generated: '2026-10-12T18:19:41'
study: serinales_vs_pichiales
script:
  path: /bigdata/stajichlab/jstajich/projects/NovInvenio_Investigations/studies/fungi/zoosporic_dikarya/analysis/enrichment/enrich_novelties_v2.py
  sha256: b96062411e1f05983aa679d2d85d6e719db6cdc15260175ccf643db400903b17
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
  --direction loss --ingroup-min-frac 0.75 --other-max-frac 0.0 --universe proteome --cluster-background --out-dir /bigdata/stajichlab/jstajich/projects/NovInvenio_Investigations/studies/fungi/serinales_vs_pichiales/analysis/enrichment/outputs/loss/proteome_clustered
class: ephemeral analysis output (not tracked; regenerate with the command above)
direction: loss
target_group:
  label: OUT
  species:
  - Komaphaf
  - Ogatpara
  - Kuracaps
  - Pichmemb
  - Pichkudr
  - Bretnaar
  - Eeninana
  - Ogatpoly
  - Pachtann
  - Sacccere
  - Kluylact
  - Lachther
  - Candglab
  - Torudelb
  - Eremgoss
other_group:
  label: IN
  species:
  - Candalbi
  - Canddubl
  - Candtrop
  - Loddelon
  - Meyeguil
  - Debahans
  - Schestip
  - Spatpass
  - Hyphburt
  - Suhotanz
  - Candtenu
  - Babjinos
  - Diutrugo
  - Yamajaro
  - Candauri
  - Clavlusi
  - Metsbicu
  - Lizaspar
universe: proteome
annotations: /bigdata/stajichlab/jstajich/projects/NovInvenio_Investigations/studies/fungi/serinales_vs_pichiales/annotations
annotation_files:
  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
  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
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: 169
  candidates_txt: 169
  symmetric_difference: 0
  candidates_file: /bigdata/stajichlab/jstajich/projects/NovInvenio_Investigations/results/serinales_vs_pichiales/loss_candidates.txt
  presence_matrix: /bigdata/stajichlab/jstajich/projects/NovInvenio_Investigations/results/serinales_vs_pichiales/loss_presence_matrix.tsv
  rule: OUT count / 15 >= 0.75 and IN count / 18 <= 0.0 (own proteome counts toward the target group)
  only_in_matrix_rule: []
  only_in_candidates_file: []
background_clustering:
  key: 306e12dfc008e240
  n_sequences: 80405
  n_clusters: 21748
  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: 60.0
  threads: 8
  created: '2026-10-12T18:19:23'
  cache_hit: false
pipeline_candidate_families: '/bigdata/stajichlab/jstajich/projects/NovInvenio_Investigations/results/serinales_vs_pichiales/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/serinales_vs_pichiales/config.csv: cc5aa30d4a241d012ee4a2dbdcd3f7689f127da3348021f039858a9b1ef371b4
  /bigdata/stajichlab/jstajich/projects/NovInvenio_Investigations/results/serinales_vs_pichiales/loss_candidates.txt: 96cc13716580d00d2b44920de65de58939e10f014faecd415caf605c87dc9e2e
  ? /bigdata/stajichlab/jstajich/projects/NovInvenio_Investigations/results/serinales_vs_pichiales/clusters/loss_clusters_cluster.tsv
  : 7ed25003ae700aac3bcefa3a39570f9b757e31323bc0c9a1603d6fe3f66c52e6
  /bigdata/stajichlab/jstajich/projects/NovInvenio_Investigations/results/serinales_vs_pichiales/loss_presence_matrix.tsv: 7ef372c08fa37c08d6e4f46ad70a8514c3f8ef8b054a59baaf6c9f7eea82c19d
  ? /bigdata/stajichlab/jstajich/projects/NovInvenio_Investigations/studies/fungi/serinales_vs_pichiales/data_dir/pep/UP000000314_644223.pep.fa
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tools:
  python: 3.12.14
  scipy: 1.18.1
  goatools: 1.6.4
  mmseqs: 18.8cc5c
runtimes_s:
  load_s: 22.7
  background_cluster_s: 60.7
  tests_s: 13.6
  total_s: 101.7
host: r11
slurm_job: '29893778'
candidate_annotation:
  frac_loss_candidates_any_annotation: 0.9467
  low_coverage: false
  rule: "low_coverage = fraction < 0.5 (flag only; no run was excluded on this value)"
  wall_s_enrichment: 104