Question: "ERROR:...Base position exceeds Integer.MAX_VALUE" using Refined IBD with map file
0
gravatar for LTDavid
3 months ago by
LTDavid20
LTDavid20 wrote:

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?

plink refined-ibd map beagle • 176 views
ADD COMMENTlink modified 3 months ago by Philipp Bayer6.5k • written 3 months ago by LTDavid20

Added plink tag to your question

ADD REPLYlink written 3 months ago by Kevin Blighe51k
0
gravatar for Philipp Bayer
3 months ago by
Philipp Bayer6.5k
Australia/Perth/UWA
Philipp Bayer6.5k wrote:

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?

ADD COMMENTlink written 3 months ago by Philipp Bayer6.5k

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.

ADD REPLYlink modified 3 months ago • written 3 months ago by LTDavid20

Did you figure this out? I'm having the same error with beagle

ADD REPLYlink written 15 days ago by nchuang200
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