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precimed / mixer

Causal Mixture Model for GWAS summary statistics
GNU General Public License v3.0
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Segmentation fault (core dumped) #93

Open olasunkanmibamidele opened 2 months ago

olasunkanmibamidele commented 2 months ago

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 generate.ld and.snp files, I kept on getting "segmentation fault (core dump)". I am new to statistical genetics studies, and I am not very good at writing codes or interpreting codes appropriately.

I would appreciate it if anyone on this platform could help me resolve this. It is putting a stop to my progress in my research;

Below are the scripts and the output for scrutiny and possible solutions.

python3 ~/my_data/MiXeR/precimed/mixer.py ld \
+    --lib ~/my_data/MiXeR/src/build/lib/libbgmg.so \
+    --bfile ~/my_data/MiXeR/python_convert/PLINK/1000G.EUR.QC.1.bim \
+    --out ~/my_data/MiXeR/python_convert/PLINK/1000G.EUR.QC.1.bim.run4.ld \
+    --r2min 0.05 --ldscore-r2min 0.05 --ld-window-kb 30000
INFO:root:__init__(lib_name=/home/my_data/MiXeR/src/build/lib/libbgmg.so, context_id=0)
INFO:root:init_log(/home/my_data/MiXeR/python_convert/PLINK/1000G.EUR.QC.1.bim.run4.ld.log)
INFO:root:log_message(***********************************************************************
* mixer.py: Univariate and Bivariate Causal Mixture for GWAS
* Version 1.2.0
* (c) 2016-2020 Oleksandr Frei, Alexey A. Shadrin, Dominic Holland
* Norwegian Centre for Mental Disorders Research / University of Oslo
* Center for Multimodal Imaging and Genetics / UCSD
* GNU General Public License v3
***********************************************************************
Call:
./mixer.py ld \
        --out /home/my_data/MiXeR/python_convert/PLINK/1000G.EUR.QC.1.bim.run4.ld \
        --lib /home/my_data/MiXeR/src/build/lib/libbgmg.so \
        --bfile /home/my_data/MiXeR/python_convert/PLINK/1000G.EUR.QC.1.bim \
        --ldscore-r2min 0.05 \
        --ld-window-kb 30000.0
)
INFO:root:__init__(lib_name=/home/my_data/MiXeR/src/build/lib/libbgmg.so, context_id=0)
Segmentation fault (core dumped)
espenhgn commented 1 month ago

Hi @olasunkanmibamidele. This could be a duplicate of https://github.com/precimed/mixer/issues/48.

Also, issues with the /build/lib/libbgmg.so extension may be solved by the container build at https://github.com/comorment/mixer. But you need a machine/HPC resource with Apptainer alternatively Singularity, or Docker. The latter may use these images but I've yet to write proper documentation for it (but should work on M1/M2 Macs with the platform=linux/amd64 option)