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Picard LiftoverVcf Log or bug?

Hi:
I try to run Picard LiftoverVcf to convert a vcf's ref which is in hg19 format,and I want to convert to hg38. so my commands:
time java -jar picard.jar LiftoverVcf I=All.merge.onlysite.VQSR.VEP.pass.per_gene.nbi.vcf O=All.merge.onlysite.VQSR.VEP.pass.per_gene.nbi.liftover_hg38.vcf CHAIN=hg19ToHg38.over.chain REJECT=All.merge.onlysite.VQSR.VEP.pass.per_gene.nbi.liftover_hg38.reject.vcf R=/Homo_sapiens_assembly38.fasta

After running,I get the final result.At the same time,I find some log:
For example:
Runtime.totalMemory()=16053698560
Exception in thread "Thread-17" Exception in thread "Thread-3" Exception in thread "Thread-7" Exception in thread "Thread-16" Exception in thread "Thread-4" Exception in thread "Thread-6" Exception in thread "Thread-11" Exception in thread "Thread-13" Exception in thread "Thread-14" Exception in thread "Thread-19" Exception in thread "Thread-2" Exception in thread "Thread-10" Exception in thread "Thread-18" Exception in thread "Thread-5" Exception in thread "Thread-8" Exception in thread "Thread-12" Exception in thread "Thread-15" Exception in thread "Thread-9" Exception in thread "Thread-1" htsjdk.samtools.util.RuntimeIOException: java.nio.file.NoSuchFileException: /tmp/liurong2/sortingcollection.5671996248650745813.tmp
at htsjdk.samtools.util.IOUtil$DeletePathThread.run(IOUtil.java:374)
Caused by: java.nio.file.NoSuchFileException: /tmp/liurong2/sortingcollection.5671996248650745813.tmp
at sun.nio.fs.UnixException.translateToIOException(UnixException.java:86)
at sun.nio.fs.UnixException.rethrowAsIOException(UnixException.java:102)
at sun.nio.fs.UnixException.rethrowAsIOException(UnixException.java:107)
at sun.nio.fs.UnixFileSystemProvider.implDelete(UnixFileSystemProvider.java:244)
at sun.nio.fs.AbstractFileSystemProvider.delete(AbstractFileSystemProvider.java:103)
at java.nio.file.Files.delete(Files.java:1126)
at htsjdk.samtools.util.IOUtil$DeletePathThread.run(IOUtil.java:372)
htsjdk.samtools.util.RuntimeIOException: java.nio.file.NoSuchFileException: /tmp/liurong2/sortingcollection.7348183798037062558.tmp
at htsjdk.samtools.util.IOUtil$DeletePathThread.run(IOUtil.java:374)

So,the final result is normal? I can use that for advanced research?

Answers

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