[ensembl-dev] VEP script error release 84

[Will McLaren]

Hi G.

This error is returned because you have an unsupported version of Perl, as
well as not having the latest version of variant_effect_predictor.pl

Ensembl and VEP support a minimum Perl version of 5.10; this error will
occur on 5.8.x versions.

However, a patch was put in to the ensembl-tools repo to suppress this
error:

https://github.com/Ensembl/ensembl-tools/commit/aaa06ff9e02faa7c10b8f5ea33b1883cec137714

You should have this patched version if you downloaded ensembl-tools after
Dec 21st 2015.

Regards

Will McLaren
Ensembl Variation

On 21 April 2016 at 14:45, Genomeo Dev <genomeodev at gmail.com> wrote:

> Hi Ensembl team,
>
> I have installed VEP script release 84 and found the error below when
> running it. Your help will be appreciated.
>
> Thanks,
>
> G.
>
> *[ggaw84 at hpclogin2 variant_annotation]$ ./ping_ensembl_v84.pl
> <http://ping_ensembl_v84.pl> *
>
> Installation is good. Connection to Ensembl works and you can query the
> human core database
>
> *[ggaw84 at hpclogin2 variant_annotation]$ ./variant_effect_predictor_v84.pl
> <http://variant_effect_predictor_v84.pl> -i example_GRCh38.vcf --database*
>
> Bareword found where operator expected at ./
> variant_effect_predictor_v84.pl line 997, near "s/\_$//r"
>
> syntax error at ./variant_effect_predictor_v84.pl line 997, near
> "s/\_$//r"
>
> Execution of ./variant_effect_predictor_v84.pl aborted due to compilation
> errors.
>
> *[ggaw84 at hpclogin2 variant_annotation]$ grep -n .
> variant_effect_predictor_v81.pl <http://variant_effect_predictor_v81.pl> |
> grep -b5 -a5 '^997'*
>
> 992:    }
>
> 993:
>
> 994:    # warn user DB will be used for SIFT/PolyPhen/HGVS/frequency/LRG
>
> 995:    if(defined($config->{cache})) {
>
> 996:
>
> 997:        # these two def depend on DB
>
> 998:        foreach my $param(grep {defined $config->{$_}} qw(hgvs lrg
> check_sv check_ref)) {
>
> 999:            debug("INFO: Database will be accessed when using
> --$param") unless defined($config->{quiet}) or ($param =~ /hgvs|check_ref/
> and defined($config->{fasta}));
>
> 1000:        }
>
> 1001:
>
> 1002:        debug("INFO: Database will be accessed when using
> --check_frequency with population ".$config->{freq_pop}) if
> !defined($config->{quiet}) and defined($config->{check_frequency}) &&
> $config->{freq_pop} !~ /1kg.*(all|afr|amr|asn|eur)/i;
>
>
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