[ensembl-dev] VEP v76

[Konrad Karczewski]

Hi Will,




Looks like re-indexing the FASTA file did it. (I feel like I've had indexing problems before and still don't understand why it works sometimes and not others).




Thanks!


-Konrad

On Mon, Sep 29, 2014 at 7:06 AM, Will McLaren <wm2 at ebi.ac.uk> wrote:

> Hi Konrad,
> I can't replicate the issue I'm afraid. A couple of things to try:
> 1) Update your ensembl-variation checkout from GitHub - there may have been
> a bug fix that caught this already
> 2) Download again and re-index your FASTA file
> 3) If neither of the above works, run perl with -d to jump into the Perl
> debugger, then:
> - press c, enter (you might need to do this twice to skip past a breakpoint)
> - the script should then fail and give you a backtrace of where it failed
> in the code hierarchy, this would help me debug.
> perl -d ./ensembl-tools-release-76/scripts/variant_effect_predictor/
> variant_effect_predictor.pl --everything --vcf --allele_number --no_stats
> --cache --offline --dir ./vep/ --force_overwrite --fasta
> ./vep/homo_sapiens/76_GRCh37/Homo_sapiens.GRCh37.75.dna.primary_assembly.fa
> --tabix -i ./test/test.vcf.gz -o test.vep.vcf.gz --gencode_basic
> Regards
> Will McLaren
> Ensembl Variation
> On 28 September 2014 20:04, Konrad Karczewski <konradk at broadinstitute.org>
> wrote:
>>  Hi dev team,
>>
>> When running v76 of VEP (with GRCh37), I'm getting a bunch of these errors
>> (command below):
>>
>>  substr outside of string at
>> /humgen/atgu1/fs03/konradk/ensembl-tools-release-76/scripts/variant_effect_predictor/Bio/EnsEMBL/Variation/Utils/Sequence.pm
>> line 511.
>> Use of uninitialized value $ref_allele in string eq at
>> /humgen/atgu1/fs03/konradk/ensembl-tools-release-76/scripts/variant_effect_predictor/Bio/EnsEMBL/Variation/Utils/Sequence.pm
>> line 514.
>> Use of uninitialized value in concatenation (.) or string at
>> /humgen/atgu1/fs03/konradk/ensembl-tools-release-76/scripts/variant_effect_predictor/Bio/EnsEMBL/Variation/Utils/Sequence.pm
>> line 643.
>>
>>  perl ./ensembl-tools-release-76/scripts/variant_effect_predictor/
>> variant_effect_predictor.pl --everything --vcf --allele_number --no_stats
>> --cache --offline --dir ./vep/ --force_overwrite --fasta
>> ./vep/homo_sapiens/76_GRCh37/Homo_sapiens.GRCh37.75.dna.primary_assembly.fa
>> --tabix -i ./test/test.vcf.gz -o test.vep.vcf.gz --gencode_basic
>>
>> Here's one line it fails on, for instance:
>>
>> 1       69995   .       G       C       282.63
>> VQSRTrancheSNP99.60to99.80      AC=1
>>
>> Thanks!
>>
>> -Konrad
>>
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