Question: Error while running Beagle for imputation
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epifaniarango • 0 wrote:
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
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modified 15 months ago
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Kevin Blighe ♦ 70k
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written
15 months ago by
epifaniarango • 0
Can you verify this:
?