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6.4 years ago
GK1610
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120
I am trying to align sample genotypes from hg19 to hg38. To do so, I am using liftover from picard on my_vcf_genotype_file (VCF file)
chainfile=hg19ToHg38.over.chain.gz
java -jar picard-tools-2.5.0/picard.jar LiftoverVcf I=$my_vcf_genotype_file O=$my_vcf_genotype_file.hg38.vcf.gz C=$chain_file REJECT=trash.vcf.gz R=GRCh38.primary_assembly.genome.fa
I am getting this error
INFO 2018-07-05 18:54:28 LiftoverVcf Loading up the target reference genome.
INFO 2018-07-05 18:54:48 LiftoverVcf Lifting variants over and sorting.
ERROR 2018-07-05 18:54:56 LiftoverVcf Encountered a contig, chr1_KI270766v1_alt that is not part of the target reference.
Can you help me to resolve this?
I am getting this error now
INFO 2018-07-06 11:52:13 LiftoverVcf Loading up the target reference genome. INFO 2018-07-06 11:52:59 LiftoverVcf Lifting variants over and sorting. WARNING 2018-07-06 11:53:06 LiftoverVcf Encountered a contig, chr1_KI270766v1_alt that is not part of the target reference. WARNING 2018-07-06 11:54:43 LiftoverVcf Encountered a contig, chr4_GL000008v2_random that is not part of the target reference. WARNING 2018-07-06 11:54:43 LiftoverVcf Encountered a contig, chr4_GL000008v2_random that is not part of the target reference. WARNING 2018-07-06 11:54:43 LiftoverVcf Encountered a contig, chr4_GL000008v2_random that is not part of the target reference. WARNING 2018-07-06 11:54:43 LiftoverVcf Encountered a contig, chr14_GL000009v2_random that is not part of the target reference. [Fri Jul 06 11:59:17 EDT 2018] picard.vcf.LiftoverVcf done. Elapsed time: 7.08 minutes. Runtime.totalMemory()=9411493888
To get help, see http://broadinstitute.github.io/picard/index.html#GettingHelp Exception in thread "main" java.lang.OutOfMemoryError: GC overhead limit exceeded at htsjdk.variant.variantcontext.GenotypeBuilder.make(GenotypeBuilder.java:192) at htsjdk.variant.vcf.AbstractVCFCodec.createGenotypeMap(AbstractVCFCodec.java:736) at htsjdk.variant.vcf.AbstractVCFCodec$LazyVCFGenotypesParser.parse(AbstractVCFCodec.java:128) at htsjdk.variant.variantcontext.LazyGenotypesContext.decode(LazyGenotypesContext.java:158) at htsjdk.variant.vcf.AbstractVCFCodec.parseVCFLine(AbstractVCFCodec.java:347) at htsjdk.variant.vcf.AbstractVCFCodec.decodeLine(AbstractVCFCodec.java:279) at htsjdk.variant.vcf.AbstractVCFCodec.decode(AbstractVCFCodec.java:257) at htsjdk.variant.vcf.AbstractVCFCodec.decode(AbstractVCFCodec.java:60) at htsjdk.tribble.TabixFeatureReader$FeatureIterator.readNextRecord(TabixFeatureReader.java:161) at htsjdk.tribble.TabixFeatureReader$FeatureIterator.next(TabixFeatureReader.java:194) at htsjdk.tribble.TabixFeatureReader$FeatureIterator.next(TabixFeatureReader.java:136) at picard.vcf.LiftoverVcf.doWork(LiftoverVcf.java:206) at picard.cmdline.CommandLineProgram.instanceMain(CommandLineProgram.java:208) at picard.cmdline.PicardCommandLine.instanceMain(PicardCommandLine.java:95) at picard.cmdline.PicardCommandLine.main(PicardCommandLine.java:105)