[ensembl-dev] Various errors with VEP
a.levine at ucl.ac.uk
Tue Jul 3 20:10:04 BST 2012
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 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
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.
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.
> 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.
> 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 P. Levine
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