Question: "ERROR:...Base position exceeds Integer.MAX_VALUE" using Refined IBD with map file
0
gravatar for LTDavid
12 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 • 336 views
ADD COMMENTlink modified 12 months ago by Philipp Bayer6.7k • written 12 months ago by LTDavid20

Added plink tag to your question

ADD REPLYlink written 12 months ago by Kevin Blighe63k
0
gravatar for Philipp Bayer
12 months ago by
Philipp Bayer6.7k
Australia/Perth/UWA
Philipp Bayer6.7k 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 12 months ago by Philipp Bayer6.7k

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 12 months ago • written 12 months ago by LTDavid20

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

ADD REPLYlink written 9 months ago by nchuang210
Please log in to add an answer.

Help
Access

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 2.3.0
Traffic: 1491 users visited in the last hour