search

precimed / mixer

Causal Mixture Model for GWAS summary statistics
GNU General Public License v3.0
59 stars 17 forks source link

Initialisation of Library Issue #69

Closed alterecho11 closed 1 year ago

alterecho11 commented 1 year ago

Hello,

When I try to run my sbatch script (as adapted from saga_ugmg_script.sh), I get the following slurm error:

.

Can you please help me with this?

ofrei commented 1 year ago

@alterecho11 thanks for reporting this! It seems you've built mixer plugin locally. An alternative that's now recommended is to use MiXeR packaged into a singularity container, as described here https://github.com/comorment/mixer .Do you have Singularity software available on your HPC environment? Please try instructions provided here https://github.com/comorment/mixer/blob/main/usecases/mixer_simu.md or here https://github.com/comorment/mixer/blob/main/usecases/mixer_real.md

alterecho11 commented 1 year ago

Hello,

Thank you for your reply! UT HPC wonder-makers have successfully installed singularity, but it seems that the mixer.sif file is corrupted...

When I run singularity shell --home $PWD:/home $SIF/mixer.sif, I got the message FATAL: While checking container encryption: could not open image /.../mixer.sif: image format not recognized

Could you please double-check this?

I have downloaded hello.sif for test, and that one seems okay.

$ file mixer.sif
mixer.sif: ASCII text
$ file hello.sif
hello.sif: a /usr/bin/env run-singularity script executable (binary data)
alterecho11 commented 1 year ago

Eh, solved it with git lfs.

Thank you for all the answers! (o•ᴗ•o)