I am using vcf2beagle.jar to convert vcf files to beagle format. In the documentation it says:
Three files will be created with extensions:".markers", ".bgl.gz", and ".int".
However the programme crashes saying that it cannot find the int file. Other programmes manage to write to the folder so I assume it is not a permissions problem. I created an empty version of the missing file using touch and it gives the same error message. My full command and error message is below.
I would be most grateful for any suggestions
Harry
zcat /pub7/harry/tgen/vcf/Chr18.batch1+2+3.beagle.phased.vcf.gz | java -jar vcf2beagle.jar missing=? prefix=/pub7/harry/tgen/vcf/Chr18.batch1+2+3.beagle.phased
java.io.FileNotFoundException: prefix=/pub7/harry/tgen/vcf/Chr18.batch1+2+3.beagle.phased.int (No such file or directory)
at java.io.FileOutputStream.open(Native Method)
at java.io.FileOutputStream.<init>(FileOutputStream.java:221)
at java.io.FileWriter.<init>(FileWriter.java:107)
at blbutil.FileUtil.printWriter(FileUtil.java:341)
at blbutil.FileUtil.printWriter(FileUtil.java:320)
at blbutil.FileUtil.printWriter(FileUtil.java:269)
at vcf.Vcf2Beagle.main(Vcf2Beagle.java:49)
Error opening prefix=/pub7/harry/tgen/vcf/Chr18.batch1+2+3.beagle.phased.int
terminating program.
Three files will be created with extensions:".markers", ".bgl.gz", and ".int".
However the programme crashes saying that it cannot find the int file. Other programmes manage to write to the folder so I assume it is not a permissions problem. I created an empty version of the missing file using touch and it gives the same error message. My full command and error message is below.
I would be most grateful for any suggestions
Harry
zcat /pub7/harry/tgen/vcf/Chr18.batch1+2+3.beagle.phased.vcf.gz | java -jar vcf2beagle.jar missing=? prefix=/pub7/harry/tgen/vcf/Chr18.batch1+2+3.beagle.phased
java.io.FileNotFoundException: prefix=/pub7/harry/tgen/vcf/Chr18.batch1+2+3.beagle.phased.int (No such file or directory)
at java.io.FileOutputStream.open(Native Method)
at java.io.FileOutputStream.<init>(FileOutputStream.java:221)
at java.io.FileWriter.<init>(FileWriter.java:107)
at blbutil.FileUtil.printWriter(FileUtil.java:341)
at blbutil.FileUtil.printWriter(FileUtil.java:320)
at blbutil.FileUtil.printWriter(FileUtil.java:269)
at vcf.Vcf2Beagle.main(Vcf2Beagle.java:49)
Error opening prefix=/pub7/harry/tgen/vcf/Chr18.batch1+2+3.beagle.phased.int
terminating program.
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