ERROR MESSAGE: Input file must have contiguous chromosomes problem

Hi,

I am running VariantFiltration on vcf files produced by GATK's (version 3.5-0-g36282e4 )UnifiedGenotyper in vcf.gz format. I tried to solve the problem many times with different solutions but its giving the same error all the time because of that I am asking you.

I have these files produced directly by UnifiedGenotyper in my working directory:

File1.vcf.gz
File1.vcf.idx

I didnt change those files produced by GATK, I did not play with them, they are directly outputs of GATK, and I want to run variantfiltration on this File1.vcf

I am running the script below:

cp File1.vcf.idx /my/directory/File1.vcf.idx
gzip -d -c File1.vcf.gz > /my/directory/File1.vcf #I am doing this because Variantfiltration didnt work with UnifiedGenotyper's output file with .gz extension

echo "vcf was uncompressed"
tail -2 ./File1.vcf

echo "Start of GATK VariantFiltration"

java -Xmx16g -jar /GATK/3.5.0/GenomeAnalysisTK.jar \
-T VariantFiltration \
-R /reference/directory/hs37d5.fa \
-V /my/directory/File1.vcf \
--filterExpression "QD < 3.0 || FS > 60.0 || MQ < 35.0 || MQRankSum < -12.5 || ReadPosRankSum < -8.0 || MQ0 >=5" \
--genotypeFilterExpression "DP < 10 || GQ < 50 || DP > 120" \
--filterName "my_snp_filter" \
--genotypeFilterName "myGQ" \
-o /my/directory/File1.filtered.vcf
echo "End of GATK VariantFiltration"

This script is not working. At first its giving a warning message saying that the .idx file is old and will be deleted and updated. And then after removing .idx file its stopping saying that the chromosomes are not contigious.

I am pasting warning and error messages here, too:

INFO 12:32:49,969 GenomeAnalysisEngine - Strictness is SILENT
INFO 12:32:50,208 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 1000
WARN 12:33:22,057 RMDTrackBuilder - Index file /scratch/10511604/ans17DR_90perc_librs_merge.hs37d5.fa.bqual5.rlgn.UG.vcf.idx is out of date (index older than input file), deleting and updating the ex file

ERROR MESSAGE: Input file must have contiguous chromosomes. Saw feature 15:20000001-20000001 followed later by 15:40620656-40620656 and then 15:40620657-40620657, for input source: File1.vcf

Could you please help me in this situation?

Thank you in advance