Question: SNPEff database building error
gravatar for ntyagi654
3.8 years ago by
ntyagi6540 wrote:
java.lang.RuntimeException: FATAL ERROR: Most Exons do not have sequences!
There might be differences in the chromosome names used in the genes file \
('/home/crpgws2/Desktop/snpEff/./data/ver6/genes.gff') \
and the chromosme names used in the 'reference sequence' file. \
Please check that chromosome names in both files match.

NOTE: (Line breaks added for clarity)

I got this error when i was running the database build command by using gff. Please let me know how to solve this. Is it possible to change the gff file or i have to change the naming of my chromosome. I am making a reference of Vigna radiata.

snp • 2.0k views
ADD COMMENTlink modified 15 months ago by trinidadmartinc0 • written 3.8 years ago by ntyagi6540

How did that happen by the way? Are you not using a matching bundle of reference sequences and annotation for the analysis? You would have to change one of them as the error says.

ADD REPLYlink written 3.8 years ago by GenoMax94k

do you have the reference genome in fasta file?

grep "^>" myRef.fa

will tell you the chromosome names, check that they match with the annotation

ADD REPLYlink modified 3.8 years ago • written 3.8 years ago by TriS4.3k

Hello all!!!

I am having the same error and I don't undestand why....

My sequences.fa has headers like this:


And my genes.gff looks like this:

tb50_4_tig00000001_BK006938 exonerate:protein2genome:local  match   771461  771859  718 +   . ID=match03090;Name=sp|A0A023PZE8|YD57W_YEAST;Target=sp|A0A023PZE8|YD57W_YEAST 1 133;Gap=M399
tb50_4_tig00000001_BK006938 exonerate:protein2genome:local  match_part  771461  771859  .   +   .   Parent=match03090

So for me, the headers are correct and same in both files... Where am I wrong???

Thanks a lot!!! Trini

ADD REPLYlink written 15 months ago by trinidadmartinc0
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