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nf-core / differentialabundance

Differential abundance analysis for feature/ observation matrices from platforms such as RNA-seq
https://nf-co.re/differentialabundance
MIT License
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"exclude" samples aren't respected in SHINYNGS_STATICEXPLORATORY - Error in cor(matrices[[g]]) : supply both 'x' and 'y' or a matrix-like 'x' #196

Closed olgabot closed 3 weeks ago

olgabot commented 7 months ago

Description of the bug

Hello, I'm running this pipeline on the star_salmon/salmon.merged.gene_counts.tsv output from nf-core/rnaseq and am having an issue with the PLOT_EXPLORATORY step, which fails with a final error message of:

  [1] "Writing sample dendrogram..."
  null device
            1
  Error in cor(matrices[[g]]) :
    supply both 'x' and 'y' or a matrix-like 'x'
  Calls: madScore -> do.call -> lapply -> FUN -> cor -> cor
  Execution halted

Do you know what may be going on?

Below are the redacted parameters

Redacted parameters ``` exploratory_final_assay = variance_stabilised custom_config_base = https://raw.githubusercontent.com/nf-core/configs/master monochrome-logs = false validation-S3Path-check = false affy_build_annotation = true plaintext_email = false features_metadata_cols = gene_id,gene_name,gene_biotype gsea_rnd_type = no_balance exploratory_cor_method = spearman deseq2_min_replicates_for_replace = 7 affy_bgversion = 2 limma_p_value = 1 css_file = /.nextflow/assets/nf-core/differentialabundance/assets/nf-core_style.css filtering_min_samples = 1 proteus_plotmv_loess = true gsea_order = descending proteus_round_digits = -1 features_id_col = gene_id gsea_median = false exploratory_clustering_method = ward.D2 exploratory_palette_name = Set1 version = false publish_dir_mode = copy input = [samplesheet.csv](https://api.tower.nf/workspaces/REDACTED/samplesheet.csv) affy_background = true gsea_zip_report = false study_type = rnaseq filtering_min_abundance = 1 validationSkipDuplicateCheck = false gsea_plot_top_x = 20 validationSchemaIgnoreParams = genomes,igenomes_base differential_subset_to_contrast_samples = false features_gtf_feature_type = transcript limma_block = None gsea_set_min = 15 gsea_rnd_seed = timestamp validation-skip-duplicate-check = false report_description = None deseq2_independent_filtering = true limma_correlation = None querygse = None proteus_palette_name = Set1 gsea_save_rnd_lists = false limma_lfc = 0 matrix = s3://REDACTED/star_salmon/salmon.merged.gene_counts.tsv observations_name_col = sample limma_trend = false shinyngs_build_app = true shinyngs_shinyapps_account = None custom_config_version = master study_abundance_type = counts proteus_measurecol_prefix = LFQ intensity proteus_norm_function = normalizeMedian gsea_set_max = 500 affy_file_name_col = file deseq2_vst_nsub = 1000 citations_file = /.nextflow/assets/nf-core/differentialabundance/CITATIONS.md differential_feature_name_column = gene_name limma_proportion = 0.01 gsea_nperm = 1000 differential_max_pval = 1 genomes: GRCh37: fasta = s3://ngi-igenomes/igenomes/Homo_sapiens/Ensembl/GRCh37/Sequence/WholeGenomeFasta/genome.fa bwa = s3://ngi-igenomes/igenomes/Homo_sapiens/Ensembl/GRCh37/Sequence/BWAIndex/version0.6.0/ bowtie2 = s3://ngi-igenomes/igenomes/Homo_sapiens/Ensembl/GRCh37/Sequence/Bowtie2Index/ star = s3://ngi-igenomes/igenomes/Homo_sapiens/Ensembl/GRCh37/Sequence/STARIndex/ bismark = s3://ngi-igenomes/igenomes/Homo_sapiens/Ensembl/GRCh37/Sequence/BismarkIndex/ gtf = s3://ngi-igenomes/igenomes/Homo_sapiens/Ensembl/GRCh37/Annotation/Genes/genes.gtf bed12 = s3://ngi-igenomes/igenomes/Homo_sapiens/Ensembl/GRCh37/Annotation/Genes/genes.bed readme = s3://ngi-igenomes/igenomes/Homo_sapiens/Ensembl/GRCh37/Annotation/README.txt mito_name = MT macs_gsize = 2.7e9 blacklist = /.nextflow/assets/nf-core/differentialabundance/assets/blacklists/GRCh37-blacklist.bed GRCh38: fasta = s3://ngi-igenomes/igenomes/Homo_sapiens/NCBI/GRCh38/Sequence/WholeGenomeFasta/genome.fa bwa = s3://ngi-igenomes/igenomes/Homo_sapiens/NCBI/GRCh38/Sequence/BWAIndex/version0.6.0/ bowtie2 = s3://ngi-igenomes/igenomes/Homo_sapiens/NCBI/GRCh38/Sequence/Bowtie2Index/ star = s3://ngi-igenomes/igenomes/Homo_sapiens/NCBI/GRCh38/Sequence/STARIndex/ bismark = s3://ngi-igenomes/igenomes/Homo_sapiens/NCBI/GRCh38/Sequence/BismarkIndex/ gtf = s3://ngi-igenomes/igenomes/Homo_sapiens/NCBI/GRCh38/Annotation/Genes/genes.gtf bed12 = s3://ngi-igenomes/igenomes/Homo_sapiens/NCBI/GRCh38/Annotation/Genes/genes.bed mito_name = chrM macs_gsize = 2.7e9 blacklist = /.nextflow/assets/nf-core/differentialabundance/assets/blacklists/hg38-blacklist.bed CHM13: fasta = s3://ngi-igenomes/igenomes/Homo_sapiens/UCSC/CHM13/Sequence/WholeGenomeFasta/genome.fa bwa = s3://ngi-igenomes/igenomes/Homo_sapiens/UCSC/CHM13/Sequence/BWAIndex/ bwamem2 = s3://ngi-igenomes/igenomes/Homo_sapiens/UCSC/CHM13/Sequence/BWAmem2Index/ gtf = s3://ngi-igenomes/igenomes/Homo_sapiens/NCBI/CHM13/Annotation/Genes/genes.gtf gff = ftp://ftp.ncbi.nlm.nih.gov/genomes/all/GCF/009/914/755/GCF_009914755.1_T2T-CHM13v2.0/GCF_009914755.1_T2T-CHM13v2.0_genomic.gff.gz mito_name = chrM GRCm38: fasta = s3://ngi-igenomes/igenomes/Mus_musculus/Ensembl/GRCm38/Sequence/WholeGenomeFasta/genome.fa bwa = s3://ngi-igenomes/igenomes/Mus_musculus/Ensembl/GRCm38/Sequence/BWAIndex/version0.6.0/ bowtie2 = s3://ngi-igenomes/igenomes/Mus_musculus/Ensembl/GRCm38/Sequence/Bowtie2Index/ star = s3://ngi-igenomes/igenomes/Mus_musculus/Ensembl/GRCm38/Sequence/STARIndex/ bismark = s3://ngi-igenomes/igenomes/Mus_musculus/Ensembl/GRCm38/Sequence/BismarkIndex/ gtf = s3://ngi-igenomes/igenomes/Mus_musculus/Ensembl/GRCm38/Annotation/Genes/genes.gtf bed12 = s3://ngi-igenomes/igenomes/Mus_musculus/Ensembl/GRCm38/Annotation/Genes/genes.bed readme = s3://ngi-igenomes/igenomes/Mus_musculus/Ensembl/GRCm38/Annotation/README.txt mito_name = MT macs_gsize = 1.87e9 blacklist = /.nextflow/assets/nf-core/differentialabundance/assets/blacklists/GRCm38-blacklist.bed TAIR10: fasta = s3://ngi-igenomes/igenomes/Arabidopsis_thaliana/Ensembl/TAIR10/Sequence/WholeGenomeFasta/genome.fa bwa = s3://ngi-igenomes/igenomes/Arabidopsis_thaliana/Ensembl/TAIR10/Sequence/BWAIndex/version0.6.0/ bowtie2 = s3://ngi-igenomes/igenomes/Arabidopsis_thaliana/Ensembl/TAIR10/Sequence/Bowtie2Index/ star = s3://ngi-igenomes/igenomes/Arabidopsis_thaliana/Ensembl/TAIR10/Sequence/STARIndex/ bismark = s3://ngi-igenomes/igenomes/Arabidopsis_thaliana/Ensembl/TAIR10/Sequence/BismarkIndex/ gtf = s3://ngi-igenomes/igenomes/Arabidopsis_thaliana/Ensembl/TAIR10/Annotation/Genes/genes.gtf bed12 = s3://ngi-igenomes/igenomes/Arabidopsis_thaliana/Ensembl/TAIR10/Annotation/Genes/genes.bed readme = s3://ngi-igenomes/igenomes/Arabidopsis_thaliana/Ensembl/TAIR10/Annotation/README.txt mito_name = Mt EB2: fasta = s3://ngi-igenomes/igenomes/Bacillus_subtilis_168/Ensembl/EB2/Sequence/WholeGenomeFasta/genome.fa bwa = s3://ngi-igenomes/igenomes/Bacillus_subtilis_168/Ensembl/EB2/Sequence/BWAIndex/version0.6.0/ bowtie2 = s3://ngi-igenomes/igenomes/Bacillus_subtilis_168/Ensembl/EB2/Sequence/Bowtie2Index/ star = s3://ngi-igenomes/igenomes/Bacillus_subtilis_168/Ensembl/EB2/Sequence/STARIndex/ bismark = s3://ngi-igenomes/igenomes/Bacillus_subtilis_168/Ensembl/EB2/Sequence/BismarkIndex/ gtf = s3://ngi-igenomes/igenomes/Bacillus_subtilis_168/Ensembl/EB2/Annotation/Genes/genes.gtf bed12 = s3://ngi-igenomes/igenomes/Bacillus_subtilis_168/Ensembl/EB2/Annotation/Genes/genes.bed readme = s3://ngi-igenomes/igenomes/Bacillus_subtilis_168/Ensembl/EB2/Annotation/README.txt UMD3.1: fasta = s3://ngi-igenomes/igenomes/Bos_taurus/Ensembl/UMD3.1/Sequence/WholeGenomeFasta/genome.fa bwa = s3://ngi-igenomes/igenomes/Bos_taurus/Ensembl/UMD3.1/Sequence/BWAIndex/version0.6.0/ bowtie2 = s3://ngi-igenomes/igenomes/Bos_taurus/Ensembl/UMD3.1/Sequence/Bowtie2Index/ star = s3://ngi-igenomes/igenomes/Bos_taurus/Ensembl/UMD3.1/Sequence/STARIndex/ bismark = s3://ngi-igenomes/igenomes/Bos_taurus/Ensembl/UMD3.1/Sequence/BismarkIndex/ gtf = s3://ngi-igenomes/igenomes/Bos_taurus/Ensembl/UMD3.1/Annotation/Genes/genes.gtf bed12 = s3://ngi-igenomes/igenomes/Bos_taurus/Ensembl/UMD3.1/Annotation/Genes/genes.bed readme = s3://ngi-igenomes/igenomes/Bos_taurus/Ensembl/UMD3.1/Annotation/README.txt mito_name = MT WBcel235: fasta = s3://ngi-igenomes/igenomes/Caenorhabditis_elegans/Ensembl/WBcel235/Sequence/WholeGenomeFasta/genome.fa bwa = s3://ngi-igenomes/igenomes/Caenorhabditis_elegans/Ensembl/WBcel235/Sequence/BWAIndex/version0.6.0/ bowtie2 = s3://ngi-igenomes/igenomes/Caenorhabditis_elegans/Ensembl/WBcel235/Sequence/Bowtie2Index/ star = s3://ngi-igenomes/igenomes/Caenorhabditis_elegans/Ensembl/WBcel235/Sequence/STARIndex/ bismark = s3://ngi-igenomes/igenomes/Caenorhabditis_elegans/Ensembl/WBcel235/Sequence/BismarkIndex/ gtf = s3://ngi-igenomes/igenomes/Caenorhabditis_elegans/Ensembl/WBcel235/Annotation/Genes/genes.gtf bed12 = s3://ngi-igenomes/igenomes/Caenorhabditis_elegans/Ensembl/WBcel235/Annotation/Genes/genes.bed mito_name = MtDNA macs_gsize = 9e7 CanFam3.1: fasta = s3://ngi-igenomes/igenomes/Canis_familiaris/Ensembl/CanFam3.1/Sequence/WholeGenomeFasta/genome.fa bwa = s3://ngi-igenomes/igenomes/Canis_familiaris/Ensembl/CanFam3.1/Sequence/BWAIndex/version0.6.0/ bowtie2 = s3://ngi-igenomes/igenomes/Canis_familiaris/Ensembl/CanFam3.1/Sequence/Bowtie2Index/ star = s3://ngi-igenomes/igenomes/Canis_familiaris/Ensembl/CanFam3.1/Sequence/STARIndex/ bismark = s3://ngi-igenomes/igenomes/Canis_familiaris/Ensembl/CanFam3.1/Sequence/BismarkIndex/ gtf = s3://ngi-igenomes/igenomes/Canis_familiaris/Ensembl/CanFam3.1/Annotation/Genes/genes.gtf bed12 = s3://ngi-igenomes/igenomes/Canis_familiaris/Ensembl/CanFam3.1/Annotation/Genes/genes.bed readme = s3://ngi-igenomes/igenomes/Canis_familiaris/Ensembl/CanFam3.1/Annotation/README.txt mito_name = MT GRCz10: fasta = s3://ngi-igenomes/igenomes/Danio_rerio/Ensembl/GRCz10/Sequence/WholeGenomeFasta/genome.fa bwa = s3://ngi-igenomes/igenomes/Danio_rerio/Ensembl/GRCz10/Sequence/BWAIndex/version0.6.0/ bowtie2 = s3://ngi-igenomes/igenomes/Danio_rerio/Ensembl/GRCz10/Sequence/Bowtie2Index/ star = s3://ngi-igenomes/igenomes/Danio_rerio/Ensembl/GRCz10/Sequence/STARIndex/ bismark = s3://ngi-igenomes/igenomes/Danio_rerio/Ensembl/GRCz10/Sequence/BismarkIndex/ gtf = s3://ngi-igenomes/igenomes/Danio_rerio/Ensembl/GRCz10/Annotation/Genes/genes.gtf bed12 = s3://ngi-igenomes/igenomes/Danio_rerio/Ensembl/GRCz10/Annotation/Genes/genes.bed mito_name = MT BDGP6: fasta = s3://ngi-igenomes/igenomes/Drosophila_melanogaster/Ensembl/BDGP6/Sequence/WholeGenomeFasta/genome.fa bwa = s3://ngi-igenomes/igenomes/Drosophila_melanogaster/Ensembl/BDGP6/Sequence/BWAIndex/version0.6.0/ bowtie2 = s3://ngi-igenomes/igenomes/Drosophila_melanogaster/Ensembl/BDGP6/Sequence/Bowtie2Index/ star = s3://ngi-igenomes/igenomes/Drosophila_melanogaster/Ensembl/BDGP6/Sequence/STARIndex/ bismark = s3://ngi-igenomes/igenomes/Drosophila_melanogaster/Ensembl/BDGP6/Sequence/BismarkIndex/ gtf = s3://ngi-igenomes/igenomes/Drosophila_melanogaster/Ensembl/BDGP6/Annotation/Genes/genes.gtf bed12 = s3://ngi-igenomes/igenomes/Drosophila_melanogaster/Ensembl/BDGP6/Annotation/Genes/genes.bed mito_name = M macs_gsize = 1.2e8 EquCab2: fasta = s3://ngi-igenomes/igenomes/Equus_caballus/Ensembl/EquCab2/Sequence/WholeGenomeFasta/genome.fa bwa = s3://ngi-igenomes/igenomes/Equus_caballus/Ensembl/EquCab2/Sequence/BWAIndex/version0.6.0/ bowtie2 = s3://ngi-igenomes/igenomes/Equus_caballus/Ensembl/EquCab2/Sequence/Bowtie2Index/ star = s3://ngi-igenomes/igenomes/Equus_caballus/Ensembl/EquCab2/Sequence/STARIndex/ bismark = s3://ngi-igenomes/igenomes/Equus_caballus/Ensembl/EquCab2/Sequence/BismarkIndex/ gtf = s3://ngi-igenomes/igenomes/Equus_caballus/Ensembl/EquCab2/Annotation/Genes/genes.gtf bed12 = s3://ngi-igenomes/igenomes/Equus_caballus/Ensembl/EquCab2/Annotation/Genes/genes.bed readme = s3://ngi-igenomes/igenomes/Equus_caballus/Ensembl/EquCab2/Annotation/README.txt mito_name = MT EB1: fasta = s3://ngi-igenomes/igenomes/Escherichia_coli_K_12_DH10B/Ensembl/EB1/Sequence/WholeGenomeFasta/genome.fa bwa = s3://ngi-igenomes/igenomes/Escherichia_coli_K_12_DH10B/Ensembl/EB1/Sequence/BWAIndex/version0.6.0/ bowtie2 = s3://ngi-igenomes/igenomes/Escherichia_coli_K_12_DH10B/Ensembl/EB1/Sequence/Bowtie2Index/ star = s3://ngi-igenomes/igenomes/Escherichia_coli_K_12_DH10B/Ensembl/EB1/Sequence/STARIndex/ bismark = s3://ngi-igenomes/igenomes/Escherichia_coli_K_12_DH10B/Ensembl/EB1/Sequence/BismarkIndex/ gtf = s3://ngi-igenomes/igenomes/Escherichia_coli_K_12_DH10B/Ensembl/EB1/Annotation/Genes/genes.gtf bed12 = s3://ngi-igenomes/igenomes/Escherichia_coli_K_12_DH10B/Ensembl/EB1/Annotation/Genes/genes.bed readme = s3://ngi-igenomes/igenomes/Escherichia_coli_K_12_DH10B/Ensembl/EB1/Annotation/README.txt Galgal4: fasta = s3://ngi-igenomes/igenomes/Gallus_gallus/Ensembl/Galgal4/Sequence/WholeGenomeFasta/genome.fa bwa = s3://ngi-igenomes/igenomes/Gallus_gallus/Ensembl/Galgal4/Sequence/BWAIndex/version0.6.0/ bowtie2 = s3://ngi-igenomes/igenomes/Gallus_gallus/Ensembl/Galgal4/Sequence/Bowtie2Index/ star = s3://ngi-igenomes/igenomes/Gallus_gallus/Ensembl/Galgal4/Sequence/STARIndex/ bismark = s3://ngi-igenomes/igenomes/Gallus_gallus/Ensembl/Galgal4/Sequence/BismarkIndex/ gtf = s3://ngi-igenomes/igenomes/Gallus_gallus/Ensembl/Galgal4/Annotation/Genes/genes.gtf bed12 = s3://ngi-igenomes/igenomes/Gallus_gallus/Ensembl/Galgal4/Annotation/Genes/genes.bed mito_name = MT Gm01: fasta = s3://ngi-igenomes/igenomes/Glycine_max/Ensembl/Gm01/Sequence/WholeGenomeFasta/genome.fa bwa = s3://ngi-igenomes/igenomes/Glycine_max/Ensembl/Gm01/Sequence/BWAIndex/version0.6.0/ bowtie2 = s3://ngi-igenomes/igenomes/Glycine_max/Ensembl/Gm01/Sequence/Bowtie2Index/ star = s3://ngi-igenomes/igenomes/Glycine_max/Ensembl/Gm01/Sequence/STARIndex/ bismark = s3://ngi-igenomes/igenomes/Glycine_max/Ensembl/Gm01/Sequence/BismarkIndex/ gtf = s3://ngi-igenomes/igenomes/Glycine_max/Ensembl/Gm01/Annotation/Genes/genes.gtf bed12 = s3://ngi-igenomes/igenomes/Glycine_max/Ensembl/Gm01/Annotation/Genes/genes.bed readme = s3://ngi-igenomes/igenomes/Glycine_max/Ensembl/Gm01/Annotation/README.txt Mmul_1: fasta = s3://ngi-igenomes/igenomes/Macaca_mulatta/Ensembl/Mmul_1/Sequence/WholeGenomeFasta/genome.fa bwa = s3://ngi-igenomes/igenomes/Macaca_mulatta/Ensembl/Mmul_1/Sequence/BWAIndex/version0.6.0/ bowtie2 = s3://ngi-igenomes/igenomes/Macaca_mulatta/Ensembl/Mmul_1/Sequence/Bowtie2Index/ star = s3://ngi-igenomes/igenomes/Macaca_mulatta/Ensembl/Mmul_1/Sequence/STARIndex/ bismark = s3://ngi-igenomes/igenomes/Macaca_mulatta/Ensembl/Mmul_1/Sequence/BismarkIndex/ gtf = s3://ngi-igenomes/igenomes/Macaca_mulatta/Ensembl/Mmul_1/Annotation/Genes/genes.gtf bed12 = s3://ngi-igenomes/igenomes/Macaca_mulatta/Ensembl/Mmul_1/Annotation/Genes/genes.bed readme = s3://ngi-igenomes/igenomes/Macaca_mulatta/Ensembl/Mmul_1/Annotation/README.txt mito_name = MT IRGSP-1.0: fasta = s3://ngi-igenomes/igenomes/Oryza_sativa_japonica/Ensembl/IRGSP-1.0/Sequence/WholeGenomeFasta/genome.fa bwa = s3://ngi-igenomes/igenomes/Oryza_sativa_japonica/Ensembl/IRGSP-1.0/Sequence/BWAIndex/version0.6.0/ bowtie2 = s3://ngi-igenomes/igenomes/Oryza_sativa_japonica/Ensembl/IRGSP-1.0/Sequence/Bowtie2Index/ star = s3://ngi-igenomes/igenomes/Oryza_sativa_japonica/Ensembl/IRGSP-1.0/Sequence/STARIndex/ bismark = s3://ngi-igenomes/igenomes/Oryza_sativa_japonica/Ensembl/IRGSP-1.0/Sequence/BismarkIndex/ gtf = s3://ngi-igenomes/igenomes/Oryza_sativa_japonica/Ensembl/IRGSP-1.0/Annotation/Genes/genes.gtf bed12 = s3://ngi-igenomes/igenomes/Oryza_sativa_japonica/Ensembl/IRGSP-1.0/Annotation/Genes/genes.bed mito_name = Mt CHIMP2.1.4: fasta = s3://ngi-igenomes/igenomes/Pan_troglodytes/Ensembl/CHIMP2.1.4/Sequence/WholeGenomeFasta/genome.fa bwa = s3://ngi-igenomes/igenomes/Pan_troglodytes/Ensembl/CHIMP2.1.4/Sequence/BWAIndex/version0.6.0/ bowtie2 = s3://ngi-igenomes/igenomes/Pan_troglodytes/Ensembl/CHIMP2.1.4/Sequence/Bowtie2Index/ star = s3://ngi-igenomes/igenomes/Pan_troglodytes/Ensembl/CHIMP2.1.4/Sequence/STARIndex/ bismark = s3://ngi-igenomes/igenomes/Pan_troglodytes/Ensembl/CHIMP2.1.4/Sequence/BismarkIndex/ gtf = s3://ngi-igenomes/igenomes/Pan_troglodytes/Ensembl/CHIMP2.1.4/Annotation/Genes/genes.gtf bed12 = s3://ngi-igenomes/igenomes/Pan_troglodytes/Ensembl/CHIMP2.1.4/Annotation/Genes/genes.bed readme = s3://ngi-igenomes/igenomes/Pan_troglodytes/Ensembl/CHIMP2.1.4/Annotation/README.txt mito_name = MT Rnor_5.0: fasta = s3://ngi-igenomes/igenomes/Rattus_norvegicus/Ensembl/Rnor_5.0/Sequence/WholeGenomeFasta/genome.fa bwa = s3://ngi-igenomes/igenomes/Rattus_norvegicus/Ensembl/Rnor_5.0/Sequence/BWAIndex/version0.6.0/ bowtie2 = s3://ngi-igenomes/igenomes/Rattus_norvegicus/Ensembl/Rnor_5.0/Sequence/Bowtie2Index/ star = s3://ngi-igenomes/igenomes/Rattus_norvegicus/Ensembl/Rnor_5.0/Sequence/STARIndex/ bismark = s3://ngi-igenomes/igenomes/Rattus_norvegicus/Ensembl/Rnor_5.0/Sequence/BismarkIndex/ gtf = s3://ngi-igenomes/igenomes/Rattus_norvegicus/Ensembl/Rnor_5.0/Annotation/Genes/genes.gtf bed12 = s3://ngi-igenomes/igenomes/Rattus_norvegicus/Ensembl/Rnor_5.0/Annotation/Genes/genes.bed mito_name = MT Rnor_6.0: fasta = s3://ngi-igenomes/igenomes/Rattus_norvegicus/Ensembl/Rnor_6.0/Sequence/WholeGenomeFasta/genome.fa bwa = s3://ngi-igenomes/igenomes/Rattus_norvegicus/Ensembl/Rnor_6.0/Sequence/BWAIndex/version0.6.0/ bowtie2 = s3://ngi-igenomes/igenomes/Rattus_norvegicus/Ensembl/Rnor_6.0/Sequence/Bowtie2Index/ star = s3://ngi-igenomes/igenomes/Rattus_norvegicus/Ensembl/Rnor_6.0/Sequence/STARIndex/ bismark = s3://ngi-igenomes/igenomes/Rattus_norvegicus/Ensembl/Rnor_6.0/Sequence/BismarkIndex/ gtf = s3://ngi-igenomes/igenomes/Rattus_norvegicus/Ensembl/Rnor_6.0/Annotation/Genes/genes.gtf bed12 = s3://ngi-igenomes/igenomes/Rattus_norvegicus/Ensembl/Rnor_6.0/Annotation/Genes/genes.bed mito_name = MT R64-1-1: fasta = s3://ngi-igenomes/igenomes/Saccharomyces_cerevisiae/Ensembl/R64-1-1/Sequence/WholeGenomeFasta/genome.fa bwa = s3://ngi-igenomes/igenomes/Saccharomyces_cerevisiae/Ensembl/R64-1-1/Sequence/BWAIndex/version0.6.0/ bowtie2 = s3://ngi-igenomes/igenomes/Saccharomyces_cerevisiae/Ensembl/R64-1-1/Sequence/Bowtie2Index/ star = s3://ngi-igenomes/igenomes/Saccharomyces_cerevisiae/Ensembl/R64-1-1/Sequence/STARIndex/ bismark = s3://ngi-igenomes/igenomes/Saccharomyces_cerevisiae/Ensembl/R64-1-1/Sequence/BismarkIndex/ gtf = s3://ngi-igenomes/igenomes/Saccharomyces_cerevisiae/Ensembl/R64-1-1/Annotation/Genes/genes.gtf bed12 = s3://ngi-igenomes/igenomes/Saccharomyces_cerevisiae/Ensembl/R64-1-1/Annotation/Genes/genes.bed mito_name = MT macs_gsize = 1.2e7 EF2: fasta = s3://ngi-igenomes/igenomes/Schizosaccharomyces_pombe/Ensembl/EF2/Sequence/WholeGenomeFasta/genome.fa bwa = s3://ngi-igenomes/igenomes/Schizosaccharomyces_pombe/Ensembl/EF2/Sequence/BWAIndex/version0.6.0/ bowtie2 = s3://ngi-igenomes/igenomes/Schizosaccharomyces_pombe/Ensembl/EF2/Sequence/Bowtie2Index/ star = s3://ngi-igenomes/igenomes/Schizosaccharomyces_pombe/Ensembl/EF2/Sequence/STARIndex/ bismark = s3://ngi-igenomes/igenomes/Schizosaccharomyces_pombe/Ensembl/EF2/Sequence/BismarkIndex/ gtf = s3://ngi-igenomes/igenomes/Schizosaccharomyces_pombe/Ensembl/EF2/Annotation/Genes/genes.gtf bed12 = s3://ngi-igenomes/igenomes/Schizosaccharomyces_pombe/Ensembl/EF2/Annotation/Genes/genes.bed readme = s3://ngi-igenomes/igenomes/Schizosaccharomyces_pombe/Ensembl/EF2/Annotation/README.txt mito_name = MT macs_gsize = 1.21e7 Sbi1: fasta = s3://ngi-igenomes/igenomes/Sorghum_bicolor/Ensembl/Sbi1/Sequence/WholeGenomeFasta/genome.fa bwa = s3://ngi-igenomes/igenomes/Sorghum_bicolor/Ensembl/Sbi1/Sequence/BWAIndex/version0.6.0/ bowtie2 = s3://ngi-igenomes/igenomes/Sorghum_bicolor/Ensembl/Sbi1/Sequence/Bowtie2Index/ star = s3://ngi-igenomes/igenomes/Sorghum_bicolor/Ensembl/Sbi1/Sequence/STARIndex/ bismark = s3://ngi-igenomes/igenomes/Sorghum_bicolor/Ensembl/Sbi1/Sequence/BismarkIndex/ gtf = s3://ngi-igenomes/igenomes/Sorghum_bicolor/Ensembl/Sbi1/Annotation/Genes/genes.gtf bed12 = s3://ngi-igenomes/igenomes/Sorghum_bicolor/Ensembl/Sbi1/Annotation/Genes/genes.bed readme = s3://ngi-igenomes/igenomes/Sorghum_bicolor/Ensembl/Sbi1/Annotation/README.txt Sscrofa10.2: fasta = s3://ngi-igenomes/igenomes/Sus_scrofa/Ensembl/Sscrofa10.2/Sequence/WholeGenomeFasta/genome.fa bwa = s3://ngi-igenomes/igenomes/Sus_scrofa/Ensembl/Sscrofa10.2/Sequence/BWAIndex/version0.6.0/ bowtie2 = s3://ngi-igenomes/igenomes/Sus_scrofa/Ensembl/Sscrofa10.2/Sequence/Bowtie2Index/ star = s3://ngi-igenomes/igenomes/Sus_scrofa/Ensembl/Sscrofa10.2/Sequence/STARIndex/ bismark = s3://ngi-igenomes/igenomes/Sus_scrofa/Ensembl/Sscrofa10.2/Sequence/BismarkIndex/ gtf = s3://ngi-igenomes/igenomes/Sus_scrofa/Ensembl/Sscrofa10.2/Annotation/Genes/genes.gtf bed12 = s3://ngi-igenomes/igenomes/Sus_scrofa/Ensembl/Sscrofa10.2/Annotation/Genes/genes.bed readme = s3://ngi-igenomes/igenomes/Sus_scrofa/Ensembl/Sscrofa10.2/Annotation/README.txt mito_name = MT AGPv3: fasta = s3://ngi-igenomes/igenomes/Zea_mays/Ensembl/AGPv3/Sequence/WholeGenomeFasta/genome.fa bwa = s3://ngi-igenomes/igenomes/Zea_mays/Ensembl/AGPv3/Sequence/BWAIndex/version0.6.0/ bowtie2 = s3://ngi-igenomes/igenomes/Zea_mays/Ensembl/AGPv3/Sequence/Bowtie2Index/ star = s3://ngi-igenomes/igenomes/Zea_mays/Ensembl/AGPv3/Sequence/STARIndex/ bismark = s3://ngi-igenomes/igenomes/Zea_mays/Ensembl/AGPv3/Sequence/BismarkIndex/ gtf = s3://ngi-igenomes/igenomes/Zea_mays/Ensembl/AGPv3/Annotation/Genes/genes.gtf bed12 = s3://ngi-igenomes/igenomes/Zea_mays/Ensembl/AGPv3/Annotation/Genes/genes.bed mito_name = Mt hg38: fasta = s3://ngi-igenomes/igenomes/Homo_sapiens/UCSC/hg38/Sequence/WholeGenomeFasta/genome.fa bwa = s3://ngi-igenomes/igenomes/Homo_sapiens/UCSC/hg38/Sequence/BWAIndex/version0.6.0/ bowtie2 = s3://ngi-igenomes/igenomes/Homo_sapiens/UCSC/hg38/Sequence/Bowtie2Index/ star = s3://ngi-igenomes/igenomes/Homo_sapiens/UCSC/hg38/Sequence/STARIndex/ bismark = s3://ngi-igenomes/igenomes/Homo_sapiens/UCSC/hg38/Sequence/BismarkIndex/ gtf = s3://ngi-igenomes/igenomes/Homo_sapiens/UCSC/hg38/Annotation/Genes/genes.gtf bed12 = s3://ngi-igenomes/igenomes/Homo_sapiens/UCSC/hg38/Annotation/Genes/genes.bed mito_name = chrM macs_gsize = 2.7e9 blacklist = /.nextflow/assets/nf-core/differentialabundance/assets/blacklists/hg38-blacklist.bed hg19: fasta = s3://ngi-igenomes/igenomes/Homo_sapiens/UCSC/hg19/Sequence/WholeGenomeFasta/genome.fa bwa = s3://ngi-igenomes/igenomes/Homo_sapiens/UCSC/hg19/Sequence/BWAIndex/version0.6.0/ bowtie2 = s3://ngi-igenomes/igenomes/Homo_sapiens/UCSC/hg19/Sequence/Bowtie2Index/ star = s3://ngi-igenomes/igenomes/Homo_sapiens/UCSC/hg19/Sequence/STARIndex/ bismark = s3://ngi-igenomes/igenomes/Homo_sapiens/UCSC/hg19/Sequence/BismarkIndex/ gtf = s3://ngi-igenomes/igenomes/Homo_sapiens/UCSC/hg19/Annotation/Genes/genes.gtf bed12 = s3://ngi-igenomes/igenomes/Homo_sapiens/UCSC/hg19/Annotation/Genes/genes.bed readme = s3://ngi-igenomes/igenomes/Homo_sapiens/UCSC/hg19/Annotation/README.txt mito_name = chrM macs_gsize = 2.7e9 blacklist = /.nextflow/assets/nf-core/differentialabundance/assets/blacklists/hg19-blacklist.bed mm10: fasta = s3://ngi-igenomes/igenomes/Mus_musculus/UCSC/mm10/Sequence/WholeGenomeFasta/genome.fa bwa = s3://ngi-igenomes/igenomes/Mus_musculus/UCSC/mm10/Sequence/BWAIndex/version0.6.0/ bowtie2 = s3://ngi-igenomes/igenomes/Mus_musculus/UCSC/mm10/Sequence/Bowtie2Index/ star = s3://ngi-igenomes/igenomes/Mus_musculus/UCSC/mm10/Sequence/STARIndex/ bismark = s3://ngi-igenomes/igenomes/Mus_musculus/UCSC/mm10/Sequence/BismarkIndex/ gtf = s3://ngi-igenomes/igenomes/Mus_musculus/UCSC/mm10/Annotation/Genes/genes.gtf bed12 = s3://ngi-igenomes/igenomes/Mus_musculus/UCSC/mm10/Annotation/Genes/genes.bed readme = s3://ngi-igenomes/igenomes/Mus_musculus/UCSC/mm10/Annotation/README.txt mito_name = chrM macs_gsize = 1.87e9 blacklist = /.nextflow/assets/nf-core/differentialabundance/assets/blacklists/mm10-blacklist.bed bosTau8: fasta = s3://ngi-igenomes/igenomes/Bos_taurus/UCSC/bosTau8/Sequence/WholeGenomeFasta/genome.fa bwa = s3://ngi-igenomes/igenomes/Bos_taurus/UCSC/bosTau8/Sequence/BWAIndex/version0.6.0/ bowtie2 = s3://ngi-igenomes/igenomes/Bos_taurus/UCSC/bosTau8/Sequence/Bowtie2Index/ star = s3://ngi-igenomes/igenomes/Bos_taurus/UCSC/bosTau8/Sequence/STARIndex/ bismark = s3://ngi-igenomes/igenomes/Bos_taurus/UCSC/bosTau8/Sequence/BismarkIndex/ gtf = s3://ngi-igenomes/igenomes/Bos_taurus/UCSC/bosTau8/Annotation/Genes/genes.gtf bed12 = s3://ngi-igenomes/igenomes/Bos_taurus/UCSC/bosTau8/Annotation/Genes/genes.bed mito_name = chrM ce10: fasta = s3://ngi-igenomes/igenomes/Caenorhabditis_elegans/UCSC/ce10/Sequence/WholeGenomeFasta/genome.fa bwa = s3://ngi-igenomes/igenomes/Caenorhabditis_elegans/UCSC/ce10/Sequence/BWAIndex/version0.6.0/ bowtie2 = s3://ngi-igenomes/igenomes/Caenorhabditis_elegans/UCSC/ce10/Sequence/Bowtie2Index/ star = s3://ngi-igenomes/igenomes/Caenorhabditis_elegans/UCSC/ce10/Sequence/STARIndex/ bismark = s3://ngi-igenomes/igenomes/Caenorhabditis_elegans/UCSC/ce10/Sequence/BismarkIndex/ gtf = s3://ngi-igenomes/igenomes/Caenorhabditis_elegans/UCSC/ce10/Annotation/Genes/genes.gtf bed12 = s3://ngi-igenomes/igenomes/Caenorhabditis_elegans/UCSC/ce10/Annotation/Genes/genes.bed readme = s3://ngi-igenomes/igenomes/Caenorhabditis_elegans/UCSC/ce10/Annotation/README.txt mito_name = chrM macs_gsize = 9e7 canFam3: fasta = s3://ngi-igenomes/igenomes/Canis_familiaris/UCSC/canFam3/Sequence/WholeGenomeFasta/genome.fa bwa = s3://ngi-igenomes/igenomes/Canis_familiaris/UCSC/canFam3/Sequence/BWAIndex/version0.6.0/ bowtie2 = s3://ngi-igenomes/igenomes/Canis_familiaris/UCSC/canFam3/Sequence/Bowtie2Index/ star = s3://ngi-igenomes/igenomes/Canis_familiaris/UCSC/canFam3/Sequence/STARIndex/ bismark = s3://ngi-igenomes/igenomes/Canis_familiaris/UCSC/canFam3/Sequence/BismarkIndex/ gtf = s3://ngi-igenomes/igenomes/Canis_familiaris/UCSC/canFam3/Annotation/Genes/genes.gtf bed12 = s3://ngi-igenomes/igenomes/Canis_familiaris/UCSC/canFam3/Annotation/Genes/genes.bed readme = s3://ngi-igenomes/igenomes/Canis_familiaris/UCSC/canFam3/Annotation/README.txt mito_name = chrM danRer10: fasta = s3://ngi-igenomes/igenomes/Danio_rerio/UCSC/danRer10/Sequence/WholeGenomeFasta/genome.fa bwa = s3://ngi-igenomes/igenomes/Danio_rerio/UCSC/danRer10/Sequence/BWAIndex/version0.6.0/ bowtie2 = s3://ngi-igenomes/igenomes/Danio_rerio/UCSC/danRer10/Sequence/Bowtie2Index/ star = s3://ngi-igenomes/igenomes/Danio_rerio/UCSC/danRer10/Sequence/STARIndex/ bismark = s3://ngi-igenomes/igenomes/Danio_rerio/UCSC/danRer10/Sequence/BismarkIndex/ gtf = s3://ngi-igenomes/igenomes/Danio_rerio/UCSC/danRer10/Annotation/Genes/genes.gtf bed12 = s3://ngi-igenomes/igenomes/Danio_rerio/UCSC/danRer10/Annotation/Genes/genes.bed mito_name = chrM macs_gsize = 1.37e9 dm6: fasta = s3://ngi-igenomes/igenomes/Drosophila_melanogaster/UCSC/dm6/Sequence/WholeGenomeFasta/genome.fa bwa = s3://ngi-igenomes/igenomes/Drosophila_melanogaster/UCSC/dm6/Sequence/BWAIndex/version0.6.0/ bowtie2 = s3://ngi-igenomes/igenomes/Drosophila_melanogaster/UCSC/dm6/Sequence/Bowtie2Index/ star = s3://ngi-igenomes/igenomes/Drosophila_melanogaster/UCSC/dm6/Sequence/STARIndex/ bismark = s3://ngi-igenomes/igenomes/Drosophila_melanogaster/UCSC/dm6/Sequence/BismarkIndex/ gtf = s3://ngi-igenomes/igenomes/Drosophila_melanogaster/UCSC/dm6/Annotation/Genes/genes.gtf bed12 = s3://ngi-igenomes/igenomes/Drosophila_melanogaster/UCSC/dm6/Annotation/Genes/genes.bed mito_name = chrM macs_gsize = 1.2e8 equCab2: fasta = s3://ngi-igenomes/igenomes/Equus_caballus/UCSC/equCab2/Sequence/WholeGenomeFasta/genome.fa bwa = s3://ngi-igenomes/igenomes/Equus_caballus/UCSC/equCab2/Sequence/BWAIndex/version0.6.0/ bowtie2 = s3://ngi-igenomes/igenomes/Equus_caballus/UCSC/equCab2/Sequence/Bowtie2Index/ star = s3://ngi-igenomes/igenomes/Equus_caballus/UCSC/equCab2/Sequence/STARIndex/ bismark = s3://ngi-igenomes/igenomes/Equus_caballus/UCSC/equCab2/Sequence/BismarkIndex/ gtf = s3://ngi-igenomes/igenomes/Equus_caballus/UCSC/equCab2/Annotation/Genes/genes.gtf bed12 = s3://ngi-igenomes/igenomes/Equus_caballus/UCSC/equCab2/Annotation/Genes/genes.bed readme = s3://ngi-igenomes/igenomes/Equus_caballus/UCSC/equCab2/Annotation/README.txt mito_name = chrM galGal4: fasta = s3://ngi-igenomes/igenomes/Gallus_gallus/UCSC/galGal4/Sequence/WholeGenomeFasta/genome.fa bwa = s3://ngi-igenomes/igenomes/Gallus_gallus/UCSC/galGal4/Sequence/BWAIndex/version0.6.0/ bowtie2 = s3://ngi-igenomes/igenomes/Gallus_gallus/UCSC/galGal4/Sequence/Bowtie2Index/ star = s3://ngi-igenomes/igenomes/Gallus_gallus/UCSC/galGal4/Sequence/STARIndex/ bismark = s3://ngi-igenomes/igenomes/Gallus_gallus/UCSC/galGal4/Sequence/BismarkIndex/ gtf = s3://ngi-igenomes/igenomes/Gallus_gallus/UCSC/galGal4/Annotation/Genes/genes.gtf bed12 = s3://ngi-igenomes/igenomes/Gallus_gallus/UCSC/galGal4/Annotation/Genes/genes.bed readme = s3://ngi-igenomes/igenomes/Gallus_gallus/UCSC/galGal4/Annotation/README.txt mito_name = chrM panTro4: fasta = s3://ngi-igenomes/igenomes/Pan_troglodytes/UCSC/panTro4/Sequence/WholeGenomeFasta/genome.fa bwa = s3://ngi-igenomes/igenomes/Pan_troglodytes/UCSC/panTro4/Sequence/BWAIndex/version0.6.0/ bowtie2 = s3://ngi-igenomes/igenomes/Pan_troglodytes/UCSC/panTro4/Sequence/Bowtie2Index/ star = s3://ngi-igenomes/igenomes/Pan_troglodytes/UCSC/panTro4/Sequence/STARIndex/ bismark = s3://ngi-igenomes/igenomes/Pan_troglodytes/UCSC/panTro4/Sequence/BismarkIndex/ gtf = s3://ngi-igenomes/igenomes/Pan_troglodytes/UCSC/panTro4/Annotation/Genes/genes.gtf bed12 = s3://ngi-igenomes/igenomes/Pan_troglodytes/UCSC/panTro4/Annotation/Genes/genes.bed readme = s3://ngi-igenomes/igenomes/Pan_troglodytes/UCSC/panTro4/Annotation/README.txt mito_name = chrM rn6: fasta = s3://ngi-igenomes/igenomes/Rattus_norvegicus/UCSC/rn6/Sequence/WholeGenomeFasta/genome.fa bwa = s3://ngi-igenomes/igenomes/Rattus_norvegicus/UCSC/rn6/Sequence/BWAIndex/version0.6.0/ bowtie2 = s3://ngi-igenomes/igenomes/Rattus_norvegicus/UCSC/rn6/Sequence/Bowtie2Index/ star = s3://ngi-igenomes/igenomes/Rattus_norvegicus/UCSC/rn6/Sequence/STARIndex/ bismark = s3://ngi-igenomes/igenomes/Rattus_norvegicus/UCSC/rn6/Sequence/BismarkIndex/ gtf = s3://ngi-igenomes/igenomes/Rattus_norvegicus/UCSC/rn6/Annotation/Genes/genes.gtf bed12 = s3://ngi-igenomes/igenomes/Rattus_norvegicus/UCSC/rn6/Annotation/Genes/genes.bed mito_name = chrM sacCer3: fasta = s3://ngi-igenomes/igenomes/Saccharomyces_cerevisiae/UCSC/sacCer3/Sequence/WholeGenomeFasta/genome.fa bwa = s3://ngi-igenomes/igenomes/Saccharomyces_cerevisiae/UCSC/sacCer3/Sequence/BWAIndex/version0.6.0/ bowtie2 = s3://ngi-igenomes/igenomes/Saccharomyces_cerevisiae/UCSC/sacCer3/Sequence/Bowtie2Index/ star = s3://ngi-igenomes/igenomes/Saccharomyces_cerevisiae/UCSC/sacCer3/Sequence/STARIndex/ bismark = s3://ngi-igenomes/igenomes/Saccharomyces_cerevisiae/UCSC/sacCer3/Sequence/BismarkIndex/ readme = s3://ngi-igenomes/igenomes/Saccharomyces_cerevisiae/UCSC/sacCer3/Annotation/README.txt mito_name = chrM macs_gsize = 1.2e7 susScr3: fasta = s3://ngi-igenomes/igenomes/Sus_scrofa/UCSC/susScr3/Sequence/WholeGenomeFasta/genome.fa bwa = s3://ngi-igenomes/igenomes/Sus_scrofa/UCSC/susScr3/Sequence/BWAIndex/version0.6.0/ bowtie2 = s3://ngi-igenomes/igenomes/Sus_scrofa/UCSC/susScr3/Sequence/Bowtie2Index/ star = s3://ngi-igenomes/igenomes/Sus_scrofa/UCSC/susScr3/Sequence/STARIndex/ bismark = s3://ngi-igenomes/igenomes/Sus_scrofa/UCSC/susScr3/Sequence/BismarkIndex/ gtf = s3://ngi-igenomes/igenomes/Sus_scrofa/UCSC/susScr3/Annotation/Genes/genes.gtf bed12 = s3://ngi-igenomes/igenomes/Sus_scrofa/UCSC/susScr3/Annotation/Genes/genes.bed readme = s3://ngi-igenomes/igenomes/Sus_scrofa/UCSC/susScr3/Annotation/README.txt mito_name = chrM logo_file = /.nextflow/assets/nf-core/differentialabundance/docs/images/nf-core-differentialabundance_logo_light.png affy_rm_mask = false exploratory_main_variable = auto_pca exploratory_n_features = 500 deseq2_minmu = 0.5 limma_adjust_method = BH gsea_gene_sets = None affy_rm_extra = false gsea_norm = meandiv differential_palette_name = Set1 outdir = s3://REDACTED limma_winsor_tail_p = 0.05,0.1 help = false shinyngs_deploy_to_shinyapps_io = false deseq2_alt_hypothesis = greaterAbs differential_foldchanges_logged = true deseq2_test = Wald limma_spacing = None study_name = RNA-Seq_Project report_author = None monochrome_logs = false deseq2_alpha = 0.1 max_cpus = 16 differential_qval_column = padj gsea_sort = real limma_robust = false limma_stdev_coef_lim = 0.1,4 validationFailUnrecognisedParams = false differential_min_fold_change = 2 gsea_make_sets = true features_gtf_table_first_field = gene_id exploratory_whisker_distance = 1.5 max_time = 240.h sizefactors_from_controls = false differential_feature_id_column = gene_id deseq2_lfc_threshold = 0 validate_params = true validationShowHiddenParams = false differential_pval_column = pvalue exploratory_mad_threshold = -5 affy_destructive = false gsea_num = 100 validationS3PathCheck = false affy_cdfname = None deseq2_fit_type = parametric exploratory_assay_names = raw,normalised,variance_stabilised igenomes_base = s3://ngi-igenomes/igenomes features_type = gene gsea_run = false validation-show-hidden-params = false validation-lenient-mode = false differential_file_suffix = .deseq2.results.tsv observations_type = sample deseq2_sf_type = ratio features_name_col = gene_name deseq2_p_adjust_method = BH deseq2_vs_blind = true deseq2_vs_method = vst gsea_scoring_scheme = weighted gsea_permute = phenotype limma_confint = false shinyngs_shinyapps_app_name = None deseq2_use_t = false gsea_metric = Signal2Noise max_memory = 128.GB monochromeLogs = false deseq2_cores = 1 contrasts = https://api.tower.nf/workspaces/REDACTED/contrasts.csv differential_max_qval = 0.05 report_file = /.nextflow/assets/nf-core/differentialabundance/assets/differentialabundance_report.Rmd report_title = None affy_cel_files_archive = None affy_rm_outliers = false validationLenientMode = false proteus_plotsd_method = violin igenomes_ignore = false validation-fail-unrecognised-params = false observations_id_col = sample limma_method = ls shinyngs_guess_unlog_matrices = true validation-schema-ignore-params = genomes,igenomes_base differential_fc_column = log2FoldChange deseq2_shrink_lfc = true ```

The final part of the error message is:

  [1] "Writing sample dendrogram..."
  null device
            1
  Error in cor(matrices[[g]]) :
    supply both 'x' and 'y' or a matrix-like 'x'
  Calls: madScore -> do.call -> lapply -> FUN -> cor -> cor
  Execution halted

Following this trace:

  1. This repo imports SHINYNGS_STATICEXPLORATORY as PLOT_EXPLORATORY:https://github.com/nf-core/differentialabundance/blob/44c449be0a703c64a7c323a2b431ec6627194f00/workflows/differentialabundance.nf#L110
  2. Following the nf-core/modules repo, SHINYNGS_STATICEXPLORATORY (https://github.com/nf-core/modules/pull/2364) calls exploratory_plots.R
  3. Stack trace references madScore in exploratory_plots.R from pinin4fjords/shinyngs: https://github.com/pinin4fjords/shinyngs/blob/develop/exec/exploratory_plots.R#L339

Command used and terminal output

I'm submitting this job via Seqera Platform which uses the following redacted command:

nextflow run 'https://github.com/nf-core/differentialabundance' \
         -name REDACTED_2 \
         -params-file 'https://api.tower.nf/ephemeral/REDACTED.json' \
         -with-tower \
         -r 44c449be0a703c64a7c323a2b431ec6627194f00 \
         -resume REDACTED

Relevant files

Here's the redacted log of this error:

Error executing process > 'NFCORE_DIFFERENTIALABUNDANCE:DIFFERENTIALABUNDANCE:PLOT_EXPLORATORY (TREATMENT)'

Caused by:
  Essential container in task exited

Command executed:

  exploratory_plots.R \
      --sample_metadata "sample_metadata.tsv" \
      --feature_metadata "matrix_as_anno.feature_metadata.tsv" \
      --assay_files "salmon.merged.gene_counts.assay.tsv,all.normalised_counts.tsv,all.vst.tsv" \
      --contrast_variable "TREATMENT" \
      --outdir "TREATMENT" \
      --sample_id_col "sample" --feature_id_col "gene_id" --assay_names "raw,normalised,variance_stabilised" --final_assay "variance_stabilised" --outlier_mad_threshold -5 --palette_name "Set1"

  cat <<-END_VERSIONS > versions.yml
  "NFCORE_DIFFERENTIALABUNDANCE:DIFFERENTIALABUNDANCE:PLOT_EXPLORATORY":
      r-base: $(echo $(R --version 2>&1) | sed 's/^.*R version //; s/ .*$//')
      r-shinyngs: $(Rscript -e "library(shinyngs); cat(as.character(packageVersion('shinyngs')))")
  END_VERSIONS

Command exit status:
  1

Command output:
  [1] "Reading inputs..."
  [1] "Creating output paths..."
  [1] "Writing boxplots..."
  [1] "... static"
  null device
            1
  [1] "Writing density plots..."
  [1] "... static"
  null device
            1
  [1] "Writing PCA plots..."
  [1] "...static (2d)"
  [1] "...static (3d)"
  NULL
  [1] "Writing sample dendrogram..."
  null device
            1

Command error:
  (more omitted..)
      anyDuplicated, aperm, append, as.data.frame, basename, cbind,
      colnames, dirname, do.call, duplicated, eval, evalq, Filter, Find,
      get, grep, grepl, intersect, is.unsorted, lapply, Map, mapply,
      match, mget, order, paste, pmax, pmax.int, pmin, pmin.int,
      Position, rank, rbind, Reduce, rownames, sapply, setdiff, sort,
      table, tapply, union, unique, unsplit, which.max, which.min
  Loading required package: S4Vectors
  Attaching package: ‘S4Vectors’
  The following object is masked from ‘package:utils’:
      findMatches
  The following objects are masked from ‘package:base’:
      expand.grid, I, unname
  Loading required package: IRanges
  Loading required package: GenomeInfoDb
  Loading required package: Biobase
  Welcome to Bioconductor
      Vignettes contain introductory material; view with
      'browseVignettes()'. To cite Bioconductor, see
      'citation("Biobase")', and for packages 'citation("pkgname")'.
  Attaching package: ‘Biobase’
  The following object is masked from ‘package:MatrixGenerics’:
      rowMedians
  The following objects are masked from ‘package:matrixStats’:
      anyMissing, rowMedians
  Attaching package: ‘shinyngs’
  The following object is masked from ‘package:MatrixGenerics’:
      colMedians
  The following object is masked from ‘package:matrixStats’:
      colMedians
  [1] "Reading inputs..."
  [1] "Creating output paths..."
  [1] "Writing boxplots..."
  [1] "... static"
  null device
            1
  [1] "Writing density plots..."
  [1] "... static"
  null device
            1
  [1] "Writing PCA plots..."
  [1] "...static (2d)"
  [1] "...static (3d)"
  NULL
  [1] "Writing sample dendrogram..."
  null device
            1
  Error in cor(matrices[[g]]) :
    supply both 'x' and 'y' or a matrix-like 'x'
  Calls: madScore -> do.call -> lapply -> FUN -> cor -> cor
  Execution halted

Work dir:
  s3://REDACTED/scratch/3jFH9XRwVZ3oVL/ff/54c1599dfd4830a927ff33f1caa023

Tip: when you have fixed the problem you can continue the execution adding the option `-resume` to the run command line

System information

This is running on AWS Batch via Sequera Tower.

olgabot commented 7 months ago

Hello, I've done a bit of digging, and I think this error is happening because exclude samples in my --contrasts file aren't getting excluded in the ShinyNGS Exploratory Plot generation.

Digging into one of the runs, I saw that this plot has three categories: green, blue, and red. But it should only show blue and red, the green samples shouldn't be there in this comparison:

image

My contrasts file (redacted) is like this, as a nicely formatted table:

id variable reference target blocking exclude_samples_col exclude_samples_values
A_vs_B A_vs_B groupA groupB A_vs_B_exclude TRUE
B_vs_C B_vs_C groupB groupC B_vs_C_exclude TRUE

And then the samplesheet is like this:

sample fastq_1 fastq_2 A_vs_B A_vs_B_exclude B_vs_C B_vs_C_exclude
groupA_sample1 groupA_sample1_R1_001.fastq.gz groupA_sample1_R1_001.fastq.gz_R2_001.fastq.gz groupA FALSE   TRUE
groupA_sample2 groupA_sample2_R1_001.fastq.gz groupA_sample2_R1_001.fastq.gz_R2_001.fastq.gz groupA FALSE   TRUE
groupA_sample3 groupA_sample3_R1_001.fastq.gz groupA_sample3_R1_001.fastq.gz_R2_001.fastq.gz groupA FALSE   TRUE
groupB_sample1 groupB_sample1_R1_001.fastq.gz groupB_sample1_R1_001.fastq.gz_R2_001.fastq.gz groupB FALSE groupB FALSE
groupB_sample2 groupB_sample2_R1_001.fastq.gz groupB_sample2_R1_001.fastq.gz_R2_001.fastq.gz groupB FALSE groupB FALSE
groupB_sample3 groupB_sample3_R1_001.fastq.gz groupB_sample3_R1_001.fastq.gz_R2_001.fastq.gz groupB FALSE groupB FALSE
groupC_sample1 groupC_sample1_R1_001.fastq.gz groupC_sample1_R1_001.fastq.gz_R2_001.fastq.gz   TRUE groupC FALSE
groupC_sample2 groupC_sample2_R1_001.fastq.gz groupC_sample2_R1_001.fastq.gz_R2_001.fastq.gz   TRUE groupC FALSE
groupC_sample3 groupC_sample3_R1_001.fastq.gz groupC_sample3_R1_001.fastq.gz_R2_001.fastq.gz   TRUE groupC FALSE

So I think the issue is in providing matrices for EXPLORATORY_PLOTS from SHINYNGS, to remove the exclude samples. Or to provide a non-null value for the exclude samples -- I'll try this for now and let you know.

olgabot commented 7 months ago

Update: Still getting the same error, even when the empty/null/None/NA values in A_vs_B are replaced with "Other":

sample fastq_1 fastq_2 A_vs_B A_vs_B_exclude B_vs_C B_vs_C_exclude
groupA_sample1 groupA_sample1_R1_001.fastq.gz groupA_sample1_R1_001.fastq.gz_R2_001.fastq.gz groupA FALSE Other TRUE
groupA_sample2 groupA_sample2_R1_001.fastq.gz groupA_sample2_R1_001.fastq.gz_R2_001.fastq.gz groupA FALSE Other TRUE
groupA_sample3 groupA_sample3_R1_001.fastq.gz groupA_sample3_R1_001.fastq.gz_R2_001.fastq.gz groupA FALSE Other TRUE
groupB_sample1 groupB_sample1_R1_001.fastq.gz groupB_sample1_R1_001.fastq.gz_R2_001.fastq.gz groupB FALSE groupB FALSE
groupB_sample2 groupB_sample2_R1_001.fastq.gz groupB_sample2_R1_001.fastq.gz_R2_001.fastq.gz groupB FALSE groupB FALSE
groupB_sample3 groupB_sample3_R1_001.fastq.gz groupB_sample3_R1_001.fastq.gz_R2_001.fastq.gz groupB FALSE groupB FALSE
groupC_sample1 groupC_sample1_R1_001.fastq.gz groupC_sample1_R1_001.fastq.gz_R2_001.fastq.gz Other TRUE groupC FALSE
groupC_sample2 groupC_sample2_R1_001.fastq.gz groupC_sample2_R1_001.fastq.gz_R2_001.fastq.gz Other TRUE groupC FALSE
groupC_sample3 groupC_sample3_R1_001.fastq.gz groupC_sample3_R1_001.fastq.gz_R2_001.fastq.gz Other TRUE groupC FALSE
pinin4fjords commented 7 months ago

Thanks for the report and the detective work- I'll look into this soon!

pinin4fjords commented 6 months ago

So, I can't reproduce this error exactly. For example, I unset the sample grouping variable in the test profile for one sample, and whilst it plotted a group with an empty legend entry, I didn't get an error at the dendrogram stage.

I'm making a PR here to prevent unlabelled samples getting plotted, and I notice a fix is also needed for GSEA.

It's important to note that the exploratory script isn't designed to plot per contrast, just per unique contrast variable, and does not pay any attention to the exclude_samples column in the contrast.

I hope that the above PR may help your case (once we update the module, and update the module in the workflow), but if not you will need to provide me with something reproducible for me to do more.

pinin4fjords commented 5 months ago

@olgabot could you test with current dev to see if the issue persists after the above fixes?

pinin4fjords commented 3 weeks ago

Closing for lack of activity