I got this error code (seen below) using Cuffdiff and don’t know what to do from here or what the issue is exactly is. I know that this program has been deprecated due to problems with SQLite, but I can’t use the new differential analysis tools because I don’t have replicates for my data and saving multiple files of the same data doesn’t work. I did bulk RNA-seq which is why I don’t have replicates.
Fatal error: Exit code 1 () [09:01:13] Loading reference annotation. Warning: No conditions are replicated, switching to 'blind' dispersion method [09:01:16] Inspecting maps and determining fragment length distributions. [09:06:47] Modeling fragment count overdispersion. > Map Properties: > Normalized Map Mass: 16277272.00 > Raw Map Mass: 16277272.00 > Fragment Length Distribution: Empirical (learned) > Estimated Mean: 201.48 > Estimated Std Dev: 77.15 > Map Properties: > Normalized Map Mass: 16277272.00 > Raw Map Mass: 16277272.00 > Fragment Length Distribution: Empirical (learned) > Estimated Mean: 201.48 > Estimated Std Dev: 77.15 [09:08:02] Calculating preliminary abundance estimates [09:08:02] Testing for differential expression and regulation in locus. Processed 42307 loci. Performed 22055 isoform-level transcription difference tests Performed 22055 tss-level transcription difference tests Performed 22055 gene-level transcription difference tests Performed 0 CDS-level transcription difference tests Performed 0 splicing tests Performed 0 promoter preference tests Performing 0 relative CDS output tests Writing isoform-level FPKM tracking Writing TSS group-level FPKM tracking Writing gene-level FPKM tracking Writing CDS-level FPKM tracking Writing isoform-level count tracking Writing TSS group-level count tracking Writing gene-level count tracking Writing CDS-level count tracking Writing isoform-level read group tracking Writing TSS group-level read group tracking Writing gene-level read group tracking Writing CDS-level read group tracking Writing read group info Writing run info 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 objects are masked from ‘package:stats’: IQR, mad, sd, var, xtabs The following objects are masked from ‘package:base’: anyDuplicated, append, as.data.frame, cbind, colMeans, colnames, colSums, do.call, duplicated, eval, evalq, Filter, Find, get, grep, grepl, intersect, is.unsorted, lapply, lengths, Map, mapply, match, mget, order, paste, pmax, pmax.int, pmin, pmin.int, Position, rank, rbind, Reduce, rowMeans, rownames, rowSums, sapply, setdiff, sort, table, tapply, union, unique, unsplit, which, which.max, which.min Loading required package: RSQLite 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: stats4 Loading required package: S4Vectors Attaching package: ‘S4Vectors’ The following objects are masked from ‘package:BiocGenerics’: colMeans, colSums, rowMeans, rowSums The following objects are masked from ‘package:base’: colMeans, colSums, expand.grid, rowMeans, rowSums 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 There were 50 or more warnings (use warnings() to see the first 50) Creating database ./cummeRbund.sqlite Reading Run Info File ./run.info Writing runInfo Table Reading Read Group Info ./read_groups.info Writing replicates Table Reading Var Model Info ./var_model.info Writing varModel Table Reading ./genes.fpkm_tracking Checking samples table... Populating samples table... Error: Column name mismatch. In addition: There were 50 or more warnings (use warnings() to see the first 50) Execution halted