Entering edit mode

13 months ago

b.ambrozio
▴
20

I'm trying run BOLT-LMM against a simulated dataset, which were generated with plink --simulate, however no success:

```
./BOLT-LMM_v2.3.4/bolt --bfile=ds1_1gt10k --phenoUseFam --statsFile ds1_1gt10k.bolt --LDscoresUseChip --lmm
...
ERROR: LOCO mixed model analysis requires >= 2 chromosomes or chunks
To run this analysis, set --numLeaveOutChunks
```

The documentation don't say nothing about `numLeaveOutChunks`

parameter. I've tried some arbitrary numbers as well, and things started working, however, after some time running, it ended up with another error:

```
./BOLT-LMM_v2.3.4/bolt --bfile=ds1_1gt10k --phenoUseFam --statsFile ds1_1gt10k.bolt --LDscoresUseChip --lmm --numLeaveOutChunks=5
...
Intel MKL ERROR: Parameter 6 was incorrect on entry to DGELS .
Intel MKL ERROR: Parameter 6 was incorrect on entry to DGELS .
Intel MKL ERROR: Parameter 6 was incorrect on entry to DGELS .
Intercept of LD Score regression for ref stats: 0.000 (0.000)
Estimated attenuation: -nan (nan)
Intercept of LD Score regression for cur stats: 0.000 (0.000)
Calibration factor (ref/cur) to multiply by: -nan (nan)
Time for computing Bayesian mixed model assoc stats = 0.802051 sec
Calibration stats: mean and lambdaGC (over SNPs used in GRM)
(note that both should be >1 because of polygenicity)
Segmentation fault
```