Post by jonmee on Jun 20, 2019 15:55:20 GMT
Hi.
I'm using gcta --mlma for the first time. I'm running this on a research cluster with slurm. I've used --make-grm to successfully create a GRM, and the --mlma command seems to be working fine up to the point where it tries to run the association test, which is when I get a segmentation fault error.
Here's my bash code:
#!/bin/bash
#SBATCH --time=00:30:00
#SBATCH --mem=2G
#SBATCH --output=gcta_mlma_%j.out
#SBATCH --job-name=gcta_mlma
module load nixpkgs/16.09 intel/2018.3
module load gcta/1.26.0
echo "Starting run at: `date`
gcta64 --mlma --bfile culaea_ts_filtered_snps_pheno --grm culaea_ts_filtered_snps_pheno_pruned --pheno culaea_ts_filtered_snps_pheno_pruned.phen --reml-alg 1 --out culaea_ts_gwas
echo "Program finished with exit code $? at: `date`"
Here's the output with the error message:
Performing MLM association analyses (including the candidate SNP) ...
Performing REML analysis ... (Note: may take hours depending on sample size).
39 observations, 1 fixed effect(s), and 2 variance component(s)(including residual variance).
Calculating prior values of variance components by EM-REML ...
Updated prior values: 0.112607 0.122778
logL: -1.87294
Running Fisher-scoring ... ...
Iter. logL V(G) V(e)
1 -1.46 0.00000 0.25226 (1 component(s) constrained)
2 5.02 0.00000 0.27661 (1 component(s) constrained)
3 4.97 0.00000 0.27661 (1 component(s) constrained)
4 4.97 0.00000 0.27661 (1 component(s) constrained)
Log-likelihood ratio converged.
Calculating allele frequencies ...
Running association tests for 927 SNPs ...
/var/spool/slurmd/job16204844/slurm_script: line 17: 19669 Segmentation fault (core dumped)
And the report on resource usage for the job (from seff):
State: COMPLETED (exit code 0)
Cores: 1
CPU Utilized: 00:00:01
CPU Efficiency: 20.00% of 00:00:05 core-walltime
Job Wall-clock time: 00:00:05
Memory Utilized: 788.00 EB
Memory Efficiency: 0.04% of 2.00 GB
Do you know what might be causing the segmentation fault? Any help would be greatly appreciated.
All the best,
jon
I'm using gcta --mlma for the first time. I'm running this on a research cluster with slurm. I've used --make-grm to successfully create a GRM, and the --mlma command seems to be working fine up to the point where it tries to run the association test, which is when I get a segmentation fault error.
Here's my bash code:
#!/bin/bash
#SBATCH --time=00:30:00
#SBATCH --mem=2G
#SBATCH --output=gcta_mlma_%j.out
#SBATCH --job-name=gcta_mlma
module load nixpkgs/16.09 intel/2018.3
module load gcta/1.26.0
echo "Starting run at: `date`
gcta64 --mlma --bfile culaea_ts_filtered_snps_pheno --grm culaea_ts_filtered_snps_pheno_pruned --pheno culaea_ts_filtered_snps_pheno_pruned.phen --reml-alg 1 --out culaea_ts_gwas
echo "Program finished with exit code $? at: `date`"
Here's the output with the error message:
Performing MLM association analyses (including the candidate SNP) ...
Performing REML analysis ... (Note: may take hours depending on sample size).
39 observations, 1 fixed effect(s), and 2 variance component(s)(including residual variance).
Calculating prior values of variance components by EM-REML ...
Updated prior values: 0.112607 0.122778
logL: -1.87294
Running Fisher-scoring ... ...
Iter. logL V(G) V(e)
1 -1.46 0.00000 0.25226 (1 component(s) constrained)
2 5.02 0.00000 0.27661 (1 component(s) constrained)
3 4.97 0.00000 0.27661 (1 component(s) constrained)
4 4.97 0.00000 0.27661 (1 component(s) constrained)
Log-likelihood ratio converged.
Calculating allele frequencies ...
Running association tests for 927 SNPs ...
/var/spool/slurmd/job16204844/slurm_script: line 17: 19669 Segmentation fault (core dumped)
And the report on resource usage for the job (from seff):
State: COMPLETED (exit code 0)
Cores: 1
CPU Utilized: 00:00:01
CPU Efficiency: 20.00% of 00:00:05 core-walltime
Job Wall-clock time: 00:00:05
Memory Utilized: 788.00 EB
Memory Efficiency: 0.04% of 2.00 GB
Do you know what might be causing the segmentation fault? Any help would be greatly appreciated.
All the best,
jon