4.11. augur_from_msa_with_subsampler¶
Build trees, and convert to json representation suitable for Nextstrain visualization. See https://nextstrain.org/docs/getting-started/ and https://nextstrain-augur.readthedocs.io/en/stable/
4.11.1. Inputs¶
4.11.1.1. Required inputs¶
augur_from_msa_with_subsampler.aligned_msa_fasta
File — Default: None
Multiple sequence alignment (aligned fasta).
augur_from_msa_with_subsampler.auspice_config
File — Default: None
A file specifying options to customize the auspice export; see: https://nextstrain.github.io/auspice/customise-client/introduction
augur_from_msa_with_subsampler.sample_metadata
Array[File]+ — Default: None
Metadata in tab-separated text format. See https://nextstrain-augur.readthedocs.io/en/stable/faq/metadata.html for details. At least one tab file must be provided--if multiple are provided, they will be joined via a full left outer join using the 'strain' column as the join ID.
augur_from_msa_with_subsampler.subsample_by_cases.case_data
File — Default: None
???
augur_from_msa_with_subsampler.subsample_by_cases.geo_column
String — Default: None
???
augur_from_msa_with_subsampler.subsample_by_cases.id_column
String — Default: None
???
4.11.1.2. Other inputs¶
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augur_from_msa_with_subsampler.ancestral_traits.confidence
Boolean — Default: true
???
augur_from_msa_with_subsampler.ancestral_traits.disk_size
Int — Default: 750
???
augur_from_msa_with_subsampler.ancestral_traits.docker
String — Default: "nextstrain/base:build-20230905T192825Z"
???
augur_from_msa_with_subsampler.ancestral_traits.machine_mem_gb
Int — Default: 32
???
augur_from_msa_with_subsampler.ancestral_traits.sampling_bias_correction
Float? — Default: None
???
augur_from_msa_with_subsampler.ancestral_traits.weights
File? — Default: None
???
augur_from_msa_with_subsampler.ancestral_traits_to_infer
Array[String]? — Default: None
A list of metadata traits to use for ancestral node inference (see https://nextstrain-augur.readthedocs.io/en/stable/usage/cli/traits.html). Multiple traits may be specified; must correspond exactly to column headers in metadata file. Omitting these values will skip ancestral trait inference, and ancestral nodes will not have estimated values for metadata.
augur_from_msa_with_subsampler.ancestral_tree.disk_size
Int — Default: 300
???
augur_from_msa_with_subsampler.ancestral_tree.docker
String — Default: "nextstrain/base:build-20230905T192825Z"
???
augur_from_msa_with_subsampler.ancestral_tree.infer_ambiguous
Boolean — Default: false
???
augur_from_msa_with_subsampler.ancestral_tree.inference
String — Default: "joint"
???
augur_from_msa_with_subsampler.ancestral_tree.keep_ambiguous
Boolean — Default: false
???
augur_from_msa_with_subsampler.ancestral_tree.keep_overhangs
Boolean — Default: false
???
augur_from_msa_with_subsampler.ancestral_tree.output_vcf
File? — Default: None
???
augur_from_msa_with_subsampler.ancestral_tree.vcf_reference
File? — Default: None
???
augur_from_msa_with_subsampler.assign_clades_to_nodes.disk_size
Int — Default: 300
???
augur_from_msa_with_subsampler.assign_clades_to_nodes.docker
String — Default: "nextstrain/base:build-20230905T192825Z"
???
augur_from_msa_with_subsampler.augur_mask_sites.disk_size
Int — Default: 750
???
augur_from_msa_with_subsampler.augur_mask_sites.docker
String — Default: "nextstrain/base:build-20230905T192825Z"
???
augur_from_msa_with_subsampler.clades_tsv
File? — Default: None
A TSV file containing clade mutation positions in four columns: [clade gene site alt]; see: https://nextstrain.org/docs/tutorials/defining-clades
augur_from_msa_with_subsampler.draft_augur_tree.cpus
Int — Default: 64
???
augur_from_msa_with_subsampler.draft_augur_tree.disk_size
Int — Default: 1250
???
augur_from_msa_with_subsampler.draft_augur_tree.docker
String — Default: "nextstrain/base:build-20230905T192825Z"
???
augur_from_msa_with_subsampler.draft_augur_tree.exclude_sites
File? — Default: None
???
augur_from_msa_with_subsampler.draft_augur_tree.machine_mem_gb
Int — Default: 32
???
augur_from_msa_with_subsampler.draft_augur_tree.method
String — Default: "iqtree"
???
augur_from_msa_with_subsampler.draft_augur_tree.substitution_model
String — Default: "GTR"
???
augur_from_msa_with_subsampler.draft_augur_tree.tree_builder_args
String? — Default: None
???
augur_from_msa_with_subsampler.draft_augur_tree.vcf_reference
File? — Default: None
???
augur_from_msa_with_subsampler.export_auspice_json.color_by_metadata
Array[String]? — Default: None
???
augur_from_msa_with_subsampler.export_auspice_json.colors_tsv
File? — Default: None
???
augur_from_msa_with_subsampler.export_auspice_json.description_md
File? — Default: None
???
augur_from_msa_with_subsampler.export_auspice_json.disk_size
Int — Default: 300
???
augur_from_msa_with_subsampler.export_auspice_json.docker
String — Default: "nextstrain/base:build-20230905T192825Z"
???
augur_from_msa_with_subsampler.export_auspice_json.geo_resolutions
Array[String]? — Default: None
???
augur_from_msa_with_subsampler.export_auspice_json.include_root_sequence
Boolean — Default: true
???
augur_from_msa_with_subsampler.export_auspice_json.lat_longs_tsv
File? — Default: None
???
augur_from_msa_with_subsampler.export_auspice_json.machine_mem_gb
Int — Default: 64
???
augur_from_msa_with_subsampler.export_auspice_json.maintainers
Array[String]? — Default: None
???
augur_from_msa_with_subsampler.export_auspice_json.out_basename
String — Default: basename(basename(tree,".nwk"),"_timetree")
???
augur_from_msa_with_subsampler.export_auspice_json.title
String? — Default: None
???
augur_from_msa_with_subsampler.filter_sequences_to_list.disk_size
Int — Default: 750
???
augur_from_msa_with_subsampler.filter_sequences_to_list.docker
String — Default: "quay.io/broadinstitute/viral-core:2.1.33"
???
augur_from_msa_with_subsampler.filter_sequences_to_list.out_fname
String — Default: sub(sub(basename(sequences,".zst"),".vcf",".filtered.vcf"),".fasta$",".filtered.fasta")
???
augur_from_msa_with_subsampler.genbank_gb
File? — Default: None
A 'genbank' formatted gene annotation file that is used to calculate coding consequences of observed mutations. Must correspond to the same coordinate space as ref_fasta. Typically downloaded from the same NCBI accession number as ref_fasta.
augur_from_msa_with_subsampler.mask_bed
File? — Default: None
Optional list of sites to mask when building trees.
augur_from_msa_with_subsampler.ref_fasta
File? — Default: None
A reference assembly (not included in assembly_fastas) to align assembly_fastas against. Typically from NCBI RefSeq or similar.
augur_from_msa_with_subsampler.refine_augur_tree.branch_length_inference
String? — Default: None
???
augur_from_msa_with_subsampler.refine_augur_tree.clock_filter_iqd
Int? — Default: 4
???
augur_from_msa_with_subsampler.refine_augur_tree.clock_rate
Float? — Default: None
???
augur_from_msa_with_subsampler.refine_augur_tree.clock_std_dev
Float? — Default: None
???
augur_from_msa_with_subsampler.refine_augur_tree.coalescent
String? — Default: None
???
augur_from_msa_with_subsampler.refine_augur_tree.covariance
Boolean? — Default: None
???
augur_from_msa_with_subsampler.refine_augur_tree.date_confidence
Boolean — Default: true
???
augur_from_msa_with_subsampler.refine_augur_tree.date_inference
String? — Default: "marginal"
???
augur_from_msa_with_subsampler.refine_augur_tree.disk_size
Int — Default: 750
???
augur_from_msa_with_subsampler.refine_augur_tree.divergence_units
String? — Default: "mutations"
???
augur_from_msa_with_subsampler.refine_augur_tree.docker
String — Default: "nextstrain/base:build-20230905T192825Z"
???
augur_from_msa_with_subsampler.refine_augur_tree.gen_per_year
Int? — Default: None
???
augur_from_msa_with_subsampler.refine_augur_tree.keep_polytomies
Boolean — Default: false
???
augur_from_msa_with_subsampler.refine_augur_tree.keep_root
Boolean — Default: true
???
augur_from_msa_with_subsampler.refine_augur_tree.machine_mem_gb
Int — Default: 75
???
augur_from_msa_with_subsampler.refine_augur_tree.precision
Int? — Default: None
???
augur_from_msa_with_subsampler.refine_augur_tree.root
String? — Default: None
???
augur_from_msa_with_subsampler.refine_augur_tree.vcf_reference
File? — Default: None
???
augur_from_msa_with_subsampler.subsample_by_cases.baseline
Float — Default: 0.0001
???
augur_from_msa_with_subsampler.subsample_by_cases.date_column
String — Default: "date"
???
augur_from_msa_with_subsampler.subsample_by_cases.docker
String — Default: "quay.io/broadinstitute/subsampler"
???
augur_from_msa_with_subsampler.subsample_by_cases.end_date
String? — Default: None
???
augur_from_msa_with_subsampler.subsample_by_cases.filter_file
File? — Default: None
???
augur_from_msa_with_subsampler.subsample_by_cases.keep_file
File? — Default: None
???
augur_from_msa_with_subsampler.subsample_by_cases.machine_mem_gb
Int — Default: 30
???
augur_from_msa_with_subsampler.subsample_by_cases.remove_file
File? — Default: None
???
augur_from_msa_with_subsampler.subsample_by_cases.seed_num
Int? — Default: None
???
augur_from_msa_with_subsampler.subsample_by_cases.start_date
String? — Default: None
???
augur_from_msa_with_subsampler.subsample_by_cases.unit
String — Default: "week"
???
augur_from_msa_with_subsampler.tip_frequencies.censored
Boolean — Default: false
???
augur_from_msa_with_subsampler.tip_frequencies.disk_size
Int — Default: 200
???
augur_from_msa_with_subsampler.tip_frequencies.docker
String — Default: "nextstrain/base:build-20230905T192825Z"
???
augur_from_msa_with_subsampler.tip_frequencies.include_internal_nodes
Boolean — Default: false
???
augur_from_msa_with_subsampler.tip_frequencies.inertia
Float? — Default: None
???
augur_from_msa_with_subsampler.tip_frequencies.machine_mem_gb
Int — Default: 64
???
augur_from_msa_with_subsampler.tip_frequencies.max_date
Float? — Default: None
???
augur_from_msa_with_subsampler.tip_frequencies.method
String — Default: "kde"
???
augur_from_msa_with_subsampler.tip_frequencies.min_date
Float? — Default: None
???
augur_from_msa_with_subsampler.tip_frequencies.minimal_frequency
Float? — Default: None
???
augur_from_msa_with_subsampler.tip_frequencies.narrow_bandwidth
Float? — Default: None
???
augur_from_msa_with_subsampler.tip_frequencies.out_basename
String — Default: basename(tree,'.nwk')
???
augur_from_msa_with_subsampler.tip_frequencies.pivot_interval
Int? — Default: None
???
augur_from_msa_with_subsampler.tip_frequencies.pivot_interval_units
String? — Default: None
???
augur_from_msa_with_subsampler.tip_frequencies.proportion_wide
Float? — Default: None
???
augur_from_msa_with_subsampler.tip_frequencies.stiffness
Float? — Default: None
???
augur_from_msa_with_subsampler.tip_frequencies.wide_bandwidth
Float? — Default: None
???
augur_from_msa_with_subsampler.translate_augur_tree.disk_size
Int — Default: 300
???
augur_from_msa_with_subsampler.translate_augur_tree.docker
String — Default: "nextstrain/base:build-20230905T192825Z"
???
augur_from_msa_with_subsampler.translate_augur_tree.genes
File? — Default: None
???
augur_from_msa_with_subsampler.translate_augur_tree.vcf_reference
File? — Default: None
???
augur_from_msa_with_subsampler.translate_augur_tree.vcf_reference_output
File? — Default: None
???
augur_from_msa_with_subsampler.tsv_join.machine_mem_gb
Int — Default: 7
???
augur_from_msa_with_subsampler.tsv_join.prefer_first
Boolean — Default: true
???
4.11.2. Outputs¶
augur_from_msa_with_subsampler.auspice_input_json
File
???
augur_from_msa_with_subsampler.masked_subsampled_msa
File
???
augur_from_msa_with_subsampler.ml_tree
File
???
augur_from_msa_with_subsampler.node_data_jsons
Array[File]
???
augur_from_msa_with_subsampler.root_sequence_json
File
???
augur_from_msa_with_subsampler.sampling_stats_file
File
???
augur_from_msa_with_subsampler.selected_metadata
File
???
augur_from_msa_with_subsampler.time_tree
File
???
augur_from_msa_with_subsampler.tip_frequencies_json
File
???
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