[maker-devel] Annotation with maker2
Carson Holt
carsonhh at gmail.com
Fri Mar 21 08:23:18 MDT 2014
Glad it's working. Let us know if anything else comes up.
--Carson
From: Chris Bioinfo <chrisbioinfo at gmail.com>
Date: Friday, March 21, 2014 at 4:57 AM
To: Carson Holt <carsonhh at gmail.com>
Subject: Re: [maker-devel] Annotation with maker2
Dear Carson
it works!! after many difficults :
I have installed sqlite3.8.4.1 yesterday: it was """better"""" (no error
message by launching sqlite3). Yet my test.db was not created..
Today I find the trick!
the problem was due to my too long path to created the db .. only that...
Thanks for your time and you help Carson!
All the best,
Christelle
2014-03-20 18:21 GMT+01:00 Carson Holt <carsonhh at gmail.com>:
> Also you can use this command line to test both before and after installing
>
> perl -MDBI -MDBD::SQLite -e 'print "$DBD::SQLite::sqlite_version\n"; $dbh =
> DBI->connect("dbi:SQLite:dbname=/path/from/maker/error/dpp_contig.db","","");'
>
> Make sure to set /path/from/maker/error/dpp_contig.db to whatever its was in
> the error.
>
> --Carson
>
>
> From: Carson Holt <carsonhh at gmail.com>
> Date: Thursday, March 20, 2014 at 11:03 AM
> To: Chris Bioinfo <chrisbioinfo at gmail.com>
>
> Subject: Re: [maker-devel] Annotation with maker2
>
> The failure is in SQLite. So you have to reinstall. I.e. 'force install
> DBD::SQLite' in CPAN. Otherwise you are just keeping whatever module is
> installed which may have broken C bindings.
>
> You may also have to install SQLite 3.8.4.1, and then reinstall the perl
> modules using the force option to force recompile.
>
> --Carson
>
>
>
> From: Chris Bioinfo <chrisbioinfo at gmail.com>
> Date: Thursday, March 20, 2014 at 10:57 AM
> To: Carson Holt <carsonhh at gmail.com>
> Subject: Re: [maker-devel] Annotation with maker2
>
> cpan[2]> install DBI
> DBI is up to date (1.631).
>
> cpan[3]> install DBD::SQLite
> DBD::SQLite is up to date (1.42).
>
> my test.db is not created effectively:
>
> sqlite3 dpp_contig.maker.output/test.db
> SQLite version 3.8.3.1 2014-02-11 14:52:19
> Enter ".help" for instructions
> Enter SQL statements terminated with a ";"
> sqlite>
>
>
>
>
> 2014-03-20 17:36 GMT+01:00 Carson Holt <carsonhh at gmail.com>:
>> I'm actually checking the mount points for the disk. SQLite won't work on
>> filesystems that don't implement locks, and 'df' is a good way to infer some
>> of that info.
>>
>> Basically I still think this is SQLlite failing on your system. You might
>> need to reinstall SQLlite and then reinstall the perl DBI and DBD::SQLite
>> modules.
>>
>> You can also do a test command --> 'sqllite3 dpp_contig.maker.output/test.db'
>>
>> This will work if you have sqllite3 installed. And any error it give may be
>> informative.
>>
>> --Carson
>>
>> From: Chris Bioinfo <chrisbioinfo at gmail.com>
>> Date: Thursday, March 20, 2014 at 10:29 AM
>>
>> To: Carson Holt <carsonhh at gmail.com>
>> Subject: Re: [maker-devel] Annotation with maker2
>>
>> oh sorry
>>
>> my disks are quite full, but still space I guess for maker
>>
>> /dev/sdc1 19T 18T 934G 95% /home
>>
>>
>> 2014-03-20 17:23 GMT+01:00 Chris Bioinfo <chrisbioinfo at gmail.com>:
>>> this :
>>>
>>> du -h dpp_contig.maker.output/
>>> 0
>>> dpp_contig.maker.output/dpp_contig_datastore/05/1F/contig-dpp-500-500/theVoi
>>> d.contig-dpp-500-500/0
>>> 88K
>>> dpp_contig.maker.output/dpp_contig_datastore/05/1F/contig-dpp-500-500/theVoi
>>> d.contig-dpp-500-500
>>> 92K dpp_contig.maker.output/dpp_contig_datastore/05/1F/contig-dpp-500-500
>>> 92K dpp_contig.maker.output/dpp_contig_datastore/05/1F
>>> 92K dpp_contig.maker.output/dpp_contig_datastore/05
>>> 92K dpp_contig.maker.output/dpp_contig_datastore
>>> 4.0K dpp_contig.maker.output/dpp_contig_master_datastore_index.log
>>> 4.0K dpp_contig.maker.output/maker_bopts.log
>>> 4.0K dpp_contig.maker.output/maker_exe.log
>>> 8.0K dpp_contig.maker.output/maker_opts.log
>>> 16K dpp_contig.maker.output/mpi_blastdb/dpp_protein%2Efasta.mpi.1
>>> 44K dpp_contig.maker.output/mpi_blastdb/dpp_contig%2Efasta.mpi.1
>>> 14M dpp_contig.maker.output/mpi_blastdb/te_proteins%2Efasta.mpi.10
>>> 32K dpp_contig.maker.output/mpi_blastdb/dpp_est%2Efasta.mpi.1
>>> 14M dpp_contig.maker.output/mpi_blastdb
>>> 0 dpp_contig.maker.output/seen.dbm
>>>
>>>
>>>
>>> 2014-03-20 17:10 GMT+01:00 Carson Holt <carsonhh at gmail.com>:
>>>
>>>> What does 'df -h dpp_contig.maker.output' show?
>>>>
>>>> --Carson
>>>>
>>>> From: Chris Bioinfo <chrisbioinfo at gmail.com>
>>>> Date: Thursday, March 20, 2014 at 10:00 AM
>>>>
>>>> To: Carson Holt <carsonhh at gmail.com>
>>>> Subject: Re: [maker-devel] Annotation with maker2
>>>>
>>>> sorry, mistake on the dir!
>>>>
>>>> I have these files:
>>>> dpp_contig_datastore dpp_contig_master_datastore_index.log
>>>> maker_bopts.log maker_exe.log maker_opts.log mpi_blastdb seen.dbm
>>>>
>>>>
>>>> 2014-03-20 16:59 GMT+01:00 Chris Bioinfo <chrisbioinfo at gmail.com>:
>>>>> no,
>>>>>
>>>>> I have theses files in the directory:
>>>>> dpp_contig.fasta dpp_est.fasta hsap_contig.fasta
>>>>> hsap_protein.fasta maker_exe.ctl
>>>>> dpp_contig.maker.output dpp_protein.fasta hsap_est.fasta
>>>>> maker_bopts.ctl maker_opts.ctl te_proteins.fasta
>>>>>
>>>>>
>>>>>
>>>>> 2014-03-20 16:53 GMT+01:00 Carson Holt <carsonhh at gmail.com>:
>>>>>
>>>>>> Did
>>>>>> /home/cdantec/cutQuality/assembly/HR/path/to/Maker/test/dpp_contig.maker.
>>>>>> output/dpp_contig.db exist?
>>>>>>
>>>>>> --Carson
>>>>>>
>>>>>>
>>>>>> From: Chris Bioinfo <chrisbioinfo at gmail.com>
>>>>>> Date: Thursday, March 20, 2014 at 9:50 AM
>>>>>>
>>>>>> To: Carson Holt <carsonhh at gmail.com>
>>>>>> Subject: Re: [maker-devel] Annotation with maker2
>>>>>>
>>>>>> cdantec at belem:~$ /usr/bin/perl -v
>>>>>>
>>>>>> This is perl 5, version 18, subversion 1 (v5.18.1) built for
>>>>>> x86_64-linux-gnu-thread-multi
>>>>>> (with 46 registered patches, see perl -V for more detail)
>>>>>>
>>>>>> Copyright 1987-2013, Larry Wall
>>>>>>
>>>>>> Perl may be copied only under the terms of either the Artistic License or
>>>>>> the
>>>>>> GNU General Public License, which may be found in the Perl 5 source kit.
>>>>>>
>>>>>> Complete documentation for Perl, including FAQ lists, should be found on
>>>>>> this system using "man perl" or "perldoc perl". If you have access to
>>>>>> the
>>>>>> Internet, point your browser at http://www.perl.org/, the Perl Home Page.
>>>>>>
>>>>>>
>>>>>>
>>>>>> 2014-03-20 16:32 GMT+01:00 Carson Holt <carsonhh at gmail.com>:
>>>>>>> What do you get for when you type --> /usr/bin/perl -v
>>>>>>>
>>>>>>> The key to the error is this line -->
>>>>>>> DBI
>>>>>>> connect('dbname=/home/cdantec/cutQuality/assembly/HR/path/to/Maker/test/
>>>>>>> dpp_contig.maker.output/dpp_contig.db','',...) failed: unable to open
>>>>>>> database file
>>>>>>>
>>>>>>> Either the database doesn't exist, or is corrupt. Does it exist?
>>>>>>>
>>>>>>> --Carson
>>>>>>>
>>>>>>> From: Chris Bioinfo <chrisbioinfo at gmail.com>
>>>>>>> Date: Thursday, March 20, 2014 at 9:25 AM
>>>>>>> To: Carson Holt <carsonhh at gmail.com>
>>>>>>> Subject: Re: [maker-devel] Annotation with maker2
>>>>>>>
>>>>>>> Dear Carson,
>>>>>>>
>>>>>>> I have reinstalled DBD::SQLite module, check the permission in my
>>>>>>> directory, configure the TMP value in maker_opts.ctl. perl is in
>>>>>>> /usr/bin/perl.
>>>>>>> I have deleted many times the output directory.. but same problem..
>>>>>>>
>>>>>>> So here the debug output :
>>>>>>> ****MODULE VERSION INFO
>>>>>>> 0.05 Acme::Damn /usr/local/lib/perl/5.18.1/Acme/Damn.pm
>>>>>>> 1.01 AnyDBM_File /usr/share/perl/5.18/AnyDBM_File.pm
>>>>>>> 5.73 AutoLoader /usr/share/perl/5.18/AutoLoader.pm
>>>>>>> UNKNOWN Bio::AnalysisParserI
>>>>>>> /usr/local/share/perl/5.18.1/Bio/AnalysisParserI.pm
>>>>>>> UNKNOWN Bio::AnnotatableI
>>>>>>> /usr/local/share/perl/5.18.1/Bio/AnnotatableI.pm
>>>>>>> UNKNOWN Bio::Annotation::Collection
>>>>>>> /usr/local/share/perl/5.18.1/Bio/Annotation/Collection.pm
>>>>>>> UNKNOWN Bio::Annotation::SimpleValue
>>>>>>> /usr/local/share/perl/5.18.1/Bio/Annotation/SimpleValue.pm
>>>>>>> UNKNOWN Bio::Annotation::TypeManager
>>>>>>> /usr/local/share/perl/5.18.1/Bio/Annotation/TypeManager.pm
>>>>>>> UNKNOWN Bio::AnnotationCollectionI
>>>>>>> /usr/local/share/perl/5.18.1/Bio/AnnotationCollectionI.pm
>>>>>>> UNKNOWN Bio::AnnotationI
>>>>>>> /usr/local/share/perl/5.18.1/Bio/AnnotationI.pm
>>>>>>> 1.006923 Bio::DB::Fasta
>>>>>>> /usr/local/share/perl/5.18.1/Bio/DB/Fasta.pm
>>>>>>> UNKNOWN Bio::DB::InMemoryCache
>>>>>>> /usr/local/share/perl/5.18.1/Bio/DB/InMemoryCache.pm
>>>>>>> UNKNOWN Bio::DB::IndexedBase
>>>>>>> /usr/local/share/perl/5.18.1/Bio/DB/IndexedBase.pm
>>>>>>> UNKNOWN Bio::DB::RandomAccessI
>>>>>>> /usr/local/share/perl/5.18.1/Bio/DB/RandomAccessI.pm
>>>>>>> UNKNOWN Bio::DB::SeqI
>>>>>>> /usr/local/share/perl/5.18.1/Bio/DB/SeqI.pm
>>>>>>> UNKNOWN Bio::DescribableI
>>>>>>> /usr/local/share/perl/5.18.1/Bio/DescribableI.pm
>>>>>>> UNKNOWN Bio::Event::EventGeneratorI
>>>>>>> /usr/local/share/perl/5.18.1/Bio/Event/EventGeneratorI.pm
>>>>>>> UNKNOWN Bio::Event::EventHandlerI
>>>>>>> /usr/local/share/perl/5.18.1/Bio/Event/EventHandlerI.pm
>>>>>>> UNKNOWN Bio::Factory::ObjectFactory
>>>>>>> /usr/local/share/perl/5.18.1/Bio/Factory/ObjectFactory.pm
>>>>>>> UNKNOWN Bio::Factory::ObjectFactoryI
>>>>>>> /usr/local/share/perl/5.18.1/Bio/Factory/ObjectFactoryI.pm
>>>>>>> UNKNOWN Bio::Factory::SequenceFactoryI
>>>>>>> /usr/local/share/perl/5.18.1/Bio/Factory/SequenceFactoryI.pm
>>>>>>> UNKNOWN Bio::FeatureHolderI
>>>>>>> /usr/local/share/perl/5.18.1/Bio/FeatureHolderI.pm
>>>>>>> UNKNOWN Bio::IdentifiableI
>>>>>>> /usr/local/share/perl/5.18.1/Bio/IdentifiableI.pm
>>>>>>> UNKNOWN Bio::LocatableSeq
>>>>>>> /usr/local/share/perl/5.18.1/Bio/LocatableSeq.pm
>>>>>>> UNKNOWN Bio::Location::Atomic
>>>>>>> /usr/local/share/perl/5.18.1/Bio/Location/Atomic.pm
>>>>>>> UNKNOWN Bio::Location::CoordinatePolicyI
>>>>>>> /usr/local/share/perl/5.18.1/Bio/Location/CoordinatePolicyI.pm
>>>>>>> UNKNOWN Bio::Location::Fuzzy
>>>>>>> /usr/local/share/perl/5.18.1/Bio/Location/Fuzzy.pm
>>>>>>> UNKNOWN Bio::Location::FuzzyLocationI
>>>>>>> /usr/local/share/perl/5.18.1/Bio/Location/FuzzyLocationI.pm
>>>>>>> UNKNOWN Bio::Location::Simple
>>>>>>> /usr/local/share/perl/5.18.1/Bio/Location/Simple.pm
>>>>>>> UNKNOWN Bio::Location::Split
>>>>>>> /usr/local/share/perl/5.18.1/Bio/Location/Split.pm
>>>>>>> UNKNOWN Bio::Location::SplitLocationI
>>>>>>> /usr/local/share/perl/5.18.1/Bio/Location/SplitLocationI.pm
>>>>>>> UNKNOWN Bio::Location::WidestCoordPolicy
>>>>>>> /usr/local/share/perl/5.18.1/Bio/Location/WidestCoordPolicy.pm
>>>>>>> UNKNOWN Bio::LocationI
>>>>>>> /usr/local/share/perl/5.18.1/Bio/LocationI.pm
>>>>>>> UNKNOWN Bio::PrimarySeq
>>>>>>> /usr/local/share/perl/5.18.1/Bio/PrimarySeq.pm
>>>>>>> 1.006923 Bio::PrimarySeqI
>>>>>>> /usr/local/share/perl/5.18.1/Bio/PrimarySeqI.pm
>>>>>>> UNKNOWN Bio::Range /usr/local/share/perl/5.18.1/Bio/Range.pm
>>>>>>> UNKNOWN Bio::RangeI /usr/local/share/perl/5.18.1/Bio/RangeI.pm
>>>>>>> 1.006923 Bio::Root::Exception
>>>>>>> /usr/local/share/perl/5.18.1/Bio/Root/Exception.pm
>>>>>>> UNKNOWN Bio::Root::HTTPget
>>>>>>> /usr/local/share/perl/5.18.1/Bio/Root/HTTPget.pm
>>>>>>> UNKNOWN Bio::Root::IO
>>>>>>> /usr/local/share/perl/5.18.1/Bio/Root/IO.pm
>>>>>>> 1.006923 Bio::Root::Root
>>>>>>> /usr/local/share/perl/5.18.1/Bio/Root/Root.pm
>>>>>>> 1.006923 Bio::Root::RootI
>>>>>>> /usr/local/share/perl/5.18.1/Bio/Root/RootI.pm
>>>>>>> 1.006923 Bio::Root::Version
>>>>>>> /usr/local/share/perl/5.18.1/Bio/Root/Version.pm
>>>>>>> UNKNOWN Bio::Search::HSP::GenericHSP
>>>>>>> /usr/local/share/perl/5.18.1/Bio/Search/HSP/GenericHSP.pm
>>>>>>> UNKNOWN Bio::Search::HSP::HSPFactory
>>>>>>> /usr/local/share/perl/5.18.1/Bio/Search/HSP/HSPFactory.pm
>>>>>>> UNKNOWN Bio::Search::HSP::HSPI
>>>>>>> /usr/local/share/perl/5.18.1/Bio/Search/HSP/HSPI.pm
>>>>>>> 0.01 Bio::Search::HSP::PhatHSP::Base
>>>>>>>
/usr/local/annotation/maker2.31/bin/../lib/Bio/Search/HSP/PhatHSP/Base.p>>>>>>>
m
>>>>>>> UNKNOWN Bio::Search::HSP::PhatHSP::augustus
>>>>>>> /usr/local/annotation/maker2.31/bin/../lib/Bio/Search/HSP/PhatHSP/august
>>>>>>> us.pm <http://augustus.pm>
>>>>>>> 0.01 Bio::Search::HSP::PhatHSP::blastn
>>>>>>> /usr/local/annotation/maker2.31/bin/../lib/Bio/Search/HSP/PhatHSP/blastn
>>>>>>> .pm <http://blastn.pm>
>>>>>>> 0.01 Bio::Search::HSP::PhatHSP::blastx
>>>>>>> /usr/local/annotation/maker2.31/bin/../lib/Bio/Search/HSP/PhatHSP/blastx
>>>>>>> .pm <http://blastx.pm>
>>>>>>> UNKNOWN Bio::Search::HSP::PhatHSP::cdna2genome
>>>>>>> /usr/local/annotation/maker2.31/bin/../lib/Bio/Search/HSP/PhatHSP/cdna2g
>>>>>>> enome.pm <http://cdna2genome.pm>
>>>>>>> UNKNOWN Bio::Search::HSP::PhatHSP::est2genome
>>>>>>> /usr/local/annotation/maker2.31/bin/../lib/Bio/Search/HSP/PhatHSP/est2ge
>>>>>>> nome.pm <http://est2genome.pm>
>>>>>>> UNKNOWN Bio::Search::HSP::PhatHSP::fgenesh
>>>>>>> /usr/local/annotation/maker2.31/bin/../lib/Bio/Search/HSP/PhatHSP/fgenes
>>>>>>> h.pm <http://fgenesh.pm>
>>>>>>> UNKNOWN Bio::Search::HSP::PhatHSP::genemark
>>>>>>> /usr/local/annotation/maker2.31/bin/../lib/Bio/Search/HSP/PhatHSP/genema
>>>>>>> rk.pm <http://genemark.pm>
>>>>>>> UNKNOWN Bio::Search::HSP::PhatHSP::gff3
>>>>>>> /usr/local/annotation/maker2.31/bin/../lib/Bio/Search/HSP/PhatHSP/gff3.p
>>>>>>> m <http://gff3.pm>
>>>>>>> UNKNOWN Bio::Search::HSP::PhatHSP::protein2genome
>>>>>>> /usr/local/annotation/maker2.31/bin/../lib/Bio/Search/HSP/PhatHSP/protei
>>>>>>> n2genome.pm <http://protein2genome.pm>
>>>>>>> UNKNOWN Bio::Search::HSP::PhatHSP::repeatmasker
>>>>>>> /usr/local/annotation/maker2.31/bin/../lib/Bio/Search/HSP/PhatHSP/repeat
>>>>>>> masker.pm <http://repeatmasker.pm>
>>>>>>> UNKNOWN Bio::Search::HSP::PhatHSP::snap
>>>>>>> /usr/local/annotation/maker2.31/bin/../lib/Bio/Search/HSP/PhatHSP/snap.p
>>>>>>> m <http://snap.pm>
>>>>>>> UNKNOWN Bio::Search::HSP::PhatHSP::snoscan
>>>>>>> /usr/local/annotation/maker2.31/bin/../lib/Bio/Search/HSP/PhatHSP/snosca
>>>>>>> n.pm <http://snoscan.pm>
>>>>>>> 0.01 Bio::Search::HSP::PhatHSP::tblastx
>>>>>>> /usr/local/annotation/maker2.31/bin/../lib/Bio/Search/HSP/PhatHSP/tblast
>>>>>>> x.pm <http://tblastx.pm>
>>>>>>> UNKNOWN Bio::Search::HSP::PhatHSP::trnascan
>>>>>>> /usr/local/annotation/maker2.31/bin/../lib/Bio/Search/HSP/PhatHSP/trnasc
>>>>>>> an.pm <http://trnascan.pm>
>>>>>>> 1.006923 Bio::Search::Hit::GenericHit
>>>>>>> /usr/local/share/perl/5.18.1/Bio/Search/Hit/GenericHit.pm
>>>>>>> UNKNOWN Bio::Search::Hit::HitFactory
>>>>>>> /usr/local/share/perl/5.18.1/Bio/Search/Hit/HitFactory.pm
>>>>>>> UNKNOWN Bio::Search::Hit::HitI
>>>>>>> /usr/local/share/perl/5.18.1/Bio/Search/Hit/HitI.pm
>>>>>>> 0.01 Bio::Search::Hit::PhatHit::Base
>>>>>>>
/usr/local/annotation/maker2.31/bin/../lib/Bio/Search/Hit/PhatHit/Base.p>>>>>>>
m
>>>>>>> UNKNOWN Bio::Search::Hit::PhatHit::augustus
>>>>>>> /usr/local/annotation/maker2.31/bin/../lib/Bio/Search/Hit/PhatHit/august
>>>>>>> us.pm <http://augustus.pm>
>>>>>>> 0.01 Bio::Search::Hit::PhatHit::blastn
>>>>>>> /usr/local/annotation/maker2.31/bin/../lib/Bio/Search/Hit/PhatHit/blastn
>>>>>>> .pm <http://blastn.pm>
>>>>>>> 0.01 Bio::Search::Hit::PhatHit::blastx
>>>>>>> /usr/local/annotation/maker2.31/bin/../lib/Bio/Search/Hit/PhatHit/blastx
>>>>>>> .pm <http://blastx.pm>
>>>>>>> UNKNOWN Bio::Search::Hit::PhatHit::cdna2genome
>>>>>>> /usr/local/annotation/maker2.31/bin/../lib/Bio/Search/Hit/PhatHit/cdna2g
>>>>>>> enome.pm <http://cdna2genome.pm>
>>>>>>> UNKNOWN Bio::Search::Hit::PhatHit::est2genome
>>>>>>> /usr/local/annotation/maker2.31/bin/../lib/Bio/Search/Hit/PhatHit/est2ge
>>>>>>> nome.pm <http://est2genome.pm>
>>>>>>> UNKNOWN Bio::Search::Hit::PhatHit::fgenesh
>>>>>>> /usr/local/annotation/maker2.31/bin/../lib/Bio/Search/Hit/PhatHit/fgenes
>>>>>>> h.pm <http://fgenesh.pm>
>>>>>>> UNKNOWN Bio::Search::Hit::PhatHit::genemark
>>>>>>> /usr/local/annotation/maker2.31/bin/../lib/Bio/Search/Hit/PhatHit/genema
>>>>>>> rk.pm <http://genemark.pm>
>>>>>>> UNKNOWN Bio::Search::Hit::PhatHit::gff3
>>>>>>> /usr/local/annotation/maker2.31/bin/../lib/Bio/Search/Hit/PhatHit/gff3.p
>>>>>>> m <http://gff3.pm>
>>>>>>> UNKNOWN Bio::Search::Hit::PhatHit::protein2genome
>>>>>>> /usr/local/annotation/maker2.31/bin/../lib/Bio/Search/Hit/PhatHit/protei
>>>>>>> n2genome.pm <http://protein2genome.pm>
>>>>>>> 1.006923 Bio::Search::Hit::PhatHit::repeatmasker
>>>>>>> /usr/local/annotation/maker2.31/bin/../lib/Bio/Search/Hit/PhatHit/repeat
>>>>>>> masker.pm <http://repeatmasker.pm>
>>>>>>> UNKNOWN Bio::Search::Hit::PhatHit::snap
>>>>>>> /usr/local/annotation/maker2.31/bin/../lib/Bio/Search/Hit/PhatHit/snap.p
>>>>>>> m <http://snap.pm>
>>>>>>> UNKNOWN Bio::Search::Hit::PhatHit::snoscan
>>>>>>> /usr/local/annotation/maker2.31/bin/../lib/Bio/Search/Hit/PhatHit/snosca
>>>>>>> n.pm <http://snoscan.pm>
>>>>>>> 0.01 Bio::Search::Hit::PhatHit::tblastx
>>>>>>> /usr/local/annotation/maker2.31/bin/../lib/Bio/Search/Hit/PhatHit/tblast
>>>>>>> x.pm <http://tblastx.pm>
>>>>>>> UNKNOWN Bio::Search::Hit::PhatHit::trnascan
>>>>>>> /usr/local/annotation/maker2.31/bin/../lib/Bio/Search/Hit/PhatHit/trnasc
>>>>>>> an.pm <http://trnascan.pm>
>>>>>>> 1.006923 Bio::Search::SearchUtils
>>>>>>> /usr/local/share/perl/5.18.1/Bio/Search/SearchUtils.pm
>>>>>>> UNKNOWN Bio::SearchIO
>>>>>>> /usr/local/share/perl/5.18.1/Bio/SearchIO.pm
>>>>>>> UNKNOWN Bio::SearchIO::EventHandlerI
>>>>>>> /usr/local/share/perl/5.18.1/Bio/SearchIO/EventHandlerI.pm
>>>>>>> UNKNOWN Bio::SearchIO::SearchResultEventBuilder
>>>>>>> /usr/local/share/perl/5.18.1/Bio/SearchIO/SearchResultEventBuilder.pm
>>>>>>> UNKNOWN Bio::Seq /usr/local/share/perl/5.18.1/Bio/Seq.pm
>>>>>>> UNKNOWN Bio::Seq::SeqFactory
>>>>>>> /usr/local/share/perl/5.18.1/Bio/Seq/SeqFactory.pm
>>>>>>> UNKNOWN Bio::SeqAnalysisParserI
>>>>>>> /usr/local/share/perl/5.18.1/Bio/SeqAnalysisParserI.pm
>>>>>>> UNKNOWN Bio::SeqFeature::FeaturePair
>>>>>>> /usr/local/share/perl/5.18.1/Bio/SeqFeature/FeaturePair.pm
>>>>>>> UNKNOWN Bio::SeqFeature::Generic
>>>>>>> /usr/local/share/perl/5.18.1/Bio/SeqFeature/Generic.pm
>>>>>>> UNKNOWN Bio::SeqFeature::Similarity
>>>>>>> /usr/local/share/perl/5.18.1/Bio/SeqFeature/Similarity.pm
>>>>>>> UNKNOWN Bio::SeqFeature::SimilarityPair
>>>>>>> /usr/local/share/perl/5.18.1/Bio/SeqFeature/SimilarityPair.pm
>>>>>>> UNKNOWN Bio::SeqFeatureI
>>>>>>> /usr/local/share/perl/5.18.1/Bio/SeqFeatureI.pm
>>>>>>> UNKNOWN Bio::SeqI /usr/local/share/perl/5.18.1/Bio/SeqI.pm
>>>>>>> UNKNOWN Bio::SeqUtils
>>>>>>> /usr/local/share/perl/5.18.1/Bio/SeqUtils.pm
>>>>>>> 1.006923 Bio::Tools::CodonTable
>>>>>>> /usr/local/share/perl/5.18.1/Bio/Tools/CodonTable.pm
>>>>>>> UNKNOWN Bio::Tools::GFF
>>>>>>> /usr/local/share/perl/5.18.1/Bio/Tools/GFF.pm
>>>>>>> 1.006923 Bio::Tools::IUPAC
>>>>>>> /usr/local/share/perl/5.18.1/Bio/Tools/IUPAC.pm
>>>>>>> 7.3 Bit::Vector /usr/local/lib/perl/5.18.1/Bit/Vector.pm
>>>>>>> 0.01 CGL::Annotation
>>>>>>> /usr/local/annotation/maker2.31/bin/../lib/CGL/Annotation.pm
>>>>>>> 0.01 CGL::Annotation::Feature
>>>>>>> /usr/local/annotation/maker2.31/bin/../lib/CGL/Annotation/Feature.pm
>>>>>>> 0.01 CGL::Annotation::Feature::Contig
>>>>>>> /usr/local/annotation/maker2.31/bin/../lib/CGL/Annotation/Feature/Contig
>>>>>>> .pm
>>>>>>> 0.01 CGL::Annotation::Feature::Exon
>>>>>>>
/usr/local/annotation/maker2.31/bin/../lib/CGL/Annotation/Feature/Exon.p>>>>>>>
m
>>>>>>> 0.01 CGL::Annotation::Feature::Gene
>>>>>>>
/usr/local/annotation/maker2.31/bin/../lib/CGL/Annotation/Feature/Gene.p>>>>>>>
m
>>>>>>> 0.01 CGL::Annotation::Feature::Intron
>>>>>>> /usr/local/annotation/maker2.31/bin/../lib/CGL/Annotation/Feature/Intron
>>>>>>> .pm
>>>>>>> 0.01 CGL::Annotation::Feature::Protein
>>>>>>> /usr/local/annotation/maker2.31/bin/../lib/CGL/Annotation/Feature/Protei
>>>>>>> n.pm
>>>>>>> 0.01 CGL::Annotation::Feature::Sequence_variant
>>>>>>> /usr/local/annotation/maker2.31/bin/../lib/CGL/Annotation/Feature/Sequen
>>>>>>> ce_variant.pm
>>>>>>> 0.01 CGL::Annotation::Feature::Transcript
>>>>>>> /usr/local/annotation/maker2.31/bin/../lib/CGL/Annotation/Feature/Transc
>>>>>>> ript.pm
>>>>>>> 0.01 CGL::Annotation::FeatureLocation
>>>>>>> /usr/local/annotation/maker2.31/bin/../lib/CGL/Annotation/FeatureLocatio
>>>>>>> n.pm
>>>>>>> 0.01 CGL::Annotation::FeatureRelationship
>>>>>>> /usr/local/annotation/maker2.31/bin/../lib/CGL/Annotation/FeatureRelatio
>>>>>>> nship.pm
>>>>>>> 0.01 CGL::Annotation::Iterator
>>>>>>> /usr/local/annotation/maker2.31/bin/../lib/CGL/Annotation/Iterator.pm
>>>>>>> 0.01 CGL::Annotation::Trace
>>>>>>> /usr/local/annotation/maker2.31/bin/../lib/CGL/Annotation/Trace.pm
>>>>>>> 0.01 CGL::Clone
>>>>>>> /usr/local/annotation/maker2.31/bin/../lib/CGL/Clone.pm
>>>>>>> 0.01 CGL::Ontology::Node
>>>>>>> /usr/local/annotation/maker2.31/bin/../lib/CGL/Ontology/Node.pm
>>>>>>> 0.01 CGL::Ontology::NodeRelationship
>>>>>>> /usr/local/annotation/maker2.31/bin/../lib/CGL/Ontology/NodeRelationship
>>>>>>> .pm
>>>>>>> 0.01 CGL::Ontology::Ontology
>>>>>>> /usr/local/annotation/maker2.31/bin/../lib/CGL/Ontology/Ontology.pm
>>>>>>> 0.01 CGL::Ontology::Parser::OBO
>>>>>>> /usr/local/annotation/maker2.31/bin/../lib/CGL/Ontology/Parser/OBO.pm
>>>>>>> 0.01 CGL::Ontology::SO
>>>>>>> /usr/local/annotation/maker2.31/bin/../lib/CGL/Ontology/SO.pm
>>>>>>> 0.01 CGL::Ontology::Trace
>>>>>>> /usr/local/annotation/maker2.31/bin/../lib/CGL/Ontology/Trace.pm
>>>>>>> 0.01 CGL::Revcomp
>>>>>>> /usr/local/annotation/maker2.31/bin/../lib/CGL/Revcomp.pm
>>>>>>> 0.01 CGL::TranslationMachine
>>>>>>> /usr/local/annotation/maker2.31/bin/../lib/CGL/TranslationMachine.pm
>>>>>>> 1.32 Carp /usr/local/share/perl/5.18.1/Carp.pm
>>>>>>> 1.32 Carp::Heavy /usr/local/share/perl/5.18.1/Carp/Heavy.pm
>>>>>>> 0.64 Class::Struct /usr/share/perl/5.18/Class/Struct.pm
>>>>>>> 0.36 Clone /usr/local/lib/perl/5.18.1/Clone.pm
>>>>>>> 5.018001 Config /usr/lib/perl/5.18/Config.pm
>>>>>>> 3.40 Cwd /usr/lib/perl/5.18/Cwd.pm
>>>>>>> 1.42 DBD::SQLite /usr/local/lib/perl/5.18.1/DBD/SQLite.pm
>>>>>>> 1.631 DBI /usr/local/lib/perl/5.18.1/DBI.pm
>>>>>>> 1.827 DB_File /usr/lib/perl/5.18/DB_File.pm
>>>>>>> 2.145 Data::Dumper /usr/lib/perl/5.18/Data/Dumper.pm
>>>>>>> 0.11 Datastore::Base
>>>>>>> /usr/local/annotation/maker2.31/bin/../lib/Datastore/Base.pm
>>>>>>> 0.01 Datastore::MD5
>>>>>>> /usr/local/annotation/maker2.31/bin/../lib/Datastore/MD5.pm
>>>>>>> 2.53 Digest::MD5 /usr/local/lib/perl/5.18.1/Digest/MD5.pm
>>>>>>> 1.16 Digest::base /usr/share/perl/5.18/Digest/base.pm
>>>>>>> <http://base.pm>
>>>>>>> UNKNOWN Dumper::GFF::GFFV3
>>>>>>> /usr/local/annotation/maker2.31/bin/../lib/Dumper/GFF/GFFV3.pm
>>>>>>> UNKNOWN Dumper::XML::Game
>>>>>>> /usr/local/annotation/maker2.31/bin/../lib/Dumper/XML/Game.pm
>>>>>>> UNKNOWN Dumper::XML::Game_Xml
>>>>>>> /usr/local/annotation/maker2.31/bin/../lib/Dumper/XML/Game_Xml.pm
>>>>>>> 1.18 DynaLoader /usr/lib/perl/5.18/DynaLoader.pm
>>>>>>> 1.18 Errno /usr/lib/perl/5.18/Errno.pm
>>>>>>> 0.17015 Error
>>>>>>> /usr/local/annotation/maker2.31/bin/../lib/Error.pm
>>>>>>> UNKNOWN Error::Simple
>>>>>>> /usr/local/annotation/maker2.31/bin/../lib/Error/Simple.pm
>>>>>>> 5.68 Exporter /usr/share/perl/5.18/Exporter.pm
>>>>>>> 5.68 Exporter::Heavy /usr/share/perl/5.18/Exporter/Heavy.pm
>>>>>>> UNKNOWN Fasta
>>>>>>> /usr/local/annotation/maker2.31/bin/../lib/Fasta.pm
>>>>>>> UNKNOWN FastaChunk
>>>>>>> /usr/local/annotation/maker2.31/bin/../lib/FastaChunk.pm
>>>>>>> UNKNOWN FastaChunker
>>>>>>> /usr/local/annotation/maker2.31/bin/../lib/FastaChunker.pm
>>>>>>> UNKNOWN FastaDB
>>>>>>> /usr/local/annotation/maker2.31/bin/../lib/FastaDB.pm
>>>>>>> UNKNOWN FastaFile
>>>>>>> /usr/local/annotation/maker2.31/bin/../lib/FastaFile.pm
>>>>>>> UNKNOWN FastaSeq
>>>>>>> /usr/local/annotation/maker2.31/bin/../lib/FastaSeq.pm
>>>>>>> 1.11 Fcntl /usr/lib/perl/5.18/Fcntl.pm
>>>>>>> 2.84 File::Basename /usr/share/perl/5.18/File/Basename.pm
>>>>>>> 2.26 File::Copy /usr/share/perl/5.18/File/Copy.pm
>>>>>>> 1.20 File::Glob /usr/lib/perl/5.18/File/Glob.pm
>>>>>>> 1.20 File::NFSLock
>>>>>>> /usr/local/annotation/maker2.31/bin/../lib/File/NFSLock.pm
>>>>>>> 2.09 File::Path /usr/share/perl/5.18/File/Path.pm
>>>>>>> 3.40 File::Spec /usr/lib/perl/5.18/File/Spec.pm
>>>>>>> 3.40 File::Spec::Unix /usr/lib/perl/5.18/File/Spec/Unix.pm
>>>>>>> 0.2304 File::Temp /usr/local/share/perl/5.18.1/File/Temp.pm
>>>>>>> 1.09 File::Which
>>>>>>> /usr/local/annotation/maker2.31/bin/../lib/File/Which.pm
>>>>>>> 2.02 FileHandle /usr/share/perl/5.18/FileHandle.pm
>>>>>>> 1.51 FindBin /usr/share/perl/5.18/FindBin.pm
>>>>>>> UNKNOWN GFFDB
>>>>>>> /usr/local/annotation/maker2.31/bin/../lib/GFFDB.pm
>>>>>>> UNKNOWN GI /usr/local/annotation/maker2.31/bin/../lib/GI.pm
>>>>>>> 2.42 Getopt::Long /usr/local/share/perl/5.18.1/Getopt/Long.pm
>>>>>>> 6.02 HTTP::Date /usr/share/perl5/HTTP/Date.pm
>>>>>>> 6.05 HTTP::Headers /usr/share/perl5/HTTP/Headers.pm
>>>>>>> 6.06 HTTP::Message /usr/share/perl5/HTTP/Message.pm
>>>>>>> 6.00 HTTP::Request /usr/share/perl5/HTTP/Request.pm
>>>>>>> 6.04 HTTP::Response /usr/share/perl5/HTTP/Response.pm
>>>>>>> 6.03 HTTP::Status /usr/share/perl5/HTTP/Status.pm
>>>>>>> 1.28 IO /usr/lib/perl/5.18/IO.pm
>>>>>>> 1.16 IO::File /usr/lib/perl/5.18/IO/File.pm
>>>>>>> 1.34 IO::Handle /usr/lib/perl/5.18/IO/Handle.pm
>>>>>>> 1.1 IO::Seekable /usr/lib/perl/5.18/IO/Seekable.pm
>>>>>>> 1.21 IO::Select /usr/lib/perl/5.18/IO/Select.pm
>>>>>>> 1.36 IO::Socket /usr/lib/perl/5.18/IO/Socket.pm
>>>>>>> 1.33 IO::Socket::INET /usr/lib/perl/5.18/IO/Socket/INET.pm
>>>>>>> 1.24 IO::Socket::UNIX /usr/lib/perl/5.18/IO/Socket/UNIX.pm
>>>>>>> 1.13 IPC::Open3 /usr/share/perl/5.18/IPC/Open3.pm
>>>>>>> 0.53 Inline /usr/local/share/perl/5.18.1/Inline.pm
>>>>>>> UNKNOWN Inline::denter
>>>>>>> /usr/local/share/perl/5.18.1/Inline/denter.pm <http://denter.pm>
>>>>>>> UNKNOWN Iterator
>>>>>>> /usr/local/annotation/maker2.31/bin/../lib/Iterator.pm
>>>>>>> UNKNOWN Iterator::Any
>>>>>>> /usr/local/annotation/maker2.31/bin/../lib/Iterator/Any.pm
>>>>>>> UNKNOWN Iterator::Fasta
>>>>>>> /usr/local/annotation/maker2.31/bin/../lib/Iterator/Fasta.pm
>>>>>>> UNKNOWN Iterator::GFF3
>>>>>>> /usr/local/annotation/maker2.31/bin/../lib/Iterator/GFF3.pm
>>>>>>> 6.05 LWP /usr/share/perl5/LWP.pm
>>>>>>> UNKNOWN LWP::MemberMixin /usr/share/perl5/LWP/MemberMixin.pm
>>>>>>> 6.00 LWP::Protocol /usr/share/perl5/LWP/Protocol.pm
>>>>>>> 6.05 LWP::UserAgent /usr/share/perl5/LWP/UserAgent.pm
>>>>>>> 0.33 List::MoreUtils
>>>>>>> /usr/local/lib/perl/5.18.1/List/MoreUtils.pm
>>>>>>> 1.38 List::Util /usr/local/lib/perl/5.18.1/List/Util.pm
>>>>>>> UNKNOWN MAKER::ConfigData
>>>>>>> /usr/local/annotation/maker2.31/bin/../perl/lib/MAKER/ConfigData.pm
>>>>>>> 1.32 POSIX /usr/lib/perl/5.18/POSIX.pm
>>>>>>> 0.01 Parallel::Application::MPI
>>>>>>> /usr/local/annotation/maker2.31/bin/../perl/lib/Parallel/Application/MPI
>>>>>>> .pm
>>>>>>> 0.02 Perl::Unsafe::Signals
>>>>>>> /usr/local/lib/perl/5.18.1/Perl/Unsafe/Signals.pm
>>>>>>> UNKNOWN PhatHit_utils
>>>>>>> /usr/local/annotation/maker2.31/bin/../lib/PhatHit_utils.pm
>>>>>>> UNKNOWN PostData
>>>>>>> /usr/local/annotation/maker2.31/bin/../lib/PostData.pm
>>>>>>> 1.0 Proc::ProcessTable_simple
>>>>>>> /usr/local/annotation/maker2.31/bin/../lib/Proc/ProcessTable_simple.pm
>>>>>>> 1.0 Proc::Signal
>>>>>>> /usr/local/annotation/maker2.31/bin/../lib/Proc/Signal.pm
>>>>>>> UNKNOWN Process::MpiChunk
>>>>>>> /usr/local/annotation/maker2.31/bin/../lib/Process/MpiChunk.pm
>>>>>>> UNKNOWN Process::MpiTiers
>>>>>>> /usr/local/annotation/maker2.31/bin/../lib/Process/MpiTiers.pm
>>>>>>> 1.38 Scalar::Util /usr/local/lib/perl/5.18.1/Scalar/Util.pm
>>>>>>> 1.02 SelectSaver /usr/share/perl/5.18/SelectSaver.pm
>>>>>>> UNKNOWN Shadower
>>>>>>> /usr/local/annotation/maker2.31/bin/../lib/Shadower.pm
>>>>>>> UNKNOWN SimpleCluster
>>>>>>> /usr/local/annotation/maker2.31/bin/../lib/SimpleCluster.pm
>>>>>>> 2.009 Socket /usr/lib/perl/5.18/Socket.pm
>>>>>>> UNKNOWN SpaceBase
>>>>>>> /usr/local/annotation/maker2.31/bin/../lib/SpaceBase.pm
>>>>>>> 2.45 Storable /usr/local/lib/perl/5.18.1/Storable.pm
>>>>>>> 1.07 Symbol /usr/share/perl/5.18/Symbol.pm
>>>>>>> 1.17 Sys::Hostname /usr/lib/perl/5.18/Sys/Hostname.pm
>>>>>>> 0.21 Sys::SigAction
>>>>>>> /usr/local/share/perl/5.18.1/Sys/SigAction.pm
>>>>>>> UNKNOWN Sys::SigAction::Alarm
>>>>>>> /usr/local/share/perl/5.18.1/Sys/SigAction/Alarm.pm
>>>>>>> 4.02 Term::ANSIColor /usr/share/perl/5.18/Term/ANSIColor.pm
>>>>>>> 4.2 Tie::Handle /usr/share/perl/5.18/Tie/Handle.pm
>>>>>>> 1.04 Tie::Hash /usr/share/perl/5.18/Tie/Hash.pm
>>>>>>> 4.3 Tie::StdHandle /usr/share/perl/5.18/Tie/StdHandle.pm
>>>>>>> 1.9726 Time::HiRes /usr/local/lib/perl/5.18.1/Time/HiRes.pm
>>>>>>> 1.2300 Time::Local /usr/share/perl/5.18/Time/Local.pm
>>>>>>> 1.60 URI /usr/share/perl5/URI.pm
>>>>>>> 3.31 URI::Escape /usr/share/perl5/URI/Escape.pm
>>>>>>> UNKNOWN Widget
>>>>>>> /usr/local/annotation/maker2.31/bin/../lib/Widget.pm
>>>>>>> UNKNOWN Widget::RepeatMasker
>>>>>>> /usr/local/annotation/maker2.31/bin/../lib/Widget/RepeatMasker.pm
>>>>>>> UNKNOWN Widget::augustus
>>>>>>> /usr/local/annotation/maker2.31/bin/../lib/Widget/augustus.pm
>>>>>>> <http://augustus.pm>
>>>>>>> UNKNOWN Widget::blastn
>>>>>>> /usr/local/annotation/maker2.31/bin/../lib/Widget/blastn.pm
>>>>>>> <http://blastn.pm>
>>>>>>> UNKNOWN Widget::blastx
>>>>>>> /usr/local/annotation/maker2.31/bin/../lib/Widget/blastx.pm
>>>>>>> <http://blastx.pm>
>>>>>>> UNKNOWN Widget::exonerate
>>>>>>> /usr/local/annotation/maker2.31/bin/../lib/Widget/exonerate.pm
>>>>>>> <http://exonerate.pm>
>>>>>>> UNKNOWN Widget::exonerate::cdna2genome
>>>>>>> /usr/local/annotation/maker2.31/bin/../lib/Widget/exonerate/cdna2genome.
>>>>>>> pm <http://cdna2genome.pm>
>>>>>>> UNKNOWN Widget::exonerate::est2genome
>>>>>>> /usr/local/annotation/maker2.31/bin/../lib/Widget/exonerate/est2genome.p
>>>>>>> m <http://est2genome.pm>
>>>>>>> UNKNOWN Widget::exonerate::protein2genome
>>>>>>> /usr/local/annotation/maker2.31/bin/../lib/Widget/exonerate/protein2geno
>>>>>>> me.pm <http://protein2genome.pm>
>>>>>>> UNKNOWN Widget::fgenesh
>>>>>>> /usr/local/annotation/maker2.31/bin/../lib/Widget/fgenesh.pm
>>>>>>> <http://fgenesh.pm>
>>>>>>> UNKNOWN Widget::formater
>>>>>>> /usr/local/annotation/maker2.31/bin/../lib/Widget/formater.pm
>>>>>>> <http://formater.pm>
>>>>>>> UNKNOWN Widget::genemark
>>>>>>> /usr/local/annotation/maker2.31/bin/../lib/Widget/genemark.pm
>>>>>>> <http://genemark.pm>
>>>>>>> UNKNOWN Widget::snap
>>>>>>> /usr/local/annotation/maker2.31/bin/../lib/Widget/snap.pm
>>>>>>> <http://snap.pm>
>>>>>>> UNKNOWN Widget::snoscan
>>>>>>> /usr/local/annotation/maker2.31/bin/../lib/Widget/snoscan.pm
>>>>>>> <http://snoscan.pm>
>>>>>>> UNKNOWN Widget::tblastx
>>>>>>> /usr/local/annotation/maker2.31/bin/../lib/Widget/tblastx.pm
>>>>>>> <http://tblastx.pm>
>>>>>>> UNKNOWN Widget::trnascan
>>>>>>> /usr/local/annotation/maker2.31/bin/../lib/Widget/trnascan.pm
>>>>>>> <http://trnascan.pm>
>>>>>>> 0.16 XSLoader /usr/share/perl/5.18/XSLoader.pm
>>>>>>> 0.21 attributes /usr/lib/perl/5.18/attributes.pm
>>>>>>> <http://attributes.pm>
>>>>>>> 2.18 base /usr/share/perl/5.18/base.pm <http://base.pm>
>>>>>>> 1.04 bytes /usr/share/perl/5.18/bytes.pm <http://bytes.pm>
>>>>>>> UNKNOWN clean
>>>>>>> /usr/local/annotation/maker2.31/bin/../lib/clean.pm <http://clean.pm>
>>>>>>> UNKNOWN cluster
>>>>>>> /usr/local/annotation/maker2.31/bin/../lib/cluster.pm
>>>>>>> <http://cluster.pm>
>>>>>>> UNKNOWN compare
>>>>>>> /usr/local/annotation/maker2.31/bin/../lib/compare.pm
>>>>>>> <http://compare.pm>
>>>>>>> 1.27 constant /usr/share/perl/5.18/constant.pm
>>>>>>> <http://constant.pm>
>>>>>>> UNKNOWN ds_utility
>>>>>>> /usr/local/annotation/maker2.31/bin/../lib/ds_utility.pm
>>>>>>> <http://ds_utility.pm>
>>>>>>> UNKNOWN exonerate::splice_info
>>>>>>> /usr/local/annotation/maker2.31/bin/../lib/exonerate/splice_info.pm
>>>>>>> <http://splice_info.pm>
>>>>>>> 0.34 forks /usr/local/lib/perl/5.18.1/forks.pm
>>>>>>> <http://forks.pm>
>>>>>>> 2.08001 forks::Devel::Symdump
>>>>>>> /usr/local/lib/perl/5.18.1/forks/Devel/Symdump.pm
>>>>>>> 0.34 forks::shared /usr/local/lib/perl/5.18.1/forks/shared.pm
>>>>>>> <http://shared.pm>
>>>>>>> 0.34 forks::signals
>>>>>>> /usr/local/lib/perl/5.18.1/forks/signals.pm <http://signals.pm>
>>>>>>> 1.00 integer /usr/share/perl/5.18/integer.pm
>>>>>>> <http://integer.pm>
>>>>>>> 0.63 lib /usr/lib/perl/5.18/lib.pm <http://lib.pm>
>>>>>>> 1.02 locale /usr/share/perl/5.18/locale.pm <http://locale.pm>
>>>>>>> UNKNOWN maker::auto_annotator
>>>>>>> /usr/local/annotation/maker2.31/bin/../lib/maker/auto_annotator.pm
>>>>>>> <http://auto_annotator.pm>
>>>>>>> UNKNOWN maker::join
>>>>>>> /usr/local/annotation/maker2.31/bin/../lib/maker/join.pm
>>>>>>> <http://join.pm>
>>>>>>> UNKNOWN maker::quality_index
>>>>>>> /usr/local/annotation/maker2.31/bin/../lib/maker/quality_index.pm
>>>>>>> <http://quality_index.pm>
>>>>>>> UNKNOWN maker::sens_spec
>>>>>>> /usr/local/annotation/maker2.31/bin/../lib/maker/sens_spec.pm
>>>>>>> <http://sens_spec.pm>
>>>>>>> 1.22 overload /usr/share/perl/5.18/overload.pm
>>>>>>> <http://overload.pm>
>>>>>>> 0.02 overloading /usr/share/perl/5.18/overloading.pm
>>>>>>> <http://overloading.pm>
>>>>>>> 0.225 parent /usr/share/perl/5.18/parent.pm <http://parent.pm>
>>>>>>> UNKNOWN polisher
>>>>>>> /usr/local/annotation/maker2.31/bin/../lib/polisher.pm
>>>>>>> <http://polisher.pm>
>>>>>>> UNKNOWN polisher::exonerate
>>>>>>> /usr/local/annotation/maker2.31/bin/../lib/polisher/exonerate.pm
>>>>>>> <http://exonerate.pm>
>>>>>>> UNKNOWN polisher::exonerate::altest
>>>>>>> /usr/local/annotation/maker2.31/bin/../lib/polisher/exonerate/altest.pm
>>>>>>> <http://altest.pm>
>>>>>>> UNKNOWN polisher::exonerate::est
>>>>>>> /usr/local/annotation/maker2.31/bin/../lib/polisher/exonerate/est.pm
>>>>>>> <http://est.pm>
>>>>>>> UNKNOWN polisher::exonerate::protein
>>>>>>> /usr/local/annotation/maker2.31/bin/../lib/polisher/exonerate/protein.pm
>>>>>>> <http://protein.pm>
>>>>>>> UNKNOWN repeat_mask_seq
>>>>>>> /usr/local/annotation/maker2.31/bin/../lib/repeat_mask_seq.pm
>>>>>>> <http://repeat_mask_seq.pm>
>>>>>>> 0.1 runlog
>>>>>>> /usr/local/annotation/maker2.31/bin/../lib/runlog.pm <http://runlog.pm>
>>>>>>> UNKNOWN shadow_AED
>>>>>>> /usr/local/annotation/maker2.31/bin/../lib/shadow_AED.pm
>>>>>>> 1.07 sigtrap /usr/share/perl/5.18/sigtrap.pm
>>>>>>> <http://sigtrap.pm>
>>>>>>> 1.07 strict /usr/share/perl/5.18/strict.pm <http://strict.pm>
>>>>>>> 1.77 threads /usr/local/lib/perl/5.18.1/forks.pm
>>>>>>> <http://forks.pm>
>>>>>>> 1.33 threads::shared
>>>>>>> /usr/local/lib/perl/5.18.1/forks/shared.pm <http://shared.pm>
>>>>>>> 1.03 vars /usr/share/perl/5.18/vars.pm <http://vars.pm>
>>>>>>> 1.18 warnings /usr/share/perl/5.18/warnings.pm
>>>>>>> <http://warnings.pm>
>>>>>>> 1.02 warnings::register
>>>>>>> /usr/share/perl/5.18/warnings/register.pm <http://register.pm>
>>>>>>> STATUS: Parsing control files...
>>>>>>> Calling GI::load_control_files at
>>>>>>> /usr/local/annotation/maker2.31/bin/maker line 452.
>>>>>>> Calling GI::new_instance_temp at
>>>>>>> /usr/local/annotation/maker2.31/bin/maker line 463.
>>>>>>> Calling GI::mount_check at /usr/local/annotation/maker2.31/bin/maker
>>>>>>> line 465.
>>>>>>> Calling GI::set_global_temp at /usr/local/annotation/maker2.31/bin/maker
>>>>>>> line 483.
>>>>>>> STATUS: Processing and indexing input FASTA files...
>>>>>>> Calling GI::s_abs_path at /usr/local/annotation/maker2.31/bin/maker line
>>>>>>> 519.
>>>>>>> Calling GI::s_abs_path at /usr/local/annotation/maker2.31/bin/maker line
>>>>>>> 519.
>>>>>>> Calling GI::s_abs_path at /usr/local/annotation/maker2.31/bin/maker line
>>>>>>> 519.
>>>>>>> Calling GI::s_abs_path at /usr/local/annotation/maker2.31/bin/maker line
>>>>>>> 519.
>>>>>>> Calling GI::s_abs_path at /usr/local/annotation/maker2.31/bin/maker line
>>>>>>> 519.
>>>>>>> Calling List::Util::shuffle at /usr/local/annotation/maker2.31/bin/maker
>>>>>>> line 529.
>>>>>>> Calling GI::split_db at /usr/local/annotation/maker2.31/bin/maker line
>>>>>>> 536.
>>>>>>> Calling File::Path::rmtree at /usr/local/annotation/maker2.31/bin/maker
>>>>>>> line 537.
>>>>>>> Calling Iterator::Any::new at /usr/local/annotation/maker2.31/bin/maker
>>>>>>> line 537.
>>>>>>> Calling Iterator::Any::nextDef at
>>>>>>> /usr/local/annotation/maker2.31/bin/maker line 537.
>>>>>>> Calling Iterator::Any::new at /usr/local/annotation/maker2.31/bin/maker
>>>>>>> line 537.
>>>>>>> Calling mkdir at /usr/local/annotation/maker2.31/bin/maker line 537.
>>>>>>> Calling Iterator::Any::nextFastaRef at
>>>>>>> /usr/local/annotation/maker2.31/bin/maker line 537.
>>>>>>> Calling system at /usr/local/annotation/maker2.31/bin/maker line 537.
>>>>>>> Calling File::NFSLock::unlock at
>>>>>>> /usr/local/annotation/maker2.31/bin/maker line 537.
>>>>>>> Calling GI::build_fasta_index at
>>>>>>> /usr/local/annotation/maker2.31/bin/maker line 538.
>>>>>>> Calling FastaDB::new at /usr/local/annotation/maker2.31/bin/maker line
>>>>>>> 539.
>>>>>>> Calling File::NFSLock::new at
>>>>>>> /usr/local/annotation/maker2.31/bin/../lib/Error.pm line 415.
>>>>>>> Calling out to BioPerl Bio::DB::Fasta::new at
>>>>>>> /usr/local/annotation/maker2.31/bin/../lib/Error.pm line 415.
>>>>>>> Calling out to BioPerl Bio::DB::Fasta::new at
>>>>>>> /usr/local/annotation/maker2.31/bin/../lib/Error.pm line 415.
>>>>>>> Calling out to BioPerl get_PrimarySeq_stream at
>>>>>>> /usr/local/annotation/maker2.31/bin/../lib/GI.pm line 1894.
>>>>>>> Calling GI::split_db at /usr/local/annotation/maker2.31/bin/maker line
>>>>>>> 536.
>>>>>>> Calling File::Path::rmtree at /usr/local/annotation/maker2.31/bin/maker
>>>>>>> line 537.
>>>>>>> Calling Iterator::Any::new at /usr/local/annotation/maker2.31/bin/maker
>>>>>>> line 537.
>>>>>>> Calling Iterator::Any::nextDef at
>>>>>>> /usr/local/annotation/maker2.31/bin/maker line 537.
>>>>>>> Calling Iterator::Any::new at /usr/local/annotation/maker2.31/bin/maker
>>>>>>> line 537.
>>>>>>> Calling mkdir at /usr/local/annotation/maker2.31/bin/maker line 537.
>>>>>>> Calling Iterator::Any::nextFastaRef at
>>>>>>> /usr/local/annotation/maker2.31/bin/maker line 537.
>>>>>>> Calling system at /usr/local/annotation/maker2.31/bin/maker line 537.
>>>>>>> Calling File::NFSLock::unlock at
>>>>>>> /usr/local/annotation/maker2.31/bin/maker line 537.
>>>>>>> Calling GI::build_fasta_index at
>>>>>>> /usr/local/annotation/maker2.31/bin/maker line 538.
>>>>>>> Calling FastaDB::new at /usr/local/annotation/maker2.31/bin/maker line
>>>>>>> 539.
>>>>>>> Calling File::NFSLock::new at
>>>>>>> /usr/local/annotation/maker2.31/bin/../lib/Error.pm line 415.
>>>>>>> Calling out to BioPerl Bio::DB::Fasta::new at
>>>>>>> /usr/local/annotation/maker2.31/bin/../lib/Error.pm line 415.
>>>>>>> Calling out to BioPerl Bio::DB::Fasta::new at
>>>>>>> /usr/local/annotation/maker2.31/bin/../lib/Error.pm line 415.
>>>>>>> Calling out to BioPerl get_PrimarySeq_stream at
>>>>>>> /usr/local/annotation/maker2.31/bin/../lib/GI.pm line 1894.
>>>>>>> Calling GI::split_db at /usr/local/annotation/maker2.31/bin/maker line
>>>>>>> 536.
>>>>>>> Calling File::Path::rmtree at /usr/local/annotation/maker2.31/bin/maker
>>>>>>> line 537.
>>>>>>> Calling Iterator::Any::new at /usr/local/annotation/maker2.31/bin/maker
>>>>>>> line 537.
>>>>>>> Calling Iterator::Any::nextDef at
>>>>>>> /usr/local/annotation/maker2.31/bin/maker line 537.
>>>>>>> Calling Iterator::Any::new at /usr/local/annotation/maker2.31/bin/maker
>>>>>>> line 537.
>>>>>>> Calling mkdir at /usr/local/annotation/maker2.31/bin/maker line 537.
>>>>>>> Calling Iterator::Any::nextFastaRef at
>>>>>>> /usr/local/annotation/maker2.31/bin/maker line 537.
>>>>>>> Calling system at /usr/local/annotation/maker2.31/bin/maker line 537.
>>>>>>> Calling File::NFSLock::unlock at
>>>>>>> /usr/local/annotation/maker2.31/bin/maker line 537.
>>>>>>> Calling GI::build_fasta_index at
>>>>>>> /usr/local/annotation/maker2.31/bin/maker line 538.
>>>>>>> Calling FastaDB::new at /usr/local/annotation/maker2.31/bin/maker line
>>>>>>> 539.
>>>>>>> Calling File::NFSLock::new at
>>>>>>> /usr/local/annotation/maker2.31/bin/../lib/Error.pm line 415.
>>>>>>> Calling out to BioPerl Bio::DB::Fasta::new at
>>>>>>> /usr/local/annotation/maker2.31/bin/../lib/Error.pm line 415.
>>>>>>> Calling out to BioPerl Bio::DB::Fasta::new at
>>>>>>> /usr/local/annotation/maker2.31/bin/../lib/Error.pm line 415.
>>>>>>> Calling out to BioPerl get_PrimarySeq_stream at
>>>>>>> /usr/local/annotation/maker2.31/bin/../lib/GI.pm line 1894.
>>>>>>> Calling GI::split_db at /usr/local/annotation/maker2.31/bin/maker line
>>>>>>> 536.
>>>>>>> Calling File::Path::rmtree at /usr/local/annotation/maker2.31/bin/maker
>>>>>>> line 537.
>>>>>>> Calling Iterator::Any::new at /usr/local/annotation/maker2.31/bin/maker
>>>>>>> line 537.
>>>>>>> Calling Iterator::Any::nextDef at
>>>>>>> /usr/local/annotation/maker2.31/bin/maker line 537.
>>>>>>> Calling Iterator::Any::new at /usr/local/annotation/maker2.31/bin/maker
>>>>>>> line 537.
>>>>>>> Calling mkdir at /usr/local/annotation/maker2.31/bin/maker line 537.
>>>>>>> Calling Iterator::Any::nextFastaRef at
>>>>>>> /usr/local/annotation/maker2.31/bin/maker line 537.
>>>>>>> Calling system at /usr/local/annotation/maker2.31/bin/maker line 537.
>>>>>>> Calling File::NFSLock::unlock at
>>>>>>> /usr/local/annotation/maker2.31/bin/maker line 537.
>>>>>>> Calling GI::build_fasta_index at
>>>>>>> /usr/local/annotation/maker2.31/bin/maker line 538.
>>>>>>> Calling FastaDB::new at /usr/local/annotation/maker2.31/bin/maker line
>>>>>>> 539.
>>>>>>> Calling File::NFSLock::new at
>>>>>>> /usr/local/annotation/maker2.31/bin/../lib/Error.pm line 415.
>>>>>>> Calling out to BioPerl Bio::DB::Fasta::new at
>>>>>>> /usr/local/annotation/maker2.31/bin/../lib/Error.pm line 415.
>>>>>>> Calling out to BioPerl Bio::DB::Fasta::new at
>>>>>>> /usr/local/annotation/maker2.31/bin/../lib/Error.pm line 415.
>>>>>>> Calling out to BioPerl get_PrimarySeq_stream at
>>>>>>> /usr/local/annotation/maker2.31/bin/../lib/GI.pm line 1894.
>>>>>>> Calling File::NFSLock::new at
>>>>>>> /usr/local/annotation/maker2.31/bin/../lib/Error.pm line 415.
>>>>>>> Calling out to BioPerl Bio::DB::Fasta::new at
>>>>>>> /usr/local/annotation/maker2.31/bin/../lib/Error.pm line 415.
>>>>>>> Calling out to BioPerl Bio::DB::Fasta::new at
>>>>>>> /usr/local/annotation/maker2.31/bin/../lib/Error.pm line 415.
>>>>>>> Calling out to BioPerl get_PrimarySeq_stream at
>>>>>>> /usr/local/annotation/maker2.31/bin/../lib/GI.pm line 1894.
>>>>>>> Calling File::NFSLock::new at
>>>>>>> /usr/local/annotation/maker2.31/bin/../lib/Error.pm line 415.
>>>>>>> Calling out to BioPerl Bio::DB::Fasta::new at
>>>>>>> /usr/local/annotation/maker2.31/bin/../lib/Error.pm line 415.
>>>>>>> Calling out to BioPerl Bio::DB::Fasta::new at
>>>>>>> /usr/local/annotation/maker2.31/bin/../lib/Error.pm line 415.
>>>>>>> Calling out to BioPerl get_PrimarySeq_stream at
>>>>>>> /usr/local/annotation/maker2.31/bin/../lib/GI.pm line 1894.
>>>>>>> Calling File::NFSLock::new at
>>>>>>> /usr/local/annotation/maker2.31/bin/../lib/Error.pm line 415.
>>>>>>> Calling out to BioPerl Bio::DB::Fasta::new at
>>>>>>> /usr/local/annotation/maker2.31/bin/../lib/Error.pm line 415.
>>>>>>> Calling out to BioPerl Bio::DB::Fasta::new at
>>>>>>> /usr/local/annotation/maker2.31/bin/../lib/Error.pm line 415.
>>>>>>> Calling out to BioPerl get_PrimarySeq_stream at
>>>>>>> /usr/local/annotation/maker2.31/bin/../lib/GI.pm line 1894.
>>>>>>> Calling File::NFSLock::new at
>>>>>>> /usr/local/annotation/maker2.31/bin/../lib/Error.pm line 415.
>>>>>>> Calling out to BioPerl Bio::DB::Fasta::new at
>>>>>>> /usr/local/annotation/maker2.31/bin/../lib/Error.pm line 415.
>>>>>>> Calling out to BioPerl Bio::DB::Fasta::new at
>>>>>>> /usr/local/annotation/maker2.31/bin/../lib/Error.pm line 415.
>>>>>>> Calling out to BioPerl get_PrimarySeq_stream at
>>>>>>> /usr/local/annotation/maker2.31/bin/../lib/GI.pm line 1894.
>>>>>>> Calling File::NFSLock::new at
>>>>>>> /usr/local/annotation/maker2.31/bin/../lib/Error.pm line 415.
>>>>>>> Calling out to BioPerl Bio::DB::Fasta::new at
>>>>>>> /usr/local/annotation/maker2.31/bin/../lib/Error.pm line 415.
>>>>>>> Calling out to BioPerl Bio::DB::Fasta::new at
>>>>>>> /usr/local/annotation/maker2.31/bin/../lib/Error.pm line 415.
>>>>>>> Calling out to BioPerl get_PrimarySeq_stream at
>>>>>>> /usr/local/annotation/maker2.31/bin/../lib/GI.pm line 1894.
>>>>>>> Calling File::NFSLock::new at
>>>>>>> /usr/local/annotation/maker2.31/bin/../lib/Error.pm line 415.
>>>>>>> Calling out to BioPerl Bio::DB::Fasta::new at
>>>>>>> /usr/local/annotation/maker2.31/bin/../lib/Error.pm line 415.
>>>>>>> Calling out to BioPerl Bio::DB::Fasta::new at
>>>>>>> /usr/local/annotation/maker2.31/bin/../lib/Error.pm line 415.
>>>>>>> Calling out to BioPerl get_PrimarySeq_stream at
>>>>>>> /usr/local/annotation/maker2.31/bin/../lib/GI.pm line 1894.
>>>>>>> Calling File::NFSLock::new at
>>>>>>> /usr/local/annotation/maker2.31/bin/../lib/Error.pm line 415.
>>>>>>> Calling out to BioPerl Bio::DB::Fasta::new at
>>>>>>> /usr/local/annotation/maker2.31/bin/../lib/Error.pm line 415.
>>>>>>> Calling out to BioPerl Bio::DB::Fasta::new at
>>>>>>> /usr/local/annotation/maker2.31/bin/../lib/Error.pm line 415.
>>>>>>> Calling out to BioPerl get_PrimarySeq_stream at
>>>>>>> /usr/local/annotation/maker2.31/bin/../lib/GI.pm line 1894.
>>>>>>> Calling File::NFSLock::new at
>>>>>>> /usr/local/annotation/maker2.31/bin/../lib/Error.pm line 415.
>>>>>>> Calling out to BioPerl Bio::DB::Fasta::new at
>>>>>>> /usr/local/annotation/maker2.31/bin/../lib/Error.pm line 415.
>>>>>>> Calling out to BioPerl Bio::DB::Fasta::new at
>>>>>>> /usr/local/annotation/maker2.31/bin/../lib/Error.pm line 415.
>>>>>>> Calling out to BioPerl get_PrimarySeq_stream at
>>>>>>> /usr/local/annotation/maker2.31/bin/../lib/GI.pm line 1894.
>>>>>>> Calling File::NFSLock::new at
>>>>>>> /usr/local/annotation/maker2.31/bin/../lib/Error.pm line 415.
>>>>>>> Calling out to BioPerl Bio::DB::Fasta::new at
>>>>>>> /usr/local/annotation/maker2.31/bin/../lib/Error.pm line 415.
>>>>>>> Calling out to BioPerl Bio::DB::Fasta::new at
>>>>>>> /usr/local/annotation/maker2.31/bin/../lib/Error.pm line 415.
>>>>>>> Calling out to BioPerl get_PrimarySeq_stream at
>>>>>>> /usr/local/annotation/maker2.31/bin/../lib/GI.pm line 1894.
>>>>>>> Calling GI::create_blastdb at /usr/local/annotation/maker2.31/bin/maker
>>>>>>> line 574.
>>>>>>> Calling File::Path::rmtree at /usr/local/annotation/maker2.31/bin/maker
>>>>>>> line 575.
>>>>>>> Calling Iterator::Any::new at /usr/local/annotation/maker2.31/bin/maker
>>>>>>> line 575.
>>>>>>> Calling Iterator::Any::nextDef at
>>>>>>> /usr/local/annotation/maker2.31/bin/maker line 575.
>>>>>>> Calling Iterator::Any::new at /usr/local/annotation/maker2.31/bin/maker
>>>>>>> line 575.
>>>>>>> Calling File::Path::rmtree at /usr/local/annotation/maker2.31/bin/maker
>>>>>>> line 575.
>>>>>>> Calling Iterator::Any::new at /usr/local/annotation/maker2.31/bin/maker
>>>>>>> line 575.
>>>>>>> Calling Iterator::Any::nextDef at
>>>>>>> /usr/local/annotation/maker2.31/bin/maker line 575.
>>>>>>> Calling Iterator::Any::new at /usr/local/annotation/maker2.31/bin/maker
>>>>>>> line 575.
>>>>>>> Calling GI::build_fasta_index at
>>>>>>> /usr/local/annotation/maker2.31/bin/maker line 622.
>>>>>>> Calling FastaDB::new at /usr/local/annotation/maker2.31/bin/maker line
>>>>>>> 623.
>>>>>>> Calling out to BioPerl Bio::DB::Fasta::new at
>>>>>>> /usr/local/annotation/maker2.31/bin/../lib/Error.pm line 415.
>>>>>>> Calling out to BioPerl get_PrimarySeq_stream at
>>>>>>> /usr/local/annotation/maker2.31/bin/../lib/GI.pm line 1894.
>>>>>>> STATUS: Setting up database for any GFF3 input...
>>>>>>> Calling GFFDB::new at /usr/local/annotation/maker2.31/bin/maker line
>>>>>>> 629.
>>>>>>> Calling GFFDB::next_build at /usr/local/annotation/maker2.31/bin/maker
>>>>>>> line 631.
>>>>>>> Calling ds_utility::new at /usr/local/annotation/maker2.31/bin/maker
>>>>>>> line 635.
>>>>>>> A data structure will be created for you at:
>>>>>>> /home/cdantec/cutQuality/assembly/HR/path/to/Maker/test/dpp_contig.maker
>>>>>>> .output/dpp_contig_datastore
>>>>>>>
>>>>>>> To access files for individual sequences use the datastore index:
>>>>>>> /home/cdantec/cutQuality/assembly/HR/path/to/Maker/test/dpp_contig.maker
>>>>>>> .output/dpp_contig_master_datastore_index.log
>>>>>>>
>>>>>>> Calling Datastore::MD5::new at /usr/local/annotation/maker2.31/bin/maker
>>>>>>> line 636.
>>>>>>> Calling Iterator::Fasta::new at
>>>>>>> /usr/local/annotation/maker2.31/bin/maker line 639.
>>>>>>> Calling Iterator::Fasta::skip_file at
>>>>>>> /usr/local/annotation/maker2.31/bin/maker line 641.
>>>>>>> Calling Iterator::Fasta::step at
>>>>>>> /usr/local/annotation/maker2.31/bin/maker line 643.
>>>>>>> STATUS: Now running MAKER...
>>>>>>> examining contents of the fasta file and run log
>>>>>>> Calling Datastore::MD5::mkdir at
>>>>>>> /usr/local/annotation/maker2.31/bin/../lib/Process/MpiChunk.pm line 439.
>>>>>>> Calling Datastore::MD5::id_to_dir at
>>>>>>> /usr/local/annotation/maker2.31/bin/../lib/Process/MpiChunk.pm line 439.
>>>>>>> Calling Datastore::MD5::mkdir at
>>>>>>> /usr/local/annotation/maker2.31/bin/../lib/Process/MpiChunk.pm line 439.
>>>>>>> Calling uri_escape at
>>>>>>> /usr/local/annotation/maker2.31/bin/../lib/Process/MpiChunk.pm line 439.
>>>>>>> Calling File::Path::mkpath at
>>>>>>> /usr/local/annotation/maker2.31/bin/../lib/Process/MpiChunk.pm line 439.
>>>>>>>
>>>>>>>
>>>>>>>
>>>>>>> --Next Contig--
>>>>>>>
>>>>>>> #---------------------------------------------------------------------
>>>>>>> Now starting the contig!!
>>>>>>> SeqID: contig-dpp-500-500
>>>>>>> Length: 32156
>>>>>>> #---------------------------------------------------------------------
>>>>>>>
>>>>>>>
>>>>>>> Calling FastaDB::new at
>>>>>>> /usr/local/annotation/maker2.31/bin/../lib/Process/MpiChunk.pm line 462.
>>>>>>> Calling out to BioPerl get_PrimarySeq_stream at
>>>>>>> /usr/local/annotation/maker2.31/bin/../lib/GI.pm line 1894.
>>>>>>> setting up GFF3 output and fasta chunks
>>>>>>> doing repeat masking
>>>>>>> DBI
>>>>>>> connect('dbname=/home/cdantec/cutQuality/assembly/HR/path/to/Maker/test/
>>>>>>> dpp_contig.maker.output/dpp_contig.db','',...) failed: unable to open
>>>>>>> database file at /usr/local/annotation/maker2.31/bin/../lib/GFFDB.pm
>>>>>>> line 107.
>>>>>>> Can't call method "do" on an undefined value at
>>>>>>> /usr/local/annotation/maker2.31/bin/../lib/GFFDB.pm line 108.
>>>>>>> --> rank=NA, hostname=belem
>>>>>>> ERROR: Failed while doing repeat masking
>>>>>>> ERROR: Chunk failed at level:0, tier_type:1
>>>>>>> FAILED CONTIG:contig-dpp-500-500
>>>>>>>
>>>>>>> ERROR: Chunk failed at level:2, tier_type:0
>>>>>>> FAILED CONTIG:contig-dpp-500-500
>>>>>>>
>>>>>>> examining contents of the fasta file and run log
>>>>>>> Calling Datastore::MD5::mkdir at
>>>>>>> /usr/local/annotation/maker2.31/bin/../lib/Process/MpiChunk.pm line 439.
>>>>>>> Calling Datastore::MD5::id_to_dir at
>>>>>>> /usr/local/annotation/maker2.31/bin/../lib/Process/MpiChunk.pm line 439.
>>>>>>> Calling Datastore::MD5::mkdir at
>>>>>>> /usr/local/annotation/maker2.31/bin/../lib/Process/MpiChunk.pm line 439.
>>>>>>> Calling uri_escape at
>>>>>>> /usr/local/annotation/maker2.31/bin/../lib/Process/MpiChunk.pm line 439.
>>>>>>> Calling File::Path::mkpath at
>>>>>>> /usr/local/annotation/maker2.31/bin/../lib/Process/MpiChunk.pm line 439.
>>>>>>>
>>>>>>>
>>>>>>>
>>>>>>> --Next Contig--
>>>>>>>
>>>>>>> Processing run.log file...
>>>>>>> #---------------------------------------------------------------------
>>>>>>> Now retrying the contig!!
>>>>>>> SeqID: contig-dpp-500-500
>>>>>>> Length: 32156
>>>>>>> Tries: 2!!
>>>>>>> #---------------------------------------------------------------------
>>>>>>>
>>>>>>>
>>>>>>> Calling FastaDB::new at
>>>>>>> /usr/local/annotation/maker2.31/bin/../lib/Process/MpiChunk.pm line 462.
>>>>>>> Calling out to BioPerl get_PrimarySeq_stream at
>>>>>>> /usr/local/annotation/maker2.31/bin/../lib/GI.pm line 1894.
>>>>>>> setting up GFF3 output and fasta chunks
>>>>>>> doing repeat masking
>>>>>>> DBI
>>>>>>> connect('dbname=/home/cdantec/cutQuality/assembly/HR/path/to/Maker/test/
>>>>>>> dpp_contig.maker.output/dpp_contig.db','',...) failed: unable to open
>>>>>>> database file at /usr/local/annotation/maker2.31/bin/../lib/GFFDB.pm
>>>>>>> line 107.
>>>>>>> Can't call method "do" on an undefined value at
>>>>>>> /usr/local/annotation/maker2.31/bin/../lib/GFFDB.pm line 108.
>>>>>>> --> rank=NA, hostname=belem
>>>>>>> ERROR: Failed while doing repeat masking
>>>>>>> ERROR: Chunk failed at level:0, tier_type:1
>>>>>>> FAILED CONTIG:contig-dpp-500-500
>>>>>>>
>>>>>>> ERROR: Chunk failed at level:2, tier_type:0
>>>>>>> FAILED CONTIG:contig-dpp-500-500
>>>>>>>
>>>>>>> examining contents of the fasta file and run log
>>>>>>> Calling Datastore::MD5::mkdir at
>>>>>>> /usr/local/annotation/maker2.31/bin/../lib/Process/MpiChunk.pm line 439.
>>>>>>> Calling Datastore::MD5::id_to_dir at
>>>>>>> /usr/local/annotation/maker2.31/bin/../lib/Process/MpiChunk.pm line 439.
>>>>>>> Calling Datastore::MD5::mkdir at
>>>>>>> /usr/local/annotation/maker2.31/bin/../lib/Process/MpiChunk.pm line 439.
>>>>>>> Calling uri_escape at
>>>>>>> /usr/local/annotation/maker2.31/bin/../lib/Process/MpiChunk.pm line 439.
>>>>>>> Calling File::Path::mkpath at
>>>>>>> /usr/local/annotation/maker2.31/bin/../lib/Process/MpiChunk.pm line 439.
>>>>>>>
>>>>>>>
>>>>>>>
>>>>>>> --Next Contig--
>>>>>>>
>>>>>>> Processing run.log file...
>>>>>>>
>>>>>>>
>>>>>>> Maker is now finished!!!
>>>>>>>
>>>>>>> Many thanks for you help
>>>>>>>
>>>>>>> Christelle
>>>>>>>
>>>>>>>
>>>>>>>
>>>>>>> 2014-03-19 14:01 GMT+01:00 Carson Holt <carsonhh at gmail.com>:
>>>>>>> Your problem is one of the following. You need to reinstall the
>>>>>>> DBD::SQLite module, you are running in a directory you don’t have
>>>>>>> permissions for, you set your TMDIR environmental variable or TMP value
>>>>>>> in maker_opts.ctl to an NFS mounted or memory mounted directory, or you
>>>>>>> are using a self compiled version of Perl (I.e. not /usr/bin/perl) that
>>>>>>> has issues (probably with DB or SQLite modules). You can also
>>>>>>> completely delete the output directory, and start again to see if it was
>>>>>>> just a random error. You should look at each of those first. You can
>>>>>>> also run MAKER with the --debug command line flag and send it to me if
>>>>>>> all of those seem not to be the issue.
>>>>>>>
>>>>>>> Thanks,
>>>>>>> Carson
>>>>>>>
>>>>>>>
>>>>>>> From: Chris Bioinfo <chrisbioinfo at gmail.com>
>>>>>>> Date: Wednesday, March 19, 2014 at 5:09 AM
>>>>>>> To: <maker-devel at yandell-lab.org>
>>>>>>> Subject: [maker-devel] Annotation with maker2
>>>>>>>
>>>>>>> Hello,
>>>>>>>
>>>>>>> I'm installing/using maker2 for the first time and I have an error by
>>>>>>> using it.
>>>>>>>
>>>>>>> I certainly missing something, but I don't know what.
>>>>>>>
>>>>>>> I compile maker with no error message and I have all these directories
>>>>>>> after compilation:
>>>>>>> bin data GMOD INSTALL lib LICENSE MWAS perl README src
>>>>>>>
>>>>>>> Nevertheless when I try maker2 on the test data (dpp_contig.fasta) I
>>>>>>> have this error:
>>>>>>>
>>>>>>> STATUS: Now running MAKER...
>>>>>>> examining contents of the fasta file and run log
>>>>>>>
>>>>>>>
>>>>>>>
>>>>>>> --Next Contig--
>>>>>>>
>>>>>>> #---------------------------------------------------------------------
>>>>>>> Now starting the contig!!
>>>>>>> SeqID: contig-dpp-500-500
>>>>>>> Length: 32156
>>>>>>> #---------------------------------------------------------------------
>>>>>>>
>>>>>>>
>>>>>>> setting up GFF3 output and fasta chunks
>>>>>>> doing repeat masking
>>>>>>> DBI
>>>>>>> connect('dbname=/path/to/dpp_contig.maker.output/dpp_contig.db','',...)
>>>>>>> failed: unable to open database file at
>>>>>>> /usr/local/annotation/maker2.31/bin/../lib/GFFDB.pm
>>>>>>>
>>>>>>> Can't call method "do" on an undefined value at
>>>>>>> /usr/local/annotation/maker2.31/bin/../lib/GFFDB.pm
>>>>>>> --> rank=NA, hostname=belem
>>>>>>> ERROR: Failed while doing repeat masking
>>>>>>> ERROR: Chunk failed at level:0, tier_type:1
>>>>>>> FAILED CONTIG:contig-dpp-500-500
>>>>>>> ...
>>>>>>>
>>>>>>> ideas?
>>>>>>>
>>>>>>> Best,
>>>>>>>
>>>>>>> Christelle
>>>>>>>
>>>>>>> _______________________________________________ maker-devel mailing list
>>>>>>> maker-devel at box290.bluehost.comhttp://box290.bluehost.com/mailman/listin
>>>>>>> fo/maker-devel_yandell-lab.org
>>>>>>>
>>>>>>
>>>>>
>>>>
>>>
>>
>
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