SNPEff database building error
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7.2 years ago
ntyagi654 • 0
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 • 3.7k views
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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.

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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

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Hello all!!!

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

My sequences.fa has headers like this:

>tb50_4_tig00000001_BK006938
>tb50_12_tig00000004_BK006945

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

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Hi, Below SNPEff database building error I am getting. "FATAL ERROR: Most Exons do not have sequences!"

The headers are correct and same in both sequence .fa and genes.gtf file. Could any one help me to solve this issue

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