generated: '2026-10-24T14:42:16' study: yc_pucciniomycotina 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/yc_pucciniomycotina --config /bigdata/stajichlab/jstajich/projects/NovInvenio_Investigations/studies/fungi/yeast_convergence/yc_pucciniomycotina/config.csv --annotations /bigdata/stajichlab/jstajich/projects/NovInvenio_Investigations/studies/fungi/yeast_convergence/yc_pucciniomycotina/annotations --study yc_pucciniomycotina --cache-dir /bigdata/stajichlab/jstajich/projects/NovInvenio_Investigations/studies/fungi/yeast_convergence/yc_pucciniomycotina/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 --direction novelty --out-dir /bigdata/stajichlab/jstajich/projects/NovInvenio_Investigations/studies/fungi/yeast_convergence/yc_pucciniomycotina/analysis/enrichment/outputs/novelty/proteome_clustered class: ephemeral analysis output (not tracked; regenerate with the command above) direction: novelty target_group: label: IN species: - Rhodtoru - Rhodmuci - Rhodgram - Sporrose - Leuccrea other_group: label: OUT species: - Micrlych - Puccgram - Melalari universe: proteome annotations: /bigdata/stajichlab/jstajich/projects/NovInvenio_Investigations/studies/fungi/yeast_convergence/yc_pucciniomycotina/annotations annotation_files: Rhodtoru: /bigdata/stajichlab/jstajich/projects/NovInvenio_Investigations/studies/fungi/yeast_convergence/yc_pucciniomycotina/annotations/GCF_000320785.1.tsv.gz Rhodmuci: /bigdata/stajichlab/jstajich/projects/NovInvenio_Investigations/studies/fungi/yeast_convergence/yc_pucciniomycotina/annotations/UP000777482.tsv.gz Rhodgram: /bigdata/stajichlab/jstajich/projects/NovInvenio_Investigations/studies/fungi/yeast_convergence/yc_pucciniomycotina/annotations/UP000053890.tsv.gz Sporrose: /bigdata/stajichlab/jstajich/projects/NovInvenio_Investigations/studies/fungi/yeast_convergence/yc_pucciniomycotina/annotations/Sporobolomyces_roseus_SR19.proteins.tsv.gz Leuccrea: /bigdata/stajichlab/jstajich/projects/NovInvenio_Investigations/studies/fungi/yeast_convergence/yc_pucciniomycotina/annotations/UP000193467.tsv.gz Micrlych: /bigdata/stajichlab/jstajich/projects/NovInvenio_Investigations/studies/fungi/yeast_convergence/yc_pucciniomycotina/annotations/UP000017200.tsv.gz Puccgram: /bigdata/stajichlab/jstajich/projects/NovInvenio_Investigations/studies/fungi/yeast_convergence/yc_pucciniomycotina/annotations/GCF_000149925.1.tsv.gz Melalari: /bigdata/stajichlab/jstajich/projects/NovInvenio_Investigations/studies/fungi/yeast_convergence/yc_pucciniomycotina/annotations/Melampsora_laricis-populina_98AG31.proteins.tsv.gz annotation_sources: Rhodtoru: Pfam-A HMM search (hmmsearch); Pfam only Rhodmuci: not recorded (no sidecar) Rhodgram: not recorded (no sidecar) Sporrose: Pfam-A HMM search (hmmsearch); Pfam only Leuccrea: not recorded (no sidecar) Micrlych: not recorded (no sidecar) Puccgram: Pfam-A HMM search (hmmsearch); Pfam only Melalari: Pfam-A HMM search (hmmsearch); Pfam only vocabulary_coverage: pfam: species_with_terms: - Rhodtoru - Rhodmuci - Rhodgram - Sporrose - Leuccrea species_without_terms: [] n_with: 5 n_species: 5 pfam_clan: species_with_terms: - Rhodtoru - Rhodmuci - Rhodgram - Sporrose - Leuccrea species_without_terms: [] n_with: 5 n_species: 5 interpro: species_with_terms: - Rhodmuci - Rhodgram - Leuccrea species_without_terms: - Rhodtoru - Sporrose n_with: 3 n_species: 5 go: species_with_terms: - Rhodmuci - Rhodgram - Leuccrea species_without_terms: - Rhodtoru - Sporrose n_with: 3 n_species: 5 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: 2406 candidates_txt: 2406 symmetric_difference: 0 candidates_file: /bigdata/stajichlab/jstajich/projects/NovInvenio_Investigations/results/yc_pucciniomycotina/candidates.txt presence_matrix: /bigdata/stajichlab/jstajich/projects/NovInvenio_Investigations/results/yc_pucciniomycotina/presence_matrix.uniprot.tsv rule: IN count / 5 >= 0.75 and OUT count / 3 <= 0.0 (own proteome counts toward the target group) only_in_matrix_rule: [] only_in_candidates_file: [] background_clustering: key: d2bf56335517e3d7 n_sequences: 38432 n_clusters: 16166 mmseqs: /bigdata/stajichlab/jstajich/projects/NovInvenio_Investigations/.pixi/envs/default/bin/mmseqs mmseqs_version: 18.8cc5c command: mmseqs easy-cluster --threads N --min-seq-id 0.3 -c 0.8 --cov-mode 0 runtime_s: 60.1 threads: 4 created: '2026-10-24T14:42:10' cache_hit: false pipeline_candidate_families: 'novelties..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/fungi/yeast_convergence/yc_pucciniomycotina/config.csv : 2012d08ed3f414d84a44ea0c42742a6d01cd5e754ac3dd3bfd2a8b9e767dd21a /bigdata/stajichlab/jstajich/projects/NovInvenio_Investigations/results/yc_pucciniomycotina/candidates.txt: 9f9e190ccd52845650500334cb6f73dbcd4d042626f51dbcd4106ca4794f12df /bigdata/stajichlab/jstajich/projects/NovInvenio_Investigations/results/yc_pucciniomycotina/novelties.Rhodtoru.tsv: ee9798043bbb490a5a10d45c5925dfa047a0276f6fbf2781256b674be1c93bfa /bigdata/stajichlab/jstajich/projects/NovInvenio_Investigations/results/yc_pucciniomycotina/novelties.Rhodmuci.tsv: 7204e61f67765ebdd29835a23dd99a40673ca7867d6d717f1244ab5e770ee96a /bigdata/stajichlab/jstajich/projects/NovInvenio_Investigations/results/yc_pucciniomycotina/novelties.Rhodgram.tsv: 458e1364190d24565e8e8e78bd07832bef11b01e9b61f421b93483a368b3ff59 /bigdata/stajichlab/jstajich/projects/NovInvenio_Investigations/results/yc_pucciniomycotina/novelties.Sporrose.tsv: ab7d05b194200a996f739d2a25c9f4b8540e2e9fbb281d5ab54a823afebcc769 /bigdata/stajichlab/jstajich/projects/NovInvenio_Investigations/results/yc_pucciniomycotina/novelties.Leuccrea.tsv: ec4d1b7e234441a0b37633dd0efecfa0331a9ea4647f733ca7ddcbdd07a63286 /bigdata/stajichlab/jstajich/projects/NovInvenio_Investigations/results/yc_pucciniomycotina/presence_matrix.uniprot.tsv: 51cd29416df937e0844afe537ac0914235e9fb59b965cee64536095a32ae87b9 ? /bigdata/stajichlab/jstajich/projects/NovInvenio_Investigations/studies/fungi/yeast_convergence/yc_pucciniomycotina/data_dir/pep/Rhodtoru.pep.fa : 6037dd04c51ebd58fbf3042d55d58ad4aa69161914a7e48578cf8bbf97d08b49 ? /bigdata/stajichlab/jstajich/projects/NovInvenio_Investigations/studies/fungi/yeast_convergence/yc_pucciniomycotina/data_dir/pep/UP000777482_5537.pep.fa : 1886ee86145128a1ab297265e005860b9eda577157c32b649d2305587ab47802 ? /bigdata/stajichlab/jstajich/projects/NovInvenio_Investigations/studies/fungi/yeast_convergence/yc_pucciniomycotina/data_dir/pep/UP000053890_578459.pep.fa : 30a9d55be4ffa3d63eff10dfdb5e4c3714695fdafe07659640e24cb759822729 ? /bigdata/stajichlab/jstajich/projects/NovInvenio_Investigations/studies/fungi/yeast_convergence/yc_pucciniomycotina/data_dir/pep/Sporrose.pep.fa : 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/bigdata/stajichlab/jstajich/projects/NovInvenio_Investigations/studies/fungi/yeast_convergence/yc_pucciniomycotina/annotations/UP000053890.tsv.gz : 0ce036b67e82f2677b0063d0965b975aa5249556d86e9502badd353c6b954439 ? /bigdata/stajichlab/jstajich/projects/NovInvenio_Investigations/studies/fungi/yeast_convergence/yc_pucciniomycotina/annotations/Sporobolomyces_roseus_SR19.proteins.tsv.gz : 14b1e7ca9faa2b0326541ac83a8170fb59ccc0f7f4d64a4e457131d1c80265a1 ? /bigdata/stajichlab/jstajich/projects/NovInvenio_Investigations/studies/fungi/yeast_convergence/yc_pucciniomycotina/annotations/UP000193467.tsv.gz : 6313562242b0454d899748a8802823f1801cdbaa117b0ab62148a03d195dd902 ? /bigdata/stajichlab/jstajich/projects/NovInvenio_Investigations/studies/fungi/yeast_convergence/yc_pucciniomycotina/annotations/UP000017200.tsv.gz : 7851737bebbe9a80f5b3a7a357d12c7f9d0e23d6a418a2d6f3440b63c87cdd0c ? 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/bigdata/stajichlab/jstajich/projects/NovInvenio_Investigations/studies/fungi/yeast_convergence/yc_pucciniomycotina/annotations/GCF_000149925.1.tsv.gz.provenance.yaml : a936fa434effbe234fdec5d1939d54d7e34132f4f7250291e9dddfa361d10b48 ? /bigdata/stajichlab/jstajich/projects/NovInvenio_Investigations/studies/fungi/yeast_convergence/yc_pucciniomycotina/annotations/Melampsora_laricis-populina_98AG31.proteins.tsv.gz.provenance.yaml : 304d672440e10066477f60482bff2155422b1a2714f971d098592b3eb47d5305 ? /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: 4.1 background_cluster_s: 60.6 tests_s: 4.4 total_s: 70.7 host: r11 slurm_job: '30452604'