Workflow Outputs

This page documents all files produced by the Episodic workflow, including:

Snakemake target outputs (requested by rule all)
Additional side-effect files produced by plotting/report scripts

Output root

All outputs are written under:

output.dir (from config), or
output.dir/YYYY-MM-DDTHH:MM:SS when output.dated: true

Examples below use OUT_DIR to represent that resolved output root.

Naming tokens

{clock}: clock model name including gamma prior suffix, e.g. flc-stem_0.5_0.1
{duplicate}: BEAST run replicate index (1..N)
{heights}: MCC summary option, e.g. mean, median, keep, ca

For BEAST run artifacts, {name} is typically {clock}_{duplicate}.

Always produced

File	Description
`OUT_DIR/config.yaml`	Rendered workflow configuration used for the run
`OUT_DIR/taxon_groups.tsv`	Taxon-to-group assignments used by local clock models

Core per-clock BEAST outputs (`beast.fit_clocks: true`)

For each {clock} and {duplicate}:

File pattern	Description
`OUT_DIR/clocks/{clock}/{clock}_{duplicate}/{clock}_{duplicate}.xml`	BEAST XML analysis file
`OUT_DIR/clocks/{clock}/{clock}_{duplicate}/{clock}_{duplicate}.stdout`	BEAST stdout log
`OUT_DIR/clocks/{clock}/{clock}_{duplicate}/{clock}_{duplicate}.log`	BEAST posterior trace log
`OUT_DIR/clocks/{clock}/{clock}_{duplicate}/{clock}_{duplicate}.trees`	Posterior tree samples
`OUT_DIR/clocks/{clock}/{clock}_{duplicate}/{clock}_{duplicate}_trace_plots/`	Trace PNGs per variable

Per-clock summaries and rate plots

Per-clock rate/comparison plots are generated for flc* clocks. Combined clocks_{shape}_{scale}-* plots aggregate all configured clocks.

File pattern	Description
`OUT_DIR/clocks/{clock}/{clock}-summary.csv`	ArviZ posterior summary table
`OUT_DIR/clocks/{clock}/{clock}-violin.svg`	Clock-rate violin plot
`OUT_DIR/clocks/{clock}/{clock}-forest.svg`	Forest plot of posterior medians and 95% HDIs for rate parameters
`OUT_DIR/clocks/{clock}/{clock}-prior-vs-posterior.svg`	Prior-versus-posterior density overlays for rate parameters
`OUT_DIR/clocks/{clock}/{clock}-contrast-violin.svg`	Violin plot of posterior rate differences relative to a baseline rate
`OUT_DIR/clocks/clocks_{shape}_{scale}-violin.svg`	Combined violin plot across clocks
`OUT_DIR/clocks/clocks_{shape}_{scale}-forest.svg`	Combined forest comparison across clocks
`OUT_DIR/clocks/clocks_{shape}_{scale}-prior-vs-posterior.svg`	Combined prior-versus-posterior density overlays across clocks
`OUT_DIR/clocks/clocks_{shape}_{scale}-contrast-violin.svg`	Combined posterior rate-difference violin plot across clocks
`OUT_DIR/clocks/clocks_{shape}_{scale}-trace.svg`	Combined trace plot across clocks

Additional side-effect files from rate plotting scripts

The plotting scripts also emit extra artifacts sharing the same output prefix:

*-violin-rug.svg
*-violin-trimmed.svg
*-violin-rug-trimmed.svg
*-trace.svg
*-trace.html

These are generated for both per-clock and combined clock prefixes.

MCC tree outputs

For each {clock}, {duplicate}, and configured {heights}:

File pattern	Description
`OUT_DIR/clocks/{clock}/{clock}_{duplicate}/{clock}_{duplicate}.mcc.{heights}.nexus`	MCC tree in NEXUS format
`OUT_DIR/clocks/{clock}/{clock}_{duplicate}/{clock}_{duplicate}.mcc.{heights}.nwk`	MCC tree in Newick format
`OUT_DIR/clocks/{clock}/{clock}_{duplicate}/{clock}_{duplicate}.mcc.{heights}.svg`	MCC tree render
`OUT_DIR/clocks/{clock}/{clock}_{duplicate}/{clock}_{duplicate}.mcc.{heights}.height_0.95_HPD.svg`	MCC tree with 95% HPD node ranges
`OUT_DIR/clocks/{clock}/{clock}_{duplicate}/{clock}_{duplicate}.mcc.{heights}.posterior.svg`	MCC tree with posterior node labels

Clock-type-specific outputs

FLC odds / effect-size Bayes factors (`flc*` clocks)

File pattern	Description
`OUT_DIR/clocks/{clock}/{clock}-odds.csv`	Per-clock odds/BF summary
`OUT_DIR/clocks/clocks_{shape}_{scale}-odds.csv`	Combined odds/BF summary concatenating all configured FLC clocks

Additional side-effect per-duplicate files:

OUT_DIR/clocks/{clock}/{clock}_{duplicate}/{clock}_{duplicate}-odds.csv

Relaxed-clock stem quantile analysis (`relaxed*` clocks)

File pattern	Description
`OUT_DIR/clocks/{clock}/{clock}_{duplicate}/{clock}_{duplicate}.stem.rate_quantiles.csv`	Stem branch rank/quantile table
`OUT_DIR/clocks/{clock}/{clock}_{duplicate}/{clock}_{duplicate}.stem.rate_quantiles.svg`	Stem branch rank/quantile plot

FLC partition local-rate posterior comparison (`flc*` clocks)

File pattern	Description
`OUT_DIR/clocks/{clock}/{clock}-partition_local_rate_posteriors.csv`	Long-format posterior rates used for plotting
`OUT_DIR/clocks/{clock}/{clock}-partition_local_rate_posteriors.svg`	Overlaid background vs local posterior frequency histograms by partition
`OUT_DIR/clocks/{clock}/{clock}-substitution_model_rates.csv`	Long-format posterior log GTR relative rates by partition
`OUT_DIR/clocks/{clock}/{clock}-substitution_model_rates.svg`	Boxplots of posterior log GTR relative rates by substitution type and partition

Marginal likelihood outputs (`marginal_likelihood.estimate: true`)

Per MLE run files:

File pattern	Description
`OUT_DIR/mle/{clock}/{clock}_mle_{duplicate}.xml`	MLE XML
`OUT_DIR/mle/{clock}/{clock}_mle_{duplicate}.stdout`	MLE stdout

Aggregated MLE summaries:

File	Description
`OUT_DIR/mle/mle.svg`	Marginal likelihood comparison plot
`OUT_DIR/mle/mle.csv`	Raw extracted MLE values
`OUT_DIR/mle/mle.grouped.csv`	Grouped/aggregated MLE values

Minimal directory example

OUT_DIR/
    config.yaml
    taxon_groups.tsv
    clocks/
        clocks_0.5_0.1-odds.csv
        flc-shared-stem-and-clade_0.5_0.1/
            flc-shared-stem-and-clade_0.5_0.1-summary.csv
            flc-shared-stem-and-clade_0.5_0.1-odds.csv
            flc-shared-stem-and-clade_0.5_0.1-partition_local_rate_posteriors.csv
            flc-shared-stem-and-clade_0.5_0.1-partition_local_rate_posteriors.svg
            flc-shared-stem-and-clade_0.5_0.1-substitution_model_rates.csv
            flc-shared-stem-and-clade_0.5_0.1-substitution_model_rates.svg
            flc-shared-stem-and-clade_0.5_0.1_1/
                flc-shared-stem-and-clade_0.5_0.1_1.log
                flc-shared-stem-and-clade_0.5_0.1_1.trees
                flc-shared-stem-and-clade_0.5_0.1_1.mcc.mean.nexus
                flc-shared-stem-and-clade_0.5_0.1_1.mcc.mean.nwk
                flc-shared-stem-and-clade_0.5_0.1_1.mcc.mean.svg
                flc-shared-stem-and-clade_0.5_0.1_1_trace_plots/
    mle/
        mle.svg
        mle.csv
        mle.grouped.csv

Which outputs are present?

beast.fit_clocks: false → suppresses most clocks/ BEAST-derived outputs
marginal_likelihood.estimate: false → no mle/ outputs
No relaxed clocks configured → no *.stem.rate_quantiles.*
No flc clocks configured → no *-partition_local_rate_posteriors.* or *-substitution_model_rates.*