generated: '2026-10-14T10:48:39' study: neocallimastigomycota_vs_early_fungi script: path: /bigdata/stajichlab/jstajich/projects/NovInvenio_Investigations/studies/fungi/zoosporic_dikarya/analysis/enrichment/enrich_novelties_v2.py sha256: d3f44fc3dc41e8838f54a472d2d5fd0d19d353757260b53f14eaba4929ca52c8 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/neocallimastigomycota_vs_early_fungi --config /bigdata/stajichlab/jstajich/projects/NovInvenio_Investigations/studies/fungi/neocallimastigomycota_vs_early_fungi/config.csv --study neocallimastigomycota_vs_early_fungi --threads 8 --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 --annotations /bigdata/stajichlab/jstajich/projects/NovInvenio_Investigations/studies/fungi/neocallimastigomycota_vs_early_fungi/annotations --cache-dir /bigdata/stajichlab/jstajich/projects/NovInvenio_Investigations/studies/fungi/neocallimastigomycota_vs_early_fungi/analysis/enrichment/outputs/cache --out-dir /bigdata/stajichlab/jstajich/projects/NovInvenio_Investigations/studies/fungi/neocallimastigomycota_vs_early_fungi/analysis/enrichment/outputs/proteome_clustered class: ephemeral analysis output (not tracked; regenerate with the command above) direction: novelty target_group: label: IN species: - Pirofinn - Anaerobu - Neocalif - Neolanat - Neoconst - PiroE2sp other_group: label: OUT species: - Spizpunc - Batrdend - Powehirt - Geravari - Chytconf - Syncendo - Allomacr - Cateangu - Rhizdele - Mucocirc - Umbevina - Sacccere - Neurcras universe: proteome annotations: /bigdata/stajichlab/jstajich/projects/NovInvenio_Investigations/studies/fungi/neocallimastigomycota_vs_early_fungi/annotations annotation_files: Pirofinn: /bigdata/stajichlab/jstajich/projects/NovInvenio_Investigations/studies/fungi/neocallimastigomycota_vs_early_fungi/annotations/UP000193719.tsv.gz Anaerobu: /bigdata/stajichlab/jstajich/projects/NovInvenio_Investigations/studies/fungi/neocallimastigomycota_vs_early_fungi/annotations/UP000193944.tsv.gz Neocalif: /bigdata/stajichlab/jstajich/projects/NovInvenio_Investigations/studies/fungi/neocallimastigomycota_vs_early_fungi/annotations/GCA_002104975.1.tsv.gz Neolanat: /bigdata/stajichlab/jstajich/projects/NovInvenio_Investigations/studies/fungi/neocallimastigomycota_vs_early_fungi/annotations/GCA_016946835.1.tsv.gz Neoconst: /bigdata/stajichlab/jstajich/projects/NovInvenio_Investigations/studies/fungi/neocallimastigomycota_vs_early_fungi/annotations/GCA_050613775.1.tsv.gz PiroE2sp: /bigdata/stajichlab/jstajich/projects/NovInvenio_Investigations/studies/fungi/neocallimastigomycota_vs_early_fungi/annotations/GCA_002157105.1.tsv.gz Spizpunc: /bigdata/stajichlab/jstajich/projects/NovInvenio_Investigations/studies/fungi/neocallimastigomycota_vs_early_fungi/annotations/UP000053201.tsv.gz Batrdend: /bigdata/stajichlab/jstajich/projects/NovInvenio_Investigations/studies/fungi/neocallimastigomycota_vs_early_fungi/annotations/UP000007241.tsv.gz Powehirt: /bigdata/stajichlab/jstajich/projects/NovInvenio_Investigations/studies/fungi/neocallimastigomycota_vs_early_fungi/annotations/UP000318582.tsv.gz Geravari: /bigdata/stajichlab/jstajich/projects/NovInvenio_Investigations/studies/fungi/neocallimastigomycota_vs_early_fungi/annotations/UP001212152.tsv.gz Chytconf: /bigdata/stajichlab/jstajich/projects/NovInvenio_Investigations/studies/fungi/neocallimastigomycota_vs_early_fungi/annotations/UP000320333.tsv.gz Syncendo: /bigdata/stajichlab/jstajich/projects/NovInvenio_Investigations/studies/fungi/neocallimastigomycota_vs_early_fungi/annotations/UP000317494.tsv.gz Allomacr: /bigdata/stajichlab/jstajich/projects/NovInvenio_Investigations/studies/fungi/neocallimastigomycota_vs_early_fungi/annotations/UP000054350.tsv.gz Cateangu: /bigdata/stajichlab/jstajich/projects/NovInvenio_Investigations/studies/fungi/neocallimastigomycota_vs_early_fungi/annotations/UP000193411.tsv.gz Rhizdele: /bigdata/stajichlab/jstajich/projects/NovInvenio_Investigations/studies/fungi/neocallimastigomycota_vs_early_fungi/annotations/UP000009138.tsv.gz Mucocirc: /bigdata/stajichlab/jstajich/projects/NovInvenio_Investigations/studies/fungi/neocallimastigomycota_vs_early_fungi/annotations/UP000014254.tsv.gz Umbevina: /bigdata/stajichlab/jstajich/projects/NovInvenio_Investigations/studies/fungi/neocallimastigomycota_vs_early_fungi/annotations/UP000612746.tsv.gz Sacccere: /bigdata/stajichlab/jstajich/projects/NovInvenio_Investigations/studies/fungi/neocallimastigomycota_vs_early_fungi/annotations/UP000002311.tsv.gz Neurcras: /bigdata/stajichlab/jstajich/projects/NovInvenio_Investigations/studies/fungi/neocallimastigomycota_vs_early_fungi/annotations/UP000001805.tsv.gz annotation_sources: Pirofinn: not recorded (no sidecar) Anaerobu: not recorded (no sidecar) Neocalif: Pfam-A HMM search (hmmsearch); Pfam only Neolanat: Pfam-A HMM search (hmmsearch); Pfam only Neoconst: Pfam-A HMM search (hmmsearch); Pfam only PiroE2sp: Pfam-A HMM search (hmmscan); Pfam only Spizpunc: not recorded (no sidecar) Batrdend: not recorded (no sidecar) Powehirt: not recorded (no sidecar) Geravari: not recorded (no sidecar) Chytconf: not recorded (no sidecar) Syncendo: not recorded (no sidecar) Allomacr: not recorded (no sidecar) Cateangu: not recorded (no sidecar) Rhizdele: not recorded (no sidecar) Mucocirc: not recorded (no sidecar) Umbevina: not recorded (no sidecar) Sacccere: not recorded (no sidecar) Neurcras: not recorded (no sidecar) vocabulary_coverage: pfam: species_with_terms: - Pirofinn - Anaerobu - Neocalif - Neolanat - Neoconst - PiroE2sp species_without_terms: [] n_with: 6 n_species: 6 pfam_clan: species_with_terms: - Pirofinn - Anaerobu - Neocalif - Neolanat - Neoconst - PiroE2sp species_without_terms: [] n_with: 6 n_species: 6 interpro: species_with_terms: - Pirofinn - Anaerobu species_without_terms: - Neocalif - Neolanat - Neoconst - PiroE2sp n_with: 2 n_species: 6 go: species_with_terms: - Pirofinn - Anaerobu species_without_terms: - Neocalif - Neolanat - Neoconst - PiroE2sp n_with: 2 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: 32717 candidates_txt: 32717 symmetric_difference: 0 candidates_file: /bigdata/stajichlab/jstajich/projects/NovInvenio_Investigations/results/neocallimastigomycota_vs_early_fungi/candidates.txt presence_matrix: /bigdata/stajichlab/jstajich/projects/NovInvenio_Investigations/results/neocallimastigomycota_vs_early_fungi/presence_matrix.uniprot.tsv rule: IN count / 6 >= 0.75 and OUT count / 13 <= 0.0 (own proteome counts toward the target group) only_in_matrix_rule: [] only_in_candidates_file: [] background_clustering: key: 16a9a2b2eaa61918 n_sequences: 76871 n_clusters: 25788 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: 35.3 threads: 8 created: '2026-10-14T10:48:10' cache_hit: true 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/neocallimastigomycota_vs_early_fungi/config.csv : a92c0fcde004bbadaec7b934c3c266f77f0af271646b06ea616947700df51c33 ? /bigdata/stajichlab/jstajich/projects/NovInvenio_Investigations/results/neocallimastigomycota_vs_early_fungi/candidates.txt : 42763268b720941469998126af0e45a13e829507c634caabd631cd57bc4cbb2c ? /bigdata/stajichlab/jstajich/projects/NovInvenio_Investigations/results/neocallimastigomycota_vs_early_fungi/novelties.Pirofinn.tsv : 0127a847d4e53581526e9711f030e4f3a6448172c19c1f063c371d7db8707d80 ? /bigdata/stajichlab/jstajich/projects/NovInvenio_Investigations/results/neocallimastigomycota_vs_early_fungi/novelties.Anaerobu.tsv : a675db6ae5882ee959b4109d1523b5a129110df28bd9d0e9d08f149f5001cdd7 ? /bigdata/stajichlab/jstajich/projects/NovInvenio_Investigations/results/neocallimastigomycota_vs_early_fungi/novelties.Neocalif.tsv : fcb6abdea191148e34951f9f837ca3e363079c61e22ed3861136b675d6bd3e97 ? /bigdata/stajichlab/jstajich/projects/NovInvenio_Investigations/results/neocallimastigomycota_vs_early_fungi/novelties.Neolanat.tsv : 244160f88920e088d83bb6be7b57263cf85fc18dfb11467afaa44feed1cd8219 ? /bigdata/stajichlab/jstajich/projects/NovInvenio_Investigations/results/neocallimastigomycota_vs_early_fungi/novelties.Neoconst.tsv : 2ca2a38cd0a87ad45f64852092810f27b8a2daa59f6b210b3fa7f13b5486f3db ? /bigdata/stajichlab/jstajich/projects/NovInvenio_Investigations/results/neocallimastigomycota_vs_early_fungi/novelties.PiroE2sp.tsv : f220d0c0b96cee2bba330237caaa24fed17b3098970d5158e1d933d84b45b9b8 ? /bigdata/stajichlab/jstajich/projects/NovInvenio_Investigations/results/neocallimastigomycota_vs_early_fungi/presence_matrix.uniprot.tsv : ec1b89867e936fdb234077ae9c7514501ab8b27fbb030f325096f241e716161d ? /bigdata/stajichlab/jstajich/projects/NovInvenio_Investigations/studies/fungi/neocallimastigomycota_vs_early_fungi/data_dir/pep/UP000193719_1754191.pep.fa : f6b43bdd5c0d2f7eef717808bb34aca5b489c9c062446101cc3adc5f0bd1b0c7 ? /bigdata/stajichlab/jstajich/projects/NovInvenio_Investigations/studies/fungi/neocallimastigomycota_vs_early_fungi/data_dir/pep/UP000193944_1754192.pep.fa : 4112aafcb0282c0e02c02501efe9f9eed17b143279d152b615d9fbafed2b1125 ? /bigdata/stajichlab/jstajich/projects/NovInvenio_Investigations/studies/fungi/neocallimastigomycota_vs_early_fungi/data_dir/pep/Neocalif.pep.fa : 3e476821f2518065d6bdefb26477bd072c3c2e51178a8078c3cb8abc9da52b90 ? /bigdata/stajichlab/jstajich/projects/NovInvenio_Investigations/studies/fungi/neocallimastigomycota_vs_early_fungi/data_dir/pep/Neolanat.pep.fa : b0591c69154f1f4b3c8f49bfdfc16aea46055bad9184a94e8cbd179aed8dd780 ? /bigdata/stajichlab/jstajich/projects/NovInvenio_Investigations/studies/fungi/neocallimastigomycota_vs_early_fungi/data_dir/pep/Neoconst.pep.fa : 1a1cf1dfb42d669a2b110c5f239ba7ce83192a8b076ba0313f272ce81d6d4469 ? /bigdata/stajichlab/jstajich/projects/NovInvenio_Investigations/studies/fungi/neocallimastigomycota_vs_early_fungi/data_dir/pep/PiroE2sp.pep.fa : ed6e14ca95f1e2d7c9040b993c0a539240696832e9fb3e890aae821b57bf1b97 ? /bigdata/stajichlab/jstajich/projects/NovInvenio_Investigations/studies/fungi/neocallimastigomycota_vs_early_fungi/species.csv : 5d8a35fef76590e0ae2e91214d315e9fbf8e25fd4b0d1944afea83f909c1b959 ? /bigdata/stajichlab/jstajich/projects/NovInvenio_Investigations/studies/fungi/neocallimastigomycota_vs_early_fungi/annotations/UP000193719.tsv.gz : 6231552a1af8da86030727068daa4b987722109caf6f0e30f6a2cbe944d0340a ? /bigdata/stajichlab/jstajich/projects/NovInvenio_Investigations/studies/fungi/neocallimastigomycota_vs_early_fungi/annotations/UP000193944.tsv.gz : 45cfc96f67e80d4742808d23881d81f82683b2707cb72aff9709d8366dff03ca ? /bigdata/stajichlab/jstajich/projects/NovInvenio_Investigations/studies/fungi/neocallimastigomycota_vs_early_fungi/annotations/GCA_002104975.1.tsv.gz : 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/bigdata/stajichlab/jstajich/projects/NovInvenio_Investigations/studies/fungi/neocallimastigomycota_vs_early_fungi/annotations/UP000317494.tsv.gz : 89a1c4f0ad8ffc1065204ef133f38f8843541b573dc4a8910533cfd0e18b9da1 ? /bigdata/stajichlab/jstajich/projects/NovInvenio_Investigations/studies/fungi/neocallimastigomycota_vs_early_fungi/annotations/UP000054350.tsv.gz : b0f8782a676f95b9384aa9de41bd053eea47423ba2210398f4d4cf9f131f59a9 ? /bigdata/stajichlab/jstajich/projects/NovInvenio_Investigations/studies/fungi/neocallimastigomycota_vs_early_fungi/annotations/UP000193411.tsv.gz : 9111592afb9e6e8b4b21acf2912c44f35d36960250cdfc698d77cd15934dfbb7 ? /bigdata/stajichlab/jstajich/projects/NovInvenio_Investigations/studies/fungi/neocallimastigomycota_vs_early_fungi/annotations/UP000009138.tsv.gz : b3311bc82307ce79a473456bf7606f9ef1e53c7b4095016972a8032dda18a927 ? /bigdata/stajichlab/jstajich/projects/NovInvenio_Investigations/studies/fungi/neocallimastigomycota_vs_early_fungi/annotations/UP000014254.tsv.gz : e370e319db954941e6006dc45c6df7e08565df2e054dd90cff4fa9e85cdc704e ? /bigdata/stajichlab/jstajich/projects/NovInvenio_Investigations/studies/fungi/neocallimastigomycota_vs_early_fungi/annotations/UP000612746.tsv.gz : f00a22c82fbd069ce0208cd540d1be07b8f54ff2e27c2064ee615d6b6ad34e99 ? /bigdata/stajichlab/jstajich/projects/NovInvenio_Investigations/studies/fungi/neocallimastigomycota_vs_early_fungi/annotations/UP000002311.tsv.gz : 6bfc0c01d44828159cd817317ad1b0954148cd39dad2770e9d48971431568d58 ? /bigdata/stajichlab/jstajich/projects/NovInvenio_Investigations/studies/fungi/neocallimastigomycota_vs_early_fungi/annotations/UP000001805.tsv.gz : a319daac8abea33c30066289a81d3064dd92ad76944e245022c1359fda4d8e81 ? /bigdata/stajichlab/jstajich/projects/NovInvenio_Investigations/studies/fungi/neocallimastigomycota_vs_early_fungi/annotations/GCA_002104975.1.tsv.gz.provenance.yaml : bff5121b8b59d1b4a2674a8404e6cb6254d7d949c34428ef9f21818eb71cc467 ? /bigdata/stajichlab/jstajich/projects/NovInvenio_Investigations/studies/fungi/neocallimastigomycota_vs_early_fungi/annotations/GCA_016946835.1.tsv.gz.provenance.yaml : db6f851cbdcab2af624d03e609b341aa116e76102248082f464b04ba0d04ea16 ? /bigdata/stajichlab/jstajich/projects/NovInvenio_Investigations/studies/fungi/neocallimastigomycota_vs_early_fungi/annotations/GCA_050613775.1.tsv.gz.provenance.yaml : 4e01ede24af8cb167e1e4017e7e992055f5ed7ba03e4d6211b4c54c853206abb ? /bigdata/stajichlab/jstajich/projects/NovInvenio_Investigations/studies/fungi/neocallimastigomycota_vs_early_fungi/annotations/GCA_002157105.1.tsv.gz.provenance.yaml : 46e643fc32835edac2e5911d8d64e23e413196b45621a9cea250b456da4dd033 ? /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: 5.6 background_cluster_s: 0.1 tests_s: 7.4 total_s: 18.8 host: r11 slurm_job: '29956230' wall_s_enrichment: 21