[ensembl-dev] error in VEP github beta version installation and custom annotation usage in VEP.pl

Tue Mar 7 10:49:07 GMT 2017

Hello,

You can safely ignore the version.t failure, this occurs if you download
ensembl-vep as a zip instead of cloning it with git. This error has been
fixed and the fix will appear in release/88.

Regarding the missing Bio::DB::HTS::Tabix module, are you running VEP from
a different directory, or did you instruct it to install to a different
directory?

INSTALL.pl should have set this up for you, but there's also a chance that
it failed, which I wouldn't know for sure without seeing the output log
from the installer run.

The following should work without error if it was installed correctly:

cd
/mnt/ris-fas1a/linux_groups2/hume_grp/Prasun/M3_F3_merged/ensembl-vep-release-87/ensembl-vep-release-87/
perl -MBio::DB::HTS::Tabix -e'print "Hello\n";'

If you installed to a different directory, you may need to add this to your
PERL5LIB or include the path at runtime:

perl -I
/mnt/ris-fas1a/linux_groups2/hume_grp/Prasun/M3_F3_merged/ensembl-vep-release-87/ensembl-vep-release-87/
vep.pl ... etc

or

perl -I [path] vep.pl ... etc

It is also fairly straightforward to install Bio::DB::HTS yourself, see
http://cpansearch.perl.org/src/RISHIDEV/Bio-DB-HTS-2.7/README or
https://github.com/Ensembl/Bio-DB-HTS

Regards

Will McLaren
Ensembl Variation

On 7 March 2017 at 10:37, DUTTA Prasun <s0928794 at sms.ed.ac.uk> wrote:

> Hi,
>
>
> So based on a recommendation, I tried the new ensemble VEP github beta
> version. Everything went fine in the installation (INSTALL.pl) except I got
> the following error at last:
>
>
>
>
>
> *./t/version.t ........................................ fatal: Not a git
> repository (or any of the parent directories): .git ./t/version.t
> ........................................ 1/? *
>
>
>
>
>
>
>
>
>
>
>
>
>
> *#   Failed test 'get current git branch' #   at ./t/version.t line 31. #
> Looks like you failed 1 test of 1. ./t/version.t
> ........................................ Dubious, test returned 1 (wstat
> 256, 0x100) Failed 1/1 subtests Test Summary Report -------------------
> ./t/version.t                                      (Wstat: 256 Tests: 1
> Failed: 1)   Failed test:  1   Non-zero exit status: 1 Files=37,
> Tests=1434, 219 wallclock secs ( 0.33 usr  0.09 sys + 214.22 cusr  5.42
> csys = 220.06 CPU) Result: FAIL Failed 1/37 test programs. 1/1434 subtests
> failed.*
>
> I ignored this error as all the required VEP files got installed
> correctly. Is this an error that I should be paying attention to? If yes, I
> have no idea what the solution is. Any help/suggestion is welcome.
>
> I also tried using my own GFF and GTF files (for water buffalo, available
> in NCBI genome database) as a source of transcript annotation. Here are the
> commands I used (according to the github manual) and the error as well:
>
>
>
>
>
> *grep -v "#" gene_anno.gff | sort -k1,1 -k4,4n -k5,5n | bgzip -c >
> gene_anno.gff.gz tabix -p gff gene_anno.gff.gz *
>
>
>
>
>
>
>
>
>
>
>
>
>
>
>
> *perl vep.pl <http://vep.pl> -i variants.vcf -gff gene_anno.gff.gz -fasta
> reference_genome.fa.gz -o variants_with_VEP.vcf --------------------
> EXCEPTION -------------------- MSG: ERROR: Cannot use format gff without
> Bio::DB::HTS::Tabix module installed STACK
> Bio::EnsEMBL::VEP::AnnotationSource::File::new
> /mnt/ris-fas1a/linux_groups2/hume_grp/Prasun/M3_F3_merged/ensembl-vep-release-87/ensembl-vep-release-87/modules/Bio/EnsEMBL/VEP/AnnotationSource/File.pm:115
> STACK Bio::EnsEMBL::VEP::AnnotationSourceAdaptor::get_all_custom
> /mnt/ris-fas1a/linux_groups2/hume_grp/Prasun/M3_F3_merged/ensembl-vep-release-87/ensembl-vep-release-87/modules/Bio/EnsEMBL/VEP/AnnotationSourceAdaptor.pm:141
> STACK Bio::EnsEMBL::VEP::AnnotationSourceAdaptor::get_all
> /mnt/ris-fas1a/linux_groups2/hume_grp/Prasun/M3_F3_merged/ensembl-vep-release-87/ensembl-vep-release-87/modules/Bio/EnsEMBL/VEP/AnnotationSourceAdaptor.pm:65
> STACK Bio::EnsEMBL::VEP::BaseRunner::get_all_AnnotationSources
> /mnt/ris-fas1a/linux_groups2/hume_grp/Prasun/M3_F3_merged/ensembl-vep-release-87/ensembl-vep-release-87/modules/Bio/EnsEMBL/VEP/BaseRunner.pm:119
> STACK Bio::EnsEMBL::VEP::Runner::init
> /mnt/ris-fas1a/linux_groups2/hume_grp/Prasun/M3_F3_merged/ensembl-vep-release-87/ensembl-vep-release-87/modules/Bio/EnsEMBL/VEP/Runner.pm:77
> STACK Bio::EnsEMBL::VEP::Runner::run
> /mnt/ris-fas1a/linux_groups2/hume_grp/Prasun/M3_F3_merged/ensembl-vep-release-87/ensembl-vep-release-87/modules/Bio/EnsEMBL/VEP/Runner.pm:111
> STACK toplevel vep.pl:193 <http://vep.pl:193> Date (localtime)    = Mon
> Mar  6 17:31:39 2017 Ensembl API version = 87 *How to resolve this error? On
> checking Bio/DB/HTS/Tabix, there was a file named 'Iterator.pm'. Is the
> installation incomplete or I am doing something wrong?
>
> Regards,
> Prasun Dutta, M.Sc. (Bioinformatics)
> PhD Student, Developmental Biology Division (Hume Group)
> The Roslin Institute, The University of Edinburgh, Scotland, UK
> M: +447438743406 <+44%207438%20743406> <%2B447438743406>
>
> The University of Edinburgh is a charitable body, registered in
> Scotland, with registration number SC005336.
>
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