CMD: /gscratch/srlab/programs/trinityrnaseq-v2.9.0/Analysis/DifferentialExpression/run_GOseq.pl --GO_assignments /gscratch/srlab/sam/data/C_bairdi/transcriptomes/20200409.cbai.trinotate.go_annotations.txt --lengths /gscratch/scrubbed/samwhite/outputs/20200422_cbai_DEG_basic_comparisons/ambient-cold/Trinity.gene_lengths.txt --genes_single_factor salmon.gene.counts.matrix.ambient_vs_cold.edgeR.DE_results.P0.05_C1.ambient-UP.subset --background salmon.gene.counts.matrix.ambient_vs_cold.edgeR.count_matrix Loading required package: BiasedUrn Loading required package: geneLenDataBase Loading required package: AnnotationDbi Loading required package: stats4 Loading required package: BiocGenerics Loading required package: parallel Attaching package: ‘BiocGenerics’ The following objects are masked from ‘package:parallel’: clusterApply, clusterApplyLB, clusterCall, clusterEvalQ, clusterExport, clusterMap, parApply, parCapply, parLapply, parLapplyLB, parRapply, parSapply, parSapplyLB The following objects are masked from ‘package:stats’: IQR, mad, sd, var, xtabs The following objects are masked from ‘package:base’: anyDuplicated, 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, which.max, which.min 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")'. Loading required package: IRanges Loading required package: S4Vectors Attaching package: ‘S4Vectors’ The following object is masked from ‘package:geneLenDataBase’: unfactor The following object is masked from ‘package:base’: expand.grid Processing category: custom_list Using manually entered categories. Calculating the p-values... 'select()' returned 1:1 mapping between keys and columns Done. CMD: /gscratch/srlab/programs/trinityrnaseq-v2.9.0/Analysis/DifferentialExpression/run_GOseq.pl --GO_assignments /gscratch/srlab/sam/data/C_bairdi/transcriptomes/20200409.cbai.trinotate.go_annotations.txt --lengths /gscratch/scrubbed/samwhite/outputs/20200422_cbai_DEG_basic_comparisons/ambient-cold/Trinity.gene_lengths.txt --genes_single_factor salmon.gene.counts.matrix.ambient_vs_cold.edgeR.DE_results.P0.05_C1.cold-UP.subset --background salmon.gene.counts.matrix.ambient_vs_cold.edgeR.count_matrix Loading required package: BiasedUrn Loading required package: geneLenDataBase Loading required package: AnnotationDbi Loading required package: stats4 Loading required package: BiocGenerics Loading required package: parallel Attaching package: ‘BiocGenerics’ The following objects are masked from ‘package:parallel’: clusterApply, clusterApplyLB, clusterCall, clusterEvalQ, clusterExport, clusterMap, parApply, parCapply, parLapply, parLapplyLB, parRapply, parSapply, parSapplyLB The following objects are masked from ‘package:stats’: IQR, mad, sd, var, xtabs The following objects are masked from ‘package:base’: anyDuplicated, 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, which.max, which.min 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")'. Loading required package: IRanges Loading required package: S4Vectors Attaching package: ‘S4Vectors’ The following object is masked from ‘package:geneLenDataBase’: unfactor The following object is masked from ‘package:base’: expand.grid Processing category: custom_list Using manually entered categories. Calculating the p-values... 'select()' returned 1:1 mapping between keys and columns Done. CMD: /gscratch/srlab/programs/trinityrnaseq-v2.9.0/Analysis/DifferentialExpression/run_GOseq.pl --GO_assignments /gscratch/srlab/sam/data/C_bairdi/transcriptomes/20200409.cbai.trinotate.go_annotations.txt --lengths /gscratch/scrubbed/samwhite/outputs/20200422_cbai_DEG_basic_comparisons/ambient-cold/Trinity.gene_lengths.txt --genes_single_factor salmon.gene.counts.matrix.ambient_vs_cold.edgeR.DE_results.P0.05_C1.DE.subset --background salmon.gene.counts.matrix.ambient_vs_cold.edgeR.count_matrix Loading required package: BiasedUrn Loading required package: geneLenDataBase Loading required package: AnnotationDbi Loading required package: stats4 Loading required package: BiocGenerics Loading required package: parallel Attaching package: ‘BiocGenerics’ The following objects are masked from ‘package:parallel’: clusterApply, clusterApplyLB, clusterCall, clusterEvalQ, clusterExport, clusterMap, parApply, parCapply, parLapply, parLapplyLB, parRapply, parSapply, parSapplyLB The following objects are masked from ‘package:stats’: IQR, mad, sd, var, xtabs The following objects are masked from ‘package:base’: anyDuplicated, 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, which.max, which.min 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")'. Loading required package: IRanges Loading required package: S4Vectors Attaching package: ‘S4Vectors’ The following object is masked from ‘package:geneLenDataBase’: unfactor The following object is masked from ‘package:base’: expand.grid Processing category: custom_list Using manually entered categories. Calculating the p-values... 'select()' returned 1:1 mapping between keys and columns Done. CMD: /gscratch/srlab/programs/trinityrnaseq-v2.9.0/Analysis/DifferentialExpression/prep_n_run_GOplot.pl --GO_annots /gscratch/srlab/sam/data/C_bairdi/transcriptomes/20200409.cbai.trinotate.go_annotations.txt --DE_subset salmon.gene.counts.matrix.ambient_vs_cold.edgeR.DE_results.P0.05_C1.DE.subset --DE_GO_enriched salmon.gene.counts.matrix.ambient_vs_cold.edgeR.DE_results.P0.05_C1.DE.subset.GOseq.enriched --tmpdir salmon.gene.counts.matrix.ambient_vs_cold.edgeR.DE_results.P0.05_C1.DE.subset.GOseq.enriched.GOplot_dat --pdf_filename salmon.gene.counts.matrix.ambient_vs_cold.edgeR.DE_results.P0.05_C1.DE.subset.GOseq.enriched.GOplot_dat.pdf CMD: mkdir -p salmon.gene.counts.matrix.ambient_vs_cold.edgeR.DE_results.P0.05_C1.DE.subset.GOseq.enriched.GOplot_dat WARNING, no GO term info found for: GO:0022891, skipping... WARNING, no GO term info found for: GO:0004872, skipping... WARNING, no GO term info found for: GO:0044699, skipping... WARNING, no GO term info found for: GO:0022892, skipping... WARNING, no GO term info found for: GO:0004871, skipping... CMD: /gscratch/srlab/programs/trinityrnaseq-v2.9.0/Analysis/DifferentialExpression/GOplot.Rscript --EC_david salmon.gene.counts.matrix.ambient_vs_cold.edgeR.DE_results.P0.05_C1.DE.subset.GOseq.enriched.GOplot_dat/EC.david --EC_genelist salmon.gene.counts.matrix.ambient_vs_cold.edgeR.DE_results.P0.05_C1.DE.subset.GOseq.enriched.GOplot_dat/EC.genelist --pdf_outfile salmon.gene.counts.matrix.ambient_vs_cold.edgeR.DE_results.P0.05_C1.DE.subset.GOseq.enriched.GOplot_dat.pdf Error in library(GOplot) : there is no package called ‘GOplot’ Execution halted Error, CMD: /gscratch/srlab/programs/trinityrnaseq-v2.9.0/Analysis/DifferentialExpression/GOplot.Rscript --EC_david salmon.gene.counts.matrix.ambient_vs_cold.edgeR.DE_results.P0.05_C1.DE.subset.GOseq.enriched.GOplot_dat/EC.david --EC_genelist salmon.gene.counts.matrix.ambient_vs_cold.edgeR.DE_results.P0.05_C1.DE.subset.GOseq.enriched.GOplot_dat/EC.genelist --pdf_outfile salmon.gene.counts.matrix.ambient_vs_cold.edgeR.DE_results.P0.05_C1.DE.subset.GOseq.enriched.GOplot_dat.pdf died with ret 256 at /gscratch/srlab/programs/trinityrnaseq-v2.9.0/Analysis/DifferentialExpression/prep_n_run_GOplot.pl line 247. WARNING: GOplot failed to run successfully on salmon.gene.counts.matrix.ambient_vs_cold.edgeR.DE_results.P0.05_C1.DE.subset.GOseq.enriched ** Found 126 features as differentially expressed. CMD: /gscratch/srlab/programs/trinityrnaseq-v2.9.0/Analysis/DifferentialExpression/PtR -m diffExpr.P0.05_C1.matrix --log2 --heatmap --min_colSums 0 --min_rowSums 0 --gene_dist euclidean --sample_dist euclidean --sample_cor_matrix --center_rows --save -s /gscratch/scrubbed/samwhite/outputs/20200422_cbai_DEG_basic_comparisons/ambient-cold/ambient-cold.samples.txt CMD: R --no-save --no-restore --no-site-file --no-init-file -q < diffExpr.P0.05_C1.matrix.R Loading required package: BiocGenerics Loading required package: parallel Attaching package: ‘BiocGenerics’ The following objects are masked from ‘package:parallel’: clusterApply, clusterApplyLB, clusterCall, clusterEvalQ, clusterExport, clusterMap, parApply, parCapply, parLapply, parLapplyLB, parRapply, parSapply, parSapplyLB The following objects are masked from ‘package:stats’: IQR, mad, sd, var, xtabs The following objects are masked from ‘package:base’: anyDuplicated, 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, which.max, which.min Welcome to Bioconductor Vignettes contain introductory material; view with 'browseVignettes()'. To cite Bioconductor, see 'citation("Biobase")', and for packages 'citation("pkgname")'. Attaching package: ‘fastcluster’ The following object is masked from ‘package:stats’: hclust for plotting:: min.raw: -0.455720026737806 max.raw: 1 for plotting:: min.raw: -13.0762535840287 max.raw: 13.0762535840287