Question: phasing vcf file
1
gravatar for mostafarafiepour
2.4 years ago by
mostafarafiepour80 wrote:

Hi all,

I am running phasing vcf file, But I'm faced with this error, In the following:

My code:

java -jar beagle.27Jan18.7e1.jar gt=BL_Population.vcf.gz out=Ind_biAll_Filtered.BL_Population.Chro1 chrom=1 window=50000 overlap=3000 niterations=5

Error snippet:

Exception in thread "main" java.lang.IllegalArgumentException: No VCF records after filtering
at vcf.VcfWindow.<init>(VcfWindow.java:53)
at vcf.TargetData.targetData(TargetData.java:62)
at main.Main.nonRefData(Main.java:279)
at main.Main.main(Main.java:111)
snp • 1.5k views
ADD COMMENTlink modified 2.4 years ago by RamRS30k • written 2.4 years ago by mostafarafiepour80
1

Hello,

how are the chromosomes named within your vcf file? With "1" or "chr1"?

fin swimmer

ADD REPLYlink written 2.4 years ago by finswimmer13k

many thanks finswimmer for your reply,

Oh my God, yes the problem has now been resolved. many thanks finswimmer...

ADD REPLYlink written 2.4 years ago by mostafarafiepour80

But now a new problem has been found,

After correcting the name of the chromosome, running is Began. But after a few minutes I faced this error, In the following:

Exception in thread "main" java.lang.StackOverflowError
    at dag.MergeableDag.similar(MergeableDag.java:374)
    at dag.MergeableDag.similar(MergeableDag.java:374)
    at dag.MergeableDag.similar(MergeableDag.java:374)
    at dag.MergeableDag.similar(MergeableDag.java:374)
    at dag.MergeableDag.similar(MergeableDag.java:374)
    at dag.MergeableDag.similar(MergeableDag.java:374)
    at dag.MergeableDag.similar(MergeableDag.java:374)
    at dag.MergeableDag.similar(MergeableDag.java:374)
    at dag.MergeableDag.similar(MergeableDag.java:374)
    at dag.MergeableDag.similar(MergeableDag.java:374)
    at dag.MergeableDag.similar(MergeableDag.java:374)
    at dag.MergeableDag.similar(MergeableDag.java:374)
    at dag.MergeableDag.similar(MergeableDag.java:374)
    at dag.MergeableDag.similar(MergeableDag.java:374)
    at dag.MergeableDag.similar(MergeableDag.java:374)
    at dag.MergeableDag.similar(MergeableDag.java:374)
    at dag.MergeableDag.similar(MergeableDag.java:374)
    at dag.MergeableDag.similar(MergeableDag.java:374)
    at dag.MergeableDag.similar(MergeableDag.java:374)
    at dag.MergeableDag.similar(MergeableDag.java:374)
    at dag.MergeableDag.similar(MergeableDag.java:374)
    at dag.MergeableDag.similar(MergeableDag.java:374)
    at dag.MergeableDag.similar(MergeableDag.java:374)
    at dag.MergeableDag.similar(MergeableDag.java:374)
    at dag.MergeableDag.similar(MergeableDag.java:374)
    at dag.MergeableDag.similar(MergeableDag.java:374)
    at dag.MergeableDag.similar(MergeableDag.java:374)
    at dag.MergeableDag.similar(MergeableDag.java:374)
    at dag.MergeableDag.similar(MergeableDag.java:374)
    at dag.MergeableDag.similar(MergeableDag.java:374)
    at dag.MergeableDag.similar(MergeableDag.java:374)
    at dag.MergeableDag.similar(MergeableDag.java:374)
    at dag.MergeableDag.similar(MergeableDag.java:374)
    at dag.MergeableDag.similar(MergeableDag.java:374)
ADD REPLYlink modified 2.4 years ago by RamRS30k • written 2.4 years ago by mostafarafiepour80
1

Hello,

have a look into the manual. The Stack needs more memory. You can set the size with the –Xss parameter. For example use –Xss5m to set the stack size to 5Mb.

Please use the code button to mark code. It is better to read.

And if you found a post helpful please upvote it.

fin swimmer

ADD REPLYlink written 2.4 years ago by finswimmer13k

Hi finswimmer,

thanks a lot for your good guidancee, It seems that the problem was solved by adding the option -Xss5m.

Now I want to see if the running was done correctly?? Please see the image below:

enter image description here

ADD REPLYlink modified 2.4 years ago • written 2.4 years ago by mostafarafiepour80

That problem is so often the cause :-D
I wonder how many hours this has costed both users and developers.

ADD REPLYlink written 2.4 years ago by WouterDeCoster44k

Please use the formatting bar (especially the code option) to present your post better. I've done it for you this time. Formatting bar

ADD REPLYlink written 2.4 years ago by RamRS30k

Hi all,

many thanks for your reply and guidance for using options. I recently joined to biostars, So i apologize if I can not good share my posts.

ADD REPLYlink written 2.4 years ago by mostafarafiepour80
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