search

broadinstitute / getzlab-PCAWG-MutSig2CV_NC

MutSig2CV for noncoding analysis as run for the PCAWG drivers paper (Rheinbay et al. 2020)
7 stars 1 forks source link

MutsigCV #4

Closed Gtt19920502 closed 4 years ago

Gtt19920502 commented 4 years ago

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

hurrialice commented 4 years ago

Hi,

Have you downloaded "all.fwb" and "all.fwi" from the bucket gs://getzlab-pcawg-mutsig2cv_nc/ as mentioned here?

julianhess commented 4 years ago

Hi @Gtt19920502,

It seems that you're trying to run the original 2010 MutSigCV algorithm. This repo contains the release of MutSig2CV specifically for noncoding element analysis.

Rather than trying to get MutSigCV to work, it will be much easier to use the latest release of MutSig2CV for coding elements, which supersedes the original MutSigCV.

Please download that here: http://software.broadinstitute.org/cancer/cga/sites/default/files/data/tools/mutsig/MutSig2CV.tar.gz

Note that it is a large download (~3 GB), since it includes all necessary reference files. Installation instructions are provided in the README.txt file. In addition to the MutSig executable, you will also need the MATLAB runtime environment, available here: http://www.mathworks.com/supportfiles/MCR_Runtime/R2013a/MCR_R2013a_glnxa64_installer.zip

Gtt19920502 commented 4 years ago

Hi @Gtt19920502,

It seems that you're trying to run the original 2010 MutSigCV algorithm. This repo contains the release of MutSig2CV specifically for noncoding element analysis.

Rather than trying to get MutSigCV to work, it will be much easier to use the latest release of MutSig2CV for coding elements, which supersedes the original MutSigCV.

Please download that here: http://software.broadinstitute.org/cancer/cga/sites/default/files/data/tools/mutsig/MutSig2CV.tar.gz

Note that it is a large download (~3 GB), since it includes all necessary reference files. Installation instructions are provided in the README.txt file. In addition to the MutSig executable, you will also need the MATLAB runtime environment, available here: http://www.mathworks.com/supportfiles/MCR_Runtime/R2013a/MCR_R2013a_glnxa64_installer.zip

Hi Julianhess,

Thank you very much for your reply and informations. I think maybe something wrong with my input file. I'll try it according your suggestion. Thank you very much.

Gtt19920502 commented 4 years ago

Hi,

Have you downloaded "all.fwb" and "all.fwi" from the bucket gs://getzlab-pcawg-mutsig2cv_nc/ as mentioned here?

Hello,

Thank you very much for your reply. I used the MutSigCV 1.3 software. I'm not whether my input file is wrong? Thank you very much. The following one is my input. Could you please help me th check it whether it's right or not? Thank you very much. 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 AADACL3 LM-BN-1 3'UTR 1 12787881 G A A AADACL3 LM-BN-1 Missense_Mutation 1 12785945 A T T AADAT LM-BN-3 3'UTR 4 170981506 TAAAAGTAGA T T AAED1 LM-BN-4 3'UTR 9 99402375 C CA CA AAED1 LM-BN-1 Missense_Mutation 9 99413690 C T T AAGAB LM-BN-4 3'UTR 15 67493515 CT C C AAGAB LM-BN-5 3'UTR 15 67493515 CT C C AAGAB LM-BN-5 3'UTR 15 67493515 CT CTT CTT AAK1 LM-BN-1 3'UTR 2 69688727 A AT AT AAK1 LM-BN-2 3'UTR 2 69709361 G A A AAK1 LM-BN-3 3'UTR 2 69688631 CA C C AAK1 LM-BN-3 3'UTR 2 69688631 CA CAA CAA AAK1 LM-BN-3 3'UTR 2 69702102 T TCCCCCCC TCCCCCCC

Gtt19920502 commented 4 years ago

Yeah, It shows closed. I'll send the input now. Could you please tell me can you check it? Thank you very much. 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

julianhess notifications@github.com 于2020年7月13日周一 下午7:02写道：

Closed #4 https://github.com/broadinstitute/getzlab-PCAWG-MutSig2CV_NC/issues/4.

— You are receiving this because you were mentioned. Reply to this email directly, view it on GitHub https://github.com/broadinstitute/getzlab-PCAWG-MutSig2CV_NC/issues/4#event-3541775184, or unsubscribe https://github.com/notifications/unsubscribe-auth/AQH2D3DGF2MO4FJEETBYYDDR3OOCPANCNFSM4OY2CIIA .

hurrialice commented 4 years ago

Hi @Gtt19920502 ,

It seems that you are still using MutSigCV. If so, please use MutSig2CV downloaded as @julianhess described. MutSigCV on GenePattern is not up-to-date and will not be further supported.

Your input file seems okay. If you are still encountering problems with MutSIg2CV, please attach the log with your reply here.

Thanks!

Gtt19920502 commented 4 years ago

Hello Qing,

Thank you very much for your reply. I will try to do it using MutSig2CV.

Thanks!

qing zhang notifications@github.com 于2020年7月17日周五 上午9:01写道：

Hi @Gtt19920502 https://github.com/Gtt19920502 ,

It seems that you are still using MutSigCV. If so, please use MutSig2CV downloaded as @julianhess https://github.com/julianhess described. MutSigCV on GenePattern is not up-to-date and will not be further supported.

Your input file seems okay. If you are still encountering problems with MutSIg2CV, please attach the log with your reply here.

Thanks!

— You are receiving this because you were mentioned. Reply to this email directly, view it on GitHub https://github.com/broadinstitute/getzlab-PCAWG-MutSig2CV_NC/issues/4#issuecomment-660123484, or unsubscribe https://github.com/notifications/unsubscribe-auth/AQH2D3HEA5U633XFR3QWLYTR4BKTPANCNFSM4OY2CIIA .

Gtt19920502 commented 4 years ago

Hello Qing,

The following one is the result of running MutSig2CV. It also shows error. Could you please tell me how to revise: [image: image.png]

Thanks

qing zhang notifications@github.com 于2020年7月17日周五 上午9:01写道：

Hi @Gtt19920502 https://github.com/Gtt19920502 ,

It seems that you are still using MutSigCV. If so, please use MutSig2CV downloaded as @julianhess https://github.com/julianhess described. MutSigCV on GenePattern is not up-to-date and will not be further supported.

Your input file seems okay. If you are still encountering problems with MutSIg2CV, please attach the log with your reply here.

Thanks!

— You are receiving this because you were mentioned. Reply to this email directly, view it on GitHub https://github.com/broadinstitute/getzlab-PCAWG-MutSig2CV_NC/issues/4#issuecomment-660123484, or unsubscribe https://github.com/notifications/unsubscribe-auth/AQH2D3HEA5U633XFR3QWLYTR4BKTPANCNFSM4OY2CIIA .

Gtt19920502 commented 4 years ago

Hello Qing,

The following one is the result of running MutSig2CV. It also shows error. Could you please tell me how to revise: -/MntsigGV/mutsig2cv$。/Mutsig2CV II-MAF, mat outputWarning: latest version of matlab app-defaults file not foundContact your system administrator to have this file installedMUTSIG VERSION E 2cv3.11 LOADING DATA Processing target list oading mutations Mutation file contains multiple columns for newbase info Tumor_seq Allele newbase ill use newbase Mutation file is missing a column named one of the following: classification Variant_Type Error using Mutsig_2CV_v3_11_core(line 169) Mutation file missing classification column Error in Mutsig-_2cV_v3_11 wrapper(line 50)

Thanks

qing zhang notifications@github.com 于2020年7月17日周五 上午9:01写道：

Hi @Gtt19920502 https://github.com/Gtt19920502 ,

It seems that you are still using MutSigCV. If so, please use MutSig2CV downloaded as @julianhess https://github.com/julianhess described. MutSigCV on GenePattern is not up-to-date and will not be further supported.

Your input file seems okay. If you are still encountering problems with MutSIg2CV, please attach the log with your reply here.

Thanks!

— You are receiving this because you were mentioned. Reply to this email directly, view it on GitHub https://github.com/broadinstitute/getzlab-PCAWG-MutSig2CV_NC/issues/4#issuecomment-660123484, or unsubscribe https://github.com/notifications/unsubscribe-auth/AQH2D3HEA5U633XFR3QWLYTR4BKTPANCNFSM4OY2CIIA .

hurrialice commented 4 years ago

HI @Gtt19920502

The error message is self-explanatory. Consider revising your table by changing column names, one example table would be 

$ head /demo-mount/M2_refs/MC3.maf 
chr pos gene    ref_allele  newbase type    classification  patient
1   13308       T   G   IGR SNP 11D-09
1   13372       G   T   IGR SNP 11D-08
1   13501       G   A   IGR SNP 11D-08
1   13515       C   A   IGR SNP 01D-08
1   13516       C   A   IGR SNP 01D-08
1   13516       C   A   IGR SNP 12D-09

MutSig2CV only expects 1 column of alt allele.

julianhess commented 4 years ago

You need to add a field for the "Variant_Type," which is described here: https://docs.gdc.cancer.gov/Data/File_Formats/MAF_Format/

Gtt19920502 commented 4 years ago

Hi Julian,

Thank you very much for your reply. I get it. I'll add the "Variant_Type" and try it again.

Thanks

julianhess notifications@github.com 于2020年7月18日周六 下午8:10写道：

You need to add a field for the "Variant_Type," which is described here: https://docs.gdc.cancer.gov/Data/File_Formats/MAF_Format/

— You are receiving this because you were mentioned. Reply to this email directly, view it on GitHub https://github.com/broadinstitute/getzlab-PCAWG-MutSig2CV_NC/issues/4#issuecomment-660567379, or unsubscribe https://github.com/notifications/unsubscribe-auth/AQH2D3GTKHBNA5NYPJ3TRNDR4JBZPANCNFSM4OY2CIIA .

Gtt19920502 commented 4 years ago

Hello Qing,

Thank you very much for your reply. I get it. I'll revise it and try it again.

Thanks

qing zhang notifications@github.com 于2020年7月18日周六 下午8:06写道：

HI @Gtt19920502 https://github.com/Gtt19920502

The error message is self-explanatory. Consider revising your table by changing column names, one example table would be

$ head /demo-mount/M2_refs/MC3.maf chr pos gene ref_allele newbase type classification patient 1 13308 T G IGR SNP 11D-09 1 13372 G T IGR SNP 11D-08 1 13501 G A IGR SNP 11D-08 1 13515 C A IGR SNP 01D-08 1 13516 C A IGR SNP 01D-08 1 13516 C A IGR SNP 12D-09

MutSig2CV only expects 1 column of alt allele.

— You are receiving this because you were mentioned. Reply to this email directly, view it on GitHub https://github.com/broadinstitute/getzlab-PCAWG-MutSig2CV_NC/issues/4#issuecomment-660566859, or unsubscribe https://github.com/notifications/unsubscribe-auth/AQH2D3CMTRJSUMTFS6UX3CLR4JBKHANCNFSM4OY2CIIA .