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

DUTTA Prasun s0928794 at sms.ed.ac.uk
Tue Mar 7 10:37:01 GMT 2017


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 -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
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<tel:%2B447438743406>
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