[ensembl-dev] Various errors with VEP

[Levine, Adam]

Dear Sarah,

I have updated ensembl-variation and repeated all of the analyses and there are now no error messages!

Thank you very much,

Adam

Adam P. Levine

-----Original Message-----
From: dev-bounces at ensembl.org [mailto:dev-bounces at ensembl.org] On Behalf Of Sarah Hunt
Sent: 05 July 2012 12:38
To: Ensembl developers list
Subject: Re: [ensembl-dev] Various errors with VEP

Hi Adam,

Thanks for the example, it made this one much easier to track down.
TranscriptVariationAllele.pm is now updated in cvs. Do let us know if you hit any further problems.

Best wishes,

Sarah

On Wed, Jul 4, 2012 at 4:54 PM, Levine, Adam <a.levine at ucl.ac.uk> wrote:
> 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;H
> aplotypeScore=219.0875;InbreedingCoeff=-0.0627;MQ=57.80;MQ0=0;MQRankSu
> m=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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