When using Refined IBD with a PLINK map file, I received the following error:
ERROR: java.lang.IllegalArgumentException: Base position exceeds Integer.MAX_VALUE
Are all genetic distances in cM units (in command line and in genetic map)?
java.lang.IllegalArgumentException: Base position exceeds Integer.MAX_VALUE
Are all genetic distances in cM units (in command line and in genetic map)?
at vcf.PlinkGenMap.basePos(PlinkGenMap.java:365)
at vcf.WindowIt$Reader.run(WindowIt.java:262)
at java.base/java.lang.Thread.run(Thread.java:835)
I'm using Windows Command Prompt.
I used the PLINK genetic map files for GCRh38 provided at the link by combining all the files into one file: http://bochet.gcc.biostat.washington.edu/beagle/genetic_maps/. The first two lines of my map files looks like this:
1 . 0 55550
1 . 0.080572 82571
I went to Disk Management to try an Extend Volume option but that option is greyed out for C:.
How do I correct for this error?
•
written
by
LTDavid •
Integer.MAX_VALUE is a Java-internal hard-coded value, googling around it should be 2,147,483,647 on most systems - do you have base positions larger than that?
No, I don't think I have base positions larger than that. My last line in my map file is this:
X . 180.837755 155699751
In the Refined IBD output, the following shows up:
Window 110 (X:37291432-93947399)
Then the error message posted in my original question followed by:
terminating program.
Window 111 (X:88981597-124619638)
And then the program ends.
Log in to answer this question.
Added
plinktag to your question