mixer.py fit2 hanging on calc_unified_bivariate_pdf

[EleniFri]

Hi,

I have successfully run ld, snp, fit1 and test1 with SLURM, but when I try to run the mixer.py fit2 command, the script runs normally for 7 hours and then appears stuck for the rest of the 24h on the first line of calc_unified_bivariate_pdf in the log file.
My script is:

#!/bin/bash
#SBATCH --job-name=qqMDDSCZfit2
#SBATCH --time=24:00:00
#SBATCH --partition=pi_polimanti,scavenge,day,week
#SBATCH --cpus-per-task=48
#SBATCH --mem-per-cpu=5G
#SBATCH --nodes=1
#SBATCH --array=1-20
#SBATCH --requeue

module load miniconda
cd /home/userid/
conda activate mixer
cd mixer/
module load GCCcore/10.2.0
module load Boost/1.71.0-GCC-10.2.0 CMake

python3 precimed/mixer.py fit2
--trait1-file prepped_sumstats/MDD_noMHC.csv
--trait2-file prepped_sumstats/SCZ_noMHC.csv
--trait1-params-file fit1/MDD.fit.rep${SLURM_ARRAY_TASK_ID}.json
--trait2-params-file fit1/SCZ.fit.rep${SLURM_ARRAY_TASK_ID}.json
--out fit2/MDD_SCZ.fit.rep${SLURM_ARRAY_TASK_ID}
--extract ~/1000G_EUR_Phase3_plink/1000G.EUR.QC.prune_maf0p05_rand2M_r2p8.rep${SLURM_ARRAY_TASK_ID}.snps
--bim-file ~/1000G_EUR_Phase3_plink/1000G.EUR.QC.@.bim
--ld-file ~/1000G_EUR_Phase3_plink/1000G.EUR.QC.@.run4.ld
--lib src/build/lib/libbgmg.so
--qq-plots
--power-curve

##############################################################################################

MDD_noMHC.csv and SCZ_noMHC.csv were prepared using the sumstats.py command and fit1 ran smoothly.
I added --qq-plots and --power-curve because when I tried to do the figures for the univariate models, an error was produced suggesting I added those two flags.

I also tried the same code adding --threads 48, but nothing changed.

Any ideas what the problem could be?

Thank you

[biomguler]

Hi Eleni,
I have the same issue; did you find any solutions?
Best,
Murat