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<p>Hi,</p>
<p><br>
</p>
<p>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:</p>
<p><b><br>
</b></p>
<p><b></b></p>
<div><b>./t/version.t ........................................ fatal: Not a git repository (or any of the parent directories): .git<br>
./t/version.t ........................................ 1/?<br>
<br>
</b>
<div><b># Failed test 'get current git branch'<br>
# at ./t/version.t line 31.<br>
# Looks like you failed 1 test of 1.<br>
./t/version.t ........................................ Dubious, test returned 1 (wstat 256, 0x100)<br>
Failed 1/1 subtests<br>
<br>
Test Summary Report<br>
-------------------<br>
./t/version.t (Wstat: 256 Tests: 1 Failed: 1)<br>
Failed test: 1<br>
Non-zero exit status: 1<br>
Files=37, Tests=1434, 219 wallclock secs ( 0.33 usr 0.09 sys + 214.22 cusr 5.42 csys = 220.06 CPU)<br>
Result: FAIL<br>
Failed 1/37 test programs. 1/1434 subtests failed.</b><br>
<br>
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.<br>
</div>
<br>
I also tried <span>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
</span>error as well:<br>
<br>
<b><span>grep -v "#" gene_anno.gff | sort -k1,1 -k4,4n -k5,5n | bgzip -c > gene_anno.gff.gz</span><br>
<br>
<span>tabix -p gff gene_anno.gff.gz</span><br>
<br>
</b>
<div><b>perl vep.pl -i variants.vcf -gff gene_anno.gff.gz -fasta reference_genome.fa.gz -o variants_with_VEP.vcf<br>
<br>
-------------------- EXCEPTION --------------------<br>
MSG: ERROR: Cannot use format gff without Bio::DB::HTS::Tabix module installed<br>
<br>
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<br>
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<br>
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<br>
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<br>
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<br>
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<br>
STACK toplevel vep.pl:193<br>
Date (localtime) = Mon Mar 6 17:31:39 2017<br>
Ensembl API version = 87<br>
<br>
</b>How to resolve this error?<b> </b>On checking Bio/DB/HTS/Tabix, there was a file named '<span>Iterator.pm</span>'. Is the installation incomplete or I am doing something wrong?<b><br>
</b></div>
<br>
</div>
<p></p>
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<span>Regards,<br>
Prasun Dutta, M.Sc. (Bioinformatics)<br>
PhD Student, Developmental Biology Division (Hume Group)<br>
The Roslin Institute, <span>The University of Edinburgh, Scotland, UK</span><br>
M: +447438743406</span><span class="HOEnZb adL"><font color="#888888"><a id="LPNoLP" title="Ctrl+Click or tap to follow the link" href="tel:%2B447438743406" value="+447438743406" target="_blank"></a></font></span>
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