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Old 01-27-2016, 05:06 AM   #1
cowman
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Default vcf2beagle.jar error "cannot find int file"

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.
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Old 01-27-2016, 05:24 AM   #2
GenoMax
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Pure speculation - I wonder if the program does not like the "+" signs in your directory path? Is it creating the other two files?
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Old 01-27-2016, 05:30 AM   #3
cowman
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Thanks GenoMax, it was an interesting thought but replacing the "+" with "." made no difference.
It has not created the other files either. I suspect that .int is just the first one that it got to.
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Old 01-27-2016, 05:36 AM   #4
GenoMax
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prefix= should point to the directory where you want the result files to go. Can you try prefix=/pub7/harry/tgen/vcf/ (or some other directory) ?
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Old 01-27-2016, 05:40 AM   #5
cowman
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I thought for a minute that you had cracked it, but:
zcat /pub7/harry/tgen/vcf/Chr18.batch1.2.3.beagle.phased.vcf.gz | java -jar vcf2beagle.jar missing=? prefix=/pub7/harry/tgen/vcf/
java.io.FileNotFoundException: prefix=/pub7/harry/tgen/vcf/.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/.int
terminating program.
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Old 01-27-2016, 05:43 AM   #6
GenoMax
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How about this: prefix=/pub7/harry/tgen/vcf/test
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Old 01-27-2016, 05:45 AM   #7
cowman
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Thanks for your perseverance but no luck with that either:
zcat /pub7/harry/tgen/vcf/Chr18.batch1.2.3.beagle.phased.vcf.gz | java -jar vcf2beagle.jar missing=? prefix=/pub7/harry/tgen/vcf/test
java.io.FileNotFoundException: prefix=/pub7/harry/tgen/vcf/test.int (No such file or directory)
at java.io.FileOutputStream.open(Native Method)
at java.io.FileOutputStream.<init>(FileOutputStream.java:221)
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Old 01-27-2016, 05:49 AM   #8
GenoMax
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That is odd indeed. I am looking at the help for vcf2beagle and that should have worked.

Since we are grasping at straws now .. can you ungzip the file and feed it to vcf2beagle using cat (instead of zcat)?

Is there an example file I can grab from the net to try this?
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Old 01-27-2016, 05:57 AM   #9
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Thanks for trying so hard with this.
Unzipping with bgzip made no difference.

Last edited by cowman; 01-27-2016 at 06:30 AM.
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Old 01-27-2016, 06:16 AM   #10
GenoMax
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@cowman: It appears that program does not like ? (or *) as value for missing. If I do this

Code:
$ zcat Chr18.batch1.2.3.beagle.phased.vcf.gz | java -jar vcf2beagle.jar ANY_CHAR ./test
the program works and makes the three files.
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Old 01-27-2016, 06:25 AM   #11
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Thanks a lot GenoMax.
It is working when I omit the parameter names and the question mark.
I thought the question mark was the beagle default for missing values. I am sure that I have used it before. I wonder if the script has been modified?

Thanks again for your help
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Old 01-27-2016, 06:29 AM   #12
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Great. Remember to remove the file (and the link) from post #9.
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Old 01-27-2016, 06:37 AM   #13
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Thanks. Links and files gone.
I have just fiddled a bit more and find that I can still use a ? as a missing value. It was the parameter names that was causing the trouble. I will write to Beagle HQ to mention this problem. At least it was not only me.
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