[ensembl-dev] Various errors with VEP

[Levine, Adam]

Dear Sarah,

It is certainly much better.

I am now only getting this error:

Use of uninitialized value in string eq at /src/ensembl-variation/modules/Bio/EnsEMBL/Variation/TranscriptVariationAllele.pm line 996, <GEN0> line 15939.

This is an example of an input for which I get this error:

##fileformat=VCFv4.1
#CHROM  POS     ID      REF     ALT     QUAL    FILTER  INFO
12      80169710        .       TA      T       158.57  FSFilter;QDFilter
AC=10;AF=0.0581;AN=172;BaseQRankSum=24.631;DP=5250;FS=514.803;HRun=1;HaplotypeScore=219.0875;InbreedingCoeff=-0.0627;MQ=57.80;MQ0=0;MQRankSum=1.246;QD=0.28;ReadPosRankSum=7.966;SB=-127.24;set=FilteredInAll

It still seems to be running through the VEP and producing an output.

Thank you,

Adam

Adam P. Levine

-----Original Message-----
From: dev-bounces at ensembl.org [mailto:dev-bounces at ensembl.org] On Behalf Of Sarah Hunt
Sent: 04 July 2012 12:15
To: Ensembl developers list
Subject: Re: [ensembl-dev] Various errors with VEP

Hi Adam,

I think I have been able to replicate the issues you found. I've just
checked the update into branch 67 - let me know if this doesn't fix
the problem you observed.

Thanks,

Sarah

On Tue, Jul 3, 2012 at 8:10 PM, Levine, Adam <a.levine at ucl.ac.uk> wrote:
> 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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>
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