Not enough mutations to analyze?

[Steve L]

Please respond with the following information as applicable:
 Complete description of the problem (ie what you were trying to do and what went wrong): Hi, I have been trying to run MutSigCV on a group of patients that have had Whole Exome Sequencing done to see which genes are significantly mutated for that group.  I have formatted the MAF file into the format required and am using the exome_full192.coverage.txt file as well as the gene.covariates.txt provide. However I am getting the stderr.txt:

Error using gp_MutSigCV>MutSig_runCV (line 850)

not enough mutations to analyze

Error in gp_MutSigCV (line 194)

 

And the stdout.txt:

MutSigCV: PREPROCESS

--------------------

Loading mutation_file...

Loading coverage file...

Processing mutation "effect"...

Will use the pre-existing "effect" column.

Processing mutation "categ"...

"categ" of mutation_file does not match coverage_file.  Ignoring it.

NOTE:  unable to perform category discovery, because Chromosome/Start_position/Reference_Allele/Tumor_Seq_Allele1/Tumor_Seq_Allele2 missing from mutation_file.Will use two categories: missense and null+indel.

Collapsing coverage...

Writing preprocessed files.

MutSig_preprocess finished.

MutSigCV: RUN

-------------

Loading mutation_file...

Loading coverage file...

Loading covariate file...

NOTE:  728/9679 gene names could not be mapped to coverage information.  Excluding them.

Building n and N tables...

I have hundreds or thousands of mutations for each sample. Is the minimum of mutations that is required? Thank you very much for your time and help in advance!

Job ID if run on a publicly available server. #1718330

If not on Public Server, please share your input files, if possible. If you need to do so privately, let us know.
 
   What were your Parameter values?
   Server Platform (Mac/Linux)?

   Any errors or warnings you see in either stderr.txt, stdout.txt or popup dialogues:

Please note that many common errors can be resolved by searching this forum or taking a look at our documentation: 

* Module Documentation - available from the "documentation" link in the upper right hand corner of the module input page or here: http://software.broadinstitute.org/cancer/software/genepattern/modules
* GenePattern FAQ - http://software.broadinstitute.org/cancer/software/genepattern/FAQ
* GenePattern  Videos - http://software.broadinstitute.org/cancer/software/genepattern/video-tutorials
* GenePattern File Formats - http://software.broadinstitute.org/cancer/software/genepattern/file-formats-guide#file-formats
* GenePattern User Guide - http://software.broadinstitute.org/cancer/software/genepattern/user-guide#user-guide
* GenePattern Programmer's Guide - http://software.broadinstitute.org/cancer/software/genepattern/programmers-guide
* GenePattern Release Notes - http://software.broadinstitute.org/cancer/software/genepattern/doc/relnotes/current

[Barbara Hill]

Hello, 

It may be that you have too few silent mutations.

https://software.broadinstitute.org/cancer/cga/node/119

That is from the archived CGA forum. 

You might also try contacting the developers at mutsi...@broadinstitute.org

You might also take a look at the stdout.txt which reports issues with gene names and categories, which may be preventing the algorithm from getting all of the information it needs to run correctly.

Best

-Barbara

[Steve L]

Hi Barbara,

Thank you for the advice! I will give that a try. What is the purpose of the silent mutations? Will those silent mutations contribute to "significant" genes?

Thanks!!

-Steve

[Barbara Hill]

Hi Steve, 

As a GenePattern team member, I'm afraid I am just the messenger here. We did not write MutSig, nor do we maintain its algorithm.

If you write to the MutSig development team, they may be able to answer that question.

All the best

-Barbara

[Steve L]

Hi Barbara,

Since I did not have any silent mutations, I put in an equal number of "dummy" silent mutations to the data. However instead of getting "not enough mutations to analyze," I am receiving the error:

Error using gp_MutSigCV>MutSig_runCV (line 854)

silent and nonsilent rates are too different

Error in gp_MutSigCV (line 194)

I am using the full coverage.txt file that is provided on the shared folder.

Thanks!

-Steve

[Barbara Hill]

Hi Steve,

Again, this is very far outside my area of expertise, but I searched the forum I linked to before and found this: https://software.broadinstitute.org/cancer/cga/node/103

 

I also found a note from gsaksena suggesting that this may be due to having only 1 sample - you have more than 1 sample, yes? 1 sample is too few.

Best

-Barbara

[tingting gao]

Hello Steve,

How are you? Have you solved this problem? I have the same probelm with you. Can you tell me how to modify it, if you solve this problem? Thank you very much.

Thanks,

Tingting

在 2018年8月21日星期二 UTC-5下午2:51:25，Steve L写道：