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?