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runtime error in LDhat
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18 months ago
prasundutta87 • 330

Hi,

I got a runtime error while running LDhat 'pairwise' program. I need some help to understand the issue so that I can take care of it. The command was:

pairwise -seq chr1.ldhat.sites -loc chr1.ldhat.locs -lk ../new_lk.txt

The error:

Run-time error

allocation failure 2 in imatrix()

On checking the error on github, I found it in this piece of code, but am unable to understand it: https://github.com/auton1/LDhat/blob/master/tools.c

To give a little background, I am working with water buffalo and have 79 samples. In order to generate a look-up table, I downloaded human-centric lookup table 'lk_n192_t0.001' from LDhat github website and used to lkgen program for generating look-up table for my species using the following command:

lkgen lk_n192_t0.001 -nseq 158

I used the generated look-up table on the 'pairwise' program. My final aim is to generate recombination maps for my species that can be used in iHS analysis downstream.

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