Results produced by the bactria pipeline v1.0.0 based on the following configuration from config.yml: # Used for parallelization by snakemakecpu_cores: 8# Used for scatter/gather processing, corresponds with the number of families within the taxon defined in fasta_filternfamilies: 17# Number of outgroups to include in each family-level analysis. Minimum is 2.outgroups: 3# Used for verbosity, see `logging` from stdliblog_level: 'INFO'# Either use COI-5P or matK_rbcLmarker: COI-5P# Substitution model in RAxML CLI syntaxmodel: GTR+G# Minimum length to include (this fits COI-5P)minlength: 600# Minimum number of sequences per alignmentminseq: 3# Maximum number of sequences per alignmentmaxseq: 12000# Nucleotide alignments (NT) or aminoacid (AA) for MACSE alignmentdatatype: NT# Choose which records to use from the database for the pipeline. filter_name only takes one name, so does filter level.# filter levels: class, order, family, genus, all (no filter)fasta_filter:filter_level: orderfilter_name: Primatesname: phylogenydependencies:- pip:- -r requirements.txtfile_names:bold_tsv: resources/BOLD_Public.18-Dec-2023/BOLD_Public.18-Dec-2023.tsvopen_tre: resources/opentree/opentree14.9_tree/labelled_supertree/labelled_supertree.trehmm: resources/hmm/COI-5P.hmmfasta_dir: results/fasta/family