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kfuku52 / amalgkit

RNA-seq data amalgamation for a large-scale evolutionary transcriptomics
BSD 3-Clause "New" or "Revised" License
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Error in if (child1_color == child2_color) { : #146

Closed kfuku52 closed 1 year ago

kfuku52 commented 1 year ago

This error occurred in csca when some species included in the metadata are missing in the curate directory.

selected_curate_groups: leaf flower root photosynthetic_leaf 
dir_work: /Volumes/kfT7/Dropbox/data/evolutionary_transcriptomics/20230527_gfe_pipeline/gfe_data 
dir_csca_input_table: /Volumes/kfT7/Dropbox/data/evolutionary_transcriptomics/20230527_gfe_pipeline/gfe_data/tmp.amalgkit.csca_input_tables 
file_orthogroup: /Volumes/kfT7/Dropbox/data/evolutionary_transcriptomics/20230527_gfe_pipeline/gfe_data/csca/multispecies_busco_table.tsv 
file_genecount: /Volumes/kfT7/Dropbox/data/evolutionary_transcriptomics/20230527_gfe_pipeline/gfe_data/tmp.amalgkit.orthogroup.genecount.tsv 
r_util_path: /Volumes/kfT7/Dropbox/repos/amalgkit/amalgkit/util.r 
dir_csca: /Volumes/kfT7/Dropbox/data/evolutionary_transcriptomics/20230527_gfe_pipeline/gfe_data/csca 
batch_effect_alg: sva 
Number of single-copy orthogroups (>=50 percent species) detected for the 109 species: 1,613
Number of orthologs in input table: 1614 
Number of single-copy orthologs: 1613 
Number of selected species: 109 
Selected species: Actinidia chinensis Amaranthus hypochondriacus Amborella trichopoda Ambrosia artemisiifolia Ananas comosus Ancistrocladus abbreviatus Andrographis paniculata Arabidopsis thaliana Arachis hypogaea Asparagus officinalis Brachypodium distachyon Brassica napus Brassica oleracea Brassica rapa Brocchinia reducta Byblis aquatica Cajanus cajan Camellia sinensis Cannabis sativa Capsella grandiflora Capsicum annuum Cephalotus follicularis Chenopodium quinoa Cicer arietinum Citrullus lanatus Citrus sinensis Coffea arabica Cucumis melo Cucumis sativus Darlingtonia californica Daucus carota Dendrobium nobile Dionaea muscipula Drosera adelae Drosera spatulata Drosophyllum lusitanicum Elaeis guineensis Erythroxylum novogranatense Fragaria vesca Genlisea subglabra Glycine max Glycine soja Gossypium arboreum Gossypium hirsutum Gossypium stocksii Heliamphora nutans Helianthus annuus Hevea brasiliensis Hordeum vulgare Lactuca sativa Leersia perrieri Linum usitatissimum Macadamia integrifolia Malus domestica Mangifera indica Melastoma candidum Mikania micrantha Morus notabilis Nelumbo nucifera Nepenthes gracilis Nicotiana tabacum Nymphaea colorata Olea europaea Oryza barthii Oryza glaberrima Oryza glumipatula Oryza meridionalis Oryza punctata Oryza rufipogon Oryza sativa Oxalis triangularis Panicum virgatum Parasponia andersonii Phalaenopsis equestris Phoenix dactylifera Pinguicula agnata Pistacia vera Pisum sativum Plumbago auriculata Prosopis cineraria Prunus armeniaca Prunus avium Prunus persica Punica granatum Raphanus sativus Ricinus communis Roridula gorgonias Salvia hispanica Sarracenia purpurea Secale cereale Sesamum indicum Setaria italica Solanum lycopersicum Solanum tuberosum Sorghum bicolor Spinacia oleracea Stylidium debile Tripterygium wilfordii Triticum aestivum Triticum dicoccoides Triticum turgidum Utricularia australis Utricularia livida Vicia faba Vigna radiata Vigna umbellata Vitis vinifera Zea mays Ziziphus jujuba 
1613 orthologs were found before filtering.
Applying expression level imputation for missing orthologs.
Number of removed rows with all NA values in the expression matrix: 0
Imputing 98,224 missing values in a total of 519,386 observations (1,613 genes x 322 samples).
Number of negative values coarced to zero in the imputed expression matrix: 5,083
Number of removed rows with all NA values in the expression matrix: 0
Imputing 1,537,761 missing values in a total of 6,914,931 observations (1,613 genes x 4,287 samples).
Number of negative values coarced to zero in the imputed expression matrix: 93,928
Number of removed rows with all NA values in the expression matrix: 0
Imputing 98,106 missing values in a total of 517,773 observations (1,613 genes x 321 samples).
Number of negative values coarced to zero in the imputed expression matrix: 4,381
Number of removed rows with all NA values in the expression matrix: 0
Imputing 1,409,370 missing values in a total of 6,285,861 observations (1,613 genes x 3,897 samples).
Number of negative values coarced to zero in the imputed expression matrix: 60,102
1613 orthologs were found after filtering and imputation.
No pvclust file found. Start bootstrapping.
Bootstrap (r = 0.5)... Done.
Bootstrap (r = 0.6)... Done.
Bootstrap (r = 0.7)... Done.
Bootstrap (r = 0.8)... Done.
Bootstrap (r = 0.9)... Done.
Bootstrap (r = 1.0)... Done.
Bootstrap (r = 1.1)... Done.
Bootstrap (r = 1.2)... Done.
Bootstrap (r = 1.3)... Done.
Bootstrap (r = 1.4)... Done.
No pvclust file found. Start bootstrapping.
Bootstrap (r = 0.5)... Done.
Bootstrap (r = 0.6)... Done.
Bootstrap (r = 0.7)... Done.
Bootstrap (r = 0.8)... Done.
Bootstrap (r = 0.9)... Done.
Bootstrap (r = 1.0)... Done.
Bootstrap (r = 1.1)... Done.
Bootstrap (r = 1.2)... Done.
Bootstrap (r = 1.3)... Done.
Bootstrap (r = 1.4)... Done.
Error in if (child1_color == child2_color) { : 
  missing value where TRUE/FALSE needed
Calls: save_averaged_dendrogram_plot ... lapply -> FUN -> lapply -> FUN -> lapply -> FUN -> FUN
Execution halted