[ensembl-dev] Various errors with VEP

[Sarah Hunt]

Hi Adam,

Thanks for letting me know!

Best wishes,

Sarah

On Thu, Jul 5, 2012 at 1:39 PM, Levine, Adam <a.levine at ucl.ac.uk> wrote:
> 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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