generated: '2026-10-24T14:46:02' study: yc_mucoromycota 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_mucoromycota --config /bigdata/stajichlab/jstajich/projects/NovInvenio_Investigations/studies/fungi/yeast_convergence/yc_mucoromycota/config.csv --annotations /bigdata/stajichlab/jstajich/projects/NovInvenio_Investigations/studies/fungi/yeast_convergence/yc_mucoromycota/annotations --study yc_mucoromycota --cache-dir /bigdata/stajichlab/jstajich/projects/NovInvenio_Investigations/studies/fungi/yeast_convergence/yc_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 --direction loss --other-max-frac 0.0 --out-dir /bigdata/stajichlab/jstajich/projects/NovInvenio_Investigations/studies/fungi/yeast_convergence/yc_mucoromycota/analysis/enrichment/outputs/loss/proteome_clustered class: ephemeral analysis output (not tracked; regenerate with the command above) direction: loss target_group: label: OUT species: - Phycblak - Rhizdele - Lichcory - Absiglau other_group: label: IN species: - Mcir - Mucorace - Thameleg universe: proteome annotations: /bigdata/stajichlab/jstajich/projects/NovInvenio_Investigations/studies/fungi/yeast_convergence/yc_mucoromycota/annotations annotation_files: Phycblak: /bigdata/stajichlab/jstajich/projects/NovInvenio_Investigations/studies/fungi/yeast_convergence/yc_mucoromycota/annotations/UP000077315.tsv.gz Rhizdele: /bigdata/stajichlab/jstajich/projects/NovInvenio_Investigations/studies/fungi/yeast_convergence/yc_mucoromycota/annotations/UP000009138.tsv.gz Lichcory: /bigdata/stajichlab/jstajich/projects/NovInvenio_Investigations/studies/fungi/yeast_convergence/yc_mucoromycota/annotations/UP000027586.tsv.gz Absiglau: /bigdata/stajichlab/jstajich/projects/NovInvenio_Investigations/studies/fungi/yeast_convergence/yc_mucoromycota/annotations/UP000078561.tsv.gz Mcir: /bigdata/stajichlab/jstajich/projects/NovInvenio_Investigations/studies/fungi/yeast_convergence/yc_mucoromycota/annotations/UP000014254.tsv.gz Mucorace: /bigdata/stajichlab/jstajich/projects/NovInvenio_Investigations/studies/fungi/yeast_convergence/yc_mucoromycota/annotations/Mucor_racemosus_CGMCC-40320.proteins.tsv.gz Thameleg: /bigdata/stajichlab/jstajich/projects/NovInvenio_Investigations/studies/fungi/yeast_convergence/yc_mucoromycota/annotations/Thamnidium_elegans_KKP_4289.proteins.tsv.gz annotation_sources: Phycblak: not recorded (no sidecar) Rhizdele: not recorded (no sidecar) Lichcory: not recorded (no sidecar) Absiglau: not recorded (no sidecar) Mcir: not recorded (no sidecar) Mucorace: Pfam-A HMM search (hmmsearch); Pfam only Thameleg: Pfam-A HMM search (hmmsearch); Pfam only vocabulary_coverage: pfam: species_with_terms: - Phycblak - Rhizdele - Lichcory - Absiglau species_without_terms: [] n_with: 4 n_species: 4 pfam_clan: species_with_terms: - Phycblak - Rhizdele - Lichcory - Absiglau species_without_terms: [] n_with: 4 n_species: 4 interpro: species_with_terms: - Phycblak - Rhizdele - Lichcory - Absiglau species_without_terms: [] n_with: 4 n_species: 4 go: species_with_terms: - Phycblak - Rhizdele - Lichcory - Absiglau species_without_terms: [] n_with: 4 n_species: 4 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: 1333 candidates_txt: 1333 symmetric_difference: 0 candidates_file: /bigdata/stajichlab/jstajich/projects/NovInvenio_Investigations/results/yc_mucoromycota/loss_candidates.txt presence_matrix: /bigdata/stajichlab/jstajich/projects/NovInvenio_Investigations/results/yc_mucoromycota/loss_presence_matrix.tsv rule: OUT count / 4 >= 0.75 and IN count / 3 <= 0.0 (own proteome counts toward the target group) only_in_matrix_rule: [] only_in_candidates_file: [] background_clustering: key: 3b0c9e0274504de9 n_sequences: 58755 n_clusters: 29659 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: 79.7 threads: 4 created: '2026-10-24T14:45:53' cache_hit: false pipeline_candidate_families: '/bigdata/stajichlab/jstajich/projects/NovInvenio_Investigations/results/yc_mucoromycota/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_mucoromycota/config.csv: f7a885928253ebbeb2d62787e32225eafdd6aced916133b4c810d081ac733c01 /bigdata/stajichlab/jstajich/projects/NovInvenio_Investigations/results/yc_mucoromycota/loss_candidates.txt: 8ff03e2a2b2e3dfac28de88db5c2ccfbcb803519c0657185055bfc325752e857 /bigdata/stajichlab/jstajich/projects/NovInvenio_Investigations/results/yc_mucoromycota/clusters/loss_clusters_cluster.tsv: f6a5d14e021395c725ec507d3b14d4079f46f60b62470ec55ca6c19615c8decb /bigdata/stajichlab/jstajich/projects/NovInvenio_Investigations/results/yc_mucoromycota/loss_presence_matrix.tsv: efc308fe8702af585f53ac052321c5483fd882b47af64cb60e9299de74b165a0 ? /bigdata/stajichlab/jstajich/projects/NovInvenio_Investigations/studies/fungi/yeast_convergence/yc_mucoromycota/data_dir/pep/UP000077315_763407.pep.fa : bf81d11d8fa875f69dbbed357058bdfa01d288787ea19dcedf225e204e2ce303 ? /bigdata/stajichlab/jstajich/projects/NovInvenio_Investigations/studies/fungi/yeast_convergence/yc_mucoromycota/data_dir/pep/UP000009138_246409.pep.fa : c7f8bbbfc379233d7d53dbd68e9df55ba747e174819a5a0bf7c91719d4c092a6 ? /bigdata/stajichlab/jstajich/projects/NovInvenio_Investigations/studies/fungi/yeast_convergence/yc_mucoromycota/data_dir/pep/UP000027586_1263082.pep.fa : d6d9bf154211859b8ee5d6ce8d268960a9a0fc0c7a3377310368835e23417c91 ? /bigdata/stajichlab/jstajich/projects/NovInvenio_Investigations/studies/fungi/yeast_convergence/yc_mucoromycota/data_dir/pep/UP000078561_4829.pep.fa : a76e2fabc040673da768be36cb28dce1277813c35a387550464c13863a26b2af ? /bigdata/stajichlab/jstajich/projects/NovInvenio_Investigations/studies/fungi/yeast_convergence/yc_mucoromycota/species.csv : 93c3ada73c2dd7567c9481660bdfffc88a2e31fcb25b519c69fd8370cf3d023d ? /bigdata/stajichlab/jstajich/projects/NovInvenio_Investigations/studies/fungi/yeast_convergence/yc_mucoromycota/annotations/UP000077315.tsv.gz : 026f6af828589dcd9a52510fa1ece222d7a543425473bb44b00bb98e1d984934 ? /bigdata/stajichlab/jstajich/projects/NovInvenio_Investigations/studies/fungi/yeast_convergence/yc_mucoromycota/annotations/UP000009138.tsv.gz : 5d973c0b2863e53494a6e640b04487102515181631f68e0b4592389e4953788b ? /bigdata/stajichlab/jstajich/projects/NovInvenio_Investigations/studies/fungi/yeast_convergence/yc_mucoromycota/annotations/UP000027586.tsv.gz : 9a7bc7ac5fcb8143c8e29729db9a356705d526e675a4ba217af5b1a66b9f0d92 ? /bigdata/stajichlab/jstajich/projects/NovInvenio_Investigations/studies/fungi/yeast_convergence/yc_mucoromycota/annotations/UP000078561.tsv.gz : 77ce72f5d4c48357a32925bdfa83dd4d72c748ec383650011f13b2cdd9d7b2cf ? /bigdata/stajichlab/jstajich/projects/NovInvenio_Investigations/studies/fungi/yeast_convergence/yc_mucoromycota/annotations/UP000014254.tsv.gz : 58ae1874928453ee53dc0b9cd14df101fd45f4ca50e81bf0e7d2ad6da1ef94db ? /bigdata/stajichlab/jstajich/projects/NovInvenio_Investigations/studies/fungi/yeast_convergence/yc_mucoromycota/annotations/Mucor_racemosus_CGMCC-40320.proteins.tsv.gz : 7a5146b3e287ba2158c3305fad7c6af41effd5f2a5b55ab15256105fe73eab30 ? /bigdata/stajichlab/jstajich/projects/NovInvenio_Investigations/studies/fungi/yeast_convergence/yc_mucoromycota/annotations/Thamnidium_elegans_KKP_4289.proteins.tsv.gz : a00ca86e0b2228fe22fc68ea3d67672e9a8b297488435f5d31b69bbfbee1e719 ? /bigdata/stajichlab/jstajich/projects/NovInvenio_Investigations/studies/fungi/yeast_convergence/yc_mucoromycota/annotations/Mucor_racemosus_CGMCC-40320.proteins.tsv.gz.provenance.yaml : 0f6511b4a46f5b4c600e1c8c25199ee4d741597f5535efa915b126f23464b323 ? /bigdata/stajichlab/jstajich/projects/NovInvenio_Investigations/studies/fungi/yeast_convergence/yc_mucoromycota/annotations/Thamnidium_elegans_KKP_4289.proteins.tsv.gz.provenance.yaml : b93bec80c57c24bb45d01984092533518c965e4a378be4ffb01d014cc0d26e80 ? /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: 4.5 background_cluster_s: 80.5 tests_s: 7.0 total_s: 94.4 host: r11 slurm_job: '30452604'