                        world you sholdn't really change it. Lowering this
                        value will probably give you too many hits from
                        neighboring genomes, which may ruin your consensus
                        taxonomy (imagine, at 90% identity you may match to a
                        single species, but at 70% identity you may match to
                        every species in a genus and your consensus assignment
                        may be influenced by that). But once in a while you
                        will have a genome that doesn't have any close match
                        in GTDB, and you will be curious to find out what it
                        could be. So, when you are getting no SCG hits
                        whatsoever, only then you may want to play with this
                        value. In those cases you can run anvi-estimate-scg-
                        taxonomy with a `--debug` flag to see what is really
                        going on. We strongly advice you to do this only with
                        single genomes, and never with metagenomes.

  -P NUM_PROCESSES, --num-parallel-processes NUM_PROCESSES
                        Maximum number of processes to run in parallel. Please
                        note that this is different than number of threads. If
                        you ask for 4 parallel processes, and 5 threads,
                        anvi'o will run four processes in parallel and assign
                        5 threads to each. For resource allocation you must
                        multiply the number of processes and threads.
  -T NUM_THREADS, --num-threads NUM_THREADS
                        Maximum number of threads to use for multithreading
                        whenever possible. Very conservatively, the default is
                        1. It is a good idea to not exceed the number of CPUs
                        / cores on your system. Plus, please be careful with
                        this option if you are running your commands on a SGE
                        --if you are clusterizing your runs, and asking for
                        multiple threads to use, you may deplete your
                        resources very fast.
  --write-buffer-size INT
                        How many items should be kept in memory before they
                        are written do the disk. The default is 500. The
                        larger the buffer size, the less frequent the program
                        will access to the disk, yet the more memory will be
                        consumed since the processed items will be cleared off
                        the memory only after they are written to the disk.
                        The default buffer size will likely work for most
                        cases, but if you feel you need to reduce it, we trust
                        you. Please keep an eye on the memory usage output to
                        make sure the memory use never exceeds the size of the
                        physical memory.

anvi-run-workflow [-h] [-w WORKFLOW]
                  [--get-default-config OUTPUT_FILENAME]
                  [--list-workflows] [--list-dependencies]
                  [-c CONFIG_FILE] [--dry-run] [--skip-dry-run]
                  [--save-workflow-graph] [-A ...]

  -w WORKFLOW, --workflow WORKFLOW
                        You must specify a workflow name. To see a list of
                        available workflows run --list-workflows.

  --get-default-config OUTPUT_FILENAME
                        Store a json formatted config file with all the
                        default settings of the workflow. This is a good draft
                        you could use in order to write your own config file.
                        This config file contains all parameters that could be
                        configured for this workflow. NOTICE: the config file
                        is provided with default values only for parameters
                        that are set by us in the workflow. The values for the
                        rest of the parameters are determined by the relevant
                        program.
  --list-workflows      Print a list of available snakemake workflows
  --list-dependencies   Print a list of the dependencies of this workflow. You
                        must provide a workflow name and a config file.
                        snakemake will figure out which rules need to be run
                        according to your config file, and according to the
                        files available on your disk. According to the rules
                        that need to be run, we will let you know which
                        programs are going to be used, so that you can make
                        sure you have all of them installed and loaded.
  -c CONFIG_FILE, --config-file CONFIG_FILE
                        A JSON-formatted configuration file.
  --dry-run             Don't do anything real. Test everything, and stop
                        right before wherever the developer said 'well, this
                        is enough testing', and decided to print out results.
  --skip-dry-run        Don't do a dry run. Just start the workflow! Useful
                        when your job is so big it takes hours to do a dry
                        run.
  --save-workflow-graph
                        Save a graph representation of the workflow. If you
                        are using this flag and if your system is unable to
                        generate such graph outputs, you will hear anvi'o
                        complaining (still, totally worth trying).
  -A ..., --additional-params ...
                        Additional snakemake parameters to add when running
                        snakemake. NOTICE: --additional-params HAS TO BE THE
                        LAST ARGUMENT THAT IS PASSED TO anvi-run-workflow,
                        ANYTHING THAT FOLLOWS WILL BE CONSIDERED AS PART OF
                        THE ADDITIONAL PARAMETERS THAT ARE PASSED TO
                        SNAKEMAKE. Any parameter that is accepted by snakemake
                        should be fair game here, but it is your
                        responsibility to make sure that whatever you added
                        makes sense. To see what parameters are available
                        please refer to the snakemake documentation. For
                        example, you could use this to set up cluster
                        submission using --additional-params --cluster 'YOUR-
                        CLUSTER-SUBMISSION-CMD'.

anvi-scan-trnas [-h] -c CONTIGS_DB [-T NUM_THREADS]
                [--log-file FILE_PATH] [--trna-hits-file FILE_PATH]
                [--trna-cutoff-score INT] [--just-do-it]

  -c CONTIGS_DB, --contigs-db CONTIGS_DB
                        Anvi'o contigs database generated by 'anvi-gen-
                        contigs-database'
  -T NUM_THREADS, --num-threads NUM_THREADS
                        Maximum number of threads to use for multithreading
                        whenever possible. Very conservatively, the default is
                        1. It is a good idea to not exceed the number of CPUs
                        / cores on your system. Plus, please be careful with
                        this option if you are running your commands on a SGE
                        --if you are clusterizing your runs, and asking for
                        multiple threads to use, you may deplete your
                        resources very fast.
  --log-file FILE_PATH  File path to store debug/output messages.
  --trna-hits-file FILE_PATH
                        File path to store raw hits from tRNA scan.
  --trna-cutoff-score INT
                        Minimum score to assume a hit comes from a proper tRNA
                        gene (passed to the tRNAScan-SE). The default is 20.
                        It can get any value between 0-100.
  --just-do-it          Don't bother me with questions or warnings, just do
                        it.

anvi-search-functions [-h] [-c CONTIGS_DB] [-p PAN_DB]
                      [-g GENOMES_STORAGE] --search-terms SEARCH_TERMS
                      [--delimiter CHAR]
                      [--annotation-sources SOURCE NAME[S]] [-l]
                      [-o FILE_PATH] [--full-report FILE_NAME]
                      [--include-sequences] [--verbose]

  -c CONTIGS_DB, --contigs-db CONTIGS_DB
                        Anvi'o contigs database generated by 'anvi-gen-
                        contigs-database'
  -p PAN_DB, --pan-db PAN_DB
                        Anvi'o pan database
  -g GENOMES_STORAGE, --genomes-storage GENOMES_STORAGE
                        Anvi'o genomes storage file

  --search-terms SEARCH_TERMS
                        Search terms. Multiple of them can be declared
                        separated by a delimiter (the default is a comma).
  --delimiter CHAR      The delimiter to parse multiple input terms. The
                        default is ','.
  --annotation-sources SOURCE NAME[S]
                        Get functional annotations for a specific list of
                        annotation sources. You can specify one or more
                        sources by separating them from each other with a
                        comma character (i.e., '--annotation-sources
                        source_1,source_2,source_3'). The default behavior is
                        to return everything
  -l, --list-annotation-sources
                        List available functional annotation sources.

  -o FILE_PATH, --output-file FILE_PATH
                        File path to store results.
  --full-report FILE_NAME
                        Optional output file with a fuller description of
                        findings.
  --include-sequences   Include sequences in the report.
  --verbose             Be verbose, print more messages whenever possible.

anvi-self-test [-h] [--suite SUITE]

  --suite SUITE  Suite of tests to execute. By default this program will
                 execute a full suite of example anvi'o commands to ensure
                 your installation is ready to run all scenarios anvi'o
                 developers could think of. Alternatively you can choose a
                 specific test to run. Here is a full list of available
                 options: mini, full, pangenomics, alons-classifier, manual-
                 interface.

anvi-setup-kegg-kofams [-h] [--kegg-data-dir KEGG_DATA_DIR]
                       [--kegg-archive KEGG_ARCHIVE] [--reset]
                       [--just-do-it]

  --kegg-data-dir KEGG_DATA_DIR
                        The directory path for your KEGG setup, which will
                        include things like KOfam profiles and KEGG MODULE
                        data. Anvi'o will try to use the default path if you
                        do not specify anything.
  --kegg-archive KEGG_ARCHIVE
                        The path to an archived KEGG directory. If you provide
                        this parameter, anvi'o will set up the KEGG data
                        directory from the archive rather than downloading and
                        building it from the KEGG website.
  --reset               Remove all the previously stored files and start over.
                        If something is feels wrong for some reason and if you
                        believe re-downloading files and setting them up could
                        address the issue, this is the flag that will tell
                        anvi'o to act like a real computer scientist
                        challenged with a computational problem.
  --just-do-it          Don't bother me with questions or warnings, just do
                        it.

anvi-setup-ncbi-cogs [-h] [--cog-data-dir COG_DATA_DIR] [--reset]
                     [--just-do-it] [-T NUM_THREADS]

  --cog-data-dir COG_DATA_DIR
                        The directory for COG data to be stored. If you leave
                        it as is without specifying anything, the default
                        destination for the data directory will be used to set
                        things up. The advantage of it is that everyone will
                        be using a single data directory, but then you may
                        need superuser privileges to do it. Using this
                        parameter you can choose the location of the data
                        directory somewhere you like. However, when it is time
                        to run COGs, you will need to remember that path and
                        provide it to the program.
  --reset               Remove all the previously stored files and start over.
                        If something is feels wrong for some reason and if you
                        believe re-downloading files and setting them up could
                        address the issue, this is the flag that will tell
                        anvi'o to act like a real computer scientist
                        challenged with a computational problem.
  --just-do-it          Don't bother me with questions or warnings, just do
                        it.
  -T NUM_THREADS, --num-threads NUM_THREADS
                        Maximum number of threads to use for multithreading
                        whenever possible. Very conservatively, the default is
                        1. It is a good idea to not exceed the number of CPUs
                        / cores on your system. Plus, please be careful with
                        this option if you are running your commands on a SGE
                        --if you are clusterizing your runs, and asking for
                        multiple threads to use, you may deplete your
                        resources very fast.

anvi-setup-pdb-database [-h] [--pdb-database-path PATH]
                        [-T NUM_THREADS] [--update]
                        [--skip-modeller-update] [--reset]

  --pdb-database-path PATH
                        The path for the PDB database to be stored. If you
                        leave it as is without specifying anything, anvi'o
                        will set up everything in a pre-defined default
                        directory. The advantage of using the default
                        directory at the time of set up is that every user of
                        anvi'o on a computer system will be using a single
                        data directory, but then you may need to run the setup
                        program with superuser privileges. If you don't have
                        superuser privileges, then you can use this parameter
                        to tell anvi'o the location you wish to use to setup
                        your database.
  -T NUM_THREADS, --num-threads NUM_THREADS
                        Maximum number of threads to use for multithreading
                        whenever possible. Very conservatively, the default is
                        1. It is a good idea to not exceed the number of CPUs
                        / cores on your system. Plus, please be careful with
                        this option if you are running your commands on a SGE
                        --if you are clusterizing your runs, and asking for
                        multiple threads to use, you may deplete your
                        resources very fast.
  --update              Use this flag if you would like to update your current
                        database.
  --skip-modeller-update
                        By default, MODELLER's search DB is updated when this
                        program is ran so that if MODELLER finds a protein,
                        its structure is guaranteed to be in this database. If
                        you don't want to touch the MODELLER database, use
                        this flag.
  --reset               Remove all the previously stored files and start over.
                        If something is feels wrong for some reason and if you
                        believe re-downloading files and setting them up could
                        address the issue, this is the flag that will tell
                        anvi'o to act like a real computer scientist
                        challenged with a computational problem.

anvi-setup-pfams [-h] [--pfam-data-dir PFAM_DATA_DIR] [--reset]

  --pfam-data-dir PFAM_DATA_DIR
                        The directory for Pfam data to be stored. If you leave
                        it as is without specifying anything, the default
                        destination for the data directory will be used to set
                        things up. The advantage of it is that everyone will
                        be using a single data directory, but then you may
                        need superuser privileges to do it. Using this
                        parameter you can choose the location of the data
                        directory somewhere you like. However, when it is time
                        to run Pfam, you will need to remember that path and
                        provide it to the program.
  --reset               This program by default attempts to use previously
                        downloaded files in your Pfam data directory if there
                        are any. If something is wrong for some reason you can
                        use this to tell anvi'o to remove everything, and
                        start over.

anvi-setup-scg-taxonomy [-h] [-T NUM_THREADS]
                        [--scgs-taxonomy-data-dir PATH]
                        [--scgs-taxonomy-remote-database-url URL]
                        [--reset] [--redo-databases]

  -T NUM_THREADS, --num-threads NUM_THREADS
                        Maximum number of threads to use for multithreading
                        whenever possible. Very conservatively, the default is
                        1. It is a good idea to not exceed the number of CPUs
                        / cores on your system. Plus, please be careful with
                        this option if you are running your commands on a SGE
                        --if you are clusterizing your runs, and asking for
                        multiple threads to use, you may deplete your
                        resources very fast.
  --scgs-taxonomy-data-dir PATH
                        The directory for SCGs data to be stored (or read
                        from, depending on the context). If you leave it as is
                        without specifying anything, anvi'o will set up
                        everything in (or try to read things from) a pre-
                        defined default directory. The advantage of using the
                        default directory at the time of set up is that every
                        user of anvi'o on a computer system will be using a
                        single data directory, but then you may need to run
                        the setup program with superuser privileges. If you
                        don't have superuser privileges, then you can use this
                        parameter to tell anvi'o the location you wish to use
                        to setup your databases. If you are using a program
                        (such as `anvi-run-scg-taxonomy` or `anvi-estimate-
                        scg-taxonomy`) you will have to use this parameter to
                        tell those programs where your data are.
  --scgs-taxonomy-remote-database-url URL
                        Anvi'o will always try to download the latest release,
                        but if there is a problem with the latest release,
                        feel free to run setup using a different URL. Just to
                        note, anvi'o will expect to find the following files
                        in the URL provided here: 'VERSION',
                        'ar122_msa_individual_genes.tar.gz',
                        'ar122_taxonomy.tsv',
                        'bac120_msa_individual_genes.tar.gz', and
                        'bac120_taxonomy.tsv'. If everything fails, you can
                        give this URL, which is supposed to work if teh server
                        in which these databases are maintained is still
                        online: https://data.ace.uq.edu.au/public/gtdb/data/re
                        leases/release89/89.0/
  --reset               Remove all the previously stored files and start over.
                        If something is feels wrong for some reason and if you
                        believe re-downloading files and setting them up could
                        address the issue, this is the flag that will tell
                        anvi'o to act like a real computer scientist
                        challenged with a computational problem.
  --redo-databases      Remove existing databases and re-create them. This can
                        be necessary when versions of programs change and
                        databases they create and use become incompatible.

anvi-show-collections-and-bins [-h] -p PAN_OR_PROFILE_DB

  -p PAN_OR_PROFILE_DB, --pan-or-profile-db PAN_OR_PROFILE_DB
                        Anvi'o pan or profile database (and even genes
                        database in appropriate contexts).

anvi-show-misc-data [-h] [-p PAN_OR_PROFILE_DB] [-c CONTIGS_DB]
                    [-t NAME] [-D NAME]

  -p PAN_OR_PROFILE_DB, --pan-or-profile-db PAN_OR_PROFILE_DB
                        Anvi'o pan or profile database (and even genes
                        database in appropriate contexts).
  -c CONTIGS_DB, --contigs-db CONTIGS_DB
                        Anvi'o contigs database generated by 'anvi-gen-
                        contigs-database'

  -t NAME, --target-data-table NAME
                        The target table is the table you are interested in
                        accessing. Currently it can be 'items','layers', or
                        'layer_orders'. Please see most up-to-date online
                        documentation for more information.
  -D NAME, --target-data-group NAME
                        Data group to focus. Anvi'o misc data tables support
                        associating a set of data keys with a data group. If
                        you have no idea what this is, then probably you don't
                        need it, and anvi'o will take care of you. Note: this
                        flag is IRRELEVANT if you are working with additional
                        order data tables.

anvi-split [-h] -p PAN_OR_PROFILE_DB [-c CONTIGS_DB]
           [-g GENOMES_STORAGE] [--skip-variability-tables]
           [--compress-auxiliary-data] [-C COLLECTION_NAME]
           [-b BIN_NAME] [-o DIR_PATH] [--list-collections]
           [--skip-hierarchical-clustering]
           [--enforce-hierarchical-clustering]
           [--distance DISTANCE_METRIC] [--linkage LINKAGE_METHOD]

  -p PAN_OR_PROFILE_DB, --pan-or-profile-db PAN_OR_PROFILE_DB
                        Anvi'o pan or profile database (and even genes
                        database in appropriate contexts).
  -c CONTIGS_DB, --contigs-db CONTIGS_DB
                        Anvi'o contigs database generated by 'anvi-gen-
                        contigs-database'
  -g GENOMES_STORAGE, --genomes-storage GENOMES_STORAGE
                        Anvi'o genomes storage file

  --skip-variability-tables
                        Processing variability tables in profile database
                        might take a very long time. With this flag you will
                        be asking anvi'o to skip them.
  --compress-auxiliary-data
                        When declared, the auxiliary data file in the
                        resulting output will be compressed. This saves space,
                        but it takes long. Also, if you are planning to
                        compress the entire later using GZIP, it is even
                        useless to do. But you are the boss!

  -C COLLECTION_NAME, --collection-name COLLECTION_NAME
                        Collection name.
  -b BIN_NAME, --bin-id BIN_NAME
                        Bin name you are interested in.

  -o DIR_PATH, --output-dir DIR_PATH
                        Directory path for output files

  --list-collections    Show available collections and exit.
  --skip-hierarchical-clustering
                        If you are not planning to use the interactive
                        interface (or if you have other means to add a tree of
                        contigs in the database) you may skip the step where
                        hierarchical clustering of your items are preformed
                        based on default clustering recipes matching to your
                        database type.
  --enforce-hierarchical-clustering
                        If you have more than 25,000 splits in your merged
                        profile, anvi-merge will automatically skip the
                        hierarchical clustering of splits (by setting --skip-
                        hierarchical-clustering flag on). This is due to the
                        fact that computational time required for hierarchical
                        clustering increases exponentially with the number of
                        items being clustered. Based on our experience we
                        decided that 25,000 splits is about the maximum we
                        should try. However, this is not a theoretical limit,
                        and you can overwrite this heuristic by using this
                        flag, which would tell anvi'o to attempt to cluster
                        splits regardless.
  --distance DISTANCE_METRIC
                        The distance metric for the hierarchical clustering.
                        If you do not use this flag, the default distance
                        metric will be used for each clustering configuration
                        which is "euclidean".
  --linkage LINKAGE_METHOD
                        The same story with the `--distance`, except, the
                        system default for this one is ward.

anvi-summarize [-h] -p PAN_OR_PROFILE_DB [-c CONTIGS_DB]
               [-g GENOMES_STORAGE] [--init-gene-coverages]
               [--reformat-contig-names]
               [--report-aa-seqs-for-gene-calls]
               [--report-DNA-sequences] [-C COLLECTION_NAME]
               [-o DIR_PATH] [--list-collections]
               [--taxonomic-level {t_domain,t_phylum,t_class,t_order,t_family,t_genus,t_species}]
               [--cog-data-dir COG_DATA_DIR] [--quick-summary]
               [--just-do-it]

  -p PAN_OR_PROFILE_DB, --pan-or-profile-db PAN_OR_PROFILE_DB
                        Anvi'o pan or profile database (and even genes
                        database in appropriate contexts).

  -c CONTIGS_DB, --contigs-db CONTIGS_DB
                        Anvi'o contigs database generated by 'anvi-gen-
                        contigs-database'
  -g GENOMES_STORAGE, --genomes-storage GENOMES_STORAGE
                        Anvi'o genomes storage file

  --init-gene-coverages
                        Initialize gene coverage and detection data. This is a
                        very computationally expensive step, but it is
                        necessary when you need gene level coverage data. The
                        reason this is very computationally expensive is
                        because anvi'o computes gene coverages by going back
                        to actual coverage values of each gene to average
                        them, instead of using contig average coverage values,
                        for extreme accuracy.
  --reformat-contig-names
                        Reformat contig names while generating the summary
                        output so they look fancy. With this flag, anvi'o will
                        replace the original names of contigs to those that
                        include the bin name as a prefix in resulting summary
                        output files per bin. Use this flag carefully as it
                        may influence your downstream analyses due to the fact
                        that your original contig names in your input FASTA
                        file for the contigs database will not be in the
                        summary output. Although, anvi'o will report a
                        conversion map per bin so you can recover the original
                        contig name if you have to.
  --report-aa-seqs-for-gene-calls
                        You can use this flag if you would like amino acid AND
                        dna sequences for your gene calls in the genes output
                        file. By default, only dna sequences are reported.

  --report-DNA-sequences
                        By default, this program reports amino acid sequences.
                        Use this flag to report DNA sequences instead. Also
                        note, since gene clusters are aligned via amino acid
                        sequences, using this flag removes alignment
                        information manifesting in the form of gap characters
                        (`-` characters) that would be present if amino acid
                        sequences were reported. Read the warnings during
                        runtime for more detailed information.

  -C COLLECTION_NAME, --collection-name COLLECTION_NAME
                        Collection name.
  -o DIR_PATH, --output-dir DIR_PATH
                        Directory path for output files
  --list-collections    Show available collections and exit.
  --taxonomic-level {t_domain,t_phylum,t_class,t_order,t_family,t_genus,t_species}
                        The taxonomic level to use whenever relevant and/or
                        available. The default taxonomic level is t_genus, but
                        if you choose something specific, anvi'o will focus on
                        that whenever possible.
  --cog-data-dir COG_DATA_DIR
                        The directory path for your COG setup. Anvi'o will try
                        to use the default path if you do not specify
                        anything.
  --quick-summary       When declared the summary output will be generated as
                        quickly as possible, with minimum amount of essential
                        information about bins.

  --just-do-it          Don't bother me with questions or warnings, just do
                        it.

anvi-update-db-description [-h] --description TEXT_FILE DB

  DB                    An anvi'o database.

  --description TEXT_FILE
                        A plain text file that contains some description about
                        the project. You can use Markdwon syntax. The
                        description text will be rendered and shown in all
                        relevant interfaces, including the anvi'o interactive
                        interface, or anvi'o summary outputs.

anvi-update-structure-database [-h] -c CONTIGS_DB -s STRUCTURE_DB
                               [--genes-of-interest FILE]
                               [--gene-caller-ids GENE_CALLER_IDS]
                               [--dump-dir DUMP_DIR]
                               [--list-modeller-params] [--rerun-genes]
                               [--modeller-executable MODELLER_EXECUTABLE]
                               [-T NUM_THREADS]
                               [--write-buffer-size-per-thread INT]

  -c CONTIGS_DB, --contigs-db CONTIGS_DB
                        Anvi'o contigs database generated by 'anvi-gen-
                        contigs-database'
  -s STRUCTURE_DB, --structure-db STRUCTURE_DB
                        Anvi'o structure database.

  --genes-of-interest FILE
                        A file with anvi'o gene caller IDs. There should be
                        only one column in the file, and each line should
                        correspond to a unique gene caller id (without a
                        column header).
  --gene-caller-ids GENE_CALLER_IDS
                        Gene caller ids. Multiple of them can be declared
                        separated by a delimiter (the default is a comma). In
                        anvi-gen-variability-profile, if you declare nothing
                        you will get all genes matching your other filtering
                        criteria. In other programs, you may get everything,
                        nothing, or an error. It really depends on the
                        situation. Fortunately, mistakes are cheap, so it's
                        worth a try.

  --dump-dir DUMP_DIR   Modeling and annotating structures requires a lot of
                        moving parts, each which have their own outputs. The
                        output of this program is a structure database
                        containing the pertinent results of this computation,
                        however a lot of stuff doesn't make the cut. By
                        providing a directory for this parameter you will get,
                        in addition to the structure database, a directory
                        containing the raw output for everything.

  --list-modeller-params
                        Since you are updating an existing DB, modeller params
                        are set in place. You can have this program list them
                        by providing this flag

  --rerun-genes         Supply if you would like to rerun structural modelling
                        for your genes of interest if they are already present
                        in your DB
  --modeller-executable MODELLER_EXECUTABLE
                        The MODELLER program to use. For example, `mod9.19`.
                        Anvi'o will try and find it if not provided.
  -T NUM_THREADS, --num-threads NUM_THREADS
                        Maximum number of threads to use for multithreading
                        whenever possible. Very conservatively, the default is
                        1. It is a good idea to not exceed the number of CPUs
                        / cores on your system. Plus, please be careful with
                        this option if you are running your commands on a SGE
                        --if you are clusterizing your runs, and asking for
                        multiple threads to use, you may deplete your
                        resources very fast.
  --write-buffer-size-per-thread INT
                        How many items should be kept in memory before they
                        are written do the disk. The default is 25 per thread.
                        So a single-threaded job would have a write buffer
                        size of 25, whereas a job with 4 threads would have a
                        write buffer size of 4*25. The larger the buffer size,
                        the less frequent the program will access to the disk,
                        yet the more memory will be consumed since the
                        processed items will be cleared off the memory only
                        after they are written to the disk. The default buffer
                        size will likely work for most cases. Please keep an
                        eye on the memory usage output to make sure the memory
                        use never exceeds the size of the physical memory. If
                        --num-threads is 1, this parameter is ignored because
                        the DB is written to after each gene

anvi-upgrade [-h] [--repository REPOSITORY]

  --repository REPOSITORY
                        Source repository to download releases, currently only
                        Github is supported. Enter in 'merenlab/anvio' format.

anvi-script-add-default-collection [-h] -p PAN_OR_PROFILE_DB
                                   [-c CONTIGS_DB] [-b BIN_NAME]
                                   [-C COLLECTION_NAME]

  -p PAN_OR_PROFILE_DB, --pan-or-profile-db PAN_OR_PROFILE_DB
                        Anvi'o pan or profile database (and even genes
                        database in appropriate contexts).
  -c CONTIGS_DB, --contigs-db CONTIGS_DB
                        Anvi'o contigs database generated by 'anvi-gen-
                        contigs-database'
  -b BIN_NAME, --bin-id BIN_NAME
                        Name for the new bin. If you don't provide any then it
                        will be named "EVERYTHING".
  -C COLLECTION_NAME, --collection-name COLLECTION_NAME
                        Name for the new collection. If you don't provide any
                        then it will be named "DEFAULT".

anvi-script-augustus-output-to-external-gene-calls [-h] -i INPUT_FILE
                                                   [-o FILE_PATH]
                                                   [--just-do-it]

  -i INPUT_FILE, --input-file INPUT_FILE
                        Gene calls file from AUGUSTUS (that ends with .gff).
                        Please note that the script is only tested with
                        AUGUSTUS v3.3.3 output (although it may still work
                        with other versions of the program).
  -o FILE_PATH, --output-file FILE_PATH
                        File path to store results.
  --just-do-it          Don't bother me with questions or warnings, just do
                        it.

anvi-script-calculate-pn-ps-ratio [-h] [-a SAAV_FILE] [-b SCV_FILE] -c
                                  CONTIGS_DB [-j FLOAT]
                                  [-i MINIMUM_NUM_VARIANTS]
                                  [-m MIN_COVERAGE] -o DIR_PATH

  -a SAAV_FILE, --saav-table SAAV_FILE
                        Filepath to the SAAV table.
  -b SCV_FILE, --scv-table SCV_FILE
                        Filepath to the SCV table.
  -c CONTIGS_DB, --contigs-db CONTIGS_DB
                        Filepath to the contigs database used to generate
                        variability tables.

  -j FLOAT, --min-departure-from-consensus FLOAT
                        Variants (either SCVs or SAAVs) will be ignored if
                        they have a departure from consensus less than this
                        value. Note: Keep in mind you may have already
                        supplied this parameter during anvi-gen-variability-
                        profile. The default value is "0.10".
  -i MINIMUM_NUM_VARIANTS, --minimum-num-variants MINIMUM_NUM_VARIANTS
                        Ignore genes with less than this number of single
                        codon variants. This avoids being impressed by pN/pS
                        values of infinite, when in reality the gene had a
                        single SAAV and no synonymous SCVs. The default is 4
                        to ensure a default value with some level of
                        statistical importance.
  -m MIN_COVERAGE, --min-coverage MIN_COVERAGE
                        If the coverage value at a codon is less than this
                        amount, any SAAVs or SCVs associated with it will be
                        ignored. The default is 30.

  -o DIR_PATH, --output-dir DIR_PATH
                        Directory path for output files

anvi-script-checkm-tree-to-interactive [-h] -t CHECKM TREE -o DIRECTORY

  -t CHECKM TREE, --tree CHECKM TREE
                        Tree file generated by CheckM.
  -o DIRECTORY, --output-dir DIRECTORY
                        The directory name that output files will be stored.

anvi-script-compute-ani-for-fasta [-h] -f FASTA -o DIR_PATH [-p PAN_DB]
                                  [-T NUM_THREADS]
                                  [--log-file FILE_PATH]
                                  [--method {ANIm,ANIb,ANIblastall,TETRA}]
                                  [--distance DISTANCE_METRIC]
                                  [--linkage LINKAGE_METHOD]
                                  [--just-do-it]

  -f FASTA, --fasta-file FASTA
                        A FASTA-formatted input file
  -o DIR_PATH, --output-dir DIR_PATH
                        Directory path for output files
  -p PAN_DB, --pan-db PAN_DB
                        Anvi'o pan database
  -T NUM_THREADS, --num-threads NUM_THREADS
                        Maximum number of threads to use for multithreading
                        whenever possible. Very conservatively, the default is
                        1. It is a good idea to not exceed the number of CPUs
                        / cores on your system. Plus, please be careful with
                        this option if you are running your commands on a SGE
                        --if you are clusterizing your runs, and asking for
                        multiple threads to use, you may deplete your
                        resources very fast.
  --log-file FILE_PATH  File path to store debug/output messages.
  --method {ANIm,ANIb,ANIblastall,TETRA}
                        Method for pyANI. The default is ANIb. You must have
                        the necessary binary in path for whichever method you
                        choose. According to the pyANI help for v0.2.7 at
                        https://github.com/widdowquinn/pyani, the method
                        'ANIm' uses MUMmer (NUCmer) to align the input
                        sequences. 'ANIb' uses BLASTN+ to align 1020nt
                        fragments of the input sequences. 'ANIblastall': uses
                        the legacy BLASTN to align 1020nt fragments Finally,
                        'TETRA': calculates tetranucleotide frequencies of
                        each input sequence
  --distance DISTANCE_METRIC
                        The distance metric for the hierarchical clustering.
                        The default is "euclidean".
  --linkage LINKAGE_METHOD
                        The linkage method for the hierarchical clustering.
                        The default is "ward".
  --just-do-it          Don't bother me with questions or warnings, just do
                        it.

anvi-script-estimate-genome-size [-h] -c CONTIGS_DB [--verbose]

  -c CONTIGS_DB, --contigs-db CONTIGS_DB
                        Anvi'o contigs database generated by 'anvi-gen-
                        contigs-database'

  --verbose             Be verbose, print more messages whenever possible.

anvi-script-filter-fasta-by-blast [-h] [-f FASTA] [-o FILE_PATH] -b TAB
                                  DELIMITED FILE -s OUTFMT -t THRESHOLD
                                  [--just-do-it]

  -f FASTA, --fasta-file FASTA
                        A FASTA-formatted input file
  -o FILE_PATH, --output-file FILE_PATH
                        File path to store results.
  -b TAB DELIMITED FILE, --blast-output TAB DELIMITED FILE
                        BLAST table generated with blastp. `--outfmt 6` as the
                        output format is assumed.
  -s OUTFMT, --outfmt OUTFMT
                        Specify the column ordering of your BLAST report. We
                        add the following paramter to our BLAST searches so
                        the output report contains the `qlen` field, which is
                        not included by default: `-outfmt '6 qseqid sseqid
                        pident length mismatch gapopen qstart qend sstart send
                        evalue bitscore qlen slen'`. You may have used a
                        different `-outfmt` paramter, and you should use this
                        parameter to explicitly define the column names in
                        your output file. For instance, if you had used the
                        parameter mentioned above, then the correct version of
                        this parameter would be: "qseqid sseqid pident length
                        mismatch gapopen qstart qend sstart send evalue
                        bitscore qlen slen". Regardless of the BLAST output
                        format, your columns MUST contain the following
                        parameters for this program to work properly:
                        'qseqid', 'bitscore', 'length', 'qlen', and 'pident'.
  -t THRESHOLD, --threshold THRESHOLD
                        What `proper_pident` threshold do you want to use for
                        filtering out sequences whose top bit-score matches
                        have `proper_pident`s less than this threshold? We
                        have defined `proper_pident` to be the percentage of
                        the query amino acids that both aligned to and were
                        identical to the corresponding matched amino acid.
                        Note that the `pident` parameter output by BLAST does
                        not include regions of the query sequence unaligned to
                        the matched sequence, whereas `proper_pident` does.
                        For example, a sequence that's only half aligned by a
                        match but with 100% identity at matched regions has a
                        `pident` of 100 but a `proper_pident` of 50. The
                        default is 30.0%.
  --just-do-it          Don't bother me with questions or warnings, just do
                        it.

anvi-script-gen-CPR-classifier [-h] [-o CLASSIFIER_FILE] MATRIX_FILE

  MATRIX_FILE           TAB-delimited matrix of CPR genome names, classes, and
                        presence absence of single-copy genes. Headers of the
                        first two rows should be "genome", and "class". The
                        rest of the rows shold be single-copy genes.

  -o CLASSIFIER_FILE, --output CLASSIFIER_FILE
                        Output file name for the classifier.

anvi-script-gen-distribution-of-genes-in-a-bin [-h] -c CONTIGS_DB
                                               [-p PROFILE_DB]
                                               [-C COLLECTION_NAME]
                                               [-b BIN_NAME]
                                               [--min-detection FLOAT]
                                               [--fraction-of-median-coverage FLOAT]

  -c CONTIGS_DB, --contigs-db CONTIGS_DB
                        Anvi'o contigs database generated by 'anvi-gen-
                        contigs-database'
  -p PROFILE_DB, --profile-db PROFILE_DB
                        Anvi'o profile database
  -C COLLECTION_NAME, --collection-name COLLECTION_NAME
                        Collection name.
  -b BIN_NAME, --bin-id BIN_NAME
                        Bin name you are interested in.
  --min-detection FLOAT
                        For this entire thing to work, the genome you are
                        focusing on should be detected in at least one
                        metagenome. If that is not the case, it would mean
                        that you do not have any sample that represents the
                        niche for this organism (or you do not have enough
                        depth of coverage) to investigate the detection of
                        genes in the environment. By default, this script
                        requires at least '0.5' of the genome to be detected
                        in at least one metagenome. This parameter allows you
                        to change that. 0 would mean no detection test
                        required, 1 would mean the entire genome must be
                        detected.
  --fraction-of-median-coverage FLOAT
                        The value set here will be used to remove a gene if
                        its total coverage across environments is less than
                        the median coverage of all genes multiplied by this
                        value. The default is 0.25, which means, if the median
                        total coverage of all genes across all samples is
                        100X, then, a gene with a total coverage of less than
                        25X across all samples will be assumed not a part of
                        the 'environmental core'.

anvi-script-gen-help-pages [-h] [-o DIR_PATH]

  -o DIR_PATH, --output-dir DIR_PATH
                        Directory path for output files

anvi-script-gen-hmm-hits-matrix-across-genomes [-h] [-e FILE_PATH]
                                               [-i FILE_PATH]
                                               [--hmm-source SOURCE NAME]
                                               [-l] -o FILE_PATH

  -e FILE_PATH, --external-genomes FILE_PATH
                        A two-column TAB-delimited flat text file that lists
                        anvi'o contigs databases. The first item in the header
                        line should read 'name', and the second should read
                        'contigs_db_path'. Each line in the file should
                        describe a single entry, where the first column is the
                        name of the genome (or MAG), and the second column is
                        the anvi'o contigs database generated for this genome.
  -i FILE_PATH, --internal-genomes FILE_PATH
                        A five-column TAB-delimited flat text file. The header
                        line must contain these columns: 'name', 'bin_id',
                        'collection_id', 'profile_db_path', 'contigs_db_path'.
                        Each line should list a single entry, where 'name' can
                        be any name to describe the anvi'o bin identified as
                        'bin_id' that is stored in a collection.

  --hmm-source SOURCE NAME
                        Use a specific HMM source. You can use '--list-hmm-
                        sources' flag to see a list of available resources.
                        The default is 'None'.
  -l, --list-hmm-sources
                        List available HMM sources in the contigs database and
                        quit.

  -o FILE_PATH, --output-file FILE_PATH
                        File path to store results.

anvi-script-gen-programs-network [-h] [-o FILE_PATH]
                                 [-p PROGRAM_NAMES_TO_FOCUS]

  -o FILE_PATH, --output-file FILE_PATH
                        File path to store results.
  -p PROGRAM_NAMES_TO_FOCUS, --program-names-to-focus PROGRAM_NAMES_TO_FOCUS
                        Comma-spearated list of program names to focus Mostly
                        for debugging purposes.

anvi-script-gen-programs-vignette [-h] [-o FILE_PATH]
                                  [-p PROGRAM_NAMES_TO_FOCUS]

  -o FILE_PATH, --output-file FILE_PATH
                        File path to store results.
  -p PROGRAM_NAMES_TO_FOCUS, --program-names-to-focus PROGRAM_NAMES_TO_FOCUS
                        Comma-spearated list of program names to focus Mostly
                        for debugging purposes.

anvi-script-gen-pseudo-paired-reads-from-fastq [-h] -f FASTQ
                                               [-O FILENAME_PREFIX]

  -f FASTQ, --fastq FASTQ
  -O FILENAME_PREFIX, --output-file-prefix FILENAME_PREFIX
                        If you want final FASTQs with the format
                        myfastq_1.fastq and myfastq_2.fastq, then this
                        parameter should be set to myfastq

anvi-script-gen-scg-domain-classifier [-h] [--genomes-dir GENOMES_DIR]
                                      [-o PATH]

  --genomes-dir GENOMES_DIR
                        This should be a directory that contains a directory
                        per domain for single-copy core gene collections a
                        given version of anvi'o knows about. For instance, if
                        there are collections for archaea, bacteria, and
                        eukarya, then this directory should contain
                        subdirectories with these names. Contents of which
                        should be contigs databases that belong to those
                        domains. These genomes will be used to generate the
                        classifier.
  -o PATH, --output PATH
                        Output file name for the classifier.

anvi-script-gen-short-reads [-h] [--output-file-path FASTA_FILE]
                            CONFIG_FILE

  CONFIG_FILE           Configuration file

  --output-file-path FASTA_FILE
                        Output FASTA file path

anvi-script-gen_stats_for_single_copy_genes.py [-h] [--list-sources]
                                               [--source SOURCE]
                                               CONTIGS_DB

  CONTIGS_DB       Contigs database to read from.

  --list-sources   Show available single-copy gene search results and exit.
  --source SOURCE  Source to focus on. If none declared, all single-copy gene
                   sources are going to be listed.

anvi-script-get-coverage-from-bam [-h] -b BAM_FILE [-c CONTIG_NAME]
                                  [-l CONTIGS_OF_INTEREST]
                                  [-C COLLECTION_TXT] -m
                                  {pos,contig,bin} -o OUTPUT
                                  [--skip-contigs-check]

  -b BAM_FILE, --bam-file BAM_FILE
                        Sorted and indexed BAM file to analyze.

  -c CONTIG_NAME, --contig-name CONTIG_NAME
                        The name of a single contig

  -l CONTIGS_OF_INTEREST, --contigs-of-interest CONTIGS_OF_INTEREST
                        Provide here a file where each line is a contig name.

  -C COLLECTION_TXT, --collection-txt COLLECTION_TXT
                        Provide a collection text file. The first column
                        should be contig names and the second column should be
                        the bin to which the contig belongs. If you have a
                        collection from a profile database, you can export it
                        in this format with anvi-export-collection.

  -m {pos,contig,bin}, --method {pos,contig,bin}
                        If pos, each nucleotide position will be reported
                        (valid for OPTION #1, #2, #3). If contig, report
                        contains contig averages (valid for OPTION #2, #3). If
                        bin, report contains bin averages (valid for OPTION
                        #3).

  -o OUTPUT, --output OUTPUT
                        Output tab-delimited file path. Will overwrite
                        existing files.

  --skip-contigs-check  Checking to see that your collection text or contigs
                        of interest file has correct names can take a really
                        long time if you have a large enough number of
                        contigs. Use this flag to forego checking, and find
                        out the hard way.

anvi-script-get-hmm-hits-per-gene-call [-h] -c CONTIGS_DB
                                       [--hmm-source SOURCE NAME] -o
                                       FILE_PATH

  -c CONTIGS_DB, --contigs-db CONTIGS_DB
                        Anvi'o contigs database generated by 'anvi-gen-
                        contigs-database'

  --hmm-source SOURCE NAME
                        Use a specific HMM source. You can use '--list-hmm-
                        sources' flag to see a list of available resources.
                        The default is 'None'.

  -o FILE_PATH, --output-file FILE_PATH
                        File path to store results.

anvi-script-get-short-reads-matching-something [-h] --match-sequence
                                               SHORT SEQUENCE [-m INT]
                                               -s NAME [-O PATH]
                                               [--report-raw]
                                               [--stop-after INT]
                                               FASTQ_FILES
                                               [FASTQ_FILES ...]

  FASTQ_FILES           One or more FASTQ formatted files

  --match-sequence SHORT SEQUENCE
                        Short sequence to look for..
  -m INT, --min-remainder-length INT
                        Minimum lenght of the remainder of the read after the
                        match. If your short read is XXXMMMMMMYYYYYYYYYYYYYY,
                        where M indicates nucleotides of matchhing sequence,
                        min remainder length is len(Y). Default is 60.
  -s NAME, --sample-name NAME
                        A short sample name (use a single word without spaces
                        or fancy chars)
  -O PATH, --output-directory PATH
                        Output directory for results to be stored. The default
                        is the current working directory.
  --report-raw          Just report them raw. Don't bother trimming.
  --stop-after INT      Stop after X number of hits because who needs data.

anvi-script-merge-collections [-h] -c CONTIGS_DB -i FILES) [FILE(S ...]
                              -o OUTPUT_FILE

  -c CONTIGS_DB, --contigs-db CONTIGS_DB
                        Anvi'o contigs database generated by 'anvi-gen-
                        contigs-database'
  -i FILE(S) [FILE(S) ...], --input-files FILE(S) [FILE(S) ...]
                        Input file(s). TAB-delimited input files should have
                        two columns, where the first column holds the contig
                        name, and the second one the bin id. This is the
                        standard ouptut of the program anvi-export-collection.
  -o OUTPUT_FILE, --output-file OUTPUT_FILE
                        Output file name.

anvi-script-predict-CPR-genomes [-h] -c CONTIGS_DB [-p PROFILE_DB]
                                [-C COLLECTION_NAME]
                                [--list-collections]
                                [--report-only-cpr]
                                [--min-genome-size MIN_GENOME_SIZE]
                                [--min-percent-completion MIN_PERCENT_COMPLETION]
                                [--max-percent-redundancy MAX_PERCENT_REDUNDANCY]
                                [--min-class-probability MIN_CLASS_PROBABILITY]
                                [-o FILE_PATH] [--just-do-it]
                                CLASSIFIER_FILE

  CLASSIFIER_FILE       Model output generated by anvi-script-gen-CPR-
                        classifier

  -c CONTIGS_DB, --contigs-db CONTIGS_DB
                        Anvi'o contigs database generated by 'anvi-gen-
                        contigs-database'
  -p PROFILE_DB, --profile-db PROFILE_DB
                        Anvi'o profile database
  -C COLLECTION_NAME, --collection-name COLLECTION_NAME
                        Collection name.
  --list-collections    Show available collections and exit.
  --report-only-cpr     Include only bins that look like CPR genomes.
  --min-genome-size MIN_GENOME_SIZE
                        Minimum genome size to consider for CPR in Mbp.
                        Default is 0.500000
  --min-percent-completion MIN_PERCENT_COMPLETION
                        Minimum percent completion estimate based on anvi'o
                        default single-copy gene collections. Default is 50
  --max-percent-redundancy MAX_PERCENT_REDUNDANCY
                        Maxumum percent redundancy or single-copy genes in an
                        anvi'o bin, or a genome to consider for
                        classification. The default is 30
  --min-class-probability MIN_CLASS_PROBABILITY
                        If the classification confidence is below this don't
                        bother. Default is 75.
  -o FILE_PATH, --output-file FILE_PATH
                        File path to store results.
  --just-do-it          Don't bother me with questions or warnings, just do
                        it.

anvi-script-process-genbank [-h] -i GENBANK [-O FILENAME_PREFIX]
                            [--output-fasta FASTA]
                            [--output-gene-calls TAB DELIMITED FILE]
                            [--output-functions TAB DELIMITED FILE]
                            [--annotation-source ANNOTATION_SOURCE]
                            [--annotation-version ANNOTATION_VERSION]

  -i GENBANK, --input-genbank GENBANK
                        Input GenBank file

  -O FILENAME_PREFIX, --output-file-prefix FILENAME_PREFIX
                        A prefix to be used while naming the output files (no
                        file type extensions please; just a prefix).
  --output-fasta FASTA  Output FASTA file path.
  --output-gene-calls TAB DELIMITED FILE
                        Output file path for external gene calls
  --output-functions TAB DELIMITED FILE
                        Output file path for anvi'o-importable gene functions
                        file

  --annotation-source ANNOTATION_SOURCE
                        Annotation source (default: "NCBI_PGAP")
  --annotation-version ANNOTATION_VERSION
                        Annotation source version to be stored in the database
                        (default: "v4.6")

anvi-script-process-genbank-metadata [-h] -m GENBANK_METADATA
                                     [-o DIR_PATH]
                                     [--output-fasta-txt OUTPUT_FASTA_TXT]
                                     [-E]

  -m GENBANK_METADATA, --metadata GENBANK_METADATA
                        This is the file you get from the program `ncbi-
                        genome-download` when you use the parameter
                        `--metadata-table`.

  -o DIR_PATH, --output-dir DIR_PATH
                        Directory path for output files
  --output-fasta-txt OUTPUT_FASTA_TXT
                        This is not a FASTA file, but a TAB-delimited file
                        with all the file names and paths processed by this
                        program. This output can directly go into the anvi'o
                        snakemake workflows because magic.

  -E, --exclude-gene-calls-from-fasta-txt
                        This flag will exclude the external gene calls and
                        functions from the fasta.txt file. Files for external
                        gene calls and functions according to the information
                        stored in GenBank file, but they will simply not be
                        included in your fasta.txt file. By doing so you will
                        *gurantee* that when you use this file from within a
                        workflow, anvi'o wil use its default gene caller to
                        identify genes.

anvi-script-reformat-fasta [-h] [-l MIN_LENGTH]
                           [--max-percentage-gaps PERCENTAGE]
                           [-i TXT FILE] [-I TXT FILE] -o FASTA FILE
                           [--simplify-names] [--prefix PREFIX]
                           [-r REPORT FILE]
                           FASTA FILE

  FASTA FILE

  -l MIN_LENGTH, --min-len MIN_LENGTH
                        Minimum length of contigs to keep (contigs shorter
                        than this value will not be included in the output
                        file). The default is 0, so nothing will be removed if
                        you do not declare a minimum size.
  --max-percentage-gaps PERCENTAGE
                        Maximum fraction of gaps in a sequence (any sequence
                        with more gaps will be removed from the output FASTA
                        file). The default is 100.000000.
  -i TXT FILE, --exclude-ids TXT FILE
                        IDs to remove from the FASTA file. You cannot provide
                        both --keep-ids and --exclude-ids.
  -I TXT FILE, --keep-ids TXT FILE
                        If provided, all IDs not in this file will be excluded
                        from the reformatted FASTA file. Any additional
                        filters (such as --min-len) will still be applied to
                        the IDs in this file. You cannot provide both
                        --exclude-ids and --keep-ids.
  -o FASTA FILE, --output-file FASTA FILE
                        Output file path.
  --simplify-names      Edit deflines to make sure they contigs have simple
                        names.
  --prefix PREFIX       Use this parameter if you would like to add a prefix
                        to your contig names while simplifying them. The
                        prefix must be a single word (you can use underscor
                        character, but nothing more!).
  -r REPORT FILE, --report-file REPORT FILE
                        Report file path. When you run this program with
                        `--simplify-names` flag, all changes to deflines will
                        be reported in this file in case you need to go back
                        to this information later. It is not mandatory to
                        declare one, but it is a very good idea to have it.

anvi-script-run-eggnog-mapper [-h] -c CONTIGS_DB
                              [--cog-data-dir COG_DATA_DIR]
                              [-T NUM_THREADS]
                              [--drop-previous-annotations]
                              [--annotation EMAPPER_ANNOTATION_FILE]
                              [--use-version EMAPPER_VERSION]

  -c CONTIGS_DB, --contigs-db CONTIGS_DB
                        Anvi'o contigs database generated by 'anvi-gen-
                        contigs-database'
  --cog-data-dir COG_DATA_DIR
                        The directory path for your COG setup if you did not
                        use the default directory.
  -T NUM_THREADS, --num-threads NUM_THREADS
                        Maximum number of threads to use for multithreading
                        whenever possible. Very conservatively, the default is
                        1. It is a good idea to not exceed the number of CPUs
                        / cores on your system. Plus, please be careful with
                        this option if you are running your commands on a SGE
                        --if you are clusterizing your runs, and asking for
                        multiple threads to use, you may deplete your
                        resources very fast.
  --drop-previous-annotations
                        When declared, previous annotations in the database
                        will be dropped.
  --annotation EMAPPER_ANNOTATION_FILE
                        If you have an annotation file from a previous run,
                        you can call this program to import the contents of
                        that file into the database instead of a run from
                        scratch. In that case, you must also use the `--use-
                        version` parameter to clarify which parser version
                        should be used to parse it.
  --use-version EMAPPER_VERSION
                        The version of eggnog-mapper that generated the
                        annotation file.

anvi-script-snvs-to-interactive [-h]
                                [--min-departure-from-consensus FLOAT]
                                [--max-departure-from-consensus FLOAT]
                                [--min-departure-from-reference FLOAT]
                                [--max-departure-from-reference FLOAT]
                                [--display-dep-from-reference]
                                [--only-in-genes] [--random INTEGER]
                                [--just-do-it] -o DIR_PATH
                                VARIABILITY_PROFILE

  VARIABILITY_PROFILE   The output file generated by anvi-gen-variability-
                        profile

  --min-departure-from-consensus FLOAT
                        Minimum departure from consensus at a given variable
                        nucleotide position. The default is 0.00.
  --max-departure-from-consensus FLOAT
                        Maximum departure from consensus at a given variable
                        nucleotide position. The default is 1.00.
  --min-departure-from-reference FLOAT
                        Minimum departure from consensus at a given variable
                        nucleotide position. The default is 0.00.
  --max-departure-from-reference FLOAT
                        Maximum departure from consensus at a given variable
                        nucleotide position. The default is 1.00.
  --display-dep-from-reference
                        By default this program will generate a matrix file
                        that displays departure from consensus values. This
                        flag will switch to departure from reference.
  --only-in-genes       With this flag you will ignore SNVs in non-coding
                        regions.
  --random INTEGER      Use this parameter to randomly subset your data. If
                        there are too many SNV positions, this script may take
                        forever to finish. You should *never* let it try to
                        deal with more than 25-30K points, but an ideal would
                        be around 4-5 thousand.
  --just-do-it          Don't bother me with questions or warnings, just do
                        it.
  -o DIR_PATH, --output-dir DIR_PATH
                        Directory path for output files

anvi-script-tabulate [-h]

anvi-script-transpose-matrix [-h] -o MATRIX_FILE MATRIX_FILE

  MATRIX_FILE           Input matrix.

  -o MATRIX_FILE, --output-file MATRIX_FILE
                        File path to store results.

anvi-script-variability-to-vcf [-h] [-i FILE_PATH] [-o FILE_PATH]

  -i FILE_PATH, --input FILE_PATH
                        Filepath to the SNV table. This is the output from the
                        anvi-gen-variability-profile program with the
                        nucleotide engine (which is the default engine).
  -o FILE_PATH, --output-file FILE_PATH
                        File path to store results.