[ensembl-dev] Fwd: Ensembl VEP: FASTA gzip to bgzip conversion failed
Rishi Nag
rishi at ebi.ac.uk
Thu Mar 31 09:24:20 BST 2016
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 ${HOME}/src directory. If you also add the directory containing the Bio directory and the so files that were copied to the PERL5LIB variable it should get picked up,
Rishi
On 30/03/16 19:09, Platon workaccount wrote:
> Hello!
>
> I tried the second set.
>
> echo PERL5LIB
> PERL5LIB
>
> Full command history:
>
> sudo cpan DBI
> sudo apt-get install libmysqlclient-dev
> sudo cpan DBD::mysql
> sudo apt-get install git
> cd src
> git clonehttps://github.com/bioperl/bioperl-live.git
> cd bioperl-live
> git checkout release-1-6-924
> cd -
> git clonehttps://github.com/Ensembl/ensembl-git-tools.git
> export PATH=$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}:${HOME}/src/ensembl-funcgen/modules
> export PERL5LIB
> git clonehttps://github.com/samtools/tabix.git
> cd tabix
> make
> cd perl
> perl Makefile.PL PREFIX=${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=1https://github.com/samtools/htslib.git
> cd htslib
> make
> export HTSLIB_DIR="$PWD"
> cd ..
> git clonehttps://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>>:
>
>
> 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>>>:
> >
> >
> > 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>>>>:
> > >
> > >
> > > 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>>>>>:
> > > >
> > > >
> > > > 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>>>>>>
> > > > > 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>>>>>>
> > > > >
> > > > >
> > > > > 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
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