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Hi

I am frequently running into a problem with Obtain_rank_score.R where the script crashes giving exit code 255 and error message below.

assertion !pthread_create(&thr->thrH, &attr, rout, arg) failed, line 119 of file /mnt/storage/home/XXXX/scratch/R-Lang/ATLAS-Build/../ATLAS//src/threads/ATL_thread_start.c

When I re-run the command with the same arguments all works fine so I know it is not the data but seems to be something with multithreading?

Here is the command

Rscript ~/apps/QUAIL/Obtain_rank_score.R --pheno data/phenotypes_quail_pheno.txt --covar data/phenotypes_quail_covar.txt --output data/pheno_rank_score.txt --num_levels 2000 --num_cores 1

Any ideas how to fix?

Thanks
Matt

Hello. I'm having trouble running T1E and power tests with QUAIL.

I've simulated data to test T1E in which there is a main genetic effect, but no variance effect:

I've also simulated data to test power in which there is a genetic effect, an environmental effect, and an interaction effect (w):

My problem seems to occur in the covariate file, which is required in the code or it will throw an error. In this simulated data I don't have any covariates I want to adjust for, so I've tried 1) including only the ID columns (this throws an error), 2) including a dummy covariate with only values of "1",

and 3) including a dummy covariate with values of "1" and changing the equation
in the Obtain_rank_score.R script to
. None of these options give me proper T1E and power results.

Can you please help me find the proper setup for the situation in which there are no covariates?
Thanks, Aubrey

p.s. I have tested the same data with other methods (though without the covariate file since they do not require one), and the T1E and power results are as expected. This confirms to me that the problem is with the covariate file.