generated: '2026-10-24T14:48:05' study: yc_pseudo_powdery_mildew 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_pseudo_powdery_mildew --config /bigdata/stajichlab/jstajich/projects/NovInvenio_Investigations/studies/fungi/yeast_convergence/yc_pseudo_powdery_mildew/config.csv --annotations /bigdata/stajichlab/jstajich/projects/NovInvenio_Investigations/studies/fungi/yeast_convergence/yc_pseudo_powdery_mildew/annotations --study yc_pseudo_powdery_mildew --cache-dir /bigdata/stajichlab/jstajich/projects/NovInvenio_Investigations/studies/fungi/yeast_convergence/yc_pseudo_powdery_mildew/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 loss --other-max-frac 0.0 --out-dir /bigdata/stajichlab/jstajich/projects/NovInvenio_Investigations/studies/fungi/yeast_convergence/yc_pseudo_powdery_mildew/analysis/enrichment/outputs/loss/proteome_clustered class: ephemeral analysis output (not tracked; regenerate with the command above) direction: loss target_group: label: OUT species: - Botrcine - Sclescle - Anid other_group: label: IN species: - Blumgram - Blumhord - Erysneca - Podoxant universe: proteome annotations: /bigdata/stajichlab/jstajich/projects/NovInvenio_Investigations/studies/fungi/yeast_convergence/yc_pseudo_powdery_mildew/annotations annotation_files: Botrcine: /bigdata/stajichlab/jstajich/projects/NovInvenio_Investigations/studies/fungi/yeast_convergence/yc_pseudo_powdery_mildew/annotations/UP000001798.tsv.gz Sclescle: /bigdata/stajichlab/jstajich/projects/NovInvenio_Investigations/studies/fungi/yeast_convergence/yc_pseudo_powdery_mildew/annotations/UP000001312.tsv.gz Anid: /bigdata/stajichlab/jstajich/projects/NovInvenio_Investigations/studies/fungi/yeast_convergence/yc_pseudo_powdery_mildew/annotations/UP000000560.tsv.gz Blumgram: /bigdata/stajichlab/jstajich/projects/NovInvenio_Investigations/studies/fungi/yeast_convergence/yc_pseudo_powdery_mildew/annotations/UP000324639.tsv.gz Blumhord: /bigdata/stajichlab/jstajich/projects/NovInvenio_Investigations/studies/fungi/yeast_convergence/yc_pseudo_powdery_mildew/annotations/UP000015441.tsv.gz Erysneca: /bigdata/stajichlab/jstajich/projects/NovInvenio_Investigations/studies/fungi/yeast_convergence/yc_pseudo_powdery_mildew/annotations/UP000030854.tsv.gz Podoxant: /bigdata/stajichlab/jstajich/projects/NovInvenio_Investigations/studies/fungi/yeast_convergence/yc_pseudo_powdery_mildew/annotations/Podosphaera_xanthii_YZU573.proteins.tsv.gz annotation_sources: Botrcine: not recorded (no sidecar) Sclescle: not recorded (no sidecar) Anid: not recorded (no sidecar) Blumgram: not recorded (no sidecar) Blumhord: not recorded (no sidecar) Erysneca: not recorded (no sidecar) Podoxant: Pfam-A HMM search (hmmsearch); Pfam only vocabulary_coverage: pfam: species_with_terms: - Botrcine - Sclescle - Anid species_without_terms: [] n_with: 3 n_species: 3 pfam_clan: species_with_terms: - Botrcine - Sclescle - Anid species_without_terms: [] n_with: 3 n_species: 3 interpro: species_with_terms: - Botrcine - Sclescle - Anid species_without_terms: [] n_with: 3 n_species: 3 go: species_with_terms: - Botrcine - Sclescle - Anid species_without_terms: [] n_with: 3 n_species: 3 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: 3538 candidates_txt: 3538 symmetric_difference: 0 candidates_file: /bigdata/stajichlab/jstajich/projects/NovInvenio_Investigations/results/yc_pseudo_powdery_mildew/loss_candidates.txt presence_matrix: /bigdata/stajichlab/jstajich/projects/NovInvenio_Investigations/results/yc_pseudo_powdery_mildew/loss_presence_matrix.tsv rule: OUT count / 3 >= 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: bdc789d26a6545ba n_sequences: 33210 n_clusters: 19924 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: 57.3 threads: 4 created: '2026-10-24T14:47:57' cache_hit: false pipeline_candidate_families: '/bigdata/stajichlab/jstajich/projects/NovInvenio_Investigations/results/yc_pseudo_powdery_mildew/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_convergence/yc_pseudo_powdery_mildew/config.csv : fac5afa72c6fb3aab482dee1872c2585a09d5939109502cd0e5b471dd69ee2df /bigdata/stajichlab/jstajich/projects/NovInvenio_Investigations/results/yc_pseudo_powdery_mildew/loss_candidates.txt: 480b3121caedbd644a24f093ed70dfa3f251e9fcc38d715cfd5f429c59cc3bcd ? /bigdata/stajichlab/jstajich/projects/NovInvenio_Investigations/results/yc_pseudo_powdery_mildew/clusters/loss_clusters_cluster.tsv : 7be362a2b3751640f7b33d9bad88b8bf546e0255a61ae87b81beda039ff0dcd6 /bigdata/stajichlab/jstajich/projects/NovInvenio_Investigations/results/yc_pseudo_powdery_mildew/loss_presence_matrix.tsv: 2e6ee1300636fde8f97ca01997a325a4d142684cc66d51eeecba5661f4086259 ? /bigdata/stajichlab/jstajich/projects/NovInvenio_Investigations/studies/fungi/yeast_convergence/yc_pseudo_powdery_mildew/data_dir/pep/UP000001798_332648.pep.fa : 95acc4c3420107b208e1aa5257d6dbcebe467d0b28c6d71724370b298f201e2b ? /bigdata/stajichlab/jstajich/projects/NovInvenio_Investigations/studies/fungi/yeast_convergence/yc_pseudo_powdery_mildew/data_dir/pep/UP000001312_665079.pep.fa : dea2df3f688c88476105dcd481869705e3997e9a2970cfabb093633a50d064f9 ? /bigdata/stajichlab/jstajich/projects/NovInvenio_Investigations/studies/fungi/yeast_convergence/yc_pseudo_powdery_mildew/data_dir/pep/UP000000560_227321.pep.fa : 929546c62a96b539b87eff1da79f95462d02f3853e6a1301cc43572bf8f3f7cc ? /bigdata/stajichlab/jstajich/projects/NovInvenio_Investigations/studies/fungi/yeast_convergence/yc_pseudo_powdery_mildew/species.csv : 116b64b3b6436765487410ffc8878027b0e9dad389bd0183265a5341f40f5991 ? /bigdata/stajichlab/jstajich/projects/NovInvenio_Investigations/studies/fungi/yeast_convergence/yc_pseudo_powdery_mildew/annotations/UP000001798.tsv.gz : f8f53d90bf1f81867d72740476cfa6cfcfe34d7a1457965220096176ba75f77e ? /bigdata/stajichlab/jstajich/projects/NovInvenio_Investigations/studies/fungi/yeast_convergence/yc_pseudo_powdery_mildew/annotations/UP000001312.tsv.gz : 1d58ef834f059d78aff2178d263ec12d0a7c555e38f537177093cedcf1e209b3 ? /bigdata/stajichlab/jstajich/projects/NovInvenio_Investigations/studies/fungi/yeast_convergence/yc_pseudo_powdery_mildew/annotations/UP000000560.tsv.gz : df6cc273d410051b9eb99039e0ac6ed30bc1847f724c5d24e56b04945bec5e35 ? /bigdata/stajichlab/jstajich/projects/NovInvenio_Investigations/studies/fungi/yeast_convergence/yc_pseudo_powdery_mildew/annotations/UP000324639.tsv.gz : aaa2a021002442a195585fa59a7116d425d94ab3540886b01679d0d73700ed27 ? /bigdata/stajichlab/jstajich/projects/NovInvenio_Investigations/studies/fungi/yeast_convergence/yc_pseudo_powdery_mildew/annotations/UP000015441.tsv.gz : 70a87b6a2e12038d9aaeea18551873972eb50db44027d598d949ef844d5762f3 ? /bigdata/stajichlab/jstajich/projects/NovInvenio_Investigations/studies/fungi/yeast_convergence/yc_pseudo_powdery_mildew/annotations/UP000030854.tsv.gz : 5a5d643acbab6ac7a74957a022566af3e7f260ccdaa7daf505f7e203a795c034 ? /bigdata/stajichlab/jstajich/projects/NovInvenio_Investigations/studies/fungi/yeast_convergence/yc_pseudo_powdery_mildew/annotations/Podosphaera_xanthii_YZU573.proteins.tsv.gz : ccafbebb9c73f885cb06cb231934ddc5b0d195521e5ff7f54ece4f6a94a91cdd ? /bigdata/stajichlab/jstajich/projects/NovInvenio_Investigations/studies/fungi/yeast_convergence/yc_pseudo_powdery_mildew/annotations/Podosphaera_xanthii_YZU573.proteins.tsv.gz.provenance.yaml : 66aa013c6cf9a916fb323ae77b34a799eb651b9bdb4c35482c9e002fc443a8dd ? /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: 57.8 tests_s: 6.2 total_s: 69.8 host: r11 slurm_job: '30452604'