refactor(benchmark): consolidate generated artifacts under run/ directory

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 Adjust documentation and dependency tracking to match the revised layout, and remove outdated temporary artifacts.

.gitignore

@@ -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

benchmark/Makefile

@@ -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)

benchmark/README.md

@@ -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/
 ```

benchmark/aggregate_stats.sh

@@ -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)

benchmark/build_reference.sh

@@ -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"
 

benchmark/build_reference_dist.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)

benchmark/compare_all_dist.py

@@ -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:

benchmark/deps.mk

@@ -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

benchmark/downloads.sh

@@ -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"

benchmark/filter_one_count.sh

@@ -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}"

benchmark/filter_one_presence.sh

@@ -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}"

benchmark/index_one_count.sh

@@ -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}"

benchmark/index_one_presence.sh

@@ -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}"

benchmark/make_deps.py

@@ -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}')
 
 

benchmark/merge_count.sh

@@ -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}"
 

benchmark/merge_presence.sh

@@ -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}"
 

benchmark/pack_dense.sh

@@ -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}"

benchmark/query_one.sh

@@ -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"
 

benchmark/simulate.sh

@@ -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}"

benchmark/test_dist.csv

@@ -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

benchmark/test_nj.nwk

@@ -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);

benchmark/test_shared.csv

@@ -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