ERROR MESSAGE: Bad input:We encountered a non-standard non-IUPAC base in the provided reference: '13

Hi,
I'm currently working with bwa, samtools and GATK to make SNP calling on Medicago truncatula. I'm using my own reference sequence, with the 8 chromosoms in the same fasta file.

C1_lenght=155648

AAAGATAGAGA..

C2_lenght=125018

ATGGATC...
etc..
I have done alignments without problem, but for GATK : I do rmdup --> CreateSequenceDictionary.jar (picard) --> samtools sort --> Read Group (picard) --> samtools index and then :
Pre alignment with :

java -jar -Xmx4g /usr/local/bioinfo/src/GATK/GenomeAnalysisTK-2.4-9-g532efad/GenomeAnalysisTK.jar -nt 8 -T RealignerTargetCreator -R REF.fa -o RTC.intervals -I INPUT_muq30_RMDUP_RG.bam

Here there is no problem, but when I want to make the realignement :

java -jar -Xmx4g /usr/local/bioinfo/src/GATK/GenomeAnalysisTK-2.4-9-g532efad/GenomeAnalysisTK.jar -T IndelRealigner -R REF.fa -I INPUT_muq30_RMDUP_RG.bam -targetIntervals RTC.intervals -o INPUT_muq30_RMDUP_RG_REAL.bam

And I got this error message :
ERROR MESSAGE: Bad input:We encountered a non-standard non-IUPAC base in the provided reference: '13'

I didn't find any explanation in google for this error.
Could you please help me ?!

vschilling