Error in binom.test_snp function

[kgaonkar6]

Hello,

Thank you developing this useful tool. I was able to run the example maf file successfully by downloading the GRCH37 fasta file however when I try to run the hotspot script by giving the my own data:
./hotspot_algo.R --input-maf=data_ext_mut.maf --rdata=hotspot_algo.Rdata --output-file=data_hotspot.maf

I get the following log and error:

No q-value entered. Using default q-value cut-off, 0.01
Using: HOMOPOLYMER_FILTER

Reading in MAF...
Prepping MAF for analysis ...
... Reducing MAF to protein-coding substitutions
... Re-annotating substitutions
... Removing putative germline SNPs based on ExAC r0.2
... Removing unexpressed genes
... Ignoring non-SNP mutations
... Making bed file
... Getting regions
WARNING. chromosome (GL000219.1) was not found in the FASTA file. Skipping.
WARNING. chromosome (GL000219.1) was not found in the FASTA file. Skipping.
WARNING. chromosome (GL000193.1) was not found in the FASTA file. Skipping.
... Adding trinucs (normalized to start from C or T)
... Writing to ___temp_maf-tri.tm
... Cleaning up

Finished prepping MAF!
Running algorithm...
Error in rep(1, aa.length - length(pval)) : invalid 'times' argument
Calls: lapply -> lapply -> FUN
Execution halted

Further investigation of the code seems to indicate the error is from the binom.test_snp function but I am not sure why I'm getting it. How do I got about identifying part that seems to break and resolve this issue?

Thanks,
Krutika

[ckandoth]

This could happen if your MAF incorrectly has Variant_Type==SNP for something that changes more than 1 amino-acid. Please limit your MAF to just SNPs and try this again.