generated: '2026-10-24T14:34:54' study: yc_dothideales 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_dothideales --config /bigdata/stajichlab/jstajich/projects/NovInvenio_Investigations/studies/fungi/yeast_convergence/yc_dothideales/config.csv --annotations /bigdata/stajichlab/jstajich/projects/NovInvenio_Investigations/studies/fungi/yeast_convergence/yc_dothideales/annotations --study yc_dothideales --cache-dir /bigdata/stajichlab/jstajich/projects/NovInvenio_Investigations/studies/fungi/yeast_convergence/yc_dothideales/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_dothideales/analysis/enrichment/outputs/loss/proteome_clustered class: ephemeral analysis output (not tracked; regenerate with the command above) direction: loss target_group: label: OUT species: - Botrdoth - Paranodo - Altealte other_group: label: IN species: - Aurepull - Auremela - Aurenami - Auresubg universe: proteome annotations: /bigdata/stajichlab/jstajich/projects/NovInvenio_Investigations/studies/fungi/yeast_convergence/yc_dothideales/annotations annotation_files: Botrdoth: /bigdata/stajichlab/jstajich/projects/NovInvenio_Investigations/studies/fungi/yeast_convergence/yc_dothideales/annotations/UP000572817.tsv.gz Paranodo: /bigdata/stajichlab/jstajich/projects/NovInvenio_Investigations/studies/fungi/yeast_convergence/yc_dothideales/annotations/UP000663193.tsv.gz Altealte: /bigdata/stajichlab/jstajich/projects/NovInvenio_Investigations/studies/fungi/yeast_convergence/yc_dothideales/annotations/UP000077248.tsv.gz Aurepull: /bigdata/stajichlab/jstajich/projects/NovInvenio_Investigations/studies/fungi/yeast_convergence/yc_dothideales/annotations/GCF_000721785.1.tsv.gz Auremela: /bigdata/stajichlab/jstajich/projects/NovInvenio_Investigations/studies/fungi/yeast_convergence/yc_dothideales/annotations/GCF_000721775.1.tsv.gz Aurenami: /bigdata/stajichlab/jstajich/projects/NovInvenio_Investigations/studies/fungi/yeast_convergence/yc_dothideales/annotations/UP000027730.tsv.gz Auresubg: /bigdata/stajichlab/jstajich/projects/NovInvenio_Investigations/studies/fungi/yeast_convergence/yc_dothideales/annotations/UP000030641.tsv.gz annotation_sources: Botrdoth: not recorded (no sidecar) Paranodo: not recorded (no sidecar) Altealte: not recorded (no sidecar) Aurepull: Pfam-A HMM search (hmmsearch); Pfam only Auremela: Pfam-A HMM search (hmmsearch); Pfam only Aurenami: not recorded (no sidecar) Auresubg: not recorded (no sidecar) vocabulary_coverage: pfam: species_with_terms: - Botrdoth - Paranodo - Altealte species_without_terms: [] n_with: 3 n_species: 3 pfam_clan: species_with_terms: - Botrdoth - Paranodo - Altealte species_without_terms: [] n_with: 3 n_species: 3 interpro: species_with_terms: - Botrdoth - Paranodo - Altealte species_without_terms: [] n_with: 3 n_species: 3 go: species_with_terms: - Botrdoth - Paranodo - Altealte species_without_terms: [] n_with: 3 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: 1663 candidates_txt: 1663 symmetric_difference: 0 candidates_file: /bigdata/stajichlab/jstajich/projects/NovInvenio_Investigations/results/yc_dothideales/loss_candidates.txt presence_matrix: /bigdata/stajichlab/jstajich/projects/NovInvenio_Investigations/results/yc_dothideales/loss_presence_matrix.tsv rule: OUT count / 3 >= 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: 30e9cd86a2fa73dd n_sequences: 42348 n_clusters: 24209 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: 77.2 threads: 4 created: '2026-10-24T14:34:47' cache_hit: false pipeline_candidate_families: '/bigdata/stajichlab/jstajich/projects/NovInvenio_Investigations/results/yc_dothideales/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_dothideales/config.csv: 64758967240a1a09f19d829c067e54032bb48967520e0658bf0b16d1fbee98fc /bigdata/stajichlab/jstajich/projects/NovInvenio_Investigations/results/yc_dothideales/loss_candidates.txt: f7997408f80de19318c39fa50763822def94fd76d0b361940d9a926e8227682d /bigdata/stajichlab/jstajich/projects/NovInvenio_Investigations/results/yc_dothideales/clusters/loss_clusters_cluster.tsv: 9df286744aafdcbfd32148b572e1276c1f9831a5ea1ce0f783808113d1c4c3fa /bigdata/stajichlab/jstajich/projects/NovInvenio_Investigations/results/yc_dothideales/loss_presence_matrix.tsv: 40995aeaa5e30cb50b15dc5d2147dff728fd7ddce2536dfb886615f98d474303 ? /bigdata/stajichlab/jstajich/projects/NovInvenio_Investigations/studies/fungi/yeast_convergence/yc_dothideales/data_dir/pep/UP000572817_55169.pep.fa : 77622e6d331f84b128562570a6361ae673ca1c9d646a8f82db7e1363d9343159 ? /bigdata/stajichlab/jstajich/projects/NovInvenio_Investigations/studies/fungi/yeast_convergence/yc_dothideales/data_dir/pep/UP000663193_321614.pep.fa : ab293be1941dfff411d9f1af8c8fb8ce2e5e87fe326f23f4f9b829ca772bbf9e ? /bigdata/stajichlab/jstajich/projects/NovInvenio_Investigations/studies/fungi/yeast_convergence/yc_dothideales/data_dir/pep/UP000077248_5599.pep.fa : ed62ef84522633acba9c07148e5da11a22e4016c87afd72c7a5c8e98a3d48153 /bigdata/stajichlab/jstajich/projects/NovInvenio_Investigations/studies/fungi/yeast_convergence/yc_dothideales/species.csv: cf7613b351d88842f6589b7273db4ba01688c639ab97c7e928ada287591cfe8c ? /bigdata/stajichlab/jstajich/projects/NovInvenio_Investigations/studies/fungi/yeast_convergence/yc_dothideales/annotations/UP000572817.tsv.gz : d31f28b5a7f7b34a932a08838c65518fc90f3285c50d3792bcea2741910b3321 ? /bigdata/stajichlab/jstajich/projects/NovInvenio_Investigations/studies/fungi/yeast_convergence/yc_dothideales/annotations/UP000663193.tsv.gz : fe6ec318960ffeb97d92743ab0540f8553ac2991529ebc9e3ec5bc02986d2de4 ? /bigdata/stajichlab/jstajich/projects/NovInvenio_Investigations/studies/fungi/yeast_convergence/yc_dothideales/annotations/UP000077248.tsv.gz : d97a3105e4f777e2de3a13942779f65964c4c92bdabdff7d5d36b9aa5e07b93c ? /bigdata/stajichlab/jstajich/projects/NovInvenio_Investigations/studies/fungi/yeast_convergence/yc_dothideales/annotations/GCF_000721785.1.tsv.gz : 09bf67ff868fb40c41c54d96f83307516029e725c43981f58f551ee3206d4c10 ? /bigdata/stajichlab/jstajich/projects/NovInvenio_Investigations/studies/fungi/yeast_convergence/yc_dothideales/annotations/GCF_000721775.1.tsv.gz : 2f4f67947d180c6ca37b5f8cbd29883ce4dd11d5e9d3d065f4b0ed36bf1c3241 ? /bigdata/stajichlab/jstajich/projects/NovInvenio_Investigations/studies/fungi/yeast_convergence/yc_dothideales/annotations/UP000027730.tsv.gz : 13b9749c4b6c01c7c925bb4a62ca401771df6134e9e185400b10b34f3e55e353 ? /bigdata/stajichlab/jstajich/projects/NovInvenio_Investigations/studies/fungi/yeast_convergence/yc_dothideales/annotations/UP000030641.tsv.gz : fbb4bf7be5a855dc5a288ad508919c05b2ac61247b2911e6437b5a7686a0173f ? /bigdata/stajichlab/jstajich/projects/NovInvenio_Investigations/studies/fungi/yeast_convergence/yc_dothideales/annotations/GCF_000721785.1.tsv.gz.provenance.yaml : ede368c6618d123b575b0f9bdb715e8f8c03b68bfe66dc4315024b6ac8c328ad ? /bigdata/stajichlab/jstajich/projects/NovInvenio_Investigations/studies/fungi/yeast_convergence/yc_dothideales/annotations/GCF_000721775.1.tsv.gz.provenance.yaml : 4f1ddc1777625ae8aaee8c0d3de9dfc943f2faa4136edaffd591a1da993bc8d8 ? /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: 4.2 background_cluster_s: 77.9 tests_s: 5.3 total_s: 89.3 host: r11 slurm_job: '30452604'