[ensembl-dev] VEP script runtime errors

[Will McLaren]

Hi Hardip,

Thanks for your help in pointing these out.

None of them are anything to be concerned about - the last one, while
it may appear bad, is just trying to format a number that hasn't been
defined (we just need to change the code to check if it is defined
before we try to format it).

We'll have all of them fixed for the next release.

Please do let us know if you spot any more!

Thanks

Will McLaren
Ensembl Variation

On 26 January 2012 12:00, Hardip Patel <hardip.patel at anu.edu.au> wrote:
> Dear all
>
> I am trying to run vep script using local database and cache using the
> following command.
>
> perl variant_effect_predictor.pl --output_file output.vep --species
> homo_sapiens --host localhost --user user --password password --port 1111
> --db_version 65 --format vcf --buffer 1000000000 --terms ensembl --canonical
> --hgnc --cache --regulatory --protein --gene --condel b --polyphen b --sift
> b --force_overwrite --input_file input.vcf -skip_db_check
>
>
> However, there are few warning thrown. Could somebody please let me know if
> these warnings are acceptable and will not affect the output in anyways?
>
> First warning:
> Use of qw(...) as parentheses is deprecated at
> /home/depressed/variant_effect_predictor/variant_effect_predictor.pl line
> 848.
>
> I am guessing this is the result of using perl v14.2 and also guessing that
> this should not have any serious consequence at this stage.
>
> Second warning is as follows:
> 2012-01-26 17:11:42 - Reading cached adaptor data
> Use of uninitialized value in join or string at
> /home/depressed/ensembl-api/ensembl-variation/modules/Bio/EnsEMBL/Variation/Utils/VEP.pm
> line 3495.
>
> Again guessing that this doesn't cascade into serious trouble while
> reporting results of the script.
>
> However I am more concerned about following warnings (I get multiple of
> them).
>
> Use of uninitialized value in sprintf at
> /home/depressed/ensembl-api/ensembl-variation/modules/Bio/EnsEMBL/Variation/Utils/VEP.pm
> line 932, <GEN0> line 315932.
>
> Trying to debug the code indicated that vcf line responsible for these are
> (examples only out of many)
>
> chr1 57005269 . AACACA AACA 217 .
> INDEL;DP=25;VDB=0.0292;AF1=0.5;AC1=1;DP4=9,5,4,6;MQ=50;FQ=217;PV4=0.41,0.00046,1,0.38
> GT:PL:DP:SP:GQ 0/1:255,0,255:24:4:99
> chr1 61542770 . GAGGGGAGAAGGGG GAGGGGAGAAGGGGAGAAGGGG 106 .
> INDEL;DP=23;VDB=0.0337;AF1=0.5;AC1=1;DP4=1,9,3,6;MQ=41;FQ=109;PV4=0.3,1,0,1
> GT:PL:DP:SP:GQ 0/1:144,0,245:19:5:99
>
> Any help on this matter is greatly appreciated.
>
> Thanking you.
>
> Kind regards
>
>
> Hardip R. Patel, PhD
> Post-doctoral Research Fellow
>
> Genome Discovery Unit and RNA Biology Lab
> Genome Biology Department
> The John Curtin School of Medical Research
> College of Medicine, Biology and Environment
> The Australian National University
> Building 131, Garran Road, ANU Campus, Acton - 0200, ACT, Australia
> Email: hardip.patel at anu.edu.au, patelhardip at gmail.com
> Phone Number: (+61) 0449 180 715
>
>
>
>
>
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