[ensembl-dev] Fwd: Ensembl VEP: FASTA gzip to bgzip conversion failed
Platon workaccount
platon.work at gmail.com
Thu Mar 31 11:33:13 BST 2016
:~/ensembl-tools-release-84/scripts/variant_effect_predictor/biodbhts$ ls
blib _build Build Build.PL Changes cpanfile DISCLAIMER INSTALL.pl lib
LICENSE MANIFEST MANIFEST.SKIP META.json META.yml MYMETA.json MYMETA.yml
ppport.h README scripts t typemap
:~/ensembl-tools-release-84/scripts/variant_effect_predictor/Bio/HTS$ ls
Alignment.pm AlignWrapper.pm Constants.pm Faidx.c Faidx.o Faidx.pm Faidx.xs
FetchIterator.pm Pileup.pm PileupWrapper.pm Query.pm ReadIterator.pm
Segment.pm Tabix Tabix.pm Target.pm VCF.pm
perl biodbhts/t/00_load.t
1..3
not ok 1 - use Bio::DB::HTS;
# Failed test 'use Bio::DB::HTS;'
# at biodbhts/t/00_load.t line 3.
# Tried to use 'Bio::DB::HTS'.
# Error: Can't locate Bio/DB/HTS.pm in @INC (you may need to install the
Bio::DB::HTS module) (@INC contains: /home/pl/src/bioperl-live
/home/pl/src/ensembl/modules /home/pl/src/ensembl-compara/modules
/home/pl/src/ensembl-variation/modules /home/pl/src/ensembl-funcgen/modules
/home/pl/src//lib/x86_64-linux-gnu/perl/5.22.1/
/home/pl/src/ensembl-io/modules
/home/pl/ensembl-tools-release-84/scripts/variant_effect_predictor
/etc/perl /usr/local/lib/x86_64-linux-gnu/perl/5.22.1
/usr/local/share/perl/5.22.1 /usr/lib/x86_64-linux-gnu/perl5/5.22
/usr/share/perl5 /usr/lib/x86_64-linux-gnu/perl/5.22 /usr/share/perl/5.22
/usr/local/lib/site_perl /usr/lib/x86_64-linux-gnu/perl-base .) at
biodbhts/t/00_load.t line 3.
# BEGIN failed--compilation aborted at biodbhts/t/00_load.t line 3.
not ok 2 - use Bio::DB::HTS::Tabix;
# Failed test 'use Bio::DB::HTS::Tabix;'
# at biodbhts/t/00_load.t line 4.
# Tried to use 'Bio::DB::HTS::Tabix'.
# Error: Can't locate Bio/DB/HTS/Tabix.pm in @INC (you may need to install
the Bio::DB::HTS::Tabix module) (@INC contains: /home/pl/src/bioperl-live
/home/pl/src/ensembl/modules /home/pl/src/ensembl-compara/modules
/home/pl/src/ensembl-variation/modules /home/pl/src/ensembl-funcgen/modules
/home/pl/src//lib/x86_64-linux-gnu/perl/5.22.1/
/home/pl/src/ensembl-io/modules
/home/pl/ensembl-tools-release-84/scripts/variant_effect_predictor
/etc/perl /usr/local/lib/x86_64-linux-gnu/perl/5.22.1
/usr/local/share/perl/5.22.1 /usr/lib/x86_64-linux-gnu/perl5/5.22
/usr/share/perl5 /usr/lib/x86_64-linux-gnu/perl/5.22 /usr/share/perl/5.22
/usr/local/lib/site_perl /usr/lib/x86_64-linux-gnu/perl-base .) at
biodbhts/t/00_load.t line 4.
# BEGIN failed--compilation aborted at biodbhts/t/00_load.t line 4.
not ok 3 - use Bio::DB::HTS::Tabix::Iterator;
# Failed test 'use Bio::DB::HTS::Tabix::Iterator;'
# at biodbhts/t/00_load.t line 5.
# Tried to use 'Bio::DB::HTS::Tabix::Iterator'.
# Error: Can't locate Bio/DB/HTS/Tabix/Iterator.pm in @INC (you may need to
install the Bio::DB::HTS::Tabix::Iterator module) (@INC contains:
/home/pl/src/bioperl-live /home/pl/src/ensembl/modules
/home/pl/src/ensembl-compara/modules /home/pl/src/ensembl-variation/modules
/home/pl/src/ensembl-funcgen/modules
/home/pl/src//lib/x86_64-linux-gnu/perl/5.22.1/
/home/pl/src/ensembl-io/modules
/home/pl/ensembl-tools-release-84/scripts/variant_effect_predictor
/etc/perl /usr/local/lib/x86_64-linux-gnu/perl/5.22.1
/usr/local/share/perl/5.22.1 /usr/lib/x86_64-linux-gnu/perl5/5.22
/usr/share/perl5 /usr/lib/x86_64-linux-gnu/perl/5.22 /usr/share/perl/5.22
/usr/local/lib/site_perl /usr/lib/x86_64-linux-gnu/perl-base .) at
biodbhts/t/00_load.t line 5.
# BEGIN failed--compilation aborted at biodbhts/t/00_load.t line 5.
# Looks like you failed 3 tests of 3.
чт, 31 мар. 2016 г. в 13:15, Rishi Nag <rishi at ebi.ac.uk>:
>
> The failure occurs as the script attempts to 'use Bio::DB::HTS::Faidx'
> to perform the conversion but then can't load it.
>
> So does
> /home/pl/ensembl-tools-release-84/scripts/variant_effect_predictor have
> a subdirectory Bio/DB/HTS and if so can you provide an ls of this
> directory please?
>
> And then from
> /home/pl/ensembl-tools-release-84/scripts/variant_effect_predictor
> try running
> perl biodbhts/t/00_load.t
>
> This should indicate a more in-depth nature of what is causing the error,
>
> Regards
>
> Rishi
>
>
>
> On 31/03/16 10:18, Platon workaccount wrote:
> >
> PERL5LIB=${PERL5LIB}:${HOME}/ensembl-tools-release-84/scripts/variant_effect_predictor
> > export PERL5LIB
> > perl INSTALL.pl
> >
> > <...>
> > Indexing failed - VEP will attempt to index the file the first time you
> > use it
> > <...>
> >
> > echo $PERL5LIB
> >
> >
> :/home/pl/src/bioperl-live:/home/pl/src/ensembl/modules:/home/pl/src/ensembl-compara/modules:/home/pl/src/ensembl-variation/modules:/home/pl/src/ensembl-funcgen/modules:/home/pl/src//lib/x86_64-linux-gnu/perl/5.22.1/:/home/pl/src/ensembl-io/modules:/home/pl/ensembl-tools-release-84/scripts/variant_effect_predictor
> >
> > чт, 31 мар. 2016 г. в 11:24, Rishi Nag <rishi at ebi.ac.uk
> > <mailto:rishi at ebi.ac.uk>>:
> >
> > Hi There
> >
> > Thanks for the information. The request should have been 'echo
> > $PERL5LIB', but it looks like (from the commands below to set the
> > PERL5LIB environment variable) that things have been set to install
> > the API in the ${HOME}/src directory. If you also add the directory
> > containing the Bio directory and the so files that were copied to
> > the PERL5LIB variable it should get picked up,
> >
> > Rishi
> >
> > On 30/03/16 19:09, Platon workaccount wrote:
> > > Hello!
> > >
> > > I tried the second set.
> > >
> > > echo PERL5LIB
> > > PERL5LIB
> > >
> > > Full command history:
> > >
> > > sudo cpan DBI
> > > sudo apt-get install libmysqlclient-dev
> > > sudo cpan DBD::mysql
> > > sudo apt-get install git
> > > cd src
> > > git clonehttps://github.com/bioperl/bioperl-live.git
> > <http://github.com/bioperl/bioperl-live.git>
> > > cd bioperl-live
> > > git checkout release-1-6-924
> > > cd -
> > > git clonehttps://github.com/Ensembl/ensembl-git-tools.git
> > <http://github.com/Ensembl/ensembl-git-tools.git>
> > > export PATH=$PWD/ensembl-git-tools/bin:$PATH
> > > git ensembl --clone api
> > > PERL5LIB=${PERL5LIB}:${HOME}/src/bioperl-live
> > > PERL5LIB=${PERL5LIB}:${HOME}/src/ensembl/modules
> > > PERL5LIB=${PERL5LIB}:${HOME}/src/ensembl-compara/modules
> > > PERL5LIB=${PERL5LIB}:${HOME}/src/ensembl-variation/modules
> > > PERL5LIB=${PERL5LIB}:${HOME}/src/ensembl-funcgen/modules
> > > export PERL5LIB
> > > git clonehttps://github.com/samtools/tabix.git
> > <http://github.com/samtools/tabix.git>
> > > cd tabix
> > > make
> > > cd perl
> > > perl Makefile.PL PREFIX=${HOME}/src/
> > > make && make install
> > >
> PERL5LIB=${PERL5LIB}:${HOME}/src//lib/x86_64-linux-gnu/perl/5.22.1/
> > > export PERL5LIB
> > > PATH=${PATH}:${HOME}/src/tabix/
> > > export PATH
> > > PERL5LIB=${PERL5LIB}:${HOME}/src/ensembl-io/modules
> > > export PERL5LIB
> > > cd ~
> > > cd ensembl-tools-release-84/scripts/variant_effect_predictor/
> > > git clone -b master --depth=1
> https://github.com/samtools/htslib.git
> > > cd htslib
> > > make
> > > export HTSLIB_DIR="$PWD"
> > > cd ..
> > > git clonehttps://github.com/Ensembl/Bio-HTS.git
> > <http://github.com/Ensembl/Bio-HTS.git> biodbhts
> > > cd biodbhts/
> > > sudo cpan Module::Build
> > > perl Build.PL
> > > ./Build
> > > cp blib/arch/auto/Bio/DB/HTS/Faidx/Faidx.so ..
> > > cp blib/arch/auto/Bio/DB/HTS/HTS.so ..
> > > cp -r lib/Bio/* ../Bio/
> > > cd ~
> > > cd ensembl-tools-release-84/scripts/variant_effect_predictor/
> > > sudo cpan Archive::Extract
> > > perl INSTALL.pl
> > >
> > >
> > > вт, 29 мар. 2016 г. в 13:35, Rishi Nag <rishi at ebi.ac.uk
> > <mailto:rishi at ebi.ac.uk>
> > > <mailto:rishi at ebi.ac.uk <mailto:rishi at ebi.ac.uk>>>:
> > >
> > >
> > > Hi
> > >
> > > Sorry to hear that and sorry for not replying earlier due to
> the
> > > Easter break.
> > >
> > > Did you try the sudo set of instructions or the second set?
> > And can
> > > I check what your PERL5LIB is set to please (run 'echo
> > PERL5LIB')?
> > >
> > > Regards
> > >
> > > Rishi
> > >
> > > On 23/03/2016 19:42, Platon workaccount wrote:
> > > > Unfortunately, your instructions did not help.
> > > >
> > > > Installation log:
> > > >
> > > >
> > > > $ perl INSTALL.pl
> > > >
> > > >
> > > > Hello! This installer is configured to install v84 of the
> > Ensembl
> > > API for use by the VEP.
> > > >
> > > > It will not affect any existing installations of the
> > Ensembl API
> > > that you may have.
> > > >
> > > >
> > > > It will also download and install cache files from
> > Ensembl's FTP
> > > server.
> > > >
> > > >
> > > > Checking for installed versions of the Ensembl
> > API...Subroutine
> > > Tabix::tabix_open redefined at
> > > /home/pl/src/lib/x86_64-linux-gnu/perl/5.20.2/Tabix.pm
> > > > line 17.
> > > >
> > > > Subroutine Tabix::tabix_close redefined at
> > > /home/pl/src/lib/x86_64-linux-gnu/perl/5.20.2/Tabix.pm line
> 17.
> > > >
> > > > Subroutine Tabix::tabix_query redefined at
> > > /home/pl/src/lib/x86_64-linux-gnu/perl/5.20.2/Tabix.pm line
> 17.
> > > >
> > > > Subroutine Tabix::tabix_read redefined at
> > > /home/pl/src/lib/x86_64-linux-gnu/perl/5.20.2/Tabix.pm line
> 17.
> > > >
> > > > Subroutine Tabix::tabix_getnames redefined at
> > > /home/pl/src/lib/x86_64-linux-gnu/perl/5.20.2/Tabix.pm line
> 17.
> > > >
> > > > Subroutine TabixIterator::tabix_iter_free redefined at
> > > /home/pl/src/lib/x86_64-linux-gnu/perl/5.20.2/Tabix.pm line
> 17.
> > > >
> > > > done
> > > >
> > > > It looks like you already have v84 of the API installed.
> > > >
> > > > You shouldn't need to install the API
> > > >
> > > >
> > > > Skip to the next step (n) to install cache files
> > > >
> > > >
> > > > Do you want to continue installing the API (y/n)? n
> > > >
> > > > - skipping API installation
> > > >
> > > >
> > > > The VEP can either connect to remote or local databases,
> > or use
> > > local cache files.
> > > >
> > > > Using local cache files is the fastest and most efficient
> > way to
> > > run the VEP
> > > >
> > > > Cache files will be stored in /home/pl/.vep
> > > >
> > > > Do you want to install any cache files (y/n)? n
> > > >
> > > > Skipping cache installation
> > > >
> > > >
> > > > The VEP can use FASTA files to retrieve sequence data for
> HGVS
> > > notations and reference sequence checks.
> > > >
> > > > FASTA files will be stored in /home/pl/.vep
> > > >
> > > > Do you want to install any FASTA files (y/n)? y
> > > >
> > > > FASTA files for the following species are available; which
> > do you
> > > want (can specify multiple separated by spaces, "0" to
> > install for
> > > species specified
> > > > for cache download):
> > > >
> > > > <...>
> > > >
> > > > 28 : homo_sapiens
> > > >
> > > > <...>
> > > >
> > > > ? 28
> > > >
> > > > - downloading
> Homo_sapiens.GRCh38.dna.primary_assembly.fa.gz
> > > >
> > > > - converting sequence data to bgzip format
> > > >
> > > > Going to run:
> > > >
> > > > ./biodbhts/scripts/convert_gz_2_bgz.sh
> > >
> >
> /home/pl/.vep/homo_sapiens/84_GRCh38/Homo_sapiens.GRCh38.dna.primary_assembly.fa.gz
> > > ./htslib/bgzip
> > > >
> > > > This may take some time and will be removed when files are
> > > provided in bgzip format
> > > >
> > > > Converted FASTA gzip file to bgzip successfully
> > > >
> > > > Indexing failed - VEP will attempt to index the file the
> first
> > > time you use it
> > > >
> > > > The FASTA file should be automatically detected by the VEP
> > when
> > > using --cache or --offline. If it is not, use "--fasta
> > > >
> > >
> >
> /home/pl/.vep/homo_sapiens/84_GRCh38/Homo_sapiens.GRCh38.dna.primary_assembly.fa.gz"
> > > >
> > > >
> > > > The VEP can use plugins to add functionality and data.
> > > >
> > > > Plugins will be installed in /home/pl/.vep/Plugins
> > > >
> > > > Do you want to install any plugins (y/n)? n# #y
> > > >
> > > > ** GET
> > >
> >
> https://raw.githubusercontent.com/Ensembl/VEP_plugins/release/84/plugin_config.txt
> > > ==> 16%#### 32%#### 48%#### 64%#### 80%####
> > > > 96%####100%####200 OK
> > > >
> > > >
> > > > ср, 23 мар. 2016 г. в 19:49, Rishi Nag <rishi at ebi.ac.uk
> > <mailto:rishi at ebi.ac.uk>
> > > <mailto:rishi at ebi.ac.uk <mailto:rishi at ebi.ac.uk>>
> > <mailto:rishi at ebi.ac.uk <mailto:rishi at ebi.ac.uk>
> > > <mailto:rishi at ebi.ac.uk <mailto:rishi at ebi.ac.uk>>>>:
> > > >
> > > >
> > > > It sounds like there has been a failure to set up . If
> you
> > > could pass on the full output from your install attempt
> > relating to
> > > the API components that
> > > > would be useful.
> > > >
> > > > There are two ways forward however to complete the
> > > installation process manually.
> > > >
> > > > The first is if you have sudo permissions on your
> > machine and
> > > are happy to have libraries installed on the system level:
> > > > cd htslib
> > > > sudo make install
> > > > cd ../biodbhts
> > > > perl Build.PL
> > > > ./Build
> > > > sudo ./Build install
> > > > cd ..
> > > >
> > > >
> > > > Alternatively the following replicates what the INSTALL
> > > script should be doing:
> > > > cd htslib
> > > > export HTSLIB_DIR="$PWD"
> > > > cd ../biodbhts
> > > > perl Build.PL
> > > > ./Build
> > > > cp blib/arch/auto/Bio/DB/HTS/Faidx/Faidx.so ..
> > > > cp blib/arch/auto/Bio/DB/HTS/HTS.so ..
> > > > cp -r lib/Bio/* ../Bio/
> > > >
> > > > And finally, if these cause issues there is the option
> of
> > > re-installing with the -NO_HTSLIB flag, which will bypass the
> > > bgzipped sequence file
> > > > process.
> > > >
> > > > Regards
> > > >
> > > > Rishi
> > > >
> > > >
> > > > On 23/03/2016 14:52, Platon workaccount wrote:
> > > > > Thanks! "Converted FASTA gzip file to bgzip
> > successfully",
> > > but this time "Indexing failed - VEP will attempt to index
> > the file
> > > the first time
> > > > you use
> > > > > it". Is it a critical error?
> > > > >
> > > > > ср, 23 мар. 2016 г. в 12:02, Rishi Nag
> > <rishi at ebi.ac.uk <mailto:rishi at ebi.ac.uk>
> > > <mailto:rishi at ebi.ac.uk <mailto:rishi at ebi.ac.uk>>
> > <mailto:rishi at ebi.ac.uk <mailto:rishi at ebi.ac.uk>
> > > <mailto:rishi at ebi.ac.uk <mailto:rishi at ebi.ac.uk>>>
> > <mailto:rishi at ebi.ac.uk <mailto:rishi at ebi.ac.uk>
> > > <mailto:rishi at ebi.ac.uk <mailto:rishi at ebi.ac.uk>>
> > <mailto:rishi at ebi.ac.uk <mailto:rishi at ebi.ac.uk>
> > > <mailto:rishi at ebi.ac.uk <mailto:rishi at ebi.ac.uk>>>>>:
> > > > >
> > > > >
> > > > > Thanks.
> > > > >
> > > > > Change into the same directory as INSTALL.pl
> > > > >
> > > > > First check for a htslib directory being
> > present with
> > > the ls command. If not then download and compile this:
> > > > > git clone -b master --depth=1
> > > https://github.com/samtools/htslib.git
> > > > > cd htslib
> > > > > make
> > > > > cd ..
> > > > >
> > > > > git clone
> > https://github.com/Ensembl/Bio-HTS.git biodbhts
> > > > > You should then be able to re-run the install
> > commands
> > > to download the sequence from this directory.
> > > > >
> > > > > Regards
> > > > >
> > > > > Rishi
> > > > >
> > > > >
> > > > > On 22/03/2016 18:17, Platon workaccount wrote:
> > > > > > VEP's install script was invoked by command
> perl
> > > INSTALL.pl
> > > > > >
> > > > > > вт, 22 мар. 2016 г. в 15:32, Rishi Nag
> > > <rishi at ebi.ac.uk <mailto:rishi at ebi.ac.uk>
> > <mailto:rishi at ebi.ac.uk <mailto:rishi at ebi.ac.uk>>
> > <mailto:rishi at ebi.ac.uk <mailto:rishi at ebi.ac.uk>
> > > <mailto:rishi at ebi.ac.uk <mailto:rishi at ebi.ac.uk>>>
> > <mailto:rishi at ebi.ac.uk <mailto:rishi at ebi.ac.uk>
> > > <mailto:rishi at ebi.ac.uk <mailto:rishi at ebi.ac.uk>>
> > <mailto:rishi at ebi.ac.uk <mailto:rishi at ebi.ac.uk>
> > > <mailto:rishi at ebi.ac.uk <mailto:rishi at ebi.ac.uk>>>>
> > > > <mailto:rishi at ebi.ac.uk <mailto:rishi at ebi.ac.uk>
> > <mailto:rishi at ebi.ac.uk <mailto:rishi at ebi.ac.uk>>
> > > <mailto:rishi at ebi.ac.uk <mailto:rishi at ebi.ac.uk>
> > <mailto:rishi at ebi.ac.uk <mailto:rishi at ebi.ac.uk>>>
> > > <mailto:rishi at ebi.ac.uk <mailto:rishi at ebi.ac.uk>
> > <mailto:rishi at ebi.ac.uk <mailto:rishi at ebi.ac.uk>>
> > > <mailto:rishi at ebi.ac.uk <mailto:rishi at ebi.ac.uk>
> > <mailto:rishi at ebi.ac.uk <mailto:rishi at ebi.ac.uk>>>>>>:
> > > > > >
> > > > > >
> > > > > > Hi
> > > > > >
> > > > > > Thanks for raising this issue. Can you
> > provide
> > > details on how the install script was invoked please?
> > > > > >
> > > > > > Regards
> > > > > >
> > > > > > Rishi
> > > > > >
> > > > > > On 22/03/2016 12:04, Platon workaccount
> > wrote:
> > > > > > >
> > > > > > >
> > > > > > > ---------- Forwarded message ---------
> > > > > > > From: Platon workaccount
> > > <platon.work at gmail.com <mailto:platon.work at gmail.com>
> > <mailto:platon.work at gmail.com <mailto:platon.work at gmail.com>>
> > > <mailto:platon.work at gmail.com <mailto:platon.work at gmail.com>
> > <mailto:platon.work at gmail.com <mailto:platon.work at gmail.com>>>
> > > <mailto:platon.work at gmail.com <mailto:platon.work at gmail.com>
> > <mailto:platon.work at gmail.com <mailto:platon.work at gmail.com>>
> > > > <mailto:platon.work at gmail.com
> > <mailto:platon.work at gmail.com>
> > > <mailto:platon.work at gmail.com
> > <mailto:platon.work at gmail.com>>>> <mailto:platon.work at gmail.com
> > <mailto:platon.work at gmail.com>
> > > <mailto:platon.work at gmail.com <mailto:platon.work at gmail.com>>
> > <mailto:platon.work at gmail.com <mailto:platon.work at gmail.com>
> > > <mailto:platon.work at gmail.com <mailto:platon.work at gmail.com
> >>>
> > > > > <mailto:platon.work at gmail.com
> > <mailto:platon.work at gmail.com>
> > > <mailto:platon.work at gmail.com <mailto:platon.work at gmail.com>>
> > <mailto:platon.work at gmail.com <mailto:platon.work at gmail.com>
> > > <mailto:platon.work at gmail.com
> > <mailto:platon.work at gmail.com>>>>> <mailto:platon.work at gmail.com
> > <mailto:platon.work at gmail.com>
> > > <mailto:platon.work at gmail.com <mailto:platon.work at gmail.com>>
> > <mailto:platon.work at gmail.com <mailto:platon.work at gmail.com>
> > > <mailto:platon.work at gmail.com <mailto:platon.work at gmail.com
> >>>
> > > > <mailto:platon.work at gmail.com
> > <mailto:platon.work at gmail.com> <mailto:platon.work at gmail.com
> > <mailto:platon.work at gmail.com>>
> > > <mailto:platon.work at gmail.com <mailto:platon.work at gmail.com>
> > <mailto:platon.work at gmail.com <mailto:platon.work at gmail.com>>>>
> > > <mailto:platon.work at gmail.com <mailto:platon.work at gmail.com>
> > <mailto:platon.work at gmail.com <mailto:platon.work at gmail.com>>
> > > <mailto:platon.work at gmail.com <mailto:platon.work at gmail.com>
> > <mailto:platon.work at gmail.com <mailto:platon.work at gmail.com>>>
> > > > > <mailto:platon.work at gmail.com
> > <mailto:platon.work at gmail.com>
> > > <mailto:platon.work at gmail.com <mailto:platon.work at gmail.com>>
> > <mailto:platon.work at gmail.com <mailto:platon.work at gmail.com>
> > > <mailto:platon.work at gmail.com
> > <mailto:platon.work at gmail.com>>>>>>>
> > > > > > > Date: вт, 22 мар. 2016 г. в 14:58
> > > > > > > Subject: Ensembl VEP: FASTA gzip to
> bgzip
> > > conversion failed
> > > > > > > To: <dev at ensembl.org
> > <mailto:dev at ensembl.org>
> > > <mailto:dev at ensembl.org <mailto:dev at ensembl.org>>
> > <mailto:dev at ensembl.org <mailto:dev at ensembl.org>
> > > <mailto:dev at ensembl.org <mailto:dev at ensembl.org>>>
> > <mailto:dev at ensembl.org <mailto:dev at ensembl.org>
> > > <mailto:dev at ensembl.org <mailto:dev at ensembl.org>>
> > <mailto:dev at ensembl.org <mailto:dev at ensembl.org>
> > > <mailto:dev at ensembl.org <mailto:dev at ensembl.org>>>>
> > <mailto:dev at ensembl.org <mailto:dev at ensembl.org>
> > > <mailto:dev at ensembl.org <mailto:dev at ensembl.org>>
> > > > <mailto:dev at ensembl.org <mailto:dev at ensembl.org>
> > <mailto:dev at ensembl.org <mailto:dev at ensembl.org>>>
> > > <mailto:dev at ensembl.org <mailto:dev at ensembl.org>
> > <mailto:dev at ensembl.org <mailto:dev at ensembl.org>>
> > > <mailto:dev at ensembl.org <mailto:dev at ensembl.org>
> > <mailto:dev at ensembl.org <mailto:dev at ensembl.org>>>>>
> > > <mailto:dev at ensembl.org <mailto:dev at ensembl.org>
> > <mailto:dev at ensembl.org <mailto:dev at ensembl.org>>
> > > <mailto:dev at ensembl.org <mailto:dev at ensembl.org>
> > <mailto:dev at ensembl.org <mailto:dev at ensembl.org>>>
> > > > > <mailto:dev at ensembl.org
> > <mailto:dev at ensembl.org> <mailto:dev at ensembl.org
> > <mailto:dev at ensembl.org>>
> > > <mailto:dev at ensembl.org <mailto:dev at ensembl.org>
> > <mailto:dev at ensembl.org <mailto:dev at ensembl.org>>>>
> > > <mailto:dev at ensembl.org <mailto:dev at ensembl.org>
> > <mailto:dev at ensembl.org <mailto:dev at ensembl.org>>
> > > <mailto:dev at ensembl.org <mailto:dev at ensembl.org>
> > <mailto:dev at ensembl.org <mailto:dev at ensembl.org>>>
> > > <mailto:dev at ensembl.org <mailto:dev at ensembl.org>
> > <mailto:dev at ensembl.org <mailto:dev at ensembl.org>>
> > > > <mailto:dev at ensembl.org <mailto:dev at ensembl.org>
> > <mailto:dev at ensembl.org <mailto:dev at ensembl.org>>>>>>>
> > > > > > >
> > > > > > >
> > > > > > > Hello.
> > > > > > >
> > > > > > > Full API end dependencies are
> installed
> > > (bioperl-live, ensembl, ensembl-compara, ensembl-variation,
> > > ensembl-funcgen; tabix; DBI,
> > > > > DBD::mysql);
> > > > > > > environment is set up
> > > > > > > my $API_VERSION = 84
> > > > > > > ubuntu-15.10-desktop-amd64
> > > > > > >
> > > > > > > Error of converting sequence data:
> > > > > > >
> > > > > > > ? 28
> > > > > > > - downloading
> > > Homo_sapiens.GRCh38.dna.primary_assembly.fa.gz
> > > > > > > - converting sequence data to bgzip
> > format
> > > > > > > Going to run:
> > > > > > > ./biodbhts/scripts/convert_gz_2_bgz.sh
> > >
> >
> /home/pl/.vep/homo_sapiens/84_GRCh38/Homo_sapiens.GRCh38.dna.primary_assembly.fa.gz
> > > > ./htslib/bgzip
> > > > > > > This may take some time and will be
> > removed
> > > when files are provided in bgzip format
> > > > > > > /bin/bash:
> > > ./biodbhts/scripts/convert_gz_2_bgz.sh: No such file or
> directory
> > > > > > > FASTA gzip to bgzip conversion failed:
> > > > > > >
> > > > > > >
> > > > > > >
> > _______________________________________________
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