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SortVcf

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The order of file Mills_and_1000G_gold_standard.indels.hg38.vcf is not same with my genome fasta file,so I need to reorder it,I use SortVcf to do it.Before I run it,I run UpdateVcfSequenceDictionary first.My scripts is as follows:

java -jar /data/share-disk/kvm72/yangzhen/programe/picard.jar UpdateVcfSequenceDictionary \
I=Mills_and_1000G_gold_standard_rename.indels.hg38.vcf \
O=Mills_and_1000G_gold_standard_dict.indels.hg38.vcf \
SEQUENCE_DICTIONARY=/data2/gminix/pipeline/toolkits/RNA_seq_SNP-INDEL/data/hg38v1.dict

java -jar /data/share-disk/kvm72/yangzhen/programe/picard.jar SortVcf \
I=Mills_and_1000G_gold_standard_dict.indels.hg38.vcf \
O=Mills_and_1000G_gold_standard_reorder.indels.hg38.vcf \
SEQUENCE_DICTIONARY=/data2/gminix/pipeline/toolkits/RNA_seq_SNP-INDEL/data/hg38v1.dict

It didn't give any error,but just counld not finish it.The report is shown in the picture:


It stops there and no longer runs,what can be the problem?

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