Commit ·
c88e8d1
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Parent(s): 0de850a
Add OrthoFinder orthogroups, rename orthogroup columns, update piper25 and processed files (#5)
Browse files- Add OrthoFinder orthogroups, rename orthogroup columns, update piper25 and processed files (61430c8de625ec2e1b7feac14e38918ac334bcf2)
- Add OrthoFinder orthogroups, rename orthogroup columns, update piper25 and processed files (part 2) (51a098eb973f2d8346903019556675c640ef98ae)
- Add OrthoFinder orthogroups, rename orthogroup columns, update piper25 and processed files (part 3) (cf7ef3dac4d54d15ef4c730ba0783e3f1410465f)
This view is limited to 50 files because it contains too many changes. See raw diff
- .gitattributes +4 -0
- README.md +9 -3
- external/molecular_networks/gnps2/fbmn_global.cys +2 -2
- external/orthogroups/orthofinder/logs/slurm-2953776.out +113 -0
- external/orthogroups/orthofinder/results/Results_Oct13/WorkingDirectory/OrthoFinder/Results_analysis_2953776/Log.txt +30 -0
- external/orthogroups/orthofinder/results/Results_Oct13/WorkingDirectory/OrthoFinder/Results_analysis_2953776/Orthogroups/Orthogroups.GeneCount.tsv +0 -0
- processed/scoring/gene_expr.npy → external/orthogroups/orthofinder/results/Results_Oct13/WorkingDirectory/OrthoFinder/Results_analysis_2953776/Orthogroups/Orthogroups.tsv +2 -2
- external/orthogroups/orthofinder/results/Results_Oct13/WorkingDirectory/OrthoFinder/Results_analysis_2953776/Orthogroups/Orthogroups_UnassignedGenes.tsv +0 -0
- external/orthogroups/orthofinder/results/Results_Oct13/WorkingDirectory/OrthoFinder/Results_analysis_2953776/Phylogenetically_Misplaced_Genes/piper06.txt +10 -0
- external/orthogroups/orthofinder/results/Results_Oct13/WorkingDirectory/OrthoFinder/Results_analysis_2953776/Phylogenetically_Misplaced_Genes/piper20.txt +27 -0
- external/orthogroups/orthofinder/results/Results_Oct13/WorkingDirectory/OrthoFinder/Results_analysis_2953776/Phylogenetically_Misplaced_Genes/piper25.txt +35 -0
- external/orthogroups/orthofinder/results/Results_Oct13/WorkingDirectory/OrthoFinder/Results_analysis_2953776/Phylogenetically_Misplaced_Genes/piper26.txt +44 -0
- external/orthogroups/orthofinder/results/Results_Oct13/WorkingDirectory/OrthoFinder/Results_analysis_2953776/Phylogenetically_Misplaced_Genes/piper27.txt +77 -0
- external/orthogroups/orthofinder/results/Results_Oct13/WorkingDirectory/OrthoFinder/Results_analysis_2953776/Phylogenetically_Misplaced_Genes/piper32.txt +73 -0
- external/orthogroups/orthofinder/results/Results_Oct13/WorkingDirectory/OrthoFinder/Results_analysis_2953776/Phylogenetically_Misplaced_Genes/piper54.txt +13 -0
- external/orthogroups/orthofinder/results/Results_Oct13/WorkingDirectory/OrthoFinder/Results_analysis_2953776/Phylogenetically_Misplaced_Genes/piper55.txt +15 -0
- external/orthogroups/orthofinder/results/Results_Oct13/WorkingDirectory/OrthoFinder/Results_analysis_2953776/Phylogenetically_Misplaced_Genes/piper56.txt +34 -0
- external/orthogroups/orthofinder/results/Results_Oct13/WorkingDirectory/OrthoFinder/Results_analysis_2953776/Species_Tree/Orthogroups_for_concatenated_alignment.txt +1540 -0
- external/orthogroups/orthofinder/results/Results_Oct13/WorkingDirectory/OrthoFinder/Results_analysis_2953776/Species_Tree/SpeciesTree_rooted.txt +1 -0
- external/orthogroups/orthofinder/results/Results_Oct13/WorkingDirectory/OrthoFinder/Results_analysis_2953776/Species_Tree/SpeciesTree_rooted_node_labels.txt +1 -0
- processed/scoring/net3d.npy → external/orthogroups/orthofinder/results/Results_Oct13/WorkingDirectory/OrthoFinder/Results_analysis_2953776/WorkingDirectory/clusters_OrthoFinder_I1.5.txt_id_pairs.txt +2 -2
- processed/scoring/gene_og_row.npy → external/orthogroups/orthofinder/results/Results_Oct13/WorkingDirectory/SequenceIDs.txt +2 -2
- external/orthogroups/orthofinder/results/Results_Oct13/WorkingDirectory/SpeciesIDs.txt +13 -0
- processed/scoring/gene_species_col.npy → external/orthogroups/sonicpd/graph_only/not_assigned_genes.ortholog_groups.tsv +2 -2
- external/orthogroups/sonicpd/graph_only/ortholog_groups.tsv +2 -2
- external/orthogroups/sonicpd/graph_only/run_info.txt +19 -18
- interim/rnaseq_clstr/piper25/transcriptome_clstr.pep +2 -2
- interim/rnaseq_clstr/piper25/transcriptome_clstr.pep.clstr +2 -2
- processed/ftable_clean.csv +2 -2
- processed/ntable_clean.csv +2 -2
- processed/proteomes/piper06/blastDB/piper06.pin +1 -1
- processed/proteomes/piper06/blastDB/piper06.pjs +1 -1
- processed/proteomes/piper06/proteome.csv +2 -2
- processed/proteomes/piper09/blastDB/piper09.pin +1 -1
- processed/proteomes/piper09/blastDB/piper09.pjs +1 -1
- processed/proteomes/piper09/proteome.csv +2 -2
- processed/proteomes/piper10/blastDB/piper10.pin +1 -1
- processed/proteomes/piper10/blastDB/piper10.pjs +1 -1
- processed/proteomes/piper10/proteome.csv +2 -2
- processed/proteomes/piper12/blastDB/piper12.pin +1 -1
- processed/proteomes/piper12/blastDB/piper12.pjs +1 -1
- processed/proteomes/piper12/proteome.csv +2 -2
- processed/proteomes/piper20/blastDB/piper20.pin +1 -1
- processed/proteomes/piper20/blastDB/piper20.pjs +1 -1
- processed/proteomes/piper20/proteome.csv +2 -2
- processed/proteomes/piper23/blastDB/piper23.pin +1 -1
- processed/proteomes/piper23/blastDB/piper23.pjs +1 -1
- processed/proteomes/piper23/proteome.csv +2 -2
- processed/proteomes/piper25/blastDB/piper25.pdb +1 -1
- processed/proteomes/piper25/blastDB/piper25.phr +2 -2
.gitattributes
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@@ -567,3 +567,7 @@ raw/lcms/rawfiles/202312_94_P25-Root-r3_1uL.mzML filter=lfs diff=lfs merge=lfs -
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raw/lcms/rawfiles/202312_96_P26-Leaf-r1_1uL.mzML filter=lfs diff=lfs merge=lfs -text
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external/orthogroups/orthofinder/results/Results_Oct13/WorkingDirectory/OrthoFinder/Results_analysis_2953776/Orthogroups/Orthogroups.tsv filter=lfs diff=lfs merge=lfs -text
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external/orthogroups/orthofinder/results/Results_Oct13/WorkingDirectory/OrthoFinder/Results_analysis_2953776/WorkingDirectory/clusters_OrthoFinder_I1.5.txt_id_pairs.txt filter=lfs diff=lfs merge=lfs -text
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external/orthogroups/orthofinder/results/Results_Oct13/WorkingDirectory/SequenceIDs.txt filter=lfs diff=lfs merge=lfs -text
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external/orthogroups/sonicpd/graph_only/not_assigned_genes.ortholog_groups.tsv filter=lfs diff=lfs merge=lfs -text
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README.md
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@@ -37,7 +37,9 @@ data/
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│ ├── molecular_networks/
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│ │ └── gnps2/ # GNPS2 feature-based molecular networking results
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│ ├── sirius/ # SIRIUS results: CSI:FingerID structures, CANOPUS classes
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-
│ ├── orthogroups/
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│ ├── speclibs/ # MS/MS spectral libraries for annotation in MZmine
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│ ├── known_enzymes/ # known enzymes table
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│ ├── customDB.csv # manually curated list of known LC-MS features, for targeted feature detection in MZmine
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├── ftable_clean.csv # LC-MS feature table
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├── ntable_clean.csv # GNPS2 node table, for Cytoscape
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├── proteomes/piperNN/ # proteome.pep, proteome.csv, blastDB/
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-
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└── scoring/ # input arrays for network-orthogroup scoring (.npy)
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```
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`scripts/README.md` in the [code repository](https://github.com/titodamiani/PiperNET) describes how each file is made.
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│ ├── molecular_networks/
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│ │ └── gnps2/ # GNPS2 feature-based molecular networking results
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│ ├── sirius/ # SIRIUS results: CSI:FingerID structures, CANOPUS classes
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│ ├── orthogroups/
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│ │ ├── sonicpd/ # SonicParanoid orthogroups and the genes in no orthogroup
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│ │ └── orthofinder/ # OrthoFinder orthogroups, MCL clusters, species tree and run log
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│ ├── speclibs/ # MS/MS spectral libraries for annotation in MZmine
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│ ├── known_enzymes/ # known enzymes table
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│ ├── customDB.csv # manually curated list of known LC-MS features, for targeted feature detection in MZmine
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├── ftable_clean.csv # LC-MS feature table
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├── ntable_clean.csv # GNPS2 node table, for Cytoscape
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├── proteomes/piperNN/ # proteome.pep, proteome.csv, blastDB/
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└── proteomes_all.csv # all proteomes with SonicParanoid and OrthoFinder orthogroups
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```
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## IDs
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- `ftable_clean.csv` and `ntable_clean.csv`: `network_id` > 0 is a molecular network. A singleton feature is its own network, with `network_id` = -`feat_id`.
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- `proteomes_all.csv`: 4 columns per orthogroup tool, with the prefix `sonicpd_` (SonicParanoid) or `orthofinder_` (OrthoFinder): `_id`, `_size` (genes), `_sp_in_grp` (species), `_intersp` (species joined with `;`).
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- A singleton transcript is its own orthogroup, with a negative ID (-1, -2, ...). `sonicpd_id` starts at 1. `orthofinder_id` is the number in the OrthoFinder ID (`OG0000123` is 123), so it starts at 0.
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`scripts/README.md` in the [code repository](https://github.com/titodamiani/PiperNET) describes how each file is made.
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external/molecular_networks/gnps2/fbmn_global.cys
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version https://git-lfs.github.com/spec/v1
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size 4521503
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external/orthogroups/orthofinder/logs/slurm-2953776.out
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[1;36;49m2026[0m[39;49m-[0m[1;36;49m10[0m[39;49m-[0m[1;36;49m13[0m[39;49m [0m[1;92;49m12:54:50[0m[39;49m : Starting [0m[33;49mOrthoFinder[0m[39;49m v[0m[36;49m3.[0m[1;36;49m1.5[0m
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32 thread(s) for highly parallel tasks (BLAST searches etc.)
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4 thread(s) for OrthoFinder algorithm
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[1;33;49mOrthoFinder[0m[39;49m version [0m[1;36;49m3.1[0m[36;49m.[0m[1;36;49m5[0m[39;49m Copyright [0m[1;39;49m([0m[39;49mC[0m[1;39;49m)[0m[39;49m [0m[1;36;49m2014[0m[39;49m [0m[1;33;49mDavid Emms[0m
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[39;49mResults directory:[0m
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[39;49m [0m[36;49m/uochb/project/pluskal_group/pipernet/data/rnaseq/external/orthogroups/ortho[0m
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[36;49mfinder/results/Results_Oct13/WorkingDirectory/OrthoFinder/Results_analysis_29537[0m
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[36;49m76/[0m
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Checking required programs are installed
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========================================
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[39;49mTest can run [0m[32;49m"[0m[33;49mmcl[0m[32;49m"[0m[39;49m - [0m[1;32;49mok[0m
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[39;49mTest can run [0m[32;49m"[0m[33;49mfamsa[0m[32;49m"[0m[39;49m - [0m[1;32;49mok[0m
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[39;49mTest can run [0m[32;49m"[0m[33;49mfasttree[0m[32;49m"[0m[39;49m - [0m[1;32;49mok[0m
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Using previously calculated BLAST results in
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/uochb/project/pluskal_group/pipernet/data/rnaseq/external/orthogroups/orthofind
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er/results/Results_Oct13/WorkingDirectory/
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Running OrthoFinder algorithm
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-----------------------------
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[1;36;49m2026[0m[39;49m-[0m[1;36;49m10[0m[39;49m-[0m[1;36;49m13[0m[39;49m [0m[1;92;49m12:54:55[0m[39;49m : Initial processing of each species[0m
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Processing... ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 13/13 0:12:57
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[1;36;49m2026[0m[39;49m-[0m[1;36;49m10[0m[39;49m-[0m[1;36;49m13[0m[39;49m [0m[1;92;49m13:07:53[0m[39;49m : Connected putative homologues[0m
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Processing... ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 13/13 0:01:01
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WARNING: program called by OrthoFinder produced output to stderr
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Command: mcl
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/uochb/project/pluskal_group/pipernet/data/rnaseq/external/orthogroups/orthofind
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er/results/Results_Oct13/WorkingDirectory/OrthoFinder/Results_analysis_2953776/W
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orkingDirectory/OrthoFinder_graph.txt -I 1.5 -o
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/uochb/project/pluskal_group/pipernet/data/rnaseq/external/orthogroups/orthofind
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er/results/Results_Oct13/WorkingDirectory/OrthoFinder/Results_analysis_2953776/W
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orkingDirectory/clusters_OrthoFinder_I1.5.txt -te 4 -V all
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stdout:
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b''
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stderr:
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b' cut <1> instances of overlap\n'
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[1;36;49m2026[0m[39;49m-[0m[1;36;49m10[0m[39;49m-[0m[1;36;49m13[0m[39;49m [0m[1;92;49m13:23:10[0m[39;49m : Ran MCL[0m
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Writing orthogroups to file
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---------------------------
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[1;36;49m2026[0m[39;49m-[0m[1;36;49m10[0m[39;49m-[0m[1;36;49m13[0m[39;49m [0m[1;92;49m13:27:03[0m[39;49m : Done orthogroups[0m
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Analysing Orthogroups
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=====================
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[1;36;49m2026[0m[39;49m-[0m[1;36;49m10[0m[39;49m-[0m[1;36;49m13[0m[39;49m [0m[1;92;49m13:27:04[0m[39;49m : Starting MSA/Trees[0m
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Species tree: Using 1540 orthogroups with minimum of 92.3% of species having
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single-copy genes in any orthogroup
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Inferring multiple sequence alignments for species tree
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-------------------------------------------------------
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Processing... ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 1540/1540 0:00:23
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Inferring remaining multiple sequence alignments and gene trees
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---------------------------------------------------------------
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Processing... ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 165084/165084 0:29:58
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[1;36;49m2026[0m[39;49m-[0m[1;36;49m10[0m[39;49m-[0m[1;36;49m13[0m[39;49m [0m[1;92;49m13:57:42[0m[39;49m : Done MSA/Trees[0m
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Best outgroup(s) for species tree
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---------------------------------
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[1;36;49m2026[0m[39;49m-[0m[1;36;49m10[0m[39;49m-[0m[1;36;49m13[0m[39;49m [0m[1;92;49m13:57:42[0m[39;49m : Starting STRIDE[0m
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[1;36;49m2026[0m[39;49m-[0m[1;36;49m10[0m[39;49m-[0m[1;36;49m13[0m[39;49m [0m[1;92;49m14:04:30[0m[39;49m : Done STRIDE[0m
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Observed 632 well-supported, non-terminal duplications. 594 support the best
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root and 38 contradict it.
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Best outgroup for species tree:
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piper23, piper09
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Reconciling gene trees and species tree
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| 74 |
+
---------------------------------------
|
| 75 |
+
Outgroup: piper23, piper09
|
| 76 |
+
[1;36;49m2026[0m[39;49m-[0m[1;36;49m10[0m[39;49m-[0m[1;36;49m13[0m[39;49m [0m[1;92;49m14:04:30[0m[39;49m : Starting reconciliation and orthologues[0m
|
| 77 |
+
[1;36;49m2026[0m[39;49m-[0m[1;36;49m10[0m[39;49m-[0m[1;36;49m13[0m[39;49m [0m[1;92;49m14:04:30[0m[39;49m : Inferring orthologues from gene trees[0m
|
| 78 |
+
Processing... ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 91855/91855 0:01:31
|
| 79 |
+
[1;36;49m2026[0m[39;49m-[0m[1;36;49m10[0m[39;49m-[0m[1;36;49m13[0m[39;49m [0m[1;92;49m14:06:01[0m[39;49m : Done of orthologues[0m
|
| 80 |
+
|
| 81 |
+
Writing results files
|
| 82 |
+
=====================
|
| 83 |
+
[1;36;49m2026[0m[39;49m-[0m[1;36;49m10[0m[39;49m-[0m[1;36;49m13[0m[39;49m [0m[1;92;49m14:06:07[0m[39;49m : Start writing hierarchical orthogroups files[0m
|
| 84 |
+
[1;36;49m2026[0m[39;49m-[0m[1;36;49m10[0m[39;49m-[0m[1;36;49m13[0m[39;49m [0m[1;92;49m14:06:07[0m[39;49m : Converting MSA/Trees[0m
|
| 85 |
+
[1;36;49m2026[0m[39;49m-[0m[1;36;49m10[0m[39;49m-[0m[1;36;49m13[0m[39;49m [0m[1;92;49m14:11:47[0m[39;49m : Updating MSA/Trees[0m
|
| 86 |
+
[1;36;49m2026[0m[39;49m-[0m[1;36;49m10[0m[39;49m-[0m[1;36;49m13[0m[39;49m [0m[1;92;49m14:17:47[0m[39;49m : Done updating MSA/Trees[0m
|
| 87 |
+
Processing... ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 122764/122764 0:01:45
|
| 88 |
+
[1;36;49m2026[0m[39;49m-[0m[1;36;49m10[0m[39;49m-[0m[1;36;49m13[0m[39;49m [0m[1;92;49m14:21:00[0m[39;49m : Done writing files[0m
|
| 89 |
+
|
| 90 |
+
Summary:
|
| 91 |
+
OrthoFinder assigned 1510954 genes (86.7% of total) to 226008 orthogroups.
|
| 92 |
+
50% of genes were in orthogroups with 9 or more genes (G50 was 9) and were
|
| 93 |
+
contained in the largest 51388 orthogroups (O50 was 51388).
|
| 94 |
+
There were 10279 orthogroups with all species present and 752 of these
|
| 95 |
+
consisted entirely of single-copy genes.
|
| 96 |
+
|
| 97 |
+
[39;49mResults directory:[0m
|
| 98 |
+
[39;49m [0m[36;49m/uochb/project/pluskal_group/pipernet/data/rnaseq/external/orthogroups/ortho[0m
|
| 99 |
+
[36;49mfinder/results/Results_Oct13/WorkingDirectory/OrthoFinder/Results_analysis_29537[0m
|
| 100 |
+
[36;49m76/[0m
|
| 101 |
+
|
| 102 |
+
|
| 103 |
+
[39;49mCITATION:[0m
|
| 104 |
+
[39;49m When publishing work that uses [0m[33;49mOrthoFinder[0m[39;49m please cite:[0m
|
| 105 |
+
[39;49m Emms D.M., Liu Y., Belcher L., Holmes J. & Kelly S. [0m[1;39;49m([0m[1;36;49m2025[0m[1;39;49m)[0m[39;49m, bioRxiv [0m]8;id=4542015;https://doi.org/10.1101/2025.07.15.664860\[4;36;49mhttps://doi.org/10.1101/2025.07.15.664860[0m]8;;\
|
| 106 |
+
[39;49m Emms D.M. & Kelly S. [0m[1;39;49m([0m[1;36;49m2019[0m[1;39;49m)[0m[39;49m, Genome Biology [0m[1;92;49m20:238[0m
|
| 107 |
+
|
| 108 |
+
[39;49m If you use the species tree in your work then please also cite:[0m
|
| 109 |
+
[39;49m Emms D.M. & Kelly S. [0m[1;39;49m([0m[1;36;49m2017[0m[1;39;49m)[0m[39;49m, MBE [0m[1;35;49m34[0m[1;39;49m([0m[1;36;49m12[0m[1;39;49m)[0m[39;49m: [0m[1;36;49m3267[0m[39;49m-[0m[1;36;49m3278[0m
|
| 110 |
+
[39;49m Emms D.M. & Kelly S. [0m[1;39;49m([0m[1;36;49m2018[0m[1;39;49m)[0m[39;49m, bioRxiv [0m]8;id=4542019;https://doi.org/10.1101/267914\[4;36;49mhttps://doi.org/10.1101/267914[0m]8;;\
|
| 111 |
+
|
| 112 |
+
[33;49mOrthoFinder[0m[39;49m finished in [0m[1;32;49m5255.[0m[32;49m456802[0m[39;49ms[0m
|
| 113 |
+
|
external/orthogroups/orthofinder/results/Results_Oct13/WorkingDirectory/OrthoFinder/Results_analysis_2953776/Log.txt
ADDED
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| 1 |
+
2026-10-13 12:54:50 : Started OrthoFinder version 3.1.5
|
| 2 |
+
Command Line: /uochb/soft/users/titodamiani/conda-envs/orthofinder/bin/orthofinder -b /uochb/project/pluskal_group/pipernet/data/rnaseq/external/orthogroups/orthofinder/results/Results_Oct13/WorkingDirectory -M msa -I 1.5 -t 32 -a 4 -n analysis_2953776
|
| 3 |
+
|
| 4 |
+
Search program: diamond
|
| 5 |
+
MSA program: famsa
|
| 6 |
+
Tree program: fasttree
|
| 7 |
+
Scoring matrix: BLOSUM62
|
| 8 |
+
Gap extend: 1
|
| 9 |
+
Gap open: 11
|
| 10 |
+
|
| 11 |
+
WorkingDirectory_Base: /uochb/project/pluskal_group/pipernet/data/rnaseq/external/orthogroups/orthofinder/results/Results_Oct13/WorkingDirectory/
|
| 12 |
+
|
| 13 |
+
Species used:
|
| 14 |
+
0: piper06.pep
|
| 15 |
+
1: piper09.pep
|
| 16 |
+
2: piper10.pep
|
| 17 |
+
3: piper12.pep
|
| 18 |
+
4: piper20.pep
|
| 19 |
+
5: piper23.pep
|
| 20 |
+
6: piper25.pep
|
| 21 |
+
7: piper26.pep
|
| 22 |
+
8: piper27.pep
|
| 23 |
+
9: piper32.pep
|
| 24 |
+
10: piper54.pep
|
| 25 |
+
11: piper55.pep
|
| 26 |
+
12: piper56.pep
|
| 27 |
+
|
| 28 |
+
FN_Orthogroups: /uochb/project/pluskal_group/pipernet/data/rnaseq/external/orthogroups/orthofinder/results/Results_Oct13/WorkingDirectory/OrthoFinder/Results_analysis_2953776/WorkingDirectory/clusters_OrthoFinder_I1.5.txt_id_pairs.txt
|
| 29 |
+
WorkingDirectory_Trees: /uochb/project/pluskal_group/pipernet/data/rnaseq/external/orthogroups/orthofinder/results/Results_Oct13/WorkingDirectory/OrthoFinder/Results_analysis_2953776/WorkingDirectory/
|
| 30 |
+
2026-10-13 14:22:25 : OrthoFinder run completed
|
external/orthogroups/orthofinder/results/Results_Oct13/WorkingDirectory/OrthoFinder/Results_analysis_2953776/Orthogroups/Orthogroups.GeneCount.tsv
ADDED
|
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|
processed/scoring/gene_expr.npy → external/orthogroups/orthofinder/results/Results_Oct13/WorkingDirectory/OrthoFinder/Results_analysis_2953776/Orthogroups/Orthogroups.tsv
RENAMED
|
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size 31967077
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external/orthogroups/orthofinder/results/Results_Oct13/WorkingDirectory/OrthoFinder/Results_analysis_2953776/Orthogroups/Orthogroups_UnassignedGenes.tsv
ADDED
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|
external/orthogroups/orthofinder/results/Results_Oct13/WorkingDirectory/OrthoFinder/Results_analysis_2953776/Phylogenetically_Misplaced_Genes/piper06.txt
ADDED
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Porn_g4_i3.p3
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|
external/orthogroups/orthofinder/results/Results_Oct13/WorkingDirectory/OrthoFinder/Results_analysis_2953776/Phylogenetically_Misplaced_Genes/piper20.txt
ADDED
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| 1 |
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Pbet_g8301_i0.p1
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| 2 |
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Pbet_g68211_i0.p1
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| 3 |
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| 5 |
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| 8 |
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| 9 |
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| 10 |
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Pbet_g1688_i0.p4
|
| 11 |
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Pbet_g733_i2.p1
|
| 12 |
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| 13 |
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| 14 |
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|
| 15 |
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| 16 |
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| 17 |
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| 18 |
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|
| 19 |
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| 21 |
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| 22 |
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| 23 |
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| 24 |
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| 25 |
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|
| 26 |
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Pbet_g10335_i5.p1
|
| 27 |
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Pbet_g34686_i0.p1
|
external/orthogroups/orthofinder/results/Results_Oct13/WorkingDirectory/OrthoFinder/Results_analysis_2953776/Phylogenetically_Misplaced_Genes/piper25.txt
ADDED
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| 1 |
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Pama_g133391_i0.p2
|
| 2 |
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Pama_g8814_i0.p1
|
| 3 |
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Pama_g26577_i0.p1
|
| 4 |
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Pama_g2877_i1.p1
|
| 5 |
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Pama_g29133_i3.p1
|
| 6 |
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|
| 7 |
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|
| 8 |
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Pama_g29133_i2.p1
|
| 9 |
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Pama_g29133_i0.p1
|
| 10 |
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Pama_g7223_i1.p1
|
| 11 |
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Pama_g7223_i0.p2
|
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Pama_g119055_i0.p1
|
| 13 |
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Pama_g64665_i0.p1
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| 26 |
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| 29 |
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|
| 30 |
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Pama_g9798_i0.p2
|
| 31 |
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Pama_g2006_i3.p1
|
| 32 |
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|
| 33 |
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Pama_g10098_i10.p1
|
| 34 |
+
Pama_g106281_i0.p1
|
| 35 |
+
Pama_g25093_i0.p1
|
external/orthogroups/orthofinder/results/Results_Oct13/WorkingDirectory/OrthoFinder/Results_analysis_2953776/Phylogenetically_Misplaced_Genes/piper26.txt
ADDED
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|
| 1 |
+
Psar_g6487_i5.p2
|
| 2 |
+
Psar_g51961_i0.p2
|
| 3 |
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Psar_g73303_i0.p1
|
| 4 |
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Psar_g130358_i0.p1
|
| 5 |
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Psar_g3102_i20.p1
|
| 6 |
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Psar_g3102_i23.p1
|
| 7 |
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Psar_g3102_i17.p1
|
| 8 |
+
Psar_g21106_i0.p3
|
| 9 |
+
Psar_g7649_i0.p1
|
| 10 |
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Psar_g5104_i1.p1
|
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|
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|
| 13 |
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Psar_g5104_i3.p1
|
| 14 |
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Psar_g6667_i18.p1
|
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|
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| 19 |
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| 21 |
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| 23 |
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Psar_g128188_i0.p1
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| 33 |
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Psar_g65681_i0.p1
|
| 44 |
+
Psar_g77759_i0.p1
|
external/orthogroups/orthofinder/results/Results_Oct13/WorkingDirectory/OrthoFinder/Results_analysis_2953776/Phylogenetically_Misplaced_Genes/piper27.txt
ADDED
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|
|
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|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
| 1 |
+
Pkad_g141287_i0.p1
|
| 2 |
+
Pkad_g123831_i0.p1
|
| 3 |
+
Pkad_g9414_i4.p1
|
| 4 |
+
Pkad_g245988_i0.p2
|
| 5 |
+
Pkad_g198627_i0.p1
|
| 6 |
+
Pkad_g10651_i3.p1
|
| 7 |
+
Pkad_g52418_i0.p1
|
| 8 |
+
Pkad_g240421_i0.p2
|
| 9 |
+
Pkad_g144905_i0.p1
|
| 10 |
+
Pkad_g139845_i0.p2
|
| 11 |
+
Pkad_g15344_i3.p1
|
| 12 |
+
Pkad_g1264_i12.p2
|
| 13 |
+
Pkad_g22354_i2.p1
|
| 14 |
+
Pkad_g6262_i0.p1
|
| 15 |
+
Pkad_g36776_i0.p1
|
| 16 |
+
Pkad_g36352_i0.p1
|
| 17 |
+
Pkad_g1472_i2.p1
|
| 18 |
+
Pkad_g1472_i1.p1
|
| 19 |
+
Pkad_g1472_i3.p1
|
| 20 |
+
Pkad_g47818_i0.p1
|
| 21 |
+
Pkad_g14176_i0.p1
|
| 22 |
+
Pkad_g34359_i0.p1
|
| 23 |
+
Pkad_g54940_i0.p1
|
| 24 |
+
Pkad_g75627_i0.p2
|
| 25 |
+
Pkad_g205581_i0.p1
|
| 26 |
+
Pkad_g2261_i5.p1
|
| 27 |
+
Pkad_g100552_i0.p3
|
| 28 |
+
Pkad_g12285_i4.p1
|
| 29 |
+
Pkad_g51836_i1.p1
|
| 30 |
+
Pkad_g48350_i0.p1
|
| 31 |
+
Pkad_g51836_i0.p1
|
| 32 |
+
Pkad_g209294_i0.p1
|
| 33 |
+
Pkad_g1779_i1.p1
|
| 34 |
+
Pkad_g69364_i0.p1
|
| 35 |
+
Pkad_g82858_i0.p1
|
| 36 |
+
Pkad_g89327_i0.p1
|
| 37 |
+
Pkad_g239038_i0.p1
|
| 38 |
+
Pkad_g18821_i0.p2
|
| 39 |
+
Pkad_g244446_i0.p1
|
| 40 |
+
Pkad_g129188_i0.p1
|
| 41 |
+
Pkad_g188394_i0.p1
|
| 42 |
+
Pkad_g98054_i0.p1
|
| 43 |
+
Pkad_g198495_i0.p2
|
| 44 |
+
Pkad_g161639_i0.p1
|
| 45 |
+
Pkad_g130018_i0.p1
|
| 46 |
+
Pkad_g3259_i3.p2
|
| 47 |
+
Pkad_g88616_i0.p1
|
| 48 |
+
Pkad_g97837_i0.p1
|
| 49 |
+
Pkad_g195427_i0.p1
|
| 50 |
+
Pkad_g47925_i0.p1
|
| 51 |
+
Pkad_g121291_i0.p1
|
| 52 |
+
Pkad_g244131_i0.p1
|
| 53 |
+
Pkad_g194111_i0.p1
|
| 54 |
+
Pkad_g47439_i0.p1
|
| 55 |
+
Pkad_g205504_i0.p1
|
| 56 |
+
Pkad_g79491_i0.p1
|
| 57 |
+
Pkad_g123_i0.p1
|
| 58 |
+
Pkad_g697_i1.p1
|
| 59 |
+
Pkad_g4888_i5.p1
|
| 60 |
+
Pkad_g4888_i6.p1
|
| 61 |
+
Pkad_g150562_i0.p1
|
| 62 |
+
Pkad_g174446_i0.p2
|
| 63 |
+
Pkad_g223531_i0.p1
|
| 64 |
+
Pkad_g14323_i1.p1
|
| 65 |
+
Pkad_g13586_i1.p2
|
| 66 |
+
Pkad_g4159_i2.p1
|
| 67 |
+
Pkad_g200186_i0.p1
|
| 68 |
+
Pkad_g6660_i4.p1
|
| 69 |
+
Pkad_g138146_i0.p2
|
| 70 |
+
Pkad_g535_i1.p3
|
| 71 |
+
Pkad_g22108_i0.p1
|
| 72 |
+
Pkad_g198997_i0.p1
|
| 73 |
+
Pkad_g122547_i0.p2
|
| 74 |
+
Pkad_g75861_i0.p1
|
| 75 |
+
Pkad_g165912_i0.p1
|
| 76 |
+
Pkad_g29284_i0.p1
|
| 77 |
+
Pkad_g141680_i0.p2
|
external/orthogroups/orthofinder/results/Results_Oct13/WorkingDirectory/OrthoFinder/Results_analysis_2953776/Phylogenetically_Misplaced_Genes/piper32.txt
ADDED
|
@@ -0,0 +1,73 @@
|
|
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|
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|
|
|
|
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|
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|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
| 1 |
+
Pgui_g3220_i1.p3
|
| 2 |
+
Pgui_g20435_i0.p1
|
| 3 |
+
Pgui_g37112_i0.p1
|
| 4 |
+
Pgui_g27561_i0.p1
|
| 5 |
+
Pgui_g77831_i0.p1
|
| 6 |
+
Pgui_g73887_i0.p1
|
| 7 |
+
Pgui_g154814_i0.p1
|
| 8 |
+
Pgui_g67373_i0.p1
|
| 9 |
+
Pgui_g35884_i0.p1
|
| 10 |
+
Pgui_g67913_i0.p1
|
| 11 |
+
Pgui_g165380_i0.p1
|
| 12 |
+
Pgui_g34248_i0.p1
|
| 13 |
+
Pgui_g12852_i0.p2
|
| 14 |
+
Pgui_g62926_i0.p1
|
| 15 |
+
Pgui_g1900_i10.p1
|
| 16 |
+
Pgui_g5408_i2.p2
|
| 17 |
+
Pgui_g25974_i0.p1
|
| 18 |
+
Pgui_g998_i0.p2
|
| 19 |
+
Pgui_g199704_i0.p1
|
| 20 |
+
Pgui_g65513_i0.p1
|
| 21 |
+
Pgui_g36200_i0.p1
|
| 22 |
+
Pgui_g68873_i0.p1
|
| 23 |
+
Pgui_g120688_i0.p1
|
| 24 |
+
Pgui_g57909_i0.p1
|
| 25 |
+
Pgui_g34361_i0.p1
|
| 26 |
+
Pgui_g84086_i0.p1
|
| 27 |
+
Pgui_g62758_i0.p1
|
| 28 |
+
Pgui_g165911_i0.p1
|
| 29 |
+
Pgui_g70210_i0.p1
|
| 30 |
+
Pgui_g124554_i0.p2
|
| 31 |
+
Pgui_g83664_i0.p2
|
| 32 |
+
Pgui_g6546_i0.p2
|
| 33 |
+
Pgui_g13179_i2.p1
|
| 34 |
+
Pgui_g94044_i0.p1
|
| 35 |
+
Pgui_g60053_i0.p1
|
| 36 |
+
Pgui_g109519_i0.p1
|
| 37 |
+
Pgui_g6275_i0.p2
|
| 38 |
+
Pgui_g160213_i0.p1
|
| 39 |
+
Pgui_g132331_i0.p1
|
| 40 |
+
Pgui_g97269_i0.p1
|
| 41 |
+
Pgui_g42244_i0.p1
|
| 42 |
+
Pgui_g85607_i0.p1
|
| 43 |
+
Pgui_g28690_i0.p1
|
| 44 |
+
Pgui_g31675_i0.p1
|
| 45 |
+
Pgui_g88277_i0.p1
|
| 46 |
+
Pgui_g96444_i0.p2
|
| 47 |
+
Pgui_g90754_i0.p1
|
| 48 |
+
Pgui_g131895_i0.p1
|
| 49 |
+
Pgui_g103806_i0.p1
|
| 50 |
+
Pgui_g27823_i0.p1
|
| 51 |
+
Pgui_g129473_i0.p1
|
| 52 |
+
Pgui_g125579_i0.p1
|
| 53 |
+
Pgui_g102282_i0.p1
|
| 54 |
+
Pgui_g4492_i0.p1
|
| 55 |
+
Pgui_g142_i11.p1
|
| 56 |
+
Pgui_g10870_i1.p1
|
| 57 |
+
Pgui_g41250_i0.p1
|
| 58 |
+
Pgui_g6633_i0.p3
|
| 59 |
+
Pgui_g106335_i0.p1
|
| 60 |
+
Pgui_g859_i2.p3
|
| 61 |
+
Pgui_g62522_i0.p1
|
| 62 |
+
Pgui_g27033_i1.p1
|
| 63 |
+
Pgui_g50874_i0.p1
|
| 64 |
+
Pgui_g10150_i1.p1
|
| 65 |
+
Pgui_g51643_i0.p1
|
| 66 |
+
Pgui_g87448_i0.p1
|
| 67 |
+
Pgui_g95779_i0.p1
|
| 68 |
+
Pgui_g81644_i0.p1
|
| 69 |
+
Pgui_g53937_i0.p1
|
| 70 |
+
Pgui_g14665_i2.p1
|
| 71 |
+
Pgui_g92951_i0.p1
|
| 72 |
+
Pgui_g68785_i0.p1
|
| 73 |
+
Pgui_g64479_i0.p1
|
external/orthogroups/orthofinder/results/Results_Oct13/WorkingDirectory/OrthoFinder/Results_analysis_2953776/Phylogenetically_Misplaced_Genes/piper54.txt
ADDED
|
@@ -0,0 +1,13 @@
|
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|
|
|
|
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|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
| 1 |
+
Paur_g291_i2.p1
|
| 2 |
+
Paur_g6234_i3.p1
|
| 3 |
+
Paur_g53673_i0.p1
|
| 4 |
+
Paur_g32901_i0.p1
|
| 5 |
+
Paur_g76961_i0.p1
|
| 6 |
+
Paur_g1759_i2.p1
|
| 7 |
+
Paur_g9710_i4.p3
|
| 8 |
+
Paur_g416_i1.p2
|
| 9 |
+
Paur_g1695_i5.p2
|
| 10 |
+
Paur_g49468_i0.p1
|
| 11 |
+
Paur_g62159_i0.p1
|
| 12 |
+
Paur_g76858_i0.p1
|
| 13 |
+
Paur_g7531_i1.p1
|
external/orthogroups/orthofinder/results/Results_Oct13/WorkingDirectory/OrthoFinder/Results_analysis_2953776/Phylogenetically_Misplaced_Genes/piper55.txt
ADDED
|
@@ -0,0 +1,15 @@
|
|
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|
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|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
| 1 |
+
Pexc_g4105_i1.p2
|
| 2 |
+
Pexc_g11376_i2.p1
|
| 3 |
+
Pexc_g4129_i0.p1
|
| 4 |
+
Pexc_g13646_i1.p1
|
| 5 |
+
Pexc_g2099_i3.p2
|
| 6 |
+
Pexc_g2099_i5.p1
|
| 7 |
+
Pexc_g4226_i1.p2
|
| 8 |
+
Pexc_g2819_i0.p1
|
| 9 |
+
Pexc_g765_i1.p2
|
| 10 |
+
Pexc_g60416_i0.p1
|
| 11 |
+
Pexc_g25883_i0.p1
|
| 12 |
+
Pexc_g5588_i0.p3
|
| 13 |
+
Pexc_g0_i4.p9
|
| 14 |
+
Pexc_g12232_i1.p1
|
| 15 |
+
Pexc_g227_i2.p2
|
external/orthogroups/orthofinder/results/Results_Oct13/WorkingDirectory/OrthoFinder/Results_analysis_2953776/Phylogenetically_Misplaced_Genes/piper56.txt
ADDED
|
@@ -0,0 +1,34 @@
|
|
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|
|
|
|
|
|
|
|
|
|
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|
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|
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|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
| 1 |
+
Pnig_g12031_i6.p1
|
| 2 |
+
Pnig_g7723_i4.p1
|
| 3 |
+
Pnig_g35394_i0.p1
|
| 4 |
+
Pnig_g38966_i0.p2
|
| 5 |
+
Pnig_g60768_i0.p1
|
| 6 |
+
Pnig_g5811_i0.p2
|
| 7 |
+
Pnig_g5811_i7.p1
|
| 8 |
+
Pnig_g5811_i6.p1
|
| 9 |
+
Pnig_g5811_i3.p2
|
| 10 |
+
Pnig_g4048_i11.p1
|
| 11 |
+
Pnig_g43288_i0.p1
|
| 12 |
+
Pnig_g5530_i2.p1
|
| 13 |
+
Pnig_g3950_i2.p1
|
| 14 |
+
Pnig_g52000_i0.p2
|
| 15 |
+
Pnig_g169_i3.p7
|
| 16 |
+
Pnig_g169_i14.p1
|
| 17 |
+
Pnig_g15346_i4.p1
|
| 18 |
+
Pnig_g16526_i5.p1
|
| 19 |
+
Pnig_g16526_i0.p1
|
| 20 |
+
Pnig_g9717_i2.p1
|
| 21 |
+
Pnig_g9717_i5.p2
|
| 22 |
+
Pnig_g8325_i0.p1
|
| 23 |
+
Pnig_g23776_i0.p1
|
| 24 |
+
Pnig_g15308_i0.p1
|
| 25 |
+
Pnig_g8670_i2.p1
|
| 26 |
+
Pnig_g1426_i9.p1
|
| 27 |
+
Pnig_g14531_i1.p1
|
| 28 |
+
Pnig_g81102_i0.p1
|
| 29 |
+
Pnig_g4143_i1.p1
|
| 30 |
+
Pnig_g72676_i0.p1
|
| 31 |
+
Pnig_g62032_i0.p1
|
| 32 |
+
Pnig_g18659_i1.p1
|
| 33 |
+
Pnig_g2250_i8.p1
|
| 34 |
+
Pnig_g10755_i0.p2
|
external/orthogroups/orthofinder/results/Results_Oct13/WorkingDirectory/OrthoFinder/Results_analysis_2953776/Species_Tree/Orthogroups_for_concatenated_alignment.txt
ADDED
|
@@ -0,0 +1,1540 @@
|
|
|
|
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|
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|
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OG0024360
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| 2 |
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|
external/orthogroups/orthofinder/results/Results_Oct13/WorkingDirectory/OrthoFinder/Results_analysis_2953776/Species_Tree/SpeciesTree_rooted.txt
ADDED
|
@@ -0,0 +1 @@
|
|
|
|
|
|
|
| 1 |
+
((piper23:0.0271839,piper09:0.0170752)1:0.00621618,(piper12:0.0338506,(piper10:0.0352404,((piper54:0.0061796,piper25:0.00692928)1:0.0368083,(piper55:0.0310378,(piper06:0.0271061,(piper26:0.0213605,((piper20:0.021423,(piper32:0.0178659,piper56:0.0187262)1:0.0041231)1:0.00235446,piper27:0.0202558)1:0.000958641)1:0.00476699)1:0.0171791)1:0.0127217)1:0.0100692)1:0.00279972)1:0.00621618);
|
external/orthogroups/orthofinder/results/Results_Oct13/WorkingDirectory/OrthoFinder/Results_analysis_2953776/Species_Tree/SpeciesTree_rooted_node_labels.txt
ADDED
|
@@ -0,0 +1 @@
|
|
|
|
|
|
|
| 1 |
+
((piper23:0.0271839,piper09:0.0170752)N1:0.00621618,(piper12:0.0338506,(piper10:0.0352404,((piper54:0.0061796,piper25:0.00692928)N5:0.0368083,(piper55:0.0310378,(piper06:0.0271061,(piper26:0.0213605,((piper20:0.021423,(piper32:0.0178659,piper56:0.0187262)N11:0.0041231)N10:0.00235446,piper27:0.0202558)N9:0.000958641)N8:0.00476699)N7:0.0171791)N6:0.0127217)N4:0.0100692)N3:0.00279972)N2:0.00621618)N0;
|
processed/scoring/net3d.npy → external/orthogroups/orthofinder/results/Results_Oct13/WorkingDirectory/OrthoFinder/Results_analysis_2953776/WorkingDirectory/clusters_OrthoFinder_I1.5.txt_id_pairs.txt
RENAMED
|
@@ -1,3 +1,3 @@
|
|
| 1 |
version https://git-lfs.github.com/spec/v1
|
| 2 |
-
oid sha256:
|
| 3 |
-
size
|
|
|
|
| 1 |
version https://git-lfs.github.com/spec/v1
|
| 2 |
+
oid sha256:231fa3558f334e99156b73b55038d590dbc4902fee708b5f016ee2861cf0a3c2
|
| 3 |
+
size 20512980
|
processed/scoring/gene_og_row.npy → external/orthogroups/orthofinder/results/Results_Oct13/WorkingDirectory/SequenceIDs.txt
RENAMED
|
@@ -1,3 +1,3 @@
|
|
| 1 |
version https://git-lfs.github.com/spec/v1
|
| 2 |
-
oid sha256:
|
| 3 |
-
size
|
|
|
|
| 1 |
version https://git-lfs.github.com/spec/v1
|
| 2 |
+
oid sha256:081eec66d871b020e17356443c4ff28a9da76ac3d1ed24d1476a3dc4d270f325
|
| 3 |
+
size 47494518
|
external/orthogroups/orthofinder/results/Results_Oct13/WorkingDirectory/SpeciesIDs.txt
ADDED
|
@@ -0,0 +1,13 @@
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
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processed/scoring/gene_species_col.npy → external/orthogroups/sonicpd/graph_only/not_assigned_genes.ortholog_groups.tsv
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Date:
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| 2 |
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SonicParanoid 2.0.
|
| 3 |
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Run ID:
|
| 4 |
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Input directory: /
|
| 5 |
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Main output directory: /
|
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Input proteomes: 13
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|
| 12 |
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|
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Sequence DB directory: /
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Alignment directory: /
|
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Pairwise tables DB directory: /
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| 25 |
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| 26 |
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|
|
@@ -29,8 +29,9 @@ Complete overwrite: False
|
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| 29 |
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|
| 30 |
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|
| 31 |
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SonicParanoid installation: /
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| 33 |
Installation type: Python
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Python version: 3.
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Date: Mon Oct 12 12:19:32 2026
|
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SonicParanoid 2.0.9
|
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Run ID: piperNET_2026-10
|
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Input directory: /uochb/project/pluskal_group/pipernet/data/rnaseq/processed/proteomes
|
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Main output directory: /uochb/project/pluskal_group/pipernet/data/rnaseq/external/orthogroups/sonicpd/graph_only
|
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Run directory: /uochb/project/pluskal_group/pipernet/data/rnaseq/external/orthogroups/sonicpd/graph_only/runs/piperNET_2026-10
|
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Input proteomes: 13
|
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|
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|
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|
| 11 |
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Threads: 32
|
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|
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| 15 |
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|
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| 21 |
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|
| 23 |
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Perform only graph-based orthology: True
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| 24 |
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| 25 |
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| 26 |
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|
|
|
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| 29 |
Skip creation of ortholog groups: False
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| 30 |
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|
| 32 |
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SonicParanoid installation: /uochb/soft/users/titodamiani/conda-envs/sonicparanoid/lib/python3.10/site-packages/sonicparanoid
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| 33 |
Installation type: Python
|
| 34 |
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Python version: 3.10.22 | packaged by conda-forge | (main, Oct 6 2026, 23:02:24) [GCC 14.4.0]
|
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Python executables: /uochb/soft/users/titodamiani/conda-envs/sonicparanoid/bin/python
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| 2 |
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oid sha256:
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| 3 |
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size
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|
| 1 |
version https://git-lfs.github.com/spec/v1
|
| 2 |
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oid sha256:cf685269e028eab44b3c4282cbcbcf6491d7a7fcebce5067105e316c814809b7
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| 3 |
+
size 8010959
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