generated: '2026-10-16T22:54:46'
study: serinales_vs_pichiales_v2
script:
  path: /bigdata/stajichlab/jstajich/projects/NovInvenio_Investigations/studies/fungi/zoosporic_dikarya/analysis/enrichment/enrich_novelties_v2.py
  sha256: d1e8fe16f6842e86fb6c226f822c8c173450a8fec660ca6879a6f8a821ad5aa7
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_v2 --config /bigdata/stajichlab/jstajich/projects/NovInvenio_Investigations/studies/fungi/serinales_vs_pichiales_v2/config.csv
  --annotations /bigdata/stajichlab/jstajich/projects/NovInvenio_Investigations/studies/fungi/serinales_vs_pichiales_v2/annotations
  --study serinales_vs_pichiales_v2 --cache-dir /bigdata/stajichlab/jstajich/projects/NovInvenio_Investigations/studies/fungi/serinales_vs_pichiales_v2/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_v2/analysis/enrichment/outputs/loss/proteome_clustered
class: ephemeral analysis output (not tracked; regenerate with the command above)
direction: loss
target_group:
  label: OUT
  species:
  - Babjinos
  - Komaphaf
  - Kuracaps
  - Pichmemb
  - Pichkudr
  - Bretnaar
  - Ogatpoly
  - Pachtann
  - Sacccere
  - Kluylact
  - Lachther
  - Candglab
  - Torudelb
other_group:
  label: IN
  species:
  - Candalbi
  - Loddelon
  - Meyeguil
  - Debahans
  - Schestip
  - Spatpass
  - Candtenu
  - Diutrugo
  - Yamajaro
  - Candauri
  - Clavlusi
  - Metsbicu
  - Lizaspar
universe: proteome
annotations: /bigdata/stajichlab/jstajich/projects/NovInvenio_Investigations/studies/fungi/serinales_vs_pichiales_v2/annotations
annotation_files:
  Babjinos: /bigdata/stajichlab/jstajich/projects/NovInvenio_Investigations/studies/fungi/serinales_vs_pichiales_v2/annotations/UP000094336.tsv.gz
  Komaphaf: /bigdata/stajichlab/jstajich/projects/NovInvenio_Investigations/studies/fungi/serinales_vs_pichiales_v2/annotations/UP000000314.tsv.gz
  Kuracaps: /bigdata/stajichlab/jstajich/projects/NovInvenio_Investigations/studies/fungi/serinales_vs_pichiales_v2/annotations/UP000019384.tsv.gz
  Pichmemb: /bigdata/stajichlab/jstajich/projects/NovInvenio_Investigations/studies/fungi/serinales_vs_pichiales_v2/annotations/UP000094455.tsv.gz
  Pichkudr: /bigdata/stajichlab/jstajich/projects/NovInvenio_Investigations/studies/fungi/serinales_vs_pichiales_v2/annotations/UP000249293.tsv.gz
  Bretnaar: /bigdata/stajichlab/jstajich/projects/NovInvenio_Investigations/studies/fungi/serinales_vs_pichiales_v2/annotations/UP000290900.tsv.gz
  Ogatpoly: /bigdata/stajichlab/jstajich/projects/NovInvenio_Investigations/studies/fungi/serinales_vs_pichiales_v2/annotations/UP000788993.tsv.gz
  Pachtann: /bigdata/stajichlab/jstajich/projects/NovInvenio_Investigations/studies/fungi/serinales_vs_pichiales_v2/annotations/UP000094236.tsv.gz
  Sacccere: /bigdata/stajichlab/jstajich/projects/NovInvenio_Investigations/studies/fungi/serinales_vs_pichiales_v2/annotations/UP000002311.tsv.gz
  Kluylact: /bigdata/stajichlab/jstajich/projects/NovInvenio_Investigations/studies/fungi/serinales_vs_pichiales_v2/annotations/UP000000598.tsv.gz
  Lachther: /bigdata/stajichlab/jstajich/projects/NovInvenio_Investigations/studies/fungi/serinales_vs_pichiales_v2/annotations/UP000002036.tsv.gz
  Candglab: /bigdata/stajichlab/jstajich/projects/NovInvenio_Investigations/studies/fungi/serinales_vs_pichiales_v2/annotations/UP000002428.tsv.gz
  Torudelb: /bigdata/stajichlab/jstajich/projects/NovInvenio_Investigations/studies/fungi/serinales_vs_pichiales_v2/annotations/UP000005627.tsv.gz
  Candalbi: /bigdata/stajichlab/jstajich/projects/NovInvenio_Investigations/studies/fungi/serinales_vs_pichiales_v2/annotations/UP000000559.tsv.gz
  Loddelon: /bigdata/stajichlab/jstajich/projects/NovInvenio_Investigations/studies/fungi/serinales_vs_pichiales_v2/annotations/UP000001996.tsv.gz
  Meyeguil: /bigdata/stajichlab/jstajich/projects/NovInvenio_Investigations/studies/fungi/serinales_vs_pichiales_v2/annotations/UP000001997.tsv.gz
  Debahans: /bigdata/stajichlab/jstajich/projects/NovInvenio_Investigations/studies/fungi/serinales_vs_pichiales_v2/annotations/UP000000599.tsv.gz
  Schestip: /bigdata/stajichlab/jstajich/projects/NovInvenio_Investigations/studies/fungi/serinales_vs_pichiales_v2/annotations/UP000002258.tsv.gz
  Spatpass: /bigdata/stajichlab/jstajich/projects/NovInvenio_Investigations/studies/fungi/serinales_vs_pichiales_v2/annotations/UP000000709.tsv.gz
  Candtenu: /bigdata/stajichlab/jstajich/projects/NovInvenio_Investigations/studies/fungi/serinales_vs_pichiales_v2/annotations/UP000000707.tsv.gz
  Diutrugo: /bigdata/stajichlab/jstajich/projects/NovInvenio_Investigations/studies/fungi/serinales_vs_pichiales_v2/annotations/UP000449547.tsv.gz
  Yamajaro: /bigdata/stajichlab/jstajich/projects/NovInvenio_Investigations/studies/fungi/serinales_vs_pichiales_v2/annotations/UP001152531.tsv.gz
  Candauri: /bigdata/stajichlab/jstajich/projects/NovInvenio_Investigations/studies/fungi/serinales_vs_pichiales_v2/annotations/UP000230249.tsv.gz
  Clavlusi: /bigdata/stajichlab/jstajich/projects/NovInvenio_Investigations/studies/fungi/serinales_vs_pichiales_v2/annotations/UP000007703.tsv.gz
  Metsbicu: /bigdata/stajichlab/jstajich/projects/NovInvenio_Investigations/studies/fungi/serinales_vs_pichiales_v2/annotations/UP000092555.tsv.gz
  Lizaspar: /bigdata/stajichlab/jstajich/projects/NovInvenio_Investigations/studies/fungi/serinales_vs_pichiales_v2/annotations/UP000790833.tsv.gz
annotation_sources:
  Babjinos: not recorded (no sidecar)
  Komaphaf: not recorded (no sidecar)
  Kuracaps: not recorded (no sidecar)
  Pichmemb: not recorded (no sidecar)
  Pichkudr: not recorded (no sidecar)
  Bretnaar: not recorded (no sidecar)
  Ogatpoly: not recorded (no sidecar)
  Pachtann: not recorded (no sidecar)
  Sacccere: not recorded (no sidecar)
  Kluylact: not recorded (no sidecar)
  Lachther: not recorded (no sidecar)
  Candglab: not recorded (no sidecar)
  Torudelb: not recorded (no sidecar)
  Candalbi: not recorded (no sidecar)
  Loddelon: not recorded (no sidecar)
  Meyeguil: not recorded (no sidecar)
  Debahans: not recorded (no sidecar)
  Schestip: not recorded (no sidecar)
  Spatpass: not recorded (no sidecar)
  Candtenu: not recorded (no sidecar)
  Diutrugo: not recorded (no sidecar)
  Yamajaro: not recorded (no sidecar)
  Candauri: not recorded (no sidecar)
  Clavlusi: not recorded (no sidecar)
  Metsbicu: not recorded (no sidecar)
  Lizaspar: not recorded (no sidecar)
vocabulary_coverage:
  pfam:
    species_with_terms:
    - Babjinos
    - Komaphaf
    - Kuracaps
    - Pichmemb
    - Pichkudr
    - Bretnaar
    - Ogatpoly
    - Pachtann
    - Sacccere
    - Kluylact
    - Lachther
    - Candglab
    - Torudelb
    species_without_terms: []
    n_with: 13
    n_species: 13
  pfam_clan:
    species_with_terms:
    - Babjinos
    - Komaphaf
    - Kuracaps
    - Pichmemb
    - Pichkudr
    - Bretnaar
    - Ogatpoly
    - Pachtann
    - Sacccere
    - Kluylact
    - Lachther
    - Candglab
    - Torudelb
    species_without_terms: []
    n_with: 13
    n_species: 13
  interpro:
    species_with_terms:
    - Babjinos
    - Komaphaf
    - Kuracaps
    - Pichmemb
    - Pichkudr
    - Bretnaar
    - Ogatpoly
    - Pachtann
    - Sacccere
    - Kluylact
    - Lachther
    - Candglab
    - Torudelb
    species_without_terms: []
    n_with: 13
    n_species: 13
  go:
    species_with_terms:
    - Babjinos
    - Komaphaf
    - Kuracaps
    - Pichmemb
    - Pichkudr
    - Bretnaar
    - Ogatpoly
    - Pachtann
    - Sacccere
    - Kluylact
    - Lachther
    - Candglab
    - Torudelb
    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: 326
  candidates_txt: 326
  symmetric_difference: 0
  candidates_file: /bigdata/stajichlab/jstajich/projects/NovInvenio_Investigations/results/serinales_vs_pichiales_v2/loss_candidates.txt
  presence_matrix: /bigdata/stajichlab/jstajich/projects/NovInvenio_Investigations/results/serinales_vs_pichiales_v2/loss_presence_matrix.tsv
  rule: OUT count / 13 >= 0.75 and IN count / 13 <= 0.0 (own proteome counts toward the target group)
  only_in_matrix_rule: []
  only_in_candidates_file: []
background_clustering:
  key: b0a71af08dce5627
  n_sequences: 71861
  n_clusters: 22669
  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: 49.3
  threads: 8
  created: '2026-10-16T22:54:29'
  cache_hit: false
pipeline_candidate_families: '/bigdata/stajichlab/jstajich/projects/NovInvenio_Investigations/results/serinales_vs_pichiales_v2/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_v2/config.csv: 85a71d46e3871a66aace8b86654dbd5f37f2bcb71d5e5910367fa9b4aa59d9b8
  /bigdata/stajichlab/jstajich/projects/NovInvenio_Investigations/results/serinales_vs_pichiales_v2/loss_candidates.txt: 733b357a4cca63f3a48d1e073c3a826be65aa9632fadecb2e4db9c20fa6a9389
  ? /bigdata/stajichlab/jstajich/projects/NovInvenio_Investigations/results/serinales_vs_pichiales_v2/clusters/loss_clusters_cluster.tsv
  : dbd02f7cb6782053ddaec13d10875273c255d1a817ace7042875814ec407c953
  /bigdata/stajichlab/jstajich/projects/NovInvenio_Investigations/results/serinales_vs_pichiales_v2/loss_presence_matrix.tsv: bbc2da2aa20aa4bb6be6803a305243d885f4c32de1852162ebe4cddc9d6dca5f
  ? /bigdata/stajichlab/jstajich/projects/NovInvenio_Investigations/studies/fungi/serinales_vs_pichiales_v2/data_dir/pep/UP000094336_984486.pep.fa
  : c94529b0c905260aac3a2c8fc6c04556128c5e72bc62cee264bfd2c2fd605303
  ? /bigdata/stajichlab/jstajich/projects/NovInvenio_Investigations/studies/fungi/serinales_vs_pichiales_v2/data_dir/pep/UP000000314_644223.pep.fa
  : 8e2149c52c9ce07421f48e313b1f7ebfa4b22ba20eb47c953b19fa91a1cae030
  ? /bigdata/stajichlab/jstajich/projects/NovInvenio_Investigations/studies/fungi/serinales_vs_pichiales_v2/data_dir/pep/UP000019384_1382522.pep.fa
  : e2f6e191eb2c7341ee431eafdc0720ed53cdd1af312a5bb0ca65576c64800dcb
  ? /bigdata/stajichlab/jstajich/projects/NovInvenio_Investigations/studies/fungi/serinales_vs_pichiales_v2/data_dir/pep/UP000094455_763406.pep.fa
  : 159c1cf14fda2f40678dae2573311ed4b4f7a9d6ae85fe825a6528af3d6f08d9
  ? /bigdata/stajichlab/jstajich/projects/NovInvenio_Investigations/studies/fungi/serinales_vs_pichiales_v2/data_dir/pep/UP000249293_4909.pep.fa
  : eb66f55e2d7697b15af4b80a73cedf402e4a1376f5a1847e8a9755be56912487
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tools:
  python: 3.12.14
  scipy: 1.18.1
  goatools: 1.6.4
  mmseqs: 18.8cc5c
runtimes_s:
  load_s: 7.5
  background_cluster_s: 50.0
  tests_s: 12.2
  total_s: 75.2
host: r11
slurm_job: '30027698'
candidate_annotation:
  frac_loss_candidates_any_annotation: 0.9571
  low_coverage: false
  rule: "low_coverage = fraction < 0.5 (flag only; no run was excluded on this value)"
  wall_s_enrichment: 77