diff --git a/.gitignore b/.gitignore index c99af57f..00fa7f0e 100644 --- a/.gitignore +++ b/.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 diff --git a/benchmark/Makefile b/benchmark/Makefile index b149e41d..46fed72c 100644 --- a/benchmark/Makefile +++ b/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) diff --git a/benchmark/README.md b/benchmark/README.md index ea683715..93cb5ba9 100644 --- a/benchmark/README.md +++ b/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 -│ └── // -├── query_data/ # generated by simulate_query (2 specimens, fixed 100k pairs) -│ └── // -├── 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 + │ └── // + ├── query_data/ # generated by simulate_query (2 specimens, fixed 100k pairs) + │ └── // + ├── 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/ ``` diff --git a/benchmark/aggregate_stats.sh b/benchmark/aggregate_stats.sh index 2e668be1..7d507e31 100755 --- a/benchmark/aggregate_stats.sh +++ b/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 "${TYPE}" in indexing_presence|indexing_count) diff --git a/benchmark/build_reference.sh b/benchmark/build_reference.sh index 3d312c17..d83c3ec8 100755 --- a/benchmark/build_reference.sh +++ b/benchmark/build_reference.sh @@ -2,8 +2,9 @@ set -euo pipefail SCRIPT_DIR="$(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" diff --git a/benchmark/build_reference_dist.py b/benchmark/build_reference_dist.py index bd851d67..51b32fcc 100755 --- a/benchmark/build_reference_dist.py +++ b/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) diff --git a/benchmark/compare_all_dist.py b/benchmark/compare_all_dist.py index 390feefc..8bfac534 100755 --- a/benchmark/compare_all_dist.py +++ b/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: diff --git a/benchmark/deps.mk b/benchmark/deps.mk index 2cf1a49f..7c38723b 100644 --- a/benchmark/deps.mk +++ b/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 diff --git a/benchmark/downloads.sh b/benchmark/downloads.sh index d86111ed..3cbe7eb2 100755 --- a/benchmark/downloads.sh +++ b/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" diff --git a/benchmark/filter_one_count.sh b/benchmark/filter_one_count.sh index 51a7a293..ba17a57d 100755 --- a/benchmark/filter_one_count.sh +++ b/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}" diff --git a/benchmark/filter_one_presence.sh b/benchmark/filter_one_presence.sh index 5e61a659..4e9e478f 100755 --- a/benchmark/filter_one_presence.sh +++ b/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}" diff --git a/benchmark/global_index_presence_sparse/.obikmer.lock b/benchmark/global_index_presence_sparse/.obikmer.lock deleted file mode 100644 index e69de29b..00000000 diff --git a/benchmark/index_one_count.sh b/benchmark/index_one_count.sh index 325ec7fc..473d9ff9 100755 --- a/benchmark/index_one_count.sh +++ b/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}" diff --git a/benchmark/index_one_presence.sh b/benchmark/index_one_presence.sh index 029c5370..7b51887c 100755 --- a/benchmark/index_one_presence.sh +++ b/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}" diff --git a/benchmark/make_deps.py b/benchmark/make_deps.py index a0381a70..121107ba 100644 --- a/benchmark/make_deps.py +++ b/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}') diff --git a/benchmark/merge_count.sh b/benchmark/merge_count.sh index 871b436b..fa3cffe0 100755 --- a/benchmark/merge_count.sh +++ b/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 "${STATS_DIR}" diff --git a/benchmark/merge_presence.sh b/benchmark/merge_presence.sh index 7a816d18..a1853abb 100755 --- a/benchmark/merge_presence.sh +++ b/benchmark/merge_presence.sh @@ -2,10 +2,11 @@ set -euo pipefail SCRIPT_DIR="$(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}" diff --git a/benchmark/pack_dense.sh b/benchmark/pack_dense.sh index 0d747c4a..bc7c4494 100755 --- a/benchmark/pack_dense.sh +++ b/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}" diff --git a/benchmark/query_one.sh b/benchmark/query_one.sh index 093ff8e6..9f40cae0 100755 --- a/benchmark/query_one.sh +++ b/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" diff --git a/benchmark/simulate.sh b/benchmark/simulate.sh index c486255f..f1deb795 100755 --- a/benchmark/simulate.sh +++ b/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}" diff --git a/benchmark/test_dist.csv b/benchmark/test_dist.csv deleted file mode 100644 index 960fc1f9..00000000 --- a/benchmark/test_dist.csv +++ /dev/null @@ -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 diff --git a/benchmark/test_nj.nwk b/benchmark/test_nj.nwk deleted file mode 100644 index 124abba9..00000000 --- a/benchmark/test_nj.nwk +++ /dev/null @@ -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); \ No newline at end of file diff --git a/benchmark/test_shared.csv b/benchmark/test_shared.csv deleted file mode 100644 index 1fbc20d5..00000000 --- a/benchmark/test_shared.csv +++ /dev/null @@ -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 diff --git a/benchmark/tmp/bacteria/.obikmer.lock b/benchmark/tmp/bacteria/.obikmer.lock deleted file mode 100644 index e69de29b..00000000 diff --git a/benchmark/tmp/bacteria/partitions/part_00000/index/layer_0/presence/matrix.pbmx b/benchmark/tmp/bacteria/partitions/part_00000/index/layer_0/presence/matrix.pbmx deleted file mode 100644 index 74f7292f..00000000 Binary files a/benchmark/tmp/bacteria/partitions/part_00000/index/layer_0/presence/matrix.pbmx and /dev/null differ diff --git a/benchmark/tmp/bacteria/partitions/part_00000/index/layer_1/presence/matrix.pbmx b/benchmark/tmp/bacteria/partitions/part_00000/index/layer_1/presence/matrix.pbmx deleted file mode 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"${BASH_SOURCE[0]}")" && pwd)" +RUN_DIR="${SCRIPT_DIR}/run" BINARY="${SCRIPT_DIR}/../src/target/release/obikmer" -INDEX="${SCRIPT_DIR}/global_index_count" -REF_DIR="${SCRIPT_DIR}/reference_index" -STATS_DIR="${SCRIPT_DIR}/stats/verify_merge_count" +INDEX="${RUN_DIR}/global_index_count" +REF_DIR="${RUN_DIR}/reference_index" +STATS_DIR="${RUN_DIR}/stats/verify_merge_count" PYTHON="${SCRIPT_DIR}/../.venv/bin/python3" VERIFY_PY="${SCRIPT_DIR}/verify_merge_count.py" diff --git a/benchmark/verify_merge_presence.sh b/benchmark/verify_merge_presence.sh index bea5ddfd..44969048 100755 --- a/benchmark/verify_merge_presence.sh +++ b/benchmark/verify_merge_presence.sh @@ -2,10 +2,11 @@ set -euo pipefail SCRIPT_DIR="$(cd "$(dirname "${BASH_SOURCE[0]}")" && pwd)" +RUN_DIR="${SCRIPT_DIR}/run" BINARY="${SCRIPT_DIR}/../src/target/release/obikmer" -INDEX="${SCRIPT_DIR}/global_index_presence" -REF_DIR="${SCRIPT_DIR}/reference_index" -STATS_DIR="${SCRIPT_DIR}/stats/verify_merge_presence" +INDEX="${RUN_DIR}/global_index_presence" +REF_DIR="${RUN_DIR}/reference_index" +STATS_DIR="${RUN_DIR}/stats/verify_merge_presence" PYTHON="${SCRIPT_DIR}/../.venv/bin/python3" VERIFY_PY="${SCRIPT_DIR}/verify_merge_presence.py" diff --git a/benchmark/verify_one_count.sh b/benchmark/verify_one_count.sh index 3dfb8d68..524f01e2 100755 --- a/benchmark/verify_one_count.sh +++ b/benchmark/verify_one_count.sh @@ -6,6 +6,7 @@ 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" PYTHON="${SCRIPT_DIR}/../.venv/bin/python3" VERIFY_PY="${SCRIPT_DIR}/verify_count.py" @@ -13,9 +14,9 @@ VERIFY_PY="${SCRIPT_DIR}/verify_count.py" species="${SPECIMEN%%--*}" strain="${SPECIMEN#*--}" -REF_NPZ="${SCRIPT_DIR}/reference_index/${SPECIMEN}.npz" -INDEX_DIR="${SCRIPT_DIR}/specimen_index_count/${SPECIMEN}" -STATS_DIR="${SCRIPT_DIR}/stats/verify_count" +REF_NPZ="${RUN_DIR}/reference_index/${SPECIMEN}.npz" +INDEX_DIR="${RUN_DIR}/specimen_index_count/${SPECIMEN}" +STATS_DIR="${RUN_DIR}/stats/verify_count" STATS_FILE="${STATS_DIR}/${SPECIMEN}.stats" mkdir -p "${STATS_DIR}" diff --git a/benchmark/verify_one_presence.sh b/benchmark/verify_one_presence.sh index 252a2c3d..9b2b264d 100755 --- a/benchmark/verify_one_presence.sh +++ b/benchmark/verify_one_presence.sh @@ -6,6 +6,7 @@ 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" PYTHON="${SCRIPT_DIR}/../.venv/bin/python3" VERIFY_PY="${SCRIPT_DIR}/verify_presence.py" @@ -13,9 +14,9 @@ VERIFY_PY="${SCRIPT_DIR}/verify_presence.py" species="${SPECIMEN%%--*}" strain="${SPECIMEN#*--}" -REF_NPZ="${SCRIPT_DIR}/reference_index/${SPECIMEN}.npz" -INDEX_DIR="${SCRIPT_DIR}/specimen_index_presence/${SPECIMEN}" -STATS_DIR="${SCRIPT_DIR}/stats/verify_presence" +REF_NPZ="${RUN_DIR}/reference_index/${SPECIMEN}.npz" +INDEX_DIR="${RUN_DIR}/specimen_index_presence/${SPECIMEN}" +STATS_DIR="${RUN_DIR}/stats/verify_presence" STATS_FILE="${STATS_DIR}/${SPECIMEN}.stats" mkdir -p "${STATS_DIR}" diff --git a/benchmark/verify_query_one.sh b/benchmark/verify_query_one.sh index ba00dc24..58c7987e 100755 --- a/benchmark/verify_query_one.sh +++ b/benchmark/verify_query_one.sh @@ -6,15 +6,16 @@ set -euo pipefail SPECIMEN="$1" SCRIPT_DIR="$(cd "$(dirname "${BASH_SOURCE[0]}")" && pwd)" +RUN_DIR="${SCRIPT_DIR}/run" PYTHON="${SCRIPT_DIR}/../.venv/bin/python3" VERIFY_PY="${SCRIPT_DIR}/verify_query.py" species="${SPECIMEN%%--*}" strain="${SPECIMEN#*--}" -DENSE="${SCRIPT_DIR}/query_presence_dense/${SPECIMEN}.fasta.gz" -SPARSE="${SCRIPT_DIR}/query_presence_sparse/${SPECIMEN}.fasta.gz" -STATS_DIR="${SCRIPT_DIR}/stats/verify_query" +DENSE="${RUN_DIR}/query_presence_dense/${SPECIMEN}.fasta.gz" +SPARSE="${RUN_DIR}/query_presence_sparse/${SPECIMEN}.fasta.gz" +STATS_DIR="${RUN_DIR}/stats/verify_query" STATS_FILE="${STATS_DIR}/${SPECIMEN}.stats" mkdir -p "${STATS_DIR}" diff --git a/src/Cargo.lock b/src/Cargo.lock index 5809d8ac..23dc3cd2 100644 --- a/src/Cargo.lock +++ b/src/Cargo.lock @@ -1480,7 +1480,7 @@ dependencies = [ [[package]] name = "obikmer" -version = "1.2.2" +version = "1.2.3" dependencies = [ "clap", "csv", diff --git a/src/obikmer/Cargo.toml b/src/obikmer/Cargo.toml index cd1f224b..a91717cb 100644 --- a/src/obikmer/Cargo.toml +++ b/src/obikmer/Cargo.toml @@ -1,6 +1,6 @@ [package] name = "obikmer" -version = "1.2.2" +version = "1.2.3" edition = "2024" [[bin]]