<div dir="ltr">Hello,<div><br></div><div>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.</div><div><br></div><div>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?</div><div><br></div><div>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.<br></div><div><br></div><div>The following should work without error if it was installed correctly:</div><br>cd /mnt/ris-fas1a/linux_groups2/hume_grp/Prasun/M3_F3_merged/ensembl-vep-release-87/ensembl-vep-release-87/<br>perl -MBio::DB::HTS::Tabix -e'print "Hello\n";'<div><br></div><div>If you installed to a different directory, you may need to add this to your PERL5LIB or include the path at runtime:</div><br>perl -I /mnt/ris-fas1a/linux_groups2/hume_grp/Prasun/M3_F3_merged/ensembl-vep-release-87/ensembl-vep-release-87/ <a href="http://vep.pl">vep.pl</a> ... etc<div><br></div><div>or</div><div><br></div><div>perl -I [path] <a href="http://vep.pl">vep.pl</a> ... etc<br><div><br></div></div><div>It is also fairly straightforward to install Bio::DB::HTS yourself, see <a href="http://cpansearch.perl.org/src/RISHIDEV/Bio-DB-HTS-2.7/README">http://cpansearch.perl.org/src/RISHIDEV/Bio-DB-HTS-2.7/README</a> or <a href="https://github.com/Ensembl/Bio-DB-HTS">https://github.com/Ensembl/Bio-DB-HTS</a></div><div><br></div><div>Regards</div><div><br></div><div>Will McLaren<br>Ensembl Variation</div></div><div class="gmail_extra"><br><div class="gmail_quote">On 7 March 2017 at 10:37, DUTTA Prasun <span dir="ltr"><<a href="mailto:s0928794@sms.ed.ac.uk" target="_blank">s0928794@sms.ed.ac.uk</a>></span> wrote:<br><blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex">
<div dir="ltr">
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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 ..............................<wbr>.......... fatal: Not a git repository (or any of the parent directories): .git<br>
./t/version.t ..............................<wbr>.......... 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 ..............................<wbr>.......... Dubious, test returned 1 (wstat 256, 0x100)<br>
Failed 1/1 subtests<br>
<br>
Test Summary Report<br>
-------------------<br>
./t/version.t <wbr> (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 <a href="http://vep.pl" target="_blank">vep.pl</a> -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::<wbr>AnnotationSource::File::new /mnt/ris-fas1a/linux_groups2/<wbr>hume_grp/Prasun/M3_F3_merged/<wbr>ensembl-vep-release-87/<wbr>ensembl-vep-release-87/<wbr>modules/Bio/EnsEMBL/VEP/<wbr>AnnotationSource/File.pm:115<br>
STACK Bio::EnsEMBL::VEP::<wbr>AnnotationSourceAdaptor::get_<wbr>all_custom /mnt/ris-fas1a/linux_groups2/<wbr>hume_grp/Prasun/M3_F3_merged/<wbr>ensembl-vep-release-87/<wbr>ensembl-vep-release-87/<wbr>modules/Bio/EnsEMBL/VEP/<wbr>AnnotationSourceAdaptor.pm:141<br>
STACK Bio::EnsEMBL::VEP::<wbr>AnnotationSourceAdaptor::get_<wbr>all /mnt/ris-fas1a/linux_groups2/<wbr>hume_grp/Prasun/M3_F3_merged/<wbr>ensembl-vep-release-87/<wbr>ensembl-vep-release-87/<wbr>modules/Bio/EnsEMBL/VEP/<wbr>AnnotationSourceAdaptor.pm:65<br>
STACK Bio::EnsEMBL::VEP::BaseRunner:<wbr>:get_all_AnnotationSources /mnt/ris-fas1a/linux_groups2/<wbr>hume_grp/Prasun/M3_F3_merged/<wbr>ensembl-vep-release-87/<wbr>ensembl-vep-release-87/<wbr>modules/Bio/EnsEMBL/VEP/<wbr>BaseRunner.pm:119<br>
STACK Bio::EnsEMBL::VEP::Runner::<wbr>init /mnt/ris-fas1a/linux_groups2/<wbr>hume_grp/Prasun/M3_F3_merged/<wbr>ensembl-vep-release-87/<wbr>ensembl-vep-release-87/<wbr>modules/Bio/EnsEMBL/VEP/<wbr>Runner.pm:77<br>
STACK Bio::EnsEMBL::VEP::Runner::run /mnt/ris-fas1a/linux_groups2/<wbr>hume_grp/Prasun/M3_F3_merged/<wbr>ensembl-vep-release-87/<wbr>ensembl-vep-release-87/<wbr>modules/Bio/EnsEMBL/VEP/<wbr>Runner.pm:111<br>
STACK toplevel <a href="http://vep.pl:193" target="_blank">vep.pl:193</a><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>
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