generated: '2026-10-12T18:27:20'
study: chytrid_vs_mucoromycota
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/chytrid_vs_mucoromycota --config /bigdata/stajichlab/jstajich/projects/NovInvenio_Investigations/studies/fungi/chytrid_vs_mucoromycota/config.csv
  --annotations /bigdata/stajichlab/jstajich/projects/NovInvenio_Investigations/studies/fungi/chytrid_vs_mucoromycota/annotations
  --study chytrid_vs_mucoromycota --cache-dir /bigdata/stajichlab/jstajich/projects/NovInvenio_Investigations/studies/fungi/chytrid_vs_mucoromycota/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/chytrid_vs_mucoromycota/analysis/enrichment/outputs/loss/proteome_clustered
class: ephemeral analysis output (not tracked; regenerate with the command above)
direction: loss
target_group:
  label: OUT
  species:
  - Mucocirc
  - Rhizdele
  - Lichcory
  - Phycblak
  - Absiglau
  - Syncrace
  - Choacucu
  - Hessvesi
  - Umbevina
  - Mortisab
  - Thamspha
other_group:
  label: IN
  species:
  - Batrdend
  - Batrsala
  - Spizpunc
  - Powehirt
  - Geravari
  - Syncendo
  - Syncmicr
  - Chytconf
  - Polystew
  - Rhizglob
  - Rhizrose
universe: proteome
annotations: /bigdata/stajichlab/jstajich/projects/NovInvenio_Investigations/studies/fungi/chytrid_vs_mucoromycota/annotations
annotation_files:
  Mucocirc: /bigdata/stajichlab/jstajich/projects/NovInvenio_Investigations/studies/fungi/chytrid_vs_mucoromycota/annotations/UP000014254.tsv.gz
  Rhizdele: /bigdata/stajichlab/jstajich/projects/NovInvenio_Investigations/studies/fungi/chytrid_vs_mucoromycota/annotations/UP000009138.tsv.gz
  Lichcory: /bigdata/stajichlab/jstajich/projects/NovInvenio_Investigations/studies/fungi/chytrid_vs_mucoromycota/annotations/UP000027586.tsv.gz
  Phycblak: /bigdata/stajichlab/jstajich/projects/NovInvenio_Investigations/studies/fungi/chytrid_vs_mucoromycota/annotations/UP000077315.tsv.gz
  Absiglau: /bigdata/stajichlab/jstajich/projects/NovInvenio_Investigations/studies/fungi/chytrid_vs_mucoromycota/annotations/UP000078561.tsv.gz
  Syncrace: /bigdata/stajichlab/jstajich/projects/NovInvenio_Investigations/studies/fungi/chytrid_vs_mucoromycota/annotations/UP000242180.tsv.gz
  Choacucu: /bigdata/stajichlab/jstajich/projects/NovInvenio_Investigations/studies/fungi/chytrid_vs_mucoromycota/annotations/UP000093000.tsv.gz
  Hessvesi: /bigdata/stajichlab/jstajich/projects/NovInvenio_Investigations/studies/fungi/chytrid_vs_mucoromycota/annotations/UP000242146.tsv.gz
  Umbevina: /bigdata/stajichlab/jstajich/projects/NovInvenio_Investigations/studies/fungi/chytrid_vs_mucoromycota/annotations/UP000612746.tsv.gz
  Mortisab: /bigdata/stajichlab/jstajich/projects/NovInvenio_Investigations/studies/fungi/chytrid_vs_mucoromycota/annotations/UP000654370.tsv.gz
  Thamspha: /bigdata/stajichlab/jstajich/projects/NovInvenio_Investigations/studies/fungi/chytrid_vs_mucoromycota/annotations/UP000271241.tsv.gz
  Batrdend: /bigdata/stajichlab/jstajich/projects/NovInvenio_Investigations/studies/fungi/chytrid_vs_mucoromycota/annotations/UP000007241.tsv.gz
  Batrsala: /bigdata/stajichlab/jstajich/projects/NovInvenio_Investigations/studies/fungi/chytrid_vs_mucoromycota/annotations/UP001648503.tsv.gz
  Spizpunc: /bigdata/stajichlab/jstajich/projects/NovInvenio_Investigations/studies/fungi/chytrid_vs_mucoromycota/annotations/UP000053201.tsv.gz
  Powehirt: /bigdata/stajichlab/jstajich/projects/NovInvenio_Investigations/studies/fungi/chytrid_vs_mucoromycota/annotations/UP000318582.tsv.gz
  Geravari: /bigdata/stajichlab/jstajich/projects/NovInvenio_Investigations/studies/fungi/chytrid_vs_mucoromycota/annotations/UP001212152.tsv.gz
  Syncendo: /bigdata/stajichlab/jstajich/projects/NovInvenio_Investigations/studies/fungi/chytrid_vs_mucoromycota/annotations/UP000317494.tsv.gz
  Syncmicr: /bigdata/stajichlab/jstajich/projects/NovInvenio_Investigations/studies/fungi/chytrid_vs_mucoromycota/annotations/UP000319731.tsv.gz
  Chytconf: /bigdata/stajichlab/jstajich/projects/NovInvenio_Investigations/studies/fungi/chytrid_vs_mucoromycota/annotations/UP000320333.tsv.gz
  Polystew: /bigdata/stajichlab/jstajich/projects/NovInvenio_Investigations/studies/fungi/chytrid_vs_mucoromycota/annotations/UP001527925.tsv.gz
  Rhizglob: /bigdata/stajichlab/jstajich/projects/NovInvenio_Investigations/studies/fungi/chytrid_vs_mucoromycota/annotations/UP000193642.tsv.gz
  Rhizrose: /bigdata/stajichlab/jstajich/projects/NovInvenio_Investigations/studies/fungi/chytrid_vs_mucoromycota/annotations/UP001212841.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: 9295
  candidates_txt: 9295
  symmetric_difference: 0
  candidates_file: /bigdata/stajichlab/jstajich/projects/NovInvenio_Investigations/results/chytrid_vs_mucoromycota/loss_candidates.txt
  presence_matrix: /bigdata/stajichlab/jstajich/projects/NovInvenio_Investigations/results/chytrid_vs_mucoromycota/loss_presence_matrix.tsv
  rule: OUT count / 11 >= 0.75 and IN count / 11 <= 0.0 (own proteome counts toward the target group)
  only_in_matrix_rule: []
  only_in_candidates_file: []
background_clustering:
  key: 25517acce90b7da3
  n_sequences: 121980
  n_clusters: 48216
  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: 80.7
  threads: 8
  created: '2026-10-12T18:26:55'
  cache_hit: false
pipeline_candidate_families: '/bigdata/stajichlab/jstajich/projects/NovInvenio_Investigations/results/chytrid_vs_mucoromycota/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/chytrid_vs_mucoromycota/config.csv: 6987c9119529729166920e02a2acb9a4cef5e6f3eed932cf1ff78cda22bf6581
  /bigdata/stajichlab/jstajich/projects/NovInvenio_Investigations/results/chytrid_vs_mucoromycota/loss_candidates.txt: b7f1f91c78854ffef824727b2f4986904c0a3f6097210e28e3af25ec5ae69c60
  ? /bigdata/stajichlab/jstajich/projects/NovInvenio_Investigations/results/chytrid_vs_mucoromycota/clusters/loss_clusters_cluster.tsv
  : 404c9294eed78de5e7873319370eae414b5a5d80fa5d09de546ee9544ea99216
  /bigdata/stajichlab/jstajich/projects/NovInvenio_Investigations/results/chytrid_vs_mucoromycota/loss_presence_matrix.tsv: 56dff5952f5e443b84063f98dc9ca183602d2a16a32b69c27dd6192bc4f43c3d
  ? /bigdata/stajichlab/jstajich/projects/NovInvenio_Investigations/studies/fungi/chytrid_vs_mucoromycota/data_dir/pep/UP000014254_1220926.pep.fa
  : 3b012673b05d0822caa95402ff9dd1ac83fd96fec77d37a9cd3fd4c598f7dc93
  ? /bigdata/stajichlab/jstajich/projects/NovInvenio_Investigations/studies/fungi/chytrid_vs_mucoromycota/data_dir/pep/UP000009138_246409.pep.fa
  : c7f8bbbfc379233d7d53dbd68e9df55ba747e174819a5a0bf7c91719d4c092a6
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  : d6d9bf154211859b8ee5d6ce8d268960a9a0fc0c7a3377310368835e23417c91
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  : bf81d11d8fa875f69dbbed357058bdfa01d288787ea19dcedf225e204e2ce303
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  : a76e2fabc040673da768be36cb28dce1277813c35a387550464c13863a26b2af
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  : 1f5f57230ffaa3a34649c6f62f2db28014e3a6bda55aaa6acc839cd9a3146e0c
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  : cda8101b4b149df18f2788bbf4e60115b6d6d28763ad4f1ad6ce7d5701bcda03
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  : f414c2815acc40eba2da1abf0a1bfdebf583111b7de5f6415730b9d664d84699
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tools:
  python: 3.12.14
  scipy: 1.18.1
  goatools: 1.6.4
  mmseqs: 18.8cc5c
runtimes_s:
  load_s: 10.7
  background_cluster_s: 82.3
  tests_s: 18.7
  total_s: 118.1
host: r11
slurm_job: '29893778'
candidate_annotation:
  frac_loss_candidates_any_annotation: 0.6298
  low_coverage: false
  rule: "low_coverage = fraction < 0.5 (flag only; no run was excluded on this value)"
  wall_s_enrichment: 121