generated: '2026-10-24T14:49:35' study: yc_pseudo_ectomycorrhizal 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_pseudo_ectomycorrhizal --config /bigdata/stajichlab/jstajich/projects/NovInvenio_Investigations/studies/fungi/yeast_convergence/yc_pseudo_ectomycorrhizal/config.csv --annotations /bigdata/stajichlab/jstajich/projects/NovInvenio_Investigations/studies/fungi/yeast_convergence/yc_pseudo_ectomycorrhizal/annotations --study yc_pseudo_ectomycorrhizal --cache-dir /bigdata/stajichlab/jstajich/projects/NovInvenio_Investigations/studies/fungi/yeast_convergence/yc_pseudo_ectomycorrhizal/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 novelty --out-dir /bigdata/stajichlab/jstajich/projects/NovInvenio_Investigations/studies/fungi/yeast_convergence/yc_pseudo_ectomycorrhizal/analysis/enrichment/outputs/novelty/proteome_clustered class: ephemeral analysis output (not tracked; regenerate with the command above) direction: novelty target_group: label: IN species: - Laccbico - Laccamet - Hebecyli - Amanmusc other_group: label: OUT species: - Amanthie - Ccin - Agbis - Pleuostr universe: proteome annotations: /bigdata/stajichlab/jstajich/projects/NovInvenio_Investigations/studies/fungi/yeast_convergence/yc_pseudo_ectomycorrhizal/annotations annotation_files: Laccbico: /bigdata/stajichlab/jstajich/projects/NovInvenio_Investigations/studies/fungi/yeast_convergence/yc_pseudo_ectomycorrhizal/annotations/UP000001194.tsv.gz Laccamet: /bigdata/stajichlab/jstajich/projects/NovInvenio_Investigations/studies/fungi/yeast_convergence/yc_pseudo_ectomycorrhizal/annotations/UP000054477.tsv.gz Hebecyli: /bigdata/stajichlab/jstajich/projects/NovInvenio_Investigations/studies/fungi/yeast_convergence/yc_pseudo_ectomycorrhizal/annotations/UP000053424.tsv.gz Amanmusc: /bigdata/stajichlab/jstajich/projects/NovInvenio_Investigations/studies/fungi/yeast_convergence/yc_pseudo_ectomycorrhizal/annotations/UP000054549.tsv.gz Amanthie: /bigdata/stajichlab/jstajich/projects/NovInvenio_Investigations/studies/fungi/yeast_convergence/yc_pseudo_ectomycorrhizal/annotations/UP000242287.tsv.gz Ccin: /bigdata/stajichlab/jstajich/projects/NovInvenio_Investigations/studies/fungi/yeast_convergence/yc_pseudo_ectomycorrhizal/annotations/UP000001861.tsv.gz Agbis: /bigdata/stajichlab/jstajich/projects/NovInvenio_Investigations/studies/fungi/yeast_convergence/yc_pseudo_ectomycorrhizal/annotations/UP000008493.tsv.gz Pleuostr: /bigdata/stajichlab/jstajich/projects/NovInvenio_Investigations/studies/fungi/yeast_convergence/yc_pseudo_ectomycorrhizal/annotations/UP000623687.tsv.gz annotation_sources: Laccbico: not recorded (no sidecar) Laccamet: not recorded (no sidecar) Hebecyli: not recorded (no sidecar) Amanmusc: not recorded (no sidecar) Amanthie: not recorded (no sidecar) Ccin: not recorded (no sidecar) Agbis: not recorded (no sidecar) Pleuostr: not recorded (no sidecar) vocabulary_coverage: pfam: species_with_terms: - Laccbico - Laccamet - Hebecyli - Amanmusc species_without_terms: [] n_with: 4 n_species: 4 pfam_clan: species_with_terms: - Laccbico - Laccamet - Hebecyli - Amanmusc species_without_terms: [] n_with: 4 n_species: 4 interpro: species_with_terms: - Laccbico - Laccamet - Hebecyli - Amanmusc species_without_terms: [] n_with: 4 n_species: 4 go: species_with_terms: - Laccbico - Laccamet - Hebecyli - Amanmusc 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: 2668 candidates_txt: 2668 symmetric_difference: 0 candidates_file: /bigdata/stajichlab/jstajich/projects/NovInvenio_Investigations/results/yc_pseudo_ectomycorrhizal/candidates.txt presence_matrix: /bigdata/stajichlab/jstajich/projects/NovInvenio_Investigations/results/yc_pseudo_ectomycorrhizal/presence_matrix.uniprot.tsv rule: IN count / 4 >= 0.75 and OUT count / 4 <= 0.0 (own proteome counts toward the target group) only_in_matrix_rule: [] only_in_candidates_file: [] background_clustering: key: 84fe326c6cc25cae n_sequences: 69378 n_clusters: 39108 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: 72.3 threads: 4 created: '2026-10-24T14:49:27' cache_hit: false pipeline_candidate_families: 'novelties..tsv family_id (nf_NovInvenio MMSEQS_CLUSTER: mmseqs easy-cluster --min-seq-id 0.3 -c 0.8 --cov-mode 0 on 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_pseudo_ectomycorrhizal/config.csv : 6eddef582c1f178b66b6e206de035800b052498ab1df98ba8bf5d2cb4c20c07b /bigdata/stajichlab/jstajich/projects/NovInvenio_Investigations/results/yc_pseudo_ectomycorrhizal/candidates.txt: b99e1c5a00a13d7667ae229b9b83970e666af9df9a6606db619d3f0c30046331 /bigdata/stajichlab/jstajich/projects/NovInvenio_Investigations/results/yc_pseudo_ectomycorrhizal/novelties.Laccbico.tsv: 9b9977c5a6f62630939d922e2a89ca418469154f208f1a223139f84955877b26 /bigdata/stajichlab/jstajich/projects/NovInvenio_Investigations/results/yc_pseudo_ectomycorrhizal/novelties.Laccamet.tsv: bb4b3db231bc0eec8db87c545d9472c9b4c5dfe98b0a660ca4d78099bb098dcc /bigdata/stajichlab/jstajich/projects/NovInvenio_Investigations/results/yc_pseudo_ectomycorrhizal/novelties.Hebecyli.tsv: a40779a0005d753c26f5bacc2282a87d6145952d873bc180e7be3074492b02d6 /bigdata/stajichlab/jstajich/projects/NovInvenio_Investigations/results/yc_pseudo_ectomycorrhizal/novelties.Amanmusc.tsv: e0c77c083261dc28f0736adabb161f5cb414a79c9e64e84fad817d99cda18f0f ? /bigdata/stajichlab/jstajich/projects/NovInvenio_Investigations/results/yc_pseudo_ectomycorrhizal/presence_matrix.uniprot.tsv : d36f28bc8d99c985ed73b9154ce23a742e8748ba62df97f42e4e75cfdcbd0092 ? /bigdata/stajichlab/jstajich/projects/NovInvenio_Investigations/studies/fungi/yeast_convergence/yc_pseudo_ectomycorrhizal/data_dir/pep/UP000001194_486041.pep.fa : b95404bee053be5f83409105f26a8f5543b3f32a4199cdbbd4319dce60a7400e ? /bigdata/stajichlab/jstajich/projects/NovInvenio_Investigations/studies/fungi/yeast_convergence/yc_pseudo_ectomycorrhizal/data_dir/pep/UP000054477_1095629.pep.fa : 162abbe0d00a683a3287f768fb33de8633b3c52b54328dc6d7d4d0162dfb8e6f ? /bigdata/stajichlab/jstajich/projects/NovInvenio_Investigations/studies/fungi/yeast_convergence/yc_pseudo_ectomycorrhizal/data_dir/pep/UP000053424_76867.pep.fa : 16af39bd70e2f5fd0b328bacbc966da8ac979480c349bef6c29edccb1bd7899b ? /bigdata/stajichlab/jstajich/projects/NovInvenio_Investigations/studies/fungi/yeast_convergence/yc_pseudo_ectomycorrhizal/data_dir/pep/UP000054549_946122.pep.fa : e57b750b723ab6e303250d25a6b469e219e177d31a417fca2d281070ae2414f0 ? /bigdata/stajichlab/jstajich/projects/NovInvenio_Investigations/studies/fungi/yeast_convergence/yc_pseudo_ectomycorrhizal/species.csv : c90b6ba069c7de6eae906cb212f0810828eb5f40d9b9558b506de3d0b987c0ef ? /bigdata/stajichlab/jstajich/projects/NovInvenio_Investigations/studies/fungi/yeast_convergence/yc_pseudo_ectomycorrhizal/annotations/UP000001194.tsv.gz : c671f268c3d82fe34920602b1524cc7d0dcffb12a41374a1690fb07088fc84b1 ? /bigdata/stajichlab/jstajich/projects/NovInvenio_Investigations/studies/fungi/yeast_convergence/yc_pseudo_ectomycorrhizal/annotations/UP000054477.tsv.gz : 7fbe17a8ec32d2540235eb7fddc99bfa4f13c971e2569a13a3836d4bdd656c87 ? /bigdata/stajichlab/jstajich/projects/NovInvenio_Investigations/studies/fungi/yeast_convergence/yc_pseudo_ectomycorrhizal/annotations/UP000053424.tsv.gz : 84cb9ae0e9bb7d9117cc31de233c4bed3d6c541a4e5b2604c45c1b2ec6ff2a3a ? /bigdata/stajichlab/jstajich/projects/NovInvenio_Investigations/studies/fungi/yeast_convergence/yc_pseudo_ectomycorrhizal/annotations/UP000054549.tsv.gz : 8837ab3248263a2d42880cf29f87ac13a1c0cf8118ea913e5dc925b5a541d81c ? /bigdata/stajichlab/jstajich/projects/NovInvenio_Investigations/studies/fungi/yeast_convergence/yc_pseudo_ectomycorrhizal/annotations/UP000242287.tsv.gz : cf4898979fe7b7fcca3bcbbd25099af62af34fd617e9c52e96f9f49dc0f56df3 ? /bigdata/stajichlab/jstajich/projects/NovInvenio_Investigations/studies/fungi/yeast_convergence/yc_pseudo_ectomycorrhizal/annotations/UP000001861.tsv.gz : 3e90bf8e6d7a60e464f904a30f9df462c29ec9fb7836d24ee9b7cfc2c4eeb4ca ? /bigdata/stajichlab/jstajich/projects/NovInvenio_Investigations/studies/fungi/yeast_convergence/yc_pseudo_ectomycorrhizal/annotations/UP000008493.tsv.gz : 33965ed8e5926dc68e862af851550a27bb3696124a3f809c2a0bdbb477938924 ? /bigdata/stajichlab/jstajich/projects/NovInvenio_Investigations/studies/fungi/yeast_convergence/yc_pseudo_ectomycorrhizal/annotations/UP000623687.tsv.gz : 0a2cde75e88da66789449ff67aa6dd1a359b1a71407c166808f303cc207fd612 ? /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: 5.2 background_cluster_s: 73.3 tests_s: 6.1 total_s: 87.0 host: r11 slurm_job: '30452604'