mixer

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Hello, thank you for developing mixer! I've sucessfully run fit1, fit2 and the bivariate analysis. However, i've encuntered a RuntimeWarning such as this: ``` /home/nico/mixer/mixer/precimed/mixer/utils.py:894: RuntimeWarning: divide by zero encountered...

NicolasC0

Segmentation fault (core dumped)

1

I am currently going through the MiXeR tutorial, which I plan to implement in my current study. When I ran the python mixer.py ld and python mixer.py snp codes to...

olasunkanmibamidele

RuntimeError: runtime_error: arg <= 0

3

Does anyone know why this error occurs and how to fix it？ Traceback (most recent call last): File "/home/lilab/software/mixer-master/precimed/mixer.py", line 23, in args.func(args) File "/home/lilab/software/mixer-master/precimed/mixer/cli.py", line 647, in execute_fit1_or_test1_parser results...

1999yangyi

mixer.py fit2 hanging on calc_unified_bivariate_pdf

1

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...

EleniFri

power plot is blank and throws a warning

1

python /media/drive12TB1/projects/software/mixer/mixer/precimed/mixer_figures.py \ one \ --json results_mixer/EUR_ancestry_subjects_results_maf_0.01_univariate_mixer_qc_noMHC.fit.json \ --out images/EUR_ancestry_subjects_results_maf_0.01_univariate_mixer_qc_noMHC.fit \ --statistic mean std The power plot is blank and throws a warning. The *power.csv file has results that look...

bardmaker

Hi, As per the title, this is a question rather than an 'issue'. I am running MiXeR v1.3 with Singularity for a bivariate analysis with two GWAS studies. One of...

yunkaig

Issue on ${SLURM_ARRAY_TASK_ID}

2

Hi, There is no SLURM on our linux server, thus , I changed the code as follows: for i in $(seq 1 20); do cmd="anaconda/anaconda3/envs/python3.8.8/bin/python3.8 mixer/mixer-master/precimed/mixer.py snps --lib mixer/mixer-master/src/build/lib/libbgmg.so --bim-file...

shenlan17

Fixes #58

espenhgn

https://github.com/comorment/mixer refers to commit 2b5ad6b2d9ab5b92d8dd24ec106338af61e27a80 as version v1.3/v1.3.0 (in [install_mixer.sh](https://github.com/comorment/mixer/blob/main/src/scripts/install_mixer.sh)), but this tag/release is missing here. These should be added.

espenhgn

mixer_figures.py combine: numpy.linalg.LinAlgError: singular matrix

6

Hi, I tried to run bivariate analysis for multiple traits with MiXeR. One of the bivariate analyses fialed to produce results with the error meaasge "numpy.linalg.LinAlgError: singular matrix". No error...

Huifang-Xu