Hollow everyone, there is error occurred when I am running GenomeAnalysisTK to fliter SNP after the calling step.

GATK Version: 3.8-1-0-gf15c1c3ef

Commond lines:

BioSoftware/bin/java -Xmx25g -Djava.io.tmpdir=./temp -jar /Software/GenomeAnalysisTK-3.8-1-0-gf15c1c3ef/GenomeAnalysisTK.jar
-T SelectVariants \
-R $ref \
-V ./Chr13.vcf.gz \
-xl_sf ./excluede-list \
-nt 10 \
-selectType SNP \
--excludeNonVariants \
--removeUnusedAlternates \
-restrictAllelesTo BIALLELIC \
--logging_level ERROR \
-o ./Chr13.SNP.vcf.gz

excluede-list includes the samples I do not need.

The error message is as follow:

##### ERROR stack trace
org.broadinstitute.gatk.utils.exceptions.ReviewedGATKException: Unable to create iterator for rod named variant
at org.broadinstitute.gatk.engine.datasources.rmd.ReferenceOrderedQueryDataPool.createIteratorFromResource(ReferenceOrderedDataSource.java:248)
at org.broadinstitute.gatk.engine.datasources.rmd.ReferenceOrderedQueryDataPool.createIteratorFromResource(ReferenceOrderedDataSource.java:185)
at org.broadinstitute.gatk.engine.datasources.rmd.ResourcePool.iterator(ResourcePool.java:93)
at org.broadinstitute.gatk.engine.datasources.rmd.ReferenceOrderedDataSource.seek(ReferenceOrderedDataSource.java:168)
at org.broadinstitute.gatk.engine.datasources.providers.RodLocusView.<init>(RodLocusView.java:82)
at org.broadinstitute.gatk.engine.traversals.TraverseLociNano.getLocusView(TraverseLociNano.java:129)
at org.broadinstitute.gatk.engine.traversals.TraverseLociNano.traverse(TraverseLociNano.java:80)
at org.broadinstitute.gatk.engine.traversals.TraverseLociNano.traverse(TraverseLociNano.java:48)
at org.broadinstitute.gatk.engine.executive.ShardTraverser.call(ShardTraverser.java:98)
at java.util.concurrent.FutureTask.run(FutureTask.java:266)
at java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1142)
at java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:617)
at java.lang.Thread.run(Thread.java:745)
Caused by: htsjdk.samtools.util.RuntimeIOException: java.io.IOException: Invalid file pointer: 2078470088699528 for  ./Chr13.vcf.gz
at htsjdk.tribble.readers.TabixIteratorLineReader.readLine(TabixIteratorLineReader.java:48)
at htsjdk.tribble.TabixFeatureReader$FeatureIterator.readNextRecord(TabixFeatureReader.java:177)
at htsjdk.tribble.TabixFeatureReader$FeatureIterator.<init>(TabixFeatureReader.java:165)
at htsjdk.tribble.TabixFeatureReader.query(TabixFeatureReader.java:138)
at org.broadinstitute.gatk.utils.refdata.tracks.RMDTrack.query(RMDTrack.java:119)
at org.broadinstitute.gatk.engine.datasources.rmd.ReferenceOrderedQueryDataPool.createIteratorFromResource(ReferenceOrderedDataSource.java:241)
... 12 more
Caused by: java.io.IOException: Invalid file pointer: 2078470088699528 for ./Chr13.vcf.gz
at htsjdk.samtools.util.BlockCompressedInputStream.seek(BlockCompressedInputStream.java:372)
at htsjdk.tribble.readers.TabixReader$IteratorImpl.next(TabixReader.java:410)
at htsjdk.tribble.readers.TabixIteratorLineReader.readLine(TabixIteratorLineReader.java:46)
... 17 more
##### ERROR ------------------------------------------------------------------------------------------
##### ERROR A GATK RUNTIME ERROR has occurred (version 3.8-1-0-gf15c1c3ef):
##### ERROR
##### ERROR This might be a bug. Please check the documentation guide to see if this is a known problem.
##### ERROR If not, please post the error message, with stack trace, to the GATK forum.
##### ERROR Visit our website and forum for extensive documentation and answers to
##### ERROR commonly asked questions https://software.broadinstitute.org/gatk
##### ERROR
##### ERROR MESSAGE: Unable to create iterator for rod named variant
##### ERROR ------------------------------------------------------------------------------------------

I have tried to remove the '-nt 10 ' commond, but it didn't work. what's going wrong here? Thankful for your ealier suggestions.