generated: '2026-10-24T14:50:59' 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 loss --other-max-frac 0.0 --out-dir /bigdata/stajichlab/jstajich/projects/NovInvenio_Investigations/studies/fungi/yeast_convergence/yc_pseudo_ectomycorrhizal/analysis/enrichment/outputs/loss/proteome_clustered class: ephemeral analysis output (not tracked; regenerate with the command above) direction: loss target_group: label: OUT species: - Amanthie - Ccin - Agbis - Pleuostr other_group: label: IN species: - Laccbico - Laccamet - Hebecyli - Amanmusc universe: proteome annotations: /bigdata/stajichlab/jstajich/projects/NovInvenio_Investigations/studies/fungi/yeast_convergence/yc_pseudo_ectomycorrhizal/annotations annotation_files: 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 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 annotation_sources: Amanthie: not recorded (no sidecar) Ccin: not recorded (no sidecar) Agbis: not recorded (no sidecar) Pleuostr: not recorded (no sidecar) Laccbico: not recorded (no sidecar) Laccamet: not recorded (no sidecar) Hebecyli: not recorded (no sidecar) Amanmusc: not recorded (no sidecar) vocabulary_coverage: pfam: species_with_terms: - Amanthie - Ccin - Agbis - Pleuostr species_without_terms: [] n_with: 4 n_species: 4 pfam_clan: species_with_terms: - Amanthie - Ccin - Agbis - Pleuostr species_without_terms: [] n_with: 4 n_species: 4 interpro: species_with_terms: - Amanthie - Ccin - Agbis - Pleuostr species_without_terms: [] n_with: 4 n_species: 4 go: species_with_terms: - Amanthie - Ccin - Agbis - Pleuostr 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: 361 candidates_txt: 361 symmetric_difference: 0 candidates_file: /bigdata/stajichlab/jstajich/projects/NovInvenio_Investigations/results/yc_pseudo_ectomycorrhizal/loss_candidates.txt presence_matrix: /bigdata/stajichlab/jstajich/projects/NovInvenio_Investigations/results/yc_pseudo_ectomycorrhizal/loss_presence_matrix.tsv rule: OUT count / 4 >= 0.75 and IN count / 4 <= 0.0 (own proteome counts toward the target group) only_in_matrix_rule: [] only_in_candidates_file: [] background_clustering: key: c52899b98e63600c n_sequences: 46144 n_clusters: 22248 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: 69.1 threads: 4 created: '2026-10-24T14:50:52' cache_hit: false pipeline_candidate_families: '/bigdata/stajichlab/jstajich/projects/NovInvenio_Investigations/results/yc_pseudo_ectomycorrhizal/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_pseudo_ectomycorrhizal/config.csv : 6eddef582c1f178b66b6e206de035800b052498ab1df98ba8bf5d2cb4c20c07b /bigdata/stajichlab/jstajich/projects/NovInvenio_Investigations/results/yc_pseudo_ectomycorrhizal/loss_candidates.txt: 30b0ac925eaab1b6931328601e82250ded7de34197739e378bf843d1432cb8d1 ? /bigdata/stajichlab/jstajich/projects/NovInvenio_Investigations/results/yc_pseudo_ectomycorrhizal/clusters/loss_clusters_cluster.tsv : 24ad33de04443541b83cbad6cd38fcd286101bf9bdcbb0d054f1e2653f67a397 /bigdata/stajichlab/jstajich/projects/NovInvenio_Investigations/results/yc_pseudo_ectomycorrhizal/loss_presence_matrix.tsv: 53f1a804d5475313854231ed9aac210f11c0efcaa9172487ad82fa55255d6743 ? /bigdata/stajichlab/jstajich/projects/NovInvenio_Investigations/studies/fungi/yeast_convergence/yc_pseudo_ectomycorrhizal/data_dir/pep/UP000242287_703135.pep.fa : ce1aecbd364888d0ead060aa327c1731f94bc5c24789e54b85d4d65b92abba33 ? /bigdata/stajichlab/jstajich/projects/NovInvenio_Investigations/studies/fungi/yeast_convergence/yc_pseudo_ectomycorrhizal/data_dir/pep/UP000001861_240176.pep.fa : 74c44aa4bf25cf5b12557eb189790357f7864197c5f0ec34b2724c338bda80c3 ? /bigdata/stajichlab/jstajich/projects/NovInvenio_Investigations/studies/fungi/yeast_convergence/yc_pseudo_ectomycorrhizal/data_dir/pep/UP000008493_597362.pep.fa : 32dd0444169cfd2e54ea9363f4f971e2aff3f5b414926ee86dbfc7ba8c9ced4a ? /bigdata/stajichlab/jstajich/projects/NovInvenio_Investigations/studies/fungi/yeast_convergence/yc_pseudo_ectomycorrhizal/data_dir/pep/UP000623687_5322.pep.fa : 5ac563f6d6c392eb063d1e762c6cdfbc7a00a1f728814a75746a6c8608de7976 ? /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/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/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/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: 4.3 background_cluster_s: 69.6 tests_s: 5.0 total_s: 81.1 host: r11 slurm_job: '30452604'