[maker-devel] Annotation with maker2

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Chris Bioinfo

unread,
Mar 19, 2014, 7:09:57 AM3/19/14
to maker...@yandell-lab.org
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

Carson Holt

unread,
Mar 19, 2014, 9:01:35 AM3/19/14
to Chris Bioinfo, maker...@yandell-lab.org
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


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Carson Holt

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Mar 21, 2014, 10:23:18 AM3/21/14
to Chris Bioinfo, maker...@yandell-lab.org
Glad it's working.  Let us know if anything else comes up.

--Carson



From: Chris Bioinfo <chrisb...@gmail.com>
Date: Friday, March 21, 2014 at 4:57 AM
To: Carson Holt <cars...@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 <cars...@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 <cars...@gmail.com>
Date: Thursday, March 20, 2014 at 11:03 AM
To: Chris Bioinfo <chrisb...@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 <chrisb...@gmail.com>
Date: Thursday, March 20, 2014 at 10:57 AM
To: Carson Holt <cars...@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 <cars...@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 <chrisb...@gmail.com>
Date: Thursday, March 20, 2014 at 10:29 AM

To: Carson Holt <cars...@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 <chrisb...@gmail.com>:
this :

 du -h dpp_contig.maker.output/
0    dpp_contig.maker.output/dpp_contig_datastore/05/1F/contig-dpp-500-500/theVoid.contig-dpp-500-500/0
88K    dpp_contig.maker.output/dpp_contig_datastore/05/1F/contig-dpp-500-500/theVoid.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 <cars...@gmail.com>:

What does 'df -h dpp_contig.maker.output' show?

--Carson

From: Chris Bioinfo <chrisb...@gmail.com>
Date: Thursday, March 20, 2014 at 10:00 AM

To: Carson Holt <cars...@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 <chrisb...@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 <cars...@gmail.com>:

Did /home/cdantec/cutQuality/assembly/HR/path/to/Maker/test/dpp_contig.maker.output/dpp_contig.db exist?

--Carson


From: Chris Bioinfo <chrisb...@gmail.com>
Date: Thursday, March 20, 2014 at 9:50 AM

To: Carson Holt <cars...@gmail.com>
Subject: Re: [maker-devel] Annotation with maker2

cdantec@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 <cars...@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 <chrisb...@gmail.com>
Date: Thursday, March 20, 2014 at 9:25 AM
To: Carson Holt <cars...@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.pm
    UNKNOWN    Bio::Search::HSP::PhatHSP::augustus    /usr/local/annotation/maker2.31/bin/../lib/Bio/Search/HSP/PhatHSP/augustus.pm
    0.01    Bio::Search::HSP::PhatHSP::blastn    /usr/local/annotation/maker2.31/bin/../lib/Bio/Search/HSP/PhatHSP/blastn.pm
    0.01    Bio::Search::HSP::PhatHSP::blastx    /usr/local/annotation/maker2.31/bin/../lib/Bio/Search/HSP/PhatHSP/blastx.pm
    UNKNOWN    Bio::Search::HSP::PhatHSP::cdna2genome    /usr/local/annotation/maker2.31/bin/../lib/Bio/Search/HSP/PhatHSP/cdna2genome.pm
    UNKNOWN    Bio::Search::HSP::PhatHSP::est2genome    /usr/local/annotation/maker2.31/bin/../lib/Bio/Search/HSP/PhatHSP/est2genome.pm
    UNKNOWN    Bio::Search::HSP::PhatHSP::fgenesh    /usr/local/annotation/maker2.31/bin/../lib/Bio/Search/HSP/PhatHSP/fgenesh.pm
    UNKNOWN    Bio::Search::HSP::PhatHSP::genemark    /usr/local/annotation/maker2.31/bin/../lib/Bio/Search/HSP/PhatHSP/genemark.pm
    UNKNOWN    Bio::Search::HSP::PhatHSP::gff3    /usr/local/annotation/maker2.31/bin/../lib/Bio/Search/HSP/PhatHSP/gff3.pm
    UNKNOWN    Bio::Search::HSP::PhatHSP::protein2genome    /usr/local/annotation/maker2.31/bin/../lib/Bio/Search/HSP/PhatHSP/protein2genome.pm
    UNKNOWN    Bio::Search::HSP::PhatHSP::repeatmasker    /usr/local/annotation/maker2.31/bin/../lib/Bio/Search/HSP/PhatHSP/repeatmasker.pm
    UNKNOWN    Bio::Search::HSP::PhatHSP::snap    /usr/local/annotation/maker2.31/bin/../lib/Bio/Search/HSP/PhatHSP/snap.pm
    UNKNOWN    Bio::Search::HSP::PhatHSP::snoscan    /usr/local/annotation/maker2.31/bin/../lib/Bio/Search/HSP/PhatHSP/snoscan.pm
    0.01    Bio::Search::HSP::PhatHSP::tblastx    /usr/local/annotation/maker2.31/bin/../lib/Bio/Search/HSP/PhatHSP/tblastx.pm
    UNKNOWN    Bio::Search::HSP::PhatHSP::trnascan    /usr/local/annotation/maker2.31/bin/../lib/Bio/Search/HSP/PhatHSP/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.pm
    UNKNOWN    Bio::Search::Hit::PhatHit::augustus    /usr/local/annotation/maker2.31/bin/../lib/Bio/Search/Hit/PhatHit/augustus.pm
    0.01    Bio::Search::Hit::PhatHit::blastn    /usr/local/annotation/maker2.31/bin/../lib/Bio/Search/Hit/PhatHit/blastn.pm
    0.01    Bio::Search::Hit::PhatHit::blastx    /usr/local/annotation/maker2.31/bin/../lib/Bio/Search/Hit/PhatHit/blastx.pm
    UNKNOWN    Bio::Search::Hit::PhatHit::cdna2genome    /usr/local/annotation/maker2.31/bin/../lib/Bio/Search/Hit/PhatHit/cdna2genome.pm
    UNKNOWN    Bio::Search::Hit::PhatHit::est2genome    /usr/local/annotation/maker2.31/bin/../lib/Bio/Search/Hit/PhatHit/est2genome.pm
    UNKNOWN    Bio::Search::Hit::PhatHit::fgenesh    /usr/local/annotation/maker2.31/bin/../lib/Bio/Search/Hit/PhatHit/fgenesh.pm
    UNKNOWN    Bio::Search::Hit::PhatHit::genemark    /usr/local/annotation/maker2.31/bin/../lib/Bio/Search/Hit/PhatHit/genemark.pm
    UNKNOWN    Bio::Search::Hit::PhatHit::gff3    /usr/local/annotation/maker2.31/bin/../lib/Bio/Search/Hit/PhatHit/gff3.pm
    UNKNOWN    Bio::Search::Hit::PhatHit::protein2genome    /usr/local/annotation/maker2.31/bin/../lib/Bio/Search/Hit/PhatHit/protein2genome.pm
    1.006923    Bio::Search::Hit::PhatHit::repeatmasker    /usr/local/annotation/maker2.31/bin/../lib/Bio/Search/Hit/PhatHit/repeatmasker.pm
    UNKNOWN    Bio::Search::Hit::PhatHit::snap    /usr/local/annotation/maker2.31/bin/../lib/Bio/Search/Hit/PhatHit/snap.pm
    UNKNOWN    Bio::Search::Hit::PhatHit::snoscan    /usr/local/annotation/maker2.31/bin/../lib/Bio/Search/Hit/PhatHit/snoscan.pm
    0.01    Bio::Search::Hit::PhatHit::tblastx    /usr/local/annotation/maker2.31/bin/../lib/Bio/Search/Hit/PhatHit/tblastx.pm
    UNKNOWN    Bio::Search::Hit::PhatHit::trnascan    /usr/local/annotation/maker2.31/bin/../lib/Bio/Search/Hit/PhatHit/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.pm
    0.01    CGL::Annotation::Feature::Gene    /usr/local/annotation/maker2.31/bin/../lib/CGL/Annotation/Feature/Gene.pm
    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/Protein.pm
    0.01    CGL::Annotation::Feature::Sequence_variant    /usr/local/annotation/maker2.31/bin/../lib/CGL/Annotation/Feature/Sequence_variant.pm
    0.01    CGL::Annotation::Feature::Transcript    /usr/local/annotation/maker2.31/bin/../lib/CGL/Annotation/Feature/Transcript.pm
    0.01    CGL::Annotation::FeatureLocation    /usr/local/annotation/maker2.31/bin/../lib/CGL/Annotation/FeatureLocation.pm
    0.01    CGL::Annotation::FeatureRelationship    /usr/local/annotation/maker2.31/bin/../lib/CGL/Annotation/FeatureRelationship.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
    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
    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
    UNKNOWN    Widget::blastn    /usr/local/annotation/maker2.31/bin/../lib/Widget/blastn.pm
    UNKNOWN    Widget::blastx    /usr/local/annotation/maker2.31/bin/../lib/Widget/blastx.pm
    UNKNOWN    Widget::exonerate    /usr/local/annotation/maker2.31/bin/../lib/Widget/exonerate.pm
    UNKNOWN    Widget::exonerate::cdna2genome    /usr/local/annotation/maker2.31/bin/../lib/Widget/exonerate/cdna2genome.pm
    UNKNOWN    Widget::exonerate::est2genome    /usr/local/annotation/maker2.31/bin/../lib/Widget/exonerate/est2genome.pm
    UNKNOWN    Widget::exonerate::protein2genome    /usr/local/annotation/maker2.31/bin/../lib/Widget/exonerate/protein2genome.pm
    UNKNOWN    Widget::fgenesh    /usr/local/annotation/maker2.31/bin/../lib/Widget/fgenesh.pm
    UNKNOWN    Widget::formater    /usr/local/annotation/maker2.31/bin/../lib/Widget/formater.pm
    UNKNOWN    Widget::genemark    /usr/local/annotation/maker2.31/bin/../lib/Widget/genemark.pm
    UNKNOWN    Widget::snap    /usr/local/annotation/maker2.31/bin/../lib/Widget/snap.pm
    UNKNOWN    Widget::snoscan    /usr/local/annotation/maker2.31/bin/../lib/Widget/snoscan.pm
    UNKNOWN    Widget::tblastx    /usr/local/annotation/maker2.31/bin/../lib/Widget/tblastx.pm
    UNKNOWN    Widget::trnascan    /usr/local/annotation/maker2.31/bin/../lib/Widget/trnascan.pm
    0.16    XSLoader    /usr/share/perl/5.18/XSLoader.pm
    0.21    attributes    /usr/lib/perl/5.18/attributes.pm
    2.18    base    /usr/share/perl/5.18/base.pm
    1.04    bytes    /usr/share/perl/5.18/bytes.pm
    UNKNOWN    clean    /usr/local/annotation/maker2.31/bin/../lib/clean.pm
    UNKNOWN    cluster    /usr/local/annotation/maker2.31/bin/../lib/cluster.pm
    UNKNOWN    compare    /usr/local/annotation/maker2.31/bin/../lib/compare.pm
    1.27    constant    /usr/share/perl/5.18/constant.pm
    UNKNOWN    ds_utility    /usr/local/annotation/maker2.31/bin/../lib/ds_utility.pm
    UNKNOWN    exonerate::splice_info    /usr/local/annotation/maker2.31/bin/../lib/exonerate/splice_info.pm
    0.34    forks    /usr/local/lib/perl/5.18.1/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
    0.34    forks::signals    /usr/local/lib/perl/5.18.1/forks/signals.pm
    1.00    integer    /usr/share/perl/5.18/integer.pm
    0.63    lib    /usr/lib/perl/5.18/lib.pm
    1.02    locale    /usr/share/perl/5.18/locale.pm
    UNKNOWN    maker::auto_annotator    /usr/local/annotation/maker2.31/bin/../lib/maker/auto_annotator.pm
    UNKNOWN    maker::join    /usr/local/annotation/maker2.31/bin/../lib/maker/join.pm
    UNKNOWN    maker::quality_index    /usr/local/annotation/maker2.31/bin/../lib/maker/quality_index.pm
    UNKNOWN    maker::sens_spec    /usr/local/annotation/maker2.31/bin/../lib/maker/sens_spec.pm
    1.22    overload    /usr/share/perl/5.18/overload.pm
    0.02    overloading    /usr/share/perl/5.18/overloading.pm
    0.225    parent    /usr/share/perl/5.18/parent.pm
    UNKNOWN    polisher    /usr/local/annotation/maker2.31/bin/../lib/polisher.pm
    UNKNOWN    polisher::exonerate    /usr/local/annotation/maker2.31/bin/../lib/polisher/exonerate.pm
    UNKNOWN    polisher::exonerate::altest    /usr/local/annotation/maker2.31/bin/../lib/polisher/exonerate/altest.pm
    UNKNOWN    polisher::exonerate::est    /usr/local/annotation/maker2.31/bin/../lib/polisher/exonerate/est.pm
    UNKNOWN    polisher::exonerate::protein    /usr/local/annotation/maker2.31/bin/../lib/polisher/exonerate/protein.pm
    UNKNOWN    repeat_mask_seq    /usr/local/annotation/maker2.31/bin/../lib/repeat_mask_seq.pm
    0.1    runlog    /usr/local/annotation/maker2.31/bin/../lib/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
    1.07    strict    /usr/share/perl/5.18/strict.pm
    1.77    threads    /usr/local/lib/perl/5.18.1/forks.pm
    1.33    threads::shared    /usr/local/lib/perl/5.18.1/forks/shared.pm
    1.03    vars    /usr/share/perl/5.18/vars.pm
    1.18    warnings    /usr/share/perl/5.18/warnings.pm
    1.02    warnings::register    /usr/share/perl/5.18/warnings/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

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