Hi many thanks for your reply. the message error was : at beagleutil.a.<init>(Unknown Source) at beagleutil.c.b(Unknown Source) at beagleutil.c.next(Unknown Source) at beagleutil.Gprobs2Beagle.main(Unknown Source)

we got this error after running the script blow:

ls *.gen.gz | sed 's/.gen.gz//g' > FileList.tmp cat FileList.tmp | while read line do inputgen=$line".gen.gz" inputsample=$line".sample" outputname=$line".call" echo "Processing : "$inputgen echo "Transforming sample : "$inputsample cut -d" " -f2 $inputsample | sed '1,2d' > Gensamp1.tmp echo "Marker" > Gensamp2.tmp echo "Allele1" >> Gensamp2.tmp echo "Allele2" >> Gensamp2.tmp cat Gensamp1.tmp | while read twoline do echo $twoline >> Gensamp2.tmp echo $twoline >> Gensamp2.tmp echo $twoline >> Gensamp2.tmp done cat Gensamp2.tmp | tr '\n' ' ' > Genfile.tmp echo "" >> Genfile.tmp gzip -dc $inputgen | cut -d" " -f2,4- >> Genfile.tmp echo "Calling : "$inputgen cat Genfile.tmp | java -jar gprobs2beagle.jar 0.34 0 > $outputname echo "Compressing : "$outputname gzip $outputname rm Genfile.tmp rm Gensamp?.tmp done rm FileList.tmp

may be we need to install some source code, if yes how please? or the error come also from the scipr itself because when I checked the Genfile.tmp file I found that only the first line was good with marker name followed by allele 1 and 2 then the probabilities but for the third line there is the chr number folowed by position then alleles and prob as shown in this example: Marker Allele1 Allele2 1 1 1 2 2 2 rs3802985 C T 1 0 0 1 0 0 1 0 11 2 G A 0.939588 0.059824 0.000588 0.978112

thanks a lot for your help

enter code here
ls *.gen.gz | sed 's/.gen.gz//g' > FileList.tmp
cat FileList.tmp | while read line
do
inputgen=$line".gen.gz"
inputsample=$line".sample"
outputname=$line".call"
echo "Processing : "$inputgen
echo "Transforming sample : "$inputsample
cut -d" " -f2 $inputsample | sed '1,2d' > Gensamp_1.tmp
echo "Marker" > Gensamp_2.tmp
echo "Allele1" >> Gensamp_2.tmp
 echo "Allele2" >> Gensamp_2.tmp
cat Gensamp_1.tmp | while read twoline
do
echo $twoline >> Gensamp_2.tmp
echo $twoline >> Gensamp_2.tmp
echo $twoline >> Gensamp_2.tmp
done
     cat Gensamp_2.tmp | tr '\n' ' ' > Genfile.tmp
      echo "" >> Genfile.tmp
       gzip -dc $inputgen | cut -d" " -f2,4- >> Genfile.tmp
       echo "Calling : "$inputgen
      cat Genfile.tmp | java -jar gprobs2beagle.jar 0.34 0 > $outputname
      echo "Compressing : "$outputname
      gzip $outputname
      rm Genfile.tmp
      rm Gensamp_?.tmp
      done
      rm FileList.tmp