Question: Error with cuffdiff
2
gravatar for drbrown
2.5 years ago by
drbrown20
European Union
drbrown20 wrote:

Hi,

I'm new to Galaxy and the tuxedo pipeline but have managed to get my data to the point where I could run cuffdiff and got the error below. (I deleted a lot of the processing locus lines so it fits!)

I'm using the galaxy main server and trying to analyze mutant versus wild-type at two different conditions of growth. Both sets of data have 2 biological replicates.

Thanks,

Dan


Fatal error: Exit code 1 ()
[09:51:02] Loading reference annotation.
[09:51:02] Inspecting maps and determining fragment length distributions.
[09:56:18] Modeling fragment count overdispersion.
[09:58:45] Modeling fragment count overdispersion.
> Map Properties:
>	Normalized Map Mass: 11390181.60
>	Raw Map Mass: 17143797.18
>	Fragment Length Distribution: Truncated Gaussian (default)
>	              Default Mean: 200
>	           Default Std Dev: 80
> Map Properties:
>	Normalized Map Mass: 11390181.60
>	Raw Map Mass: 11136236.08
>	Fragment Length Distribution: Truncated Gaussian (default)
>	              Default Mean: 200
>	           Default Std Dev: 80
> Map Properties:
>	Normalized Map Mass: 11390181.60
>	Raw Map Mass: 18071033.85
>	Fragment Length Distribution: Truncated Gaussian (default)
>	              Default Mean: 200
>	           Default Std Dev: 80
> Map Properties:
>	Normalized Map Mass: 11390181.60
>	Raw Map Mass: 12434663.38
>	Fragment Length Distribution: Truncated Gaussian (default)
>	              Default Mean: 200
>	           Default Std Dev: 80
> Map Properties:
>	Normalized Map Mass: 11390181.60
>	Raw Map Mass: 11933159.24
>	Fragment Length Distribution: Truncated Gaussian (default)
>	              Default Mean: 200
>	           Default Std Dev: 80
> Map Properties:
>	Normalized Map Mass: 11390181.60
>	Raw Map Mass: 4301014.51
>	Fragment Length Distribution: Truncated Gaussian (default)
>	              Default Mean: 200
>	           Default Std Dev: 80
> Map Properties:
>	Normalized Map Mass: 11390181.60
>	Raw Map Mass: 8139011.11
>	Fragment Length Distribution: Truncated Gaussian (default)
>	              Default Mean: 200
>	           Default Std Dev: 80
> Map Properties:
>	Normalized Map Mass: 11390181.60
>	Raw Map Mass: 4206573.23
>	Fragment Length Distribution: Truncated Gaussian (default)
>	              Default Mean: 200
>	           Default Std Dev: 80
[10:01:14] Calculating preliminary abundance estimates
[10:01:14] Testing for differential expression and regulation in locus.

> Processing Locus Chromosome:189-255          [                         ]   0%

> Processing Locus C
..
[***********************  ]  94%
> Processed 3692 loci.                         [*************************] 100%
Performed 4348 isoform-level transcription difference tests
Performed 4331 tss-level transcription difference tests
Performed 3710 gene-level transcription difference tests
Performed 0 CDS-level transcription difference tests
Performed 17 splicing tests
Performed 450 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: parallel
Error: package 'parallel' could not be loaded
In addition: Warning messages:
1: package 'cummeRbund' was built under R version 3.1.2 
2: package 'BiocGenerics' was built under R version 3.1.2 
3: In library(pkg, character.only = TRUE, logical.return = TRUE, lib.loc = lib.loc) :
  there is no package called 'parallel'
Execution halted

Could anyone help me with this?

ADD COMMENTlink modified 2.5 years ago by Martin Čech ♦♦ 4.2k • written 2.5 years ago by drbrown20
1

Hi there:

 

I'm having the same problem today, Dan.  I think it's something systemic, and not with your approach/data.

 

-Cory

ADD REPLYlink written 2.5 years ago by Cory Dunn40
1

Add me to the list, also experiencing this error.

ADD REPLYlink written 2.5 years ago by gsolis10

I'm not getting an error message now, but the output seems to be an SQLite database file, rather than the tabular data that has previously been the output of Cuffdiff.  I've never used R or cummeRbund - the tabular data were easy to handle and are preferred.  Are we now forced to receive our output in this new format, or is there a way to convert/obtain tabular data?

Thank you,

-Cory

 

ADD REPLYlink written 2.5 years ago by Cory Dunn40

I am getting same error message. Any changes you have made Cory?

ADD REPLYlink written 2.5 years ago by merops990
1
gravatar for Martin Čech
2.5 years ago by
Martin Čech ♦♦ 4.2k
United States
Martin Čech ♦♦ 4.2k wrote:

This is a known issue and is currently being worked on. Sorry for the inconvenience.

Regarding the output format it will be switched to provide both sqlite and tabular datasets.

edit: the missing parallel issue should be resolved on usegalaxy.org - please give it a try; if you installed cummerbund on your Galaxy see https://github.com/galaxyproject/tools-iuc/pull/176 for fix or wait for the fix to be merged and pushed to the Tool Shed

Thank you for using Galaxy

ADD COMMENTlink modified 2.5 years ago • written 2.5 years ago by Martin Čech ♦♦ 4.2k

Thanks Martin,

I have managed to run it with no errors now, but as above I only have sqlite database file.... I can't extract as in the video from Galaxy 101 series because the Extract Cuffdiff and plot cuffdiff tools are no longer present? Will the output be returning to tabular? I imagine then I can get to my data.

Best, Dan

ADD REPLYlink written 2.5 years ago by drbrown20

Yes, there is an update currently under review to restore the original behavior of the cuffdiff tool, in addition to generating a SQLite file appropriate for plotting the data with cummeRbund.

ADD REPLYlink written 2.5 years ago by Dave B.410

Thanks Dave!

ADD REPLYlink written 2.5 years ago by drbrown20
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