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lindenb / jvarkit

Java utilities for Bioinformatics
https://jvarkit.readthedocs.io/
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java.lang.StackOverflowError [Biostar175929] #221

Closed vkulaganathan closed 1 year ago

vkulaganathan commented 1 year ago

Am I doing something wrong? I get the following error.

$ java -Xms1024m -Xmx8g -jar dist/biostar175929.jar -x 2 -R hg19.p13.plusMT.fa -b rn-3.vcf.gz | more

[INFO][Biostar175929]chrom:chr10 N=254953
[SEVERE][Biostar175929]null
java.lang.StackOverflowError
    at java.base/java.lang.StringCoding.decodeUTF8(StringCoding.java:732)
    at java.base/java.lang.StringCoding.decode(StringCoding.java:257)
    at java.base/java.lang.String.<init>(String.java:507)
    at java.base/java.lang.String.<init>(String.java:561)
    at htsjdk.variant.variantcontext.SimpleAllele.getBaseString(SimpleAllele.java:166)
    at com.github.lindenb.jvarkit.tools.biostar.Biostar175929.recursive(Biostar175929.java:229)
    at com.github.lindenb.jvarkit.tools.biostar.Biostar175929.recursive(Biostar175929.java:233)
    at com.github.lindenb.jvarkit.tools.biostar.Biostar175929.recursive(Biostar175929.java:233)
    at com.github.lindenb.jvarkit.tools.biostar.Biostar175929.recursive(Biostar175929.java:233)
    at com.github.lindenb.jvarkit.tools.biostar.Biostar175929.recursive(Biostar175929.java:233)
    at com.github.lindenb.jvarkit.tools.biostar.Biostar175929.recursive(Biostar175929.java:233)
    at com.github.lindenb.jvarkit.tools.biostar.Biostar175929.recursive(Biostar175929.java:233)
    at com.github.lindenb.jvarkit.tools.biostar.Biostar175929.recursive(Biostar175929.java:233)
    at com.github.lindenb.jvarkit.tools.biostar.Biostar175929.recursive(Biostar175929.java:233)
    at com.github.lindenb.jvarkit.tools.biostar.Biostar175929.recursive(Biostar175929.java:233)
    at com.github.lindenb.jvarkit.tools.biostar.Biostar175929.recursive(Biostar175929.java:233)
    at com.github.lindenb.jvarkit.tools.biostar.Biostar175929.recursive(Biostar175929.java:233)
    at com.github.lindenb.jvarkit.tools.biostar.Biostar175929.recursive(Biostar175929.java:233)
    at com.github.lindenb.jvarkit.tools.biostar.Biostar175929.recursive(Biostar175929.java:233)
    at com.github.lindenb.jvarkit.tools.biostar.Biostar175929.recursive(Biostar175929.java:233)
    at com.github.lindenb.jvarkit.tools.biostar.Biostar175929.recursive(Biostar175929.java:233)
    at com.github.lindenb.jvarkit.tools.biostar.Biostar175929.recursive(Biostar175929.java:233)
    at com.github.lindenb.jvarkit.tools.biostar.Biostar175929.recursive(Biostar175929.java:233)
    at com.github.lindenb.jvarkit.tools.biostar.Biostar175929.recursive(Biostar175929.java:233)
    at com.github.lindenb.jvarkit.tools.biostar.Biostar175929.recursive(Biostar175929.java:233)
    at com.github.lindenb.jvarkit.tools.biostar.Biostar175929.recursive(Biostar175929.java:233)
    at com.github.lindenb.jvarkit.tools.biostar.Biostar175929.recursive(Biostar175929.java:233)
    at com.github.lindenb.jvarkit.tools.biostar.Biostar175929.recursive(Biostar175929.java:233)
    at com.github.lindenb.jvarkit.tools.biostar.Biostar175929.recursive(Biostar175929.java:233)
    at com.github.lindenb.jvarkit.tools.biostar.Biostar175929.recursive(Biostar175929.java:233)
    at com.github.lindenb.jvarkit.tools.biostar.Biostar175929.recursive(Biostar175929.java:233)
    at com.github.lindenb.jvarkit.tools.biostar.Biostar175929.recursive(Biostar175929.java:233)
.
.
.
    at com.github.lindenb.jvarkit.tools.biostar.Biostar175929.recursive(Biostar175929.java:233)
    at com.github.lindenb.jvarkit.tools.biostar.Biostar175929.recursive(Biostar175929.java:233)
    at com.github.lindenb.jvarkit.tools.biostar.Biostar175929.recursive(Biostar175929.java:233)
    at com.github.lindenb.jvarkit.tools.biostar.Biostar175929.recursive(Biostar175929.java:233)
    at com.github.lindenb.jvarkit.tools.biostar.Biostar175929.recursive(Biostar175929.java:233)
    at com.github.lindenb.jvarkit.tools.biostar.Biostar175929.recursive(Biostar175929.java:233)
    at com.github.lindenb.jvarkit.tools.biostar.Biostar175929.recursive(Biostar175929.java:233)
    at com.github.lindenb.jvarkit.tools.biostar.Biostar175929.recursive(Biostar175929.java:233)
    at com.github.lindenb.jvarkit.tools.biostar.Biostar175929.recursive(Biostar175929.java:233)
    at com.github.lindenb.jvarkit.tools.biostar.Biostar175929.recursive(Biostar175929.java:233)
    at com.github.lindenb.jvarkit.tools.biostar.Biostar175929.recursive(Biostar175929.java:233)
    at com.github.lindenb.jvarkit.tools.biostar.Biostar175929.recursive(Biostar175929.java:233)
    at com.github.lindenb.jvarkit.tools.biostar.Biostar175929.recursive(Biostar175929.java:233)
    at com.github.lindenb.jvarkit.tools.biostar.Biostar175929.recursive(Biostar175929.java:233)
    at com.github.lindenb.jvarkit.tools.biostar.Biostar175929.recursive(Biostar175929.java:233)
    at com.github.lindenb.jvarkit.tools.biostar.Biostar175929.recursive(Biostar175929.java:233)
    at com.github.lindenb.jvarkit.tools.biostar.Biostar175929.recursive(Biostar175929.java:233)
    at com.github.lindenb.jvarkit.tools.biostar.Biostar175929.recursive(Biostar175929.java:233)
    at com.github.lindenb.jvarkit.tools.biostar.Biostar175929.recursive(Biostar175929.java:233)
    at com.github.lindenb.jvarkit.tools.biostar.Biostar175929.recursive(Biostar175929.java:233)
    at com.github.lindenb.jvarkit.tools.biostar.Biostar175929.recursive(Biostar175929.java:233)
    at com.github.lindenb.jvarkit.tools.biostar.Biostar175929.recursive(Biostar175929.java:233)
    at com.github.lindenb.jvarkit.tools.biostar.Biostar175929.recursive(Biostar175929.java:233)
    at com.github.lindenb.jvarkit.tools.biostar.Biostar175929.recursive(Biostar175929.java:233)
    at com.github.lindenb.jvarkit.tools.biostar.Biostar175929.recursive(Biostar175929.java:233)
    at com.github.lindenb.jvarkit.tools.biostar.Biostar175929.recursive(Biostar175929.java:233)
    at com.github.lindenb.jvarkit.tools.biostar.Biostar175929.recursive(Biostar175929.java:233)
    at com.github.lindenb.jvarkit.tools.biostar.Biostar175929.recursive(Biostar175929.java:233)
    at com.github.lindenb.jvarkit.tools.biostar.Biostar175929.recursive(Biostar175929.java:233)
    at com.github.lindenb.jvarkit.tools.biostar.Biostar175929.recursive(Biostar175929.java:233)
    at com.github.lindenb.jvarkit.tools.biostar.Biostar175929.recursive(Biostar175929.java:233)
    at com.github.lindenb.jvarkit.tools.biostar.Biostar175929.recursive(Biostar175929.java:233)
    at com.github.lindenb.jvarkit.tools.biostar.Biostar175929.recursive(Biostar175929.java:233)
    at com.github.lindenb.jvarkit.tools.biostar.Biostar175929.recursive(Biostar175929.java:233)
    at com.github.lindenb.jvarkit.tools.biostar.Biostar175929.recursive(Biostar175929.java:233)
    at com.github.lindenb.jvarkit.tools.biostar.Biostar175929.recursive(Biostar175929.java:233)
    at com.github.lindenb.jvarkit.tools.biostar.Biostar175929.recursive(Biostar175929.java:233)
    at com.github.lindenb.jvarkit.tools.biostar.Biostar175929.recursive(Biostar175929.java:233)
    at com.github.lindenb.jvarkit.tools.biostar.Biostar175929.recursive(Biostar175929.java:233)
    at com.github.lindenb.jvarkit.tools.biostar.Biostar175929.recursive(Biostar175929.java:233)
    at com.github.lindenb.jvarkit.tools.biostar.Biostar175929.recursive(Biostar175929.java:233)
    at com.github.lindenb.jvarkit.tools.biostar.Biostar175929.recursive(Biostar175929.java:233)
    at com.github.lindenb.jvarkit.tools.biostar.Biostar175929.recursive(Biostar175929.java:233)
    at com.github.lindenb.jvarkit.tools.biostar.Biostar175929.recursive(Biostar175929.java:233)
    at com.github.lindenb.jvarkit.tools.biostar.Biostar175929.recursive(Biostar175929.java:233)
    at com.github.lindenb.jvarkit.tools.biostar.Biostar175929.recursive(Biostar175929.java:233)
    at com.github.lindenb.jvarkit.tools.biostar.Biostar175929.recursive(Biostar175929.java:233)
    at com.github.lindenb.jvarkit.tools.biostar.Biostar175929.recursive(Biostar175929.java:233)
    at com.github.lindenb.jvarkit.tools.biostar.Biostar175929.recursive(Biostar175929.java:233)
    at com.github.lindenb.jvarkit.tools.biostar.Biostar175929.recursive(Biostar175929.java:233)
    at com.github.lindenb.jvarkit.tools.biostar.Biostar175929.recursive(Biostar175929.java:233)
    at com.github.lindenb.jvarkit.tools.biostar.Biostar175929.recursive(Biostar175929.java:233)
    at com.github.lindenb.jvarkit.tools.biostar.Biostar175929.recursive(Biostar175929.java:233)
    at com.github.lindenb.jvarkit.tools.biostar.Biostar175929.recursive(Biostar175929.java:233)
    at com.github.lindenb.jvarkit.tools.biostar.Biostar175929.recursive(Biostar175929.java:233)
    at com.github.lindenb.jvarkit.tools.biostar.Biostar175929.recursive(Biostar175929.java:233)
    at com.github.lindenb.jvarkit.tools.biostar.Biostar175929.recursive(Biostar175929.java:233)
    at com.github.lindenb.jvarkit.tools.biostar.Biostar175929.recursive(Biostar175929.java:233)
    at com.github.lindenb.jvarkit.tools.biostar.Biostar175929.recursive(Biostar175929.java:233)
    at com.github.lindenb.jvarkit.tools.biostar.Biostar175929.recursive(Biostar175929.java:233)
    at com.github.lindenb.jvarkit.tools.biostar.Biostar175929.recursive(Biostar175929.java:233)
[INFO][Launcher]biostar175929 Exited with failure (-1)
lindenb commented 1 year ago

Hi, I think it's because you have too many variants in the VCF. The tool builds a combination of all the possible variants in the VCF using a recursive process.

The tool is not dedicated to build all the possible sequences for a large set of variants. You might be interested in GATK https://gatk.broadinstitute.org/hc/en-us/articles/360037594571-FastaAlternateReferenceMaker

vkulaganathan commented 1 year ago

Thanks ! That was helpful.