GLUE Error in bash

Screenshot 2023-11-14 at 5 43 08 PM

I have just configured the conda and when I try to run evaluation on GPU, I get the following error.

Your guidance in resolving this issue will be highly appreciated and if you guide me to run only GLUE or 2,3 methods instead of all. I tried to comment on other methods in the config file but seems like it's not working.

Thanks

Nov 14 '23 08:11 Khalid-Usman

Hi @Khalid-Usman! Which lines did you comment out in the config file? There are multiple types of benchmarks in the config file, you may try commenting out all but one benchmark (https://github.com/gao-lab/GLUE/blob/fc6c2093ecc218e686586eb5fd4ea5f3e7a87e13/evaluation/config/config.yaml#L182-L333), and then removing all but 2-3 methods in that benchmark.

Nov 16 '23 05:11 Jeff1995

@Jeff1995 , I comment out two datasets and all the methods except GLUE, UnionCom, and Harmony. Still it showing me the above attached error.

Nov 16 '23 17:11 Khalid-Usman

Oh that should be a problem with the snakemake profile. Unless you are using a slurm cluster, the local profile should be used:

snakemake -j32 --profile profiles/local  # On local server

Nov 22 '23 08:11 Jeff1995

@Jeff1995 I have modified the attached two files, please let me know if I am supposed to change other files, like GLUE -> evaluation -> workflow -> methods.smk or another file to run the code successfully.

config.docx display.docx

Dec 02 '23 04:12 Khalid-Usman

@Jeff1995 When I run the following command after the above configurations. I got the error as attached.

GLUE_Error