generated: '2026-10-24T14:57:38' study: yc_rev_eremothecium 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_rev_eremothecium --config /bigdata/stajichlab/jstajich/projects/NovInvenio_Investigations/studies/fungi/yeast_convergence/yc_rev_eremothecium/config.csv --annotations /bigdata/stajichlab/jstajich/projects/NovInvenio_Investigations/studies/fungi/yeast_convergence/yc_rev_eremothecium/annotations --study yc_rev_eremothecium --cache-dir /bigdata/stajichlab/jstajich/projects/NovInvenio_Investigations/studies/fungi/yeast_convergence/yc_rev_eremothecium/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_rev_eremothecium/analysis/enrichment/outputs/loss/proteome_clustered class: ephemeral analysis output (not tracked; regenerate with the command above) direction: loss target_group: label: OUT species: - Kluylact - Lachther - Torudelb - Scer other_group: label: IN species: - Eremgoss - Eremcymb - Eremsine universe: proteome annotations: /bigdata/stajichlab/jstajich/projects/NovInvenio_Investigations/studies/fungi/yeast_convergence/yc_rev_eremothecium/annotations annotation_files: Kluylact: /bigdata/stajichlab/jstajich/projects/NovInvenio_Investigations/studies/fungi/yeast_convergence/yc_rev_eremothecium/annotations/UP000000598.tsv.gz Lachther: /bigdata/stajichlab/jstajich/projects/NovInvenio_Investigations/studies/fungi/yeast_convergence/yc_rev_eremothecium/annotations/UP000002036.tsv.gz Torudelb: /bigdata/stajichlab/jstajich/projects/NovInvenio_Investigations/studies/fungi/yeast_convergence/yc_rev_eremothecium/annotations/UP000005627.tsv.gz Scer: /bigdata/stajichlab/jstajich/projects/NovInvenio_Investigations/studies/fungi/yeast_convergence/yc_rev_eremothecium/annotations/UP000002311.tsv.gz Eremgoss: /bigdata/stajichlab/jstajich/projects/NovInvenio_Investigations/studies/fungi/yeast_convergence/yc_rev_eremothecium/annotations/UP000000591.tsv.gz Eremcymb: /bigdata/stajichlab/jstajich/projects/NovInvenio_Investigations/studies/fungi/yeast_convergence/yc_rev_eremothecium/annotations/UP000006790.tsv.gz Eremsine: /bigdata/stajichlab/jstajich/projects/NovInvenio_Investigations/studies/fungi/yeast_convergence/yc_rev_eremothecium/annotations/UP000243052.tsv.gz annotation_sources: Kluylact: not recorded (no sidecar) Lachther: not recorded (no sidecar) Torudelb: not recorded (no sidecar) Scer: not recorded (no sidecar) Eremgoss: not recorded (no sidecar) Eremcymb: not recorded (no sidecar) Eremsine: not recorded (no sidecar) vocabulary_coverage: pfam: species_with_terms: - Kluylact - Lachther - Torudelb - Scer species_without_terms: [] n_with: 4 n_species: 4 pfam_clan: species_with_terms: - Kluylact - Lachther - Torudelb - Scer species_without_terms: [] n_with: 4 n_species: 4 interpro: species_with_terms: - Kluylact - Lachther - Torudelb - Scer species_without_terms: [] n_with: 4 n_species: 4 go: species_with_terms: - Kluylact - Lachther - Torudelb - Scer species_without_terms: [] n_with: 4 n_species: 4 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: 716 candidates_txt: 716 symmetric_difference: 0 candidates_file: /bigdata/stajichlab/jstajich/projects/NovInvenio_Investigations/results/yc_rev_eremothecium/loss_candidates.txt presence_matrix: /bigdata/stajichlab/jstajich/projects/NovInvenio_Investigations/results/yc_rev_eremothecium/loss_presence_matrix.tsv rule: OUT count / 4 >= 0.75 and IN count / 3 <= 0.0 (own proteome counts toward the target group) only_in_matrix_rule: [] only_in_candidates_file: [] background_clustering: key: bc0c9b6549fe9d91 n_sequences: 20488 n_clusters: 7005 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: 29.4 threads: 4 created: '2026-10-24T14:57:32' cache_hit: false pipeline_candidate_families: '/bigdata/stajichlab/jstajich/projects/NovInvenio_Investigations/results/yc_rev_eremothecium/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_rev_eremothecium/config.csv : 09a73ac572da099f076eef129c6bd33673646f536aee3d66ea89138cf94f1c73 /bigdata/stajichlab/jstajich/projects/NovInvenio_Investigations/results/yc_rev_eremothecium/loss_candidates.txt: 03323ec066afb4f3ab43c3df12d911c148a954d1edec19bdc6675d23898d52d9 ? /bigdata/stajichlab/jstajich/projects/NovInvenio_Investigations/results/yc_rev_eremothecium/clusters/loss_clusters_cluster.tsv : 430c07c31184e2cf13ab0fa4b1e0dcf4f810d5ba195404e9bf70302c5f88ed9d /bigdata/stajichlab/jstajich/projects/NovInvenio_Investigations/results/yc_rev_eremothecium/loss_presence_matrix.tsv: ffd849cdc8b1842c77725e21a25d94cda449a90b64cb8965cc1a52c3977f8375 ? /bigdata/stajichlab/jstajich/projects/NovInvenio_Investigations/studies/fungi/yeast_convergence/yc_rev_eremothecium/data_dir/pep/UP000000598_284590.pep.fa : d90b1665b282db52cec6656b69c3facf6d35464f98a666e2f0004bd29bc5e5b9 ? /bigdata/stajichlab/jstajich/projects/NovInvenio_Investigations/studies/fungi/yeast_convergence/yc_rev_eremothecium/data_dir/pep/UP000002036_559295.pep.fa : 2c116f665af04fb7858d711f3ab4b0ec3bac6532e97e61b20be9018f41712427 ? /bigdata/stajichlab/jstajich/projects/NovInvenio_Investigations/studies/fungi/yeast_convergence/yc_rev_eremothecium/data_dir/pep/UP000005627_1076872.pep.fa : df804cb98350944d51afc62cf45353cef5e83d1af7b75de24472905fe7c31a68 ? /bigdata/stajichlab/jstajich/projects/NovInvenio_Investigations/studies/fungi/yeast_convergence/yc_rev_eremothecium/data_dir/pep/UP000002311_559292.pep.fa : 8ca7d8ccfd337f039527d136c3d10ec9c81be3aae33578cadef3abf2093792cb ? /bigdata/stajichlab/jstajich/projects/NovInvenio_Investigations/studies/fungi/yeast_convergence/yc_rev_eremothecium/species.csv : 7bc3c250ccb58501953ffd4ce3f48ed07caa416c9ccd8582030111501914c00f ? /bigdata/stajichlab/jstajich/projects/NovInvenio_Investigations/studies/fungi/yeast_convergence/yc_rev_eremothecium/annotations/UP000000598.tsv.gz : 2d9dd1b5b8bc031eb256c8c5a4606513367fb68594af22ac0b6c481c73ce6860 ? /bigdata/stajichlab/jstajich/projects/NovInvenio_Investigations/studies/fungi/yeast_convergence/yc_rev_eremothecium/annotations/UP000002036.tsv.gz : 2d6b71ac9748c00fb4a236986ec21eaf31430733ca9f0db4193c68e0b568586e ? /bigdata/stajichlab/jstajich/projects/NovInvenio_Investigations/studies/fungi/yeast_convergence/yc_rev_eremothecium/annotations/UP000005627.tsv.gz : 125d08fc0e7decdc85807580f1d221ce2c015da8dd36bdd9c64178382eb1c639 ? /bigdata/stajichlab/jstajich/projects/NovInvenio_Investigations/studies/fungi/yeast_convergence/yc_rev_eremothecium/annotations/UP000002311.tsv.gz : 83a0c1436d2357898e74c648a772b30ee1cb962e7cca7b975394bde1bb61d690 ? /bigdata/stajichlab/jstajich/projects/NovInvenio_Investigations/studies/fungi/yeast_convergence/yc_rev_eremothecium/annotations/UP000000591.tsv.gz : 27e5e67968a888e408ec7aaba955d94c20c6af32708b9f5945519cb21e13fb53 ? /bigdata/stajichlab/jstajich/projects/NovInvenio_Investigations/studies/fungi/yeast_convergence/yc_rev_eremothecium/annotations/UP000006790.tsv.gz : 5831d5fcfd3b8a28e4e6078777975416e8295e2dd3c41a405c300a544c1fc187 ? /bigdata/stajichlab/jstajich/projects/NovInvenio_Investigations/studies/fungi/yeast_convergence/yc_rev_eremothecium/annotations/UP000243052.tsv.gz : 5149f9de4ffa7a254079a1bf1423a1ff6edb48ead8f567805c4fafc612f2828a ? /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: 3.4 background_cluster_s: 29.6 tests_s: 5.1 total_s: 39.1 host: r11 slurm_job: '30452604'