Question: Allocation error from PolyRelatedness
gravatar for lovestowell
3.8 years ago by
United States
lovestowell10 wrote:

Anyone out there using PolyRelatedness? I have 1000s of SNPs from 16 individuals and I would like to calculate pairwise relatedness. I'm looking for a relatedness estimator that allows for both polyploidy and inbreeding. When I run PolyRelatedness I get an error and I'm not sure what's causing it. Any help would be appreciated!

I am running Ubuntu 14.04.3 on a Dell PowerEdgeT620. I have 16 individuals and 5000-9000 SNPs (depending on filtering).

I tried to run PolyRelatedness like this:

~/polyrelatedness-master/PolyRelatedness-1.6$ ./PolyRelatedness.out myinfile.txt myoutfile.txt e 1 0

This returns an error:
terminate called after throwing an instance of 'std::bad_alloc'
  what():  std::bad_alloc
Aborted (core dumped)

The top of myinfile.txt looks like this:
//#alleledigits(1~4)    #outputdigits(0~10)    #missingallele    #ambiguousallele    #nthreads(1~64)
3    6    000    999    10
Ind Pop 1 2 3 4 5 6 7 8 9 10 11 12 13 14 [...]
CAR_F1 car  130130 100100 100100 110110 110100 110120 130120 [...]
//end of file

ADD COMMENTlink written 3.8 years ago by lovestowell10
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