generated: '2026-10-24T14:52:54' study: yc_pseudo_dermatophyte 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_dermatophyte --config /bigdata/stajichlab/jstajich/projects/NovInvenio_Investigations/studies/fungi/yeast_convergence/yc_pseudo_dermatophyte/config.csv --annotations /bigdata/stajichlab/jstajich/projects/NovInvenio_Investigations/studies/fungi/yeast_convergence/yc_pseudo_dermatophyte/annotations --study yc_pseudo_dermatophyte --cache-dir /bigdata/stajichlab/jstajich/projects/NovInvenio_Investigations/studies/fungi/yeast_convergence/yc_pseudo_dermatophyte/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_dermatophyte/analysis/enrichment/outputs/loss/proteome_clustered class: ephemeral analysis output (not tracked; regenerate with the command above) direction: loss target_group: label: OUT species: - Anid - Talastip other_group: label: IN species: - Tricrubr - Micrcani - Tricinte - Nanngyps universe: proteome annotations: /bigdata/stajichlab/jstajich/projects/NovInvenio_Investigations/studies/fungi/yeast_convergence/yc_pseudo_dermatophyte/annotations annotation_files: Anid: /bigdata/stajichlab/jstajich/projects/NovInvenio_Investigations/studies/fungi/yeast_convergence/yc_pseudo_dermatophyte/annotations/UP000000560.tsv.gz Talastip: /bigdata/stajichlab/jstajich/projects/NovInvenio_Investigations/studies/fungi/yeast_convergence/yc_pseudo_dermatophyte/annotations/UP000001745.tsv.gz Tricrubr: /bigdata/stajichlab/jstajich/projects/NovInvenio_Investigations/studies/fungi/yeast_convergence/yc_pseudo_dermatophyte/annotations/UP000008864.tsv.gz Micrcani: /bigdata/stajichlab/jstajich/projects/NovInvenio_Investigations/studies/fungi/yeast_convergence/yc_pseudo_dermatophyte/annotations/Microsporum_canis_BMU_08102.proteins.tsv.gz Tricinte: /bigdata/stajichlab/jstajich/projects/NovInvenio_Investigations/studies/fungi/yeast_convergence/yc_pseudo_dermatophyte/annotations/UP000024533.tsv.gz Nanngyps: /bigdata/stajichlab/jstajich/projects/NovInvenio_Investigations/studies/fungi/yeast_convergence/yc_pseudo_dermatophyte/annotations/Nannizzia_gypsea_CBS_118893.proteins.tsv.gz annotation_sources: Anid: not recorded (no sidecar) Talastip: not recorded (no sidecar) Tricrubr: not recorded (no sidecar) Micrcani: Pfam-A HMM search (hmmsearch); Pfam only Tricinte: not recorded (no sidecar) Nanngyps: Pfam-A HMM search (hmmsearch); Pfam only vocabulary_coverage: pfam: species_with_terms: - Anid - Talastip species_without_terms: [] n_with: 2 n_species: 2 pfam_clan: species_with_terms: - Anid - Talastip species_without_terms: [] n_with: 2 n_species: 2 interpro: species_with_terms: - Anid - Talastip species_without_terms: [] n_with: 2 n_species: 2 go: species_with_terms: - Anid - Talastip species_without_terms: [] n_with: 2 n_species: 2 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: 2367 candidates_txt: 2367 symmetric_difference: 0 candidates_file: /bigdata/stajichlab/jstajich/projects/NovInvenio_Investigations/results/yc_pseudo_dermatophyte/loss_candidates.txt presence_matrix: /bigdata/stajichlab/jstajich/projects/NovInvenio_Investigations/results/yc_pseudo_dermatophyte/loss_presence_matrix.tsv rule: OUT count / 2 >= 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: 7791b87dfc3a6789 n_sequences: 20662 n_clusters: 12690 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: 50.4 threads: 4 created: '2026-10-24T14:52:49' cache_hit: false pipeline_candidate_families: '/bigdata/stajichlab/jstajich/projects/NovInvenio_Investigations/results/yc_pseudo_dermatophyte/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_dermatophyte/config.csv : 5b58378692ee5449b1c71d3bb5754ae6cd18b3d75449c49bc2c98b58396ccd3e /bigdata/stajichlab/jstajich/projects/NovInvenio_Investigations/results/yc_pseudo_dermatophyte/loss_candidates.txt: 3ff3d9fbbf201da8742842549fb89cc6b54a95139e9e62a5ec20974df82000f6 ? /bigdata/stajichlab/jstajich/projects/NovInvenio_Investigations/results/yc_pseudo_dermatophyte/clusters/loss_clusters_cluster.tsv : 0b7fab804b9de65f10fa6f455d3696eed5e13b0a75b9750d8fb258de5fe774a5 /bigdata/stajichlab/jstajich/projects/NovInvenio_Investigations/results/yc_pseudo_dermatophyte/loss_presence_matrix.tsv: 6c317b9be70acd7d0f36fc5e4426c61083c820406da48f9d3dc899ae06213a08 ? /bigdata/stajichlab/jstajich/projects/NovInvenio_Investigations/studies/fungi/yeast_convergence/yc_pseudo_dermatophyte/data_dir/pep/UP000000560_227321.pep.fa : 929546c62a96b539b87eff1da79f95462d02f3853e6a1301cc43572bf8f3f7cc ? /bigdata/stajichlab/jstajich/projects/NovInvenio_Investigations/studies/fungi/yeast_convergence/yc_pseudo_dermatophyte/data_dir/pep/UP000001745_441959.pep.fa : cc316aa77be8787586f854588410334e3e68226f9005d61092a1194232274bcd ? /bigdata/stajichlab/jstajich/projects/NovInvenio_Investigations/studies/fungi/yeast_convergence/yc_pseudo_dermatophyte/species.csv : ed23d1e53ebe264ac291beb81fffc874d4988461587eb14c5c8f0ee45a851b4b ? /bigdata/stajichlab/jstajich/projects/NovInvenio_Investigations/studies/fungi/yeast_convergence/yc_pseudo_dermatophyte/annotations/UP000000560.tsv.gz : 39c8a51f76bbfcff402e73adc4af1bba62df58f8e76af87a63c2aa7e5204de3d ? /bigdata/stajichlab/jstajich/projects/NovInvenio_Investigations/studies/fungi/yeast_convergence/yc_pseudo_dermatophyte/annotations/UP000001745.tsv.gz : d858b84e6e03b950834d4b036778b406329a9d34422b86c46b4f160e07ec4961 ? /bigdata/stajichlab/jstajich/projects/NovInvenio_Investigations/studies/fungi/yeast_convergence/yc_pseudo_dermatophyte/annotations/UP000008864.tsv.gz : 60d1ad081da989724c1872832a69e6432385210eab61f4f64c38fa353e246885 ? /bigdata/stajichlab/jstajich/projects/NovInvenio_Investigations/studies/fungi/yeast_convergence/yc_pseudo_dermatophyte/annotations/Microsporum_canis_BMU_08102.proteins.tsv.gz : 44cb98c7f909340843ae4a17e266b1c8ba1ed7b3052e01c8b023a6c7628c0f6a ? /bigdata/stajichlab/jstajich/projects/NovInvenio_Investigations/studies/fungi/yeast_convergence/yc_pseudo_dermatophyte/annotations/UP000024533.tsv.gz : ddad87128940f1113360060c513b9cc875fda30514e36cf87fefe320bc1fe544 ? /bigdata/stajichlab/jstajich/projects/NovInvenio_Investigations/studies/fungi/yeast_convergence/yc_pseudo_dermatophyte/annotations/Nannizzia_gypsea_CBS_118893.proteins.tsv.gz : b2afc566d13c29cd870b4f1346c53ac43007164c23dd7c97f43575c6bf924fbe ? /bigdata/stajichlab/jstajich/projects/NovInvenio_Investigations/studies/fungi/yeast_convergence/yc_pseudo_dermatophyte/annotations/Microsporum_canis_BMU_08102.proteins.tsv.gz.provenance.yaml : 9572ec90a81441c87a703f29ae41460da94edd780eb608448c8cf7ce932c1ebf ? /bigdata/stajichlab/jstajich/projects/NovInvenio_Investigations/studies/fungi/yeast_convergence/yc_pseudo_dermatophyte/annotations/Nannizzia_gypsea_CBS_118893.proteins.tsv.gz.provenance.yaml : 3b66639f8b38cf9d8776070047d11597050d5073e616d0d06878d9f6087ea186 ? /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: 3.0 background_cluster_s: 50.7 tests_s: 4.1 total_s: 59.1 host: r11 slurm_job: '30452604'