I'm having a problem calculating delta K with the admixture32 pipeline on my RADseq data generated by STACKS.
Here is the command I use:
#!/bin/bash
#SBATCH -J mpi_job
#SBATCH --nodes=1
#SBATCH --time=80:00:00
#SBATCH --cpus-per-task=10
#SBATCH --mem=20G
for K in 4 5; \
do /usr/local/bioinfo/src/ADMIXTURE/admixture_linux-1.3.0/admixture32 --cv /home/groux/work/populations_48.bed $K -j1 | tee log${K}.out; done
and here is the log obtained :
**** ADMIXTURE Version 1.3.0 ****
**** Copyright 2008-2015 ****
**** David Alexander, Suyash Shringarpure, ****
**** John Novembre, Ken Lange ****
**** ****
**** Please cite our paper! ****
**** Information at www.genetics.ucla.edu/software/admixture ****
Cross-validation will be performed. Folds=5.
Parallel execution requested. Will use 2 threads.
Random seed: 43
Point estimation method: Block relaxation algorithm
Convergence acceleration algorithm: QuasiNewton, 3 secant conditions
Point estimation will terminate when objective function delta < 0.0001
Estimation of standard errors disabled; will compute point estimates only.
Size of G: 133x5009874
Performing five EM steps to prime main algorithm
1 (EM) Elapsed: 15.909 Loglikelihood: -7.33575e+07 (delta): 5.53733e+07
2 (EM) Elapsed: 15.246 Loglikelihood: -6.91772e+07 (delta): 4.18036e+06
3 (EM) Elapsed: 15.131 Loglikelihood: -6.74197e+07 (delta): 1.75748e+06
4 (EM) Elapsed: 15.221 Loglikelihood: -6.62251e+07 (delta): 1.19455e+06
5 (EM) Elapsed: 15.182 Loglikelihood: -6.53358e+07 (delta): 889323
Initial loglikelihood: -6.53358e+07
Starting main algorithm
1 (QN/Block) Elapsed: 45.736 Loglikelihood: -6.24718e+07 (delta): 2.86401e+06
terminate called after throwing an instance of 'std::bad_alloc'
what(): std::bad_alloc
**** ADMIXTURE Version 1.3.0 ****
**** Copyright 2008-2015 ****
**** David Alexander, Suyash Shringarpure, ****
**** John Novembre, Ken Lange ****
**** ****
**** Please cite our paper! ****
**** Information at www.genetics.ucla.edu/software/admixture ****
Cross-validation will be performed. Folds=5.
Parallel execution requested. Will use 2 threads.
Random seed: 43
Point estimation method: Block relaxation algorithm
Convergence acceleration algorithm: QuasiNewton, 3 secant conditions
Point estimation will terminate when objective function delta < 0.0001
Estimation of standard errors disabled; will compute point estimates only.
Size of G: 133x5009874
Performing five EM steps to prime main algorithm
1 (EM) Elapsed: 18.231 Loglikelihood: -7.30901e+07 (delta): 5.31587e+07
2 (EM) Elapsed: 17.638 Loglikelihood: -6.8697e+07 (delta): 4.39313e+06
3 (EM) Elapsed: 17.708 Loglikelihood: -6.68036e+07 (delta): 1.89339e+06
4 (EM) Elapsed: 17.788 Loglikelihood: -6.54971e+07 (delta): 1.30655e+06
5 (EM) Elapsed: 17.843 Loglikelihood: -6.4523e+07 (delta): 974028
Initial loglikelihood: -6.4523e+07
Starting main algorithm
terminate called after throwing an instance of 'std::bad_alloc'
what(): std::bad_alloc
Do you have any idea what the problem is and how to solve it?
Thank you and have a nice day
Loïs
