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snpEff build Error

While building snpEff database for Mitochondrial DNA using Revised Cambridge Reference Sequence genbank(NC_012920.1) file the tool was unable to read protein sequence data and was displaying following error message.

Protein check: NC_012920.1 OK: 0 Not found: 0 Errors: 13 Error percentage: 100.0%

Using the verbose mode I observed the error was caused by the mismatch between SnpEff predicted protein sequence and the Reference protein sequence in genbank file. Has anyone faced a similar issue? Also looking for other alternatives for annotating( to genes & amino acid changes) mitochondrial variants.

annotation software error
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written by Arup Ghosh Arup Ghosh

Were you able to solve this problem? I've tried renaming the chromosome names in gff and fasta files to same name however, ended up having Protein check: mtDNA OK: 0 Not found: 13 Errors: 0 Error percentage: NaN%

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written by ozankiratli ozankiratli

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