Question: Error in Geneland
gravatar for oklagirl
4.0 years ago by
oklagirl0 wrote:

Hello, I have used Geneland in R in the past with no issues. I am working on a SNP dataset of approximately 35,353 SNPs. I have run these SNPs through Geneland using the MCMC function with no issues. When I try to run the PostProcessChain function, I get the Fortran runtime error below. I have used used the same scripts I used with dataset with a much smaller subset of the dataset and everything ran fine. I have received this error running R in both Linux and Windows. Does anyone have any advice?

Error: Read 625 items [1] "Iteration with highest posterior density: 70" [1] "Calling Fortran function postprocesschain2" At line 12379 of file main.f (unit = 13, file = '/scratch/mtrope/Geneland_bald1/frequencie$ Fortran runtime error: End of file

snp geneland • 1.5k views
ADD COMMENTlink written 4.0 years ago by oklagirl0

"Error in Geneland" sounds like such an amazing title for a bioinformatics docu-soap. I'm so disappointed.

I would recommend checking line 12379 of the file to check if something is odd there...

ADD REPLYlink written 4.0 years ago by WouterDeCoster44k

Thanks for the reply. That file is installed on installation. I have searched for the path that it was installed on and I cannot actually find the file but I can see that it gets installed when I install Geneland if I watch the installation in the R window. It works fine in other analyses. I am wondering if this is some sort of memory error, but I am not overly familiar with Fortran errors so I am not sure. This is actually the first one I have received. I have extensively looked on the internet and I have not come up with anything.

ADD REPLYlink written 4.0 years ago by oklagirl0

Perhaps you should then monitor the memory usage to find out if it's indeed a memory issue. My knowledge of fortran is non-existent, so I can't give more specific help.

ADD REPLYlink written 4.0 years ago by WouterDeCoster44k
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