generated: '2026-10-14T21:59:54'
study: UHM_Koxytoca
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/UHM_Koxytoca --config /bigdata/stajichlab/jstajich/projects/NovInvenio_Investigations/studies/bacteria/UHM_Koxytoca/config.csv
  --presence-matrix /bigdata/stajichlab/jstajich/projects/NovInvenio_Investigations/results/UHM_Koxytoca/presence_matrix.tsv
  --proteins-dir /bigdata/stajichlab/jstajich/projects/NovInvenio_Investigations/studies/bacteria/UHM_Koxytoca/data_dir_enrich_prefixed/pep
  --annotations /bigdata/stajichlab/jstajich/projects/NovInvenio_Investigations/studies/bacteria/UHM_Koxytoca/data_dir_enrich_prefixed/annotations
  --study UHM_Koxytoca --cache-dir /bigdata/stajichlab/jstajich/projects/NovInvenio_Investigations/studies/bacteria/UHM_Koxytoca/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/bacteria/UHM_Koxytoca/analysis/enrichment/outputs/proteome_clustered
class: ephemeral analysis output (not tracked; regenerate with the command above)
direction: novelty
target_group:
  label: IN
  species:
  - UHM102bin47
  - UHM125bin22
  - UHM125bin48
  - UHM145bin17
  - UHM145bin33
  - UHM145bin28
  - UHM17bin35
  - UHM18bin40
  - UHM20bin40
  - UHM20bin12
  - UHM22bin50
  - UHM22bin54
  - UHM22bin8
  - UHM40bin4
  - UHM40bin27
  - UHM43bin53
  - UHM56bin19
  - UHM72bin19
other_group:
  label: OUT
  species:
  - KoxO_050916275
  - KoxO_017310465
  - KoxO_929608445
  - KoxO_040561445
  - KoxO_900083795
  - KoxO_024918735
  - KoxO_902162875
  - KoxO_053276915
  - KoxO_030343105
  - KoxO_030343375
  - KoxO_016734995
  - KoxO_030343565
  - KoxO_900083995
  - KoxO_004360035
  - KoxO_030344075
  - KoxO_051951865
universe: proteome
annotations: /bigdata/stajichlab/jstajich/projects/NovInvenio_Investigations/studies/bacteria/UHM_Koxytoca/data_dir_enrich_prefixed/annotations
annotation_files:
  UHM102bin47: /bigdata/stajichlab/jstajich/projects/NovInvenio_Investigations/studies/bacteria/UHM_Koxytoca/data_dir_enrich_prefixed/annotations/UHM102.35765_R.bin.47.tsv.gz
  UHM125bin22: /bigdata/stajichlab/jstajich/projects/NovInvenio_Investigations/studies/bacteria/UHM_Koxytoca/data_dir_enrich_prefixed/annotations/UHM125.35768_R.bin.22.tsv.gz
  UHM125bin48: /bigdata/stajichlab/jstajich/projects/NovInvenio_Investigations/studies/bacteria/UHM_Koxytoca/data_dir_enrich_prefixed/annotations/UHM125.35770_R.bin.48.tsv.gz
  UHM145bin17: /bigdata/stajichlab/jstajich/projects/NovInvenio_Investigations/studies/bacteria/UHM_Koxytoca/data_dir_enrich_prefixed/annotations/UHM145.35771_R.bin.17.tsv.gz
  UHM145bin33: /bigdata/stajichlab/jstajich/projects/NovInvenio_Investigations/studies/bacteria/UHM_Koxytoca/data_dir_enrich_prefixed/annotations/UHM145.35772_R.bin.33.tsv.gz
  UHM145bin28: /bigdata/stajichlab/jstajich/projects/NovInvenio_Investigations/studies/bacteria/UHM_Koxytoca/data_dir_enrich_prefixed/annotations/UHM145.35773_R.bin.28.tsv.gz
  UHM17bin35: /bigdata/stajichlab/jstajich/projects/NovInvenio_Investigations/studies/bacteria/UHM_Koxytoca/data_dir_enrich_prefixed/annotations/UHM17.35739_R.bin.35.tsv.gz
  UHM18bin40: /bigdata/stajichlab/jstajich/projects/NovInvenio_Investigations/studies/bacteria/UHM_Koxytoca/data_dir_enrich_prefixed/annotations/UHM18.35742_R.bin.40.tsv.gz
  UHM20bin40: /bigdata/stajichlab/jstajich/projects/NovInvenio_Investigations/studies/bacteria/UHM_Koxytoca/data_dir_enrich_prefixed/annotations/UHM20.35743_R.bin.40.tsv.gz
  UHM20bin12: /bigdata/stajichlab/jstajich/projects/NovInvenio_Investigations/studies/bacteria/UHM_Koxytoca/data_dir_enrich_prefixed/annotations/UHM20.35744_R.bin.12.tsv.gz
  UHM22bin50: /bigdata/stajichlab/jstajich/projects/NovInvenio_Investigations/studies/bacteria/UHM_Koxytoca/data_dir_enrich_prefixed/annotations/UHM22.35745_R.bin.50.tsv.gz
  UHM22bin54: /bigdata/stajichlab/jstajich/projects/NovInvenio_Investigations/studies/bacteria/UHM_Koxytoca/data_dir_enrich_prefixed/annotations/UHM22.35746_R.bin.54.tsv.gz
  UHM22bin8: /bigdata/stajichlab/jstajich/projects/NovInvenio_Investigations/studies/bacteria/UHM_Koxytoca/data_dir_enrich_prefixed/annotations/UHM22.35747_R.bin.8.tsv.gz
  UHM40bin4: /bigdata/stajichlab/jstajich/projects/NovInvenio_Investigations/studies/bacteria/UHM_Koxytoca/data_dir_enrich_prefixed/annotations/UHM40.35754_R.bin.4.tsv.gz
  UHM40bin27: /bigdata/stajichlab/jstajich/projects/NovInvenio_Investigations/studies/bacteria/UHM_Koxytoca/data_dir_enrich_prefixed/annotations/UHM40.35755_R.bin.27.tsv.gz
  UHM43bin53: /bigdata/stajichlab/jstajich/projects/NovInvenio_Investigations/studies/bacteria/UHM_Koxytoca/data_dir_enrich_prefixed/annotations/UHM43.10836_R.bin.53.tsv.gz
  UHM56bin19: /bigdata/stajichlab/jstajich/projects/NovInvenio_Investigations/studies/bacteria/UHM_Koxytoca/data_dir_enrich_prefixed/annotations/UHM56.35760_R.bin.19.tsv.gz
  UHM72bin19: /bigdata/stajichlab/jstajich/projects/NovInvenio_Investigations/studies/bacteria/UHM_Koxytoca/data_dir_enrich_prefixed/annotations/UHM72.35762_R.bin.19.tsv.gz
  KoxO_050916275: /bigdata/stajichlab/jstajich/projects/NovInvenio_Investigations/studies/bacteria/UHM_Koxytoca/data_dir_enrich_prefixed/annotations/GCF_050916275.1.tsv.gz
  KoxO_017310465: /bigdata/stajichlab/jstajich/projects/NovInvenio_Investigations/studies/bacteria/UHM_Koxytoca/data_dir_enrich_prefixed/annotations/GCF_017310465.1.tsv.gz
  KoxO_929608445: /bigdata/stajichlab/jstajich/projects/NovInvenio_Investigations/studies/bacteria/UHM_Koxytoca/data_dir_enrich_prefixed/annotations/GCF_929608445.1.tsv.gz
  KoxO_040561445: /bigdata/stajichlab/jstajich/projects/NovInvenio_Investigations/studies/bacteria/UHM_Koxytoca/data_dir_enrich_prefixed/annotations/GCF_040561445.1.tsv.gz
  KoxO_900083795: /bigdata/stajichlab/jstajich/projects/NovInvenio_Investigations/studies/bacteria/UHM_Koxytoca/data_dir_enrich_prefixed/annotations/GCF_900083795.1.tsv.gz
  KoxO_024918735: /bigdata/stajichlab/jstajich/projects/NovInvenio_Investigations/studies/bacteria/UHM_Koxytoca/data_dir_enrich_prefixed/annotations/GCF_024918735.1.tsv.gz
  KoxO_902162875: /bigdata/stajichlab/jstajich/projects/NovInvenio_Investigations/studies/bacteria/UHM_Koxytoca/data_dir_enrich_prefixed/annotations/GCF_902162875.1.tsv.gz
  KoxO_053276915: /bigdata/stajichlab/jstajich/projects/NovInvenio_Investigations/studies/bacteria/UHM_Koxytoca/data_dir_enrich_prefixed/annotations/GCF_053276915.1.tsv.gz
  KoxO_030343105: /bigdata/stajichlab/jstajich/projects/NovInvenio_Investigations/studies/bacteria/UHM_Koxytoca/data_dir_enrich_prefixed/annotations/GCF_030343105.1.tsv.gz
  KoxO_030343375: /bigdata/stajichlab/jstajich/projects/NovInvenio_Investigations/studies/bacteria/UHM_Koxytoca/data_dir_enrich_prefixed/annotations/GCF_030343375.1.tsv.gz
  KoxO_016734995: /bigdata/stajichlab/jstajich/projects/NovInvenio_Investigations/studies/bacteria/UHM_Koxytoca/data_dir_enrich_prefixed/annotations/GCF_016734995.1.tsv.gz
  KoxO_030343565: /bigdata/stajichlab/jstajich/projects/NovInvenio_Investigations/studies/bacteria/UHM_Koxytoca/data_dir_enrich_prefixed/annotations/GCF_030343565.1.tsv.gz
  KoxO_900083995: /bigdata/stajichlab/jstajich/projects/NovInvenio_Investigations/studies/bacteria/UHM_Koxytoca/data_dir_enrich_prefixed/annotations/GCF_900083995.1.tsv.gz
  KoxO_004360035: /bigdata/stajichlab/jstajich/projects/NovInvenio_Investigations/studies/bacteria/UHM_Koxytoca/data_dir_enrich_prefixed/annotations/GCF_004360035.1.tsv.gz
  KoxO_030344075: /bigdata/stajichlab/jstajich/projects/NovInvenio_Investigations/studies/bacteria/UHM_Koxytoca/data_dir_enrich_prefixed/annotations/GCF_030344075.1.tsv.gz
  KoxO_051951865: /bigdata/stajichlab/jstajich/projects/NovInvenio_Investigations/studies/bacteria/UHM_Koxytoca/data_dir_enrich_prefixed/annotations/GCF_051951865.1.tsv.gz
annotation_sources:
  UHM102bin47: Pfam-A HMM search (hmmsearch); Pfam only
  UHM125bin22: Pfam-A HMM search (hmmsearch); Pfam only
  UHM125bin48: Pfam-A HMM search (hmmsearch); Pfam only
  UHM145bin17: Pfam-A HMM search (hmmsearch); Pfam only
  UHM145bin33: Pfam-A HMM search (hmmsearch); Pfam only
  UHM145bin28: Pfam-A HMM search (hmmsearch); Pfam only
  UHM17bin35: Pfam-A HMM search (hmmsearch); Pfam only
  UHM18bin40: Pfam-A HMM search (hmmsearch); Pfam only
  UHM20bin40: Pfam-A HMM search (hmmsearch); Pfam only
  UHM20bin12: Pfam-A HMM search (hmmsearch); Pfam only
  UHM22bin50: Pfam-A HMM search (hmmsearch); Pfam only
  UHM22bin54: Pfam-A HMM search (hmmsearch); Pfam only
  UHM22bin8: Pfam-A HMM search (hmmsearch); Pfam only
  UHM40bin4: Pfam-A HMM search (hmmsearch); Pfam only
  UHM40bin27: Pfam-A HMM search (hmmsearch); Pfam only
  UHM43bin53: Pfam-A HMM search (hmmsearch); Pfam only
  UHM56bin19: Pfam-A HMM search (hmmsearch); Pfam only
  UHM72bin19: Pfam-A HMM search (hmmsearch); Pfam only
  KoxO_050916275: Pfam-A HMM search (hmmsearch); Pfam only
  KoxO_017310465: Pfam-A HMM search (hmmsearch); Pfam only
  KoxO_929608445: Pfam-A HMM search (hmmsearch); Pfam only
  KoxO_040561445: Pfam-A HMM search (hmmsearch); Pfam only
  KoxO_900083795: Pfam-A HMM search (hmmsearch); Pfam only
  KoxO_024918735: Pfam-A HMM search (hmmsearch); Pfam only
  KoxO_902162875: Pfam-A HMM search (hmmsearch); Pfam only
  KoxO_053276915: Pfam-A HMM search (hmmsearch); Pfam only
  KoxO_030343105: Pfam-A HMM search (hmmsearch); Pfam only
  KoxO_030343375: Pfam-A HMM search (hmmsearch); Pfam only
  KoxO_016734995: Pfam-A HMM search (hmmsearch); Pfam only
  KoxO_030343565: Pfam-A HMM search (hmmsearch); Pfam only
  KoxO_900083995: Pfam-A HMM search (hmmsearch); Pfam only
  KoxO_004360035: Pfam-A HMM search (hmmsearch); Pfam only
  KoxO_030344075: Pfam-A HMM search (hmmsearch); Pfam only
  KoxO_051951865: Pfam-A HMM search (hmmsearch); Pfam only
vocabulary_coverage:
  pfam:
    species_with_terms:
    - UHM102bin47
    - UHM125bin22
    - UHM125bin48
    - UHM145bin17
    - UHM145bin33
    - UHM145bin28
    - UHM17bin35
    - UHM18bin40
    - UHM20bin40
    - UHM20bin12
    - UHM22bin50
    - UHM22bin54
    - UHM22bin8
    - UHM40bin4
    - UHM40bin27
    - UHM43bin53
    - UHM56bin19
    - UHM72bin19
    species_without_terms: []
    n_with: 18
    n_species: 18
  pfam_clan:
    species_with_terms:
    - UHM102bin47
    - UHM125bin22
    - UHM125bin48
    - UHM145bin17
    - UHM145bin33
    - UHM145bin28
    - UHM17bin35
    - UHM18bin40
    - UHM20bin40
    - UHM20bin12
    - UHM22bin50
    - UHM22bin54
    - UHM22bin8
    - UHM40bin4
    - UHM40bin27
    - UHM43bin53
    - UHM56bin19
    - UHM72bin19
    species_without_terms: []
    n_with: 18
    n_species: 18
  interpro:
    species_with_terms: []
    species_without_terms:
    - UHM102bin47
    - UHM125bin22
    - UHM125bin48
    - UHM145bin17
    - UHM145bin33
    - UHM145bin28
    - UHM17bin35
    - UHM18bin40
    - UHM20bin40
    - UHM20bin12
    - UHM22bin50
    - UHM22bin54
    - UHM22bin8
    - UHM40bin4
    - UHM40bin27
    - UHM43bin53
    - UHM56bin19
    - UHM72bin19
    n_with: 0
    n_species: 18
  go:
    species_with_terms: []
    species_without_terms:
    - UHM102bin47
    - UHM125bin22
    - UHM125bin48
    - UHM145bin17
    - UHM145bin33
    - UHM145bin28
    - UHM17bin35
    - UHM18bin40
    - UHM20bin40
    - UHM20bin12
    - UHM22bin50
    - UHM22bin54
    - UHM22bin8
    - UHM40bin4
    - UHM40bin27
    - UHM43bin53
    - UHM56bin19
    - UHM72bin19
    n_with: 0
    n_species: 18
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: 697
  candidates_txt: 697
  symmetric_difference: 0
  candidates_file: /bigdata/stajichlab/jstajich/projects/NovInvenio_Investigations/results/UHM_Koxytoca/candidates.txt
  presence_matrix: /bigdata/stajichlab/jstajich/projects/NovInvenio_Investigations/results/UHM_Koxytoca/presence_matrix.tsv
  rule: IN count / 18 >= 0.75 and OUT count / 16 <= 0.0 (own proteome counts toward the target group)
  only_in_matrix_rule: []
  only_in_candidates_file: []
background_clustering:
  key: cfdaa8d7df847b96
  n_sequences: 84356
  n_clusters: 8840
  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: 13.4
  threads: 8
  created: '2026-10-14T21:59:44'
  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)'
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/bacteria/UHM_Koxytoca/config.csv: cfb62f71e826777ec08b4ab7d30814b8e870f7569e70b26f2fba927b847d7057
  /bigdata/stajichlab/jstajich/projects/NovInvenio_Investigations/results/UHM_Koxytoca/candidates.txt: 26338c1e2a8a52e010ab172e21d736a02026f207d03fd4f178ac259645f7e710
  /bigdata/stajichlab/jstajich/projects/NovInvenio_Investigations/results/UHM_Koxytoca/novelties.UHM102bin47.tsv: 3a7897a335d7e6794304f20093541e131d9fce7855828aa4ffbf5c99ea340548
  /bigdata/stajichlab/jstajich/projects/NovInvenio_Investigations/results/UHM_Koxytoca/novelties.UHM125bin22.tsv: 258e48f7daa0cb1951891b57931838ee59a65e7eb09f08113996829901e93d9d
  /bigdata/stajichlab/jstajich/projects/NovInvenio_Investigations/results/UHM_Koxytoca/novelties.UHM125bin48.tsv: 8c77f0c042dac79819a9b9bd2f41973a2a6de3f073213b9586d61dc660402ba2
  /bigdata/stajichlab/jstajich/projects/NovInvenio_Investigations/results/UHM_Koxytoca/novelties.UHM145bin17.tsv: e40906b48ba963a246bf76d71828f5c97ae723017c39efa0b02cb2dbd5b3db39
  /bigdata/stajichlab/jstajich/projects/NovInvenio_Investigations/results/UHM_Koxytoca/novelties.UHM145bin33.tsv: 2b86530712470aad99f59aeb9a5eeb4edf204b760e242bc90c85773bf8b03123
  /bigdata/stajichlab/jstajich/projects/NovInvenio_Investigations/results/UHM_Koxytoca/novelties.UHM145bin28.tsv: 45e86fd11bb14e2d7f1e257019bf6b6737138bdddc7f70042062d9f5244f832d
  /bigdata/stajichlab/jstajich/projects/NovInvenio_Investigations/results/UHM_Koxytoca/novelties.UHM17bin35.tsv: c79cb07b7325041fa963fcaee746d0930ab13507f935ab3ae9e41c5f774afd43
  /bigdata/stajichlab/jstajich/projects/NovInvenio_Investigations/results/UHM_Koxytoca/novelties.UHM18bin40.tsv: 4ece524df916e0cb42a534abf1350119668994055e54a19b26878fff7286bae1
  /bigdata/stajichlab/jstajich/projects/NovInvenio_Investigations/results/UHM_Koxytoca/novelties.UHM20bin40.tsv: a4125980377ef8e12501821eb47e08b87c50deb87586cf185a124431e548fc0f
  /bigdata/stajichlab/jstajich/projects/NovInvenio_Investigations/results/UHM_Koxytoca/novelties.UHM20bin12.tsv: aca60a239efb5d60deb40c1bb50b68436bcfca2407fcaf50a5111bffc6230b61
  /bigdata/stajichlab/jstajich/projects/NovInvenio_Investigations/results/UHM_Koxytoca/novelties.UHM22bin50.tsv: df4a02e0c069a59489c4e9db94aeb822f10d6691bd55ba878036edb6d0fb5cb3
  /bigdata/stajichlab/jstajich/projects/NovInvenio_Investigations/results/UHM_Koxytoca/novelties.UHM22bin54.tsv: a96479f284396fd8b5a1ebc14afecdc007bb0a0aade61bb3553dda5cfdc8235e
  /bigdata/stajichlab/jstajich/projects/NovInvenio_Investigations/results/UHM_Koxytoca/novelties.UHM22bin8.tsv: 0f86426c36ebdbb909cf108bfdd03d95cf42105cebdb98a5d270f8ae6d8280d7
  /bigdata/stajichlab/jstajich/projects/NovInvenio_Investigations/results/UHM_Koxytoca/novelties.UHM40bin4.tsv: a29dec12cbeb5a51dca46e2e80099c7b101f270862cfa148770050a993ee1572
  /bigdata/stajichlab/jstajich/projects/NovInvenio_Investigations/results/UHM_Koxytoca/novelties.UHM40bin27.tsv: c5960c81e4a297ba0a2923c061a87f7927fc2559969d81a6a361f49dde4fc944
  /bigdata/stajichlab/jstajich/projects/NovInvenio_Investigations/results/UHM_Koxytoca/novelties.UHM43bin53.tsv: dd2d4e5621f745a391e1ec89e9206df46d68ac6666e1a97f2a051025f054582f
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tools:
  python: 3.12.14
  scipy: 1.18.1
  goatools: 1.6.4
  mmseqs: 18.8cc5c
runtimes_s:
  load_s: 5.2
  background_cluster_s: 14.2
  tests_s: 4.9
  total_s: 29.8
host: r22
slurm_job: '29966708'
wall_s_enrichment: 32