Question: Error with Cuffdiff
1
Yiwei Ai • 20 wrote:
Hi,
I have used cuffdiff on my cuffmerge results. Then an error occurred. Could anyone tell me what should I do? Thanks!
Fatal error: Exit code 1 ()
[14:42:15] Loading reference annotation.
Warning: No conditions are replicated, switching to 'blind' dispersion method
[14:42:19] Inspecting maps and determining fragment length distributions.
[14:49:53] Modeling fragment count overdispersion.
> Map Properties:
> Normalized Map Mass: 23388927.85
> Raw Map Mass: 22136508.03
> Fragment Length Distribution: Empirical (learned)
> Estimated Mean: 183.41
> Estimated Std Dev: 62.30
> Map Properties:
> Normalized Map Mass: 23388927.85
> Raw Map Mass: 24719433.31
> Fragment Length Distribution: Empirical (learned)
> Estimated Mean: 185.83
> Estimated Std Dev: 63.77
[14:51:21] Calculating preliminary abundance estimates
[14:51:21] Testing for differential expression and regulation in locus.
> Processing Locus chr1:89313-91069 [ ] 0%
> Processing Locus chr1:236563-259102 [
> Processing Locus chr1:15853354-15911570 [ ] 1%
> Processing Locus chr1:15736403-15756818
..
[************************ ] 98%
> Processing Locus chrX:118708468-118718371 [************************ ] 98%
> Processing Locus chrX:118722419-118740432 [************************ ] 98%
> Processing Locus chrX:118892984-118894092 [************************ ] 98%
> Processing Locus chrX:118749692-118827268 [************************ ] 98%
> Processing Locus chrX:118964015-118966912 [************************ ] 98%
> Processing Locus chrX:118923196-118939781 [************************ ] 98%
> Processing Locus chrX:118968083-118987008 [************************ ] 98%
> Processing Locus chrX:119054722-119057638 [************************ ] 98%
> Processing Locus chrX:119370348-119379126 [************************ ] 99%
> Processing Locus chrY:21152707-21154677 [************************ ] 99%
> Processed 18444 loci. [*************************] 100%
Performed 39644 isoform-level transcription difference tests
Performed 31248 tss-level transcription difference tests
Performed 21542 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
Error in library("cummeRbund") : there is no package called 'cummeRbund'
Execution halted
The tool produced the following additional output:
R version 3.1.2 (2014-10-31) -- "Pumpkin Helmet"
Copyright (C) 2014 The R Foundation for Statistical Computing
Platform: x86_64-unknown-linux-gnu (64-bit)
R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.
R is a collaborative project with many contributors.
Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.
Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.
> library("cummeRbund")
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modified 3.5 years ago
by
Jennifer Hillman Jackson ♦ 25k
•
written
3.5 years ago by
Yiwei Ai • 20
I also met this problem. How to interpret the following information? Thank you very much!
Log: tool progress Log: tool progress [16:26:26] Loading reference annotation. Warning: No conditions are replicated, switching to 'blind' dispersion method [16:26:27] Inspecting maps and determining fragment length distributions. [16:26:29] Modeling fra