Error while running Beagle for imputation

Question

[epifaniarango]

Hi everyone!

I am trying to run Beagle for imputation. My script is this one:

java -jar $Beagle_jar gt=/srv/kenlab/epifania/GelatoHO_dataset/GelatoHO_by_chr/GelatoHO_1.vcf.gz ref=/srv/kenlab/epifania/GelatoHO/phased_no_ref_panel/phased_no_ref_panel_1.filterNOalt.vcf map=/srv/kenlab/epifania/GelatoHO_dataset/GelatoHO_by_chr/GelatoHO_1.map out=/srv/kenlab/epifania/GelatoHO/imputed_no_ref_panel/GelatoHO_imputed_no_ref_panel_chr21 impute=true nthreads=8

and it gives me this 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.lang.Thread.run(Thread.java:745)

I have tried to use flags like IllegalArgumentException: NaN and -Xss5m but it is not working. Do you have any clue of what I could use?

Thank you

[Kevin Blighe]

Can you verify this:

Are all genetic distances in cM units (in command line and in genetic map)?

?