[ensembl-dev] Fwd: Ensembl VEP: FASTA gzip to bgzip conversion failed
Rishi Nag
rishi at ebi.ac.uk
Thu Mar 31 11:15:45 BST 2016
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=1https://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:
> > > > > >
> > > > > >
> > > > > >
> _______________________________________________
> > > > > > Dev mailing list Dev at ensembl.org
> <mailto:Dev at ensembl.org>
> > <mailto:Dev at ensembl.org <mailto:Dev at ensembl.org>>
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> > <mailto:Dev at ensembl.org <mailto:Dev at ensembl.org>>>
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> > <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>
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> > > > >
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