Saving results... Reference to non-existent field 'longname'.

[yusufdjuanda]

Hi getzlab team,

I ran the MutSigCV2 for the hg38 samples with the following command:

bin/MutSig2CV ${MAF_FILE} ${OUTPUT_DIR} params.txt

The params.txt follows the default params for hg38 with a caveat. I changed the file name of hg38 to hg19 default file (e.g., from "target_list.gencode25.txt" to "reference/target_list.hg19.v1a.txt" for target list file) this is because I had a problem when specifying file in the params.txt

I got the significant genes. However, the running is not 100% complete and it gave some errors:

## Multiple genes gave the same error
Operands to the || and && operators must be convertible to logical scalar values.
ERROR with gene ZZEF1
  MException with properties:

    identifier: 'MATLAB:nonLogicalConditional'
       message: [1x81 char]
         cause: {}
         stack: [2x1 struct]

Operands to the || and && operators must be convertible to logical scalar values.
ERROR with gene ZZZ3
  MException with properties:

    identifier: 'MATLAB:nonLogicalConditional'
       message: [1x81 char]
         cause: {}
         stack: [2x1 struct]
         
         
         Saving results... Reference to non-existent field 'longname'.

Error in getfield (line 37)

Error in keep_fields (line 16)

Error in MutSig_2CV_v3_11_core (line 1178)

Error in MutSig_2CV_v3_11_wrapper (line 51)

MATLAB:nonExistentField

I have all the output file except the per_gene.mutation_counts.txt. So my questions are:

1. I am wondering if the output of the significant genes is valid and how I can troubleshoot the error shown.
2. Additionally, I am wondering why in hg38, the skip permutations is set to True

Thanks in advance!

[vmelichar]

Hi, I am just joining the thread since I have the exact same issue and exact same questions.

Thanks for any clarification.

[lypeng7]

Hi, I hope you're doing well. I saw your issue regarding MutSig2CV, and I was wondering if you were able to resolve it? I'm currently facing the same problem while processing hg19 results using MutSig2CV. My command is: bin/MutSig2CV ${MAF_FILE} ${OUTPUT_DIR}