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Oryza.log
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# WARNING : folder 'Oryza' exists, files might be overwritten
# pangene_analysis.pl -d Plants -c Oryza -r oryza_sativa -o -f Oryza -t protein -G 0 -W 0 -L 0 -S 0
# supported species in NCBI taxon Oryza : 11
# total selected species : 11
# re-using plant_tools/compara/downloads/Compara.98.protein_default.homologies.oryza_sativa.tsv.gz
# re-using Oryza_sativa.IRGSP-1.0.pep.all.fa.gz
# re-using plant_tools/compara/downloads/Compara.98.protein_default.homologies.oryza_indica.tsv.gz
# re-using Oryza_indica.ASM465v1.pep.all.fa.gz
# re-using plant_tools/compara/downloads/Compara.98.protein_default.homologies.oryza_brachyantha.tsv.gz
# re-using Oryza_brachyantha.Oryza_brachyantha.v1.4b.pep.all.fa.gz
# re-using plant_tools/compara/downloads/Compara.98.protein_default.homologies.oryza_meridionalis.tsv.gz
# re-using Oryza_meridionalis.Oryza_meridionalis_v1.3.pep.all.fa.gz
# re-using plant_tools/compara/downloads/Compara.98.protein_default.homologies.oryza_glaberrima.tsv.gz
# re-using Oryza_glaberrima.Oryza_glaberrima_V1.pep.all.fa.gz
# re-using plant_tools/compara/downloads/Compara.98.protein_default.homologies.oryza_punctata.tsv.gz
# re-using Oryza_punctata.Oryza_punctata_v1.2.pep.all.fa.gz
# re-using plant_tools/compara/downloads/Compara.98.protein_default.homologies.oryza_longistaminata.tsv.gz
# re-using Oryza_longistaminata.O_longistaminata_v1.0.pep.all.fa.gz
# re-using plant_tools/compara/downloads/Compara.98.protein_default.homologies.oryza_barthii.tsv.gz
# re-using Oryza_barthii.O.barthii_v1.pep.all.fa.gz
# re-using plant_tools/compara/downloads/Compara.98.protein_default.homologies.oryza_nivara.tsv.gz
# re-using Oryza_nivara.Oryza_nivara_v1.0.pep.all.fa.gz
# re-using plant_tools/compara/downloads/Compara.98.protein_default.homologies.oryza_rufipogon.tsv.gz
# re-using Oryza_rufipogon.OR_W1943.pep.all.fa.gz
# re-using plant_tools/compara/downloads/Compara.98.protein_default.homologies.oryza_glumipatula.tsv.gz
# re-using Oryza_glumipatula.Oryza_glumaepatula_v1.5.pep.all.fa.gz
# oryza_sativa : sequences = 35775 clusters = 35419 (singletons = 8371)
# oryza_indica : sequences = 40745 clusters = 39590 (singletons = 7645)
# oryza_brachyantha : sequences = 32037 clusters = 31856 (singletons = 10421)
# oryza_meridionalis : sequences = 29308 clusters = 28659 (singletons = 4605)
# oryza_glaberrima : sequences = 33164 clusters = 31710 (singletons = 4051)
# oryza_punctata : sequences = 31762 clusters = 30673 (singletons = 6246)
# oryza_longistaminata : sequences = 31686 clusters = 30034 (singletons = 7460)
# oryza_barthii : sequences = 34575 clusters = 33903 (singletons = 3263)
# oryza_nivara : sequences = 36313 clusters = 35918 (singletons = 3387)
# oryza_rufipogon : sequences = 37071 clusters = 36716 (singletons = 3837)
# oryza_glumipatula : sequences = 35735 clusters = 35231 (singletons = 4249)
# total sequences = 378171
# number_of_clusters = 110289 (core = 8052)
# cluster_list = Oryza/oryzasativa_Oryza_algEnsemblCompara.cluster_list
# cluster_directory = Oryza/oryzasativa_Oryza_algEnsemblCompara
# percent_conserved_proteins_file = Oryza/POCP.matrix.tab
# pangenome_file = Oryza/pangenome_matrix.tab tranposed = Oryza/pangenome_matrix.tr.tab
# pangenome_genes = Oryza/pangenome_matrix_genes.tab transposed = Oryza/pangenome_matrix_genes.tr.tab
# pangenome_FASTA_file = Oryza/pangenome_matrix.fasta
# genome composition report (samples=10,seed=12345)
## sample 0 (oryza_sativa | 0,1,2,3,4,5,6,7,8,9,10,)
## sample 1 (oryza_meridionalis | 3,2,4,8,10,0,6,9,1,7,5,)
## sample 2 (oryza_meridionalis | 3,0,1,9,4,2,6,8,7,5,10,)
## sample 3 (oryza_barthii | 7,10,2,8,6,5,3,9,1,0,4,)
## sample 4 (oryza_indica | 1,4,2,6,7,3,0,10,8,9,5,)
## sample 5 (oryza_sativa | 0,6,3,5,10,4,8,7,2,1,9,)
## sample 6 (oryza_barthii | 7,8,4,1,9,5,0,10,2,6,3,)
## sample 7 (oryza_glaberrima | 4,10,3,9,8,1,7,6,2,0,5,)
## sample 8 (oryza_indica | 1,0,2,3,6,8,10,9,5,4,7,)
## sample 9 (oryza_glaberrima | 4,6,1,5,0,2,10,9,8,7,3,)
# pan-gene (number of clusters) = Oryza/pan_gene.tab
# core-gene (number of clusters) = Oryza/core_gene.tab
# runtime: 146 wallclock secs (79.95 usr 4.76 sys + 29.57 cusr 1.52 csys = 115.80 CPU)