[ensembl-dev] Various errors with VEP

[Levine, Adam]

Dear Sarah,

Thank you for your help.

I have updated to branch 67 and repeated all of the analyses. I now only have errors 1 and 4. Was it error 3 or error 4 that was corrected in branch 67?

I will segment my input file into small sections to try and identify the problematic variant(s) and will get back to you when I have this information.

Thank you again,

Adam

Adam P. Levine
________________________________________
From: dev-bounces at ensembl.org [dev-bounces at ensembl.org] on behalf of Sarah Hunt [seh at ebi.ac.uk]
Sent: 03 July 2012 17:27
To: Ensembl developers list
Subject: Re: [ensembl-dev] Various errors with VEP

Hi Adam,

Could you supply examples of input causing errors 1 and 3 to help us
check them out? The other issues are fixed in branch 67 in cvs.

Best wishes,

Sarah



On Tue, Jul 3, 2012 at 4:04 PM, Levine, Adam <a.levine at ucl.ac.uk> wrote:
> I seem to be getting a number of different errors when using the VEP Perl script with various VCF input files all generated by GATK.
>
> ****START****
> 1. Use of uninitialized value in concatenation (.) or string src/ensemble-variation/modules/Bio/EnsEMBL/Variation/TranscriptVariationAllele.pm line 778, <GEN0> line 82338.
>
> 2. Quantifier follows nothing in regex; marked by <-- HERE in m/* <-- HERE K$/ at /src/ensemble-variation/modules/Bio/EnsEMBL/Variation/TranscriptVariationAllele.pm line 1196, <GEN0> line 653.
>
> 3. Use of uninitialized value in length at /src/ensembl-variation/modules/Bio/EnsEMBL/Variation/TranscriptVariationAllele.pm line 980, <GEN0> line 15939.
>
> 4. Use of uninitialized value in string eq /src/ensembl-variation/modules/Bio/EnsEMBL/Variation/TranscriptVariationAllele.pm line 761, <GEN0> line 15939.
>
> 5. Use of uninitialized value in substitution (s///) at /src/ensemble-variation/modules/Bio/EnsEMBL/Variation/TranscriptVariationAllele.pm line 997, <GEN0> line 15939.
>
> 6. Quantifier follows nothing in regex; marked by <-- HERE in m/* <-- HERE K$/ at /src/ensembl-variation/modules/Bio/EnsEMBL/Variation/TranscriptVariationAllele.pm line 1196, <GEN0> line 653.
> ****END****
>
> I was wondering whether anyone might be able to help me work out what these errors are. For all of these except for error 6, the analyses still ran.
>
> Thank you,
>
> Adam
>
> Adam P. Levine
>
>
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