[ensembl-dev] Fwd: Ensembl VEP: FASTA gzip to bgzip conversion failed
Platon workaccount
platon.work at gmail.com
Wed Mar 30 19:09:31 BST 2016
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 clone https://github.com/bioperl/bioperl-live.git
cd bioperl-live
git checkout release-1-6-924
cd -
git clone https://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 clone https://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 clone https://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>:
>
> 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>>:
> >
> >
> > 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>>>:
> > >
> > >
> > > 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>>>>:
> > > >
> > > >
> > > > 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
> >>>>>
> > > > > 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>>>>>
> > > > >
> > > > >
> > > > > 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:
> > > > >
> > > > >
> > > > > _______________________________________________
> > > > > Dev mailing list 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:
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