generated: '2026-10-24T14:30:08' study: yc_taphrinomycotina script: path: /bigdata/stajichlab/jstajich/projects/NovInvenio_Investigations/studies/fungi/zoosporic_dikarya/analysis/enrichment/enrich_novelties_v2.py sha256: d1e8fe16f6842e86fb6c226f822c8c173450a8fec660ca6879a6f8a821ad5aa7 command: /bigdata/stajichlab/jstajich/projects/NovInvenio_Investigations/.pixi/envs/default/bin/python3 /bigdata/stajichlab/jstajich/projects/NovInvenio_Investigations/studies/fungi/zoosporic_dikarya/analysis/enrichment/enrich_novelties_v2.py --results /bigdata/stajichlab/jstajich/projects/NovInvenio_Investigations/results/yc_taphrinomycotina --config /bigdata/stajichlab/jstajich/projects/NovInvenio_Investigations/studies/fungi/yeast_convergence/yc_taphrinomycotina/config.csv --annotations /bigdata/stajichlab/jstajich/projects/NovInvenio_Investigations/studies/fungi/yeast_convergence/yc_taphrinomycotina/annotations --study yc_taphrinomycotina --cache-dir /bigdata/stajichlab/jstajich/projects/NovInvenio_Investigations/studies/fungi/yeast_convergence/yc_taphrinomycotina/analysis/enrichment/outputs/cache --threads 4 --pfam-dat /srv/projects/db/pfam/2026-01-27-Pfam38.2/Pfam-A.hmm.dat --interpro-entries /srv/projects/db/interproscan/6.0.0/110.0/interpro/110.0/entries.json --controls /bigdata/stajichlab/jstajich/projects/NovInvenio_Investigations/studies/fungi/zoosporic_dikarya/analysis/enrichment/actin_controls.tsv --ingroup-min-frac 0.75 --universe proteome --cluster-background --direction loss --other-max-frac 0.0 --out-dir /bigdata/stajichlab/jstajich/projects/NovInvenio_Investigations/studies/fungi/yeast_convergence/yc_taphrinomycotina/analysis/enrichment/outputs/loss/proteome_clustered class: ephemeral analysis output (not tracked; regenerate with the command above) direction: loss target_group: label: OUT species: - Nirr - Amega - Ncra other_group: label: IN species: - Spom - Schiocto - Schijapo - Saitcomp - Taphdefo - Protinou universe: proteome annotations: /bigdata/stajichlab/jstajich/projects/NovInvenio_Investigations/studies/fungi/yeast_convergence/yc_taphrinomycotina/annotations annotation_files: Nirr: /bigdata/stajichlab/jstajich/projects/NovInvenio_Investigations/studies/fungi/yeast_convergence/yc_taphrinomycotina/annotations/UP000186594.tsv.gz Amega: /bigdata/stajichlab/jstajich/projects/NovInvenio_Investigations/studies/fungi/yeast_convergence/yc_taphrinomycotina/annotations/UP001658139.tsv.gz Ncra: /bigdata/stajichlab/jstajich/projects/NovInvenio_Investigations/studies/fungi/yeast_convergence/yc_taphrinomycotina/annotations/UP000001805.tsv.gz Spom: /bigdata/stajichlab/jstajich/projects/NovInvenio_Investigations/studies/fungi/yeast_convergence/yc_taphrinomycotina/annotations/UP000002485.tsv.gz Schiocto: /bigdata/stajichlab/jstajich/projects/NovInvenio_Investigations/studies/fungi/yeast_convergence/yc_taphrinomycotina/annotations/UP000016088.tsv.gz Schijapo: /bigdata/stajichlab/jstajich/projects/NovInvenio_Investigations/studies/fungi/yeast_convergence/yc_taphrinomycotina/annotations/UP000001744.tsv.gz Saitcomp: /bigdata/stajichlab/jstajich/projects/NovInvenio_Investigations/studies/fungi/yeast_convergence/yc_taphrinomycotina/annotations/UP000033140.tsv.gz Taphdefo: /bigdata/stajichlab/jstajich/projects/NovInvenio_Investigations/studies/fungi/yeast_convergence/yc_taphrinomycotina/annotations/UP000013776.tsv.gz Protinou: /bigdata/stajichlab/jstajich/projects/NovInvenio_Investigations/studies/fungi/yeast_convergence/yc_taphrinomycotina/annotations/Protomyces_inouyei_NRRL_YB-4354.proteins.tsv.gz annotation_sources: Nirr: not recorded (no sidecar) Amega: not recorded (no sidecar) Ncra: not recorded (no sidecar) Spom: not recorded (no sidecar) Schiocto: not recorded (no sidecar) Schijapo: not recorded (no sidecar) Saitcomp: not recorded (no sidecar) Taphdefo: not recorded (no sidecar) Protinou: Pfam-A HMM search (hmmsearch); Pfam only vocabulary_coverage: pfam: species_with_terms: - Nirr - Amega - Ncra species_without_terms: [] n_with: 3 n_species: 3 pfam_clan: species_with_terms: - Nirr - Amega - Ncra species_without_terms: [] n_with: 3 n_species: 3 interpro: species_with_terms: - Nirr - Amega - Ncra species_without_terms: [] n_with: 3 n_species: 3 go: species_with_terms: - Nirr - Ncra species_without_terms: - Amega n_with: 2 n_species: 3 parameters: min_bg: 5 exclude_iea: false report_ids_fdr: 0.05 ingroup_min_frac: 0.75 other_max_frac: 0.0 cluster_background: true statistics: one-sided hypergeometric scipy.stats.hypergeom.sf(k-1,M,n,N); BH (lib/stats_util.bh_fdr) within scope x level x vocabulary; scope-B fdr_bh_all_species = BH across species tests of one level x vocabulary. goatools only parses the OBO and gives is_a ancestors. candidate_check: matrix_in_rule_and_0_out: 174 candidates_txt: 174 symmetric_difference: 0 candidates_file: /bigdata/stajichlab/jstajich/projects/NovInvenio_Investigations/results/yc_taphrinomycotina/loss_candidates.txt presence_matrix: /bigdata/stajichlab/jstajich/projects/NovInvenio_Investigations/results/yc_taphrinomycotina/loss_presence_matrix.tsv rule: OUT count / 3 >= 0.75 and IN count / 6 <= 0.0 (own proteome counts toward the target group) only_in_matrix_rule: [] only_in_candidates_file: [] background_clustering: key: 3df251977c88cf28 n_sequences: 26974 n_clusters: 19854 mmseqs: /bigdata/stajichlab/jstajich/projects/NovInvenio_Investigations/.pixi/envs/default/bin/mmseqs mmseqs_version: 18.8cc5c command: mmseqs easy-cluster --threads N --min-seq-id 0.3 -c 0.8 --cov-mode 0 runtime_s: 62.1 threads: 4 created: '2026-10-24T14:30:04' cache_hit: false pipeline_candidate_families: '/bigdata/stajichlab/jstajich/projects/NovInvenio_Investigations/results/yc_taphrinomycotina/clusters/loss_clusters_cluster.tsv (nf_NovInvenio MMSEQS_CLUSTER: mmseqs easy-cluster --min-seq-id 0.3 -c 0.8 --cov-mode 0 on loss_candidates.fa)' candidates_without_family_row: 0 go_obo: path: /bigdata/stajichlab/jstajich/projects/NovInvenio_Investigations/data/go/go-basic.obo data_version: releases/2026-07-26 sha256: b08d45b268b8c24ccb2513dbbbc7d4df9f6521c099b413f79eb31e06e0fa3bcc pfam_dat: path: /srv/projects/db/pfam/2026-01-27-Pfam38.2/Pfam-A.hmm.dat sha256: ead9a40cdb871e1e6ceb151ea15c7aeaff083add2558031b4811afb9d7496b2d release_note: release taken from directory name; the .dat file has no version line interpro_entries: /srv/projects/db/interproscan/6.0.0/110.0/interpro/110.0/entries.json inputs_sha256: ? /bigdata/stajichlab/jstajich/projects/NovInvenio_Investigations/studies/fungi/yeast_convergence/yc_taphrinomycotina/config.csv : 1c052e1abd02e511c3bf2628a29ccc21718fe4fab28564b02b56ee175c12ed23 /bigdata/stajichlab/jstajich/projects/NovInvenio_Investigations/results/yc_taphrinomycotina/loss_candidates.txt: 01c2d453847ca3788fa82bb5ff99258394ed4f79f6a0a6479473c26ca2236a6a ? /bigdata/stajichlab/jstajich/projects/NovInvenio_Investigations/results/yc_taphrinomycotina/clusters/loss_clusters_cluster.tsv : 891270048938a22e3d8c1e6b1661046fd23887622f4d24f6842c741d1771768d /bigdata/stajichlab/jstajich/projects/NovInvenio_Investigations/results/yc_taphrinomycotina/loss_presence_matrix.tsv: 1fb18b6fa0663d7ba319318884960464572b5225c7e191bfccb7dce8bd90c5fb ? /bigdata/stajichlab/jstajich/projects/NovInvenio_Investigations/studies/fungi/yeast_convergence/yc_taphrinomycotina/data_dir/pep/UP000186594_1198029.pep.fa : 7517c626df1b99b5a688e5151f3c7fe5a66b45db510a8adf61b57a8600133f0e ? /bigdata/stajichlab/jstajich/projects/NovInvenio_Investigations/studies/fungi/yeast_convergence/yc_taphrinomycotina/data_dir/pep/UP001658139_2528406.pep.fa : 2f3e3fabaa24307b063911f3ad1f01c2d9b49d0602fc56e31679894476facde4 ? /bigdata/stajichlab/jstajich/projects/NovInvenio_Investigations/studies/fungi/yeast_convergence/yc_taphrinomycotina/data_dir/pep/UP000001805_367110.pep.fa : 6c3a6d498fb30b129e2ab084f95789b3c510164f34661a5c85acb6a14e5f3dde ? /bigdata/stajichlab/jstajich/projects/NovInvenio_Investigations/studies/fungi/yeast_convergence/yc_taphrinomycotina/species.csv : 4c778b62e3ed6bb8a73df615366bcedb13b39705107c4e0849c2d0f0591fc108 ? /bigdata/stajichlab/jstajich/projects/NovInvenio_Investigations/studies/fungi/yeast_convergence/yc_taphrinomycotina/annotations/UP000186594.tsv.gz : 8e4b602b8dfc7c96e2679d70c92d4f8720bfa9380bb2aac6ecda0d2b5b2ab0bc ? /bigdata/stajichlab/jstajich/projects/NovInvenio_Investigations/studies/fungi/yeast_convergence/yc_taphrinomycotina/annotations/UP001658139.tsv.gz : f0960624740d07e6e2197b0d08b62dee72b3cb63fbbe2353d0f2375350d69a02 ? /bigdata/stajichlab/jstajich/projects/NovInvenio_Investigations/studies/fungi/yeast_convergence/yc_taphrinomycotina/annotations/UP000001805.tsv.gz : a1f3d317c188519a6f6b199e85b0099d384ed7ec3601e1a620cabc831356e920 ? /bigdata/stajichlab/jstajich/projects/NovInvenio_Investigations/studies/fungi/yeast_convergence/yc_taphrinomycotina/annotations/UP000002485.tsv.gz : 63b0e656b692fc431786bf3175391ab5ab41380a00319fd378f3933accdd3154 ? /bigdata/stajichlab/jstajich/projects/NovInvenio_Investigations/studies/fungi/yeast_convergence/yc_taphrinomycotina/annotations/UP000016088.tsv.gz : 51bdd4fca20412dd789920f4bc8bff2ba663fe854c6e48efb887dc24c64c89de ? /bigdata/stajichlab/jstajich/projects/NovInvenio_Investigations/studies/fungi/yeast_convergence/yc_taphrinomycotina/annotations/UP000001744.tsv.gz : 4b097ec1594d6aed4eb7601482782e5d53f891d92bc0999bb3ca7435ab5eb0ec ? /bigdata/stajichlab/jstajich/projects/NovInvenio_Investigations/studies/fungi/yeast_convergence/yc_taphrinomycotina/annotations/UP000033140.tsv.gz : 5925fc1c8bb9a3acd13d5ea3298f70480aea1fab7fbd4eba323e531a69b16f8c ? /bigdata/stajichlab/jstajich/projects/NovInvenio_Investigations/studies/fungi/yeast_convergence/yc_taphrinomycotina/annotations/UP000013776.tsv.gz : d762d02130351381ea75e9a082ac243ba61280a6d97c02fd01592305c3e12d32 ? /bigdata/stajichlab/jstajich/projects/NovInvenio_Investigations/studies/fungi/yeast_convergence/yc_taphrinomycotina/annotations/Protomyces_inouyei_NRRL_YB-4354.proteins.tsv.gz : e94a842ec3f1b4d62e8ed8e506fb47689c27e6e38ac06f6104a0a25a9d0d91a5 ? /bigdata/stajichlab/jstajich/projects/NovInvenio_Investigations/studies/fungi/yeast_convergence/yc_taphrinomycotina/annotations/Protomyces_inouyei_NRRL_YB-4354.proteins.tsv.gz.provenance.yaml : 44d7e3fb5f2f20ee9e6182a1ef079fd9f8e819c5c89071f05e958d515617e5d5 ? /bigdata/stajichlab/jstajich/projects/NovInvenio_Investigations/studies/fungi/zoosporic_dikarya/analysis/enrichment/actin_controls.tsv : dd7c85c91f413f3eee48b75b51c1ad75f7e2de6afcb611c5e0b3659f777a23d1 tools: python: 3.12.14 scipy: 1.18.1 goatools: 1.6.4 mmseqs: 18.8cc5c runtimes_s: load_s: 3.3 background_cluster_s: 62.5 tests_s: 3.1 total_s: 70.2 host: r11 slurm_job: '30452604'