convert /mnt/max/c/genomics_facility/proton/run299/wwwSCR/cuffdiff_M14_vs_M14mut/isoform_exp.diff.csv -> /mnt/max/c/genomics_facility/proton/run299/wwwSCR/cuffdiff_M14_vs_M14mut/isoform_exp.diff.xlsx using Calc MS Excel 2007 XML Overwriting: /mnt/max/c/genomics_facility/proton/run299/wwwSCR/cuffdiff_M14_vs_M14mut/isoform_exp.diff.xlsx convert /mnt/max/c/genomics_facility/proton/run299/wwwSCR/cuffdiff_M14_vs_M14mut/gene_exp.diff.csv -> /mnt/max/c/genomics_facility/proton/run299/wwwSCR/cuffdiff_M14_vs_M14mut/gene_exp.diff.xlsx using Calc MS Excel 2007 XML Overwriting: /mnt/max/c/genomics_facility/proton/run299/wwwSCR/cuffdiff_M14_vs_M14mut/gene_exp.diff.xlsx Loading required package: BiocGenerics Loading required package: methods 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 object is masked from ‘package:stats’: xtabs The following objects are masked from ‘package:base’: anyDuplicated, append, as.data.frame, as.vector, cbind, colnames, do.call, duplicated, eval, evalq, Filter, Find, get, intersect, is.unsorted, lapply, Map, mapply, match, mget, order, paste, pmax, pmax.int, pmin, pmin.int, Position, rank, rbind, Reduce, rep.int, rownames, sapply, setdiff, sort, table, tapply, union, unique, unlist, unsplit Loading required package: RSQLite Loading required package: DBI Loading required package: ggplot2 Loading required package: reshape2 Loading required package: fastcluster Attaching package: ‘fastcluster’ The following object is masked from ‘package:stats’: hclust Loading required package: rtracklayer Loading required package: GenomicRanges Loading required package: S4Vectors Loading required package: stats4 Loading required package: IRanges Loading required package: GenomeInfoDb Loading required package: Gviz Loading required package: grid Attaching package: ‘cummeRbund’ The following object is masked from ‘package:GenomicRanges’: promoters The following object is masked from ‘package:IRanges’: promoters The following object is masked from ‘package:BiocGenerics’: conditions Error in file(file, "rt") : cannot open the connection Calls: read.table -> file In addition: Warning message: In file(file, "rt") : cannot open file '../reads.txt': No such file or directory Execution halted convert /mnt/max/c/genomics_facility/proton/run299/wwwSCR/cuffdiff_F16_vs_F16mut/isoform_exp.diff.csv -> /mnt/max/c/genomics_facility/proton/run299/wwwSCR/cuffdiff_F16_vs_F16mut/isoform_exp.diff.xlsx using Calc MS Excel 2007 XML convert /mnt/max/c/genomics_facility/proton/run299/wwwSCR/cuffdiff_F16_vs_F16mut/gene_exp.diff.csv -> /mnt/max/c/genomics_facility/proton/run299/wwwSCR/cuffdiff_F16_vs_F16mut/gene_exp.diff.xlsx using Calc MS Excel 2007 XML Loading required package: BiocGenerics Loading required package: methods 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 object is masked from ‘package:stats’: xtabs The following objects are masked from ‘package:base’: anyDuplicated, append, as.data.frame, as.vector, cbind, colnames, do.call, duplicated, eval, evalq, Filter, Find, get, intersect, is.unsorted, lapply, Map, mapply, match, mget, order, paste, pmax, pmax.int, pmin, pmin.int, Position, rank, rbind, Reduce, rep.int, rownames, sapply, setdiff, sort, table, tapply, union, unique, unlist, unsplit Loading required package: RSQLite Loading required package: DBI Loading required package: ggplot2 Loading required package: reshape2 Loading required package: fastcluster Attaching package: ‘fastcluster’ The following object is masked from ‘package:stats’: hclust Loading required package: rtracklayer Loading required package: GenomicRanges Loading required package: S4Vectors Loading required package: stats4 Loading required package: IRanges Loading required package: GenomeInfoDb Loading required package: Gviz Loading required package: grid Attaching package: ‘cummeRbund’ The following object is masked from ‘package:GenomicRanges’: promoters The following object is masked from ‘package:IRanges’: promoters The following object is masked from ‘package:BiocGenerics’: conditions Creating database /mnt/max/c/genomics_facility/proton/run299/wwwSCR/cuffdiff_F16_vs_F16mut/cuffData.db Reading Run Info File /mnt/max/c/genomics_facility/proton/run299/wwwSCR/cuffdiff_F16_vs_F16mut/run.info Writing runInfo Table Reading Read Group Info /mnt/max/c/genomics_facility/proton/run299/wwwSCR/cuffdiff_F16_vs_F16mut/read_groups.info Writing replicates Table Reading Var Model Info /mnt/max/c/genomics_facility/proton/run299/wwwSCR/cuffdiff_F16_vs_F16mut/var_model.info Writing varModel Table Reading /mnt/max/c/genomics_facility/proton/run299/wwwSCR/cuffdiff_F16_vs_F16mut/genes.fpkm_tracking Checking samples table... Populating samples table... Writing genes table Reshaping geneData table Recasting Writing geneData table Reading /mnt/max/c/genomics_facility/proton/run299/wwwSCR/cuffdiff_F16_vs_F16mut/gene_exp.diff Writing geneExpDiffData table Reading /mnt/max/c/genomics_facility/proton/run299/wwwSCR/cuffdiff_F16_vs_F16mut/promoters.diff Writing promoterDiffData table Reading /mnt/max/c/genomics_facility/proton/run299/wwwSCR/cuffdiff_F16_vs_F16mut/genes.count_tracking Reshaping geneCount table Recasting Writing geneCount table Reading read group info in /mnt/max/c/genomics_facility/proton/run299/wwwSCR/cuffdiff_F16_vs_F16mut/genes.read_group_tracking Writing geneReplicateData table Reading /mnt/max/c/genomics_facility/proton/run299/wwwSCR/cuffdiff_F16_vs_F16mut/isoforms.fpkm_tracking Checking samples table... OK! Writing isoforms table Reshaping isoformData table Recasting Writing isoformData table Reading /mnt/max/c/genomics_facility/proton/run299/wwwSCR/cuffdiff_F16_vs_F16mut/isoform_exp.diff Writing isoformExpDiffData table Reading /mnt/max/c/genomics_facility/proton/run299/wwwSCR/cuffdiff_F16_vs_F16mut/isoforms.count_tracking Reshaping isoformCount table Recasting Writing isoformCount table Reading read group info in /mnt/max/c/genomics_facility/proton/run299/wwwSCR/cuffdiff_F16_vs_F16mut/isoforms.read_group_tracking Writing isoformReplicateData table Reading /mnt/max/c/genomics_facility/proton/run299/wwwSCR/cuffdiff_F16_vs_F16mut/tss_groups.fpkm_tracking Checking samples table... OK! Writing TSS table Reshaping TSSData table Recasting Writing TSSData table Reading /mnt/max/c/genomics_facility/proton/run299/wwwSCR/cuffdiff_F16_vs_F16mut/tss_group_exp.diff Writing TSSExpDiffData table Reading /mnt/max/c/genomics_facility/proton/run299/wwwSCR/cuffdiff_F16_vs_F16mut/splicing.diff Writing splicingDiffData table Reading /mnt/max/c/genomics_facility/proton/run299/wwwSCR/cuffdiff_F16_vs_F16mut/tss_groups.count_tracking Reshaping TSSCount table Recasting Writing TSSCount table Reading read group info in /mnt/max/c/genomics_facility/proton/run299/wwwSCR/cuffdiff_F16_vs_F16mut/tss_groups.read_group_tracking Writing TSSReplicateData table Reading /mnt/max/c/genomics_facility/proton/run299/wwwSCR/cuffdiff_F16_vs_F16mut/cds.fpkm_tracking Checking samples table... OK! Writing CDS table No records found in /mnt/max/c/genomics_facility/proton/run299/wwwSCR/cuffdiff_F16_vs_F16mut/cds.fpkm_tracking CDS FPKM tracking file was empty. Reading /mnt/max/c/genomics_facility/proton/run299/wwwSCR/cuffdiff_F16_vs_F16mut/cds_exp.diff No records found in /mnt/max/c/genomics_facility/proton/run299/wwwSCR/cuffdiff_F16_vs_F16mut/cds_exp.diff Reading /mnt/max/c/genomics_facility/proton/run299/wwwSCR/cuffdiff_F16_vs_F16mut/cds.diff No records found in /mnt/max/c/genomics_facility/proton/run299/wwwSCR/cuffdiff_F16_vs_F16mut/cds.diff Reading /mnt/max/c/genomics_facility/proton/run299/wwwSCR/cuffdiff_F16_vs_F16mut/cds.count_tracking No records found in /mnt/max/c/genomics_facility/proton/run299/wwwSCR/cuffdiff_F16_vs_F16mut/cds.count_tracking Reading read group info in /mnt/max/c/genomics_facility/proton/run299/wwwSCR/cuffdiff_F16_vs_F16mut/cds.read_group_tracking No records found in /mnt/max/c/genomics_facility/proton/run299/wwwSCR/cuffdiff_F16_vs_F16mut/cds.read_group_tracking Indexing Tables... Warning messages: 1: attributes are not identical across measure variables; they will be dropped 2: attributes are not identical across measure variables; they will be dropped 3: attributes are not identical across measure variables; they will be dropped 4: attributes are not identical across measure variables; they will be dropped 5: attributes are not identical across measure variables; they will be dropped 6: attributes are not identical across measure variables; they will be dropped Getting gene information: FPKM Differential Expression Data Annotation Data Replicate FPKMs Counts Getting isoforms information: FPKM Differential Expression Data Annotation Data Replicate FPKMs Counts Getting CDS information: FPKM Differential Expression Data Annotation Data Replicate FPKMs Counts Getting TSS information: FPKM Differential Expression Data Annotation Data Replicate FPKMs Counts Getting promoter information: distData Getting splicing information: distData Getting relCDS information: distData Getting gene information: FPKM Differential Expression Data Annotation Data Replicate FPKMs Counts Getting isoforms information: FPKM Differential Expression Data Annotation Data Replicate FPKMs Counts Getting CDS information: FPKM Differential Expression Data Annotation Data Replicate FPKMs Counts Getting TSS information: FPKM Differential Expression Data Annotation Data Replicate FPKMs Counts Getting promoter information: distData Getting splicing information: distData Getting relCDS information: distData Getting gene information: FPKM Differential Expression Data Annotation Data Replicate FPKMs Counts Getting isoforms information: FPKM Differential Expression Data Annotation Data Replicate FPKMs Counts Getting CDS information: FPKM Differential Expression Data Annotation Data Replicate FPKMs Counts Getting TSS information: FPKM Differential Expression Data Annotation Data Replicate FPKMs Counts Getting promoter information: distData Getting splicing information: distData Getting relCDS information: distData Heatmap F16_vs_F16mut_alpha0.05_heatmap.png qval=0.05 #sig=100 ww=4 hh=30 Using tracking_id, sample_name as id variables No id variables; using all as measure variables null device 1 Getting gene information: FPKM Differential Expression Data Annotation Data Replicate FPKMs Counts Getting isoforms information: FPKM Differential Expression Data Annotation Data Replicate FPKMs Counts Getting CDS information: FPKM Differential Expression Data Annotation Data Replicate FPKMs Counts Getting TSS information: FPKM Differential Expression Data Annotation Data Replicate FPKMs Counts Getting promoter information: distData Getting splicing information: distData Getting relCDS information: distData Getting gene information: FPKM Differential Expression Data Annotation Data Replicate FPKMs Counts Getting isoforms information: FPKM Differential Expression Data Annotation Data Replicate FPKMs Counts Getting CDS information: FPKM Differential Expression Data Annotation Data Replicate FPKMs Counts Getting TSS information: FPKM Differential Expression Data Annotation Data Replicate FPKMs Counts Getting promoter information: distData Getting splicing information: distData Getting relCDS information: distData Using tracking_id, sample_name as id variables No id variables; using all as measure variables HeatmapB F16_vs_F16mut_alpha0.05_heatmap.png qval=0.05 #sig=100 ww=5 hh=14.1 null device 1 null device 1 Error in sqliteSendQuery(con, statement, bind.data) : error in statement: near ")": syntax error Calls: getGenes ... .local -> sqliteGetQuery -> sqliteSendQuery -> .Call Execution halted