Hi everyone,
I was trying to run ADMIXTURE using a merged vcf file with 82 samples. I pruned the data using a set of plink command:
plink --vcf 82_samples.vcf.gz --make-bed --double-id
plink --bfile 82_samples --indep-pairwise 50 5 0.5 --out 82_samples_pruned
plink --bfile plink --extract 82_samples_pruned.prune.in --make-bed --out 82_samples_pruned
Then I edited the .bim file ADMIXTURE does not accept chromosome names that are not human chromosomes using an awk command:
awk '{$1=0;print $0}' 82_samples_pruned.bim > 82_samples_pruned.bim.tmp
After this, I ran ADMIXTURE using k=2,3,4,5 with a for loop:
for i in {2..5}; do admixture --cv 82_samples_pruned.bed $i > log${i}.out; done
But I'm geting a Segmentation Fault error.
The log file for k=2 has the following information:
**** 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.
Size of G: 82x35511617
Can anyone help me?
Thanks in advance,
Pedro
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pmc.sa •
Hello! Maybe this little thing will be useful to someone. I also encountered a problem "Segmentation fault (core dumped)". Installing admixture32 helped me. But I didn’t immediately understand that to run version 32, the command should look like this
admixture32 hapmap3.bed 3
not
admixture hapmap3.bed 3
With best regards, Olesya
First check your syslog (might require sudo):
grep admixture /var/log/syslog
If you see something that looks like
admixture[26825] vsyscall attempted with vsyscall=none ...
Try this:
/etc/default/grub fileGRUB_CMDLINE_LINUX_DEFAULT="vga=normal nomodeset vsyscall=emulate")update-grubHello,
I encountered the same problem of getting segmentation faults only when trying to compute bootstraps with ADMIXTURE v1.30. I figured out the problem comes at least in part from chromosome names in the input files. For some reason, it seems ADMIXTURE expects chromosome names that correspond to the standard code for human karyotype. See plink doc for details.
Using admixture32 as suggested in this thread did not work for me.
I work with a fragmented assembly of >200 contigs, so I replaced my chromosome names by "fake" numbers expected for the human karyotype (1,2,3...23).
Of course this is not an ideal solution but it did the trick.
Etienne DVRK, but if you have >200 contigs how does numbers 1-23 help? What do you enter as the names for the other contigs?
Log in to answer this question.
Could it be due to memory issues. Most of time segmentation fault are related to memory issues.
Can you try these suggestions?
Hi.
I've tried running the time command but I can't seem to be able to. I'm getting the "command not found" error and I think it's because the executable either doesn't have this name or isn't there.
Check the mentioned post replies, please
Using the 32-bit version of the admixture worked for me in WSL.
Can confirm! Gihanjay you're a legend! Thank you so much!
How to change to 32 bit version? Thank you
Hi Little, sorry for the delay.
You can download the latest version of ADMIXTURE from https://github.com/NovembreLab/admixture, and then run the "admixture32" file that comes within the "admixture_linux-1.3.0" folder.
Hope it helps!
Thanks. I had this same issue while running linux ubuntu in WSL. Segmentation fault with admixture while the run is successful with admixture32.
What can be done to WSL admixture to run? I saw a suggestion below about editing the grub file. Unfortunately, I donot have grub file in etc directory.
I have re-run the analysis in linux ubuntu in virtualbox, it runs perfectly - no segmentation fault.
thank u ！！！！！！！