generated: '2026-10-14T10:49:23' 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 --direction loss --other-max-frac 0.0 --out-dir /bigdata/stajichlab/jstajich/projects/NovInvenio_Investigations/studies/fungi/neocallimastigomycota_vs_early_fungi/analysis/enrichment/outputs/loss/proteome_clustered class: ephemeral analysis output (not tracked; regenerate with the command above) direction: loss target_group: label: OUT species: - Spizpunc - Batrdend - Powehirt - Geravari - Chytconf - Syncendo - Allomacr - Cateangu - Rhizdele - Mucocirc - Umbevina - Sacccere - Neurcras other_group: label: IN species: - Pirofinn - Anaerobu - Neocalif - Neolanat - Neoconst - PiroE2sp universe: proteome annotations: /bigdata/stajichlab/jstajich/projects/NovInvenio_Investigations/studies/fungi/neocallimastigomycota_vs_early_fungi/annotations annotation_files: 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 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 annotation_sources: 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) 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 vocabulary_coverage: pfam: species_with_terms: - Spizpunc - Batrdend - Powehirt - Geravari - Chytconf - Syncendo - Allomacr - Cateangu - Rhizdele - Mucocirc - Umbevina - Sacccere - Neurcras species_without_terms: [] n_with: 13 n_species: 13 pfam_clan: species_with_terms: - Spizpunc - Batrdend - Powehirt - Geravari - Chytconf - Syncendo - Allomacr - Cateangu - Rhizdele - Mucocirc - Umbevina - Sacccere - Neurcras species_without_terms: [] n_with: 13 n_species: 13 interpro: species_with_terms: - Spizpunc - Batrdend - Powehirt - Geravari - Chytconf - Syncendo - Allomacr - Cateangu - Rhizdele - Mucocirc - Umbevina - Sacccere - Neurcras species_without_terms: [] n_with: 13 n_species: 13 go: species_with_terms: - Spizpunc - Batrdend - Powehirt - Geravari - Chytconf - Syncendo - Allomacr - Cateangu - Rhizdele - Mucocirc - Umbevina - Sacccere - Neurcras species_without_terms: [] n_with: 13 n_species: 13 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: 9173 candidates_txt: 9173 symmetric_difference: 0 candidates_file: /bigdata/stajichlab/jstajich/projects/NovInvenio_Investigations/results/neocallimastigomycota_vs_early_fungi/loss_candidates.txt presence_matrix: /bigdata/stajichlab/jstajich/projects/NovInvenio_Investigations/results/neocallimastigomycota_vs_early_fungi/loss_presence_matrix.tsv rule: OUT count / 13 >= 0.75 and IN count / 6 <= 0.0 (own proteome counts toward the target group) only_in_matrix_rule: [] only_in_candidates_file: [] background_clustering: key: 8d1d473106d133dd n_sequences: 127537 n_clusters: 70280 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: 116.2 threads: 8 created: '2026-10-12T18:29:38' cache_hit: true pipeline_candidate_families: '/bigdata/stajichlab/jstajich/projects/NovInvenio_Investigations/results/neocallimastigomycota_vs_early_fungi/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/neocallimastigomycota_vs_early_fungi/config.csv : a92c0fcde004bbadaec7b934c3c266f77f0af271646b06ea616947700df51c33 ? /bigdata/stajichlab/jstajich/projects/NovInvenio_Investigations/results/neocallimastigomycota_vs_early_fungi/loss_candidates.txt : 4a8aa4ff4541e5c74295c7dffa3569a8ffb648fe9dcae8a56baf544128fba972 ? /bigdata/stajichlab/jstajich/projects/NovInvenio_Investigations/results/neocallimastigomycota_vs_early_fungi/clusters/loss_clusters_cluster.tsv : 398d08d1bf694b1643ab1c8d5b8ab3535352527e753e9e6e46af1d344e7b2f79 ? /bigdata/stajichlab/jstajich/projects/NovInvenio_Investigations/results/neocallimastigomycota_vs_early_fungi/loss_presence_matrix.tsv : b10052cc8df2a1c6febbc1744f1c3125faff192bddb64502d0c6f9eea2883410 ? /bigdata/stajichlab/jstajich/projects/NovInvenio_Investigations/studies/fungi/neocallimastigomycota_vs_early_fungi/data_dir/pep/UP000053201_645134.pep.fa : 8bd4d9ebed9f723020afc4ea42cff0fbd940dc7922870dedfbb5f9a4cfc2f9c0 ? /bigdata/stajichlab/jstajich/projects/NovInvenio_Investigations/studies/fungi/neocallimastigomycota_vs_early_fungi/data_dir/pep/UP000007241_684364.pep.fa : 4e4c6abb18055c8c0ed97e584c71e1919acb4afb8aa9afd89ed5870347126ae4 ? /bigdata/stajichlab/jstajich/projects/NovInvenio_Investigations/studies/fungi/neocallimastigomycota_vs_early_fungi/data_dir/pep/UP000318582_109895.pep.fa : 9bda96b8b8b1102754d22304a37d4ade9dab495d1007aff23f5018bfb7938ec4 ? /bigdata/stajichlab/jstajich/projects/NovInvenio_Investigations/studies/fungi/neocallimastigomycota_vs_early_fungi/data_dir/pep/UP001212152_109894.pep.fa : ca499d9289158588d1939cf83bd3ac94e09fc00a58fb7de3fcf31ebccc8a5205 ? /bigdata/stajichlab/jstajich/projects/NovInvenio_Investigations/studies/fungi/neocallimastigomycota_vs_early_fungi/data_dir/pep/UP000320333_246404.pep.fa : 1d4b846fd4db60adf1d1808b4c6dd8e7ac63b7bf2a1a23e3586b97fcdcd2d199 ? /bigdata/stajichlab/jstajich/projects/NovInvenio_Investigations/studies/fungi/neocallimastigomycota_vs_early_fungi/data_dir/pep/UP000317494_286115.pep.fa : c56505ba0725d49584a4b0b3c378dc4341ad59547d23ee3c5989ebf05c71975e ? /bigdata/stajichlab/jstajich/projects/NovInvenio_Investigations/studies/fungi/neocallimastigomycota_vs_early_fungi/data_dir/pep/UP000054350_578462.pep.fa : f874160443aa6627a1165bc333271882998af5b69dad5ca6dbbec76d68e6d04c ? 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/bigdata/stajichlab/jstajich/projects/NovInvenio_Investigations/studies/fungi/neocallimastigomycota_vs_early_fungi/data_dir/pep/UP000002311_559292.pep.fa : 8ca7d8ccfd337f039527d136c3d10ec9c81be3aae33578cadef3abf2093792cb ? /bigdata/stajichlab/jstajich/projects/NovInvenio_Investigations/studies/fungi/neocallimastigomycota_vs_early_fungi/data_dir/pep/UP000001805_367110.pep.fa : 6c3a6d498fb30b129e2ab084f95789b3c510164f34661a5c85acb6a14e5f3dde ? /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/UP000053201.tsv.gz : 3bfce2c6f78a64a4c07111580ebe5b1a115e0ad4f2030d2f581070f70a3df5d2 ? 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/bigdata/stajichlab/jstajich/projects/NovInvenio_Investigations/studies/fungi/neocallimastigomycota_vs_early_fungi/annotations/GCA_050613775.1.tsv.gz : 5caee8093b38c92eb7b27b9e41fd61d32f3d3270cc35769956696b3ce7169c83 ? /bigdata/stajichlab/jstajich/projects/NovInvenio_Investigations/studies/fungi/neocallimastigomycota_vs_early_fungi/annotations/GCA_002157105.1.tsv.gz : 120aab50ca4795298608934ab645bf7c49351fb862e4c4a2b7502a8744c65e89 ? /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: 8.8 background_cluster_s: 0.2 tests_s: 22.0 total_s: 39.7 host: r11 slurm_job: '29956230' candidate_annotation: frac_loss_candidates_any_annotation: 0.9959 low_coverage: false rule: "low_coverage = fraction < 0.5 (flag only; no run was excluded on this value)" wall_s_enrichment: 41