Error with "......too long a vector"

[gbnci]

I merged joint mutect VCF results with facets output as input for the pictograph analysis. After a few hours of running, the program stopped with error shows below:

Error in 1:K : result would be too long a vector
Calls: runMCMCForAllBoxes ... writeClusterMCFsTable -> as.data.frame -> estimateMCFs -> matrix
In addition: Warning messages:
1: In FUN(X[[i]], ...) : Failed to set trace monitor for mcf
Variable mcf not found

2: In FUN(X[[i]], ...) : Failed to set trace monitor for ystar
Variable ystar not found

3: In max(.) : no non-missing arguments to max; returning -Inf
4: In max(.) : no non-missing arguments to max; returning -Inf
Execution halted

while the same or similar errors generated for two different input files, I am wondering:

1. What is the requirement for the input file (except the specific columns, what I mean here is that whether I should remove some mutations with "0" values for some columns)?
2. For the variant calls, should I generated vcf using joint calls or it is doesn't matter?
3. What kind of trimming I should apply in order to make the input file smaller (as you know joint calls from multiple samples normally give big file)?
4. The last question is how to avoid above errors by changing some of the configurations?
   Thanks for your help

[jiaying2508]

Hi @gbnci

What is the requirement for the input file (except the specific columns, what I mean here is that whether I should remove some mutations with "0" values for some columns)?

In order to help, could you share how many samples and how many mutations you have for a file? Also are there cases where the tool would run, or do you always get this error message? When you say mutations with "0" values, is it "0" for all samples?

For the variant calls, should I generated vcf using joint calls or it is doesn't matter?

it doesn't matter.

What kind of trimming I should apply in order to make the input file smaller (as you know joint calls from multiple samples normally give big file)?

you would need to apply filtering criteria based on your samples. For example, include mutations if variant read count is at least certain number.

The last question is how to avoid above errors by changing some of the configurations?

I have never encountered the above issue, and without having the exact input files you are using, I would not be able to identify the source of error or how to fix.

I hope that helps.