Is there anyone who did snpEff annotation with MSUv6.1 rice reference.

Currently, I am working to identify the Heat shock gene from weedy rice. I have 9 WGS sequences which 5 belong to heat tolerance and 4 belong to heat susceptible. So, to identify the heat shock gene I aligned all those weedy rice WGS sequences with MSUv6.1 reference genome and finally create filtred SNP vcf file. So until SNP filtered there was no error. So once I did with variant calling further proceed to the SNP annotation by snpEff tools and I found no proper SNP database for MSUv6.1. So far i try to annotated by snpEFF version 4.2 database like rice_rap201304, rice_rap201503, rice5, rice6.1 and rice7. The error come like the below output.

`WARNING: Chromosome 'chr12|13112' not found. File '/home/songbk/Mainul_bin/Bioinfo/022MA2_filtered_snpsfinal.vcf', line 3645356
WARNING: Chromosome 'chr12|13112' not found. File '/home/songbk/Mainul_bin/Bioinfo/022MA2_filtered_snpsfinal.vcf', line 3645357
WARNING: Chromosome 'chr12|13112' not found. File '/home/songbk/Mainul_bin/Bioinfo/022MA2_filtered_snpsfinal.vcf', line 3645358
WARNING: Chromosome 'chr12|13112' not found. File '/home/songbk/Mainul_bin/Bioinfo/022MA2_filtered_snpsfinal.vcf', line 3645359
WARNING: Chromosome 'chr12|13112' not found. File '/home/songbk/Mainul_bin/Bioinfo/022MA2_filtered_snpsfinal.vcf', line 3645360
WARNING: Chromosome 'chr12|13112' not found. File '/home/songbk/Mainul_bin/Bioinfo/022MA2_filtered_snpsfinal.vcf', line 3645361
WARNING: Chromosome 'chr12|13112' not found. File '/home/songbk/Mainul_bin/Bioinfo/022MA2_filtered_snpsfinal.vcf', line 3645362
WARNING: Chromosome 'chr12|13112' not found. File '/home/songbk/Mainul_bin/Bioinfo/022MA2_filtered_snpsfinal.vcf', line 3645363
WARNING: Chromosome 'chr12|13112' not found. File '/home/songbk/Mainul_bin/Bioinfo/022MA2_filtered_snpsfinal.vcf', line 3645364
WARNING: Chromosome 'chr12|13112' not found. File '/home/songbk/Mainul_bin/Bioinfo/022MA2_filtered_snpsfinal.vcf', line 3645365
WARNING: Chromosome 'chr12|13112' not found. File '/home/songbk/Mainul_bin/Bioinfo/022MA2_filtered_snpsfinal.vcf', line 3645366

ERRORS: Some errors were detected
Error type  Number of errors
ERROR_CHROMOSOME_NOT_FOUND  3651011`

So my question is which snpEff database should I use. After that, I also tried to build my own reference snpEff file as collect gff3 and fasat from http://rice.plantbiology.msu.edu/ by following this method (java -jar snpEff.jar build -gff3 -v MSU6v1). The gff file was namely all.gff3 (change to genes.gff) and fasta file was all.con (change to sequences.fa) and kept in MSU6v1 directory and result come with below output

FATAL ERROR: Most Exons do not have sequences!
    There might be differences in the chromosome names used in the genes file '/home/songbk/Mainul_bin/Bioinfo/snpEff/./data/MSU6v1/genes.gff'
    and the chromosme names used in the 'reference sequence' file.
    Please check that chromosome names in both files match.
        Chromosome names missing in 'reference sequence' file:  '1', '10', '11', '12', '2', '3', '4', '5', '6', '7', '8', '9', 'Sy', 'Un', , , , , , , , , , , 
        Chromosome names missing in 'genes' file             :  '10|13110''11|13111''12|13112''1|13101''2|13102''3|13103''4|13104''5|13105''6|13106''7|13107''8|13108''9|13109')
    Fatal Error # see screenshot 2

    WARNING: Cannot find first exonic position after 27061823 for transcript '13105.m05011'
    WARNING: Cannot find first exonic position after 20836530 for transcript '13102.m03765'
    WARNING: Cannot find first exonic position after 28133402 for transcript '13103.m13008'
    WARNING: Cannot find first exonic position after 21074629 for transcript '13102.m03809'
    WARNING: Cannot find last exonic position before 25987811 for transcript '13105.m04749'
    WARNING: Cannot find first exonic position after 2434416 for transcript '13106.m00521'
    no sequence found`

If anyone face same problem before and is there any solution of that?