generated: '2026-10-12T18:32:53'
study: malassezia_vs_ustilaginomycotina
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/malassezia_vs_ustilaginomycotina --config
  /bigdata/stajichlab/jstajich/projects/NovInvenio_Investigations/studies/fungi/malassezia_vs_ustilaginomycotina/config.csv
  --annotations /bigdata/stajichlab/jstajich/projects/NovInvenio_Investigations/studies/fungi/malassezia_vs_ustilaginomycotina/annotations
  --study malassezia_vs_ustilaginomycotina --cache-dir /bigdata/stajichlab/jstajich/projects/NovInvenio_Investigations/studies/fungi/malassezia_vs_ustilaginomycotina/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/malassezia_vs_ustilaginomycotina/analysis/enrichment/outputs/loss/proteome_clustered
class: ephemeral analysis output (not tracked; regenerate with the command above)
direction: loss
target_group:
  label: OUT
  species:
  - Mycomayd
  - Ustihord
  - Sporreil
  - Moesaphi
  - Kalmbras
  - Pseufloc
  - Sporgram
  - Testcype
  - Tillindi
  - Tillcari
  - Meirmilt
  - Acaringo
  - Jamirose
  - Micrgluc
  - Tillwash
  - Cerabomb
  - Violpalu
  - Tillanom
other_group:
  label: IN
  species:
  - Malaglob
  - Malasymp
  - Malarest
  - Malafurf
  - Malapach
  - Malavesp
  - Malanana
  - Malabras
  - Malajapo
  - Malaarun
universe: proteome
annotations: /bigdata/stajichlab/jstajich/projects/NovInvenio_Investigations/studies/fungi/malassezia_vs_ustilaginomycotina/annotations
annotation_files:
  Mycomayd: /bigdata/stajichlab/jstajich/projects/NovInvenio_Investigations/studies/fungi/malassezia_vs_ustilaginomycotina/annotations/UP000000561.tsv.gz
  Ustihord: /bigdata/stajichlab/jstajich/projects/NovInvenio_Investigations/studies/fungi/malassezia_vs_ustilaginomycotina/annotations/UP000006174.tsv.gz
  Sporreil: /bigdata/stajichlab/jstajich/projects/NovInvenio_Investigations/studies/fungi/malassezia_vs_ustilaginomycotina/annotations/UP000008867.tsv.gz
  Moesaphi: /bigdata/stajichlab/jstajich/projects/NovInvenio_Investigations/studies/fungi/malassezia_vs_ustilaginomycotina/annotations/UP000019462.tsv.gz
  Kalmbras: /bigdata/stajichlab/jstajich/projects/NovInvenio_Investigations/studies/fungi/malassezia_vs_ustilaginomycotina/annotations/UP000019377.tsv.gz
  Pseufloc: /bigdata/stajichlab/jstajich/projects/NovInvenio_Investigations/studies/fungi/malassezia_vs_ustilaginomycotina/annotations/UP000323386.tsv.gz
  Sporgram: /bigdata/stajichlab/jstajich/projects/NovInvenio_Investigations/studies/fungi/malassezia_vs_ustilaginomycotina/annotations/UP000306050.tsv.gz
  Testcype: /bigdata/stajichlab/jstajich/projects/NovInvenio_Investigations/studies/fungi/malassezia_vs_ustilaginomycotina/annotations/UP000246740.tsv.gz
  Tillindi: /bigdata/stajichlab/jstajich/projects/NovInvenio_Investigations/studies/fungi/malassezia_vs_ustilaginomycotina/annotations/UP000077521.tsv.gz
  Tillcari: /bigdata/stajichlab/jstajich/projects/NovInvenio_Investigations/studies/fungi/malassezia_vs_ustilaginomycotina/annotations/UP000836402.tsv.gz
  Meirmilt: /bigdata/stajichlab/jstajich/projects/NovInvenio_Investigations/studies/fungi/malassezia_vs_ustilaginomycotina/annotations/UP000245771.tsv.gz
  Acaringo: /bigdata/stajichlab/jstajich/projects/NovInvenio_Investigations/studies/fungi/malassezia_vs_ustilaginomycotina/annotations/UP000245768.tsv.gz
  Jamirose: /bigdata/stajichlab/jstajich/projects/NovInvenio_Investigations/studies/fungi/malassezia_vs_ustilaginomycotina/annotations/UP000245884.tsv.gz
  Micrgluc: /bigdata/stajichlab/jstajich/projects/NovInvenio_Investigations/studies/fungi/malassezia_vs_ustilaginomycotina/annotations/UP000245942.tsv.gz
  Tillwash: /bigdata/stajichlab/jstajich/projects/NovInvenio_Investigations/studies/fungi/malassezia_vs_ustilaginomycotina/annotations/UP000245946.tsv.gz
  Cerabomb: /bigdata/stajichlab/jstajich/projects/NovInvenio_Investigations/studies/fungi/malassezia_vs_ustilaginomycotina/annotations/UP000054845.tsv.gz
  Violpalu: /bigdata/stajichlab/jstajich/projects/NovInvenio_Investigations/studies/fungi/malassezia_vs_ustilaginomycotina/annotations/UP000245626.tsv.gz
  Tillanom: /bigdata/stajichlab/jstajich/projects/NovInvenio_Investigations/studies/fungi/malassezia_vs_ustilaginomycotina/annotations/UP000027361.tsv.gz
  Malaglob: /bigdata/stajichlab/jstajich/projects/NovInvenio_Investigations/studies/fungi/malassezia_vs_ustilaginomycotina/annotations/UP000008837.tsv.gz
  Malasymp: /bigdata/stajichlab/jstajich/projects/NovInvenio_Investigations/studies/fungi/malassezia_vs_ustilaginomycotina/annotations/UP000186303.tsv.gz
  Malarest: /bigdata/stajichlab/jstajich/projects/NovInvenio_Investigations/studies/fungi/malassezia_vs_ustilaginomycotina/annotations/UP000269793.tsv.gz
  Malafurf: /bigdata/stajichlab/jstajich/projects/NovInvenio_Investigations/studies/fungi/malassezia_vs_ustilaginomycotina/annotations/UP000818624.tsv.gz
  Malapach: /bigdata/stajichlab/jstajich/projects/NovInvenio_Investigations/studies/fungi/malassezia_vs_ustilaginomycotina/annotations/UP000037751.tsv.gz
  Malavesp: /bigdata/stajichlab/jstajich/projects/NovInvenio_Investigations/studies/fungi/malassezia_vs_ustilaginomycotina/annotations/UP000232875.tsv.gz
  Malanana: /bigdata/stajichlab/jstajich/projects/NovInvenio_Investigations/studies/fungi/malassezia_vs_ustilaginomycotina/annotations/UP001213623.tsv.gz
  Malabras: /bigdata/stajichlab/jstajich/projects/NovInvenio_Investigations/studies/fungi/malassezia_vs_ustilaginomycotina/annotations/UP001216638.tsv.gz
  Malajapo: /bigdata/stajichlab/jstajich/projects/NovInvenio_Investigations/studies/fungi/malassezia_vs_ustilaginomycotina/annotations/UP001217754.tsv.gz
  Malaarun: /bigdata/stajichlab/jstajich/projects/NovInvenio_Investigations/studies/fungi/malassezia_vs_ustilaginomycotina/annotations/UP001217582.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: 11852
  candidates_txt: 11852
  symmetric_difference: 0
  candidates_file: /bigdata/stajichlab/jstajich/projects/NovInvenio_Investigations/results/malassezia_vs_ustilaginomycotina/loss_candidates.txt
  presence_matrix: /bigdata/stajichlab/jstajich/projects/NovInvenio_Investigations/results/malassezia_vs_ustilaginomycotina/loss_presence_matrix.tsv
  rule: OUT count / 18 >= 0.75 and IN count / 10 <= 0.0 (own proteome counts toward the target group)
  only_in_matrix_rule: []
  only_in_candidates_file: []
background_clustering:
  key: 4f30c682eabdb155
  n_sequences: 120231
  n_clusters: 42252
  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: 102.9
  threads: 8
  created: '2026-10-12T18:32:20'
  cache_hit: false
pipeline_candidate_families: '/bigdata/stajichlab/jstajich/projects/NovInvenio_Investigations/results/malassezia_vs_ustilaginomycotina/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/malassezia_vs_ustilaginomycotina/config.csv: 708781d6d9020eaeb844b1f685f8c04ca32191cf42ef9b6b7a9a56d76d48b617
  ? /bigdata/stajichlab/jstajich/projects/NovInvenio_Investigations/results/malassezia_vs_ustilaginomycotina/loss_candidates.txt
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  ? /bigdata/stajichlab/jstajich/projects/NovInvenio_Investigations/results/malassezia_vs_ustilaginomycotina/clusters/loss_clusters_cluster.tsv
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tools:
  python: 3.12.14
  scipy: 1.18.1
  goatools: 1.6.4
  mmseqs: 18.8cc5c
runtimes_s:
  load_s: 19.6
  background_cluster_s: 107.0
  tests_s: 22.3
  total_s: 158.3
host: r11
slurm_job: '29893778'
candidate_annotation:
  frac_loss_candidates_any_annotation: 0.797
  low_coverage: false
  rule: "low_coverage = fraction < 0.5 (flag only; no run was excluded on this value)"
  wall_s_enrichment: 166