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HaplotypeCaller error in the middle of processing

danangcrysnantodanangcrysnanto EdinburghMember

I run the GATK4 using this command:

GATK4 HaplotypeCaller \
-I ${input_file}\
-R umd_3_1.fa \
-L ~/helper/location.bed \
-O ${file_name}.gatk4.g.vcf.gz \
-ERC GVCF \

And got error as follow:

16:42:14.507 WARN DepthPerSampleHC - Annotation will not be calculated, genotype is not called or alleleLikelihoodMap is null
16:42:14.507 WARN StrandBiasBySample - Annotation will not be calculated, genotype is not called or alleleLikelihoodMap is null
16:42:55.522 INFO HaplotypeCaller - Shutting down engine
[January 12, 2018 4:42:55 PM CET] org.broadinstitute.hellbender.tools.walkers.haplotypecaller.HaplotypeCaller done. Elapsed time: 63.53 minutes.
Runtime.totalMemory()=12507938816
htsjdk.samtools.util.RuntimeIOException: Unable to close index for /cluster/scratch/cdanang/BSWCHEM110280223340.gatk4.g.vcf.gz

I was running previously on the smaller chromosomes using the same script and it worked. Anyone has any ideas how to resolve the problem?
I notice that the GVCF is produced but stopped (not finished) on all regions indicated in -L.

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