Error while running Beagle for imputation
0
0
Entering edit mode
5.6 years ago

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

snp vcf Beagle software error genome • 1.1k views
ADD COMMENT
0
Entering edit mode

Can you verify this:

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

?

ADD REPLY

Login before adding your answer.

Traffic: 2508 users visited in the last hour
Help About
FAQ
Access RSS
API
Stats

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.

Powered by the version 2.3.6