[ensembl-dev] Uninitialized variable in reverse in Sequence.pm

[Giulietta]

On 03/09/2014 21:02, James Knight wrote:
> I am running VEP, from release 76, using —offline, --everything and "--fasta genome.fa" (to get HGVS annotations while still offline).  When I do this, this error message is output numerous times:
>
> Use of uninitialized value in reverse at /home/jk2269/soft/ensembl-tools-release-76/scripts/variant_effect_predictor/Bio/EnsEMBL/Utils/Sequence.pm line 90.
>
> Is this a bug?

Someone else had this this week and it was resolved by re-indexing the 
FASTA file.

Remove genome.fa.index (and if you want to be really thorough 
re-generate/unpack/download genome.fa too) and re-run.

It could also be that the FASTA file does not have the sequence for a 
chromosome referenced in your input file. Check that all of the 
chromosomes you are referencing in your VEP input file are found in the 
FASTA file.
>
>
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