S

    binchicken iterate

    Run a further iteration of coassemble, including newly recovered bins. All coassemble options are available and can be altered for the new iteration (see example workflow).

    # Example: rerun coassemble, adding new bins to database
binchicken iterate --coassemble-output coassemble_dir

# Example: rerun coassemble, adding new bins to database, providing genomes directly
binchicken iterate --coassemble-output coassemble_dir \
    --new-genomes new_genome_1.fna

    Defaults to using genomes (from the provided coassemble outputs) with at least 70% complete and at most 10% contamination as estimated by CheckM2. Automatically excludes previous coassemblies.

    OPTIONS

    ITERATION OPTIONS

    --iteration ITERATION

    Iteration number used for unique bin naming [default: 0]

    --aviary-outputs AVIARY_OUTPUTS [AVIARY_OUTPUTS ...]

    Output dir from Aviary coassembly and recover commands produced by coassemble subcommand

    --new-genomes NEW_GENOMES [NEW_GENOMES ...]

    New genomes to iterate (alternative to --aviary-outputs)

    --new-genomes-list NEW_GENOMES_LIST

    New genomes to iterate (alternative to --aviary-outputs) newline separated

    --new-genome-singlem NEW_GENOME_SINGLEM

    Combined SingleM otu tables for new genome transcripts. If provided, genome SingleM is skipped

    --elusive-clusters ELUSIVE_CLUSTERS [ELUSIVE_CLUSTERS ...]

    Previous elusive_clusters.tsv files produced by coassemble subcommand (used to check for duplicated coassembly suggestions)

    --coassemble-output COASSEMBLE_OUTPUT

    Output dir from coassemble subcommand

    --coassemble-unbinned COASSEMBLE_UNBINNED

    SingleM appraise unbinned output from Bin Chicken coassemble (alternative to --coassemble-output)

    --coassemble-binned COASSEMBLE_BINNED

    SingleM appraise binned output from Bin Chicken coassemble (alternative to --coassemble-output)

    --checkm-version CHECKM_VERSION

    CheckM version to use to quality cutoffs [default: 2]

    --min-completeness MIN_COMPLETENESS

    Include bins with at least this minimum completeness [default: 70]

    --max-contamination MAX_CONTAMINATION

    Include bins with at most this maximum contamination [default: 10]

    BASE INPUT ARGUMENTS

    --forward, --reads, --sequences FORWARD [FORWARD ...]

    input forward/unpaired nucleotide read sequence(s)

    --forward-list, --reads-list, --sequences-list FORWARD_LIST

    input forward/unpaired nucleotide read sequence(s) newline separated

    --reverse REVERSE [REVERSE ...]

    input reverse nucleotide read sequence(s)

    --reverse-list REVERSE_LIST

    input reverse nucleotide read sequence(s) newline separated

    --genomes GENOMES [GENOMES ...]

    Reference genomes for read mapping

    --genomes-list GENOMES_LIST

    Reference genomes for read mapping newline separated

    --coassembly-samples COASSEMBLY_SAMPLES [COASSEMBLY_SAMPLES ...]

    Restrict coassembly to these samples. Remaining samples will still be used for recovery [default: use all samples]

    --coassembly-samples-list COASSEMBLY_SAMPLES_LIST

    Restrict coassembly to these samples, newline separated. Remaining samples will still be used for recovery [default: use all samples]

    --singlem-metapackage SINGLEM_METAPACKAGE

    SingleM metapackage for sequence searching. [default: use path from SINGLEM_METAPACKAGE_PATH env variable]

    INTERMEDIATE RESULTS INPUT ARGUMENTS

    --sample-singlem SAMPLE_SINGLEM [SAMPLE_SINGLEM ...]

    SingleM otu tables for each sample, in the form "[sample name]_read.otu_table.tsv". If provided, SingleM pipe sample is skipped

    --sample-singlem-list SAMPLE_SINGLEM_LIST

    SingleM otu tables for each sample, in the form "[sample name]_read.otu_table.tsv" newline separated. If provided, SingleM pipe sample is skipped

    --sample-singlem-dir SAMPLE_SINGLEM_DIR

    Directory containing SingleM otu tables for each sample, in the form "[sample name]_read.otu_table.tsv". If provided, SingleM pipe sample is skipped

    --sample-query SAMPLE_QUERY [SAMPLE_QUERY ...]

    Queried SingleM otu tables for each sample against genome database, in the form "[sample name]_query.otu_table.tsv". If provided, SingleM pipe and appraise are skipped

    --sample-query-list SAMPLE_QUERY_LIST

    Queried SingleM otu tables for each sample against genome database, in the form "[sample name]_query.otu_table.tsv" newline separated. If provided, SingleM pipe and appraise are skipped

    --sample-query-dir SAMPLE_QUERY_DIR

    Directory containing Queried SingleM otu tables for each sample against genome database, in the form "[sample name]_query.otu_table.tsv". If provided, SingleM pipe and appraise are skipped

    --sample-read-size SAMPLE_READ_SIZE

    Comma separated list of sample name and size (bp). If provided, sample read counting is skipped

    --genome-transcripts GENOME_TRANSCRIPTS [GENOME_TRANSCRIPTS ...]

    Genome transcripts for reference database, in the form "[genome]_protein.fna"

    --genome-transcripts-list GENOME_TRANSCRIPTS_LIST

    Genome transcripts for reference database, in the form "[genome]_protein.fna" newline separated

    --genome-singlem GENOME_SINGLEM

    Combined SingleM otu tables for genome transcripts. If provided, genome SingleM is skipped

    CLUSTERING OPTIONS

    --taxa-of-interest TAXA_OF_INTEREST

    Only consider sequences from this GTDB taxa (e.g. p__Planctomycetota) [default: all]

    --appraise-sequence-identity APPRAISE_SEQUENCE_IDENTITY

    Minimum sequence identity for SingleM appraise against reference database [default: 86%, Genus-level]

    --min-sequence-coverage MIN_SEQUENCE_COVERAGE

    Minimum combined coverage for sequence inclusion [default: 10]

    --single-assembly

    Skip appraise to discover samples to differential abundance binning. Forces --num-coassembly-samples and --max-coassembly-samples to 1 and sets --max- coassembly-size to None

    --exclude-coassemblies EXCLUDE_COASSEMBLIES [EXCLUDE_COASSEMBLIES ...]

    List of coassemblies to exclude, space separated, in the form "sample_1,sample_2"

    --exclude-coassemblies-list EXCLUDE_COASSEMBLIES_LIST

    List of coassemblies to exclude, space separated, in the form "sample_1,sample_2", newline separated

    --num-coassembly-samples NUM_COASSEMBLY_SAMPLES

    Number of samples per coassembly cluster [default: 2]

    --max-coassembly-samples MAX_COASSEMBLY_SAMPLES

    Upper bound for number of samples per coassembly cluster [default: --num- coassembly-samples]

    --max-coassembly-size MAX_COASSEMBLY_SIZE

    Maximum size (Gbp) of coassembly cluster [default: 50Gbp]

    --max-recovery-samples MAX_RECOVERY_SAMPLES

    Upper bound for number of related samples to use for differential abundance binning [default: 20]

    --abundance-weighted

    Weight sequences by mean sample abundance when ranking clusters [default: False]

    --abundance-weighted-samples ABUNDANCE_WEIGHTED_SAMPLES [ABUNDANCE_WEIGHTED_SAMPLES ...]

    Restrict sequence weighting to these samples. Remaining samples will still be used for coassembly [default: use all samples]

    --abundance-weighted-samples-list ABUNDANCE_WEIGHTED_SAMPLES_LIST

    Restrict sequence weighting to these samples, newline separated. Remaining samples will still be used for coassembly [default: use all samples]

    --kmer-precluster {never,large,always}

    Run kmer preclustering using unbinned window sequences as kmers. [default: large; perform preclustering when given >1000 samples]

    --precluster-size PRECLUSTER_SIZE

    # of samples within each sample's precluster [default: 5 * max-recovery- samples]

    --prodigal-meta

    Use prodigal "-p meta" argument (for testing)

    COASSEMBLY OPTIONS

    --assemble-unmapped

    Only assemble reads that do not map to reference genomes

    --run-qc

    Run Fastp QC on reads

    --unmapping-min-appraised UNMAPPING_MIN_APPRAISED

    Minimum fraction of sequences binned to justify unmapping [default: 0.1]

    --unmapping-max-identity UNMAPPING_MAX_IDENTITY

    Maximum sequence identity of mapped sequences kept for coassembly [default: 99%]

    --unmapping-max-alignment UNMAPPING_MAX_ALIGNMENT

    Maximum percent alignment of mapped sequences kept for coassembly [default: 99%]

    --run-aviary

    Run Aviary commands for all identified coassemblies (unless specific coassemblies are chosen with --coassemblies) [default: do not]

    --cluster-submission

    Flag that cluster submission will occur through `--snakemake-profile`. This sets the local threads of Aviary recover to 1, allowing parallel job submission [default: do not]

    --aviary-speed {fast,comprehensive}

    Run Aviary recover in 'fast' or 'comprehensive' mode. Fast mode skips slow binners and refinement steps. [default: fast]

    --assembly-strategy {dynamic,metaspades,megahit}

    Assembly strategy to use with Aviary. [default: dynamic; attempts metaspades and if fails, switches to megahit]

    --aviary-gtdbtk-db AVIARY_GTDBTK_DB

    Path to GTDB-Tk database directory for Aviary. Only required if --aviary-speed is set to comprehensive [default: use path from GTDBTK_DATA_PATH env variable]

    --aviary-checkm2-db AVIARY_CHECKM2_DB

    Path to CheckM2 database directory for Aviary. [default: use path from CHECKM2DB env variable]

    --aviary-assemble-cores AVIARY_ASSEMBLE_CORES

    Maximum number of cores for Aviary assemble to use. [default: 64]

    --aviary-assemble-memory AVIARY_ASSEMBLE_MEMORY

    Maximum amount of memory for Aviary assemble to use (Gigabytes). [default: 500]

    --aviary-recover-cores AVIARY_RECOVER_CORES

    Maximum number of cores for Aviary recover to use. [default: 32]

    --aviary-recover-memory AVIARY_RECOVER_MEMORY

    Maximum amount of memory for Aviary recover to use (Gigabytes). [default: 250]

    GENERAL OPTIONS

    --output OUTPUT

    Output directory [default: .]

    --conda-prefix CONDA_PREFIX

    Path to conda environment install location. [default: Use path from CONDA_ENV_PATH env variable]

    --cores CORES

    Maximum number of cores to use [default: 1]

    --dryrun

    dry run workflow

    --snakemake-profile SNAKEMAKE_PROFILE

    Snakemake profile (see https://snakemake.readthedocs.io/en/v7.32.3/executing/cli.html#profiles). Can be used to submit rules as jobs to cluster engine (see https://snakemake.readthedocs.io/en/v7.32.3/executing/cluster.html).

    --local-cores LOCAL_CORES

    Maximum number of cores to use on localrules when running in cluster mode [default: 1]

    --cluster-retries CLUSTER_RETRIES

    Number of times to retry a failed job when using cluster submission (see `--snakemake-profile`) [default: 3].

    --snakemake-args SNAKEMAKE_ARGS

    Additional commands to be supplied to snakemake in the form of a space- prefixed single string e.g. " --quiet"

    --tmp-dir TMP_DIR

    Path to temporary directory. [default: no default]

    OTHER GENERAL OPTIONS

    --debug

    output debug information

    --version

    output version information and quit

    --quiet

    only output errors

    --full-help

    print longer help message

    --full-help-roff

    print longer help message in ROFF (manpage) format

    EXAMPLES

    rerun coassemble, adding new bins to database

    $ binchicken iterate --coassemble-output coassemble_dir

    rerun coassemble, adding new bins to database, providing genomes directly

    $ binchicken iterate --coassemble-output coassemble_dir --new-genomes new_genome_1.fna

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