This is a test version of Biostars. For the public version, visit https://www.biostars.org.
Admixture - Abort trap: 6

I have just installed Admixture, and it fails to run on my data files, giving the following output:

ou056055:public veaan84p$ ./admixture --cv public.mm.bysubspecies.bed 5 * ADMIXTURE Version 1.3.0 * * Copyright 2008-2015 * * David Alexander, Suyash Shringarpure, * * John Novembre, Ken Lange * * * * Please cite our paper! * * Information at www.genetics.ucla.edu/software/admixture *

Cross-validation will be performed. Folds=5. Random seed: 43 Point estimation method: Block relaxation algorithm Convergence acceleration algorithm: QuasiNewton, 3 secant conditions Point estimation will terminate when objective function delta < 0.0001 Estimation of standard errors disabled; will compute point estimates only. Abort trap: 6

It does run on the hapmap3 file provided, but not on my plink input files. I do not have a .map file in the directory, but this should not be required for a .bed file. I do have the .bim and .fam files in the directory.

Any ideas would be greatly appreciated.

Thanks!

software error
• 5,011 views • link
updated by beausoleilmo beausoleilmo • written by Andrew Veale • Andrew Veale

2 answers

"Abort trap: 6" usually means a buffer overflow or other memory management bug: the program is perhaps trying to read from or write to memory it doesn't own. I'd suggest contacting the developers.

• 0 views • link
written by Alex Reynolds Alex Reynolds

In my case, it was because the chromosome names, in the .bim file, were not supported by ADMIXTURE. 

# Make the first column a bunch of zeros.
awk '{$1=0;print $0}' public.mm.bysubspecies.bim > public.mm.bysubspecies.bim.tmp
# Rename the .bim file 
mv public.mm.bysubspecies.bim.tmp public.mm.bysubspecies.bim

Then run the command:

./admixture --cv public.mm.bysubspecies.bed 5
• 0 views • link
written by beausoleilmo beausoleilmo

Log in to answer this question.

More posts like this