generated: '2026-10-24T14:37:02' study: yc_capnodiales 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_capnodiales --config /bigdata/stajichlab/jstajich/projects/NovInvenio_Investigations/studies/fungi/yeast_convergence/yc_capnodiales/config.csv --annotations /bigdata/stajichlab/jstajich/projects/NovInvenio_Investigations/studies/fungi/yeast_convergence/yc_capnodiales/annotations --study yc_capnodiales --cache-dir /bigdata/stajichlab/jstajich/projects/NovInvenio_Investigations/studies/fungi/yeast_convergence/yc_capnodiales/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_capnodiales/analysis/enrichment/outputs/loss/proteome_clustered class: ephemeral analysis output (not tracked; regenerate with the command above) direction: loss target_group: label: OUT species: - Pseufiji - Dothsept - Cladclad other_group: label: IN species: - Hortwern - Hortthai universe: proteome annotations: /bigdata/stajichlab/jstajich/projects/NovInvenio_Investigations/studies/fungi/yeast_convergence/yc_capnodiales/annotations annotation_files: Pseufiji: /bigdata/stajichlab/jstajich/projects/NovInvenio_Investigations/studies/fungi/yeast_convergence/yc_capnodiales/annotations/UP000016932.tsv.gz Dothsept: /bigdata/stajichlab/jstajich/projects/NovInvenio_Investigations/studies/fungi/yeast_convergence/yc_capnodiales/annotations/UP000016933.tsv.gz Cladclad: /bigdata/stajichlab/jstajich/projects/NovInvenio_Investigations/studies/fungi/yeast_convergence/yc_capnodiales/annotations/Cladosporium_cladosporioides_SYC63.proteins.tsv.gz Hortwern: /bigdata/stajichlab/jstajich/projects/NovInvenio_Investigations/studies/fungi/yeast_convergence/yc_capnodiales/annotations/UP000194280.tsv.gz Hortthai: /bigdata/stajichlab/jstajich/projects/NovInvenio_Investigations/studies/fungi/yeast_convergence/yc_capnodiales/annotations/UP000308549.tsv.gz annotation_sources: Pseufiji: not recorded (no sidecar) Dothsept: not recorded (no sidecar) Cladclad: Pfam-A HMM search (hmmsearch); Pfam only Hortwern: not recorded (no sidecar) Hortthai: not recorded (no sidecar) vocabulary_coverage: pfam: species_with_terms: - Pseufiji - Dothsept - Cladclad species_without_terms: [] n_with: 3 n_species: 3 pfam_clan: species_with_terms: - Pseufiji - Dothsept - Cladclad species_without_terms: [] n_with: 3 n_species: 3 interpro: species_with_terms: - Pseufiji - Dothsept species_without_terms: - Cladclad n_with: 2 n_species: 3 go: species_with_terms: - Pseufiji - Dothsept species_without_terms: - Cladclad n_with: 2 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: 683 candidates_txt: 683 symmetric_difference: 0 candidates_file: /bigdata/stajichlab/jstajich/projects/NovInvenio_Investigations/results/yc_capnodiales/loss_candidates.txt presence_matrix: /bigdata/stajichlab/jstajich/projects/NovInvenio_Investigations/results/yc_capnodiales/loss_presence_matrix.tsv rule: OUT count / 3 >= 0.75 and IN count / 2 <= 0.0 (own proteome counts toward the target group) only_in_matrix_rule: [] only_in_candidates_file: [] background_clustering: key: 924bfc9d2fa914bc n_sequences: 37122 n_clusters: 21207 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: 57.5 threads: 4 created: '2026-10-24T14:36:56' cache_hit: false pipeline_candidate_families: '/bigdata/stajichlab/jstajich/projects/NovInvenio_Investigations/results/yc_capnodiales/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_capnodiales/config.csv: 1f20536239d96325dce916060160832828580fd3f1b4eae8829f78f806e6f231 /bigdata/stajichlab/jstajich/projects/NovInvenio_Investigations/results/yc_capnodiales/loss_candidates.txt: c44bce4d18871bf58cd70a9488653b175f49834471ea9cea77297afc580ced31 /bigdata/stajichlab/jstajich/projects/NovInvenio_Investigations/results/yc_capnodiales/clusters/loss_clusters_cluster.tsv: e8f2522a2f5a2279b73a63238f8625e3343d6b42c442ba324c78d28c5b9e192d /bigdata/stajichlab/jstajich/projects/NovInvenio_Investigations/results/yc_capnodiales/loss_presence_matrix.tsv: 5f1f98270dff582a588ed83849a9df0ed8bfba0c3746e51fcd9b1cdddaa7e964 ? /bigdata/stajichlab/jstajich/projects/NovInvenio_Investigations/studies/fungi/yeast_convergence/yc_capnodiales/data_dir/pep/UP000016932_383855.pep.fa : 6d451f9d1072082393194bbd89f201540276731a78866d5be73f7962fd10d86f ? /bigdata/stajichlab/jstajich/projects/NovInvenio_Investigations/studies/fungi/yeast_convergence/yc_capnodiales/data_dir/pep/UP000016933_675120.pep.fa : 75ef024a039186d0d95e5145ef4dac1dd39e059b9ab786247a0bd310234b3b4e ? /bigdata/stajichlab/jstajich/projects/NovInvenio_Investigations/studies/fungi/yeast_convergence/yc_capnodiales/data_dir/pep/Cladclad.pep.fa : 2b52ec30d5f463ab0900e03667ccc047e33b3c291d7e683c45e599909a6f920d /bigdata/stajichlab/jstajich/projects/NovInvenio_Investigations/studies/fungi/yeast_convergence/yc_capnodiales/species.csv: 3a70fe395ca4973171415c64c3d305fa09bbde0547c1771454e4b91b4dc18dab ? /bigdata/stajichlab/jstajich/projects/NovInvenio_Investigations/studies/fungi/yeast_convergence/yc_capnodiales/annotations/UP000016932.tsv.gz : 83107018015d4e9272147459b3dc9d7496adb09ec47fd35f268c28c99826c926 ? /bigdata/stajichlab/jstajich/projects/NovInvenio_Investigations/studies/fungi/yeast_convergence/yc_capnodiales/annotations/UP000016933.tsv.gz : 3154c0a7f45133fa3f5b3c288ac5171eac91b3bdde0fca1bbd592c494cb729ce ? /bigdata/stajichlab/jstajich/projects/NovInvenio_Investigations/studies/fungi/yeast_convergence/yc_capnodiales/annotations/Cladosporium_cladosporioides_SYC63.proteins.tsv.gz : 6c0756d8fcb49130e74aff91dc736fe5651558b48732e39b023a0d90a74663e1 ? /bigdata/stajichlab/jstajich/projects/NovInvenio_Investigations/studies/fungi/yeast_convergence/yc_capnodiales/annotations/UP000194280.tsv.gz : 99375c520d235a1818cf99cf77991cc5c098f15f3eb46c27c083067c472af786 ? /bigdata/stajichlab/jstajich/projects/NovInvenio_Investigations/studies/fungi/yeast_convergence/yc_capnodiales/annotations/UP000308549.tsv.gz : e24246e2f44f86442362c504acb21b4fd978bde6f17b8a0c2da82156604b427f ? /bigdata/stajichlab/jstajich/projects/NovInvenio_Investigations/studies/fungi/yeast_convergence/yc_capnodiales/annotations/Cladosporium_cladosporioides_SYC63.proteins.tsv.gz.provenance.yaml : 22c3d574368b9691b690b946033d3b875e874e29c9d29c5c2f3ae53ecdaa217d ? /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: 5.1 background_cluster_s: 57.9 tests_s: 4.3 total_s: 68.8 host: r11 slurm_job: '30452604'