generated: '2026-10-12T15:21:05'
study: serinales_vs_pichiales
script:
  path: /bigdata/stajichlab/jstajich/projects/NovInvenio_Investigations/studies/fungi/zoosporic_dikarya/analysis/enrichment/enrich_novelties_v2.py
  sha256: 199f750f1ebbeb473fc6204d0435b712f565039b8460e5f08108c49d9752ccf2
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/serinales_vs_pichiales --config /bigdata/stajichlab/jstajich/projects/NovInvenio_Investigations/studies/fungi/serinales_vs_pichiales/config.csv
  --annotations /bigdata/stajichlab/jstajich/projects/NovInvenio_Investigations/studies/fungi/serinales_vs_pichiales/annotations
  --study serinales_vs_pichiales --cache-dir /bigdata/stajichlab/jstajich/projects/NovInvenio_Investigations/studies/fungi/serinales_vs_pichiales/analysis/enrichment/outputs/cache
  --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 --out-dir /bigdata/stajichlab/jstajich/projects/NovInvenio_Investigations/studies/fungi/serinales_vs_pichiales/analysis/enrichment/outputs/proteome_clustered
class: ephemeral analysis output (not tracked; regenerate with the command above)
universe: proteome
annotations: /bigdata/stajichlab/jstajich/projects/NovInvenio_Investigations/studies/fungi/serinales_vs_pichiales/annotations
annotation_files:
  Candalbi: /bigdata/stajichlab/jstajich/projects/NovInvenio_Investigations/studies/fungi/serinales_vs_pichiales/annotations/UP000000559.tsv.gz
  Canddubl: /bigdata/stajichlab/jstajich/projects/NovInvenio_Investigations/studies/fungi/serinales_vs_pichiales/annotations/UP000002605.tsv.gz
  Candtrop: /bigdata/stajichlab/jstajich/projects/NovInvenio_Investigations/studies/fungi/serinales_vs_pichiales/annotations/UP000002037.tsv.gz
  Loddelon: /bigdata/stajichlab/jstajich/projects/NovInvenio_Investigations/studies/fungi/serinales_vs_pichiales/annotations/UP000001996.tsv.gz
  Meyeguil: /bigdata/stajichlab/jstajich/projects/NovInvenio_Investigations/studies/fungi/serinales_vs_pichiales/annotations/UP000001997.tsv.gz
  Debahans: /bigdata/stajichlab/jstajich/projects/NovInvenio_Investigations/studies/fungi/serinales_vs_pichiales/annotations/UP000000599.tsv.gz
  Schestip: /bigdata/stajichlab/jstajich/projects/NovInvenio_Investigations/studies/fungi/serinales_vs_pichiales/annotations/UP000002258.tsv.gz
  Spatpass: /bigdata/stajichlab/jstajich/projects/NovInvenio_Investigations/studies/fungi/serinales_vs_pichiales/annotations/UP000000709.tsv.gz
  Hyphburt: /bigdata/stajichlab/jstajich/projects/NovInvenio_Investigations/studies/fungi/serinales_vs_pichiales/annotations/UP000095085.tsv.gz
  Suhotanz: /bigdata/stajichlab/jstajich/projects/NovInvenio_Investigations/studies/fungi/serinales_vs_pichiales/annotations/UP000094285.tsv.gz
  Candtenu: /bigdata/stajichlab/jstajich/projects/NovInvenio_Investigations/studies/fungi/serinales_vs_pichiales/annotations/UP000000707.tsv.gz
  Babjinos: /bigdata/stajichlab/jstajich/projects/NovInvenio_Investigations/studies/fungi/serinales_vs_pichiales/annotations/UP000094336.tsv.gz
  Diutrugo: /bigdata/stajichlab/jstajich/projects/NovInvenio_Investigations/studies/fungi/serinales_vs_pichiales/annotations/UP000449547.tsv.gz
  Yamajaro: /bigdata/stajichlab/jstajich/projects/NovInvenio_Investigations/studies/fungi/serinales_vs_pichiales/annotations/UP001152531.tsv.gz
  Candauri: /bigdata/stajichlab/jstajich/projects/NovInvenio_Investigations/studies/fungi/serinales_vs_pichiales/annotations/UP000230249.tsv.gz
  Clavlusi: /bigdata/stajichlab/jstajich/projects/NovInvenio_Investigations/studies/fungi/serinales_vs_pichiales/annotations/UP000007703.tsv.gz
  Metsbicu: /bigdata/stajichlab/jstajich/projects/NovInvenio_Investigations/studies/fungi/serinales_vs_pichiales/annotations/UP000092555.tsv.gz
  Lizaspar: /bigdata/stajichlab/jstajich/projects/NovInvenio_Investigations/studies/fungi/serinales_vs_pichiales/annotations/UP000790833.tsv.gz
  Komaphaf: /bigdata/stajichlab/jstajich/projects/NovInvenio_Investigations/studies/fungi/serinales_vs_pichiales/annotations/UP000000314.tsv.gz
  Ogatpara: /bigdata/stajichlab/jstajich/projects/NovInvenio_Investigations/studies/fungi/serinales_vs_pichiales/annotations/UP000008673.tsv.gz
  Kuracaps: /bigdata/stajichlab/jstajich/projects/NovInvenio_Investigations/studies/fungi/serinales_vs_pichiales/annotations/UP000019384.tsv.gz
  Pichmemb: /bigdata/stajichlab/jstajich/projects/NovInvenio_Investigations/studies/fungi/serinales_vs_pichiales/annotations/UP000094455.tsv.gz
  Pichkudr: /bigdata/stajichlab/jstajich/projects/NovInvenio_Investigations/studies/fungi/serinales_vs_pichiales/annotations/UP000249293.tsv.gz
  Bretnaar: /bigdata/stajichlab/jstajich/projects/NovInvenio_Investigations/studies/fungi/serinales_vs_pichiales/annotations/UP000290900.tsv.gz
  Eeninana: /bigdata/stajichlab/jstajich/projects/NovInvenio_Investigations/studies/fungi/serinales_vs_pichiales/annotations/UP000662931.tsv.gz
  Ogatpoly: /bigdata/stajichlab/jstajich/projects/NovInvenio_Investigations/studies/fungi/serinales_vs_pichiales/annotations/UP000788993.tsv.gz
  Pachtann: /bigdata/stajichlab/jstajich/projects/NovInvenio_Investigations/studies/fungi/serinales_vs_pichiales/annotations/UP000094236.tsv.gz
  Sacccere: /bigdata/stajichlab/jstajich/projects/NovInvenio_Investigations/studies/fungi/serinales_vs_pichiales/annotations/UP000002311.tsv.gz
  Kluylact: /bigdata/stajichlab/jstajich/projects/NovInvenio_Investigations/studies/fungi/serinales_vs_pichiales/annotations/UP000000598.tsv.gz
  Lachther: /bigdata/stajichlab/jstajich/projects/NovInvenio_Investigations/studies/fungi/serinales_vs_pichiales/annotations/UP000002036.tsv.gz
  Candglab: /bigdata/stajichlab/jstajich/projects/NovInvenio_Investigations/studies/fungi/serinales_vs_pichiales/annotations/UP000002428.tsv.gz
  Torudelb: /bigdata/stajichlab/jstajich/projects/NovInvenio_Investigations/studies/fungi/serinales_vs_pichiales/annotations/UP000005627.tsv.gz
  Eremgoss: /bigdata/stajichlab/jstajich/projects/NovInvenio_Investigations/studies/fungi/serinales_vs_pichiales/annotations/UP000000591.tsv.gz
parameters:
  min_bg: 5
  exclude_iea: false
  report_ids_fdr: 0.05
  ingroup_min_frac: 0.75
  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: 2995
  candidates_txt: 2995
  symmetric_difference: 0
background_clustering:
  key: c3fa4eb7f93e736b
  n_sequences: 102522
  n_clusters: 23051
  mmseqs: /bigdata/stajichlab/jstajich/projects/NovInvenio_Investigations/.pixi/envs/default/bin/mmseqs
  mmseqs_version: 18.8cc5c
  command: mmseqs easy-cluster <bg.fa> <out> <tmp> --threads N --min-seq-id 0.3 -c 0.8 --cov-mode 0
  runtime_s: 72.5
  threads: 8
  created: '2026-10-12T15:20:39'
  cache_hit: false
pipeline_candidate_families: 'novelties.<Short>.tsv family_id (nf_NovInvenio MMSEQS_CLUSTER: mmseqs easy-cluster --min-seq-id
  0.3 -c 0.8 --cov-mode 0 on candidates.fa)'
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/serinales_vs_pichiales/config.csv: cc5aa30d4a241d012ee4a2dbdcd3f7689f127da3348021f039858a9b1ef371b4
  /bigdata/stajichlab/jstajich/projects/NovInvenio_Investigations/results/serinales_vs_pichiales/candidates.txt: 7249b6d9d53d293a38eab0ae418d1aa96e95ec28595092f3cef96e54c2389dcd
  /bigdata/stajichlab/jstajich/projects/NovInvenio_Investigations/results/serinales_vs_pichiales/novelties.Candalbi.tsv: d650eaa92a711c346b122ccbbf249149622deef6dbfb240ef793fa254d8141b2
  /bigdata/stajichlab/jstajich/projects/NovInvenio_Investigations/results/serinales_vs_pichiales/novelties.Canddubl.tsv: ace07302a35ddcae75cc6361b6d143b592059bd2159648daed4974c63b218388
  /bigdata/stajichlab/jstajich/projects/NovInvenio_Investigations/results/serinales_vs_pichiales/novelties.Candtrop.tsv: 95e5da9e79ae785a223e757dc0e91af7af68067f60befaf1ae2ba73e8d7a2d87
  /bigdata/stajichlab/jstajich/projects/NovInvenio_Investigations/results/serinales_vs_pichiales/novelties.Loddelon.tsv: 86ccb0020afd24a06f94270ecca831dbf6ff9a8e2b29a964d4b5745af7f7db04
  /bigdata/stajichlab/jstajich/projects/NovInvenio_Investigations/results/serinales_vs_pichiales/novelties.Meyeguil.tsv: d111a5bc3ed799783f13761ef59f684cd08c4c8d864f530908a03d594c61a8e0
  /bigdata/stajichlab/jstajich/projects/NovInvenio_Investigations/results/serinales_vs_pichiales/novelties.Debahans.tsv: 31465a8b0f0ba877571ee656e05c2ca5b851248e0a3d187d8b81257a5b68165b
  /bigdata/stajichlab/jstajich/projects/NovInvenio_Investigations/results/serinales_vs_pichiales/novelties.Schestip.tsv: dbee6ea02c7a7a035e70ce8aabba0dcd2a9336e99f77c35e91b36eb497cede0c
  /bigdata/stajichlab/jstajich/projects/NovInvenio_Investigations/results/serinales_vs_pichiales/novelties.Spatpass.tsv: 91cab7d8efe79cb9d4f442479f9bf116fb0ab802d83bae0fa897e01686574581
  /bigdata/stajichlab/jstajich/projects/NovInvenio_Investigations/results/serinales_vs_pichiales/novelties.Hyphburt.tsv: 4ab2a41847960932f39e6a2f202e6e24a0dc9c55c6efa5f8aa6d9d438e44997f
  /bigdata/stajichlab/jstajich/projects/NovInvenio_Investigations/results/serinales_vs_pichiales/novelties.Suhotanz.tsv: 4cda99eb2755bd5ca42e4af81665480f9cfcdfcd25d09ce7332cd99baa9f37fe
  /bigdata/stajichlab/jstajich/projects/NovInvenio_Investigations/results/serinales_vs_pichiales/novelties.Candtenu.tsv: f1aba4214b212a1429d5271cbfe579fd221cbd214d29537d0f84987b835b475f
  /bigdata/stajichlab/jstajich/projects/NovInvenio_Investigations/results/serinales_vs_pichiales/novelties.Babjinos.tsv: 809de80a3a70c2a2668fffb3e523a0c6de95bd447156e811f547116ec9410eb8
  /bigdata/stajichlab/jstajich/projects/NovInvenio_Investigations/results/serinales_vs_pichiales/novelties.Diutrugo.tsv: c5c083cf8b900a510d55f544afecd3ae2253259e505b7691eee3eaa3795e25c3
  /bigdata/stajichlab/jstajich/projects/NovInvenio_Investigations/results/serinales_vs_pichiales/novelties.Yamajaro.tsv: bba051d565551440ae17e7b1469362efc99f09ab18e8e740e82948ad70606d16
  /bigdata/stajichlab/jstajich/projects/NovInvenio_Investigations/results/serinales_vs_pichiales/novelties.Candauri.tsv: a63c4f904b88a5c7e5cf409f92c854aaa19f5ef7b7536f9f7c33196faf89f7fb
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  /bigdata/stajichlab/jstajich/projects/NovInvenio_Investigations/results/serinales_vs_pichiales/novelties.Metsbicu.tsv: a3c7c58746e496286d05aa5d1f3809656b23f0cf28c3bb50fd5909840d5f40d4
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tools:
  python: 3.12.14
  scipy: 1.18.1
  goatools: 1.6.4
  mmseqs: 18.8cc5c
runtimes_s:
  load_s: 17.3
  background_cluster_s: 73.5
  tests_s: 16.6
  total_s: 117.4
host: r11
slurm_job: '29892705'