a problem on "ApplyRecalibration"

I've finished calling the SNPs and Indels with "HaplotypeCaller" and built the SNP recalibration model. When I started to "Apply the desired level of recalibration to the SNPs in the call set", some errors turned up.

my commandline is as follows(which are almostly the same as the command line in the "best pactice"):

java -Xmx10g -Djava.io.tmpdir=pwd/tmp \
|_______-jar ./GATK/GenomeAnalysisTK.jar \
|_______-T ApplyRecalibration \
|_______-R ./hg19/ucsc.hg19.fasta \
|_______-input ./bamByChr/chr6.output.indel_HaplotypeCaller.vcf \
|_______-mode SNP \
|_______--ts_filter_level 99.9 \
|_______-recalFile ./bamByChr/chr6.recalibrate_SNP.recal \
|_______-tranchesFile ./bamByChr/chr6.recalibrate_SNP.tranches \
|_______-o ./bamByChr/recalibrated_snps_raw_indels.vcf

============================================================

and the ERROR information is :

ERROR ------------------------------------------------------------------------------------------
ERROR A USER ERROR has occurred (version 3.3-0-g37228af):
ERROR
ERROR This means that one or more arguments or inputs in your command are incorrect.
ERROR The error message below tells you what is the problem.
ERROR
ERROR If the problem is an invalid argument, please check the online documentation guide
ERROR (or rerun your command with --help) to view allowable command-line arguments for this tool.
ERROR
ERROR Visit our website and forum for extensive documentation and answers to
ERROR commonly asked questions http://www.broadinstitute.org/gatk
ERROR
ERROR Please do NOT post this error to the GATK forum unless you have really tried to fix it yourself.
ERROR
ERROR MESSAGE: Invalid command line: No tribble type was provided on the command line and the type of the file could not be determined dynamicaly. Please add an explicit type tag :NAME listing the correct type from among the supported types:
ERROR Name FeatureType Documentation
ERROR BCF2 VariantContext (this is an external codec and is not documented within GATK)
ERROR VCF VariantContext (this is an external codec and is not documented within GATK)
ERROR VCF3 VariantContext (this is an external codec and is not documented within GATK)

##### ERROR ------------------------------------------------------------------------------------------

I can't find what's the problem, for my augments are nearly the same as those in the "best practice".

Answers

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