generated: '2026-10-12T14:46:00'
study: chytrid_vs_mucoromycota
script:
  path: /bigdata/stajichlab/jstajich/projects/NovInvenio_Investigations/studies/fungi/zoosporic_dikarya/analysis/enrichment/enrich_novelties_v2.py
  sha256: 199f750f1ebbeb473fc6204d0435b712f565039b8460e5f08108c49d9752ccf2
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 4 --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/fungi/chytrid_vs_mucoromycota/analysis/enrichment/outputs/proteome_clustered
class: ephemeral analysis output (not tracked; regenerate with the command above)
universe: proteome
annotations: /bigdata/stajichlab/jstajich/projects/NovInvenio_Investigations/studies/fungi/chytrid_vs_mucoromycota/annotations
annotation_files:
  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
  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
parameters:
  min_bg: 5
  exclude_iea: false
  report_ids_fdr: 0.05
  ingroup_min_frac: 0.75
  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: 4868
  candidates_txt: 4868
  symmetric_difference: 0
background_clustering:
  key: 867b83fe8f946aec
  n_sequences: 101239
  n_clusters: 49924
  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: 183.4
  threads: 4
  created: '2026-10-12T14:45:39'
  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)'
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/candidates.txt: 9c55ef41e5e49da4f0cbb605364fbf14bea8a211ac4cf36d29fc3b3f01fd63cd
  /bigdata/stajichlab/jstajich/projects/NovInvenio_Investigations/results/chytrid_vs_mucoromycota/novelties.Batrdend.tsv: b27c867cd2334eac7ffe004ebce2a079124ef6ce67fa6528c246dfccf7e583d3
  /bigdata/stajichlab/jstajich/projects/NovInvenio_Investigations/results/chytrid_vs_mucoromycota/novelties.Batrsala.tsv: 2f24645bee46f01083bda28fea2334723dbdc1c821c2e45fc5ff16c96f127e3c
  /bigdata/stajichlab/jstajich/projects/NovInvenio_Investigations/results/chytrid_vs_mucoromycota/novelties.Spizpunc.tsv: 35cf687868bd604d30142c6c93ef5e94561f6723b0159e0204c2f7e565e0fb49
  /bigdata/stajichlab/jstajich/projects/NovInvenio_Investigations/results/chytrid_vs_mucoromycota/novelties.Powehirt.tsv: 98f26d5c72cdb0b2bb888f2879ecb255617f910c6caec6819c8273134090202e
  /bigdata/stajichlab/jstajich/projects/NovInvenio_Investigations/results/chytrid_vs_mucoromycota/novelties.Geravari.tsv: b4ecb7dc647386f20ecd26ed8c495700953aa97b34dcb4c77395ff4015e09341
  /bigdata/stajichlab/jstajich/projects/NovInvenio_Investigations/results/chytrid_vs_mucoromycota/novelties.Syncendo.tsv: 9bc28651bcbe60018dd3ec965c2a0929b400cc1ef87623b563088a397b340b79
  /bigdata/stajichlab/jstajich/projects/NovInvenio_Investigations/results/chytrid_vs_mucoromycota/novelties.Syncmicr.tsv: 6c935f1b0897ed8caa11ec12ab7f0d7c13667e72fbff82dd8ab9868ff18786fe
  /bigdata/stajichlab/jstajich/projects/NovInvenio_Investigations/results/chytrid_vs_mucoromycota/novelties.Chytconf.tsv: 3b39e9a97eeef6c1c0171c5b9bff070989c2248078ae6249d141086e365b16a6
  /bigdata/stajichlab/jstajich/projects/NovInvenio_Investigations/results/chytrid_vs_mucoromycota/novelties.Polystew.tsv: 720307e8697209be8939a85a0f278a54c9d7f743138c9e481e5fdb6dbf90b5b5
  /bigdata/stajichlab/jstajich/projects/NovInvenio_Investigations/results/chytrid_vs_mucoromycota/novelties.Rhizglob.tsv: d411a11748fd84b1e000d3d01f6a295177c1346bfe7e92f6b59f86561a374957
  /bigdata/stajichlab/jstajich/projects/NovInvenio_Investigations/results/chytrid_vs_mucoromycota/novelties.Rhizrose.tsv: ec802c4d2ddd8388225be29d8dd7e23ac577929c876d2b69321c88990d9f6700
  ? /bigdata/stajichlab/jstajich/projects/NovInvenio_Investigations/results/chytrid_vs_mucoromycota/presence_matrix.uniprot.tsv
  : b6983b9c18e42ea48ffb7f3a2da0d38c8e6392ed5500c98b9d7bafdec7d80a77
  ? /bigdata/stajichlab/jstajich/projects/NovInvenio_Investigations/studies/fungi/chytrid_vs_mucoromycota/data_dir/pep/UP000007241_684364.pep.fa
  : 4e4c6abb18055c8c0ed97e584c71e1919acb4afb8aa9afd89ed5870347126ae4
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tools:
  python: 3.12.14
  scipy: 1.18.1
  goatools: 1.6.4
  mmseqs: 18.8cc5c
runtimes_s:
  load_s: 10.2
  background_cluster_s: 185.0
  tests_s: 15.0
  total_s: 216.2
host: r11
slurm_job: '29892523'