generated: '2026-10-24T14:59:06' study: yc_rev_neolecta 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_neolecta --config /bigdata/stajichlab/jstajich/projects/NovInvenio_Investigations/studies/fungi/yeast_convergence/yc_rev_neolecta/config.csv --annotations /bigdata/stajichlab/jstajich/projects/NovInvenio_Investigations/studies/fungi/yeast_convergence/yc_rev_neolecta/annotations --study yc_rev_neolecta --cache-dir /bigdata/stajichlab/jstajich/projects/NovInvenio_Investigations/studies/fungi/yeast_convergence/yc_rev_neolecta/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_neolecta/analysis/enrichment/outputs/loss/proteome_clustered class: ephemeral analysis output (not tracked; regenerate with the command above) direction: loss target_group: label: OUT species: - Spom - Schiocto - Schijapo - Saitcomp - Taphdefo - Protinou other_group: label: IN species: - Nirr universe: proteome annotations: /bigdata/stajichlab/jstajich/projects/NovInvenio_Investigations/studies/fungi/yeast_convergence/yc_rev_neolecta/annotations annotation_files: Spom: /bigdata/stajichlab/jstajich/projects/NovInvenio_Investigations/studies/fungi/yeast_convergence/yc_rev_neolecta/annotations/UP000002485.tsv.gz Schiocto: /bigdata/stajichlab/jstajich/projects/NovInvenio_Investigations/studies/fungi/yeast_convergence/yc_rev_neolecta/annotations/UP000016088.tsv.gz Schijapo: /bigdata/stajichlab/jstajich/projects/NovInvenio_Investigations/studies/fungi/yeast_convergence/yc_rev_neolecta/annotations/UP000001744.tsv.gz Saitcomp: /bigdata/stajichlab/jstajich/projects/NovInvenio_Investigations/studies/fungi/yeast_convergence/yc_rev_neolecta/annotations/UP000033140.tsv.gz Taphdefo: /bigdata/stajichlab/jstajich/projects/NovInvenio_Investigations/studies/fungi/yeast_convergence/yc_rev_neolecta/annotations/UP000013776.tsv.gz Protinou: /bigdata/stajichlab/jstajich/projects/NovInvenio_Investigations/studies/fungi/yeast_convergence/yc_rev_neolecta/annotations/Protomyces_inouyei_NRRL_YB-4354.proteins.tsv.gz Nirr: /bigdata/stajichlab/jstajich/projects/NovInvenio_Investigations/studies/fungi/yeast_convergence/yc_rev_neolecta/annotations/UP000186594.tsv.gz annotation_sources: 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 Nirr: not recorded (no sidecar) vocabulary_coverage: pfam: species_with_terms: - Spom - Schiocto - Schijapo - Saitcomp - Taphdefo - Protinou species_without_terms: [] n_with: 6 n_species: 6 pfam_clan: species_with_terms: - Spom - Schiocto - Schijapo - Saitcomp - Taphdefo - Protinou species_without_terms: [] n_with: 6 n_species: 6 interpro: species_with_terms: - Spom - Schiocto - Schijapo - Saitcomp - Taphdefo species_without_terms: - Protinou n_with: 5 n_species: 6 go: species_with_terms: - Spom - Schiocto - Schijapo - Saitcomp - Taphdefo species_without_terms: - Protinou n_with: 5 n_species: 6 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: 2638 candidates_txt: 2638 symmetric_difference: 0 candidates_file: /bigdata/stajichlab/jstajich/projects/NovInvenio_Investigations/results/yc_rev_neolecta/loss_candidates.txt presence_matrix: /bigdata/stajichlab/jstajich/projects/NovInvenio_Investigations/results/yc_rev_neolecta/loss_presence_matrix.tsv rule: OUT count / 6 >= 0.75 and IN count / 1 <= 0.0 (own proteome counts toward the target group) only_in_matrix_rule: [] only_in_candidates_file: [] background_clustering: key: 7a40aeca5f30420a n_sequences: 30331 n_clusters: 14714 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: 50.5 threads: 4 created: '2026-10-24T14:58:57' cache_hit: false pipeline_candidate_families: '/bigdata/stajichlab/jstajich/projects/NovInvenio_Investigations/results/yc_rev_neolecta/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_neolecta/config.csv: dfef664a66e24360de120cccc93fc6a1b5caad99295d85b36ec6e71838cf2055 /bigdata/stajichlab/jstajich/projects/NovInvenio_Investigations/results/yc_rev_neolecta/loss_candidates.txt: c90699e4f18fedca8ed286b448d596ca2f9c0940b88af3f0707ae42e7401389c /bigdata/stajichlab/jstajich/projects/NovInvenio_Investigations/results/yc_rev_neolecta/clusters/loss_clusters_cluster.tsv: 6ddeb2c975f7f0c6e360624ff63d5e24eadaaf02825abc4bf171ed235a954fdb /bigdata/stajichlab/jstajich/projects/NovInvenio_Investigations/results/yc_rev_neolecta/loss_presence_matrix.tsv: 5b8dd2af571f5f9afd86f153d95066c9c05b15e4e9dfbe49a4bea00d483d91f2 ? /bigdata/stajichlab/jstajich/projects/NovInvenio_Investigations/studies/fungi/yeast_convergence/yc_rev_neolecta/data_dir/pep/UP000002485_284812.pep.fa : b5d0a365078dc93e90244f462ebdead02b85de578db20ef20b9d7af9caa0de47 ? /bigdata/stajichlab/jstajich/projects/NovInvenio_Investigations/studies/fungi/yeast_convergence/yc_rev_neolecta/data_dir/pep/UP000016088_483514.pep.fa : f406958f7002d46466caf40ec15af10a55f99e72229816e10a62a0e0398a4bfd ? /bigdata/stajichlab/jstajich/projects/NovInvenio_Investigations/studies/fungi/yeast_convergence/yc_rev_neolecta/data_dir/pep/UP000001744_402676.pep.fa : cfdd3ece460f711449d28a6069fdf93e8e4d788863d81ef5d91bbca07441a3d0 ? /bigdata/stajichlab/jstajich/projects/NovInvenio_Investigations/studies/fungi/yeast_convergence/yc_rev_neolecta/data_dir/pep/UP000033140_698492.pep.fa : eb69f19616ec6ca9efca93c8265cdaa8679f07292d670a8b002f1c2e6f7e1ab7 ? /bigdata/stajichlab/jstajich/projects/NovInvenio_Investigations/studies/fungi/yeast_convergence/yc_rev_neolecta/data_dir/pep/UP000013776_1097556.pep.fa : e8cb37745877b35a67b2dc7f52932b6e6a665147dcbc309da04db83584aa34fd ? /bigdata/stajichlab/jstajich/projects/NovInvenio_Investigations/studies/fungi/yeast_convergence/yc_rev_neolecta/data_dir/pep/Protinou.pep.fa : 2b32099912b241a4cab3bad4e897f0a63bdae4cfc127827009660547e326eb6e ? /bigdata/stajichlab/jstajich/projects/NovInvenio_Investigations/studies/fungi/yeast_convergence/yc_rev_neolecta/species.csv : 1f265a7720fc69446058c8e424ac2056b4371dceaac85f97b2d1deb8fde89e6f ? /bigdata/stajichlab/jstajich/projects/NovInvenio_Investigations/studies/fungi/yeast_convergence/yc_rev_neolecta/annotations/UP000002485.tsv.gz : 14ce839f5423c2728641631260a90c21d5b5e1b2de47095722e63ffe6d1b4619 ? /bigdata/stajichlab/jstajich/projects/NovInvenio_Investigations/studies/fungi/yeast_convergence/yc_rev_neolecta/annotations/UP000016088.tsv.gz : d9933f4e0a8ff3a497a968fce5de6a7a9ba220441370db345a222681ff2f2224 ? /bigdata/stajichlab/jstajich/projects/NovInvenio_Investigations/studies/fungi/yeast_convergence/yc_rev_neolecta/annotations/UP000001744.tsv.gz : 2c8b230c43b831dac49afcb69afc98e626a8217136424a64bb5f345bfd5352a4 ? /bigdata/stajichlab/jstajich/projects/NovInvenio_Investigations/studies/fungi/yeast_convergence/yc_rev_neolecta/annotations/UP000033140.tsv.gz : 6c60aa212dab8ca0765541becf6816a3c5e09b053a9a33db25818a86312e2bbb ? /bigdata/stajichlab/jstajich/projects/NovInvenio_Investigations/studies/fungi/yeast_convergence/yc_rev_neolecta/annotations/UP000013776.tsv.gz : b13e6a3551add0f26a4eb41898970f6ddfb9d108ae936b12a9410b5de93361f2 ? /bigdata/stajichlab/jstajich/projects/NovInvenio_Investigations/studies/fungi/yeast_convergence/yc_rev_neolecta/annotations/Protomyces_inouyei_NRRL_YB-4354.proteins.tsv.gz : e94a842ec3f1b4d62e8ed8e506fb47689c27e6e38ac06f6104a0a25a9d0d91a5 ? /bigdata/stajichlab/jstajich/projects/NovInvenio_Investigations/studies/fungi/yeast_convergence/yc_rev_neolecta/annotations/UP000186594.tsv.gz : 25c6cd3e59c70d9bb2c477815385b7870f138d40bf71955fba5bd30b64843152 ? /bigdata/stajichlab/jstajich/projects/NovInvenio_Investigations/studies/fungi/yeast_convergence/yc_rev_neolecta/annotations/Protomyces_inouyei_NRRL_YB-4354.proteins.tsv.gz.provenance.yaml : b94508ce41f862b983d46fbd2371b8384707f67d855590457fd22f3aa61506f0 ? /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: 3.7 background_cluster_s: 50.8 tests_s: 7.3 total_s: 63.5 host: r11 slurm_job: '30452604'