Merge pull request 'Implement NUMA topology detection and CPU budget capping' (#74 ) from push-tnkxqmwztnmm into main

Reviewed-on: #74
Implement NUMA topology detection and CPU budget capping
2026-09-11 05:23:42 +00:00 · 2026-09-11 07:22:35 +02:00 · 2026-09-10 15:10:19 +00:00 · 2026-09-10 17:08:32 +02:00 · 2026-08-31 09:09:40 +02:00 · 2026-08-29 06:18:11 +00:00
1082 changed files with 610 additions and 853 deletions
@@ -30,25 +30,7 @@ data-stress
 *.bin.idx
 *.prsb
 Betula_exilis--IGA-24-33
-benchmark/genomes
-benchmark/genomes_orig
-benchmark/simulated_data
-benchmark/specimen_index_presence
-benchmark/global_index_count_dense
-benchmark/global_index_presence
-benchmark/global_index_presence_orig
-benchmark/global_index_presence_sav
-benchmark/global_index_presence_dense
-benchmark/all_specific
-benchmark/global_index_count
-benchmark/specimen_index_count
-benchmark/stats
-benchmark/reference_index
-benchmark/reference_dist
-benchmark/obikmer_dist
-benchmark/specific_index_count
-benchmark/specific_index_presence
-benchmark/query_data
+benchmark/run/
 TNT
 phyg
 biblio
@@ -1,87 +0,0 @@
-# Plan d'amélioration technique - obiskio
-
-## 1. Contexte et objectifs
- **Objectif** : Renforcer la robustesse, la maintenabilité et les performances de la crate `obiskio`.
- **Priorités** : 
-  1. Gestion des erreurs
-  2. Optimisation de la mémoire du pool
-  3. Robustesse concurrente
-  4. Couverture de tests
-  5. Documentation
-
---
-
-## 2. Axes d'amélioration détaillés
-
-### 2.1 Gestion des erreurs
- **Problème** : `SKError` ne couvre pas tous les cas (format invalide, taille maximale, CRC)
- **Actions** :
-  - Ajouter variante `ParseError(String)` dans `src/error.rs`
-  - Valider les tailles de SuperKmer avant parsing
-  - Remplacer `expect()` par `unwrap_or_else` avec messages explicites
-  - Documenter chaque variante d’erreur dans le README
-
-### 2.2 Optimisation du pool de fichiers
- **Problème** : `SKFilePool` utilise un `Vec<WriteEntry>` non contraint et n’effectue pas de nettoyage en cas d’erreur
- **Actions** :
-  - Implémenter un `LimitedVec` avec limite stricte à `MAX_POOL_SIZE`
-  - Créer `clear_memory()` qui supprime les entrées orphelines
-  - Ajouter `evict_lru_threshold()` pour éviction proactive
-  - Introduire un `RwLock` pour les opérations de lecture massives
-
-### 2.3 Robustesse concurrente
- **Problème** : Risque de deadlocks dans `SKFileWriter::write_batch()` et `SKFileReader::reopen_and_seek()`
- **Actions** :
-  - Remplacer `Mutex` par `RwLock` pour les accès en lecture
-  - Ajouter un compteur de blocage et logs de timeout
-  - Utiliser `std::thread::park_timeout` pour débloquer
-  - Insérer `debug_assert!` sur les états invariants
-
-### 2.4 Couverture de tests
- **Problème** : Absence de benchmarks, de tests de migration, de résilience de fichiers corrompus
- **Actions** :
-  - Benchmarks I/O sur 10k+ SuperKmer avec `criterion`
-  - Tests de migration de version de fichier `.meta` → `.v2.meta`
-  - Tests de corruption volontaire (truncature, inversion de bits)
-  - Tests de stress sur pool saturation (100 threads)
-
-### 2.5 Documentation & exemples
- **Actions** :
-  - Ajouter des examples dans chaque module (`# Examples`)
-  - Documenter la logique LRU avec diagrammes Mermaid
-  - Créer un guide « How to recover from eviction »
-  - Mettre à jour le `README.md` avec tableau des variantes d’erreur
-
---
-
-## 3. Plan d'exécution (Roadmap)
-
-| Sprint | Durée | Livrables clés |
-|--------|-------|----------------|
-| **S1** | 2 jours | Refactorisation `SKError`, ajout de tests unitaires |
-| **S2** | 3 jours | Implémentation `clear_memory()` + `LimitedVec` |
-| **S3** | 2 jours | Passage à `RwLock`, ajout de compteurs de blocage |
-| **S4** | 2 jours | Benchmarks + tests de migration |
-| **S5** | 1 jour | Documentation finale & mise à jour du README |
-
---
-
-## 4. Dépendances externes
- Mettre à jour `niffler` vers la version 2.0 (performance compression)
- Évaluer `bincode` vs `serde_json` pour les métas (I/O)
- Ajouter dépendance `criterion` (dev‑dependencies)
-
---
-
-## 5. KPI de suivi
- **Couverture de tests** : ≥85 % des chemins critiques
- **Latence moyenne d’écriture** : ↓15 % après optimisation du pool
- **Taux d’erreurs résolues** : 100 % des nouvelles variantes couvertes
- **Temps de build CI** : ≤5 min pour l’ensemble des benchmarks
-
---
-
-## 6. Validation finale
- Revue de code avec `cargo clippy -- -D warnings`
- Analyse de toxicité avec `cargo deny open-source-licenses`
- Vérification de la conformité aux standards de naming du projet
@@ -1,2 +0,0 @@
-/cache
-/project.local.yml
@@ -1,169 +0,0 @@
-# the name by which the project can be referenced within Serena/when chatting with the LLM.
-project_name: "obikmer"
-
-# the encoding used by text files in the project
-# For a list of possible encodings, see https://docs.python.org/3.11/library/codecs.html#standard-encodings
-encoding: "utf-8"
-
-# line ending convention to use when writing source files.
-# Possible values: unset (use global setting), "lf", "crlf", or "native" (platform default)
-# This does not affect Serena's own files (e.g. memories and configuration files), which always use native line endings.
-line_ending:
-
-# The language backend to use for this project.
-# If not set, the global setting from serena_config.yml is used.
-# Valid values: LSP, JetBrains
-# Note: the backend is fixed at startup. If a project with a different backend
-# is activated post-init, an error will be returned.
-language_backend:
-
-# whether to use project's .gitignore files to ignore files
-ignore_all_files_in_gitignore: true
-
-# advanced configuration option allowing to configure language server-specific options.
-# Maps the language key to the options.
-# The settings are considered only if the project is trusted (see global configuration to define trusted projects).
-# See https://oraios.github.io/serena/02-usage/050_configuration.html#language-server-specific-settings
-ls_specific_settings: {}
-
-# list of additional paths to ignore in this project.
-# Same syntax as gitignore, so you can use * and **.
-# Important: quote patterns that start with `*`, otherwise YAML treats them as aliases.
-# Example:
-#   ignored_paths:
-#     - "examples/**"
-#     - ".worktrees/**"
-#     - "**/bin/**"
-#     - "**/obj/**"
-# Note: global ignored_paths from serena_config.yml are also applied additively.
-ignored_paths: []
-
-# whether the project is in read-only mode
-# If set to true, all editing tools will be disabled and attempts to use them will result in an error
-# Added on 2025-04-18
-read_only: false
-
-# list of tool names to exclude.
-# This extends the existing exclusions (e.g. from the global configuration)
-# Find the list of tools here: https://oraios.github.io/serena/01-about/035_tools.html
-excluded_tools: []
-
-# list of tools to include that would otherwise be disabled (particularly optional tools that are disabled by default).
-# This extends the existing inclusions (e.g. from the global configuration).
-# Find the list of tools here: https://oraios.github.io/serena/01-about/035_tools.html
-included_optional_tools: []
-
-# fixed set of tools to use as the base tool set (if non-empty), replacing Serena's default set of tools.
-# This cannot be combined with non-empty excluded_tools or included_optional_tools.
-# Find the list of tools here: https://oraios.github.io/serena/01-about/035_tools.html
-fixed_tools: []
-
-# list of mode names that are to be activated by default, overriding the setting in the global configuration.
-# The full set of modes to be activated is base_modes (from global config) + default_modes + added_modes.
-# If the setting is undefined/empty, the default_modes from the global configuration (serena_config.yml) apply.
-# Otherwise, this overrides the setting from the global configuration (serena_config.yml).
-# Therefore, you can set this to [] if you do not want the default modes defined in the global config to apply
-# for this project.
-# This setting can, in turn, be overridden by CLI parameters (--mode).
-# See https://oraios.github.io/serena/02-usage/050_configuration.html#modes
-default_modes:
-
-# list of mode names to be activated additionally for this project, e.g. ["query-projects"]
-# The full set of modes to be activated is base_modes (from global config) + default_modes + added_modes.
-# See https://oraios.github.io/serena/02-usage/050_configuration.html#modes
-added_modes:
-
-# initial prompt for the project. It will always be given to the LLM upon activating the project
-# (contrary to the memories, which are loaded on demand).
-initial_prompt: ""
-
-# time budget (seconds) per tool call for the retrieval of additional symbol information
-# such as docstrings or parameter information.
-# This overrides the corresponding setting in the global configuration; see the documentation there.
-# If null or missing, use the setting from the global configuration.
-symbol_info_budget:
-
-# list of regex patterns which, when matched, mark a memory entry as read‑only.
-# Extends the list from the global configuration, merging the two lists.
-read_only_memory_patterns: []
-
-# list of regex patterns for memories to completely ignore.
-# Matching memories will not appear in list_memories or activate_project output
-# and cannot be accessed via read_memory or write_memory.
-# To access ignored memory files, use the read_file tool on the raw file path.
-# Extends the list from the global configuration, merging the two lists.
-# Example: ["_archive/.*", "_episodes/.*"]
-ignored_memory_patterns: []
-
-# list of additional workspace folder paths for cross-package reference support.
-# Paths can be absolute or relative to the project root.
-# Each folder is registered as an LSP workspace folder, enabling language servers to discover
-# symbols and references across package boundaries, but these folders are not indexed by Serena,
-# i.e. the respective symbols will not be found using Serena's symbol search tools.
-# Example:
-#   additional_workspace_folders:
-#     - ../sibling-package
-#     - ../shared-lib
-ls_additional_workspace_folders: []
-
-# list of language servers to start when using the LSP backend; choose from:
-#   ada                    al                     angular                ansible                bash
-#   bsl                    clojure                cpp                    cpp_ccls               crystal
-#   csharp                 csharp_omnisharp       cue                    dart                   deno
-#   elixir                 elm                    erlang                 fortran                fsharp
-#   gdscript               gleam                  go                     groovy                 haskell
-#   haxe                   hlsl                   html                   java                   json
-#   julia                  kotlin                 latex                  lean4                  lua
-#   luau                   markdown               matlab                 msl                    nextflow
-#   nix                    ocaml                  pascal                 perl                   php
-#   php_phpactor           php_phpantom           powershell             python                 python_basedpyright
-#   python_jedi            python_pyrefly         python_ty              qml                    r
-#   rego                   ruby                   ruby_solargraph        rust                   scala
-#   scss                   solidity               svelte                 swift                  systemverilog
-#   terraform              toml                   typescript             typescript_vts         vue
-#   wolfram                yaml                   zig
-#   (This list may be outdated; generated with scripts/print_language_list.py;
-#   For the current list, see values of the LanguageServerId enum here:
-#   https://github.com/oraios/serena/blob/main/src/solidlsp/ls_config.py)
-# For some languages, there are several alternative language servers, e.g. csharp_omnisharp, ruby_solargraph.)
-# Note:
-#   - For C, use cpp
-#   - For JavaScript, use typescript
-#   - For Angular projects, use angular (subsumes typescript+html; requires `npm install` in the project root)
-#   - For Svelte projects, use svelte (subsumes typescript/javascript for .svelte projects; requires npm)
-#   - For Deno projects, use deno (serves the same .ts/.js files as typescript; requires the deno CLI on PATH)
-#   - For SCSS / Sass / plain CSS, use scss (some-sass-language-server handles all three)
-#   - For Free Pascal/Lazarus, use pascal
-# Special requirements:
-#   Some language servers require additional setup/installations.
-#   See here for details: https://oraios.github.io/serena/01-about/020_programming-languages.html#language-servers
-# When using multiple language servers, the first language server that supports a given file will be used for that file.
-# The first language server is the default language and the respective language server will be used as a fallback.
-# Note that when using the JetBrains backend, language servers are not used and this list is correspondingly ignored.
-language_servers:
- rust
-
-# list of workspace folder paths (LSP backend only).
-# These folders will be used to build up Serena's symbol index.
-# Paths must be within the project root and should thus be relative to the project root.
-# Furthermore, the paths should not be filtered by ignore settings.
-# Default setting: The entire project root folder (".") is considered.
-# In (large) monorepos, this can be used to index only subfolders of the project root, e.g.
-#   ls_workspace_folders:
-#     - "./subproject1"
-#     - "./subproject2"
-ls_workspace_folders:
- .
-
-# optional shell command to run before the language backend (LSP or JetBrains) is initialised.
-# the command runs in the project root directory and is only executed if the project is trusted
-# (see trusted_project_path_patterns in the global configuration).
-# serena waits for the command to exit: a non-zero exit code is logged as an error but does not
-# abort activation. a per-project timeout (activation_command_timeout, default 180s) is the safety
-# backstop for non-terminating commands; on expiry the process is killed and activation continues.
-# example: activation_command: "npx nx run-many -t build"
-activation_command:
-
-# maximum time in seconds to wait for activation_command to complete before killing it (default 180s).
-# must be a positive number.
-activation_command_timeout: 180.0
@@ -1,59 +0,0 @@
-// Project tasks configuration. See https://zed.dev/docs/tasks for documentation.
-//
-// Example:
-[
-  {
-    "label": "Example task",
-    "command": "for i in {1..5}; do echo \"Hello $i/5\"; sleep 1; done",
-    //"args": [],
-    // Env overrides for the command, will be appended to the terminal's environment from the settings.
-    "env": { "foo": "bar" },
-    // Current working directory to spawn the command into, defaults to current project root.
-    //"cwd": "/path/to/working/directory",
-    // Whether to use a new terminal tab or reuse the existing one to spawn the process, defaults to `false`.
-    "use_new_terminal": false,
-    // Whether to allow multiple instances of the same task to be run, or rather wait for the existing ones to finish, defaults to `false`.
-    "allow_concurrent_runs": false,
-    // What to do with the terminal pane and tab, after the command was started:
-    // * `always` — always show the task's pane, and focus the corresponding tab in it (default)
-    // * `no_focus` — always show the task's pane, add the task's tab in it, but don't focus it
-    // * `never` — do not alter focus, but still add/reuse the task's tab in its pane
-    "reveal": "always",
-    // Where to place the task's terminal item after starting the task:
-    // * `dock` — in the terminal dock, "regular" terminal items' place (default)
-    // * `center` — in the central pane group, "main" editor area
-    "reveal_target": "dock",
-    // What to do with the terminal pane and tab, after the command had finished:
-    // * `never` — Do nothing when the command finishes (default)
-    // * `always` — always hide the terminal tab, hide the pane also if it was the last tab in it
-    // * `on_success` — hide the terminal tab on task success only, otherwise behaves similar to `always`
-    "hide": "never",
-    // Which shell to use when running a task inside the terminal.
-    // May take 3 values:
-    // 1. (default) Use the system's default terminal configuration in /etc/passwd
-    //      "shell": "system"
-    // 2. A program:
-    //      "shell": {
-    //        "program": "sh"
-    //      }
-    // 3. A program with arguments:
-    //     "shell": {
-    //         "with_arguments": {
-    //           "program": "/bin/bash",
-    //           "args": ["--login"]
-    //         }
-    //     }
-    "shell": "system",
-    // Whether to show the task line in the output of the spawned task, defaults to `true`.
-    "show_summary": true,
-    // Whether to show the command line in the output of the spawned task, defaults to `true`.
-    "show_command": true,
-    // Which edited buffers to save before running the task:
-    // * `all` — save all edited buffers
-    // * `current` — save currently active buffer only
-    // * `none` — don't save any buffers
-    "save": "none",
-    // Represents the tags for inline runnable indicators, or spawning multiple tasks at once.
-    // "tags": []
-  },
-]
@@ -2,23 +2,27 @@
 BINARY  := ../src/target/release/obikmer
 VENV_PY := ../.venv/bin/python3

-GENOMES := $(wildcard genomes/*.fna.gz)
+# All generated/downloaded artifacts live under RUN/ so the whole tree can be
+# gitignored with a single entry (benchmark/run/) — see benchmark/README.md.
+RUN := run
+
+GENOMES := $(wildcard $(RUN)/genomes/*.fna.gz)

 # SPECIMENS, SPECIES, and the full dependency graph are generated by
 # make_deps.py from the genome FASTA headers — like .d files in C.
 # Make rebuilds deps.mk whenever genomes/ changes and restarts.
 -include deps.mk

-REF_NPZS              := $(SPECIMENS:%=reference_index/%.npz)
-REF_DIST_CSVS         := $(addprefix reference_dist/, \
+REF_NPZS              := $(SPECIMENS:%=$(RUN)/reference_index/%.npz)
+REF_DIST_CSVS         := $(addprefix $(RUN)/reference_dist/, \
 	shared_kmers.csv hamming_dist.csv jaccard_dist.csv \
 	bray_curtis_dist.csv relfreq_bray_curtis_dist.csv \
 	euclidean_dist.csv relfreq_euclidean_dist.csv \
 	hellinger_dist.csv hellinger_euclidean_dist.csv)
-OBIKMER_PRESENCE_DIST := $(addprefix obikmer_dist/presence/, \
+OBIKMER_PRESENCE_DIST := $(addprefix $(RUN)/obikmer_dist/presence/, \
 	jaccard_dist.csv jaccard_shared.csv jaccard_nj.nwk \
 	hamming_dist.csv hamming_nj.nwk)
-OBIKMER_COUNT_DIST    := $(addprefix obikmer_dist/count/, \
+OBIKMER_COUNT_DIST    := $(addprefix $(RUN)/obikmer_dist/count/, \
 	jaccard_dist.csv jaccard_shared.csv jaccard_nj.nwk \
 	bray_curtis_dist.csv bray_curtis_nj.nwk \
 	relfreq_bray_curtis_dist.csv relfreq_bray_curtis_nj.nwk \
@@ -26,28 +30,28 @@ OBIKMER_COUNT_DIST    := $(addprefix obikmer_dist/count/, \
 	relfreq_euclidean_dist.csv relfreq_euclidean_nj.nwk \
 	hellinger_dist.csv hellinger_nj.nwk \
 	hellinger_euclidean_dist.csv hellinger_euclidean_nj.nwk)
-DIST_COMPARISON       := stats/dist_comparison/summary.csv
-PRESENCE_DONE         := $(SPECIMENS:%=specimen_index_presence/%/index.done)
-PRESENCE_STATS        := $(SPECIMENS:%=stats/indexing_presence/%.stats)
-COUNT_DONE            := $(SPECIMENS:%=specimen_index_count/%/index.done)
-COUNT_STATS           := $(SPECIMENS:%=stats/indexing_count/%.stats)
-VERIFY_PRESENCE_STATS := $(SPECIMENS:%=stats/verify_presence/%.stats)
-VERIFY_COUNT_STATS    := $(SPECIMENS:%=stats/verify_count/%.stats)
-SPECIFIC_PRESENCE_DONE  := $(SPECIES:%=specific_index_presence/%/index.done)
-SPECIFIC_PRESENCE_STATS := $(SPECIES:%=stats/specific_kmer_presence/%.stats)
-SPECIFIC_COUNT_DONE     := $(SPECIES:%=specific_index_count/%/index.done)
-SPECIFIC_COUNT_STATS    := $(SPECIES:%=stats/specific_kmer_count/%.stats)
-SIMULATED_READS := $(foreach s,$(SPECIMENS),simulated_data/$(subst --,/,$s)/reads_R1.fastq.gz)
-QUERY_READS      := $(foreach s,$(QUERY_SPECIMENS),query_data/$(subst --,/,$s)/reads_R1.fastq.gz)
-QUERY_PRESENCE_DENSE_DONE   := $(QUERY_SPECIMENS:%=query_presence_dense/%.fasta.gz)
-QUERY_PRESENCE_DENSE_STATS  := $(QUERY_SPECIMENS:%=stats/query_presence_dense/%.stats)
-QUERY_PRESENCE_SPARSE_DONE  := $(QUERY_SPECIMENS:%=query_presence_sparse/%.fasta.gz)
-QUERY_PRESENCE_SPARSE_STATS := $(QUERY_SPECIMENS:%=stats/query_presence_sparse/%.stats)
-QUERY_COUNT_DENSE_DONE      := $(QUERY_SPECIMENS:%=query_count_dense/%.fasta.gz)
-QUERY_COUNT_DENSE_STATS     := $(QUERY_SPECIMENS:%=stats/query_count_dense/%.stats)
-QUERY_COUNT_SPARSE_DONE     := $(QUERY_SPECIMENS:%=query_count_sparse/%.fasta.gz)
-QUERY_COUNT_SPARSE_STATS    := $(QUERY_SPECIMENS:%=stats/query_count_sparse/%.stats)
-VERIFY_QUERY_STATS := $(QUERY_SPECIMENS:%=stats/verify_query/%.stats)
+DIST_COMPARISON       := $(RUN)/stats/dist_comparison/summary.csv
+PRESENCE_DONE         := $(SPECIMENS:%=$(RUN)/specimen_index_presence/%/index.done)
+PRESENCE_STATS        := $(SPECIMENS:%=$(RUN)/stats/indexing_presence/%.stats)
+COUNT_DONE            := $(SPECIMENS:%=$(RUN)/specimen_index_count/%/index.done)
+COUNT_STATS           := $(SPECIMENS:%=$(RUN)/stats/indexing_count/%.stats)
+VERIFY_PRESENCE_STATS := $(SPECIMENS:%=$(RUN)/stats/verify_presence/%.stats)
+VERIFY_COUNT_STATS    := $(SPECIMENS:%=$(RUN)/stats/verify_count/%.stats)
+SPECIFIC_PRESENCE_DONE  := $(SPECIES:%=$(RUN)/specific_index_presence/%/index.done)
+SPECIFIC_PRESENCE_STATS := $(SPECIES:%=$(RUN)/stats/specific_kmer_presence/%.stats)
+SPECIFIC_COUNT_DONE     := $(SPECIES:%=$(RUN)/specific_index_count/%/index.done)
+SPECIFIC_COUNT_STATS    := $(SPECIES:%=$(RUN)/stats/specific_kmer_count/%.stats)
+SIMULATED_READS := $(foreach s,$(SPECIMENS),$(RUN)/simulated_data/$(subst --,/,$s)/reads_R1.fastq.gz)
+QUERY_READS      := $(foreach s,$(QUERY_SPECIMENS),$(RUN)/query_data/$(subst --,/,$s)/reads_R1.fastq.gz)
+QUERY_PRESENCE_DENSE_DONE   := $(QUERY_SPECIMENS:%=$(RUN)/query_presence_dense/%.fasta.gz)
+QUERY_PRESENCE_DENSE_STATS  := $(QUERY_SPECIMENS:%=$(RUN)/stats/query_presence_dense/%.stats)
+QUERY_PRESENCE_SPARSE_DONE  := $(QUERY_SPECIMENS:%=$(RUN)/query_presence_sparse/%.fasta.gz)
+QUERY_PRESENCE_SPARSE_STATS := $(QUERY_SPECIMENS:%=$(RUN)/stats/query_presence_sparse/%.stats)
+QUERY_COUNT_DENSE_DONE      := $(QUERY_SPECIMENS:%=$(RUN)/query_count_dense/%.fasta.gz)
+QUERY_COUNT_DENSE_STATS     := $(QUERY_SPECIMENS:%=$(RUN)/stats/query_count_dense/%.stats)
+QUERY_COUNT_SPARSE_DONE     := $(QUERY_SPECIMENS:%=$(RUN)/query_count_sparse/%.fasta.gz)
+QUERY_COUNT_SPARSE_STATS    := $(QUERY_SPECIMENS:%=$(RUN)/stats/query_count_sparse/%.stats)
+VERIFY_QUERY_STATS := $(QUERY_SPECIMENS:%=$(RUN)/stats/verify_query/%.stats)

 .NOTPARALLEL:

@@ -69,8 +73,8 @@ VERIFY_QUERY_STATS := $(QUERY_SPECIMENS:%=stats/verify_query/%.stats)
        aggregate_query_count_dense aggregate_query_count_sparse \
        verify_query aggregate_verify_query

-verify_merge_presence: stats/verify_merge_presence/current.csv
-verify_merge_count:    stats/verify_merge_count/current.csv
+verify_merge_presence: $(RUN)/stats/verify_merge_presence/current.csv
+verify_merge_count:    $(RUN)/stats/verify_merge_count/current.csv

 all: aggregate_verify_presence aggregate_verify_count \
     verify_merge_presence verify_merge_count \
@@ -104,7 +108,7 @@ simulate_query: $(QUERY_READS)
 # ── reference kmer sets ───────────────────────────────────────────────────────
 # Prerequisites (reads → npz) are in deps.mk.

-reference_index/%.npz:
+$(RUN)/reference_index/%.npz:
 	bash build_reference.sh $*

 reference: $(REF_NPZS)
@@ -112,57 +116,58 @@ reference: $(REF_NPZS)
 # ── reference distance matrices ───────────────────────────────────────────────

 $(REF_DIST_CSVS) &: $(REF_NPZS) build_reference_dist.py
-	$(VENV_PY) build_reference_dist.py
+	$(VENV_PY) build_reference_dist.py \
+		--ref-dir $(RUN)/reference_index --out-dir $(RUN)/reference_dist

 reference_dist: $(REF_DIST_CSVS)

 # ── obikmer phylo (presence index) ──────────────────────────────────────────

-$(OBIKMER_PRESENCE_DIST) &: global_index_presence/index.done $(BINARY)
-	mkdir -p obikmer_dist/presence
+$(OBIKMER_PRESENCE_DIST) &: $(RUN)/global_index_presence/index.done $(BINARY)
+	mkdir -p $(RUN)/obikmer_dist/presence
 	$(BINARY) phylo \
-		--output obikmer_dist/presence/jaccard \
+		--output $(RUN)/obikmer_dist/presence/jaccard \
 		--distance jaccard --csv --shared-kmers --nj \
-		global_index_presence
+		$(RUN)/global_index_presence
 	$(BINARY) phylo \
-		--output obikmer_dist/presence/hamming \
+		--output $(RUN)/obikmer_dist/presence/hamming \
 		--distance hamming --csv --nj \
-		global_index_presence
+		$(RUN)/global_index_presence

 obikmer_dist_presence: $(OBIKMER_PRESENCE_DIST)

 # ── obikmer phylo (count index) ─────────────────────────────────────────────

-$(OBIKMER_COUNT_DIST) &: global_index_count/index.done $(BINARY)
-	mkdir -p obikmer_dist/count
+$(OBIKMER_COUNT_DIST) &: $(RUN)/global_index_count/index.done $(BINARY)
+	mkdir -p $(RUN)/obikmer_dist/count
 	$(BINARY) phylo \
-		--output obikmer_dist/count/jaccard \
+		--output $(RUN)/obikmer_dist/count/jaccard \
 		--distance jaccard --csv --shared-kmers --nj \
-		global_index_count
+		$(RUN)/global_index_count
 	$(BINARY) phylo \
-		--output obikmer_dist/count/bray_curtis \
+		--output $(RUN)/obikmer_dist/count/bray_curtis \
 		--distance bray-curtis --csv --nj \
-		global_index_count
+		$(RUN)/global_index_count
 	$(BINARY) phylo \
-		--output obikmer_dist/count/relfreq_bray_curtis \
+		--output $(RUN)/obikmer_dist/count/relfreq_bray_curtis \
 		--distance relfreq-bray-curtis --csv --nj \
-		global_index_count
+		$(RUN)/global_index_count
 	$(BINARY) phylo \
-		--output obikmer_dist/count/euclidean \
+		--output $(RUN)/obikmer_dist/count/euclidean \
 		--distance euclidean --csv --nj \
-		global_index_count
+		$(RUN)/global_index_count
 	$(BINARY) phylo \
-		--output obikmer_dist/count/relfreq_euclidean \
+		--output $(RUN)/obikmer_dist/count/relfreq_euclidean \
 		--distance relfreq-euclidean --csv --nj \
-		global_index_count
+		$(RUN)/global_index_count
 	$(BINARY) phylo \
-		--output obikmer_dist/count/hellinger \
+		--output $(RUN)/obikmer_dist/count/hellinger \
 		--distance hellinger --csv --nj \
-		global_index_count
+		$(RUN)/global_index_count
 	$(BINARY) phylo \
-		--output obikmer_dist/count/hellinger_euclidean \
+		--output $(RUN)/obikmer_dist/count/hellinger_euclidean \
 		--distance hellinger-euclidean --csv --nj \
-		global_index_count
+		$(RUN)/global_index_count

 obikmer_dist_count: $(OBIKMER_COUNT_DIST)

@@ -171,19 +176,19 @@ obikmer_dist: obikmer_dist_presence obikmer_dist_count
 # ── distance comparison ───────────────────────────────────────────────────────

 $(DIST_COMPARISON): $(REF_DIST_CSVS) $(OBIKMER_PRESENCE_DIST) $(OBIKMER_COUNT_DIST) compare_all_dist.py
-	$(VENV_PY) compare_all_dist.py --out $(DIST_COMPARISON)
+	$(VENV_PY) compare_all_dist.py --run-dir $(RUN) --out $(DIST_COMPARISON)

 dist_comparison: $(DIST_COMPARISON)

 # ── per-specimen indexing ─────────────────────────────────────────────────────
 # Prerequisites (reads → index.done + .stats) are in deps.mk.

-specimen_index_presence/%/index.done \
-stats/indexing_presence/%.stats &: $(BINARY)
+$(RUN)/specimen_index_presence/%/index.done \
+$(RUN)/stats/indexing_presence/%.stats &: $(BINARY)
 	bash index_one_presence.sh $*

-specimen_index_count/%/index.done \
-stats/indexing_count/%.stats &: $(BINARY)
+$(RUN)/specimen_index_count/%/index.done \
+$(RUN)/stats/indexing_count/%.stats &: $(BINARY)
 	bash index_one_count.sh $*

 index_presence: $(PRESENCE_DONE)
@@ -199,22 +204,22 @@ aggregate_index_count: $(COUNT_STATS)

 # ── global merge ──────────────────────────────────────────────────────────────

-global_index_presence/index.done: $(PRESENCE_DONE) $(BINARY)
+$(RUN)/global_index_presence/index.done: $(PRESENCE_DONE) $(BINARY)
 	bash merge_presence.sh

-global_index_count/index.done: $(COUNT_DONE) $(BINARY)
+$(RUN)/global_index_count/index.done: $(COUNT_DONE) $(BINARY)
 	bash merge_count.sh

-merge_presence: global_index_presence/index.done
-merge_count:    global_index_count/index.done
+merge_presence: $(RUN)/global_index_presence/index.done
+merge_count:    $(RUN)/global_index_count/index.done

 # ── per-specimen verification ─────────────────────────────────────────────────
 # Prerequisites (index.done + npz → .stats) are in deps.mk.

-stats/verify_presence/%.stats:
+$(RUN)/stats/verify_presence/%.stats:
 	bash verify_one_presence.sh $*

-stats/verify_count/%.stats:
+$(RUN)/stats/verify_count/%.stats:
 	bash verify_one_count.sh $*

 verify_presence: $(VERIFY_PRESENCE_STATS)
@@ -231,12 +236,12 @@ aggregate_verify_count: $(VERIFY_COUNT_STATS)
 # ── species-specific indexes ──────────────────────────────────────────────────
 # Prerequisites (global index → specific index) are in deps.mk.

-specific_index_presence/%/index.done \
-stats/specific_kmer_presence/%.stats &: $(BINARY)
+$(RUN)/specific_index_presence/%/index.done \
+$(RUN)/stats/specific_kmer_presence/%.stats &: $(BINARY)
 	bash filter_one_presence.sh $*

-specific_index_count/%/index.done \
-stats/specific_kmer_count/%.stats &: $(BINARY)
+$(RUN)/specific_index_count/%/index.done \
+$(RUN)/stats/specific_kmer_count/%.stats &: $(BINARY)
 	bash filter_one_count.sh $*

 filter_presence: $(SPECIFIC_PRESENCE_DONE)
@@ -250,10 +255,10 @@ aggregate_filter_count: $(SPECIFIC_COUNT_STATS)

 # ── merged index verification ─────────────────────────────────────────────────

-stats/verify_merge_presence/current.csv: $(REF_NPZS) global_index_presence/index.done
+$(RUN)/stats/verify_merge_presence/current.csv: $(REF_NPZS) $(RUN)/global_index_presence/index.done
 	bash verify_merge_presence.sh

-stats/verify_merge_count/current.csv: $(REF_NPZS) global_index_count/index.done
+$(RUN)/stats/verify_merge_count/current.csv: $(REF_NPZS) $(RUN)/global_index_count/index.done
 	bash verify_merge_count.sh

 # ── dense variants (query benchmark) ────────────────────────────────────────────
@@ -262,34 +267,34 @@ stats/verify_merge_count/current.csv: $(REF_NPZS) global_index_count/index.done
 # built explicitly here, from a hard-link-based copy (see
 # copy_index_hardlink.sh) rather than a full `cp -r`.

-global_index_presence_dense/index.done: global_index_presence/index.done $(BINARY)
+$(RUN)/global_index_presence_dense/index.done: $(RUN)/global_index_presence/index.done $(BINARY)
 	bash pack_dense.sh presence

 # Rebuilt from the per-specimen count sources directly (via `merge --dense`),
 # not repacked from global_index_count — see pack_dense.sh's own comment.
-global_index_count_dense/index.done: $(COUNT_DONE) $(BINARY)
+$(RUN)/global_index_count_dense/index.done: $(COUNT_DONE) $(BINARY)
 	bash pack_dense.sh count

-pack_dense_presence: global_index_presence_dense/index.done
-pack_dense_count:    global_index_count_dense/index.done
+pack_dense_presence: $(RUN)/global_index_presence_dense/index.done
+pack_dense_count:    $(RUN)/global_index_count_dense/index.done

 # ── query: dense vs sparse, presence and count ──────────────────────────────────
 # Prerequisites (reads + index → output + .stats) are in deps.mk.

-query_presence_dense/%.fasta.gz \
-stats/query_presence_dense/%.stats &: $(BINARY) global_index_presence_dense/index.done
+$(RUN)/query_presence_dense/%.fasta.gz \
+$(RUN)/stats/query_presence_dense/%.stats &: $(BINARY) $(RUN)/global_index_presence_dense/index.done
 	bash query_one.sh presence dense $*

-query_presence_sparse/%.fasta.gz \
-stats/query_presence_sparse/%.stats &: $(BINARY) global_index_presence/index.done
+$(RUN)/query_presence_sparse/%.fasta.gz \
+$(RUN)/stats/query_presence_sparse/%.stats &: $(BINARY) $(RUN)/global_index_presence/index.done
 	bash query_one.sh presence sparse $*

-query_count_dense/%.fasta.gz \
-stats/query_count_dense/%.stats &: $(BINARY) global_index_count_dense/index.done
+$(RUN)/query_count_dense/%.fasta.gz \
+$(RUN)/stats/query_count_dense/%.stats &: $(BINARY) $(RUN)/global_index_count_dense/index.done
 	bash query_one.sh count dense $*

-query_count_sparse/%.fasta.gz \
-stats/query_count_sparse/%.stats &: $(BINARY) global_index_count/index.done
+$(RUN)/query_count_sparse/%.fasta.gz \
+$(RUN)/stats/query_count_sparse/%.stats &: $(BINARY) $(RUN)/global_index_count/index.done
 	bash query_one.sh count sparse $*

 query_presence_dense:  $(QUERY_PRESENCE_DENSE_DONE)
@@ -311,7 +316,7 @@ aggregate_query_count_sparse: $(QUERY_COUNT_SPARSE_STATS)

 # ── query: dense/sparse regression ──────────────────────────────────────────────

-stats/verify_query/%.stats:
+$(RUN)/stats/verify_query/%.stats:
 	bash verify_query_one.sh $*

 verify_query: $(VERIFY_QUERY_STATS)
@@ -8,108 +8,124 @@ gmake simulate     # simulation only
 gmake reference    # reference kmer sets only
 ```

+All generated and downloaded artifacts live under `run/` (see
+[Directory layout](#directory-layout)), so the whole tree is gitignored with
+a single `benchmark/run/` entry.
+
 ## Pipeline overview

 ```mermaid
 flowchart TD
-    GENOMES["genomes/*.fna.gz"]
+    GENOMES["run/genomes/*.fna.gz"]
    BIN["obikmer binary"]

    GENOMES --> simulate
-    simulate --> simdata[("simulated_data/")]
+    simulate --> simdata[("run/simulated_data/")]

    simdata --> reference
-    reference --> refnpz[("reference_index/*.npz")]
+    reference --> refnpz[("run/reference_index/*.npz")]

    subgraph presence ["Presence track"]
        simdata  --> index_presence
        BIN      --> index_presence
-        index_presence --> pres_done[("specimen_index_presence/")]
-        index_presence --> pres_istats[("stats/indexing_presence/")]
+        index_presence --> pres_done[("run/specimen_index_presence/")]
+        index_presence --> pres_istats[("run/stats/indexing_presence/")]
        pres_istats --> aggregate_index_presence

        pres_done --> merge_presence
        BIN       --> merge_presence
-        merge_presence --> gpres[("global_index_presence/")]
+        merge_presence --> gpres[("run/global_index_presence/")]

        refnpz    --> verify_presence
        pres_done --> verify_presence
-        verify_presence --> vpres_stats[("stats/verify_presence/")]
+        verify_presence --> vpres_stats[("run/stats/verify_presence/")]
        vpres_stats --> aggregate_verify_presence

        gpres --> filter_presence
        BIN   --> filter_presence
-        filter_presence --> spec_pres[("specific_index_presence/")]
-        filter_presence --> spec_pres_stats[("stats/specific_kmer_presence/")]
+        filter_presence --> spec_pres[("run/specific_index_presence/")]
+        filter_presence --> spec_pres_stats[("run/stats/specific_kmer_presence/")]
        spec_pres_stats --> aggregate_filter_presence

        refnpz --> verify_merge_presence
        gpres  --> verify_merge_presence
-        verify_merge_presence --> vmp[("stats/verify_merge_presence/")]
+        verify_merge_presence --> vmp[("run/stats/verify_merge_presence/")]
    end

    subgraph count ["Count track"]
        simdata --> index_count
        BIN     --> index_count
-        index_count --> count_done[("specimen_index_count/")]
-        index_count --> count_istats[("stats/indexing_count/")]
+        index_count --> count_done[("run/specimen_index_count/")]
+        index_count --> count_istats[("run/stats/indexing_count/")]
        count_istats --> aggregate_index_count

        count_done --> merge_count
        BIN        --> merge_count
-        merge_count --> gcount[("global_index_count/")]
+        merge_count --> gcount[("run/global_index_count/")]

        refnpz     --> verify_count
        count_done --> verify_count
-        verify_count --> vcount_stats[("stats/verify_count/")]
+        verify_count --> vcount_stats[("run/stats/verify_count/")]
        vcount_stats --> aggregate_verify_count

        gcount --> filter_count
        BIN    --> filter_count
-        filter_count --> spec_count[("specific_index_count/")]
-        filter_count --> spec_count_stats[("stats/specific_kmer_count/")]
+        filter_count --> spec_count[("run/specific_index_count/")]
+        filter_count --> spec_count_stats[("run/stats/specific_kmer_count/")]
        spec_count_stats --> aggregate_filter_count

        refnpz --> verify_merge_count
        gcount --> verify_merge_count
-        verify_merge_count --> vmc[("stats/verify_merge_count/")]
+        verify_merge_count --> vmc[("run/stats/verify_merge_count/")]
    end

    subgraph query ["Query track (2 specimens: E. coli + archaeon)"]
        GENOMES --> simulate_query
-        simulate_query --> qdata[("query_data/")]
+        simulate_query --> qdata[("run/query_data/")]

-        gpres --> pack_sparse
-        BIN   --> pack_sparse
-        pack_sparse --> gsparse[("global_index_presence_sparse/")]
+        gpres --> pack_dense_presence
+        BIN   --> pack_dense_presence
+        pack_dense_presence --> gpresd[("run/global_index_presence_dense/")]

-        qdata  --> query_dense
-        gpres  --> query_dense
-        BIN    --> query_dense
-        query_dense --> qd[("query_dense/")]
-        query_dense --> qd_stats[("stats/query_dense/")]
-        qd_stats --> aggregate_query_dense
+        count_done --> pack_dense_count
+        BIN        --> pack_dense_count
+        pack_dense_count --> gcountd[("run/global_index_count_dense/")]

-        qdata   --> query_sparse
-        gsparse --> query_sparse
-        BIN     --> query_sparse
-        query_sparse --> qs[("query_sparse/")]
-        query_sparse --> qs_stats[("stats/query_sparse/")]
-        qs_stats --> aggregate_query_sparse
+        qdata  --> query_presence_dense
+        gpresd --> query_presence_dense
+        query_presence_dense --> qpd[("run/query_presence_dense/")]
+        qpd --> aggregate_query_presence_dense

-        qd --> verify_query
-        qs --> verify_query
-        verify_query --> vq_stats[("stats/verify_query/")]
+        qdata  --> query_presence_sparse
+        gpres  --> query_presence_sparse
+        query_presence_sparse --> qps[("run/query_presence_sparse/")]
+        qps --> aggregate_query_presence_sparse
+
+        qdata   --> query_count_dense
+        gcountd --> query_count_dense
+        query_count_dense --> qcd[("run/query_count_dense/")]
+        qcd --> aggregate_query_count_dense
+
+        qdata  --> query_count_sparse
+        gcount --> query_count_sparse
+        query_count_sparse --> qcs[("run/query_count_sparse/")]
+        qcs --> aggregate_query_count_sparse
+
+        qpd --> verify_query
+        qps --> verify_query
+        verify_query --> vq_stats[("run/stats/verify_query/")]
        vq_stats --> aggregate_verify_query
    end

-    aggregate_verify_presence  --> all
-    aggregate_verify_count     --> all
-    vmp                        --> all
-    vmc                        --> all
-    aggregate_query_dense      --> all
-    aggregate_query_sparse     --> all
-    aggregate_verify_query     --> all
+    aggregate_verify_presence         --> all
+    aggregate_verify_count            --> all
+    vmp                               --> all
+    vmc                               --> all
+    aggregate_query_presence_dense    --> all
+    aggregate_query_presence_sparse   --> all
+    aggregate_query_count_dense       --> all
+    aggregate_query_count_sparse      --> all
+    aggregate_verify_query            --> all
    all -. "$(MAKE) re-eval" .-> aggregate_filter_presence
    all -. "$(MAKE) re-eval" .-> aggregate_filter_count
 ```
@@ -137,44 +153,59 @@ flowchart TD
 | `verify_merge_presence` | `verify_merge_presence.sh` | Verify global presence index against all reference sets |
 | `verify_merge_count` | `verify_merge_count.sh` | Verify global count index against all reference sets |
 | `simulate_query` | `simulate_query_one.sh` | Simulate a fixed-size (100k pairs) read set per query specimen |
-| `pack_sparse` | `pack_sparse.sh` | Build `global_index_presence_sparse/` from `global_index_presence/` |
-| `query_dense` | `query_one.sh dense` | Query each query specimen's reads against the dense global index |
-| `query_sparse` | `query_one.sh sparse` | Query each query specimen's reads against the sparse global index |
-| `aggregate_query_dense` | `aggregate_stats.sh` | Aggregate dense query wall/RSS stats |
-| `aggregate_query_sparse` | `aggregate_stats.sh` | Aggregate sparse query wall/RSS stats |
-| `verify_query` | `verify_query_one.sh` | Diff dense vs sparse query output per specimen (regression check) |
+| `pack_dense_presence` | `pack_dense.sh presence` | Build `global_index_presence_dense/` from `global_index_presence/` |
+| `pack_dense_count` | `pack_dense.sh count` | Build `global_index_count_dense/` from the per-specimen count sources |
+| `query_presence_dense` | `query_one.sh presence dense` | Query against the dense presence global index |
+| `query_presence_sparse` | `query_one.sh presence sparse` | Query against the sparse (as-merged) presence global index |
+| `query_count_dense` | `query_one.sh count dense` | Query against the dense count global index |
+| `query_count_sparse` | `query_one.sh count sparse` | Query against the sparse (as-merged) count global index |
+| `aggregate_query_presence_dense` | `aggregate_stats.sh` | Aggregate dense presence-query wall/RSS stats |
+| `aggregate_query_presence_sparse` | `aggregate_stats.sh` | Aggregate sparse presence-query wall/RSS stats |
+| `aggregate_query_count_dense` | `aggregate_stats.sh` | Aggregate dense count-query wall/RSS stats |
+| `aggregate_query_count_sparse` | `aggregate_stats.sh` | Aggregate sparse count-query wall/RSS stats |
+| `verify_query` | `verify_query_one.sh` | Diff dense vs sparse presence-query output per specimen (regression check) |
 | `aggregate_verify_query` | `aggregate_stats.sh` | Aggregate dense/sparse query regression stats |

 ## Directory layout

 ```
 benchmark/
-├── genomes/                        # input reference genomes (.fna.gz)
-├── simulated_data/                 # generated by simulate
-│   └── <species>/<specimen>/
-├── query_data/                     # generated by simulate_query (2 specimens, fixed 100k pairs)
-│   └── <species>/<specimen>/
-├── reference_index/                # reference kmer sets (.npz)
-├── specimen_index_presence/        # per-specimen presence indexes
-├── specimen_index_count/           # per-specimen count indexes
-├── global_index_presence/          # merged global presence index (dense-packed)
-├── global_index_presence_sparse/   # global presence index, sparse-packed (query benchmark)
-├── global_index_count/             # merged global count index
-├── specific_index_presence/        # species-specific presence indexes
-├── specific_index_count/           # species-specific count indexes
-├── query_dense/                    # query output against global_index_presence
-├── query_sparse/                   # query output against global_index_presence_sparse
-└── stats/                          # all benchmark statistics
-    ├── indexing_presence/
-    ├── indexing_count/
-    ├── verify_presence/
-    ├── verify_count/
-    ├── specific_kmer_presence/
-    ├── specific_kmer_count/
-    ├── verify_merge_presence/
-    ├── verify_merge_count/
-    ├── pack_sparse/
-    ├── query_dense/
-    ├── query_sparse/
-    └── verify_query/
+└── run/                                 # everything generated/downloaded — gitignored as a whole
+    ├── genomes/                         # input reference genomes (.fna.gz), downloaded by downloads.sh
+    ├── simulated_data/                  # generated by simulate
+    │   └── <species>/<specimen>/
+    ├── query_data/                      # generated by simulate_query (2 specimens, fixed 100k pairs)
+    │   └── <species>/<specimen>/
+    ├── reference_index/                 # reference kmer sets (.npz)
+    ├── reference_dist/                  # reference pairwise distance matrices
+    ├── obikmer_dist/                    # obikmer phylo distance matrices (presence/, count/)
+    ├── specimen_index_presence/         # per-specimen presence indexes
+    ├── specimen_index_count/            # per-specimen count indexes
+    ├── global_index_presence/           # merged global presence index (sparse, as merged)
+    ├── global_index_presence_dense/     # global presence index, dense-repacked (query benchmark)
+    ├── global_index_count/              # merged global count index (sparse, as merged)
+    ├── global_index_count_dense/        # global count index, dense-repacked (query benchmark)
+    ├── specific_index_presence/         # species-specific presence indexes
+    ├── specific_index_count/            # species-specific count indexes
+    ├── query_presence_dense/            # query output against global_index_presence_dense
+    ├── query_presence_sparse/           # query output against global_index_presence
+    ├── query_count_dense/               # query output against global_index_count_dense
+    ├── query_count_sparse/              # query output against global_index_count
+    └── stats/                           # all benchmark statistics
+        ├── indexing_presence/
+        ├── indexing_count/
+        ├── verify_presence/
+        ├── verify_count/
+        ├── specific_kmer_presence/
+        ├── specific_kmer_count/
+        ├── verify_merge_presence/
+        ├── verify_merge_count/
+        ├── pack_dense_presence/
+        ├── pack_dense_count/
+        ├── query_presence_dense/
+        ├── query_presence_sparse/
+        ├── query_count_dense/
+        ├── query_count_sparse/
+        ├── dist_comparison/
+        └── verify_query/
 ```
@@ -11,7 +11,7 @@ set -euo pipefail

 TYPE="$1"
 SCRIPT_DIR="$(cd "$(dirname "${BASH_SOURCE[0]}")" && pwd)"
-STATS_DIR="${SCRIPT_DIR}/stats/${TYPE}"
+STATS_DIR="${SCRIPT_DIR}/run/stats/${TYPE}"

 case "${TYPE}" in
    indexing_presence|indexing_count)
@@ -2,8 +2,9 @@
 set -euo pipefail

 SCRIPT_DIR="$(cd "$(dirname "${BASH_SOURCE[0]}")" && pwd)"
-SIMDATA_DIR="${SCRIPT_DIR}/simulated_data"
-REF_DIR="${SCRIPT_DIR}/reference_index"
+RUN_DIR="${SCRIPT_DIR}/run"
+SIMDATA_DIR="${RUN_DIR}/simulated_data"
+REF_DIR="${RUN_DIR}/reference_index"
 PYTHON="${SCRIPT_DIR}/../.venv/bin/python3"
 BUILD_PY="${SCRIPT_DIR}/build_reference.py"

@@ -176,10 +176,10 @@ def write_csv(path: Path, labels: list[str], mat: np.ndarray, fmt: str) -> None:
 def main() -> None:
    ap = argparse.ArgumentParser(description=__doc__,
                                 formatter_class=argparse.RawDescriptionHelpFormatter)
-    ap.add_argument('--ref-dir', default='reference_index',
-                    help='Directory with per-specimen .npz files (default: reference_index)')
-    ap.add_argument('--out-dir', default='reference_dist',
-                    help='Output directory for CSV files (default: reference_dist)')
+    ap.add_argument('--ref-dir', default='run/reference_index',
+                    help='Directory with per-specimen .npz files (default: run/reference_index)')
+    ap.add_argument('--out-dir', default='run/reference_dist',
+                    help='Output directory for CSV files (default: run/reference_dist)')
    args = ap.parse_args()

    ref_dir = Path(args.ref_dir)
@@ -150,17 +150,20 @@ def main() -> None:
                                 formatter_class=argparse.RawDescriptionHelpFormatter)
    ap.add_argument('--tol', type=float, default=1e-4,
                    help='Max abs diff threshold for PASS/FAIL (default 1e-4)')
-    ap.add_argument('--out', default='stats/dist_comparison/summary.csv',
+    ap.add_argument('--run-dir', default='run',
+                    help='Root directory holding reference_dist/ and obikmer_dist/ (default: run)')
+    ap.add_argument('--out', default='run/stats/dist_comparison/summary.csv',
                    help='Output summary CSV path')
    args = ap.parse_args()

    out_path = Path(args.out)
    out_path.parent.mkdir(parents=True, exist_ok=True)

+    run_dir = Path(args.run_dir)
    print(f'Comparing {len(COMPARISONS)} matrix pairs…', file=sys.stderr)
    rows = []
    for label, ref, obi in COMPARISONS:
-        rows.append(compare(label, Path(ref), Path(obi), tol=args.tol))
+        rows.append(compare(label, run_dir / ref, run_dir / obi, tol=args.tol))

    fields = ['comparison', 'max_abs', 'mean_abs', 'rmse', 'n_pairs', 'status']
    with out_path.open('w', newline='') as fh:
@@ -2,212 +2,212 @@ SPECIMENS := Escherichia_coli--K-12_MG1655 Escherichia_coli--EDL933 Salmonella_e
 SPECIES   := Escherichia_coli Salmonella_enterica Bacillus_subtilis Shouchella_clausii Klebsiella_pneumoniae Opitutus_terrae Saccharolobus_islandicus Acidobacterium_capsulatum Proteus_mirabilis Wolbachia_endosymbiont Yersinia_ruckeri Candidozyma_auris

 # Escherichia_coli--K-12_MG1655
-simulated_data/Escherichia_coli/K-12_MG1655/reads_R1.fastq.gz: genomes/GCF_000005845.2_ASM584v2_genomic.fna.gz
-reference_index/Escherichia_coli--K-12_MG1655.npz: simulated_data/Escherichia_coli/K-12_MG1655/reads_R1.fastq.gz
-specimen_index_presence/Escherichia_coli--K-12_MG1655/index.done stats/indexing_presence/Escherichia_coli--K-12_MG1655.stats: simulated_data/Escherichia_coli/K-12_MG1655/reads_R1.fastq.gz
-specimen_index_count/Escherichia_coli--K-12_MG1655/index.done stats/indexing_count/Escherichia_coli--K-12_MG1655.stats: simulated_data/Escherichia_coli/K-12_MG1655/reads_R1.fastq.gz
-stats/verify_presence/Escherichia_coli--K-12_MG1655.stats: reference_index/Escherichia_coli--K-12_MG1655.npz specimen_index_presence/Escherichia_coli--K-12_MG1655/index.done
-stats/verify_count/Escherichia_coli--K-12_MG1655.stats: reference_index/Escherichia_coli--K-12_MG1655.npz specimen_index_count/Escherichia_coli--K-12_MG1655/index.done
+run/simulated_data/Escherichia_coli/K-12_MG1655/reads_R1.fastq.gz: run/genomes/GCF_000005845.2_ASM584v2_genomic.fna.gz
+run/reference_index/Escherichia_coli--K-12_MG1655.npz: run/simulated_data/Escherichia_coli/K-12_MG1655/reads_R1.fastq.gz
+run/specimen_index_presence/Escherichia_coli--K-12_MG1655/index.done run/stats/indexing_presence/Escherichia_coli--K-12_MG1655.stats: run/simulated_data/Escherichia_coli/K-12_MG1655/reads_R1.fastq.gz
+run/specimen_index_count/Escherichia_coli--K-12_MG1655/index.done run/stats/indexing_count/Escherichia_coli--K-12_MG1655.stats: run/simulated_data/Escherichia_coli/K-12_MG1655/reads_R1.fastq.gz
+run/stats/verify_presence/Escherichia_coli--K-12_MG1655.stats: run/reference_index/Escherichia_coli--K-12_MG1655.npz run/specimen_index_presence/Escherichia_coli--K-12_MG1655/index.done
+run/stats/verify_count/Escherichia_coli--K-12_MG1655.stats: run/reference_index/Escherichia_coli--K-12_MG1655.npz run/specimen_index_count/Escherichia_coli--K-12_MG1655/index.done

 # Escherichia_coli--EDL933
-simulated_data/Escherichia_coli/EDL933/reads_R1.fastq.gz: genomes/GCF_000006665.1_ASM666v1_genomic.fna.gz
-reference_index/Escherichia_coli--EDL933.npz: simulated_data/Escherichia_coli/EDL933/reads_R1.fastq.gz
-specimen_index_presence/Escherichia_coli--EDL933/index.done stats/indexing_presence/Escherichia_coli--EDL933.stats: simulated_data/Escherichia_coli/EDL933/reads_R1.fastq.gz
-specimen_index_count/Escherichia_coli--EDL933/index.done stats/indexing_count/Escherichia_coli--EDL933.stats: simulated_data/Escherichia_coli/EDL933/reads_R1.fastq.gz
-stats/verify_presence/Escherichia_coli--EDL933.stats: reference_index/Escherichia_coli--EDL933.npz specimen_index_presence/Escherichia_coli--EDL933/index.done
-stats/verify_count/Escherichia_coli--EDL933.stats: reference_index/Escherichia_coli--EDL933.npz specimen_index_count/Escherichia_coli--EDL933/index.done
+run/simulated_data/Escherichia_coli/EDL933/reads_R1.fastq.gz: run/genomes/GCF_000006665.1_ASM666v1_genomic.fna.gz
+run/reference_index/Escherichia_coli--EDL933.npz: run/simulated_data/Escherichia_coli/EDL933/reads_R1.fastq.gz
+run/specimen_index_presence/Escherichia_coli--EDL933/index.done run/stats/indexing_presence/Escherichia_coli--EDL933.stats: run/simulated_data/Escherichia_coli/EDL933/reads_R1.fastq.gz
+run/specimen_index_count/Escherichia_coli--EDL933/index.done run/stats/indexing_count/Escherichia_coli--EDL933.stats: run/simulated_data/Escherichia_coli/EDL933/reads_R1.fastq.gz
+run/stats/verify_presence/Escherichia_coli--EDL933.stats: run/reference_index/Escherichia_coli--EDL933.npz run/specimen_index_presence/Escherichia_coli--EDL933/index.done
+run/stats/verify_count/Escherichia_coli--EDL933.stats: run/reference_index/Escherichia_coli--EDL933.npz run/specimen_index_count/Escherichia_coli--EDL933/index.done

 # Salmonella_enterica--LT2
-simulated_data/Salmonella_enterica/LT2/reads_R1.fastq.gz: genomes/GCF_000006945.2_ASM694v2_genomic.fna.gz
-reference_index/Salmonella_enterica--LT2.npz: simulated_data/Salmonella_enterica/LT2/reads_R1.fastq.gz
-specimen_index_presence/Salmonella_enterica--LT2/index.done stats/indexing_presence/Salmonella_enterica--LT2.stats: simulated_data/Salmonella_enterica/LT2/reads_R1.fastq.gz
-specimen_index_count/Salmonella_enterica--LT2/index.done stats/indexing_count/Salmonella_enterica--LT2.stats: simulated_data/Salmonella_enterica/LT2/reads_R1.fastq.gz
-stats/verify_presence/Salmonella_enterica--LT2.stats: reference_index/Salmonella_enterica--LT2.npz specimen_index_presence/Salmonella_enterica--LT2/index.done
-stats/verify_count/Salmonella_enterica--LT2.stats: reference_index/Salmonella_enterica--LT2.npz specimen_index_count/Salmonella_enterica--LT2/index.done
+run/simulated_data/Salmonella_enterica/LT2/reads_R1.fastq.gz: run/genomes/GCF_000006945.2_ASM694v2_genomic.fna.gz
+run/reference_index/Salmonella_enterica--LT2.npz: run/simulated_data/Salmonella_enterica/LT2/reads_R1.fastq.gz
+run/specimen_index_presence/Salmonella_enterica--LT2/index.done run/stats/indexing_presence/Salmonella_enterica--LT2.stats: run/simulated_data/Salmonella_enterica/LT2/reads_R1.fastq.gz
+run/specimen_index_count/Salmonella_enterica--LT2/index.done run/stats/indexing_count/Salmonella_enterica--LT2.stats: run/simulated_data/Salmonella_enterica/LT2/reads_R1.fastq.gz
+run/stats/verify_presence/Salmonella_enterica--LT2.stats: run/reference_index/Salmonella_enterica--LT2.npz run/specimen_index_presence/Salmonella_enterica--LT2/index.done
+run/stats/verify_count/Salmonella_enterica--LT2.stats: run/reference_index/Salmonella_enterica--LT2.npz run/specimen_index_count/Salmonella_enterica--LT2/index.done

 # Escherichia_coli--CFT073
-simulated_data/Escherichia_coli/CFT073/reads_R1.fastq.gz: genomes/GCF_000007445.1_ASM744v1_genomic.fna.gz
-reference_index/Escherichia_coli--CFT073.npz: simulated_data/Escherichia_coli/CFT073/reads_R1.fastq.gz
-specimen_index_presence/Escherichia_coli--CFT073/index.done stats/indexing_presence/Escherichia_coli--CFT073.stats: simulated_data/Escherichia_coli/CFT073/reads_R1.fastq.gz
-specimen_index_count/Escherichia_coli--CFT073/index.done stats/indexing_count/Escherichia_coli--CFT073.stats: simulated_data/Escherichia_coli/CFT073/reads_R1.fastq.gz
-stats/verify_presence/Escherichia_coli--CFT073.stats: reference_index/Escherichia_coli--CFT073.npz specimen_index_presence/Escherichia_coli--CFT073/index.done
-stats/verify_count/Escherichia_coli--CFT073.stats: reference_index/Escherichia_coli--CFT073.npz specimen_index_count/Escherichia_coli--CFT073/index.done
+run/simulated_data/Escherichia_coli/CFT073/reads_R1.fastq.gz: run/genomes/GCF_000007445.1_ASM744v1_genomic.fna.gz
+run/reference_index/Escherichia_coli--CFT073.npz: run/simulated_data/Escherichia_coli/CFT073/reads_R1.fastq.gz
+run/specimen_index_presence/Escherichia_coli--CFT073/index.done run/stats/indexing_presence/Escherichia_coli--CFT073.stats: run/simulated_data/Escherichia_coli/CFT073/reads_R1.fastq.gz
+run/specimen_index_count/Escherichia_coli--CFT073/index.done run/stats/indexing_count/Escherichia_coli--CFT073.stats: run/simulated_data/Escherichia_coli/CFT073/reads_R1.fastq.gz
+run/stats/verify_presence/Escherichia_coli--CFT073.stats: run/reference_index/Escherichia_coli--CFT073.npz run/specimen_index_presence/Escherichia_coli--CFT073/index.done
+run/stats/verify_count/Escherichia_coli--CFT073.stats: run/reference_index/Escherichia_coli--CFT073.npz run/specimen_index_count/Escherichia_coli--CFT073/index.done

 # Bacillus_subtilis--168
-simulated_data/Bacillus_subtilis/168/reads_R1.fastq.gz: genomes/GCF_000009045.1_ASM904v1_genomic.fna.gz
-reference_index/Bacillus_subtilis--168.npz: simulated_data/Bacillus_subtilis/168/reads_R1.fastq.gz
-specimen_index_presence/Bacillus_subtilis--168/index.done stats/indexing_presence/Bacillus_subtilis--168.stats: simulated_data/Bacillus_subtilis/168/reads_R1.fastq.gz
-specimen_index_count/Bacillus_subtilis--168/index.done stats/indexing_count/Bacillus_subtilis--168.stats: simulated_data/Bacillus_subtilis/168/reads_R1.fastq.gz
-stats/verify_presence/Bacillus_subtilis--168.stats: reference_index/Bacillus_subtilis--168.npz specimen_index_presence/Bacillus_subtilis--168/index.done
-stats/verify_count/Bacillus_subtilis--168.stats: reference_index/Bacillus_subtilis--168.npz specimen_index_count/Bacillus_subtilis--168/index.done
+run/simulated_data/Bacillus_subtilis/168/reads_R1.fastq.gz: run/genomes/GCF_000009045.1_ASM904v1_genomic.fna.gz
+run/reference_index/Bacillus_subtilis--168.npz: run/simulated_data/Bacillus_subtilis/168/reads_R1.fastq.gz
+run/specimen_index_presence/Bacillus_subtilis--168/index.done run/stats/indexing_presence/Bacillus_subtilis--168.stats: run/simulated_data/Bacillus_subtilis/168/reads_R1.fastq.gz
+run/specimen_index_count/Bacillus_subtilis--168/index.done run/stats/indexing_count/Bacillus_subtilis--168.stats: run/simulated_data/Bacillus_subtilis/168/reads_R1.fastq.gz
+run/stats/verify_presence/Bacillus_subtilis--168.stats: run/reference_index/Bacillus_subtilis--168.npz run/specimen_index_presence/Bacillus_subtilis--168/index.done
+run/stats/verify_count/Bacillus_subtilis--168.stats: run/reference_index/Bacillus_subtilis--168.npz run/specimen_index_count/Bacillus_subtilis--168/index.done

 # Salmonella_enterica--P125109
-simulated_data/Salmonella_enterica/P125109/reads_R1.fastq.gz: genomes/GCF_000009505.1_ASM950v1_genomic.fna.gz
-reference_index/Salmonella_enterica--P125109.npz: simulated_data/Salmonella_enterica/P125109/reads_R1.fastq.gz
-specimen_index_presence/Salmonella_enterica--P125109/index.done stats/indexing_presence/Salmonella_enterica--P125109.stats: simulated_data/Salmonella_enterica/P125109/reads_R1.fastq.gz
-specimen_index_count/Salmonella_enterica--P125109/index.done stats/indexing_count/Salmonella_enterica--P125109.stats: simulated_data/Salmonella_enterica/P125109/reads_R1.fastq.gz
-stats/verify_presence/Salmonella_enterica--P125109.stats: reference_index/Salmonella_enterica--P125109.npz specimen_index_presence/Salmonella_enterica--P125109/index.done
-stats/verify_count/Salmonella_enterica--P125109.stats: reference_index/Salmonella_enterica--P125109.npz specimen_index_count/Salmonella_enterica--P125109/index.done
+run/simulated_data/Salmonella_enterica/P125109/reads_R1.fastq.gz: run/genomes/GCF_000009505.1_ASM950v1_genomic.fna.gz
+run/reference_index/Salmonella_enterica--P125109.npz: run/simulated_data/Salmonella_enterica/P125109/reads_R1.fastq.gz
+run/specimen_index_presence/Salmonella_enterica--P125109/index.done run/stats/indexing_presence/Salmonella_enterica--P125109.stats: run/simulated_data/Salmonella_enterica/P125109/reads_R1.fastq.gz
+run/specimen_index_count/Salmonella_enterica--P125109/index.done run/stats/indexing_count/Salmonella_enterica--P125109.stats: run/simulated_data/Salmonella_enterica/P125109/reads_R1.fastq.gz
+run/stats/verify_presence/Salmonella_enterica--P125109.stats: run/reference_index/Salmonella_enterica--P125109.npz run/specimen_index_presence/Salmonella_enterica--P125109/index.done
+run/stats/verify_count/Salmonella_enterica--P125109.stats: run/reference_index/Salmonella_enterica--P125109.npz run/specimen_index_count/Salmonella_enterica--P125109/index.done

 # Shouchella_clausii--KSM-K16
-simulated_data/Shouchella_clausii/KSM-K16/reads_R1.fastq.gz: genomes/GCF_000009825.1_ASM982v1_genomic.fna.gz
-reference_index/Shouchella_clausii--KSM-K16.npz: simulated_data/Shouchella_clausii/KSM-K16/reads_R1.fastq.gz
-specimen_index_presence/Shouchella_clausii--KSM-K16/index.done stats/indexing_presence/Shouchella_clausii--KSM-K16.stats: simulated_data/Shouchella_clausii/KSM-K16/reads_R1.fastq.gz
-specimen_index_count/Shouchella_clausii--KSM-K16/index.done stats/indexing_count/Shouchella_clausii--KSM-K16.stats: simulated_data/Shouchella_clausii/KSM-K16/reads_R1.fastq.gz
-stats/verify_presence/Shouchella_clausii--KSM-K16.stats: reference_index/Shouchella_clausii--KSM-K16.npz specimen_index_presence/Shouchella_clausii--KSM-K16/index.done
-stats/verify_count/Shouchella_clausii--KSM-K16.stats: reference_index/Shouchella_clausii--KSM-K16.npz specimen_index_count/Shouchella_clausii--KSM-K16/index.done
+run/simulated_data/Shouchella_clausii/KSM-K16/reads_R1.fastq.gz: run/genomes/GCF_000009825.1_ASM982v1_genomic.fna.gz
+run/reference_index/Shouchella_clausii--KSM-K16.npz: run/simulated_data/Shouchella_clausii/KSM-K16/reads_R1.fastq.gz
+run/specimen_index_presence/Shouchella_clausii--KSM-K16/index.done run/stats/indexing_presence/Shouchella_clausii--KSM-K16.stats: run/simulated_data/Shouchella_clausii/KSM-K16/reads_R1.fastq.gz
+run/specimen_index_count/Shouchella_clausii--KSM-K16/index.done run/stats/indexing_count/Shouchella_clausii--KSM-K16.stats: run/simulated_data/Shouchella_clausii/KSM-K16/reads_R1.fastq.gz
+run/stats/verify_presence/Shouchella_clausii--KSM-K16.stats: run/reference_index/Shouchella_clausii--KSM-K16.npz run/specimen_index_presence/Shouchella_clausii--KSM-K16/index.done
+run/stats/verify_count/Shouchella_clausii--KSM-K16.stats: run/reference_index/Shouchella_clausii--KSM-K16.npz run/specimen_index_count/Shouchella_clausii--KSM-K16/index.done

 # Escherichia_coli--K-12_W3110
-simulated_data/Escherichia_coli/K-12_W3110/reads_R1.fastq.gz: genomes/GCF_000010245.2_ASM1024v1_genomic.fna.gz
-reference_index/Escherichia_coli--K-12_W3110.npz: simulated_data/Escherichia_coli/K-12_W3110/reads_R1.fastq.gz
-specimen_index_presence/Escherichia_coli--K-12_W3110/index.done stats/indexing_presence/Escherichia_coli--K-12_W3110.stats: simulated_data/Escherichia_coli/K-12_W3110/reads_R1.fastq.gz
-specimen_index_count/Escherichia_coli--K-12_W3110/index.done stats/indexing_count/Escherichia_coli--K-12_W3110.stats: simulated_data/Escherichia_coli/K-12_W3110/reads_R1.fastq.gz
-stats/verify_presence/Escherichia_coli--K-12_W3110.stats: reference_index/Escherichia_coli--K-12_W3110.npz specimen_index_presence/Escherichia_coli--K-12_W3110/index.done
-stats/verify_count/Escherichia_coli--K-12_W3110.stats: reference_index/Escherichia_coli--K-12_W3110.npz specimen_index_count/Escherichia_coli--K-12_W3110/index.done
+run/simulated_data/Escherichia_coli/K-12_W3110/reads_R1.fastq.gz: run/genomes/GCF_000010245.2_ASM1024v1_genomic.fna.gz
+run/reference_index/Escherichia_coli--K-12_W3110.npz: run/simulated_data/Escherichia_coli/K-12_W3110/reads_R1.fastq.gz
+run/specimen_index_presence/Escherichia_coli--K-12_W3110/index.done run/stats/indexing_presence/Escherichia_coli--K-12_W3110.stats: run/simulated_data/Escherichia_coli/K-12_W3110/reads_R1.fastq.gz
+run/specimen_index_count/Escherichia_coli--K-12_W3110/index.done run/stats/indexing_count/Escherichia_coli--K-12_W3110.stats: run/simulated_data/Escherichia_coli/K-12_W3110/reads_R1.fastq.gz
+run/stats/verify_presence/Escherichia_coli--K-12_W3110.stats: run/reference_index/Escherichia_coli--K-12_W3110.npz run/specimen_index_presence/Escherichia_coli--K-12_W3110/index.done
+run/stats/verify_count/Escherichia_coli--K-12_W3110.stats: run/reference_index/Escherichia_coli--K-12_W3110.npz run/specimen_index_count/Escherichia_coli--K-12_W3110/index.done

 # Klebsiella_pneumoniae--MGH_78578
-simulated_data/Klebsiella_pneumoniae/MGH_78578/reads_R1.fastq.gz: genomes/GCF_000016305.1_ASM1630v1_genomic.fna.gz
-reference_index/Klebsiella_pneumoniae--MGH_78578.npz: simulated_data/Klebsiella_pneumoniae/MGH_78578/reads_R1.fastq.gz
-specimen_index_presence/Klebsiella_pneumoniae--MGH_78578/index.done stats/indexing_presence/Klebsiella_pneumoniae--MGH_78578.stats: simulated_data/Klebsiella_pneumoniae/MGH_78578/reads_R1.fastq.gz
-specimen_index_count/Klebsiella_pneumoniae--MGH_78578/index.done stats/indexing_count/Klebsiella_pneumoniae--MGH_78578.stats: simulated_data/Klebsiella_pneumoniae/MGH_78578/reads_R1.fastq.gz
-stats/verify_presence/Klebsiella_pneumoniae--MGH_78578.stats: reference_index/Klebsiella_pneumoniae--MGH_78578.npz specimen_index_presence/Klebsiella_pneumoniae--MGH_78578/index.done
-stats/verify_count/Klebsiella_pneumoniae--MGH_78578.stats: reference_index/Klebsiella_pneumoniae--MGH_78578.npz specimen_index_count/Klebsiella_pneumoniae--MGH_78578/index.done
+run/simulated_data/Klebsiella_pneumoniae/MGH_78578/reads_R1.fastq.gz: run/genomes/GCF_000016305.1_ASM1630v1_genomic.fna.gz
+run/reference_index/Klebsiella_pneumoniae--MGH_78578.npz: run/simulated_data/Klebsiella_pneumoniae/MGH_78578/reads_R1.fastq.gz
+run/specimen_index_presence/Klebsiella_pneumoniae--MGH_78578/index.done run/stats/indexing_presence/Klebsiella_pneumoniae--MGH_78578.stats: run/simulated_data/Klebsiella_pneumoniae/MGH_78578/reads_R1.fastq.gz
+run/specimen_index_count/Klebsiella_pneumoniae--MGH_78578/index.done run/stats/indexing_count/Klebsiella_pneumoniae--MGH_78578.stats: run/simulated_data/Klebsiella_pneumoniae/MGH_78578/reads_R1.fastq.gz
+run/stats/verify_presence/Klebsiella_pneumoniae--MGH_78578.stats: run/reference_index/Klebsiella_pneumoniae--MGH_78578.npz run/specimen_index_presence/Klebsiella_pneumoniae--MGH_78578/index.done
+run/stats/verify_count/Klebsiella_pneumoniae--MGH_78578.stats: run/reference_index/Klebsiella_pneumoniae--MGH_78578.npz run/specimen_index_count/Klebsiella_pneumoniae--MGH_78578/index.done

 # Opitutus_terrae--PB90-1
-simulated_data/Opitutus_terrae/PB90-1/reads_R1.fastq.gz: genomes/GCF_000019965.1_ASM1996v1_genomic.fna.gz
-reference_index/Opitutus_terrae--PB90-1.npz: simulated_data/Opitutus_terrae/PB90-1/reads_R1.fastq.gz
-specimen_index_presence/Opitutus_terrae--PB90-1/index.done stats/indexing_presence/Opitutus_terrae--PB90-1.stats: simulated_data/Opitutus_terrae/PB90-1/reads_R1.fastq.gz
-specimen_index_count/Opitutus_terrae--PB90-1/index.done stats/indexing_count/Opitutus_terrae--PB90-1.stats: simulated_data/Opitutus_terrae/PB90-1/reads_R1.fastq.gz
-stats/verify_presence/Opitutus_terrae--PB90-1.stats: reference_index/Opitutus_terrae--PB90-1.npz specimen_index_presence/Opitutus_terrae--PB90-1/index.done
-stats/verify_count/Opitutus_terrae--PB90-1.stats: reference_index/Opitutus_terrae--PB90-1.npz specimen_index_count/Opitutus_terrae--PB90-1/index.done
+run/simulated_data/Opitutus_terrae/PB90-1/reads_R1.fastq.gz: run/genomes/GCF_000019965.1_ASM1996v1_genomic.fna.gz
+run/reference_index/Opitutus_terrae--PB90-1.npz: run/simulated_data/Opitutus_terrae/PB90-1/reads_R1.fastq.gz
+run/specimen_index_presence/Opitutus_terrae--PB90-1/index.done run/stats/indexing_presence/Opitutus_terrae--PB90-1.stats: run/simulated_data/Opitutus_terrae/PB90-1/reads_R1.fastq.gz
+run/specimen_index_count/Opitutus_terrae--PB90-1/index.done run/stats/indexing_count/Opitutus_terrae--PB90-1.stats: run/simulated_data/Opitutus_terrae/PB90-1/reads_R1.fastq.gz
+run/stats/verify_presence/Opitutus_terrae--PB90-1.stats: run/reference_index/Opitutus_terrae--PB90-1.npz run/specimen_index_presence/Opitutus_terrae--PB90-1/index.done
+run/stats/verify_count/Opitutus_terrae--PB90-1.stats: run/reference_index/Opitutus_terrae--PB90-1.npz run/specimen_index_count/Opitutus_terrae--PB90-1/index.done

 # Saccharolobus_islandicus--M.16.4
-simulated_data/Saccharolobus_islandicus/M.16.4/reads_R1.fastq.gz: genomes/GCF_000022445.1_ASM2244v1_genomic.fna.gz
-reference_index/Saccharolobus_islandicus--M.16.4.npz: simulated_data/Saccharolobus_islandicus/M.16.4/reads_R1.fastq.gz
-specimen_index_presence/Saccharolobus_islandicus--M.16.4/index.done stats/indexing_presence/Saccharolobus_islandicus--M.16.4.stats: simulated_data/Saccharolobus_islandicus/M.16.4/reads_R1.fastq.gz
-specimen_index_count/Saccharolobus_islandicus--M.16.4/index.done stats/indexing_count/Saccharolobus_islandicus--M.16.4.stats: simulated_data/Saccharolobus_islandicus/M.16.4/reads_R1.fastq.gz
-stats/verify_presence/Saccharolobus_islandicus--M.16.4.stats: reference_index/Saccharolobus_islandicus--M.16.4.npz specimen_index_presence/Saccharolobus_islandicus--M.16.4/index.done
-stats/verify_count/Saccharolobus_islandicus--M.16.4.stats: reference_index/Saccharolobus_islandicus--M.16.4.npz specimen_index_count/Saccharolobus_islandicus--M.16.4/index.done
+run/simulated_data/Saccharolobus_islandicus/M.16.4/reads_R1.fastq.gz: run/genomes/GCF_000022445.1_ASM2244v1_genomic.fna.gz
+run/reference_index/Saccharolobus_islandicus--M.16.4.npz: run/simulated_data/Saccharolobus_islandicus/M.16.4/reads_R1.fastq.gz
+run/specimen_index_presence/Saccharolobus_islandicus--M.16.4/index.done run/stats/indexing_presence/Saccharolobus_islandicus--M.16.4.stats: run/simulated_data/Saccharolobus_islandicus/M.16.4/reads_R1.fastq.gz
+run/specimen_index_count/Saccharolobus_islandicus--M.16.4/index.done run/stats/indexing_count/Saccharolobus_islandicus--M.16.4.stats: run/simulated_data/Saccharolobus_islandicus/M.16.4/reads_R1.fastq.gz
+run/stats/verify_presence/Saccharolobus_islandicus--M.16.4.stats: run/reference_index/Saccharolobus_islandicus--M.16.4.npz run/specimen_index_presence/Saccharolobus_islandicus--M.16.4/index.done
+run/stats/verify_count/Saccharolobus_islandicus--M.16.4.stats: run/reference_index/Saccharolobus_islandicus--M.16.4.npz run/specimen_index_count/Saccharolobus_islandicus--M.16.4/index.done

 # Acidobacterium_capsulatum--ATCC_51196
-simulated_data/Acidobacterium_capsulatum/ATCC_51196/reads_R1.fastq.gz: genomes/GCF_000022565.1_ASM2256v1_genomic.fna.gz
-reference_index/Acidobacterium_capsulatum--ATCC_51196.npz: simulated_data/Acidobacterium_capsulatum/ATCC_51196/reads_R1.fastq.gz
-specimen_index_presence/Acidobacterium_capsulatum--ATCC_51196/index.done stats/indexing_presence/Acidobacterium_capsulatum--ATCC_51196.stats: simulated_data/Acidobacterium_capsulatum/ATCC_51196/reads_R1.fastq.gz
-specimen_index_count/Acidobacterium_capsulatum--ATCC_51196/index.done stats/indexing_count/Acidobacterium_capsulatum--ATCC_51196.stats: simulated_data/Acidobacterium_capsulatum/ATCC_51196/reads_R1.fastq.gz
-stats/verify_presence/Acidobacterium_capsulatum--ATCC_51196.stats: reference_index/Acidobacterium_capsulatum--ATCC_51196.npz specimen_index_presence/Acidobacterium_capsulatum--ATCC_51196/index.done
-stats/verify_count/Acidobacterium_capsulatum--ATCC_51196.stats: reference_index/Acidobacterium_capsulatum--ATCC_51196.npz specimen_index_count/Acidobacterium_capsulatum--ATCC_51196/index.done
+run/simulated_data/Acidobacterium_capsulatum/ATCC_51196/reads_R1.fastq.gz: run/genomes/GCF_000022565.1_ASM2256v1_genomic.fna.gz
+run/reference_index/Acidobacterium_capsulatum--ATCC_51196.npz: run/simulated_data/Acidobacterium_capsulatum/ATCC_51196/reads_R1.fastq.gz
+run/specimen_index_presence/Acidobacterium_capsulatum--ATCC_51196/index.done run/stats/indexing_presence/Acidobacterium_capsulatum--ATCC_51196.stats: run/simulated_data/Acidobacterium_capsulatum/ATCC_51196/reads_R1.fastq.gz
+run/specimen_index_count/Acidobacterium_capsulatum--ATCC_51196/index.done run/stats/indexing_count/Acidobacterium_capsulatum--ATCC_51196.stats: run/simulated_data/Acidobacterium_capsulatum/ATCC_51196/reads_R1.fastq.gz
+run/stats/verify_presence/Acidobacterium_capsulatum--ATCC_51196.stats: run/reference_index/Acidobacterium_capsulatum--ATCC_51196.npz run/specimen_index_presence/Acidobacterium_capsulatum--ATCC_51196/index.done
+run/stats/verify_count/Acidobacterium_capsulatum--ATCC_51196.stats: run/reference_index/Acidobacterium_capsulatum--ATCC_51196.npz run/specimen_index_count/Acidobacterium_capsulatum--ATCC_51196/index.done

 # Salmonella_enterica--AKU_12601
-simulated_data/Salmonella_enterica/AKU_12601/reads_R1.fastq.gz: genomes/GCF_000026565.1_ASM2656v1_genomic.fna.gz
-reference_index/Salmonella_enterica--AKU_12601.npz: simulated_data/Salmonella_enterica/AKU_12601/reads_R1.fastq.gz
-specimen_index_presence/Salmonella_enterica--AKU_12601/index.done stats/indexing_presence/Salmonella_enterica--AKU_12601.stats: simulated_data/Salmonella_enterica/AKU_12601/reads_R1.fastq.gz
-specimen_index_count/Salmonella_enterica--AKU_12601/index.done stats/indexing_count/Salmonella_enterica--AKU_12601.stats: simulated_data/Salmonella_enterica/AKU_12601/reads_R1.fastq.gz
-stats/verify_presence/Salmonella_enterica--AKU_12601.stats: reference_index/Salmonella_enterica--AKU_12601.npz specimen_index_presence/Salmonella_enterica--AKU_12601/index.done
-stats/verify_count/Salmonella_enterica--AKU_12601.stats: reference_index/Salmonella_enterica--AKU_12601.npz specimen_index_count/Salmonella_enterica--AKU_12601/index.done
+run/simulated_data/Salmonella_enterica/AKU_12601/reads_R1.fastq.gz: run/genomes/GCF_000026565.1_ASM2656v1_genomic.fna.gz
+run/reference_index/Salmonella_enterica--AKU_12601.npz: run/simulated_data/Salmonella_enterica/AKU_12601/reads_R1.fastq.gz
+run/specimen_index_presence/Salmonella_enterica--AKU_12601/index.done run/stats/indexing_presence/Salmonella_enterica--AKU_12601.stats: run/simulated_data/Salmonella_enterica/AKU_12601/reads_R1.fastq.gz
+run/specimen_index_count/Salmonella_enterica--AKU_12601/index.done run/stats/indexing_count/Salmonella_enterica--AKU_12601.stats: run/simulated_data/Salmonella_enterica/AKU_12601/reads_R1.fastq.gz
+run/stats/verify_presence/Salmonella_enterica--AKU_12601.stats: run/reference_index/Salmonella_enterica--AKU_12601.npz run/specimen_index_presence/Salmonella_enterica--AKU_12601/index.done
+run/stats/verify_count/Salmonella_enterica--AKU_12601.stats: run/reference_index/Salmonella_enterica--AKU_12601.npz run/specimen_index_count/Salmonella_enterica--AKU_12601/index.done

 # Proteus_mirabilis--HI4320
-simulated_data/Proteus_mirabilis/HI4320/reads_R1.fastq.gz: genomes/GCF_000069965.1_ASM6996v1_genomic.fna.gz
-reference_index/Proteus_mirabilis--HI4320.npz: simulated_data/Proteus_mirabilis/HI4320/reads_R1.fastq.gz
-specimen_index_presence/Proteus_mirabilis--HI4320/index.done stats/indexing_presence/Proteus_mirabilis--HI4320.stats: simulated_data/Proteus_mirabilis/HI4320/reads_R1.fastq.gz
-specimen_index_count/Proteus_mirabilis--HI4320/index.done stats/indexing_count/Proteus_mirabilis--HI4320.stats: simulated_data/Proteus_mirabilis/HI4320/reads_R1.fastq.gz
-stats/verify_presence/Proteus_mirabilis--HI4320.stats: reference_index/Proteus_mirabilis--HI4320.npz specimen_index_presence/Proteus_mirabilis--HI4320/index.done
-stats/verify_count/Proteus_mirabilis--HI4320.stats: reference_index/Proteus_mirabilis--HI4320.npz specimen_index_count/Proteus_mirabilis--HI4320/index.done
+run/simulated_data/Proteus_mirabilis/HI4320/reads_R1.fastq.gz: run/genomes/GCF_000069965.1_ASM6996v1_genomic.fna.gz
+run/reference_index/Proteus_mirabilis--HI4320.npz: run/simulated_data/Proteus_mirabilis/HI4320/reads_R1.fastq.gz
+run/specimen_index_presence/Proteus_mirabilis--HI4320/index.done run/stats/indexing_presence/Proteus_mirabilis--HI4320.stats: run/simulated_data/Proteus_mirabilis/HI4320/reads_R1.fastq.gz
+run/specimen_index_count/Proteus_mirabilis--HI4320/index.done run/stats/indexing_count/Proteus_mirabilis--HI4320.stats: run/simulated_data/Proteus_mirabilis/HI4320/reads_R1.fastq.gz
+run/stats/verify_presence/Proteus_mirabilis--HI4320.stats: run/reference_index/Proteus_mirabilis--HI4320.npz run/specimen_index_presence/Proteus_mirabilis--HI4320/index.done
+run/stats/verify_count/Proteus_mirabilis--HI4320.stats: run/reference_index/Proteus_mirabilis--HI4320.npz run/specimen_index_count/Proteus_mirabilis--HI4320/index.done

 # Salmonella_enterica--CT18
-simulated_data/Salmonella_enterica/CT18/reads_R1.fastq.gz: genomes/GCF_000195995.1_ASM19599v1_genomic.fna.gz
-reference_index/Salmonella_enterica--CT18.npz: simulated_data/Salmonella_enterica/CT18/reads_R1.fastq.gz
-specimen_index_presence/Salmonella_enterica--CT18/index.done stats/indexing_presence/Salmonella_enterica--CT18.stats: simulated_data/Salmonella_enterica/CT18/reads_R1.fastq.gz
-specimen_index_count/Salmonella_enterica--CT18/index.done stats/indexing_count/Salmonella_enterica--CT18.stats: simulated_data/Salmonella_enterica/CT18/reads_R1.fastq.gz
-stats/verify_presence/Salmonella_enterica--CT18.stats: reference_index/Salmonella_enterica--CT18.npz specimen_index_presence/Salmonella_enterica--CT18/index.done
-stats/verify_count/Salmonella_enterica--CT18.stats: reference_index/Salmonella_enterica--CT18.npz specimen_index_count/Salmonella_enterica--CT18/index.done
+run/simulated_data/Salmonella_enterica/CT18/reads_R1.fastq.gz: run/genomes/GCF_000195995.1_ASM19599v1_genomic.fna.gz
+run/reference_index/Salmonella_enterica--CT18.npz: run/simulated_data/Salmonella_enterica/CT18/reads_R1.fastq.gz
+run/specimen_index_presence/Salmonella_enterica--CT18/index.done run/stats/indexing_presence/Salmonella_enterica--CT18.stats: run/simulated_data/Salmonella_enterica/CT18/reads_R1.fastq.gz
+run/specimen_index_count/Salmonella_enterica--CT18/index.done run/stats/indexing_count/Salmonella_enterica--CT18.stats: run/simulated_data/Salmonella_enterica/CT18/reads_R1.fastq.gz
+run/stats/verify_presence/Salmonella_enterica--CT18.stats: run/reference_index/Salmonella_enterica--CT18.npz run/specimen_index_presence/Salmonella_enterica--CT18/index.done
+run/stats/verify_count/Salmonella_enterica--CT18.stats: run/reference_index/Salmonella_enterica--CT18.npz run/specimen_index_count/Salmonella_enterica--CT18/index.done

 # Klebsiella_pneumoniae--HS11286
-simulated_data/Klebsiella_pneumoniae/HS11286/reads_R1.fastq.gz: genomes/GCF_000240185.1_ASM24018v2_genomic.fna.gz
-reference_index/Klebsiella_pneumoniae--HS11286.npz: simulated_data/Klebsiella_pneumoniae/HS11286/reads_R1.fastq.gz
-specimen_index_presence/Klebsiella_pneumoniae--HS11286/index.done stats/indexing_presence/Klebsiella_pneumoniae--HS11286.stats: simulated_data/Klebsiella_pneumoniae/HS11286/reads_R1.fastq.gz
-specimen_index_count/Klebsiella_pneumoniae--HS11286/index.done stats/indexing_count/Klebsiella_pneumoniae--HS11286.stats: simulated_data/Klebsiella_pneumoniae/HS11286/reads_R1.fastq.gz
-stats/verify_presence/Klebsiella_pneumoniae--HS11286.stats: reference_index/Klebsiella_pneumoniae--HS11286.npz specimen_index_presence/Klebsiella_pneumoniae--HS11286/index.done
-stats/verify_count/Klebsiella_pneumoniae--HS11286.stats: reference_index/Klebsiella_pneumoniae--HS11286.npz specimen_index_count/Klebsiella_pneumoniae--HS11286/index.done
+run/simulated_data/Klebsiella_pneumoniae/HS11286/reads_R1.fastq.gz: run/genomes/GCF_000240185.1_ASM24018v2_genomic.fna.gz
+run/reference_index/Klebsiella_pneumoniae--HS11286.npz: run/simulated_data/Klebsiella_pneumoniae/HS11286/reads_R1.fastq.gz
+run/specimen_index_presence/Klebsiella_pneumoniae--HS11286/index.done run/stats/indexing_presence/Klebsiella_pneumoniae--HS11286.stats: run/simulated_data/Klebsiella_pneumoniae/HS11286/reads_R1.fastq.gz
+run/specimen_index_count/Klebsiella_pneumoniae--HS11286/index.done run/stats/indexing_count/Klebsiella_pneumoniae--HS11286.stats: run/simulated_data/Klebsiella_pneumoniae/HS11286/reads_R1.fastq.gz
+run/stats/verify_presence/Klebsiella_pneumoniae--HS11286.stats: run/reference_index/Klebsiella_pneumoniae--HS11286.npz run/specimen_index_presence/Klebsiella_pneumoniae--HS11286/index.done
+run/stats/verify_count/Klebsiella_pneumoniae--HS11286.stats: run/reference_index/Klebsiella_pneumoniae--HS11286.npz run/specimen_index_count/Klebsiella_pneumoniae--HS11286/index.done

 # Wolbachia_endosymbiont--GCF_000306885.1_ASM30688v1
-simulated_data/Wolbachia_endosymbiont/GCF_000306885.1_ASM30688v1/reads_R1.fastq.gz: genomes/GCF_000306885.1_ASM30688v1_genomic.fna.gz
-reference_index/Wolbachia_endosymbiont--GCF_000306885.1_ASM30688v1.npz: simulated_data/Wolbachia_endosymbiont/GCF_000306885.1_ASM30688v1/reads_R1.fastq.gz
-specimen_index_presence/Wolbachia_endosymbiont--GCF_000306885.1_ASM30688v1/index.done stats/indexing_presence/Wolbachia_endosymbiont--GCF_000306885.1_ASM30688v1.stats: simulated_data/Wolbachia_endosymbiont/GCF_000306885.1_ASM30688v1/reads_R1.fastq.gz
-specimen_index_count/Wolbachia_endosymbiont--GCF_000306885.1_ASM30688v1/index.done stats/indexing_count/Wolbachia_endosymbiont--GCF_000306885.1_ASM30688v1.stats: simulated_data/Wolbachia_endosymbiont/GCF_000306885.1_ASM30688v1/reads_R1.fastq.gz
-stats/verify_presence/Wolbachia_endosymbiont--GCF_000306885.1_ASM30688v1.stats: reference_index/Wolbachia_endosymbiont--GCF_000306885.1_ASM30688v1.npz specimen_index_presence/Wolbachia_endosymbiont--GCF_000306885.1_ASM30688v1/index.done
-stats/verify_count/Wolbachia_endosymbiont--GCF_000306885.1_ASM30688v1.stats: reference_index/Wolbachia_endosymbiont--GCF_000306885.1_ASM30688v1.npz specimen_index_count/Wolbachia_endosymbiont--GCF_000306885.1_ASM30688v1/index.done
+run/simulated_data/Wolbachia_endosymbiont/GCF_000306885.1_ASM30688v1/reads_R1.fastq.gz: run/genomes/GCF_000306885.1_ASM30688v1_genomic.fna.gz
+run/reference_index/Wolbachia_endosymbiont--GCF_000306885.1_ASM30688v1.npz: run/simulated_data/Wolbachia_endosymbiont/GCF_000306885.1_ASM30688v1/reads_R1.fastq.gz
+run/specimen_index_presence/Wolbachia_endosymbiont--GCF_000306885.1_ASM30688v1/index.done run/stats/indexing_presence/Wolbachia_endosymbiont--GCF_000306885.1_ASM30688v1.stats: run/simulated_data/Wolbachia_endosymbiont/GCF_000306885.1_ASM30688v1/reads_R1.fastq.gz
+run/specimen_index_count/Wolbachia_endosymbiont--GCF_000306885.1_ASM30688v1/index.done run/stats/indexing_count/Wolbachia_endosymbiont--GCF_000306885.1_ASM30688v1.stats: run/simulated_data/Wolbachia_endosymbiont/GCF_000306885.1_ASM30688v1/reads_R1.fastq.gz
+run/stats/verify_presence/Wolbachia_endosymbiont--GCF_000306885.1_ASM30688v1.stats: run/reference_index/Wolbachia_endosymbiont--GCF_000306885.1_ASM30688v1.npz run/specimen_index_presence/Wolbachia_endosymbiont--GCF_000306885.1_ASM30688v1/index.done
+run/stats/verify_count/Wolbachia_endosymbiont--GCF_000306885.1_ASM30688v1.stats: run/reference_index/Wolbachia_endosymbiont--GCF_000306885.1_ASM30688v1.npz run/specimen_index_count/Wolbachia_endosymbiont--GCF_000306885.1_ASM30688v1/index.done

 # Klebsiella_pneumoniae--ATCC_13883
-simulated_data/Klebsiella_pneumoniae/ATCC_13883/reads_R1.fastq.gz: genomes/GCF_000742135.1_ASM74213v1_genomic.fna.gz
-reference_index/Klebsiella_pneumoniae--ATCC_13883.npz: simulated_data/Klebsiella_pneumoniae/ATCC_13883/reads_R1.fastq.gz
-specimen_index_presence/Klebsiella_pneumoniae--ATCC_13883/index.done stats/indexing_presence/Klebsiella_pneumoniae--ATCC_13883.stats: simulated_data/Klebsiella_pneumoniae/ATCC_13883/reads_R1.fastq.gz
-specimen_index_count/Klebsiella_pneumoniae--ATCC_13883/index.done stats/indexing_count/Klebsiella_pneumoniae--ATCC_13883.stats: simulated_data/Klebsiella_pneumoniae/ATCC_13883/reads_R1.fastq.gz
-stats/verify_presence/Klebsiella_pneumoniae--ATCC_13883.stats: reference_index/Klebsiella_pneumoniae--ATCC_13883.npz specimen_index_presence/Klebsiella_pneumoniae--ATCC_13883/index.done
-stats/verify_count/Klebsiella_pneumoniae--ATCC_13883.stats: reference_index/Klebsiella_pneumoniae--ATCC_13883.npz specimen_index_count/Klebsiella_pneumoniae--ATCC_13883/index.done
+run/simulated_data/Klebsiella_pneumoniae/ATCC_13883/reads_R1.fastq.gz: run/genomes/GCF_000742135.1_ASM74213v1_genomic.fna.gz
+run/reference_index/Klebsiella_pneumoniae--ATCC_13883.npz: run/simulated_data/Klebsiella_pneumoniae/ATCC_13883/reads_R1.fastq.gz
+run/specimen_index_presence/Klebsiella_pneumoniae--ATCC_13883/index.done run/stats/indexing_presence/Klebsiella_pneumoniae--ATCC_13883.stats: run/simulated_data/Klebsiella_pneumoniae/ATCC_13883/reads_R1.fastq.gz
+run/specimen_index_count/Klebsiella_pneumoniae--ATCC_13883/index.done run/stats/indexing_count/Klebsiella_pneumoniae--ATCC_13883.stats: run/simulated_data/Klebsiella_pneumoniae/ATCC_13883/reads_R1.fastq.gz
+run/stats/verify_presence/Klebsiella_pneumoniae--ATCC_13883.stats: run/reference_index/Klebsiella_pneumoniae--ATCC_13883.npz run/specimen_index_presence/Klebsiella_pneumoniae--ATCC_13883/index.done
+run/stats/verify_count/Klebsiella_pneumoniae--ATCC_13883.stats: run/reference_index/Klebsiella_pneumoniae--ATCC_13883.npz run/specimen_index_count/Klebsiella_pneumoniae--ATCC_13883/index.done

 # Yersinia_ruckeri--YRB
-simulated_data/Yersinia_ruckeri/YRB/reads_R1.fastq.gz: genomes/GCF_000834255.1_ASM83425v1_genomic.fna.gz
-reference_index/Yersinia_ruckeri--YRB.npz: simulated_data/Yersinia_ruckeri/YRB/reads_R1.fastq.gz
-specimen_index_presence/Yersinia_ruckeri--YRB/index.done stats/indexing_presence/Yersinia_ruckeri--YRB.stats: simulated_data/Yersinia_ruckeri/YRB/reads_R1.fastq.gz
-specimen_index_count/Yersinia_ruckeri--YRB/index.done stats/indexing_count/Yersinia_ruckeri--YRB.stats: simulated_data/Yersinia_ruckeri/YRB/reads_R1.fastq.gz
-stats/verify_presence/Yersinia_ruckeri--YRB.stats: reference_index/Yersinia_ruckeri--YRB.npz specimen_index_presence/Yersinia_ruckeri--YRB/index.done
-stats/verify_count/Yersinia_ruckeri--YRB.stats: reference_index/Yersinia_ruckeri--YRB.npz specimen_index_count/Yersinia_ruckeri--YRB/index.done
+run/simulated_data/Yersinia_ruckeri/YRB/reads_R1.fastq.gz: run/genomes/GCF_000834255.1_ASM83425v1_genomic.fna.gz
+run/reference_index/Yersinia_ruckeri--YRB.npz: run/simulated_data/Yersinia_ruckeri/YRB/reads_R1.fastq.gz
+run/specimen_index_presence/Yersinia_ruckeri--YRB/index.done run/stats/indexing_presence/Yersinia_ruckeri--YRB.stats: run/simulated_data/Yersinia_ruckeri/YRB/reads_R1.fastq.gz
+run/specimen_index_count/Yersinia_ruckeri--YRB/index.done run/stats/indexing_count/Yersinia_ruckeri--YRB.stats: run/simulated_data/Yersinia_ruckeri/YRB/reads_R1.fastq.gz
+run/stats/verify_presence/Yersinia_ruckeri--YRB.stats: run/reference_index/Yersinia_ruckeri--YRB.npz run/specimen_index_presence/Yersinia_ruckeri--YRB/index.done
+run/stats/verify_count/Yersinia_ruckeri--YRB.stats: run/reference_index/Yersinia_ruckeri--YRB.npz run/specimen_index_count/Yersinia_ruckeri--YRB/index.done

 # Candidozyma_auris--GCF_003013715.1_ASM301371v2
-simulated_data/Candidozyma_auris/GCF_003013715.1_ASM301371v2/reads_R1.fastq.gz: genomes/GCF_003013715.1_ASM301371v2_genomic.fna.gz
-reference_index/Candidozyma_auris--GCF_003013715.1_ASM301371v2.npz: simulated_data/Candidozyma_auris/GCF_003013715.1_ASM301371v2/reads_R1.fastq.gz
-specimen_index_presence/Candidozyma_auris--GCF_003013715.1_ASM301371v2/index.done stats/indexing_presence/Candidozyma_auris--GCF_003013715.1_ASM301371v2.stats: simulated_data/Candidozyma_auris/GCF_003013715.1_ASM301371v2/reads_R1.fastq.gz
-specimen_index_count/Candidozyma_auris--GCF_003013715.1_ASM301371v2/index.done stats/indexing_count/Candidozyma_auris--GCF_003013715.1_ASM301371v2.stats: simulated_data/Candidozyma_auris/GCF_003013715.1_ASM301371v2/reads_R1.fastq.gz
-stats/verify_presence/Candidozyma_auris--GCF_003013715.1_ASM301371v2.stats: reference_index/Candidozyma_auris--GCF_003013715.1_ASM301371v2.npz specimen_index_presence/Candidozyma_auris--GCF_003013715.1_ASM301371v2/index.done
-stats/verify_count/Candidozyma_auris--GCF_003013715.1_ASM301371v2.stats: reference_index/Candidozyma_auris--GCF_003013715.1_ASM301371v2.npz specimen_index_count/Candidozyma_auris--GCF_003013715.1_ASM301371v2/index.done
+run/simulated_data/Candidozyma_auris/GCF_003013715.1_ASM301371v2/reads_R1.fastq.gz: run/genomes/GCF_003013715.1_ASM301371v2_genomic.fna.gz
+run/reference_index/Candidozyma_auris--GCF_003013715.1_ASM301371v2.npz: run/simulated_data/Candidozyma_auris/GCF_003013715.1_ASM301371v2/reads_R1.fastq.gz
+run/specimen_index_presence/Candidozyma_auris--GCF_003013715.1_ASM301371v2/index.done run/stats/indexing_presence/Candidozyma_auris--GCF_003013715.1_ASM301371v2.stats: run/simulated_data/Candidozyma_auris/GCF_003013715.1_ASM301371v2/reads_R1.fastq.gz
+run/specimen_index_count/Candidozyma_auris--GCF_003013715.1_ASM301371v2/index.done run/stats/indexing_count/Candidozyma_auris--GCF_003013715.1_ASM301371v2.stats: run/simulated_data/Candidozyma_auris/GCF_003013715.1_ASM301371v2/reads_R1.fastq.gz
+run/stats/verify_presence/Candidozyma_auris--GCF_003013715.1_ASM301371v2.stats: run/reference_index/Candidozyma_auris--GCF_003013715.1_ASM301371v2.npz run/specimen_index_presence/Candidozyma_auris--GCF_003013715.1_ASM301371v2/index.done
+run/stats/verify_count/Candidozyma_auris--GCF_003013715.1_ASM301371v2.stats: run/reference_index/Candidozyma_auris--GCF_003013715.1_ASM301371v2.npz run/specimen_index_count/Candidozyma_auris--GCF_003013715.1_ASM301371v2/index.done

 # Escherichia_coli
-specific_index_presence/Escherichia_coli/index.done stats/specific_kmer_presence/Escherichia_coli.stats: global_index_presence/index.done
-specific_index_count/Escherichia_coli/index.done stats/specific_kmer_count/Escherichia_coli.stats: global_index_count/index.done
+run/specific_index_presence/Escherichia_coli/index.done run/stats/specific_kmer_presence/Escherichia_coli.stats: run/global_index_presence/index.done
+run/specific_index_count/Escherichia_coli/index.done run/stats/specific_kmer_count/Escherichia_coli.stats: run/global_index_count/index.done
 # Salmonella_enterica
-specific_index_presence/Salmonella_enterica/index.done stats/specific_kmer_presence/Salmonella_enterica.stats: global_index_presence/index.done
-specific_index_count/Salmonella_enterica/index.done stats/specific_kmer_count/Salmonella_enterica.stats: global_index_count/index.done
+run/specific_index_presence/Salmonella_enterica/index.done run/stats/specific_kmer_presence/Salmonella_enterica.stats: run/global_index_presence/index.done
+run/specific_index_count/Salmonella_enterica/index.done run/stats/specific_kmer_count/Salmonella_enterica.stats: run/global_index_count/index.done
 # Bacillus_subtilis
-specific_index_presence/Bacillus_subtilis/index.done stats/specific_kmer_presence/Bacillus_subtilis.stats: global_index_presence/index.done
-specific_index_count/Bacillus_subtilis/index.done stats/specific_kmer_count/Bacillus_subtilis.stats: global_index_count/index.done
+run/specific_index_presence/Bacillus_subtilis/index.done run/stats/specific_kmer_presence/Bacillus_subtilis.stats: run/global_index_presence/index.done
+run/specific_index_count/Bacillus_subtilis/index.done run/stats/specific_kmer_count/Bacillus_subtilis.stats: run/global_index_count/index.done
 # Shouchella_clausii
-specific_index_presence/Shouchella_clausii/index.done stats/specific_kmer_presence/Shouchella_clausii.stats: global_index_presence/index.done
-specific_index_count/Shouchella_clausii/index.done stats/specific_kmer_count/Shouchella_clausii.stats: global_index_count/index.done
+run/specific_index_presence/Shouchella_clausii/index.done run/stats/specific_kmer_presence/Shouchella_clausii.stats: run/global_index_presence/index.done
+run/specific_index_count/Shouchella_clausii/index.done run/stats/specific_kmer_count/Shouchella_clausii.stats: run/global_index_count/index.done
 # Klebsiella_pneumoniae
-specific_index_presence/Klebsiella_pneumoniae/index.done stats/specific_kmer_presence/Klebsiella_pneumoniae.stats: global_index_presence/index.done
-specific_index_count/Klebsiella_pneumoniae/index.done stats/specific_kmer_count/Klebsiella_pneumoniae.stats: global_index_count/index.done
+run/specific_index_presence/Klebsiella_pneumoniae/index.done run/stats/specific_kmer_presence/Klebsiella_pneumoniae.stats: run/global_index_presence/index.done
+run/specific_index_count/Klebsiella_pneumoniae/index.done run/stats/specific_kmer_count/Klebsiella_pneumoniae.stats: run/global_index_count/index.done
 # Opitutus_terrae
-specific_index_presence/Opitutus_terrae/index.done stats/specific_kmer_presence/Opitutus_terrae.stats: global_index_presence/index.done
-specific_index_count/Opitutus_terrae/index.done stats/specific_kmer_count/Opitutus_terrae.stats: global_index_count/index.done
+run/specific_index_presence/Opitutus_terrae/index.done run/stats/specific_kmer_presence/Opitutus_terrae.stats: run/global_index_presence/index.done
+run/specific_index_count/Opitutus_terrae/index.done run/stats/specific_kmer_count/Opitutus_terrae.stats: run/global_index_count/index.done
 # Saccharolobus_islandicus
-specific_index_presence/Saccharolobus_islandicus/index.done stats/specific_kmer_presence/Saccharolobus_islandicus.stats: global_index_presence/index.done
-specific_index_count/Saccharolobus_islandicus/index.done stats/specific_kmer_count/Saccharolobus_islandicus.stats: global_index_count/index.done
+run/specific_index_presence/Saccharolobus_islandicus/index.done run/stats/specific_kmer_presence/Saccharolobus_islandicus.stats: run/global_index_presence/index.done
+run/specific_index_count/Saccharolobus_islandicus/index.done run/stats/specific_kmer_count/Saccharolobus_islandicus.stats: run/global_index_count/index.done
 # Acidobacterium_capsulatum
-specific_index_presence/Acidobacterium_capsulatum/index.done stats/specific_kmer_presence/Acidobacterium_capsulatum.stats: global_index_presence/index.done
-specific_index_count/Acidobacterium_capsulatum/index.done stats/specific_kmer_count/Acidobacterium_capsulatum.stats: global_index_count/index.done
+run/specific_index_presence/Acidobacterium_capsulatum/index.done run/stats/specific_kmer_presence/Acidobacterium_capsulatum.stats: run/global_index_presence/index.done
+run/specific_index_count/Acidobacterium_capsulatum/index.done run/stats/specific_kmer_count/Acidobacterium_capsulatum.stats: run/global_index_count/index.done
 # Proteus_mirabilis
-specific_index_presence/Proteus_mirabilis/index.done stats/specific_kmer_presence/Proteus_mirabilis.stats: global_index_presence/index.done
-specific_index_count/Proteus_mirabilis/index.done stats/specific_kmer_count/Proteus_mirabilis.stats: global_index_count/index.done
+run/specific_index_presence/Proteus_mirabilis/index.done run/stats/specific_kmer_presence/Proteus_mirabilis.stats: run/global_index_presence/index.done
+run/specific_index_count/Proteus_mirabilis/index.done run/stats/specific_kmer_count/Proteus_mirabilis.stats: run/global_index_count/index.done
 # Wolbachia_endosymbiont
-specific_index_presence/Wolbachia_endosymbiont/index.done stats/specific_kmer_presence/Wolbachia_endosymbiont.stats: global_index_presence/index.done
-specific_index_count/Wolbachia_endosymbiont/index.done stats/specific_kmer_count/Wolbachia_endosymbiont.stats: global_index_count/index.done
+run/specific_index_presence/Wolbachia_endosymbiont/index.done run/stats/specific_kmer_presence/Wolbachia_endosymbiont.stats: run/global_index_presence/index.done
+run/specific_index_count/Wolbachia_endosymbiont/index.done run/stats/specific_kmer_count/Wolbachia_endosymbiont.stats: run/global_index_count/index.done
 # Yersinia_ruckeri
-specific_index_presence/Yersinia_ruckeri/index.done stats/specific_kmer_presence/Yersinia_ruckeri.stats: global_index_presence/index.done
-specific_index_count/Yersinia_ruckeri/index.done stats/specific_kmer_count/Yersinia_ruckeri.stats: global_index_count/index.done
+run/specific_index_presence/Yersinia_ruckeri/index.done run/stats/specific_kmer_presence/Yersinia_ruckeri.stats: run/global_index_presence/index.done
+run/specific_index_count/Yersinia_ruckeri/index.done run/stats/specific_kmer_count/Yersinia_ruckeri.stats: run/global_index_count/index.done
 # Candidozyma_auris
-specific_index_presence/Candidozyma_auris/index.done stats/specific_kmer_presence/Candidozyma_auris.stats: global_index_presence/index.done
-specific_index_count/Candidozyma_auris/index.done stats/specific_kmer_count/Candidozyma_auris.stats: global_index_count/index.done
+run/specific_index_presence/Candidozyma_auris/index.done run/stats/specific_kmer_presence/Candidozyma_auris.stats: run/global_index_presence/index.done
+run/specific_index_count/Candidozyma_auris/index.done run/stats/specific_kmer_count/Candidozyma_auris.stats: run/global_index_count/index.done

 QUERY_SPECIMENS := Escherichia_coli--K-12_MG1655 Saccharolobus_islandicus--M.16.4

 # query: Escherichia_coli--K-12_MG1655
-query_data/Escherichia_coli/K-12_MG1655/reads_R1.fastq.gz: genomes/GCF_000005845.2_ASM584v2_genomic.fna.gz
-query_dense/Escherichia_coli--K-12_MG1655.fasta.gz stats/query_dense/Escherichia_coli--K-12_MG1655.stats: query_data/Escherichia_coli/K-12_MG1655/reads_R1.fastq.gz global_index_presence/index.done
-query_sparse/Escherichia_coli--K-12_MG1655.fasta.gz stats/query_sparse/Escherichia_coli--K-12_MG1655.stats: query_data/Escherichia_coli/K-12_MG1655/reads_R1.fastq.gz global_index_presence_sparse/index.done
-stats/verify_query/Escherichia_coli--K-12_MG1655.stats: query_dense/Escherichia_coli--K-12_MG1655.fasta.gz query_sparse/Escherichia_coli--K-12_MG1655.fasta.gz
+run/query_data/Escherichia_coli/K-12_MG1655/reads_R1.fastq.gz: run/genomes/GCF_000005845.2_ASM584v2_genomic.fna.gz
+run/query_presence_dense/Escherichia_coli--K-12_MG1655.fasta.gz run/stats/query_presence_dense/Escherichia_coli--K-12_MG1655.stats: run/query_data/Escherichia_coli/K-12_MG1655/reads_R1.fastq.gz run/global_index_presence_dense/index.done
+run/query_presence_sparse/Escherichia_coli--K-12_MG1655.fasta.gz run/stats/query_presence_sparse/Escherichia_coli--K-12_MG1655.stats: run/query_data/Escherichia_coli/K-12_MG1655/reads_R1.fastq.gz run/global_index_presence/index.done
+run/stats/verify_query/Escherichia_coli--K-12_MG1655.stats: run/query_presence_dense/Escherichia_coli--K-12_MG1655.fasta.gz run/query_presence_sparse/Escherichia_coli--K-12_MG1655.fasta.gz

 # query: Saccharolobus_islandicus--M.16.4
-query_data/Saccharolobus_islandicus/M.16.4/reads_R1.fastq.gz: genomes/GCF_000022445.1_ASM2244v1_genomic.fna.gz
-query_dense/Saccharolobus_islandicus--M.16.4.fasta.gz stats/query_dense/Saccharolobus_islandicus--M.16.4.stats: query_data/Saccharolobus_islandicus/M.16.4/reads_R1.fastq.gz global_index_presence/index.done
-query_sparse/Saccharolobus_islandicus--M.16.4.fasta.gz stats/query_sparse/Saccharolobus_islandicus--M.16.4.stats: query_data/Saccharolobus_islandicus/M.16.4/reads_R1.fastq.gz global_index_presence_sparse/index.done
-stats/verify_query/Saccharolobus_islandicus--M.16.4.stats: query_dense/Saccharolobus_islandicus--M.16.4.fasta.gz query_sparse/Saccharolobus_islandicus--M.16.4.fasta.gz
+run/query_data/Saccharolobus_islandicus/M.16.4/reads_R1.fastq.gz: run/genomes/GCF_000022445.1_ASM2244v1_genomic.fna.gz
+run/query_presence_dense/Saccharolobus_islandicus--M.16.4.fasta.gz run/stats/query_presence_dense/Saccharolobus_islandicus--M.16.4.stats: run/query_data/Saccharolobus_islandicus/M.16.4/reads_R1.fastq.gz run/global_index_presence_dense/index.done
+run/query_presence_sparse/Saccharolobus_islandicus--M.16.4.fasta.gz run/stats/query_presence_sparse/Saccharolobus_islandicus--M.16.4.stats: run/query_data/Saccharolobus_islandicus/M.16.4/reads_R1.fastq.gz run/global_index_presence/index.done
+run/stats/verify_query/Saccharolobus_islandicus--M.16.4.stats: run/query_presence_dense/Saccharolobus_islandicus--M.16.4.fasta.gz run/query_presence_sparse/Saccharolobus_islandicus--M.16.4.fasta.gz
@@ -29,7 +29,10 @@ assemblies=(
    GCF_000834255.1
 )

-mkdir -p genomes
+SCRIPT_DIR="$(cd "$(dirname "${BASH_SOURCE[0]}")" && pwd)"
+GENOMES_DIR="${SCRIPT_DIR}/run/genomes"
+
+mkdir -p "${GENOMES_DIR}"

 for acc in "${assemblies[@]}"; do
    echo "Downloading ${acc}"
@@ -41,7 +44,7 @@ for acc in "${assemblies[@]}"; do
    unzip -q "${acc}.zip" -d "${acc}"
    find "${acc}" -name "*.fna" |
        while read file; do
-            obiconvert -Z ${file} >genomes/$(basename ${file}).gz
+            obiconvert -Z ${file} >"${GENOMES_DIR}/$(basename ${file}).gz"
        done

    rm -rf "${acc}" "${acc}.zip"
@@ -12,11 +12,12 @@ set -euo pipefail

 SPECIES="$1"
 SCRIPT_DIR="$(cd "$(dirname "${BASH_SOURCE[0]}")" && pwd)"
+RUN_DIR="${SCRIPT_DIR}/run"
 BINARY="${SCRIPT_DIR}/../src/target/release/obikmer"

-SOURCE="${SCRIPT_DIR}/global_index_count"
-OUTPUT="${SCRIPT_DIR}/specific_index_count/${SPECIES}"
-STATS_DIR="${SCRIPT_DIR}/stats/specific_kmer_count"
+SOURCE="${RUN_DIR}/global_index_count"
+OUTPUT="${RUN_DIR}/specific_index_count/${SPECIES}"
+STATS_DIR="${RUN_DIR}/stats/specific_kmer_count"
 STATS_FILE="${STATS_DIR}/${SPECIES}.stats"

 mkdir -p "${STATS_DIR}"
@@ -12,11 +12,12 @@ set -euo pipefail

 SPECIES="$1"
 SCRIPT_DIR="$(cd "$(dirname "${BASH_SOURCE[0]}")" && pwd)"
+RUN_DIR="${SCRIPT_DIR}/run"
 BINARY="${SCRIPT_DIR}/../src/target/release/obikmer"

-SOURCE="${SCRIPT_DIR}/global_index_presence"
-OUTPUT="${SCRIPT_DIR}/specific_index_presence/${SPECIES}"
-STATS_DIR="${SCRIPT_DIR}/stats/specific_kmer_presence"
+SOURCE="${RUN_DIR}/global_index_presence"
+OUTPUT="${RUN_DIR}/specific_index_presence/${SPECIES}"
+STATS_DIR="${RUN_DIR}/stats/specific_kmer_presence"
 STATS_FILE="${STATS_DIR}/${SPECIES}.stats"

 mkdir -p "${STATS_DIR}"
@@ -8,14 +8,15 @@ set -euo pipefail

 SPECIMEN="$1"
 SCRIPT_DIR="$(cd "$(dirname "${BASH_SOURCE[0]}")" && pwd)"
+RUN_DIR="${SCRIPT_DIR}/run"
 BINARY="${SCRIPT_DIR}/../src/target/release/obikmer"

 species="${SPECIMEN%%--*}"
 strain="${SPECIMEN#*--}"

-READS_DIR="${SCRIPT_DIR}/simulated_data/${species}/${strain}"
-INDEX_PATH="${SCRIPT_DIR}/specimen_index_count/${SPECIMEN}"
-STATS_DIR="${SCRIPT_DIR}/stats/indexing_count"
+READS_DIR="${RUN_DIR}/simulated_data/${species}/${strain}"
+INDEX_PATH="${RUN_DIR}/specimen_index_count/${SPECIMEN}"
+STATS_DIR="${RUN_DIR}/stats/indexing_count"
 STATS_FILE="${STATS_DIR}/${SPECIMEN}.stats"

 mkdir -p "${STATS_DIR}"
@@ -8,14 +8,15 @@ set -euo pipefail

 SPECIMEN="$1"
 SCRIPT_DIR="$(cd "$(dirname "${BASH_SOURCE[0]}")" && pwd)"
+RUN_DIR="${SCRIPT_DIR}/run"
 BINARY="${SCRIPT_DIR}/../src/target/release/obikmer"

 species="${SPECIMEN%%--*}"
 strain="${SPECIMEN#*--}"

-READS_DIR="${SCRIPT_DIR}/simulated_data/${species}/${strain}"
-INDEX_PATH="${SCRIPT_DIR}/specimen_index_presence/${SPECIMEN}"
-STATS_DIR="${SCRIPT_DIR}/stats/indexing_presence"
+READS_DIR="${RUN_DIR}/simulated_data/${species}/${strain}"
+INDEX_PATH="${RUN_DIR}/specimen_index_presence/${SPECIMEN}"
+STATS_DIR="${RUN_DIR}/stats/indexing_presence"
 STATS_FILE="${STATS_DIR}/${SPECIMEN}.stats"

 mkdir -p "${STATS_DIR}"
@@ -13,6 +13,10 @@ STOP_WORDS    = {'complete', 'chromosome', 'whole', 'sequence', 'genome',
                 'endosymbiont', 'of'}
 STOP_PREFIXES = ('scaffold', 'contig', 'plasmid')

+# All generated paths live under RUN/ (see Makefile) so the whole tree can be
+# gitignored with a single entry.
+RUN = 'run'
+
 # Specimens used as read sources for the query benchmark (see
 # DevDocMD/implementation/benchmark_query_testing.md): one common bacterium,
 # one distant lineage (the only archaeon in SPECIES).
@@ -80,7 +84,7 @@ def main():
        defn    = first_definition(path)
        sp, st  = parse_organism(defn, gcf_id)
        specimen = f'{sp}--{st}'
-        sim_dir  = f'simulated_data/{sp}/{st}'
+        sim_dir  = f'{RUN}/simulated_data/{sp}/{st}'
        entries.append((specimen, sp, sim_dir, path))
        if sp not in species_seen:
            species_seen.append(sp)
@@ -91,13 +95,13 @@ def main():

    for specimen, species, sim_dir, genome in entries:
        reads = f'{sim_dir}/reads_R1.fastq.gz'
-        p_done  = f'specimen_index_presence/{specimen}/index.done'
-        p_stats = f'stats/indexing_presence/{specimen}.stats'
-        c_done  = f'specimen_index_count/{specimen}/index.done'
-        c_stats = f'stats/indexing_count/{specimen}.stats'
-        ref     = f'reference_index/{specimen}.npz'
-        vp      = f'stats/verify_presence/{specimen}.stats'
-        vc      = f'stats/verify_count/{specimen}.stats'
+        p_done  = f'{RUN}/specimen_index_presence/{specimen}/index.done'
+        p_stats = f'{RUN}/stats/indexing_presence/{specimen}.stats'
+        c_done  = f'{RUN}/specimen_index_count/{specimen}/index.done'
+        c_stats = f'{RUN}/stats/indexing_count/{specimen}.stats'
+        ref     = f'{RUN}/reference_index/{specimen}.npz'
+        vp      = f'{RUN}/stats/verify_presence/{specimen}.stats'
+        vc      = f'{RUN}/stats/verify_count/{specimen}.stats'

        print()
        print(f'# {specimen}')
@@ -110,13 +114,13 @@ def main():

    print()
    for sp in species_seen:
-        sp_done  = f'specific_index_presence/{sp}/index.done'
-        sp_stats = f'stats/specific_kmer_presence/{sp}.stats'
-        sc_done  = f'specific_index_count/{sp}/index.done'
-        sc_stats = f'stats/specific_kmer_count/{sp}.stats'
+        sp_done  = f'{RUN}/specific_index_presence/{sp}/index.done'
+        sp_stats = f'{RUN}/stats/specific_kmer_presence/{sp}.stats'
+        sc_done  = f'{RUN}/specific_index_count/{sp}/index.done'
+        sc_stats = f'{RUN}/stats/specific_kmer_count/{sp}.stats'
        print(f'# {sp}')
-        print(f'{sp_done} {sp_stats}: global_index_presence/index.done')
-        print(f'{sc_done} {sc_stats}: global_index_count/index.done')
+        print(f'{sp_done} {sp_stats}: {RUN}/global_index_presence/index.done')
+        print(f'{sc_done} {sc_stats}: {RUN}/global_index_count/index.done')

    print()
    print('QUERY_SPECIMENS :=', ' '.join(QUERY_SPECIMENS))
@@ -126,17 +130,17 @@ def main():
        _, species, sim_dir, genome = by_specimen[specimen]
        query_dir = sim_dir.replace('simulated_data/', 'query_data/', 1)
        reads      = f'{query_dir}/reads_R1.fastq.gz'
-        dense_out  = f'query_dense/{specimen}.fasta.gz'
-        dense_stat = f'stats/query_dense/{specimen}.stats'
-        sparse_out  = f'query_sparse/{specimen}.fasta.gz'
-        sparse_stat = f'stats/query_sparse/{specimen}.stats'
-        vq_stat     = f'stats/verify_query/{specimen}.stats'
+        dense_out  = f'{RUN}/query_presence_dense/{specimen}.fasta.gz'
+        dense_stat = f'{RUN}/stats/query_presence_dense/{specimen}.stats'
+        sparse_out  = f'{RUN}/query_presence_sparse/{specimen}.fasta.gz'
+        sparse_stat = f'{RUN}/stats/query_presence_sparse/{specimen}.stats'
+        vq_stat     = f'{RUN}/stats/verify_query/{specimen}.stats'

        print()
        print(f'# query: {specimen}')
        print(f'{reads}: {genome}')
-        print(f'{dense_out} {dense_stat}: {reads} global_index_presence/index.done')
-        print(f'{sparse_out} {sparse_stat}: {reads} global_index_presence_sparse/index.done')
+        print(f'{dense_out} {dense_stat}: {reads} {RUN}/global_index_presence_dense/index.done')
+        print(f'{sparse_out} {sparse_stat}: {reads} {RUN}/global_index_presence/index.done')
        print(f'{vq_stat}: {dense_out} {sparse_out}')


@@ -2,10 +2,11 @@
 set -euo pipefail

 SCRIPT_DIR="$(cd "$(dirname "${BASH_SOURCE[0]}")" && pwd)"
+RUN_DIR="${SCRIPT_DIR}/run"
 BINARY="${SCRIPT_DIR}/../src/target/release/obikmer"
-IDX_DIR="${SCRIPT_DIR}/specimen_index_count"
-OUTPUT="${SCRIPT_DIR}/global_index_count"
-STATS_DIR="${SCRIPT_DIR}/stats/merge_count"
+IDX_DIR="${RUN_DIR}/specimen_index_count"
+OUTPUT="${RUN_DIR}/global_index_count"
+STATS_DIR="${RUN_DIR}/stats/merge_count"

 mkdir -p "${STATS_DIR}"

@@ -2,10 +2,11 @@
 set -euo pipefail

 SCRIPT_DIR="$(cd "$(dirname "${BASH_SOURCE[0]}")" && pwd)"
+RUN_DIR="${SCRIPT_DIR}/run"
 BINARY="${SCRIPT_DIR}/../src/target/release/obikmer"
-IDX_DIR="${SCRIPT_DIR}/specimen_index_presence"
-OUTPUT="${SCRIPT_DIR}/global_index_presence"
-STATS_DIR="${SCRIPT_DIR}/stats/merge_presence"
+IDX_DIR="${RUN_DIR}/specimen_index_presence"
+OUTPUT="${RUN_DIR}/global_index_presence"
+STATS_DIR="${RUN_DIR}/stats/merge_presence"

 mkdir -p "${STATS_DIR}"

@@ -30,10 +30,11 @@ set -euo pipefail

 KIND="$1"
 SCRIPT_DIR="$(cd "$(dirname "${BASH_SOURCE[0]}")" && pwd)"
+RUN_DIR="${SCRIPT_DIR}/run"
 BINARY="${SCRIPT_DIR}/../src/target/release/obikmer"
-SOURCE="${SCRIPT_DIR}/global_index_${KIND}"
-OUTPUT="${SCRIPT_DIR}/global_index_${KIND}_dense"
-STATS_DIR="${SCRIPT_DIR}/stats/pack_dense_${KIND}"
+SOURCE="${RUN_DIR}/global_index_${KIND}"
+OUTPUT="${RUN_DIR}/global_index_${KIND}_dense"
+STATS_DIR="${RUN_DIR}/stats/pack_dense_${KIND}"
 STATS_FILE="${STATS_DIR}/current.stats"

 mkdir -p "${STATS_DIR}"
@@ -14,6 +14,7 @@ KIND="$1"
 MODE="$2"
 SPECIMEN="$3"
 SCRIPT_DIR="$(cd "$(dirname "${BASH_SOURCE[0]}")" && pwd)"
+RUN_DIR="${SCRIPT_DIR}/run"
 BINARY="${SCRIPT_DIR}/../src/target/release/obikmer"

 case "${KIND}" in
@@ -22,17 +23,17 @@ case "${KIND}" in
 esac

 case "${MODE}" in
-    sparse) INDEX="${SCRIPT_DIR}/global_index_${KIND}" ;;
-    dense)  INDEX="${SCRIPT_DIR}/global_index_${KIND}_dense" ;;
+    sparse) INDEX="${RUN_DIR}/global_index_${KIND}" ;;
+    dense)  INDEX="${RUN_DIR}/global_index_${KIND}_dense" ;;
    *) echo "ERROR: unknown mode '${MODE}' (expected dense|sparse)" >&2; exit 1 ;;
 esac

 species="${SPECIMEN%%--*}"
 strain="${SPECIMEN#*--}"

-READS_DIR="${SCRIPT_DIR}/query_data/${species}/${strain}"
-OUT_DIR="${SCRIPT_DIR}/query_${KIND}_${MODE}"
-STATS_DIR="${SCRIPT_DIR}/stats/query_${KIND}_${MODE}"
+READS_DIR="${RUN_DIR}/query_data/${species}/${strain}"
+OUT_DIR="${RUN_DIR}/query_${KIND}_${MODE}"
+STATS_DIR="${RUN_DIR}/stats/query_${KIND}_${MODE}"
 OUT_FILE="${OUT_DIR}/${SPECIMEN}.fasta.gz"
 STATS_FILE="${STATS_DIR}/${SPECIMEN}.stats"

@@ -4,8 +4,9 @@
 set -euo pipefail

 SCRIPT_DIR="$(cd "$(dirname "${BASH_SOURCE[0]}")" && pwd)"
+RUN_DIR="${SCRIPT_DIR}/run"

-for genome_file in "${SCRIPT_DIR}"/genomes/*.fna.gz; do
+for genome_file in "${RUN_DIR}"/genomes/*.fna.gz; do
    out_dir=$("${SCRIPT_DIR}/../.venv/bin/python3" "${SCRIPT_DIR}/make_deps.py" \
        --dir-for "${genome_file}")
    bash "${SCRIPT_DIR}/simulate_one.sh" "${genome_file}" "${out_dir}"
@@ -1,21 +0,0 @@
-genome,Candidozyma_auris--GCF_003013715.1_ASM301371v2,Acidobacterium_capsulatum--ATCC_51196,Bacillus_subtilis--168,Escherichia_coli--CFT073,Escherichia_coli--EDL933,Escherichia_coli--K-12_MG1655,Escherichia_coli--K-12_W3110,Klebsiella_pneumoniae--ATCC_13883,Klebsiella_pneumoniae--HS11286,Klebsiella_pneumoniae--MGH_78578,Opitutus_terrae--PB90-1,Proteus_mirabilis--HI4320,Saccharolobus_islandicus--M.16.4,Salmonella_enterica--AKU_12601,Salmonella_enterica--CT18,Salmonella_enterica--LT2,Salmonella_enterica--P125109,Shouchella_clausii--KSM-K16,Wolbachia_endosymbiont--GCF_000306885.1_ASM30688v1,Yersinia_ruckeri--YRB
-Candidozyma_auris--GCF_003013715.1_ASM301371v2,0.000000,1.000000,1.000000,1.000000,1.000000,1.000000,1.000000,1.000000,1.000000,1.000000,1.000000,1.000000,1.000000,1.000000,1.000000,1.000000,1.000000,1.000000,1.000000,1.000000
-Acidobacterium_capsulatum--ATCC_51196,1.000000,0.000000,0.999981,0.999990,0.999989,0.999987,0.999987,0.999990,0.999988,0.999988,0.999994,0.999989,1.000000,0.999988,0.999987,0.999987,0.999988,0.999989,0.999991,0.999987
-Bacillus_subtilis--168,1.000000,0.999981,0.000000,0.999990,0.999989,0.999989,0.999989,0.999989,0.999988,0.999986,0.999995,0.999985,0.999999,0.999988,0.999987,0.999989,0.999988,0.999778,0.999993,0.999987
-Escherichia_coli--CFT073,1.000000,0.999990,0.999990,0.000000,0.825741,0.807495,0.807218,0.991156,0.996855,0.997849,0.999996,0.999633,1.000000,0.993885,0.996736,0.994148,0.993821,0.999991,0.999984,0.999291
-Escherichia_coli--EDL933,1.000000,0.999989,0.999989,0.825741,0.000000,0.735107,0.734775,0.996126,0.998058,0.997908,0.999997,0.999640,1.000000,0.993993,0.997126,0.994390,0.994059,0.999991,0.999986,0.999292
-Escherichia_coli--K-12_MG1655,1.000000,0.999987,0.999989,0.807495,0.735107,0.000000,0.382567,0.996190,0.997747,0.997455,0.999996,0.999604,1.000000,0.993444,0.996645,0.993773,0.993431,0.999989,0.999984,0.999174
-Escherichia_coli--K-12_W3110,1.000000,0.999987,0.999989,0.807218,0.734775,0.382567,0.000000,0.996220,0.997761,0.997467,0.999995,0.999604,1.000000,0.993445,0.996669,0.993769,0.993443,0.999990,0.999985,0.999165
-Klebsiella_pneumoniae--ATCC_13883,1.000000,0.999990,0.999989,0.991156,0.996126,0.996190,0.996220,0.000000,0.845220,0.840545,0.999997,0.999648,1.000000,0.996177,0.998128,0.996268,0.996052,0.999990,0.999987,0.999325
-Klebsiella_pneumoniae--HS11286,1.000000,0.999988,0.999988,0.996855,0.998058,0.997747,0.997761,0.845220,0.000000,0.906475,0.999996,0.999683,1.000000,0.997724,0.995697,0.997776,0.997769,0.999989,0.999979,0.999463
-Klebsiella_pneumoniae--MGH_78578,1.000000,0.999988,0.999986,0.997849,0.997908,0.997455,0.997467,0.840545,0.906475,0.000000,0.999996,0.999704,1.000000,0.997928,0.995054,0.997844,0.997868,0.999990,0.999980,0.999479
-Opitutus_terrae--PB90-1,1.000000,0.999994,0.999995,0.999996,0.999997,0.999996,0.999995,0.999997,0.999996,0.999996,0.000000,0.999997,0.999998,0.999996,0.999996,0.999996,0.999995,0.999997,0.999993,0.999996
-Proteus_mirabilis--HI4320,1.000000,0.999989,0.999985,0.999633,0.999640,0.999604,0.999604,0.999648,0.999683,0.999704,0.999997,0.000000,1.000000,0.999604,0.999699,0.999622,0.999613,0.999987,0.999983,0.999505
-Saccharolobus_islandicus--M.16.4,1.000000,1.000000,0.999999,1.000000,1.000000,1.000000,1.000000,1.000000,1.000000,1.000000,0.999998,1.000000,0.000000,1.000000,1.000000,1.000000,1.000000,1.000000,1.000000,1.000000
-Salmonella_enterica--AKU_12601,1.000000,0.999988,0.999988,0.993885,0.993993,0.993444,0.993445,0.996177,0.997724,0.997928,0.999996,0.999604,1.000000,0.000000,0.869238,0.682277,0.663383,0.999990,0.999985,0.999260
-Salmonella_enterica--CT18,1.000000,0.999987,0.999987,0.996736,0.997126,0.996645,0.996669,0.998128,0.995697,0.995054,0.999996,0.999699,1.000000,0.869238,0.000000,0.890872,0.886148,0.999988,0.999976,0.999524
-Salmonella_enterica--LT2,1.000000,0.999987,0.999989,0.994148,0.994390,0.993773,0.993769,0.996268,0.997776,0.997844,0.999996,0.999622,1.000000,0.682277,0.890872,0.000000,0.622606,0.999989,0.999985,0.999296
-Salmonella_enterica--P125109,1.000000,0.999988,0.999988,0.993821,0.994059,0.993431,0.993443,0.996052,0.997769,0.997868,0.999995,0.999613,1.000000,0.663383,0.886148,0.622606,0.000000,0.999988,0.999983,0.999270
-Shouchella_clausii--KSM-K16,1.000000,0.999989,0.999778,0.999991,0.999991,0.999989,0.999990,0.999990,0.999989,0.999990,0.999997,0.999987,1.000000,0.999990,0.999988,0.999989,0.999988,0.000000,0.999991,0.999988
-Wolbachia_endosymbiont--GCF_000306885.1_ASM30688v1,1.000000,0.999991,0.999993,0.999984,0.999986,0.999984,0.999985,0.999987,0.999979,0.999980,0.999993,0.999983,1.000000,0.999985,0.999976,0.999985,0.999983,0.999991,0.000000,0.999983
-Yersinia_ruckeri--YRB,1.000000,0.999987,0.999987,0.999291,0.999292,0.999174,0.999165,0.999325,0.999463,0.999479,0.999996,0.999505,1.000000,0.999260,0.999524,0.999296,0.999270,0.999988,0.999983,0.000000
@@ -1 +0,0 @@
-(((((((((((Candidozyma_auris--GCF_003013715.1_ASM301371v2:0.5000001881725941,Saccharolobus_islandicus--M.16.4:0.4999993211600824):0.0000023411501775538747,Opitutus_terrae--PB90-1:0.499997075187947):0.0000029791191795691675,(Acidobacterium_capsulatum--ATCC_51196:0.49999227771334689,(Bacillus_subtilis--168:0.49988797935621456,Shouchella_clausii--KSM-K16:0.49988984146059159):0.0001037210285571577):0.0000023959836053522034):0.0000034093646568700288,Wolbachia_endosymbiont--GCF_000306885.1_ASM30688v1:0.4999920159222422):0.000199555100890203,Proteus_mirabilis--HI4320:0.49979129185300427):0.00010103619067070024,Yersinia_ruckeri--YRB:0.4996806650749249):0.0013719139155004,(Klebsiella_pneumoniae--HS11286:0.43798845051648258,(Klebsiella_pneumoniae--ATCC_13883:0.41780293826821265,Klebsiella_pneumoniae--MGH_78578:0.42274184870836559):0.017586732339732737):0.0604124197073832):0.0006482538063555254,(Salmonella_enterica--CT18:0.43952894448143017,(Salmonella_enterica--AKU_12601:0.3357977326267918,(Salmonella_enterica--LT2:0.31203395843666389,Salmonella_enterica--P125109:0.31057217324861216):0.025729515856701136):0.10292985918524672):0.05825411485542886):0.08937928015651564,Escherichia_coli--CFT073:0.40806501650701029):0.0410131211869626,Escherichia_coli--EDL933:0.3681464750911808):0.1755112579711463,Escherichia_coli--K-12_MG1655:0.19129818036662728,Escherichia_coli--K-12_W3110:0.19126872019906239);
@@ -1,21 +0,0 @@
-genome,Candidozyma_auris--GCF_003013715.1_ASM301371v2,Acidobacterium_capsulatum--ATCC_51196,Bacillus_subtilis--168,Escherichia_coli--CFT073,Escherichia_coli--EDL933,Escherichia_coli--K-12_MG1655,Escherichia_coli--K-12_W3110,Klebsiella_pneumoniae--ATCC_13883,Klebsiella_pneumoniae--HS11286,Klebsiella_pneumoniae--MGH_78578,Opitutus_terrae--PB90-1,Proteus_mirabilis--HI4320,Saccharolobus_islandicus--M.16.4,Salmonella_enterica--AKU_12601,Salmonella_enterica--CT18,Salmonella_enterica--LT2,Salmonella_enterica--P125109,Shouchella_clausii--KSM-K16,Wolbachia_endosymbiont--GCF_000306885.1_ASM30688v1,Yersinia_ruckeri--YRB
-Candidozyma_auris--GCF_003013715.1_ASM301371v2,0,0,0,0,0,0,0,0,0,0,0,0,8,0,1,0,0,0,0,3
-Acidobacterium_capsulatum--ATCC_51196,0,0,203,119,128,141,140,116,109,111,78,112,0,136,109,147,134,117,55,129
-Bacillus_subtilis--168,0,203,0,124,132,128,123,133,109,130,66,158,6,131,112,124,135,2393,46,124
-Escherichia_coli--CFT073,0,119,124,0,1966777,1998059,1999094,117743,32029,22312,63,4225,0,74946,31918,73311,76585,113,128,7854
-Escherichia_coli--EDL933,0,128,132,1966777,0,2627885,2628700,52488,20134,22064,48,4202,0,74655,28602,71244,74665,112,108,7963
-Escherichia_coli--K-12_MG1655,0,141,128,1998059,2627885,0,4452541,48302,21382,24602,47,4277,0,75729,30449,73622,76778,119,111,8566
-Escherichia_coli--K-12_W3110,0,140,123,1999094,2628700,4452541,0,47894,21226,24470,68,4278,0,75658,30207,73614,76583,112,108,8660
-Klebsiella_pneumoniae--ATCC_13883,0,116,133,117743,52488,48302,47894,0,1416091,1477759,42,4172,0,48296,18988,48144,50416,120,106,7712
-Klebsiella_pneumoniae--HS11286,0,109,109,32029,20134,21382,21226,1416091,0,644063,42,2738,0,21498,29758,21606,21376,99,102,4417
-Klebsiella_pneumoniae--MGH_78578,0,111,130,22312,22064,24602,24470,1477759,644063,0,42,2614,0,19948,35067,21330,20813,97,102,4374
-Opitutus_terrae--PB90-1,0,78,66,63,48,47,68,42,42,42,0,43,18,57,42,53,66,39,58,43
-Proteus_mirabilis--HI4320,0,112,158,4225,4202,4277,4278,4172,2738,2614,43,0,0,4254,2481,4166,4215,131,103,4704
-Saccharolobus_islandicus--M.16.4,8,0,6,0,0,0,0,0,0,0,18,0,0,0,0,0,0,0,0,0
-Salmonella_enterica--AKU_12601,0,136,131,74946,74655,75729,75658,48296,21498,19948,57,4254,0,0,1047731,2857146,2951421,117,108,7643
-Salmonella_enterica--CT18,1,109,112,31918,28602,30449,30207,18988,29758,35067,42,2481,0,1047731,0,917948,940297,106,106,3716
-Salmonella_enterica--LT2,0,147,124,73311,71244,73622,73614,48144,21606,21330,53,4166,0,2857146,917948,0,3284800,122,108,7460
-Salmonella_enterica--P125109,0,134,135,76585,74665,76778,76583,50416,21376,20813,66,4215,0,2951421,940297,3284800,0,134,124,7645
-Shouchella_clausii--KSM-K16,0,117,2393,113,112,119,112,120,99,97,39,131,0,117,106,122,134,0,58,124
-Wolbachia_endosymbiont--GCF_000306885.1_ASM30688v1,0,55,46,128,108,111,108,106,102,102,58,103,0,108,106,108,124,58,0,96
-Yersinia_ruckeri--YRB,3,129,124,7854,7963,8566,8660,7712,4417,4374,43,4704,0,7643,3716,7460,7645,124,96,0
--- a/Show More
+++ b/Show More
Author	SHA1	Message	Date
coissac	e280b6d0a3	Merge pull request 'Implement NUMA topology detection and CPU budget capping' (#74 ) from push-tnkxqmwztnmm into main Reviewed-on: #74	2026-09-11 05:23:42 +00:00
Eric Coissac	98dba1802d	Implement NUMA topology detection and CPU budget capping Release / create-release (push) Successful in 2m30s Details ci.yml / build (pull_request) Successful in 3m50s Details Release / build-linux-x86_64 (push) Successful in 8m23s Details Release / build-macos-arm64 (push) Successful in 1m57s Details This change introduces logic to detect NUMA topology, calculate per-node worker limits based on available CPU cores, and cap resource allocation to ensure worker counts respect the physical capacity of each node.	2026-09-11 07:22:35 +02:00
coissac	dd4285b269	Merge pull request 'Introduce CPU budget and dynamic thread limiting' (#73 ) from push-lztkokoxqpuw into main Reviewed-on: #73	2026-09-10 15:10:19 +00:00
Eric Coissac	b66a488277	Introduce CPU budget and dynamic thread limiting Release / create-release (push) Successful in 3m4s Details ci.yml / build (pull_request) Successful in 4m17s Details Release / build-linux-x86_64 (push) Successful in 8m11s Details Release / build-macos-arm64 (push) Successful in 2m2s Details This change implements mechanisms to enforce resource limits based on the available CPU budget, including setting a hard CPU ceiling and calculating effective thread counts for CLI, query, and superkmer operations.	2026-09-10 17:08:32 +02:00
Eric Coissac	b954032faa	chore: remove obsolete configuration and memory files Deletes unused tool configurations, planning plans, and local memory files across multiple directories.	2026-08-31 09:09:40 +02:00
coissac	43d89d8f02	Merge pull request 'disable default features for obisys dependency' (#72 ) from push-wvkttrwzkqoo into main Reviewed-on: #72	2026-08-29 06:18:11 +00:00
Eric Coissac	8bb1d52514	disable default features for obisys dependency Release / create-release (push) Successful in 2m32s Details Release / build-linux-x86_64 (push) Successful in 7m57s Details Release / build-macos-arm64 (push) Successful in 1m53s Details ci.yml / build (pull_request) Successful in 3m42s Details Update obisys dependency configuration across multiple crates to explicitly set default-features = false. This restricts compilation to only explicitly enabled feature flags, affecting build resolution and potentially compile-time paths or binary size. Also updates the obikmer package version to 1.3.1.	2026-08-29 08:13:49 +02:00
coissac	77d4429645	Merge pull request 'chore: bump obikmer to 1.3.0 and disable obisys default features' (#71 ) from push-sllyqzuztwkr into main Reviewed-on: #71	2026-08-29 05:51:37 +00:00
Eric Coissac	4d55258ada	chore: bump obikmer to 1.3.0 and disable obisys default features Release / create-release (push) Successful in 2m32s Details Release / build-linux-x86_64 (push) Successful in 8m22s Details Release / build-macos-arm64 (push) Failing after 1m15s Details ci.yml / build (pull_request) Successful in 3m33s Details Updates package version and explicitly disables default features for the local obisys dependency.	2026-08-29 07:46:56 +02:00
coissac	7e28ca4853	Merge pull request 'Push zunrplorkwkt' (#70 ) from push-zunrplorkwkt into main Reviewed-on: #70	2026-08-28 23:15:37 +00:00
Eric Coissac	52f26809af	refactor(benchmark): consolidate generated artifacts under run/ directory ci.yml / build (pull_request) Successful in 3m49s Details Restructure the benchmark pipeline to direct all simulated data, indices, statistics, and query outputs into a unified `run/` directory. Update Makefile targets, shell scripts, and Python utilities to resolve paths relative to this new base. Adjust documentation and dependency tracking to match the revised layout, and remove outdated temporary artifacts.	2026-08-29 00:19:31 +02:00
				`@@ -1 +0,0 @@`
				(((((((((((Candidozyma_auris--GCF_003013715.1_ASM301371v2:0.5000001881725941,Saccharolobus_islandicus--M.16.4:0.4999993211600824):0.0000023411501775538747,Opitutus_terrae--PB90-1:0.499997075187947):0.0000029791191795691675,(Acidobacterium_capsulatum--ATCC_51196:0.49999227771334689,(Bacillus_subtilis--168:0.49988797935621456,Shouchella_clausii--KSM-K16:0.49988984146059159):0.0001037210285571577):0.0000023959836053522034):0.0000034093646568700288,Wolbachia_endosymbiont--GCF_000306885.1_ASM30688v1:0.4999920159222422):0.000199555100890203,Proteus_mirabilis--HI4320:0.49979129185300427):0.00010103619067070024,Yersinia_ruckeri--YRB:0.4996806650749249):0.0013719139155004,(Klebsiella_pneumoniae--HS11286:0.43798845051648258,(Klebsiella_pneumoniae--ATCC_13883:0.41780293826821265,Klebsiella_pneumoniae--MGH_78578:0.42274184870836559):0.017586732339732737):0.0604124197073832):0.0006482538063555254,(Salmonella_enterica--CT18:0.43952894448143017,(Salmonella_enterica--AKU_12601:0.3357977326267918,(Salmonella_enterica--LT2:0.31203395843666389,Salmonella_enterica--P125109:0.31057217324861216):0.025729515856701136):0.10292985918524672):0.05825411485542886):0.08937928015651564,Escherichia_coli--CFT073:0.40806501650701029):0.0410131211869626,Escherichia_coli--EDL933:0.3681464750911808):0.1755112579711463,Escherichia_coli--K-12_MG1655:0.19129818036662728,Escherichia_coli--K-12_W3110:0.19126872019906239);