Hi,

I am trying to run Mutsig2CV_NC on my own HCC WGS data with MATLAB v2019a on Windows and MCR on linux, like
"
MutSig2CV_NC('input/input.fiveCol.maf', 'output', 'run/params/Liver-HCC_alt_prom.params.txt') "
Then it showed
"
WILL LOAD+RUN.
LOADING DATA
"
But then I encountered errors said
"
errors when using require_fields (line 9)
Structure is missing required field "num"
Error: demand_fields (line 2)
require_fields(varargin{:});
Error: map_categories_to_65 (line 15)
demand_fields(C,{'num','name'});
Error MutSig2CV_v5_load (line 78)
M.context_and_effect.context65 =
map_categories_to_65(context_and_effect_categs_file); %XXX: make sure this works
Error MutSig2CV_NC (line 96)
[M P] = MutSig2CV_v5_load(args{:});
"
in Windows and
"
Structure is missing required field "num"
Error in demand_fields (line 2)
Error in map_categories_to_65 (line 15)
Error in MutSig2CV_v5_load (line 78)
Error in MutSig2CV_v5_wrapper (line 96)
" in linux.

Could you please tell me how should I avoid such errors? Many thanks.

Best wishes,
Jennifer

Hello,

I use MutSigCV analyzed my mutation data. It shows some error. I think maybe something is wrong with my input file. Could you please tell me how to revise it? The error is:

Error using gp_MutSigCV>MutSig_runCV (line 850)
not enough mutations to analyze

Error in gp_MutSigCV (line 194)
MutSigCV
v1.3

(c) Mike Lawrence and Gaddy Getz
Broad Institute of MIT and Harvard
MutSigCV: PREPROCESS
Loading mutation_file...
Loading coverage file...
Processing mutation "effect"...
WARNING: 2/21453 mutations could not be mapped to effect using mutation_type_dictionary_file:

     : [2]

----TOTAL: [2]
They will be removed from the analysis.
Processing mutation "categ"...
NOTE: unable to perform category discovery, because no chr_files available.Will use two categories: missense and null+indel.
Collapsing coverage...
Writing preprocessed files.
MutSig_preprocess finished.

The following one is input file:
Hugo_Symbol Tumor_Sample_Barcode Variant_Classification Chromosome Start_position Reference_Allele Tumor_Seq_Allele1 Tumor_Seq_Allele2
A1CF LM-BN-1 3'UTR 10 52563029 GT G G
A1CF LM-BN-4 3'UTR 10 52563029 GT G G
A1CF LM-BN-5 3'UTR 10 52566432 CT C C
A2M LM-BN-1 Intron 12 9220823 G GA GA
A2M LM-BN-4 Intron 12 9220823 G GA GA
A2ML1 LM-BN-1 3'UTR 12 9028242 T C C
A2ML1 LM-BN-1 3'UTR 12 9028264 G A A
AAAS LM-BN-1 Missense_Mutation 12 53715218 G A A
AACS LM-BN-1 5'UTR 12 125586335 TG CA CA
AACS LM-BN-2 5'UTR 12 125607905 A G G
AACS LM-BN-2 5'UTR 12 125607960 C G G
AACS LM-BN-3 5'UTR 12 125586308 CTT C C
AACS LM-BN-3 5'UTR 12 125586308 CTT CTTT CTTT
AACS LM-BN-4 5'UTR 12 125586308 CT C C
AACS LM-BN-4 5'UTR 12 125586308 CT CTT CTT
AACS LM-BN-1 5'UTR 12 125586359 G C C

Thanks.

Hello, Julianhess

I use MutSigCV module of Genepattern analyzed my mutation data. It shows some error. I think maybe something is wrong with my input file. Could you please tell me how to revise it? The error is:

Error using gp_MutSigCV>MutSig_runCV (line 850)
not enough mutations to analyze

Error in gp_MutSigCV (line 194)
MutSigCV
v1.3

(c) Mike Lawrence and Gaddy Getz
Broad Institute of MIT and Harvard
MutSigCV: PREPROCESS
Loading mutation_file...
Loading coverage file...
Processing mutation "effect"...
WARNING: 2/21453 mutations could not be mapped to effect using mutation_type_dictionary_file:

 : [2]

----TOTAL: [2]
They will be removed from the analysis.
Processing mutation "categ"...
NOTE: unable to perform category discovery, because no chr_files available.Will use two categories: missense and null+indel.
Collapsing coverage...
Writing preprocessed files.
MutSig_preprocess finished.

The following one is input file:
Hugo_Symbol Tumor_Sample_Barcode Variant_Classification Chromosome Start_position Reference_Allele Tumor_Seq_Allele1 Tumor_Seq_Allele2
A1CF LM-BN-1 3'UTR 10 52563029 GT G G
A1CF LM-BN-4 3'UTR 10 52563029 GT G G
A1CF LM-BN-5 3'UTR 10 52566432 CT C C
A2M LM-BN-1 Intron 12 9220823 G GA GA
A2M LM-BN-4 Intron 12 9220823 G GA GA
A2ML1 LM-BN-1 3'UTR 12 9028242 T C C
A2ML1 LM-BN-1 3'UTR 12 9028264 G A A
AAAS LM-BN-1 Missense_Mutation 12 53715218 G A A
AACS LM-BN-1 5'UTR 12 125586335 TG CA CA
AACS LM-BN-2 5'UTR 12 125607905 A G G
AACS LM-BN-2 5'UTR 12 125607960 C G G
AACS LM-BN-3 5'UTR 12 125586308 CTT C C
AACS LM-BN-3 5'UTR 12 125586308 CTT CTTT CTTT
AACS LM-BN-4 5'UTR 12 125586308 CT C C
AACS LM-BN-4 5'UTR 12 125586308 CT CTT CTT
AACS LM-BN-1 5'UTR 12 125586359 G C C

Thanks.

Dear developer team,

Thank you for developing the new Mutsig for non-coding regions. I'm trying to download the provided resources (cohort_parameter) and appreciate help with that.

I am new to google cloud bucket. At first, I try to install the gsutil on my server but failed, so I install it in my local desktop. However, one file seems too large to download and the error shows that my local desktop doesn't allow for a "lustre" file. Later I also try to install the google cloud python package for downloading but also stuck at somewhere.

May I ask is there any other places I could download the files from, except the google bucket?

Many Thanks,
Jue

Is there a reason why in run/params there are no files available for PanCan cohort for miRNA (neither mature, pre or promotors)?

Hello,

I use MutSigCV analyzed my mutation data. It shows some error. I think maybe something is wrong with my input file. Could you please tell me how to revise it? The error is:

Error using gp_MutSigCV>MutSig_runCV (line 850)
not enough mutations to analyze

Error in gp_MutSigCV (line 194)
MutSigCV
v1.3

(c) Mike Lawrence and Gaddy Getz
Broad Institute of MIT and Harvard

MutSigCV: PREPROCESS

Loading mutation_file...
Loading coverage file...
Processing mutation "effect"...
WARNING: 2/21453 mutations could not be mapped to effect using mutation_type_dictionary_file:

         : [2]
----TOTAL: [2]
      They will be removed from the analysis.

Processing mutation "categ"...
NOTE: unable to perform category discovery, because no chr_files available.Will use two categories: missense and null+indel.
Collapsing coverage...
Writing preprocessed files.
MutSig_preprocess finished.

Thanks.
The following one is input file:
Hugo_Symbol Tumor_Sample_Barcode Variant_Classification Chromosome Start_position Reference_Allele Tumor_Seq_Allele1 Tumor_Seq_Allele2
A1CF LM-BN-1 3'UTR 10 52563029 GT G G
A1CF LM-BN-4 3'UTR 10 52563029 GT G G
A1CF LM-BN-5 3'UTR 10 52566432 CT C C
A2M LM-BN-1 Intron 12 9220823 G GA GA
A2M LM-BN-4 Intron 12 9220823 G GA GA
A2ML1 LM-BN-1 3'UTR 12 9028242 T C C
A2ML1 LM-BN-1 3'UTR 12 9028264 G A A
AAAS LM-BN-1 Missense_Mutation 12 53715218 G A A
AACS LM-BN-1 5'UTR 12 125586335 TG CA CA
AACS LM-BN-2 5'UTR 12 125607905 A G G
AACS LM-BN-2 5'UTR 12 125607960 C G G
AACS LM-BN-3 5'UTR 12 125586308 CTT C C
AACS LM-BN-3 5'UTR 12 125586308 CTT CTTT CTTT
AACS LM-BN-4 5'UTR 12 125586308 CT C C
AACS LM-BN-4 5'UTR 12 125586308 CT CTT CTT
AACS LM-BN-1 5'UTR 12 125586359 G C C

Hi Julian,

I run the software on my own data on linux. The results seems weird. For example, in enhancers' output file, the first 5 lines is:
"
codelen nnei nind nnon npat nsite pCL pFN pCL2 pFN2 pCF q
97 13 15 15 15 2 NaN NaN NaN NaN NaN 1.000000e-16
607 18 8 11 11 4 NaN NaN NaN NaN NaN 1.000000e-16
1333 15 4 11 11 10 NaN NaN NaN NaN NaN 1.000000e-16
375 3 10 10 10 2 NaN NaN NaN NaN NaN 1.000000e-16
193 43 10 10 10 4 NaN NaN NaN NaN NaN 1.000000e-16
"
During the process there were 2 warnings：
“Warning: NARGCHK will be removed in a future release. Use NARGINCHK or NARGOUTCHK instead.

In sparse_to_csr (line 26)
In scomponents (line 31)
In new_find_duplicate_samples (line 68)
In MutSig2CV_v5_load (line 218)
In MutSig2CV_v5_wrapper (line 96)
Warning: The KEYBOARD function cannot be used in compiled applications.
In keyboard (line 4)
In MutSig2CV_v5_load (line 272)
In MutSig2CV_v5_wrapper (line 96)
”

And I also used Matlab 2016b on Windows, and encountered errors like:
"
Undefined function or variable 'str2doubleq'。

Error: str2doubleq_wrapper (line 3)
out = real(str2doubleq(in));

Error: make_numeric (line 37)
x = str2doubleq_wrapper(x);

Error: MutSig2CV_v5_load (line 197)
M.mut = make_numeric(M.mut,'pos');

Error: MutSig2CV_NC (line 96)
[M P] = MutSig2CV_v5_load(args{:});
"

Could you please tell me how should I proceed? Thank you very much.

Best,
Jennifer