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Rosemeis / pcangsd

Framework for analyzing low depth NGS data in heterogeneous populations using PCA.
GNU General Public License v3.0
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Segmentation fault (core dumped) #60

Closed katcatalano closed 2 years ago

katcatalano commented 2 years ago

Hi! I am have a beagle.gz file output from ANGSD, and I am running into a segmentation fault error:

pcangsd -b angsd.beagle.gz -e 2 -t 40 -o output.pcangsd 

PCAngsd v.1.10.
Jonas Meisner and Anders Albrechtsen.
Using 40 thread(s).

Parsing Beagle file.
Loaded 5886700 sites and 159 individuals.
Estimating minor allele frequencies.
EM (MAF) converged at iteration: 57
Number of sites after MAF filtering (0.05): 5886700

Estimating covariance matrix.
Using 2 principal components (manually selected).
Segmentation fault (core dumped)

I don't see any formatting issues in my input file... thank you for any ideas you might have for me to troubleshoot!

katcatalano commented 2 years ago

Running on 1 thread solved this issue, thanks!

agentzero93 commented 1 year ago

For future reference, I received this same error and running on 1 thread did not resolve this issue. Turns out I had a blank line on the end of my beagle file, once I removed it the issue was solved.