*** caught segfault *** address cause 'invalid permissions'

[SamMod1]

Hello,

Me and a college are trying to run rMVP on a cluster, however we keep getting segmentation fault during the MVP.Data() run:

MVP.Data(fileVCF=genotype_vcf,
         filePhe=phenotype,
         fileKin=FALSE,
         filePC=FALSE,
         sep.phe="\t",
         ncpus=1,
         out=output
)

The function does generate output before it errors, it generates output.geno.bin, output.geno.desc and output.geno.map, however not output.phe. Furthermore, while most of these files do appear to have output, the output.geno.bin file, while it does have content it seems to be just filled with zeros. When I try to run MVP() on this output it errors saying "NA is not allowed in genotype, use 'MVP.Data.impute' to impute.". However, I am thinking this may be related to the failure of MVP.Data() to run successfully.

Here is the full output MVP.Data() generates:

Full description, Bug report, Suggestion and the latest version:
https://github.com/xiaolei-lab/rMVP
[1] "phenotype.tab"
[1] "modified.recode.vcf"
[1] "rMVP/snapper_sd"
Preparing data for MVP...
Reading file...
inds: 12 markers: 5025424
Loading genotype at a step of 10000...
0% 10 20 30 40 50 60 70 80 90 100%
[----|----|----|----|----|----|----|----|----|----|

*** caught segfault ***
address 0x1538b97f5aa0, cause 'invalid permissions'

Traceback:
1: vcf_parser_genotype(vcf_file = vcf_file, pBigMat = bigmat@address, maxLine = maxLine, threads = threads, verbose = verbose)
2: MVP.Data.VCF2MVP(vcf_file = fileVCF, out = out, verbose = verbose, threads = ncpus)
3: MVP.Data(fileVCF = genotype_vcf, filePhe = phenotype, fileKin = FALSE, filePC = FALSE, sep.phe = "\t", ncpus = 1, out = output)
An irrecoverable exception occurred. R is aborting now ...
/var/spool/slurmd/job8190498/slurm_script: line 4: 637543 Segmentation fault (core dumped) Rscript init_vcf_data.R phenotype.tab modified.recode.vcf rMVP/snapper_sd

[SamMod1]

It seems like this might be an issue with our computer cluster.