Entering edit mode
7.4 years ago
oklagirl
•
0
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
"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...
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.
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.