generated: '2026-10-13T22:10:41'
study: yeast_filamentous
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/yeast_filamentous --config /bigdata/stajichlab/jstajich/projects/NovInvenio_Investigations/studies/fungi/yeast_filamentous/config.csv
  --annotations /bigdata/stajichlab/jstajich/projects/NovInvenio_Investigations/studies/fungi/yeast_filamentous/annotations
  --study yeast_filamentous --cache-dir /bigdata/stajichlab/jstajich/projects/NovInvenio_Investigations/studies/fungi/yeast_filamentous/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/yeast_filamentous/analysis/enrichment/outputs/loss/proteome_clustered
class: ephemeral analysis output (not tracked; regenerate with the command above)
direction: loss
target_group:
  label: OUT
  species:
  - Ncra
  - Afum
  - Ztri
  - Cimm
other_group:
  label: IN
  species:
  - Scer
  - Ylip
  - Spom
  - Nirr
universe: proteome
annotations: /bigdata/stajichlab/jstajich/projects/NovInvenio_Investigations/studies/fungi/yeast_filamentous/annotations
annotation_files:
  Ncra: /bigdata/stajichlab/jstajich/projects/NovInvenio_Investigations/studies/fungi/yeast_filamentous/annotations/UP000001805.tsv.gz
  Afum: /bigdata/stajichlab/jstajich/projects/NovInvenio_Investigations/studies/fungi/yeast_filamentous/annotations/UP000002530.tsv.gz
  Ztri: /bigdata/stajichlab/jstajich/projects/NovInvenio_Investigations/studies/fungi/yeast_filamentous/annotations/UP000008062.tsv.gz
  Cimm: /bigdata/stajichlab/jstajich/projects/NovInvenio_Investigations/studies/fungi/yeast_filamentous/annotations/UP000001261.tsv.gz
  Scer: /bigdata/stajichlab/jstajich/projects/NovInvenio_Investigations/studies/fungi/yeast_filamentous/annotations/UP000002311.tsv.gz
  Ylip: /bigdata/stajichlab/jstajich/projects/NovInvenio_Investigations/studies/fungi/yeast_filamentous/annotations/UP000001300.tsv.gz
  Spom: /bigdata/stajichlab/jstajich/projects/NovInvenio_Investigations/studies/fungi/yeast_filamentous/annotations/UP000002485.tsv.gz
  Nirr: /bigdata/stajichlab/jstajich/projects/NovInvenio_Investigations/studies/fungi/yeast_filamentous/annotations/UP000186594.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: 5060
  candidates_txt: 5060
  symmetric_difference: 0
  candidates_file: /bigdata/stajichlab/jstajich/projects/NovInvenio_Investigations/results/yeast_filamentous/loss_candidates.txt
  presence_matrix: /bigdata/stajichlab/jstajich/projects/NovInvenio_Investigations/results/yeast_filamentous/loss_presence_matrix.tsv
  rule: OUT count / 4 >= 0.75 and IN count / 4 <= 0.0 (own proteome counts toward the target group)
  only_in_matrix_rule: []
  only_in_candidates_file: []
background_clustering:
  key: 8c67b54b9fea3e10
  n_sequences: 34884
  n_clusters: 19574
  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: 39.5
  threads: 8
  created: '2026-10-13T22:10:32'
  cache_hit: false
pipeline_candidate_families: '/bigdata/stajichlab/jstajich/projects/NovInvenio_Investigations/results/yeast_filamentous/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/yeast_filamentous/config.csv: 7d9f4aed52daccafe58dd82b33898e496d8ab8ee320442a1f978ba5ad9e183f1
  /bigdata/stajichlab/jstajich/projects/NovInvenio_Investigations/results/yeast_filamentous/loss_candidates.txt: 5cca00ba68c78aa3733c7a284d22b5980651b7eabbb8b6559bd3245c7a250073
  ? /bigdata/stajichlab/jstajich/projects/NovInvenio_Investigations/results/yeast_filamentous/clusters/loss_clusters_cluster.tsv
  : fe2d460c2db9d1dd7b7613b873d1d292c01ee8a289b9d40237c1efce34db253e
  /bigdata/stajichlab/jstajich/projects/NovInvenio_Investigations/results/yeast_filamentous/loss_presence_matrix.tsv: 730659df7e4331096c5882a5fa2abd34264d5609d10bc929ba18b0ecc239f05b
  /bigdata/stajichlab/jstajich/projects/NovInvenio_Investigations/studies/fungi/yeast_filamentous/data_dir/pep/Ncra.pep.fa: 64510ca60f0efbd7831689a409eafcd1ad5251eb1a541663a223f396148d54eb
  /bigdata/stajichlab/jstajich/projects/NovInvenio_Investigations/studies/fungi/yeast_filamentous/data_dir/pep/Afum.pep.fa: 1e888bb1a1aa58b9ff6adf3eb221affa7a67c57618aa4663eebaeea81eea7a28
  /bigdata/stajichlab/jstajich/projects/NovInvenio_Investigations/studies/fungi/yeast_filamentous/data_dir/pep/Ztri.pep.fa: 3224be4a0ac028418b7571d322c8e837d85c1a3923bb0a606d4e2898b6b3673a
  /bigdata/stajichlab/jstajich/projects/NovInvenio_Investigations/studies/fungi/yeast_filamentous/data_dir/pep/Cimm.pep.fa: 71b0445457051f4e4faaf2fbf45f35c4c88e5722e5f890c28ed5deac1d7e9e3a
  /bigdata/stajichlab/jstajich/projects/NovInvenio_Investigations/studies/fungi/yeast_filamentous/species.csv: 3f5cf348c1336045eb6a1accb7c8a4caff183853ed34d361e31df675137acaa4
  ? /bigdata/stajichlab/jstajich/projects/NovInvenio_Investigations/studies/fungi/yeast_filamentous/annotations/UP000001805.tsv.gz
  : 2fe385fe609645a3e1f85faf672397e2e1998eabb9cddfc5bf182e1af77622f5
  ? /bigdata/stajichlab/jstajich/projects/NovInvenio_Investigations/studies/fungi/yeast_filamentous/annotations/UP000002530.tsv.gz
  : 2dbbdd01574c9ea2b90088f120aab8fc29a67c1bdb744e1f73d61abc5bcdfea9
  ? /bigdata/stajichlab/jstajich/projects/NovInvenio_Investigations/studies/fungi/yeast_filamentous/annotations/UP000008062.tsv.gz
  : af1e9dbdce9292f6b38b276f773511f1ef51c150861c865f258a98ab6858aac9
  ? /bigdata/stajichlab/jstajich/projects/NovInvenio_Investigations/studies/fungi/yeast_filamentous/annotations/UP000001261.tsv.gz
  : e6b9f7a7dc7bcb925b751f075bd9c9f6c6fbc62873683af47e8ce789c45047d8
  ? /bigdata/stajichlab/jstajich/projects/NovInvenio_Investigations/studies/fungi/yeast_filamentous/annotations/UP000002311.tsv.gz
  : c48e3f8fb0332e1ef974268e7601151dd797a6881a2970da74baf5f28bd07e91
  ? /bigdata/stajichlab/jstajich/projects/NovInvenio_Investigations/studies/fungi/yeast_filamentous/annotations/UP000001300.tsv.gz
  : 47a6a7ddf6ddf464fe4f06d78e2f51e63a694cf9a50535581ef60dadec7f84ac
  ? /bigdata/stajichlab/jstajich/projects/NovInvenio_Investigations/studies/fungi/yeast_filamentous/annotations/UP000002485.tsv.gz
  : cbb108172f3b7d110f33717cc1dde0153d1600da9996f2943d2e0176788cff4f
  ? /bigdata/stajichlab/jstajich/projects/NovInvenio_Investigations/studies/fungi/yeast_filamentous/annotations/UP000186594.tsv.gz
  : b1b704ae1cc5788961c4712e2abc76d7dc4dae06e62d3ef3265048f24c1bb03c
  ? /bigdata/stajichlab/jstajich/projects/NovInvenio_Investigations/studies/fungi/zoosporic_dikarya/analysis/enrichment/actin_controls.tsv
  : dd7c85c91f413f3eee48b75b51c1ad75f7e2de6afcb611c5e0b3659f777a23d1
tools:
  python: 3.12.14
  scipy: 1.18.1
  goatools: 1.6.4
  mmseqs: 18.8cc5c
runtimes_s:
  load_s: 10.0
  background_cluster_s: 40.0
  tests_s: 7.2
  total_s: 58.9
host: r11
slurm_job: '29949100'
candidate_annotation:
  frac_loss_candidates_any_annotation: 0.8065
  low_coverage: false
  rule: "low_coverage = fraction < 0.5 (flag only; no run was excluded on this value)"
  wall_s_enrichment: 114