Error Code with Cuffdiff

cuffdiff

#1

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

#2

Is the option to output the SQLite output checked on the tool form? If so, remove that and run again.