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diff --git a/figures/ani_profile_benchmark_times.svg b/figures/ani_profile_benchmark_times.svg
diff --git a/figures/ani_r89_benchmark.svg b/figures/ani_r89_benchmark.svg
diff --git a/figures/bio+ocean.svg b/figures/bio+ocean.svg
diff --git a/figures/biofloc.svg b/figures/biofloc.svg
diff --git a/figures/cami2_marine.png b/figures/cami2_marine.png
diff --git a/figures/cami2_marine.svg b/figures/cami2_marine.svg
diff --git a/figures/database_sketching_time.svg b/figures/database_sketching_time.svg
diff --git a/figures/f2-ani_profile_benchmark_times.svg b/figures/f2-ani_profile_benchmark_times.svg
diff --git a/figures/f2-ani_r89_benchmark.svg b/figures/f2-ani_r89_benchmark.svg
diff --git a/figures/f2-cami2_marine.svg b/figures/f2-cami2_marine.svg
diff --git a/figures/f2-stratified_plots.svg b/figures/f2-stratified_plots.svg
diff --git a/figures/f3-meslier_profiling.svg b/figures/f3-meslier_profiling.svg
diff --git a/figures/l1_metric_benchmark.svg b/figures/l1_metric_benchmark.svg
diff --git a/figures/meslier_profiling.svg b/figures/meslier_profiling.svg
diff --git a/figures/mock_community_box.svg b/figures/mock_community_box.svg
diff --git a/figures/real_biofloc.svg b/figures/real_biofloc.svg
diff --git a/figures/real_database_sketching_time.svg b/figures/real_database_sketching_time.svg
diff --git a/figures/real_profiling_gtdbvsrefseq.svg b/figures/real_profiling_gtdbvsrefseq.svg
diff --git a/figures/real_soil+ocean.svg b/figures/real_soil+ocean.svg
diff --git a/figures/soil+ocean.svg b/figures/soil+ocean.svg
diff --git a/figures/stratified_plots.svg b/figures/stratified_plots.svg
diff --git a/figures/virus_results.svg b/figures/virus_results.svg
diff --git a/precomputed_results/D2_aniu.txt b/precomputed_results/D2_aniu.txt
diff --git a/precomputed_results/D2_contain.tsv b/precomputed_results/D2_contain.tsv
diff --git a/precomputed_results/D2_contain_k21.tsv b/precomputed_results/D2_contain_k21.tsv
diff --git a/precomputed_results/D2_contain_k31.tsv b/precomputed_results/D2_contain_k31.tsv
diff --git a/profile_analysis.ipynb b/profile_analysis.ipynb
diff --git a/real_profile_analysis.ipynb b/real_profile_analysis.ipynb
diff --git a/real_profiles/PRJEB61010_all.tsv b/real_profiles/PRJEB61010_all.tsv
diff --git a/real_profiles/PRJEB61010_gtdb.tsv b/real_profiles/PRJEB61010_gtdb.tsv
diff --git a/real_profiles/PRJEB61010_refseq.tsv b/real_profiles/PRJEB61010_refseq.tsv
diff --git a/real_profiles/PRJNA1014704_rhizo_gtdb.tsv b/real_profiles/PRJNA1014704_rhizo_gtdb.tsv
diff --git a/real_profiles/PRJNA1014704_rhizo_refseq.tsv b/real_profiles/PRJNA1014704_rhizo_refseq.tsv
diff --git a/real_profiles/PRJNA1014704_rhizo_soildb+gtdb.tsv b/real_profiles/PRJNA1014704_rhizo_soildb+gtdb.tsv
diff --git a/real_profiles/PRJNA904562_all.tsv b/real_profiles/PRJNA904562_all.tsv
diff --git a/real_profiles/PRJNA904562_gtdb.tsv b/real_profiles/PRJNA904562_gtdb.tsv
diff --git a/real_profiles/PRJNA904562_refseq.tsv b/real_profiles/PRJNA904562_refseq.tsv
diff --git a/real_profiles/biofilm_gtdb_only.tsv b/real_profiles/biofilm_gtdb_only.tsv
diff --git a/real_profiles/biofilm_profile.tsv b/real_profiles/biofilm_profile.tsv
diff --git a/real_profiles/biofilm_refseq.tsv b/real_profiles/biofilm_refseq.tsv
diff --git a/real_profiles/biofilm_with_mags.tsv b/real_profiles/biofilm_with_mags.tsv
diff --git a/real_profiles/mouse_profile.tsv b/real_profiles/mouse_profile.tsv
diff --git a/real_profiles/mouse_profile_refseq.tsv b/real_profiles/mouse_profile_refseq.tsv
diff --git a/rerun_opal/by_rank/class.tsv b/rerun_opal/by_rank/class.tsv
diff --git a/rerun_opal/by_rank/family.tsv b/rerun_opal/by_rank/family.tsv
diff --git a/rerun_opal/by_rank/genus.tsv b/rerun_opal/by_rank/genus.tsv
diff --git a/rerun_opal/by_rank/order.tsv b/rerun_opal/by_rank/order.tsv
diff --git a/rerun_opal/by_rank/phylum.tsv b/rerun_opal/by_rank/phylum.tsv
diff --git a/rerun_opal/by_rank/species.tsv b/rerun_opal/by_rank/species.tsv
diff --git a/rerun_opal/by_rank/strain.tsv b/rerun_opal/by_rank/strain.tsv
diff --git a/rerun_opal/by_rank/superkingdom.tsv b/rerun_opal/by_rank/superkingdom.tsv
diff --git a/rerun_opal/by_tool/marmgCAMI2_short_read_sample_0-9.LSHvec_1dfe822.profile.tsv b/rerun_opal/by_tool/marmgCAMI2_short_read_sample_0-9.LSHvec_1dfe822.profile.tsv
diff --git a/..._tool/marmgCAMI2_short_read_sample_0-9.LSHvec_1dfe822.profile/beta_diversity_bc_class.pdf b/..._tool/marmgCAMI2_short_read_sample_0-9.LSHvec_1dfe822.profile/beta_diversity_bc_class.pdf
diff --git a/...gCAMI2_short_read_sample_0-9.LSHvec_1dfe822.profile/beta_diversity_bc_class.png b/...gCAMI2_short_read_sample_0-9.LSHvec_1dfe822.profile/beta_diversity_bc_class.png
diff --git a/...tool/marmgCAMI2_short_read_sample_0-9.LSHvec_1dfe822.profile/beta_diversity_bc_family.pdf b/...tool/marmgCAMI2_short_read_sample_0-9.LSHvec_1dfe822.profile/beta_diversity_bc_family.pdf
diff --git a/...CAMI2_short_read_sample_0-9.LSHvec_1dfe822.profile/beta_diversity_bc_family.png b/...CAMI2_short_read_sample_0-9.LSHvec_1dfe822.profile/beta_diversity_bc_family.png
diff --git a/..._tool/marmgCAMI2_short_read_sample_0-9.LSHvec_1dfe822.profile/beta_diversity_bc_genus.pdf b/..._tool/marmgCAMI2_short_read_sample_0-9.LSHvec_1dfe822.profile/beta_diversity_bc_genus.pdf
diff --git a/...gCAMI2_short_read_sample_0-9.LSHvec_1dfe822.profile/beta_diversity_bc_genus.png b/...gCAMI2_short_read_sample_0-9.LSHvec_1dfe822.profile/beta_diversity_bc_genus.png
diff --git a/..._tool/marmgCAMI2_short_read_sample_0-9.LSHvec_1dfe822.profile/beta_diversity_bc_order.pdf b/..._tool/marmgCAMI2_short_read_sample_0-9.LSHvec_1dfe822.profile/beta_diversity_bc_order.pdf
diff --git a/...gCAMI2_short_read_sample_0-9.LSHvec_1dfe822.profile/beta_diversity_bc_order.png b/...gCAMI2_short_read_sample_0-9.LSHvec_1dfe822.profile/beta_diversity_bc_order.png
diff --git a/...tool/marmgCAMI2_short_read_sample_0-9.LSHvec_1dfe822.profile/beta_diversity_bc_phylum.pdf b/...tool/marmgCAMI2_short_read_sample_0-9.LSHvec_1dfe822.profile/beta_diversity_bc_phylum.pdf
diff --git a/...CAMI2_short_read_sample_0-9.LSHvec_1dfe822.profile/beta_diversity_bc_phylum.png b/...CAMI2_short_read_sample_0-9.LSHvec_1dfe822.profile/beta_diversity_bc_phylum.png
diff --git a/...ool/marmgCAMI2_short_read_sample_0-9.LSHvec_1dfe822.profile/beta_diversity_bc_species.pdf b/...ool/marmgCAMI2_short_read_sample_0-9.LSHvec_1dfe822.profile/beta_diversity_bc_species.pdf
diff --git a/...AMI2_short_read_sample_0-9.LSHvec_1dfe822.profile/beta_diversity_bc_species.png b/...AMI2_short_read_sample_0-9.LSHvec_1dfe822.profile/beta_diversity_bc_species.png
diff --git a/...armgCAMI2_short_read_sample_0-9.LSHvec_1dfe822.profile/beta_diversity_bc_superkingdom.pdf b/...armgCAMI2_short_read_sample_0-9.LSHvec_1dfe822.profile/beta_diversity_bc_superkingdom.pdf
diff --git a/...short_read_sample_0-9.LSHvec_1dfe822.profile/beta_diversity_bc_superkingdom.png b/...short_read_sample_0-9.LSHvec_1dfe822.profile/beta_diversity_bc_superkingdom.png
diff --git a/.../marmgCAMI2_short_read_sample_0-9.LSHvec_1dfe822.profile/purity_completeness_per_rank.pdf b/.../marmgCAMI2_short_read_sample_0-9.LSHvec_1dfe822.profile/purity_completeness_per_rank.pdf
diff --git a/...2_short_read_sample_0-9.LSHvec_1dfe822.profile/purity_completeness_per_rank.png b/...2_short_read_sample_0-9.LSHvec_1dfe822.profile/purity_completeness_per_rank.png
diff --git a/rerun_opal/by_tool/marmgCAMI2_short_read_sample_0-9.bracken_2.2.profile.tsv b/rerun_opal/by_tool/marmgCAMI2_short_read_sample_0-9.bracken_2.2.profile.tsv
diff --git a/.../by_tool/marmgCAMI2_short_read_sample_0-9.bracken_2.2.profile/beta_diversity_bc_class.pdf b/.../by_tool/marmgCAMI2_short_read_sample_0-9.bracken_2.2.profile/beta_diversity_bc_class.pdf
diff --git a/...armgCAMI2_short_read_sample_0-9.bracken_2.2.profile/beta_diversity_bc_class.png b/...armgCAMI2_short_read_sample_0-9.bracken_2.2.profile/beta_diversity_bc_class.png
diff --git a/...by_tool/marmgCAMI2_short_read_sample_0-9.bracken_2.2.profile/beta_diversity_bc_family.pdf b/...by_tool/marmgCAMI2_short_read_sample_0-9.bracken_2.2.profile/beta_diversity_bc_family.pdf
diff --git a/...rmgCAMI2_short_read_sample_0-9.bracken_2.2.profile/beta_diversity_bc_family.png b/...rmgCAMI2_short_read_sample_0-9.bracken_2.2.profile/beta_diversity_bc_family.png
diff --git a/.../by_tool/marmgCAMI2_short_read_sample_0-9.bracken_2.2.profile/beta_diversity_bc_genus.pdf b/.../by_tool/marmgCAMI2_short_read_sample_0-9.bracken_2.2.profile/beta_diversity_bc_genus.pdf
diff --git a/...armgCAMI2_short_read_sample_0-9.bracken_2.2.profile/beta_diversity_bc_genus.png b/...armgCAMI2_short_read_sample_0-9.bracken_2.2.profile/beta_diversity_bc_genus.png
diff --git a/.../by_tool/marmgCAMI2_short_read_sample_0-9.bracken_2.2.profile/beta_diversity_bc_order.pdf b/.../by_tool/marmgCAMI2_short_read_sample_0-9.bracken_2.2.profile/beta_diversity_bc_order.pdf
diff --git a/...armgCAMI2_short_read_sample_0-9.bracken_2.2.profile/beta_diversity_bc_order.png b/...armgCAMI2_short_read_sample_0-9.bracken_2.2.profile/beta_diversity_bc_order.png
diff --git a/...y_tool/marmgCAMI2_short_read_sample_0-9.bracken_2.2.profile/beta_diversity_bc_species.pdf b/...y_tool/marmgCAMI2_short_read_sample_0-9.bracken_2.2.profile/beta_diversity_bc_species.pdf
diff --git a/...mgCAMI2_short_read_sample_0-9.bracken_2.2.profile/beta_diversity_bc_species.png b/...mgCAMI2_short_read_sample_0-9.bracken_2.2.profile/beta_diversity_bc_species.png
diff --git a/...ool/marmgCAMI2_short_read_sample_0-9.bracken_2.2.profile/purity_completeness_per_rank.pdf b/...ool/marmgCAMI2_short_read_sample_0-9.bracken_2.2.profile/purity_completeness_per_rank.pdf
diff --git a/...AMI2_short_read_sample_0-9.bracken_2.2.profile/purity_completeness_per_rank.png b/...AMI2_short_read_sample_0-9.bracken_2.2.profile/purity_completeness_per_rank.png
diff --git a/rerun_opal/by_tool/marmgCAMI2_short_read_sample_0-9.ccmetagen_1.1.3.profile.tsv b/rerun_opal/by_tool/marmgCAMI2_short_read_sample_0-9.ccmetagen_1.1.3.profile.tsv
diff --git a/...tool/marmgCAMI2_short_read_sample_0-9.ccmetagen_1.1.3.profile/beta_diversity_bc_class.pdf b/...tool/marmgCAMI2_short_read_sample_0-9.ccmetagen_1.1.3.profile/beta_diversity_bc_class.pdf
diff --git a/...CAMI2_short_read_sample_0-9.ccmetagen_1.1.3.profile/beta_diversity_bc_class.png b/...CAMI2_short_read_sample_0-9.ccmetagen_1.1.3.profile/beta_diversity_bc_class.png
diff --git a/...ool/marmgCAMI2_short_read_sample_0-9.ccmetagen_1.1.3.profile/beta_diversity_bc_family.pdf b/...ool/marmgCAMI2_short_read_sample_0-9.ccmetagen_1.1.3.profile/beta_diversity_bc_family.pdf
diff --git a/...AMI2_short_read_sample_0-9.ccmetagen_1.1.3.profile/beta_diversity_bc_family.png b/...AMI2_short_read_sample_0-9.ccmetagen_1.1.3.profile/beta_diversity_bc_family.png
diff --git a/...tool/marmgCAMI2_short_read_sample_0-9.ccmetagen_1.1.3.profile/beta_diversity_bc_genus.pdf b/...tool/marmgCAMI2_short_read_sample_0-9.ccmetagen_1.1.3.profile/beta_diversity_bc_genus.pdf
diff --git a/...CAMI2_short_read_sample_0-9.ccmetagen_1.1.3.profile/beta_diversity_bc_genus.png b/...CAMI2_short_read_sample_0-9.ccmetagen_1.1.3.profile/beta_diversity_bc_genus.png
diff --git a/...tool/marmgCAMI2_short_read_sample_0-9.ccmetagen_1.1.3.profile/beta_diversity_bc_order.pdf b/...tool/marmgCAMI2_short_read_sample_0-9.ccmetagen_1.1.3.profile/beta_diversity_bc_order.pdf
diff --git a/...CAMI2_short_read_sample_0-9.ccmetagen_1.1.3.profile/beta_diversity_bc_order.png b/...CAMI2_short_read_sample_0-9.ccmetagen_1.1.3.profile/beta_diversity_bc_order.png
diff --git a/...ool/marmgCAMI2_short_read_sample_0-9.ccmetagen_1.1.3.profile/beta_diversity_bc_phylum.pdf b/...ool/marmgCAMI2_short_read_sample_0-9.ccmetagen_1.1.3.profile/beta_diversity_bc_phylum.pdf
diff --git a/...AMI2_short_read_sample_0-9.ccmetagen_1.1.3.profile/beta_diversity_bc_phylum.png b/...AMI2_short_read_sample_0-9.ccmetagen_1.1.3.profile/beta_diversity_bc_phylum.png
diff --git a/...ol/marmgCAMI2_short_read_sample_0-9.ccmetagen_1.1.3.profile/beta_diversity_bc_species.pdf b/...ol/marmgCAMI2_short_read_sample_0-9.ccmetagen_1.1.3.profile/beta_diversity_bc_species.pdf
diff --git a/...MI2_short_read_sample_0-9.ccmetagen_1.1.3.profile/beta_diversity_bc_species.png b/...MI2_short_read_sample_0-9.ccmetagen_1.1.3.profile/beta_diversity_bc_species.png
diff --git a/...rmgCAMI2_short_read_sample_0-9.ccmetagen_1.1.3.profile/beta_diversity_bc_superkingdom.pdf b/...rmgCAMI2_short_read_sample_0-9.ccmetagen_1.1.3.profile/beta_diversity_bc_superkingdom.pdf
diff --git a/...hort_read_sample_0-9.ccmetagen_1.1.3.profile/beta_diversity_bc_superkingdom.png b/...hort_read_sample_0-9.ccmetagen_1.1.3.profile/beta_diversity_bc_superkingdom.png
diff --git a/...marmgCAMI2_short_read_sample_0-9.ccmetagen_1.1.3.profile/purity_completeness_per_rank.pdf b/...marmgCAMI2_short_read_sample_0-9.ccmetagen_1.1.3.profile/purity_completeness_per_rank.pdf
diff --git a/..._short_read_sample_0-9.ccmetagen_1.1.3.profile/purity_completeness_per_rank.png b/..._short_read_sample_0-9.ccmetagen_1.1.3.profile/purity_completeness_per_rank.png
diff --git a/rerun_opal/by_tool/marmgCAMI2_short_read_sample_0-9.centrifuge_1.0.4_beta.profile.tsv b/rerun_opal/by_tool/marmgCAMI2_short_read_sample_0-9.centrifuge_1.0.4_beta.profile.tsv
diff --git a/...armgCAMI2_short_read_sample_0-9.centrifuge_1.0.4_beta.profile/beta_diversity_bc_class.pdf b/...armgCAMI2_short_read_sample_0-9.centrifuge_1.0.4_beta.profile/beta_diversity_bc_class.pdf
diff --git a/...short_read_sample_0-9.centrifuge_1.0.4_beta.profile/beta_diversity_bc_class.png b/...short_read_sample_0-9.centrifuge_1.0.4_beta.profile/beta_diversity_bc_class.png
diff --git a/...rmgCAMI2_short_read_sample_0-9.centrifuge_1.0.4_beta.profile/beta_diversity_bc_family.pdf b/...rmgCAMI2_short_read_sample_0-9.centrifuge_1.0.4_beta.profile/beta_diversity_bc_family.pdf
diff --git a/...hort_read_sample_0-9.centrifuge_1.0.4_beta.profile/beta_diversity_bc_family.png b/...hort_read_sample_0-9.centrifuge_1.0.4_beta.profile/beta_diversity_bc_family.png
diff --git a/...armgCAMI2_short_read_sample_0-9.centrifuge_1.0.4_beta.profile/beta_diversity_bc_genus.pdf b/...armgCAMI2_short_read_sample_0-9.centrifuge_1.0.4_beta.profile/beta_diversity_bc_genus.pdf
diff --git a/...short_read_sample_0-9.centrifuge_1.0.4_beta.profile/beta_diversity_bc_genus.png b/...short_read_sample_0-9.centrifuge_1.0.4_beta.profile/beta_diversity_bc_genus.png
diff --git a/...armgCAMI2_short_read_sample_0-9.centrifuge_1.0.4_beta.profile/beta_diversity_bc_order.pdf b/...armgCAMI2_short_read_sample_0-9.centrifuge_1.0.4_beta.profile/beta_diversity_bc_order.pdf
diff --git a/...short_read_sample_0-9.centrifuge_1.0.4_beta.profile/beta_diversity_bc_order.png b/...short_read_sample_0-9.centrifuge_1.0.4_beta.profile/beta_diversity_bc_order.png
diff --git a/...rmgCAMI2_short_read_sample_0-9.centrifuge_1.0.4_beta.profile/beta_diversity_bc_phylum.pdf b/...rmgCAMI2_short_read_sample_0-9.centrifuge_1.0.4_beta.profile/beta_diversity_bc_phylum.pdf
diff --git a/...hort_read_sample_0-9.centrifuge_1.0.4_beta.profile/beta_diversity_bc_phylum.png b/...hort_read_sample_0-9.centrifuge_1.0.4_beta.profile/beta_diversity_bc_phylum.png
diff --git a/...mgCAMI2_short_read_sample_0-9.centrifuge_1.0.4_beta.profile/beta_diversity_bc_species.pdf b/...mgCAMI2_short_read_sample_0-9.centrifuge_1.0.4_beta.profile/beta_diversity_bc_species.pdf
diff --git a/...ort_read_sample_0-9.centrifuge_1.0.4_beta.profile/beta_diversity_bc_species.png b/...ort_read_sample_0-9.centrifuge_1.0.4_beta.profile/beta_diversity_bc_species.png
diff --git a/...I2_short_read_sample_0-9.centrifuge_1.0.4_beta.profile/beta_diversity_bc_superkingdom.pdf b/...I2_short_read_sample_0-9.centrifuge_1.0.4_beta.profile/beta_diversity_bc_superkingdom.pdf
diff --git a/...ead_sample_0-9.centrifuge_1.0.4_beta.profile/beta_diversity_bc_superkingdom.png b/...ead_sample_0-9.centrifuge_1.0.4_beta.profile/beta_diversity_bc_superkingdom.png
diff --git a/...AMI2_short_read_sample_0-9.centrifuge_1.0.4_beta.profile/purity_completeness_per_rank.pdf b/...AMI2_short_read_sample_0-9.centrifuge_1.0.4_beta.profile/purity_completeness_per_rank.pdf
diff --git a/..._read_sample_0-9.centrifuge_1.0.4_beta.profile/purity_completeness_per_rank.png b/..._read_sample_0-9.centrifuge_1.0.4_beta.profile/purity_completeness_per_rank.png
diff --git a/rerun_opal/by_tool/marmgCAMI2_short_read_sample_0-9.dudes_0.08.profile.tsv b/rerun_opal/by_tool/marmgCAMI2_short_read_sample_0-9.dudes_0.08.profile.tsv
diff --git a/...l/by_tool/marmgCAMI2_short_read_sample_0-9.dudes_0.08.profile/beta_diversity_bc_class.pdf b/...l/by_tool/marmgCAMI2_short_read_sample_0-9.dudes_0.08.profile/beta_diversity_bc_class.pdf
diff --git a/...marmgCAMI2_short_read_sample_0-9.dudes_0.08.profile/beta_diversity_bc_class.png b/...marmgCAMI2_short_read_sample_0-9.dudes_0.08.profile/beta_diversity_bc_class.png
diff --git a/.../by_tool/marmgCAMI2_short_read_sample_0-9.dudes_0.08.profile/beta_diversity_bc_family.pdf b/.../by_tool/marmgCAMI2_short_read_sample_0-9.dudes_0.08.profile/beta_diversity_bc_family.pdf
diff --git a/...armgCAMI2_short_read_sample_0-9.dudes_0.08.profile/beta_diversity_bc_family.png b/...armgCAMI2_short_read_sample_0-9.dudes_0.08.profile/beta_diversity_bc_family.png
diff --git a/...l/by_tool/marmgCAMI2_short_read_sample_0-9.dudes_0.08.profile/beta_diversity_bc_genus.pdf b/...l/by_tool/marmgCAMI2_short_read_sample_0-9.dudes_0.08.profile/beta_diversity_bc_genus.pdf
diff --git a/...marmgCAMI2_short_read_sample_0-9.dudes_0.08.profile/beta_diversity_bc_genus.png b/...marmgCAMI2_short_read_sample_0-9.dudes_0.08.profile/beta_diversity_bc_genus.png
diff --git a/...l/by_tool/marmgCAMI2_short_read_sample_0-9.dudes_0.08.profile/beta_diversity_bc_order.pdf b/...l/by_tool/marmgCAMI2_short_read_sample_0-9.dudes_0.08.profile/beta_diversity_bc_order.pdf
diff --git a/...marmgCAMI2_short_read_sample_0-9.dudes_0.08.profile/beta_diversity_bc_order.png b/...marmgCAMI2_short_read_sample_0-9.dudes_0.08.profile/beta_diversity_bc_order.png
diff --git a/.../by_tool/marmgCAMI2_short_read_sample_0-9.dudes_0.08.profile/beta_diversity_bc_phylum.pdf b/.../by_tool/marmgCAMI2_short_read_sample_0-9.dudes_0.08.profile/beta_diversity_bc_phylum.pdf
diff --git a/...armgCAMI2_short_read_sample_0-9.dudes_0.08.profile/beta_diversity_bc_phylum.png b/...armgCAMI2_short_read_sample_0-9.dudes_0.08.profile/beta_diversity_bc_phylum.png
diff --git a/...by_tool/marmgCAMI2_short_read_sample_0-9.dudes_0.08.profile/beta_diversity_bc_species.pdf b/...by_tool/marmgCAMI2_short_read_sample_0-9.dudes_0.08.profile/beta_diversity_bc_species.pdf
diff --git a/...rmgCAMI2_short_read_sample_0-9.dudes_0.08.profile/beta_diversity_bc_species.png b/...rmgCAMI2_short_read_sample_0-9.dudes_0.08.profile/beta_diversity_bc_species.png
diff --git a/...ol/marmgCAMI2_short_read_sample_0-9.dudes_0.08.profile/beta_diversity_bc_superkingdom.pdf b/...ol/marmgCAMI2_short_read_sample_0-9.dudes_0.08.profile/beta_diversity_bc_superkingdom.pdf
diff --git a/...MI2_short_read_sample_0-9.dudes_0.08.profile/beta_diversity_bc_superkingdom.png b/...MI2_short_read_sample_0-9.dudes_0.08.profile/beta_diversity_bc_superkingdom.png
diff --git a/...tool/marmgCAMI2_short_read_sample_0-9.dudes_0.08.profile/purity_completeness_per_rank.pdf b/...tool/marmgCAMI2_short_read_sample_0-9.dudes_0.08.profile/purity_completeness_per_rank.pdf
diff --git a/...CAMI2_short_read_sample_0-9.dudes_0.08.profile/purity_completeness_per_rank.png b/...CAMI2_short_read_sample_0-9.dudes_0.08.profile/purity_completeness_per_rank.png
diff --git a/rerun_opal/by_tool/marmgCAMI2_short_read_sample_0-9.focus_1.5.profile.tsv b/rerun_opal/by_tool/marmgCAMI2_short_read_sample_0-9.focus_1.5.profile.tsv
diff --git a/...al/by_tool/marmgCAMI2_short_read_sample_0-9.focus_1.5.profile/beta_diversity_bc_class.pdf b/...al/by_tool/marmgCAMI2_short_read_sample_0-9.focus_1.5.profile/beta_diversity_bc_class.pdf
diff --git a/.../marmgCAMI2_short_read_sample_0-9.focus_1.5.profile/beta_diversity_bc_class.png b/.../marmgCAMI2_short_read_sample_0-9.focus_1.5.profile/beta_diversity_bc_class.png
diff --git a/...l/by_tool/marmgCAMI2_short_read_sample_0-9.focus_1.5.profile/beta_diversity_bc_family.pdf b/...l/by_tool/marmgCAMI2_short_read_sample_0-9.focus_1.5.profile/beta_diversity_bc_family.pdf
diff --git a/...marmgCAMI2_short_read_sample_0-9.focus_1.5.profile/beta_diversity_bc_family.png b/...marmgCAMI2_short_read_sample_0-9.focus_1.5.profile/beta_diversity_bc_family.png
diff --git a/...al/by_tool/marmgCAMI2_short_read_sample_0-9.focus_1.5.profile/beta_diversity_bc_genus.pdf b/...al/by_tool/marmgCAMI2_short_read_sample_0-9.focus_1.5.profile/beta_diversity_bc_genus.pdf
diff --git a/.../marmgCAMI2_short_read_sample_0-9.focus_1.5.profile/beta_diversity_bc_genus.png b/.../marmgCAMI2_short_read_sample_0-9.focus_1.5.profile/beta_diversity_bc_genus.png
diff --git a/...al/by_tool/marmgCAMI2_short_read_sample_0-9.focus_1.5.profile/beta_diversity_bc_order.pdf b/...al/by_tool/marmgCAMI2_short_read_sample_0-9.focus_1.5.profile/beta_diversity_bc_order.pdf
diff --git a/.../marmgCAMI2_short_read_sample_0-9.focus_1.5.profile/beta_diversity_bc_order.png b/.../marmgCAMI2_short_read_sample_0-9.focus_1.5.profile/beta_diversity_bc_order.png
diff --git a/...l/by_tool/marmgCAMI2_short_read_sample_0-9.focus_1.5.profile/beta_diversity_bc_phylum.pdf b/...l/by_tool/marmgCAMI2_short_read_sample_0-9.focus_1.5.profile/beta_diversity_bc_phylum.pdf
diff --git a/...marmgCAMI2_short_read_sample_0-9.focus_1.5.profile/beta_diversity_bc_phylum.png b/...marmgCAMI2_short_read_sample_0-9.focus_1.5.profile/beta_diversity_bc_phylum.png
diff --git a/.../by_tool/marmgCAMI2_short_read_sample_0-9.focus_1.5.profile/beta_diversity_bc_species.pdf b/.../by_tool/marmgCAMI2_short_read_sample_0-9.focus_1.5.profile/beta_diversity_bc_species.pdf
diff --git a/...armgCAMI2_short_read_sample_0-9.focus_1.5.profile/beta_diversity_bc_species.png b/...armgCAMI2_short_read_sample_0-9.focus_1.5.profile/beta_diversity_bc_species.png
diff --git a/...l/by_tool/marmgCAMI2_short_read_sample_0-9.focus_1.5.profile/beta_diversity_bc_strain.pdf b/...l/by_tool/marmgCAMI2_short_read_sample_0-9.focus_1.5.profile/beta_diversity_bc_strain.pdf
diff --git a/...marmgCAMI2_short_read_sample_0-9.focus_1.5.profile/beta_diversity_bc_strain.png b/...marmgCAMI2_short_read_sample_0-9.focus_1.5.profile/beta_diversity_bc_strain.png
diff --git a/...ool/marmgCAMI2_short_read_sample_0-9.focus_1.5.profile/beta_diversity_bc_superkingdom.pdf b/...ool/marmgCAMI2_short_read_sample_0-9.focus_1.5.profile/beta_diversity_bc_superkingdom.pdf
diff --git a/...AMI2_short_read_sample_0-9.focus_1.5.profile/beta_diversity_bc_superkingdom.png b/...AMI2_short_read_sample_0-9.focus_1.5.profile/beta_diversity_bc_superkingdom.png
diff --git a/..._tool/marmgCAMI2_short_read_sample_0-9.focus_1.5.profile/purity_completeness_per_rank.pdf b/..._tool/marmgCAMI2_short_read_sample_0-9.focus_1.5.profile/purity_completeness_per_rank.pdf
diff --git a/...gCAMI2_short_read_sample_0-9.focus_1.5.profile/purity_completeness_per_rank.png b/...gCAMI2_short_read_sample_0-9.focus_1.5.profile/purity_completeness_per_rank.png
diff --git a/rerun_opal/by_tool/marmgCAMI2_short_read_sample_0-9.metalign_0.6.2_default.profile.tsv b/rerun_opal/by_tool/marmgCAMI2_short_read_sample_0-9.metalign_0.6.2_default.profile.tsv
diff --git a/...rmgCAMI2_short_read_sample_0-9.metalign_0.6.2_default.profile/beta_diversity_bc_class.pdf b/...rmgCAMI2_short_read_sample_0-9.metalign_0.6.2_default.profile/beta_diversity_bc_class.pdf
diff --git a/...hort_read_sample_0-9.metalign_0.6.2_default.profile/beta_diversity_bc_class.png b/...hort_read_sample_0-9.metalign_0.6.2_default.profile/beta_diversity_bc_class.png
diff --git a/...mgCAMI2_short_read_sample_0-9.metalign_0.6.2_default.profile/beta_diversity_bc_family.pdf b/...mgCAMI2_short_read_sample_0-9.metalign_0.6.2_default.profile/beta_diversity_bc_family.pdf
diff --git a/...ort_read_sample_0-9.metalign_0.6.2_default.profile/beta_diversity_bc_family.png b/...ort_read_sample_0-9.metalign_0.6.2_default.profile/beta_diversity_bc_family.png
diff --git a/...rmgCAMI2_short_read_sample_0-9.metalign_0.6.2_default.profile/beta_diversity_bc_genus.pdf b/...rmgCAMI2_short_read_sample_0-9.metalign_0.6.2_default.profile/beta_diversity_bc_genus.pdf
diff --git a/...hort_read_sample_0-9.metalign_0.6.2_default.profile/beta_diversity_bc_genus.png b/...hort_read_sample_0-9.metalign_0.6.2_default.profile/beta_diversity_bc_genus.png
diff --git a/...rmgCAMI2_short_read_sample_0-9.metalign_0.6.2_default.profile/beta_diversity_bc_order.pdf b/...rmgCAMI2_short_read_sample_0-9.metalign_0.6.2_default.profile/beta_diversity_bc_order.pdf
diff --git a/...hort_read_sample_0-9.metalign_0.6.2_default.profile/beta_diversity_bc_order.png b/...hort_read_sample_0-9.metalign_0.6.2_default.profile/beta_diversity_bc_order.png
diff --git a/...mgCAMI2_short_read_sample_0-9.metalign_0.6.2_default.profile/beta_diversity_bc_phylum.pdf b/...mgCAMI2_short_read_sample_0-9.metalign_0.6.2_default.profile/beta_diversity_bc_phylum.pdf
diff --git a/...ort_read_sample_0-9.metalign_0.6.2_default.profile/beta_diversity_bc_phylum.png b/...ort_read_sample_0-9.metalign_0.6.2_default.profile/beta_diversity_bc_phylum.png
diff --git a/...gCAMI2_short_read_sample_0-9.metalign_0.6.2_default.profile/beta_diversity_bc_species.pdf b/...gCAMI2_short_read_sample_0-9.metalign_0.6.2_default.profile/beta_diversity_bc_species.pdf
diff --git a/...rt_read_sample_0-9.metalign_0.6.2_default.profile/beta_diversity_bc_species.png b/...rt_read_sample_0-9.metalign_0.6.2_default.profile/beta_diversity_bc_species.png
diff --git a/...mgCAMI2_short_read_sample_0-9.metalign_0.6.2_default.profile/beta_diversity_bc_strain.pdf b/...mgCAMI2_short_read_sample_0-9.metalign_0.6.2_default.profile/beta_diversity_bc_strain.pdf
diff --git a/...ort_read_sample_0-9.metalign_0.6.2_default.profile/beta_diversity_bc_strain.png b/...ort_read_sample_0-9.metalign_0.6.2_default.profile/beta_diversity_bc_strain.png
diff --git a/...2_short_read_sample_0-9.metalign_0.6.2_default.profile/beta_diversity_bc_superkingdom.pdf b/...2_short_read_sample_0-9.metalign_0.6.2_default.profile/beta_diversity_bc_superkingdom.pdf
diff --git a/...ad_sample_0-9.metalign_0.6.2_default.profile/beta_diversity_bc_superkingdom.png b/...ad_sample_0-9.metalign_0.6.2_default.profile/beta_diversity_bc_superkingdom.png
diff --git a/...MI2_short_read_sample_0-9.metalign_0.6.2_default.profile/purity_completeness_per_rank.pdf b/...MI2_short_read_sample_0-9.metalign_0.6.2_default.profile/purity_completeness_per_rank.pdf
diff --git a/...read_sample_0-9.metalign_0.6.2_default.profile/purity_completeness_per_rank.png b/...read_sample_0-9.metalign_0.6.2_default.profile/purity_completeness_per_rank.png
diff --git a/rerun_opal/by_tool/marmgCAMI2_short_read_sample_0-9.metalign_0.6.2_precise.profile.tsv b/rerun_opal/by_tool/marmgCAMI2_short_read_sample_0-9.metalign_0.6.2_precise.profile.tsv
diff --git a/...rmgCAMI2_short_read_sample_0-9.metalign_0.6.2_precise.profile/beta_diversity_bc_class.pdf b/...rmgCAMI2_short_read_sample_0-9.metalign_0.6.2_precise.profile/beta_diversity_bc_class.pdf
diff --git a/...hort_read_sample_0-9.metalign_0.6.2_precise.profile/beta_diversity_bc_class.png b/...hort_read_sample_0-9.metalign_0.6.2_precise.profile/beta_diversity_bc_class.png
diff --git a/...mgCAMI2_short_read_sample_0-9.metalign_0.6.2_precise.profile/beta_diversity_bc_family.pdf b/...mgCAMI2_short_read_sample_0-9.metalign_0.6.2_precise.profile/beta_diversity_bc_family.pdf
diff --git a/...ort_read_sample_0-9.metalign_0.6.2_precise.profile/beta_diversity_bc_family.png b/...ort_read_sample_0-9.metalign_0.6.2_precise.profile/beta_diversity_bc_family.png
diff --git a/...rmgCAMI2_short_read_sample_0-9.metalign_0.6.2_precise.profile/beta_diversity_bc_genus.pdf b/...rmgCAMI2_short_read_sample_0-9.metalign_0.6.2_precise.profile/beta_diversity_bc_genus.pdf
diff --git a/...hort_read_sample_0-9.metalign_0.6.2_precise.profile/beta_diversity_bc_genus.png b/...hort_read_sample_0-9.metalign_0.6.2_precise.profile/beta_diversity_bc_genus.png
diff --git a/...rmgCAMI2_short_read_sample_0-9.metalign_0.6.2_precise.profile/beta_diversity_bc_order.pdf b/...rmgCAMI2_short_read_sample_0-9.metalign_0.6.2_precise.profile/beta_diversity_bc_order.pdf
diff --git a/...hort_read_sample_0-9.metalign_0.6.2_precise.profile/beta_diversity_bc_order.png b/...hort_read_sample_0-9.metalign_0.6.2_precise.profile/beta_diversity_bc_order.png
diff --git a/...mgCAMI2_short_read_sample_0-9.metalign_0.6.2_precise.profile/beta_diversity_bc_phylum.pdf b/...mgCAMI2_short_read_sample_0-9.metalign_0.6.2_precise.profile/beta_diversity_bc_phylum.pdf
diff --git a/...ort_read_sample_0-9.metalign_0.6.2_precise.profile/beta_diversity_bc_phylum.png b/...ort_read_sample_0-9.metalign_0.6.2_precise.profile/beta_diversity_bc_phylum.png
diff --git a/...gCAMI2_short_read_sample_0-9.metalign_0.6.2_precise.profile/beta_diversity_bc_species.pdf b/...gCAMI2_short_read_sample_0-9.metalign_0.6.2_precise.profile/beta_diversity_bc_species.pdf
diff --git a/...rt_read_sample_0-9.metalign_0.6.2_precise.profile/beta_diversity_bc_species.png b/...rt_read_sample_0-9.metalign_0.6.2_precise.profile/beta_diversity_bc_species.png
diff --git a/...mgCAMI2_short_read_sample_0-9.metalign_0.6.2_precise.profile/beta_diversity_bc_strain.pdf b/...mgCAMI2_short_read_sample_0-9.metalign_0.6.2_precise.profile/beta_diversity_bc_strain.pdf
diff --git a/...ort_read_sample_0-9.metalign_0.6.2_precise.profile/beta_diversity_bc_strain.png b/...ort_read_sample_0-9.metalign_0.6.2_precise.profile/beta_diversity_bc_strain.png
diff --git a/...2_short_read_sample_0-9.metalign_0.6.2_precise.profile/beta_diversity_bc_superkingdom.pdf b/...2_short_read_sample_0-9.metalign_0.6.2_precise.profile/beta_diversity_bc_superkingdom.pdf
diff --git a/...ad_sample_0-9.metalign_0.6.2_precise.profile/beta_diversity_bc_superkingdom.png b/...ad_sample_0-9.metalign_0.6.2_precise.profile/beta_diversity_bc_superkingdom.png
diff --git a/...MI2_short_read_sample_0-9.metalign_0.6.2_precise.profile/purity_completeness_per_rank.pdf b/...MI2_short_read_sample_0-9.metalign_0.6.2_precise.profile/purity_completeness_per_rank.pdf
diff --git a/...read_sample_0-9.metalign_0.6.2_precise.profile/purity_completeness_per_rank.png b/...read_sample_0-9.metalign_0.6.2_precise.profile/purity_completeness_per_rank.png
diff --git a/rerun_opal/by_tool/marmgCAMI2_short_read_sample_0-9.metapalette_1.0.0.profile.tsv b/rerun_opal/by_tool/marmgCAMI2_short_read_sample_0-9.metapalette_1.0.0.profile.tsv
diff --git a/...ol/marmgCAMI2_short_read_sample_0-9.metapalette_1.0.0.profile/beta_diversity_bc_class.pdf b/...ol/marmgCAMI2_short_read_sample_0-9.metapalette_1.0.0.profile/beta_diversity_bc_class.pdf
diff --git a/...MI2_short_read_sample_0-9.metapalette_1.0.0.profile/beta_diversity_bc_class.png b/...MI2_short_read_sample_0-9.metapalette_1.0.0.profile/beta_diversity_bc_class.png
diff --git a/...l/marmgCAMI2_short_read_sample_0-9.metapalette_1.0.0.profile/beta_diversity_bc_family.pdf b/...l/marmgCAMI2_short_read_sample_0-9.metapalette_1.0.0.profile/beta_diversity_bc_family.pdf
diff --git a/...I2_short_read_sample_0-9.metapalette_1.0.0.profile/beta_diversity_bc_family.png b/...I2_short_read_sample_0-9.metapalette_1.0.0.profile/beta_diversity_bc_family.png
diff --git a/...ol/marmgCAMI2_short_read_sample_0-9.metapalette_1.0.0.profile/beta_diversity_bc_genus.pdf b/...ol/marmgCAMI2_short_read_sample_0-9.metapalette_1.0.0.profile/beta_diversity_bc_genus.pdf
diff --git a/...MI2_short_read_sample_0-9.metapalette_1.0.0.profile/beta_diversity_bc_genus.png b/...MI2_short_read_sample_0-9.metapalette_1.0.0.profile/beta_diversity_bc_genus.png
diff --git a/...ol/marmgCAMI2_short_read_sample_0-9.metapalette_1.0.0.profile/beta_diversity_bc_order.pdf b/...ol/marmgCAMI2_short_read_sample_0-9.metapalette_1.0.0.profile/beta_diversity_bc_order.pdf
diff --git a/...MI2_short_read_sample_0-9.metapalette_1.0.0.profile/beta_diversity_bc_order.png b/...MI2_short_read_sample_0-9.metapalette_1.0.0.profile/beta_diversity_bc_order.png
diff --git a/...l/marmgCAMI2_short_read_sample_0-9.metapalette_1.0.0.profile/beta_diversity_bc_phylum.pdf b/...l/marmgCAMI2_short_read_sample_0-9.metapalette_1.0.0.profile/beta_diversity_bc_phylum.pdf
diff --git a/...I2_short_read_sample_0-9.metapalette_1.0.0.profile/beta_diversity_bc_phylum.png b/...I2_short_read_sample_0-9.metapalette_1.0.0.profile/beta_diversity_bc_phylum.png
diff --git a/.../marmgCAMI2_short_read_sample_0-9.metapalette_1.0.0.profile/beta_diversity_bc_species.pdf b/.../marmgCAMI2_short_read_sample_0-9.metapalette_1.0.0.profile/beta_diversity_bc_species.pdf
diff --git a/...2_short_read_sample_0-9.metapalette_1.0.0.profile/beta_diversity_bc_species.png b/...2_short_read_sample_0-9.metapalette_1.0.0.profile/beta_diversity_bc_species.png
diff --git a/...l/marmgCAMI2_short_read_sample_0-9.metapalette_1.0.0.profile/beta_diversity_bc_strain.pdf b/...l/marmgCAMI2_short_read_sample_0-9.metapalette_1.0.0.profile/beta_diversity_bc_strain.pdf
diff --git a/...I2_short_read_sample_0-9.metapalette_1.0.0.profile/beta_diversity_bc_strain.png b/...I2_short_read_sample_0-9.metapalette_1.0.0.profile/beta_diversity_bc_strain.png
diff --git a/...gCAMI2_short_read_sample_0-9.metapalette_1.0.0.profile/beta_diversity_bc_superkingdom.pdf b/...gCAMI2_short_read_sample_0-9.metapalette_1.0.0.profile/beta_diversity_bc_superkingdom.pdf
diff --git a/...rt_read_sample_0-9.metapalette_1.0.0.profile/beta_diversity_bc_superkingdom.png b/...rt_read_sample_0-9.metapalette_1.0.0.profile/beta_diversity_bc_superkingdom.png
diff --git a/...rmgCAMI2_short_read_sample_0-9.metapalette_1.0.0.profile/purity_completeness_per_rank.pdf b/...rmgCAMI2_short_read_sample_0-9.metapalette_1.0.0.profile/purity_completeness_per_rank.pdf
diff --git a/...hort_read_sample_0-9.metapalette_1.0.0.profile/purity_completeness_per_rank.png b/...hort_read_sample_0-9.metapalette_1.0.0.profile/purity_completeness_per_rank.png
diff --git a/rerun_opal/by_tool/marmgCAMI2_short_read_sample_0-9.metaphlan2_2.9.22.profile.tsv b/rerun_opal/by_tool/marmgCAMI2_short_read_sample_0-9.metaphlan2_2.9.22.profile.tsv
diff --git a/...ol/marmgCAMI2_short_read_sample_0-9.metaphlan2_2.9.22.profile/beta_diversity_bc_class.pdf b/...ol/marmgCAMI2_short_read_sample_0-9.metaphlan2_2.9.22.profile/beta_diversity_bc_class.pdf
diff --git a/...MI2_short_read_sample_0-9.metaphlan2_2.9.22.profile/beta_diversity_bc_class.png b/...MI2_short_read_sample_0-9.metaphlan2_2.9.22.profile/beta_diversity_bc_class.png
diff --git a/...l/marmgCAMI2_short_read_sample_0-9.metaphlan2_2.9.22.profile/beta_diversity_bc_family.pdf b/...l/marmgCAMI2_short_read_sample_0-9.metaphlan2_2.9.22.profile/beta_diversity_bc_family.pdf
diff --git a/...I2_short_read_sample_0-9.metaphlan2_2.9.22.profile/beta_diversity_bc_family.png b/...I2_short_read_sample_0-9.metaphlan2_2.9.22.profile/beta_diversity_bc_family.png
diff --git a/...ol/marmgCAMI2_short_read_sample_0-9.metaphlan2_2.9.22.profile/beta_diversity_bc_genus.pdf b/...ol/marmgCAMI2_short_read_sample_0-9.metaphlan2_2.9.22.profile/beta_diversity_bc_genus.pdf
diff --git a/...MI2_short_read_sample_0-9.metaphlan2_2.9.22.profile/beta_diversity_bc_genus.png b/...MI2_short_read_sample_0-9.metaphlan2_2.9.22.profile/beta_diversity_bc_genus.png
diff --git a/...ol/marmgCAMI2_short_read_sample_0-9.metaphlan2_2.9.22.profile/beta_diversity_bc_order.pdf b/...ol/marmgCAMI2_short_read_sample_0-9.metaphlan2_2.9.22.profile/beta_diversity_bc_order.pdf
diff --git a/...MI2_short_read_sample_0-9.metaphlan2_2.9.22.profile/beta_diversity_bc_order.png b/...MI2_short_read_sample_0-9.metaphlan2_2.9.22.profile/beta_diversity_bc_order.png
diff --git a/...l/marmgCAMI2_short_read_sample_0-9.metaphlan2_2.9.22.profile/beta_diversity_bc_phylum.pdf b/...l/marmgCAMI2_short_read_sample_0-9.metaphlan2_2.9.22.profile/beta_diversity_bc_phylum.pdf
diff --git a/...I2_short_read_sample_0-9.metaphlan2_2.9.22.profile/beta_diversity_bc_phylum.png b/...I2_short_read_sample_0-9.metaphlan2_2.9.22.profile/beta_diversity_bc_phylum.png
diff --git a/.../marmgCAMI2_short_read_sample_0-9.metaphlan2_2.9.22.profile/beta_diversity_bc_species.pdf b/.../marmgCAMI2_short_read_sample_0-9.metaphlan2_2.9.22.profile/beta_diversity_bc_species.pdf
diff --git a/...2_short_read_sample_0-9.metaphlan2_2.9.22.profile/beta_diversity_bc_species.png b/...2_short_read_sample_0-9.metaphlan2_2.9.22.profile/beta_diversity_bc_species.png
diff --git a/...gCAMI2_short_read_sample_0-9.metaphlan2_2.9.22.profile/beta_diversity_bc_superkingdom.pdf b/...gCAMI2_short_read_sample_0-9.metaphlan2_2.9.22.profile/beta_diversity_bc_superkingdom.pdf
diff --git a/...rt_read_sample_0-9.metaphlan2_2.9.22.profile/beta_diversity_bc_superkingdom.png b/...rt_read_sample_0-9.metaphlan2_2.9.22.profile/beta_diversity_bc_superkingdom.png
diff --git a/...rmgCAMI2_short_read_sample_0-9.metaphlan2_2.9.22.profile/purity_completeness_per_rank.pdf b/...rmgCAMI2_short_read_sample_0-9.metaphlan2_2.9.22.profile/purity_completeness_per_rank.pdf
diff --git a/...hort_read_sample_0-9.metaphlan2_2.9.22.profile/purity_completeness_per_rank.png b/...hort_read_sample_0-9.metaphlan2_2.9.22.profile/purity_completeness_per_rank.png
diff --git a/rerun_opal/by_tool/marmgCAMI2_short_read_sample_0-9.metaphyler_1.25.profile.tsv b/rerun_opal/by_tool/marmgCAMI2_short_read_sample_0-9.metaphyler_1.25.profile.tsv
diff --git a/...tool/marmgCAMI2_short_read_sample_0-9.metaphyler_1.25.profile/beta_diversity_bc_class.pdf b/...tool/marmgCAMI2_short_read_sample_0-9.metaphyler_1.25.profile/beta_diversity_bc_class.pdf
diff --git a/...CAMI2_short_read_sample_0-9.metaphyler_1.25.profile/beta_diversity_bc_class.png b/...CAMI2_short_read_sample_0-9.metaphyler_1.25.profile/beta_diversity_bc_class.png
diff --git a/...ool/marmgCAMI2_short_read_sample_0-9.metaphyler_1.25.profile/beta_diversity_bc_family.pdf b/...ool/marmgCAMI2_short_read_sample_0-9.metaphyler_1.25.profile/beta_diversity_bc_family.pdf
diff --git a/...AMI2_short_read_sample_0-9.metaphyler_1.25.profile/beta_diversity_bc_family.png b/...AMI2_short_read_sample_0-9.metaphyler_1.25.profile/beta_diversity_bc_family.png
diff --git a/...tool/marmgCAMI2_short_read_sample_0-9.metaphyler_1.25.profile/beta_diversity_bc_genus.pdf b/...tool/marmgCAMI2_short_read_sample_0-9.metaphyler_1.25.profile/beta_diversity_bc_genus.pdf
diff --git a/...CAMI2_short_read_sample_0-9.metaphyler_1.25.profile/beta_diversity_bc_genus.png b/...CAMI2_short_read_sample_0-9.metaphyler_1.25.profile/beta_diversity_bc_genus.png
diff --git a/...tool/marmgCAMI2_short_read_sample_0-9.metaphyler_1.25.profile/beta_diversity_bc_order.pdf b/...tool/marmgCAMI2_short_read_sample_0-9.metaphyler_1.25.profile/beta_diversity_bc_order.pdf
diff --git a/...CAMI2_short_read_sample_0-9.metaphyler_1.25.profile/beta_diversity_bc_order.png b/...CAMI2_short_read_sample_0-9.metaphyler_1.25.profile/beta_diversity_bc_order.png
diff --git a/...ool/marmgCAMI2_short_read_sample_0-9.metaphyler_1.25.profile/beta_diversity_bc_phylum.pdf b/...ool/marmgCAMI2_short_read_sample_0-9.metaphyler_1.25.profile/beta_diversity_bc_phylum.pdf
diff --git a/...AMI2_short_read_sample_0-9.metaphyler_1.25.profile/beta_diversity_bc_phylum.png b/...AMI2_short_read_sample_0-9.metaphyler_1.25.profile/beta_diversity_bc_phylum.png
diff --git a/...rmgCAMI2_short_read_sample_0-9.metaphyler_1.25.profile/beta_diversity_bc_superkingdom.pdf b/...rmgCAMI2_short_read_sample_0-9.metaphyler_1.25.profile/beta_diversity_bc_superkingdom.pdf
diff --git a/...hort_read_sample_0-9.metaphyler_1.25.profile/beta_diversity_bc_superkingdom.png b/...hort_read_sample_0-9.metaphyler_1.25.profile/beta_diversity_bc_superkingdom.png
diff --git a/...marmgCAMI2_short_read_sample_0-9.metaphyler_1.25.profile/purity_completeness_per_rank.pdf b/...marmgCAMI2_short_read_sample_0-9.metaphyler_1.25.profile/purity_completeness_per_rank.pdf
diff --git a/..._short_read_sample_0-9.metaphyler_1.25.profile/purity_completeness_per_rank.png b/..._short_read_sample_0-9.metaphyler_1.25.profile/purity_completeness_per_rank.png
diff --git a/rerun_opal/by_tool/marmgCAMI2_short_read_sample_0-9.motus_2.5.1.profile.tsv b/rerun_opal/by_tool/marmgCAMI2_short_read_sample_0-9.motus_2.5.1.profile.tsv
diff --git a/.../by_tool/marmgCAMI2_short_read_sample_0-9.motus_2.5.1.profile/beta_diversity_bc_class.pdf b/.../by_tool/marmgCAMI2_short_read_sample_0-9.motus_2.5.1.profile/beta_diversity_bc_class.pdf
diff --git a/...armgCAMI2_short_read_sample_0-9.motus_2.5.1.profile/beta_diversity_bc_class.png b/...armgCAMI2_short_read_sample_0-9.motus_2.5.1.profile/beta_diversity_bc_class.png
diff --git a/...by_tool/marmgCAMI2_short_read_sample_0-9.motus_2.5.1.profile/beta_diversity_bc_family.pdf b/...by_tool/marmgCAMI2_short_read_sample_0-9.motus_2.5.1.profile/beta_diversity_bc_family.pdf
diff --git a/...rmgCAMI2_short_read_sample_0-9.motus_2.5.1.profile/beta_diversity_bc_family.png b/...rmgCAMI2_short_read_sample_0-9.motus_2.5.1.profile/beta_diversity_bc_family.png
diff --git a/.../by_tool/marmgCAMI2_short_read_sample_0-9.motus_2.5.1.profile/beta_diversity_bc_genus.pdf b/.../by_tool/marmgCAMI2_short_read_sample_0-9.motus_2.5.1.profile/beta_diversity_bc_genus.pdf
diff --git a/...armgCAMI2_short_read_sample_0-9.motus_2.5.1.profile/beta_diversity_bc_genus.png b/...armgCAMI2_short_read_sample_0-9.motus_2.5.1.profile/beta_diversity_bc_genus.png
diff --git a/.../by_tool/marmgCAMI2_short_read_sample_0-9.motus_2.5.1.profile/beta_diversity_bc_order.pdf b/.../by_tool/marmgCAMI2_short_read_sample_0-9.motus_2.5.1.profile/beta_diversity_bc_order.pdf
diff --git a/...armgCAMI2_short_read_sample_0-9.motus_2.5.1.profile/beta_diversity_bc_order.png b/...armgCAMI2_short_read_sample_0-9.motus_2.5.1.profile/beta_diversity_bc_order.png
diff --git a/...by_tool/marmgCAMI2_short_read_sample_0-9.motus_2.5.1.profile/beta_diversity_bc_phylum.pdf b/...by_tool/marmgCAMI2_short_read_sample_0-9.motus_2.5.1.profile/beta_diversity_bc_phylum.pdf
diff --git a/...rmgCAMI2_short_read_sample_0-9.motus_2.5.1.profile/beta_diversity_bc_phylum.png b/...rmgCAMI2_short_read_sample_0-9.motus_2.5.1.profile/beta_diversity_bc_phylum.png
diff --git a/...y_tool/marmgCAMI2_short_read_sample_0-9.motus_2.5.1.profile/beta_diversity_bc_species.pdf b/...y_tool/marmgCAMI2_short_read_sample_0-9.motus_2.5.1.profile/beta_diversity_bc_species.pdf
diff --git a/...mgCAMI2_short_read_sample_0-9.motus_2.5.1.profile/beta_diversity_bc_species.png b/...mgCAMI2_short_read_sample_0-9.motus_2.5.1.profile/beta_diversity_bc_species.png
diff --git a/...l/marmgCAMI2_short_read_sample_0-9.motus_2.5.1.profile/beta_diversity_bc_superkingdom.pdf b/...l/marmgCAMI2_short_read_sample_0-9.motus_2.5.1.profile/beta_diversity_bc_superkingdom.pdf
diff --git a/...I2_short_read_sample_0-9.motus_2.5.1.profile/beta_diversity_bc_superkingdom.png b/...I2_short_read_sample_0-9.motus_2.5.1.profile/beta_diversity_bc_superkingdom.png
diff --git a/...ool/marmgCAMI2_short_read_sample_0-9.motus_2.5.1.profile/purity_completeness_per_rank.pdf b/...ool/marmgCAMI2_short_read_sample_0-9.motus_2.5.1.profile/purity_completeness_per_rank.pdf
diff --git a/...AMI2_short_read_sample_0-9.motus_2.5.1.profile/purity_completeness_per_rank.png b/...AMI2_short_read_sample_0-9.motus_2.5.1.profile/purity_completeness_per_rank.png
diff --git a/rerun_opal/by_tool/marmgCAMI2_short_read_sample_0-9.tipp_4.3.10.profile.tsv b/rerun_opal/by_tool/marmgCAMI2_short_read_sample_0-9.tipp_4.3.10.profile.tsv
diff --git a/.../by_tool/marmgCAMI2_short_read_sample_0-9.tipp_4.3.10.profile/beta_diversity_bc_class.pdf b/.../by_tool/marmgCAMI2_short_read_sample_0-9.tipp_4.3.10.profile/beta_diversity_bc_class.pdf
diff --git a/...armgCAMI2_short_read_sample_0-9.tipp_4.3.10.profile/beta_diversity_bc_class.png b/...armgCAMI2_short_read_sample_0-9.tipp_4.3.10.profile/beta_diversity_bc_class.png
diff --git a/...by_tool/marmgCAMI2_short_read_sample_0-9.tipp_4.3.10.profile/beta_diversity_bc_family.pdf b/...by_tool/marmgCAMI2_short_read_sample_0-9.tipp_4.3.10.profile/beta_diversity_bc_family.pdf
diff --git a/...rmgCAMI2_short_read_sample_0-9.tipp_4.3.10.profile/beta_diversity_bc_family.png b/...rmgCAMI2_short_read_sample_0-9.tipp_4.3.10.profile/beta_diversity_bc_family.png
diff --git a/.../by_tool/marmgCAMI2_short_read_sample_0-9.tipp_4.3.10.profile/beta_diversity_bc_genus.pdf b/.../by_tool/marmgCAMI2_short_read_sample_0-9.tipp_4.3.10.profile/beta_diversity_bc_genus.pdf
diff --git a/...armgCAMI2_short_read_sample_0-9.tipp_4.3.10.profile/beta_diversity_bc_genus.png b/...armgCAMI2_short_read_sample_0-9.tipp_4.3.10.profile/beta_diversity_bc_genus.png
diff --git a/.../by_tool/marmgCAMI2_short_read_sample_0-9.tipp_4.3.10.profile/beta_diversity_bc_order.pdf b/.../by_tool/marmgCAMI2_short_read_sample_0-9.tipp_4.3.10.profile/beta_diversity_bc_order.pdf
diff --git a/...armgCAMI2_short_read_sample_0-9.tipp_4.3.10.profile/beta_diversity_bc_order.png b/...armgCAMI2_short_read_sample_0-9.tipp_4.3.10.profile/beta_diversity_bc_order.png
diff --git a/...by_tool/marmgCAMI2_short_read_sample_0-9.tipp_4.3.10.profile/beta_diversity_bc_phylum.pdf b/...by_tool/marmgCAMI2_short_read_sample_0-9.tipp_4.3.10.profile/beta_diversity_bc_phylum.pdf
diff --git a/...rmgCAMI2_short_read_sample_0-9.tipp_4.3.10.profile/beta_diversity_bc_phylum.png b/...rmgCAMI2_short_read_sample_0-9.tipp_4.3.10.profile/beta_diversity_bc_phylum.png
diff --git a/...y_tool/marmgCAMI2_short_read_sample_0-9.tipp_4.3.10.profile/beta_diversity_bc_species.pdf b/...y_tool/marmgCAMI2_short_read_sample_0-9.tipp_4.3.10.profile/beta_diversity_bc_species.pdf
diff --git a/...mgCAMI2_short_read_sample_0-9.tipp_4.3.10.profile/beta_diversity_bc_species.png b/...mgCAMI2_short_read_sample_0-9.tipp_4.3.10.profile/beta_diversity_bc_species.png
diff --git a/...l/marmgCAMI2_short_read_sample_0-9.tipp_4.3.10.profile/beta_diversity_bc_superkingdom.pdf b/...l/marmgCAMI2_short_read_sample_0-9.tipp_4.3.10.profile/beta_diversity_bc_superkingdom.pdf
diff --git a/...I2_short_read_sample_0-9.tipp_4.3.10.profile/beta_diversity_bc_superkingdom.png b/...I2_short_read_sample_0-9.tipp_4.3.10.profile/beta_diversity_bc_superkingdom.png
diff --git a/...ool/marmgCAMI2_short_read_sample_0-9.tipp_4.3.10.profile/purity_completeness_per_rank.pdf b/...ool/marmgCAMI2_short_read_sample_0-9.tipp_4.3.10.profile/purity_completeness_per_rank.pdf
diff --git a/...AMI2_short_read_sample_0-9.tipp_4.3.10.profile/purity_completeness_per_rank.png b/...AMI2_short_read_sample_0-9.tipp_4.3.10.profile/purity_completeness_per_rank.png
diff --git a/rerun_opal/gold_standard/rarefaction_curves.pdf b/rerun_opal/gold_standard/rarefaction_curves.pdf
diff --git a/rerun_opal/gold_standard/rarefaction_curves.png b/rerun_opal/gold_standard/rarefaction_curves.png
diff --git a/rerun_opal/gold_standard/rarefaction_curves_log_scale.pdf b/rerun_opal/gold_standard/rarefaction_curves_log_scale.pdf
diff --git a/rerun_opal/gold_standard/rarefaction_curves_log_scale.png b/rerun_opal/gold_standard/rarefaction_curves_log_scale.png
diff --git a/rerun_opal/heatmap_bar.png b/rerun_opal/heatmap_bar.png
diff --git a/rerun_opal/log.txt b/rerun_opal/log.txt
@@ -0,0 +1,18 @@
+2023-11-03 18:10:19,470 INFO /home/jimshawster/mambaforge/bin/opal.py -g gs_marine_short.noplasmids.profile marmgCAMI2_short_read_sample_0-9.bracken_2.2.profile marmgCAMI2_short_read_sample_0-9.ccmetagen_1.1.3.profile marmgCAMI2_short_read_sample_0-9.centrifuge_1.0.4_beta.profile marmgCAMI2_short_read_sample_0-9.dudes_0.08.profile marmgCAMI2_short_read_sample_0-9.focus_1.5.profile marmgCAMI2_short_read_sample_0-9.LSHvec_1dfe822.profile marmgCAMI2_short_read_sample_0-9.metalign_0.6.2_default.profile marmgCAMI2_short_read_sample_0-9.metalign_0.6.2_precise.profile marmgCAMI2_short_read_sample_0-9.metapalette_1.0.0.profile marmgCAMI2_short_read_sample_0-9.metaphlan2_2.9.22.profile marmgCAMI2_short_read_sample_0-9.metaphyler_1.25.profile marmgCAMI2_short_read_sample_0-9.motus_2.5.1.profile marmgCAMI2_short_read_sample_0-9.tipp_4.3.10.profile -o rerun_opal
+2023-11-03 18:10:19,470 INFO Loading profiles...
+2023-11-03 18:10:20,209 INFO done
+2023-11-03 18:10:20,209 INFO Computing metrics...
+2023-11-03 18:11:54,812 INFO done
+2023-11-03 18:11:54,813 INFO Saving computed metrics...
+2023-11-03 18:11:55,136 INFO done
+2023-11-03 18:11:55,136 INFO Creating beta diversity plots...
+2023-11-03 18:12:18,943 INFO done
+2023-11-03 18:12:18,944 INFO Creating rarefaction curves...
+2023-11-03 18:12:19,575 INFO done
+2023-11-03 18:12:19,575 INFO Creating more plots...
+2023-11-03 18:12:28,764 INFO done
+2023-11-03 18:12:28,764 INFO Computing rankings...
+2023-11-03 18:12:29,262 INFO done
+2023-11-03 18:12:29,262 INFO Creating HTML page...
+2023-11-03 18:12:37,668 INFO done
+2023-11-03 18:12:37,668 INFO OPAL finished successfully. All results have been saved to /mnt/disks/1tb/cami/kmcp-manuscript-data-r2/3.figures/fig2-cami2-marine/rerun_opal
diff --git a/rerun_opal/plot_shannon.pdf b/rerun_opal/plot_shannon.pdf
diff --git a/rerun_opal/plot_shannon.png b/rerun_opal/plot_shannon.png
diff --git a/rerun_opal/plot_shannon_diff.pdf b/rerun_opal/plot_shannon_diff.pdf
diff --git a/rerun_opal/plot_shannon_diff.png b/rerun_opal/plot_shannon_diff.png
diff --git a/rerun_opal/results.html b/rerun_opal/results.html
diff --git a/rerun_opal/results.tsv b/rerun_opal/results.tsv
diff --git a/rerun_opal/spider_plot_absolute.pdf b/rerun_opal/spider_plot_absolute.pdf
diff --git a/rerun_opal/spider_plot_absolute.png b/rerun_opal/spider_plot_absolute.png
diff --git a/rerun_opal/spider_plot_relative.pdf b/rerun_opal/spider_plot_relative.pdf
diff --git a/rerun_opal/spider_plot_relative.png b/rerun_opal/spider_plot_relative.png
diff --git a/sylph_opal/by_rank/class.tsv b/sylph_opal/by_rank/class.tsv
@@ -0,0 +1,11 @@
+tool	sample	Sum of abundances	Weighted UniFrac error	Unweighted UniFrac error	L1 norm error	Completeness	Purity	F1 score	True positives	False positives	False negatives	Taxon counts	Jaccard index	Shannon diversity	Shannon equitability	Bray-Curtis distance
+sylph.profile	marmgCAMI2_short_read_sample_0	0.964527	0.010903953047618946	0.36183516115397124	0.056838999999999924	0.92	0.9583333333333334	0.9387755102040817	23.0	1.0	2.0	24.0	0.8846153846153846	1.699649493117513	0.5348082769672371	0.029548596183048517
+sylph.profile	marmgCAMI2_short_read_sample_1	0.9568490000000002	0.010003745333333368	0.2995216209806135	0.04710299999999989	0.9032258064516129	0.9333333333333333	0.9180327868852459	28.0	2.0	3.0	30.0	0.8484848484848485	1.8381406385101637	0.5404392724811136	0.02467263695977039
+sylph.profile	marmgCAMI2_short_read_sample_2	0.9688589999999998	0.009245576190476225	0.3353639863396895	0.03463299999999978	0.9285714285714286	0.9285714285714286	0.9285714285714286	26.0	2.0	2.0	28.0	0.8666666666666667	1.840279803039785	0.5522709657886589	0.01791477279487101
+sylph.profile	marmgCAMI2_short_read_sample_3	0.9658090000000003	0.010895430095238037	0.36421382744569464	0.05239099999999998	0.9354838709677419	0.9354838709677419	0.9354838709677419	29.0	2.0	2.0	31.0	0.8787878787878788	1.9404704467236091	0.565077949093448	0.02721131187806406
+sylph.profile	marmgCAMI2_short_read_sample_4	0.9764860000000002	0.011672512761904716	0.3584009754524677	0.06349600000000014	0.9629629629629629	0.9629629629629629	0.9629629629629629	26.0	1.0	1.0	27.0	0.9285714285714286	1.8991519627930435	0.5762275379531934	0.03263961640123254
+sylph.profile	marmgCAMI2_short_read_sample_5	0.968562	0.0122195338095238	0.341361243777129	0.05775799999999981	0.9310344827586207	0.9310344827586207	0.9310344827586207	27.0	2.0	2.0	29.0	0.8709677419354839	1.8895566050163097	0.5611495693931648	0.030091820743235263
+sylph.profile	marmgCAMI2_short_read_sample_6	0.9722749999999998	0.013912765714285694	0.38900349314162064	0.05937699999999993	0.9333333333333333	0.9333333333333333	0.9333333333333333	28.0	2.0	2.0	30.0	0.875	1.8228652572213382	0.5359480949413495	0.030998091886995826
+sylph.profile	marmgCAMI2_short_read_sample_7	0.9787009999999999	0.014075738095238101	0.3829796341646111	0.06870899999999992	0.9285714285714286	0.9629629629629629	0.9454545454545454	26.0	1.0	2.0	27.0	0.896551724137931	1.738398519134503	0.5274528412087431	0.03560215989234733
+sylph.profile	marmgCAMI2_short_read_sample_8	0.9711089999999999	0.010765023523809515	0.3801890812188627	0.04759100000000004	0.9333333333333333	0.9333333333333333	0.9333333333333333	28.0	2.0	2.0	30.0	0.875	1.6990523132061477	0.49954534316847726	0.024618254370178574
+sylph.profile	marmgCAMI2_short_read_sample_9	0.9751080000000001	0.014167886095238107	0.36343428458822324	0.0963460000000001	0.9310344827586207	0.9642857142857143	0.9473684210526316	27.0	1.0	2.0	28.0	0.9	1.7894050123053484	0.5370033582396369	0.049743964131228356
diff --git a/sylph_opal/by_rank/family.tsv b/sylph_opal/by_rank/family.tsv
@@ -0,0 +1,11 @@
+tool	sample	Sum of abundances	Weighted UniFrac error	Unweighted UniFrac error	L1 norm error	Completeness	Purity	F1 score	True positives	False positives	False negatives	Taxon counts	Jaccard index	Shannon diversity	Shannon equitability	Bray-Curtis distance
+sylph.profile	marmgCAMI2_short_read_sample_0	0.9556239999999999	0.010903953047618946	0.36183516115397124	0.12028000000000004	0.9357798165137615	0.9714285714285714	0.9532710280373832	102.0	3.0	7.0	105.0	0.9107142857142857	3.22497356746813	0.6929525231900555	0.06320001849551589
+sylph.profile	marmgCAMI2_short_read_sample_1	0.9549090000000007	0.010003745333333368	0.2995216209806135	0.07665299999999994	0.9401709401709402	0.9649122807017544	0.9523809523809523	110.0	4.0	7.0	114.0	0.9090909090909091	3.5771290944076264	0.7552743267377706	0.04027862363372004
+sylph.profile	marmgCAMI2_short_read_sample_2	0.9492160000000007	0.009245576190476225	0.3353639863396895	0.076676	0.9433962264150944	0.9615384615384616	0.9523809523809524	100.0	4.0	6.0	104.0	0.9090909090909091	3.354536317279872	0.7222769121135	0.04052180089376691
+sylph.profile	marmgCAMI2_short_read_sample_3	0.9405480000000003	0.010895430095238037	0.36421382744569464	0.10368199999999997	0.9583333333333334	0.9663865546218487	0.9623430962343097	115.0	4.0	5.0	119.0	0.9274193548387096	3.446420080673652	0.7211406203755161	0.05530213971628329
+sylph.profile	marmgCAMI2_short_read_sample_4	0.9390279999999998	0.011672512761904716	0.3584009754524677	0.11434600000000003	0.9405940594059405	0.95	0.9452736318407959	95.0	5.0	6.0	100.0	0.8962264150943396	3.2622336886476093	0.7083850448292738	0.06099240541979286
+sylph.profile	marmgCAMI2_short_read_sample_5	0.9591670000000004	0.0122195338095238	0.341361243777129	0.09982700000000007	0.9532710280373832	0.9532710280373832	0.9532710280373832	102.0	5.0	5.0	107.0	0.9107142857142857	3.34834618236741	0.7165565658372729	0.0521478529828288
+sylph.profile	marmgCAMI2_short_read_sample_6	0.9674250000000003	0.013912765714285694	0.38900349314162064	0.11942299999999996	0.9727272727272728	0.963963963963964	0.9683257918552037	107.0	4.0	3.0	111.0	0.9385964912280702	3.4274733816852447	0.7277739466943353	0.061824827154198396
+sylph.profile	marmgCAMI2_short_read_sample_7	0.9617490000000004	0.014075738095238101	0.3829796341646111	0.11989099999999998	0.9519230769230769	0.9705882352941176	0.9611650485436893	99.0	3.0	5.0	102.0	0.9252336448598131	3.3186794961759194	0.7175565414446771	0.06241562975538422
+sylph.profile	marmgCAMI2_short_read_sample_8	0.9687920000000001	0.010765023523809515	0.3801890812188627	0.103256	0.9568965517241379	0.9652173913043478	0.961038961038961	111.0	4.0	5.0	115.0	0.925	3.336628521565405	0.7031983664466798	0.053450612433365324
+sylph.profile	marmgCAMI2_short_read_sample_9	0.9675549999999999	0.014167886095238107	0.36343428458822324	0.13350099999999998	0.9489795918367347	0.9489795918367347	0.9489795918367347	93.0	5.0	5.0	98.0	0.9029126213592233	3.353915382211019	0.7315025456153287	0.06922045902931347
diff --git a/sylph_opal/by_rank/genus.tsv b/sylph_opal/by_rank/genus.tsv
@@ -0,0 +1,11 @@
+tool	sample	Sum of abundances	Weighted UniFrac error	Unweighted UniFrac error	L1 norm error	Completeness	Purity	F1 score	True positives	False positives	False negatives	Taxon counts	Jaccard index	Shannon diversity	Shannon equitability	Bray-Curtis distance
+sylph.profile	marmgCAMI2_short_read_sample_0	0.9955159999999985	0.010903953047618946	0.36183516115397124	0.11941000000000006	0.9226519337016574	0.9488636363636364	0.9355742296918768	167.0	9.0	14.0	176.0	0.8789473684210526	3.7282620104209454	0.7210663477536663	0.06043915440860127
+sylph.profile	marmgCAMI2_short_read_sample_1	0.9967020000000006	0.010003745333333368	0.2995216209806135	0.106304	0.9261083743842364	0.9591836734693877	0.9423558897243107	188.0	8.0	15.0	196.0	0.8909952606635071	4.154312926817719	0.7870827359827317	0.053618156250441355
+sylph.profile	marmgCAMI2_short_read_sample_2	0.9961570000000005	0.009245576190476225	0.3353639863396895	0.08807700000000002	0.9438775510204082	0.9487179487179487	0.9462915601023018	185.0	10.0	11.0	195.0	0.8980582524271845	3.9773586050909087	0.7542876802694549	0.04455428265313401
+sylph.profile	marmgCAMI2_short_read_sample_3	0.9913029999999999	0.010895430095238037	0.36421382744569464	0.11504299999999992	0.9353448275862069	0.9475982532751092	0.9414316702819957	217.0	12.0	15.0	229.0	0.889344262295082	4.158050475851228	0.7652306233427869	0.05848584383609139
+sylph.profile	marmgCAMI2_short_read_sample_4	0.9913179999999993	0.011672512761904716	0.3584009754524677	0.11475200000000005	0.9243243243243243	0.9447513812154696	0.9344262295081968	171.0	10.0	14.0	181.0	0.8769230769230769	3.9028095315015	0.7507572877369081	0.05815327669632306
+sylph.profile	marmgCAMI2_short_read_sample_5	0.9955710000000008	0.0122195338095238	0.341361243777129	0.11273300000000008	0.9439252336448598	0.9619047619047619	0.9528301886792454	202.0	8.0	12.0	210.0	0.9099099099099099	4.0079343198240895	0.7495518458904659	0.056789839861245674
+sylph.profile	marmgCAMI2_short_read_sample_6	0.996096	0.013912765714285694	0.38900349314162064	0.13968599999999998	0.9476190476190476	0.9754901960784313	0.961352657004831	199.0	5.0	11.0	204.0	0.9255813953488372	4.050581283426682	0.7616566170216685	0.07034646968352497
+sylph.profile	marmgCAMI2_short_read_sample_7	0.9923819999999995	0.014075738095238101	0.3829796341646111	0.1446619999999999	0.9421052631578948	0.9623655913978495	0.9521276595744681	179.0	7.0	11.0	186.0	0.9086294416243654	3.8746737515546226	0.7414583969493183	0.07323130567193073
+sylph.profile	marmgCAMI2_short_read_sample_8	0.9928499999999998	0.010765023523809515	0.3801890812188627	0.10682400000000007	0.9444444444444444	0.9488372093023256	0.9466357308584686	204.0	11.0	12.0	215.0	0.8986784140969163	3.8963904242821323	0.7254986100116135	0.054219876154705096
+sylph.profile	marmgCAMI2_short_read_sample_9	0.9902860000000004	0.014167886095238107	0.36343428458822324	0.14709600000000003	0.9388888888888889	0.9388888888888889	0.9388888888888889	169.0	11.0	11.0	180.0	0.8848167539267016	3.9301781645096674	0.7568285809723088	0.07479422131555986
diff --git a/sylph_opal/by_rank/order.tsv b/sylph_opal/by_rank/order.tsv
@@ -0,0 +1,11 @@
+tool	sample	Sum of abundances	Weighted UniFrac error	Unweighted UniFrac error	L1 norm error	Completeness	Purity	F1 score	True positives	False positives	False negatives	Taxon counts	Jaccard index	Shannon diversity	Shannon equitability	Bray-Curtis distance
+sylph.profile	marmgCAMI2_short_read_sample_0	0.9612600000000002	0.010903953047618946	0.36183516115397124	0.09064600000000002	0.9402985074626866	0.984375	0.9618320610687023	63.0	1.0	4.0	64.0	0.9264705882352942	2.8274373248511178	0.6798549678311775	0.04731125551293094
+sylph.profile	marmgCAMI2_short_read_sample_1	0.9613740000000002	0.010003745333333368	0.2995216209806135	0.07012800000000001	0.9166666666666666	0.9565217391304348	0.9361702127659574	66.0	3.0	6.0	69.0	0.88	3.068760307096111	0.7247716380691293	0.036605761461223824
+sylph.profile	marmgCAMI2_short_read_sample_2	0.9570910000000009	0.009245576190476225	0.3353639863396895	0.06164500000000003	0.9558823529411765	0.9848484848484849	0.9701492537313432	65.0	1.0	3.0	66.0	0.9420289855072463	2.933049627398927	0.7000695303069981	0.03227552813905625
+sylph.profile	marmgCAMI2_short_read_sample_3	0.9525040000000007	0.010895430095238037	0.36421382744569464	0.08760800000000002	0.9324324324324325	0.9583333333333334	0.9452054794520548	69.0	3.0	5.0	72.0	0.8961038961038961	3.057817415400941	0.7150002666339691	0.04608924293231286
+sylph.profile	marmgCAMI2_short_read_sample_4	0.9612369999999999	0.011672512761904716	0.3584009754524677	0.0906210000000001	0.90625	0.9830508474576272	0.943089430894309	58.0	1.0	6.0	59.0	0.8923076923076924	2.9600483953541468	0.7259402117271124	0.047180327134844637
+sylph.profile	marmgCAMI2_short_read_sample_5	0.968798	0.0122195338095238	0.341361243777129	0.10098399999999998	0.9242424242424242	0.953125	0.9384615384615383	61.0	3.0	5.0	64.0	0.8840579710144928	2.9651406213151668	0.7129656116516352	0.05221218256684734
+sylph.profile	marmgCAMI2_short_read_sample_6	0.9756820000000002	0.013912765714285694	0.38900349314162064	0.10543600000000004	0.9571428571428572	0.9571428571428572	0.9571428571428572	67.0	3.0	3.0	70.0	0.9178082191780822	3.0047136770116847	0.7072418599584666	0.054108812927488176
+sylph.profile	marmgCAMI2_short_read_sample_7	0.9730539999999998	0.014075738095238101	0.3829796341646111	0.11113	0.9545454545454546	0.9692307692307692	0.9618320610687022	63.0	2.0	3.0	65.0	0.9264705882352942	2.925434624619603	0.7008057555457093	0.05713289812319485
+sylph.profile	marmgCAMI2_short_read_sample_8	0.975194	0.010765023523809515	0.3801890812188627	0.090276	0.9305555555555556	0.9571428571428572	0.943661971830986	67.0	3.0	5.0	70.0	0.8933333333333333	2.8876637170136807	0.6796909382016277	0.0463761504651177
+sylph.profile	marmgCAMI2_short_read_sample_9	0.9795439999999997	0.014167886095238107	0.36343428458822324	0.11792599999999992	0.9193548387096774	0.9661016949152542	0.9421487603305785	57.0	2.0	5.0	59.0	0.890625	2.963824602719845	0.7268663117121271	0.0603543488029545
diff --git a/sylph_opal/by_rank/phylum.tsv b/sylph_opal/by_rank/phylum.tsv
@@ -0,0 +1,11 @@
+tool	sample	Sum of abundances	Weighted UniFrac error	Unweighted UniFrac error	L1 norm error	Completeness	Purity	F1 score	True positives	False positives	False negatives	Taxon counts	Jaccard index	Shannon diversity	Shannon equitability	Bray-Curtis distance
+sylph.profile	marmgCAMI2_short_read_sample_0	1.0000109999999987	0.010903953047618946	0.36183516115397124	0.05586299999999894	0.8823529411764706	1.0	0.9375	15.0	0.0	2.0	15.0	0.8823529411764706	1.2043493063624582	0.4447293133163754	0.027943361957150296
+sylph.profile	marmgCAMI2_short_read_sample_1	0.9999970000000006	0.010003745333333368	0.2995216209806135	0.04737900000000025	0.9047619047619048	1.0	0.9500000000000001	19.0	0.0	2.0	19.0	0.9047619047619048	1.2905426507693833	0.4382983175744845	0.023693563446131133
+sylph.profile	marmgCAMI2_short_read_sample_2	0.999997	0.009245576190476225	0.3353639863396895	0.03574900000000016	0.8636363636363636	1.0	0.9268292682926829	19.0	0.0	3.0	19.0	0.8636363636363636	1.267147349719388	0.430352728884914	0.01787443743946904
+sylph.profile	marmgCAMI2_short_read_sample_3	1.0000010000000001	0.010895430095238037	0.36421382744569464	0.05834700000000012	0.9090909090909091	1.0	0.9523809523809523	20.0	0.0	2.0	20.0	0.9090909090909091	1.280778435921671	0.4275343451843972	0.029173193681466394
+sylph.profile	marmgCAMI2_short_read_sample_4	0.9999999999999996	0.011672512761904716	0.3584009754524677	0.06787599999999987	0.9444444444444444	1.0	0.9714285714285714	17.0	0.0	1.0	17.0	0.9444444444444444	1.1956607818808018	0.42201579502975745	0.03393799999999994
+sylph.profile	marmgCAMI2_short_read_sample_5	1.0000029999999998	0.0122195338095238	0.341361243777129	0.0715410000000001	0.9	1.0	0.9473684210526316	18.0	0.0	2.0	18.0	0.9	1.2048577075742029	0.41685215899396666	0.03577062519718824
+sylph.profile	marmgCAMI2_short_read_sample_6	0.9999959999999994	0.013912765714285694	0.38900349314162064	0.08586199999999967	0.8636363636363636	1.0	0.9268292682926829	19.0	0.0	3.0	19.0	0.8636363636363636	1.1911641331918286	0.4045470602787098	0.04293087120738623
+sylph.profile	marmgCAMI2_short_read_sample_7	1.0000010000000004	0.014075738095238101	0.3829796341646111	0.0944570000000006	0.9	1.0	0.9473684210526316	18.0	0.0	2.0	18.0	0.9	1.1217010014669206	0.38808191313195683	0.047228712529206664
+sylph.profile	marmgCAMI2_short_read_sample_8	1.0000059999999995	0.010765023523809515	0.3801890812188627	0.05327399999999974	0.8695652173913043	1.0	0.9302325581395349	20.0	0.0	3.0	20.0	0.8695652173913043	1.1531030253867542	0.38491524612069855	0.026637053274106426
+sylph.profile	marmgCAMI2_short_read_sample_9	0.9999990000000006	0.014167886095238107	0.36343428458822324	0.10525300000000071	0.9047619047619048	1.0	0.9500000000000001	19.0	0.0	2.0	19.0	0.9047619047619048	1.161804319902714	0.3945757844272312	0.05262652631326349
diff --git a/sylph_opal/by_rank/species.tsv b/sylph_opal/by_rank/species.tsv
@@ -0,0 +1,11 @@
+tool	sample	Sum of abundances	Weighted UniFrac error	Unweighted UniFrac error	L1 norm error	Completeness	Purity	F1 score	True positives	False positives	False negatives	Taxon counts	Jaccard index	Shannon diversity	Shannon equitability	Bray-Curtis distance
+sylph.profile	marmgCAMI2_short_read_sample_0	1.0000109999999984	0.010903953047618946	0.36183516115397124	0.24874499999999997	0.9140625	0.8666666666666667	0.8897338403041826	234.0	36.0	22.0	270.0	0.8013698630136986	4.272292629098523	0.7631244412064444	0.13138650275639896
+sylph.profile	marmgCAMI2_short_read_sample_1	0.9999970000000016	0.010003745333333368	0.2995216209806135	0.19277900000000003	0.92	0.8903225806451613	0.9049180327868852	276.0	34.0	24.0	310.0	0.8263473053892215	4.71230496035125	0.821449589752746	0.10112323008513006
+sylph.profile	marmgCAMI2_short_read_sample_2	0.9999970000000001	0.009245576190476225	0.3353639863396895	0.19543700000000008	0.9306569343065694	0.8614864864864865	0.8947368421052633	255.0	41.0	19.0	296.0	0.8095238095238095	4.5025557088832375	0.7912603316231245	0.10304070708183753
+sylph.profile	marmgCAMI2_short_read_sample_3	1.0000009999999986	0.010895430095238037	0.36421382744569464	0.22324299999999983	0.9133858267716536	0.8765743073047859	0.8946015424164525	348.0	49.0	33.0	397.0	0.8093023255813954	4.737638645682766	0.79172611863753	0.11894234165787117
+sylph.profile	marmgCAMI2_short_read_sample_4	0.9999999999999999	0.011672512761904716	0.3584009754524677	0.254078	0.9133574007220217	0.8605442176870748	0.8861646234676007	253.0	41.0	24.0	294.0	0.7955974842767296	4.404113727351743	0.7748837717841964	0.13792695372722732
+sylph.profile	marmgCAMI2_short_read_sample_5	1.0000030000000006	0.0122195338095238	0.341361243777129	0.2579989999999997	0.9365558912386707	0.8985507246376812	0.9171597633136095	310.0	35.0	21.0	345.0	0.8469945355191257	4.472792004698084	0.7654244899143512	0.13883655591448713
+sylph.profile	marmgCAMI2_short_read_sample_6	0.9999959999999996	0.013912765714285694	0.38900349314162064	0.28937999999999986	0.9202453987730062	0.8797653958944281	0.8995502248875561	300.0	41.0	26.0	341.0	0.8174386920980926	4.598102549772598	0.7884422513113447	0.15427461927147915
+sylph.profile	marmgCAMI2_short_read_sample_7	1.0000009999999997	0.014075738095238101	0.3829796341646111	0.25606899999999977	0.9219858156028369	0.8783783783783784	0.8996539792387545	260.0	36.0	22.0	296.0	0.8176100628930818	4.427458052756383	0.7780629832429992	0.13708330009780614
+sylph.profile	marmgCAMI2_short_read_sample_8	1.0000059999999993	0.010765023523809515	0.3801890812188627	0.2235680000000001	0.9130434782608695	0.8848314606741573	0.8987161198288159	315.0	41.0	30.0	356.0	0.8160621761658031	4.44804006691153	0.7571221297219345	0.11937658986883783
+sylph.profile	marmgCAMI2_short_read_sample_9	0.999999	0.014167886095238107	0.36343428458822324	0.29776099999999966	0.922509225092251	0.8741258741258742	0.8976660682226213	250.0	36.0	21.0	286.0	0.8143322475570033	4.51593826542751	0.7984343712783616	0.16375709519119136