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WGLab / doc-ANNOVAR

Documentation for the ANNOVAR software
http://annovar.openbioinformatics.org
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invalid triplets found in DNA sequence to be translated #98

Open CongqianyouYz opened 4 years ago

CongqianyouYz commented 4 years ago

hi developer,

I tried to annotate rabbit SNVs with Annovar. I downloaded http://hgdownload.cse.ucsc.edu/goldenPath/oryCun2/bigZips/oryCun2.fa.gz and http://hgdownload.cse.ucsc.edu/goldenPath/oryCun2/database/ensGene.txt.gz and build the oryCun2_ensGeneMrna.fa.

The SNVs I was working on: 3 140275163 140275163 T C 14 19837413 19837413 A G

When I ran Annovar the STDOUT was like: Died at /home/disk/pengying/tools/annovar/coding_change.pl line 677. and reported no other information.

In *.ensGene.fa I can find this: WARNING: invalid triplets found in DNA sequence to be translated: \<TAN> in \<ACGTCAAAGCCTCCTGTGTCATCTCTGCCCACATTTCTTCAGAACCCGTGTGTTACTTGCTTAAGGACAGACAACTGGGACAAGTACCGGTACTTTGCTTGCTTGTTGAGAGCCCGGTTTGATGAACATAAGAATGAAAAGGATATGATGAAAGCCACCCGGCTGCTGAGGGACGCAGAGGAAGAGTTCTGGTGCAATCAGCACCCGCAGCCGTACATCTTCCCCGACTCCCCTGGGGGGACCTCCTATGAGAGATACGAGTGCTACAAGGTTCCGGAATGGTGCTTAGATTACTGGCATCCTTCTGAGAAGGCGATGTATCCTGACTACTTTGCCAAGAGAGAGCAGTGGAAGAAACTGCGGAGAGAAAGCTGGGAACGAGAGGTGTGTCCTGCTTGCCCTTCACCGTGCACTTGGTCAGCACAGGACAGGGCTTTGGTCCTGTGGGCAGATACACGGATTCCAGGCCTGGCCCCTTGCTTCTCCGACATACTGGAGTTTCTAATTGTCTCCAGCTTACCACCTCCTGCCGTCTTACAAATGGGTTATGATGTCTTCCCTCGTTTGTTTGCTTCCTCCCCTCCTTAGCCCTTGGACCCTTTTGCTGTACCTCCCTCTCCCTTGAGCTTCACGAGTTACCAGGTGGTGCTCACTCAGAGTTATATTTACTGTACTGGAGAGGCCCAGGGAAGAGACCGATTTGGGGTTTTTGCAGTAGTGTAGCTGAAAGGTTACGGTGTCTANNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNGTTT> But I have no idea what to do next......

Could you please give me some advice? Thank you very much.

Version: $Date: 2020-06-07 23:56:37 -0400 (Sun, 7 Jun 2020) $