generated: '2026-10-12T14:56:47'
study: zoosporic_holozoa_vs_dikarya
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/zoosporic_holozoa_vs_dikarya --config
  /bigdata/stajichlab/jstajich/projects/NovInvenio_Investigations/studies/eukaryotes/zoosporic_holozoa_vs_dikarya/config.csv
  --annotations /bigdata/stajichlab/jstajich/projects/NovInvenio_Investigations/studies/eukaryotes/zoosporic_holozoa_vs_dikarya/annotations
  --study zoosporic_holozoa_vs_dikarya --cache-dir /bigdata/stajichlab/jstajich/projects/NovInvenio_Investigations/studies/eukaryotes/zoosporic_holozoa_vs_dikarya/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/eukaryotes/zoosporic_holozoa_vs_dikarya/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/eukaryotes/zoosporic_holozoa_vs_dikarya/annotations
annotation_files:
  Monobrev: /bigdata/stajichlab/jstajich/projects/NovInvenio_Investigations/studies/eukaryotes/zoosporic_holozoa_vs_dikarya/annotations/UP000001357.tsv.gz
  Salprose: /bigdata/stajichlab/jstajich/projects/NovInvenio_Investigations/studies/eukaryotes/zoosporic_holozoa_vs_dikarya/annotations/UP000007799.tsv.gz
  Capsowcz: /bigdata/stajichlab/jstajich/projects/NovInvenio_Investigations/studies/eukaryotes/zoosporic_holozoa_vs_dikarya/annotations/UP000008743.tsv.gz
  Sphaarct: /bigdata/stajichlab/jstajich/projects/NovInvenio_Investigations/studies/eukaryotes/zoosporic_holozoa_vs_dikarya/annotations/UP000054560.tsv.gz
  Amphquee: /bigdata/stajichlab/jstajich/projects/NovInvenio_Investigations/studies/eukaryotes/zoosporic_holozoa_vs_dikarya/annotations/UP000007879.tsv.gz
  Tricadha: /bigdata/stajichlab/jstajich/projects/NovInvenio_Investigations/studies/eukaryotes/zoosporic_holozoa_vs_dikarya/annotations/UP000009022.tsv.gz
  Nemavect: /bigdata/stajichlab/jstajich/projects/NovInvenio_Investigations/studies/eukaryotes/zoosporic_holozoa_vs_dikarya/annotations/UP000001593.tsv.gz
  Mnemleid: /bigdata/stajichlab/jstajich/projects/NovInvenio_Investigations/studies/eukaryotes/zoosporic_holozoa_vs_dikarya/annotations/UP001729289.tsv.gz
  Caeneleg: /bigdata/stajichlab/jstajich/projects/NovInvenio_Investigations/studies/eukaryotes/zoosporic_holozoa_vs_dikarya/annotations/UP000001940.tsv.gz
  Drosmela: /bigdata/stajichlab/jstajich/projects/NovInvenio_Investigations/studies/eukaryotes/zoosporic_holozoa_vs_dikarya/annotations/UP000000803.tsv.gz
  Homosapi: /bigdata/stajichlab/jstajich/projects/NovInvenio_Investigations/studies/eukaryotes/zoosporic_holozoa_vs_dikarya/annotations/UP000005640.tsv.gz
  Batrdend: /bigdata/stajichlab/jstajich/projects/NovInvenio_Investigations/studies/eukaryotes/zoosporic_holozoa_vs_dikarya/annotations/UP000007241.tsv.gz
  Batrsala: /bigdata/stajichlab/jstajich/projects/NovInvenio_Investigations/studies/eukaryotes/zoosporic_holozoa_vs_dikarya/annotations/UP001648503.tsv.gz
  Spizpunc: /bigdata/stajichlab/jstajich/projects/NovInvenio_Investigations/studies/eukaryotes/zoosporic_holozoa_vs_dikarya/annotations/UP000053201.tsv.gz
  Powehirt: /bigdata/stajichlab/jstajich/projects/NovInvenio_Investigations/studies/eukaryotes/zoosporic_holozoa_vs_dikarya/annotations/UP000318582.tsv.gz
  Geravari: /bigdata/stajichlab/jstajich/projects/NovInvenio_Investigations/studies/eukaryotes/zoosporic_holozoa_vs_dikarya/annotations/UP001212152.tsv.gz
  Syncendo: /bigdata/stajichlab/jstajich/projects/NovInvenio_Investigations/studies/eukaryotes/zoosporic_holozoa_vs_dikarya/annotations/UP000317494.tsv.gz
  Syncmicr: /bigdata/stajichlab/jstajich/projects/NovInvenio_Investigations/studies/eukaryotes/zoosporic_holozoa_vs_dikarya/annotations/UP000319731.tsv.gz
  Chytconf: /bigdata/stajichlab/jstajich/projects/NovInvenio_Investigations/studies/eukaryotes/zoosporic_holozoa_vs_dikarya/annotations/UP000320333.tsv.gz
  Polystew: /bigdata/stajichlab/jstajich/projects/NovInvenio_Investigations/studies/eukaryotes/zoosporic_holozoa_vs_dikarya/annotations/UP001527925.tsv.gz
  Rhizglob: /bigdata/stajichlab/jstajich/projects/NovInvenio_Investigations/studies/eukaryotes/zoosporic_holozoa_vs_dikarya/annotations/UP000193642.tsv.gz
  Rhizrose: /bigdata/stajichlab/jstajich/projects/NovInvenio_Investigations/studies/eukaryotes/zoosporic_holozoa_vs_dikarya/annotations/UP001212841.tsv.gz
  Cateangu: /bigdata/stajichlab/jstajich/projects/NovInvenio_Investigations/studies/eukaryotes/zoosporic_holozoa_vs_dikarya/annotations/UP000193411.tsv.gz
  Allomacr: /bigdata/stajichlab/jstajich/projects/NovInvenio_Investigations/studies/eukaryotes/zoosporic_holozoa_vs_dikarya/annotations/UP000054350.tsv.gz
  Pirofinn: /bigdata/stajichlab/jstajich/projects/NovInvenio_Investigations/studies/eukaryotes/zoosporic_holozoa_vs_dikarya/annotations/UP000193719.tsv.gz
  Sacccere: /bigdata/stajichlab/jstajich/projects/NovInvenio_Investigations/studies/eukaryotes/zoosporic_holozoa_vs_dikarya/annotations/UP000002311.tsv.gz
  Schipomb: /bigdata/stajichlab/jstajich/projects/NovInvenio_Investigations/studies/eukaryotes/zoosporic_holozoa_vs_dikarya/annotations/UP000002485.tsv.gz
  Neurcras: /bigdata/stajichlab/jstajich/projects/NovInvenio_Investigations/studies/eukaryotes/zoosporic_holozoa_vs_dikarya/annotations/UP000001805.tsv.gz
  Aspenidu: /bigdata/stajichlab/jstajich/projects/NovInvenio_Investigations/studies/eukaryotes/zoosporic_holozoa_vs_dikarya/annotations/UP000000560.tsv.gz
  Mycomayd: /bigdata/stajichlab/jstajich/projects/NovInvenio_Investigations/studies/eukaryotes/zoosporic_holozoa_vs_dikarya/annotations/UP000000561.tsv.gz
  Crypneof: /bigdata/stajichlab/jstajich/projects/NovInvenio_Investigations/studies/eukaryotes/zoosporic_holozoa_vs_dikarya/annotations/UP000010091.tsv.gz
  Coprcine: /bigdata/stajichlab/jstajich/projects/NovInvenio_Investigations/studies/eukaryotes/zoosporic_holozoa_vs_dikarya/annotations/UP000001861.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: 6615
  candidates_txt: 6615
  symmetric_difference: 0
background_clustering:
  key: 1845b2ec434f81b3
  n_sequences: 318843
  n_clusters: 182816
  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: 360.9
  threads: 8
  created: '2026-10-12T14:55:17'
  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/eukaryotes/zoosporic_holozoa_vs_dikarya/config.csv: bec465ef33372ed010bca6d6b3737ceb2bf3b6890558ce2e6d2e106bfb722580
  /bigdata/stajichlab/jstajich/projects/NovInvenio_Investigations/results/zoosporic_holozoa_vs_dikarya/candidates.txt: f43e40c1a9a0c1df2969dc57a3098c3fe164dea0d8e55c94f4b3a68026167dcf
  ? /bigdata/stajichlab/jstajich/projects/NovInvenio_Investigations/results/zoosporic_holozoa_vs_dikarya/novelties.Monobrev.tsv
  : 31c5ed4d49476323ad06fb9f612871c67881baab101c75e72e0a7e0846fa5cd8
  ? /bigdata/stajichlab/jstajich/projects/NovInvenio_Investigations/results/zoosporic_holozoa_vs_dikarya/novelties.Salprose.tsv
  : b82942debcbf3febae5c8f96dc1c86c84470a7b85dedb23a20a8c6111e437c04
  ? /bigdata/stajichlab/jstajich/projects/NovInvenio_Investigations/results/zoosporic_holozoa_vs_dikarya/novelties.Capsowcz.tsv
  : eb9c6aa6ab3a8303541d02b49ba685db79b697515132727f659fe0b8b9f3bcb1
  ? /bigdata/stajichlab/jstajich/projects/NovInvenio_Investigations/results/zoosporic_holozoa_vs_dikarya/novelties.Sphaarct.tsv
  : 0f92837fa09e80668e3af31f99791a38a1aaf76d3f91fe82bf1761ecdba2c30f
  ? /bigdata/stajichlab/jstajich/projects/NovInvenio_Investigations/results/zoosporic_holozoa_vs_dikarya/novelties.Amphquee.tsv
  : 7365326d4c07628dfeea729031eab55ae7630dd8b293ea19d956eac3965d748d
  ? /bigdata/stajichlab/jstajich/projects/NovInvenio_Investigations/results/zoosporic_holozoa_vs_dikarya/novelties.Tricadha.tsv
  : a7d6c4100a8d6e791bc5a6296adffc7f5ab47f75904272febe40be8b7d98f920
  ? /bigdata/stajichlab/jstajich/projects/NovInvenio_Investigations/results/zoosporic_holozoa_vs_dikarya/novelties.Nemavect.tsv
  : d0108bd5bb738b4701d3b6d232aa527092370a2d229863ab85d3e01152836ecd
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tools:
  python: 3.12.14
  scipy: 1.18.1
  goatools: 1.6.4
  mmseqs: 18.8cc5c
runtimes_s:
  load_s: 26.3
  background_cluster_s: 380.7
  tests_s: 66.7
  total_s: 488.9
host: r11
slurm_job: '29892648'