<html><head></head><body style="word-wrap: break-word; -webkit-nbsp-mode: space; -webkit-line-break: after-white-space; color: rgb(0, 0, 0); font-size: 14px; font-family: Calibri, sans-serif;"><div>Glad it's working. Let us know if anything else comes up.</div><div><br></div><div>--Carson</div><div><br></div><div><br></div><div><br></div><span id="OLK_SRC_BODY_SECTION"><div style="font-family:Calibri; font-size:11pt; text-align:left; color:black; BORDER-BOTTOM: medium none; BORDER-LEFT: medium none; PADDING-BOTTOM: 0in; PADDING-LEFT: 0in; PADDING-RIGHT: 0in; BORDER-TOP: #b5c4df 1pt solid; BORDER-RIGHT: medium none; PADDING-TOP: 3pt"><span style="font-weight:bold">From: </span> Chris Bioinfo <<a href="mailto:chrisbioinfo@gmail.com">chrisbioinfo@gmail.com</a>><br><span style="font-weight:bold">Date: </span> Friday, March 21, 2014 at 4:57 AM<br><span style="font-weight:bold">To: </span> Carson Holt <<a href="mailto:carsonhh@gmail.com">carsonhh@gmail.com</a>><br><span style="font-weight:bold">Subject: </span> Re: [maker-devel] Annotation with maker2<br></div><div><br></div><div dir="ltr">Dear Carson<br><div><br>it works!! after many difficults :<br><br></div><div>I have installed sqlite3.8.4.1 yesterday: it was """better"""" (no error message by launching sqlite3). Yet my test.db was not created..<br><br></div><div>Today I find the trick!<br></div><div>the problem was due to my too long path to created the db .. only that... <br><br></div><div>Thanks for your time and you help Carson!<br><br></div><div>All the best,<br><br></div><div>Christelle<br></div><div><br><br></div></div><div class="gmail_extra"><br><br><div class="gmail_quote">2014-03-20 18:21 GMT+01:00 Carson Holt <span dir="ltr"><<a href="mailto:carsonhh@gmail.com" target="_blank">carsonhh@gmail.com</a>></span>:<br><blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex"><div style="font-size:14px;font-family:Calibri,sans-serif;word-wrap:break-word"><div><div>Also you can use this command line to test both before and after installing</div><div><br></div><div style="font-family:Calibri;font-size:medium"><font face="Calibri,sans-serif">perl -MDBI -MDBD::SQLite -e 'print "$DBD::SQLite::sqlite_version\n"; $dbh = DBI->connect("dbi:SQLite:dbname=/path/from/maker/error/dpp_contig.db","","");'</font></div><div style="font-family:Calibri;font-size:medium"><font face="Calibri,sans-serif"><br></font></div><div style="font-family:Calibri;font-size:medium"><font face="Calibri,sans-serif">Make sure to set </font><font face="Calibri,sans-serif">/path/from/maker/error/dpp_contig.db to whatever its was in the error.</font></div><div style="font-family:Calibri;font-size:medium"><font face="Calibri,sans-serif"><br></font></div><div style="font-family:Calibri;font-size:medium"><font face="Calibri,sans-serif">--Carson</font></div></div><div><font face="Calibri,sans-serif"><br></font></div><div><br></div><span><div style="border-right:medium none;padding-right:0in;padding-left:0in;padding-top:3pt;text-align:left;font-size:11pt;border-bottom:medium none;font-family:Calibri;border-top:#b5c4df 1pt solid;padding-bottom:0in;border-left:medium none"><span style="font-weight:bold">From: </span> Carson Holt <<a href="mailto:carsonhh@gmail.com" target="_blank">carsonhh@gmail.com</a>><br><span style="font-weight:bold">Date: </span> Thursday, March 20, 2014 at 11:03 AM<br><span style="font-weight:bold">To: </span> Chris Bioinfo <<a href="mailto:chrisbioinfo@gmail.com" target="_blank">chrisbioinfo@gmail.com</a>><div><div class="h5"><br><span style="font-weight:bold">Subject: </span> Re: [maker-devel] Annotation with maker2<br></div></div></div><div><div class="h5"><div><br></div><div><div style="word-wrap:break-word"><div><font face="Calibri,sans-serif">The failure is in SQLite. So you have to reinstall. I.e. 'force install </font>DBD::SQLite' in CPAN. Otherwise you are just keeping whatever module is installed which may have broken C bindings.</div><div><br></div><div>You may also have to install SQLite 3.8.4.1, and then reinstall the perl modules using the force option to force recompile.</div><div><br></div><div>--Carson</div><div><br></div><div style="font-size:14px;font-family:Calibri,sans-serif"><br></div><div style="font-size:14px;font-family:Calibri,sans-serif"><br></div><span style="font-size: 14px; font-family: Calibri, sans-serif;"><div style="border-right:medium none;padding-right:0in;padding-left:0in;padding-top:3pt;text-align:left;font-size:11pt;border-bottom:medium none;font-family:Calibri;border-top:#b5c4df 1pt solid;padding-bottom:0in;border-left:medium none"><span style="font-weight:bold">From: </span> Chris Bioinfo <<a href="mailto:chrisbioinfo@gmail.com" target="_blank">chrisbioinfo@gmail.com</a>><br><span style="font-weight:bold">Date: </span> Thursday, March 20, 2014 at 10:57 AM<br><span style="font-weight:bold">To: </span> Carson Holt <<a href="mailto:carsonhh@gmail.com" target="_blank">carsonhh@gmail.com</a>><br><span style="font-weight:bold">Subject: </span> Re: [maker-devel] Annotation with maker2<br></div><div><br></div><div dir="ltr"><div>cpan[2]> install DBI<br>DBI is up to date (1.631).<br><br>cpan[3]> install DBD::SQLite<br>DBD::SQLite is up to date (1.42).<br><br></div>my test.db is not created effectively:<br><div><br>sqlite3 dpp_contig.maker.output/test.db <br>
SQLite version 3.8.3.1 2014-02-11 14:52:19<br>Enter ".help" for instructions<br>Enter SQL statements terminated with a ";"<br>sqlite> <br><br><br></div></div><div class="gmail_extra"><br><br><div class="gmail_quote">
2014-03-20 17:36 GMT+01:00 Carson Holt <span dir="ltr"><<a href="mailto:carsonhh@gmail.com" target="_blank">carsonhh@gmail.com</a>></span>:<br><blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex"><div style="font-size:14px;font-family:Calibri,sans-serif;word-wrap:break-word"><div>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.</div><div><br></div><div>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.</div><div><br></div><div>You can also do a test command --> 'sqllite3 dpp_contig.maker.output/test.db'</div><div><br></div><div>This will work if you have sqllite3 installed. And any error it give may be informative.</div><div><br></div><div>--Carson</div><div><br></div><span><div style="border-right:medium none;padding-right:0in;padding-left:0in;padding-top:3pt;text-align:left;font-size:11pt;border-bottom:medium none;font-family:Calibri;border-top:#b5c4df 1pt solid;padding-bottom:0in;border-left:medium none"><span style="font-weight:bold">From: </span> Chris Bioinfo <<a href="mailto:chrisbioinfo@gmail.com" target="_blank">chrisbioinfo@gmail.com</a>><br><span style="font-weight:bold">Date: </span> Thursday, March 20, 2014 at 10:29 AM<div><div><br><span style="font-weight:bold">To: </span> Carson Holt <<a href="mailto:carsonhh@gmail.com" target="_blank">carsonhh@gmail.com</a>><br><span style="font-weight:bold">Subject: </span> Re: [maker-devel] Annotation with maker2<br></div></div></div><div><div><div><br></div><div dir="ltr"><div>oh sorry<br><br></div>my disks are quite full, but still space I guess for maker<br><br> /dev/sdc1 19T 18T 934G 95% /home<br></div><div class="gmail_extra"><br><br><div class="gmail_quote">
2014-03-20 17:23 GMT+01:00 Chris Bioinfo <span dir="ltr"><<a href="mailto:chrisbioinfo@gmail.com" target="_blank">chrisbioinfo@gmail.com</a>></span>:<br><blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex"><div dir="ltr">this :<br><div><br> du -h dpp_contig.maker.output/<br>0 dpp_contig.maker.output/dpp_contig_datastore/05/1F/contig-dpp-500-500/theVoid.contig-dpp-500-500/0<br>88K dpp_contig.maker.output/dpp_contig_datastore/05/1F/contig-dpp-500-500/theVoid.contig-dpp-500-500<br>
92K dpp_contig.maker.output/dpp_contig_datastore/05/1F/contig-dpp-500-500<br>92K dpp_contig.maker.output/dpp_contig_datastore/05/1F<br>92K dpp_contig.maker.output/dpp_contig_datastore/05<br>92K dpp_contig.maker.output/dpp_contig_datastore<br>
4.0K dpp_contig.maker.output/dpp_contig_master_datastore_index.log<br>4.0K dpp_contig.maker.output/maker_bopts.log<br>4.0K dpp_contig.maker.output/maker_exe.log<br>8.0K dpp_contig.maker.output/maker_opts.log<br>
16K dpp_contig.maker.output/mpi_blastdb/dpp_protein%2Efasta.mpi.1<br>44K dpp_contig.maker.output/mpi_blastdb/dpp_contig%2Efasta.mpi.1<br>14M dpp_contig.maker.output/mpi_blastdb/te_proteins%2Efasta.mpi.10<br>32K dpp_contig.maker.output/mpi_blastdb/dpp_est%2Efasta.mpi.1<br>
14M dpp_contig.maker.output/mpi_blastdb<br>0 dpp_contig.maker.output/seen.dbm<br><br></div></div><div class="gmail_extra"><br><br><div class="gmail_quote">2014-03-20 17:10 GMT+01:00 Carson Holt <span dir="ltr"><<a href="mailto:carsonhh@gmail.com" target="_blank">carsonhh@gmail.com</a>></span>:<div><div><br><blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex"><div style="font-size:14px;font-family:Calibri,sans-serif;word-wrap:break-word"><div>What does 'df -h <span style="font-family:Calibri;font-size:medium">dpp_contig.maker.output' show?</span></div><div><span style="font-family:Calibri;font-size:medium"><br></span></div><div><span style="font-family:Calibri;font-size:medium">--Carson</span></div><div><br></div><span><div style="border-right:medium none;padding-right:0in;padding-left:0in;padding-top:3pt;text-align:left;font-size:11pt;border-bottom:medium none;font-family:Calibri;border-top:#b5c4df 1pt solid;padding-bottom:0in;border-left:medium none"><span style="font-weight:bold">From: </span> Chris Bioinfo <<a href="mailto:chrisbioinfo@gmail.com" target="_blank">chrisbioinfo@gmail.com</a>><br><span style="font-weight:bold">Date: </span> Thursday, March 20, 2014 at 10:00 AM<div><div><br><span style="font-weight:bold">To: </span> Carson Holt <<a href="mailto:carsonhh@gmail.com" target="_blank">carsonhh@gmail.com</a>><br><span style="font-weight:bold">Subject: </span> Re: [maker-devel] Annotation with maker2<br></div></div></div><div><div><div><br></div><div dir="ltr"><div>sorry, mistake on the dir!<br><br></div>I have these files:<br>dpp_contig_datastore dpp_contig_master_datastore_index.log maker_bopts.log maker_exe.log maker_opts.log mpi_blastdb seen.dbm<br></div><div class="gmail_extra"><br><br><div class="gmail_quote">2014-03-20 16:59 GMT+01:00 Chris Bioinfo <span dir="ltr"><<a href="mailto:chrisbioinfo@gmail.com" target="_blank">chrisbioinfo@gmail.com</a>></span>:<br><blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex"><div dir="ltr"><div>no,<br><br></div>I have theses files in the directory:<br>dpp_contig.fasta dpp_est.fasta hsap_contig.fasta hsap_protein.fasta maker_exe.ctl <br>
dpp_contig.maker.output dpp_protein.fasta hsap_est.fasta maker_bopts.ctl maker_opts.ctl te_proteins.fasta<br><br></div><div class="gmail_extra"><br><br><div class="gmail_quote">2014-03-20 16:53 GMT+01:00 Carson Holt <span dir="ltr"><<a href="mailto:carsonhh@gmail.com" target="_blank">carsonhh@gmail.com</a>></span>:<div><div><br><blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex"><div style="word-wrap:break-word"><div><font face="Calibri,sans-serif">Did </font><span style="font-size:medium;font-family:Calibri">/home/cdantec/cutQuality/assembly/HR/path/to/Maker/test/dpp_contig.maker.output/dpp_contig.db </span>exist?</div><div style="font-size:14px;font-family:Calibri,sans-serif"><br></div><div style="font-size:14px;font-family:Calibri,sans-serif">--Carson</div><div style="font-size:14px;font-family:Calibri,sans-serif"><br></div><div style="font-size:14px;font-family:Calibri,sans-serif"><br></div><span style="font-size: 14px; font-family: Calibri, sans-serif;"><div style="border-right:medium none;padding-right:0in;padding-left:0in;padding-top:3pt;text-align:left;font-size:11pt;border-bottom:medium none;font-family:Calibri;border-top:#b5c4df 1pt solid;padding-bottom:0in;border-left:medium none"><span style="font-weight:bold">From: </span> Chris Bioinfo <<a href="mailto:chrisbioinfo@gmail.com" target="_blank">chrisbioinfo@gmail.com</a>><br><span style="font-weight:bold">Date: </span> Thursday, March 20, 2014 at 9:50 AM<div><div><br><span style="font-weight:bold">To: </span> Carson Holt <<a href="mailto:carsonhh@gmail.com" target="_blank">carsonhh@gmail.com</a>><br><span style="font-weight:bold">Subject: </span> Re: [maker-devel] Annotation with maker2<br></div></div></div><div><div><div><br></div><div dir="ltr">cdantec@belem:~$ /usr/bin/perl -v<br><br>This is perl 5, version 18, subversion 1 (v5.18.1) built for x86_64-linux-gnu-thread-multi<br>(with 46 registered patches, see perl -V for more detail)<br><br>Copyright 1987-2013, Larry Wall<br><br>Perl may be copied only under the terms of either the Artistic License or the<br>GNU General Public License, which may be found in the Perl 5 source kit.<br><br>Complete documentation for Perl, including FAQ lists, should be found on<br>
this system using "man perl" or "perldoc perl". If you have access to the<br>Internet, point your browser at <a href="http://www.perl.org/" target="_blank">http://www.perl.org/</a>, the Perl Home Page.<br><br></div><div class="gmail_extra"><br><br><div class="gmail_quote">2014-03-20 16:32 GMT+01:00 Carson Holt <span dir="ltr"><<a href="mailto:carsonhh@gmail.com" target="_blank">carsonhh@gmail.com</a>></span>:<br><blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex"><div style="font-size:14px;font-family:Calibri,sans-serif;word-wrap:break-word"><div>What do you get for when you type --> /usr/bin/perl -v</div><div><br></div><div>The key to the error is this line --></div><div><div><span style="font-family:Calibri;font-size:medium">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</span></div><div><br></div></div><div>Either the database doesn't exist, or is corrupt. Does it exist?</div><div><br></div><div>--Carson</div><div><br></div><span><div style="border-right:medium none;padding-right:0in;padding-left:0in;padding-top:3pt;text-align:left;font-size:11pt;border-bottom:medium none;font-family:Calibri;border-top:#b5c4df 1pt solid;padding-bottom:0in;border-left:medium none"><span style="font-weight:bold">From: </span> Chris Bioinfo <<a href="mailto:chrisbioinfo@gmail.com" target="_blank">chrisbioinfo@gmail.com</a>><br><span style="font-weight:bold">Date: </span> Thursday, March 20, 2014 at 9:25 AM<br><span style="font-weight:bold">To: </span> Carson Holt <<a href="mailto:carsonhh@gmail.com" target="_blank">carsonhh@gmail.com</a>><br><span style="font-weight:bold">Subject: </span> Re: [maker-devel] Annotation with maker2<br></div><div><div><div><br></div><div dir="ltr"><div><div><div><div><div>Dear Carson,<br><br></div>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.<br></div>
I have deleted many times the output directory.. but same problem..<br><br></div>So here the debug output :<br>****MODULE VERSION INFO<br> 0.05 Acme::Damn /usr/local/lib/perl/5.18.1/Acme/Damn.pm<br> 1.01 AnyDBM_File /usr/share/perl/5.18/AnyDBM_File.pm<br>
5.73 AutoLoader /usr/share/perl/5.18/AutoLoader.pm<br> UNKNOWN Bio::AnalysisParserI /usr/local/share/perl/5.18.1/Bio/AnalysisParserI.pm<br> UNKNOWN Bio::AnnotatableI /usr/local/share/perl/5.18.1/Bio/AnnotatableI.pm<br>
UNKNOWN Bio::Annotation::Collection /usr/local/share/perl/5.18.1/Bio/Annotation/Collection.pm<br> UNKNOWN Bio::Annotation::SimpleValue /usr/local/share/perl/5.18.1/Bio/Annotation/SimpleValue.pm<br> UNKNOWN Bio::Annotation::TypeManager /usr/local/share/perl/5.18.1/Bio/Annotation/TypeManager.pm<br>
UNKNOWN Bio::AnnotationCollectionI /usr/local/share/perl/5.18.1/Bio/AnnotationCollectionI.pm<br> UNKNOWN Bio::AnnotationI /usr/local/share/perl/5.18.1/Bio/AnnotationI.pm<br> 1.006923 Bio::DB::Fasta /usr/local/share/perl/5.18.1/Bio/DB/Fasta.pm<br>
UNKNOWN Bio::DB::InMemoryCache /usr/local/share/perl/5.18.1/Bio/DB/InMemoryCache.pm<br> UNKNOWN Bio::DB::IndexedBase /usr/local/share/perl/5.18.1/Bio/DB/IndexedBase.pm<br> UNKNOWN Bio::DB::RandomAccessI /usr/local/share/perl/5.18.1/Bio/DB/RandomAccessI.pm<br>
UNKNOWN Bio::DB::SeqI /usr/local/share/perl/5.18.1/Bio/DB/SeqI.pm<br> UNKNOWN Bio::DescribableI /usr/local/share/perl/5.18.1/Bio/DescribableI.pm<br> UNKNOWN Bio::Event::EventGeneratorI /usr/local/share/perl/5.18.1/Bio/Event/EventGeneratorI.pm<br>
UNKNOWN Bio::Event::EventHandlerI /usr/local/share/perl/5.18.1/Bio/Event/EventHandlerI.pm<br> UNKNOWN Bio::Factory::ObjectFactory /usr/local/share/perl/5.18.1/Bio/Factory/ObjectFactory.pm<br> UNKNOWN Bio::Factory::ObjectFactoryI /usr/local/share/perl/5.18.1/Bio/Factory/ObjectFactoryI.pm<br>
UNKNOWN Bio::Factory::SequenceFactoryI /usr/local/share/perl/5.18.1/Bio/Factory/SequenceFactoryI.pm<br> UNKNOWN Bio::FeatureHolderI /usr/local/share/perl/5.18.1/Bio/FeatureHolderI.pm<br> UNKNOWN Bio::IdentifiableI /usr/local/share/perl/5.18.1/Bio/IdentifiableI.pm<br>
UNKNOWN Bio::LocatableSeq /usr/local/share/perl/5.18.1/Bio/LocatableSeq.pm<br> UNKNOWN Bio::Location::Atomic /usr/local/share/perl/5.18.1/Bio/Location/Atomic.pm<br> UNKNOWN Bio::Location::CoordinatePolicyI /usr/local/share/perl/5.18.1/Bio/Location/CoordinatePolicyI.pm<br>
UNKNOWN Bio::Location::Fuzzy /usr/local/share/perl/5.18.1/Bio/Location/Fuzzy.pm<br> UNKNOWN Bio::Location::FuzzyLocationI /usr/local/share/perl/5.18.1/Bio/Location/FuzzyLocationI.pm<br> UNKNOWN Bio::Location::Simple /usr/local/share/perl/5.18.1/Bio/Location/Simple.pm<br>
UNKNOWN Bio::Location::Split /usr/local/share/perl/5.18.1/Bio/Location/Split.pm<br> UNKNOWN Bio::Location::SplitLocationI /usr/local/share/perl/5.18.1/Bio/Location/SplitLocationI.pm<br> UNKNOWN Bio::Location::WidestCoordPolicy /usr/local/share/perl/5.18.1/Bio/Location/WidestCoordPolicy.pm<br>
UNKNOWN Bio::LocationI /usr/local/share/perl/5.18.1/Bio/LocationI.pm<br> UNKNOWN Bio::PrimarySeq /usr/local/share/perl/5.18.1/Bio/PrimarySeq.pm<br> 1.006923 Bio::PrimarySeqI /usr/local/share/perl/5.18.1/Bio/PrimarySeqI.pm<br>
UNKNOWN Bio::Range /usr/local/share/perl/5.18.1/Bio/Range.pm<br> UNKNOWN Bio::RangeI /usr/local/share/perl/5.18.1/Bio/RangeI.pm<br> 1.006923 Bio::Root::Exception /usr/local/share/perl/5.18.1/Bio/Root/Exception.pm<br>
UNKNOWN Bio::Root::HTTPget /usr/local/share/perl/5.18.1/Bio/Root/HTTPget.pm<br> UNKNOWN Bio::Root::IO /usr/local/share/perl/5.18.1/Bio/Root/IO.pm<br> 1.006923 Bio::Root::Root /usr/local/share/perl/5.18.1/Bio/Root/Root.pm<br>
1.006923 Bio::Root::RootI /usr/local/share/perl/5.18.1/Bio/Root/RootI.pm<br> 1.006923 Bio::Root::Version /usr/local/share/perl/5.18.1/Bio/Root/Version.pm<br> UNKNOWN Bio::Search::HSP::GenericHSP /usr/local/share/perl/5.18.1/Bio/Search/HSP/GenericHSP.pm<br>
UNKNOWN Bio::Search::HSP::HSPFactory /usr/local/share/perl/5.18.1/Bio/Search/HSP/HSPFactory.pm<br> UNKNOWN Bio::Search::HSP::HSPI /usr/local/share/perl/5.18.1/Bio/Search/HSP/HSPI.pm<br> 0.01 Bio::Search::HSP::PhatHSP::Base /usr/local/annotation/maker2.31/bin/../lib/Bio/Search/HSP/PhatHSP/Base.pm<br>
UNKNOWN Bio::Search::HSP::PhatHSP::augustus /usr/local/annotation/maker2.31/bin/../lib/Bio/Search/HSP/PhatHSP/<a href="http://augustus.pm" target="_blank">augustus.pm</a><br> 0.01 Bio::Search::HSP::PhatHSP::blastn /usr/local/annotation/maker2.31/bin/../lib/Bio/Search/HSP/PhatHSP/<a href="http://blastn.pm" target="_blank">blastn.pm</a><br>
0.01 Bio::Search::HSP::PhatHSP::blastx /usr/local/annotation/maker2.31/bin/../lib/Bio/Search/HSP/PhatHSP/<a href="http://blastx.pm" target="_blank">blastx.pm</a><br> UNKNOWN Bio::Search::HSP::PhatHSP::cdna2genome /usr/local/annotation/maker2.31/bin/../lib/Bio/Search/HSP/PhatHSP/<a href="http://cdna2genome.pm" target="_blank">cdna2genome.pm</a><br>
UNKNOWN Bio::Search::HSP::PhatHSP::est2genome /usr/local/annotation/maker2.31/bin/../lib/Bio/Search/HSP/PhatHSP/<a href="http://est2genome.pm" target="_blank">est2genome.pm</a><br> UNKNOWN Bio::Search::HSP::PhatHSP::fgenesh /usr/local/annotation/maker2.31/bin/../lib/Bio/Search/HSP/PhatHSP/<a href="http://fgenesh.pm" target="_blank">fgenesh.pm</a><br>
UNKNOWN Bio::Search::HSP::PhatHSP::genemark /usr/local/annotation/maker2.31/bin/../lib/Bio/Search/HSP/PhatHSP/<a href="http://genemark.pm" target="_blank">genemark.pm</a><br> UNKNOWN Bio::Search::HSP::PhatHSP::gff3 /usr/local/annotation/maker2.31/bin/../lib/Bio/Search/HSP/PhatHSP/<a href="http://gff3.pm" target="_blank">gff3.pm</a><br>
UNKNOWN Bio::Search::HSP::PhatHSP::protein2genome /usr/local/annotation/maker2.31/bin/../lib/Bio/Search/HSP/PhatHSP/<a href="http://protein2genome.pm" target="_blank">protein2genome.pm</a><br> UNKNOWN Bio::Search::HSP::PhatHSP::repeatmasker /usr/local/annotation/maker2.31/bin/../lib/Bio/Search/HSP/PhatHSP/<a href="http://repeatmasker.pm" target="_blank">repeatmasker.pm</a><br>
UNKNOWN Bio::Search::HSP::PhatHSP::snap /usr/local/annotation/maker2.31/bin/../lib/Bio/Search/HSP/PhatHSP/<a href="http://snap.pm" target="_blank">snap.pm</a><br> UNKNOWN Bio::Search::HSP::PhatHSP::snoscan /usr/local/annotation/maker2.31/bin/../lib/Bio/Search/HSP/PhatHSP/<a href="http://snoscan.pm" target="_blank">snoscan.pm</a><br>
0.01 Bio::Search::HSP::PhatHSP::tblastx /usr/local/annotation/maker2.31/bin/../lib/Bio/Search/HSP/PhatHSP/<a href="http://tblastx.pm" target="_blank">tblastx.pm</a><br> UNKNOWN Bio::Search::HSP::PhatHSP::trnascan /usr/local/annotation/maker2.31/bin/../lib/Bio/Search/HSP/PhatHSP/<a href="http://trnascan.pm" target="_blank">trnascan.pm</a><br>
1.006923 Bio::Search::Hit::GenericHit /usr/local/share/perl/5.18.1/Bio/Search/Hit/GenericHit.pm<br> UNKNOWN Bio::Search::Hit::HitFactory /usr/local/share/perl/5.18.1/Bio/Search/Hit/HitFactory.pm<br> UNKNOWN Bio::Search::Hit::HitI /usr/local/share/perl/5.18.1/Bio/Search/Hit/HitI.pm<br>
0.01 Bio::Search::Hit::PhatHit::Base /usr/local/annotation/maker2.31/bin/../lib/Bio/Search/Hit/PhatHit/Base.pm<br> UNKNOWN Bio::Search::Hit::PhatHit::augustus /usr/local/annotation/maker2.31/bin/../lib/Bio/Search/Hit/PhatHit/<a href="http://augustus.pm" target="_blank">augustus.pm</a><br>
0.01 Bio::Search::Hit::PhatHit::blastn /usr/local/annotation/maker2.31/bin/../lib/Bio/Search/Hit/PhatHit/<a href="http://blastn.pm" target="_blank">blastn.pm</a><br> 0.01 Bio::Search::Hit::PhatHit::blastx /usr/local/annotation/maker2.31/bin/../lib/Bio/Search/Hit/PhatHit/<a href="http://blastx.pm" target="_blank">blastx.pm</a><br>
UNKNOWN Bio::Search::Hit::PhatHit::cdna2genome /usr/local/annotation/maker2.31/bin/../lib/Bio/Search/Hit/PhatHit/<a href="http://cdna2genome.pm" target="_blank">cdna2genome.pm</a><br> UNKNOWN Bio::Search::Hit::PhatHit::est2genome /usr/local/annotation/maker2.31/bin/../lib/Bio/Search/Hit/PhatHit/<a href="http://est2genome.pm" target="_blank">est2genome.pm</a><br>
UNKNOWN Bio::Search::Hit::PhatHit::fgenesh /usr/local/annotation/maker2.31/bin/../lib/Bio/Search/Hit/PhatHit/<a href="http://fgenesh.pm" target="_blank">fgenesh.pm</a><br> UNKNOWN Bio::Search::Hit::PhatHit::genemark /usr/local/annotation/maker2.31/bin/../lib/Bio/Search/Hit/PhatHit/<a href="http://genemark.pm" target="_blank">genemark.pm</a><br>
UNKNOWN Bio::Search::Hit::PhatHit::gff3 /usr/local/annotation/maker2.31/bin/../lib/Bio/Search/Hit/PhatHit/<a href="http://gff3.pm" target="_blank">gff3.pm</a><br> UNKNOWN Bio::Search::Hit::PhatHit::protein2genome /usr/local/annotation/maker2.31/bin/../lib/Bio/Search/Hit/PhatHit/<a href="http://protein2genome.pm" target="_blank">protein2genome.pm</a><br>
1.006923 Bio::Search::Hit::PhatHit::repeatmasker /usr/local/annotation/maker2.31/bin/../lib/Bio/Search/Hit/PhatHit/<a href="http://repeatmasker.pm" target="_blank">repeatmasker.pm</a><br> UNKNOWN Bio::Search::Hit::PhatHit::snap /usr/local/annotation/maker2.31/bin/../lib/Bio/Search/Hit/PhatHit/<a href="http://snap.pm" target="_blank">snap.pm</a><br>
UNKNOWN Bio::Search::Hit::PhatHit::snoscan /usr/local/annotation/maker2.31/bin/../lib/Bio/Search/Hit/PhatHit/<a href="http://snoscan.pm" target="_blank">snoscan.pm</a><br> 0.01 Bio::Search::Hit::PhatHit::tblastx /usr/local/annotation/maker2.31/bin/../lib/Bio/Search/Hit/PhatHit/<a href="http://tblastx.pm" target="_blank">tblastx.pm</a><br>
UNKNOWN Bio::Search::Hit::PhatHit::trnascan /usr/local/annotation/maker2.31/bin/../lib/Bio/Search/Hit/PhatHit/<a href="http://trnascan.pm" target="_blank">trnascan.pm</a><br> 1.006923 Bio::Search::SearchUtils /usr/local/share/perl/5.18.1/Bio/Search/SearchUtils.pm<br>
UNKNOWN Bio::SearchIO /usr/local/share/perl/5.18.1/Bio/SearchIO.pm<br> UNKNOWN Bio::SearchIO::EventHandlerI /usr/local/share/perl/5.18.1/Bio/SearchIO/EventHandlerI.pm<br> UNKNOWN Bio::SearchIO::SearchResultEventBuilder /usr/local/share/perl/5.18.1/Bio/SearchIO/SearchResultEventBuilder.pm<br>
UNKNOWN Bio::Seq /usr/local/share/perl/5.18.1/Bio/Seq.pm<br> UNKNOWN Bio::Seq::SeqFactory /usr/local/share/perl/5.18.1/Bio/Seq/SeqFactory.pm<br> UNKNOWN Bio::SeqAnalysisParserI /usr/local/share/perl/5.18.1/Bio/SeqAnalysisParserI.pm<br>
UNKNOWN Bio::SeqFeature::FeaturePair /usr/local/share/perl/5.18.1/Bio/SeqFeature/FeaturePair.pm<br> UNKNOWN Bio::SeqFeature::Generic /usr/local/share/perl/5.18.1/Bio/SeqFeature/Generic.pm<br> UNKNOWN Bio::SeqFeature::Similarity /usr/local/share/perl/5.18.1/Bio/SeqFeature/Similarity.pm<br>
UNKNOWN Bio::SeqFeature::SimilarityPair /usr/local/share/perl/5.18.1/Bio/SeqFeature/SimilarityPair.pm<br> UNKNOWN Bio::SeqFeatureI /usr/local/share/perl/5.18.1/Bio/SeqFeatureI.pm<br> UNKNOWN Bio::SeqI /usr/local/share/perl/5.18.1/Bio/SeqI.pm<br>
UNKNOWN Bio::SeqUtils /usr/local/share/perl/5.18.1/Bio/SeqUtils.pm<br> 1.006923 Bio::Tools::CodonTable /usr/local/share/perl/5.18.1/Bio/Tools/CodonTable.pm<br> UNKNOWN Bio::Tools::GFF /usr/local/share/perl/5.18.1/Bio/Tools/GFF.pm<br>
1.006923 Bio::Tools::IUPAC /usr/local/share/perl/5.18.1/Bio/Tools/IUPAC.pm<br> 7.3 Bit::Vector /usr/local/lib/perl/5.18.1/Bit/Vector.pm<br> 0.01 CGL::Annotation /usr/local/annotation/maker2.31/bin/../lib/CGL/Annotation.pm<br>
0.01 CGL::Annotation::Feature /usr/local/annotation/maker2.31/bin/../lib/CGL/Annotation/Feature.pm<br> 0.01 CGL::Annotation::Feature::Contig /usr/local/annotation/maker2.31/bin/../lib/CGL/Annotation/Feature/Contig.pm<br>
0.01 CGL::Annotation::Feature::Exon /usr/local/annotation/maker2.31/bin/../lib/CGL/Annotation/Feature/Exon.pm<br> 0.01 CGL::Annotation::Feature::Gene /usr/local/annotation/maker2.31/bin/../lib/CGL/Annotation/Feature/Gene.pm<br>
0.01 CGL::Annotation::Feature::Intron /usr/local/annotation/maker2.31/bin/../lib/CGL/Annotation/Feature/Intron.pm<br> 0.01 CGL::Annotation::Feature::Protein /usr/local/annotation/maker2.31/bin/../lib/CGL/Annotation/Feature/Protein.pm<br>
0.01 CGL::Annotation::Feature::Sequence_variant /usr/local/annotation/maker2.31/bin/../lib/CGL/Annotation/Feature/Sequence_variant.pm<br> 0.01 CGL::Annotation::Feature::Transcript /usr/local/annotation/maker2.31/bin/../lib/CGL/Annotation/Feature/Transcript.pm<br>
0.01 CGL::Annotation::FeatureLocation /usr/local/annotation/maker2.31/bin/../lib/CGL/Annotation/FeatureLocation.pm<br> 0.01 CGL::Annotation::FeatureRelationship /usr/local/annotation/maker2.31/bin/../lib/CGL/Annotation/FeatureRelationship.pm<br>
0.01 CGL::Annotation::Iterator /usr/local/annotation/maker2.31/bin/../lib/CGL/Annotation/Iterator.pm<br> 0.01 CGL::Annotation::Trace /usr/local/annotation/maker2.31/bin/../lib/CGL/Annotation/Trace.pm<br>
0.01 CGL::Clone /usr/local/annotation/maker2.31/bin/../lib/CGL/Clone.pm<br> 0.01 CGL::Ontology::Node /usr/local/annotation/maker2.31/bin/../lib/CGL/Ontology/Node.pm<br> 0.01 CGL::Ontology::NodeRelationship /usr/local/annotation/maker2.31/bin/../lib/CGL/Ontology/NodeRelationship.pm<br>
0.01 CGL::Ontology::Ontology /usr/local/annotation/maker2.31/bin/../lib/CGL/Ontology/Ontology.pm<br> 0.01 CGL::Ontology::Parser::OBO /usr/local/annotation/maker2.31/bin/../lib/CGL/Ontology/Parser/OBO.pm<br>
0.01 CGL::Ontology::SO /usr/local/annotation/maker2.31/bin/../lib/CGL/Ontology/SO.pm<br> 0.01 CGL::Ontology::Trace /usr/local/annotation/maker2.31/bin/../lib/CGL/Ontology/Trace.pm<br> 0.01 CGL::Revcomp /usr/local/annotation/maker2.31/bin/../lib/CGL/Revcomp.pm<br>
0.01 CGL::TranslationMachine /usr/local/annotation/maker2.31/bin/../lib/CGL/TranslationMachine.pm<br> 1.32 Carp /usr/local/share/perl/5.18.1/Carp.pm<br> 1.32 Carp::Heavy /usr/local/share/perl/5.18.1/Carp/Heavy.pm<br>
0.64 Class::Struct /usr/share/perl/5.18/Class/Struct.pm<br> 0.36 Clone /usr/local/lib/perl/5.18.1/Clone.pm<br> 5.018001 Config /usr/lib/perl/5.18/Config.pm<br> 3.40 Cwd /usr/lib/perl/5.18/Cwd.pm<br>
1.42 DBD::SQLite /usr/local/lib/perl/5.18.1/DBD/SQLite.pm<br> 1.631 DBI /usr/local/lib/perl/5.18.1/DBI.pm<br> 1.827 DB_File /usr/lib/perl/5.18/DB_File.pm<br> 2.145 Data::Dumper /usr/lib/perl/5.18/Data/Dumper.pm<br>
0.11 Datastore::Base /usr/local/annotation/maker2.31/bin/../lib/Datastore/Base.pm<br> 0.01 Datastore::MD5 /usr/local/annotation/maker2.31/bin/../lib/Datastore/MD5.pm<br> 2.53 Digest::MD5 /usr/local/lib/perl/5.18.1/Digest/MD5.pm<br>
1.16 Digest::base /usr/share/perl/5.18/Digest/<a href="http://base.pm" target="_blank">base.pm</a><br> UNKNOWN Dumper::GFF::GFFV3 /usr/local/annotation/maker2.31/bin/../lib/Dumper/GFF/GFFV3.pm<br> UNKNOWN Dumper::XML::Game /usr/local/annotation/maker2.31/bin/../lib/Dumper/XML/Game.pm<br>
UNKNOWN Dumper::XML::Game_Xml /usr/local/annotation/maker2.31/bin/../lib/Dumper/XML/Game_Xml.pm<br> 1.18 DynaLoader /usr/lib/perl/5.18/DynaLoader.pm<br> 1.18 Errno /usr/lib/perl/5.18/Errno.pm<br>
0.17015 Error /usr/local/annotation/maker2.31/bin/../lib/Error.pm<br> UNKNOWN Error::Simple /usr/local/annotation/maker2.31/bin/../lib/Error/Simple.pm<br> 5.68 Exporter /usr/share/perl/5.18/Exporter.pm<br>
5.68 Exporter::Heavy /usr/share/perl/5.18/Exporter/Heavy.pm<br> UNKNOWN Fasta /usr/local/annotation/maker2.31/bin/../lib/Fasta.pm<br> UNKNOWN FastaChunk /usr/local/annotation/maker2.31/bin/../lib/FastaChunk.pm<br>
UNKNOWN FastaChunker /usr/local/annotation/maker2.31/bin/../lib/FastaChunker.pm<br> UNKNOWN FastaDB /usr/local/annotation/maker2.31/bin/../lib/FastaDB.pm<br> UNKNOWN FastaFile /usr/local/annotation/maker2.31/bin/../lib/FastaFile.pm<br>
UNKNOWN FastaSeq /usr/local/annotation/maker2.31/bin/../lib/FastaSeq.pm<br> 1.11 Fcntl /usr/lib/perl/5.18/Fcntl.pm<br> 2.84 File::Basename /usr/share/perl/5.18/File/Basename.pm<br> 2.26 File::Copy /usr/share/perl/5.18/File/Copy.pm<br>
1.20 File::Glob /usr/lib/perl/5.18/File/Glob.pm<br> 1.20 File::NFSLock /usr/local/annotation/maker2.31/bin/../lib/File/NFSLock.pm<br> 2.09 File::Path /usr/share/perl/5.18/File/Path.pm<br> 3.40 File::Spec /usr/lib/perl/5.18/File/Spec.pm<br>
3.40 File::Spec::Unix /usr/lib/perl/5.18/File/Spec/Unix.pm<br> 0.2304 File::Temp /usr/local/share/perl/5.18.1/File/Temp.pm<br> 1.09 File::Which /usr/local/annotation/maker2.31/bin/../lib/File/Which.pm<br>
2.02 FileHandle /usr/share/perl/5.18/FileHandle.pm<br> 1.51 FindBin /usr/share/perl/5.18/FindBin.pm<br> UNKNOWN GFFDB /usr/local/annotation/maker2.31/bin/../lib/GFFDB.pm<br> UNKNOWN GI /usr/local/annotation/maker2.31/bin/../lib/GI.pm<br>
2.42 Getopt::Long /usr/local/share/perl/5.18.1/Getopt/Long.pm<br> 6.02 HTTP::Date /usr/share/perl5/HTTP/Date.pm<br> 6.05 HTTP::Headers /usr/share/perl5/HTTP/Headers.pm<br> 6.06 HTTP::Message /usr/share/perl5/HTTP/Message.pm<br>
6.00 HTTP::Request /usr/share/perl5/HTTP/Request.pm<br> 6.04 HTTP::Response /usr/share/perl5/HTTP/Response.pm<br> 6.03 HTTP::Status /usr/share/perl5/HTTP/Status.pm<br> 1.28 IO /usr/lib/perl/5.18/IO.pm<br>
1.16 IO::File /usr/lib/perl/5.18/IO/File.pm<br> 1.34 IO::Handle /usr/lib/perl/5.18/IO/Handle.pm<br> 1.1 IO::Seekable /usr/lib/perl/5.18/IO/Seekable.pm<br> 1.21 IO::Select /usr/lib/perl/5.18/IO/Select.pm<br>
1.36 IO::Socket /usr/lib/perl/5.18/IO/Socket.pm<br> 1.33 IO::Socket::INET /usr/lib/perl/5.18/IO/Socket/INET.pm<br> 1.24 IO::Socket::UNIX /usr/lib/perl/5.18/IO/Socket/UNIX.pm<br> 1.13 IPC::Open3 /usr/share/perl/5.18/IPC/Open3.pm<br>
0.53 Inline /usr/local/share/perl/5.18.1/Inline.pm<br> UNKNOWN Inline::denter /usr/local/share/perl/5.18.1/Inline/<a href="http://denter.pm" target="_blank">denter.pm</a><br> UNKNOWN Iterator /usr/local/annotation/maker2.31/bin/../lib/Iterator.pm<br>
UNKNOWN Iterator::Any /usr/local/annotation/maker2.31/bin/../lib/Iterator/Any.pm<br> UNKNOWN Iterator::Fasta /usr/local/annotation/maker2.31/bin/../lib/Iterator/Fasta.pm<br> UNKNOWN Iterator::GFF3 /usr/local/annotation/maker2.31/bin/../lib/Iterator/GFF3.pm<br>
6.05 LWP /usr/share/perl5/LWP.pm<br> UNKNOWN LWP::MemberMixin /usr/share/perl5/LWP/MemberMixin.pm<br> 6.00 LWP::Protocol /usr/share/perl5/LWP/Protocol.pm<br> 6.05 LWP::UserAgent /usr/share/perl5/LWP/UserAgent.pm<br>
0.33 List::MoreUtils /usr/local/lib/perl/5.18.1/List/MoreUtils.pm<br> 1.38 List::Util /usr/local/lib/perl/5.18.1/List/Util.pm<br> UNKNOWN MAKER::ConfigData /usr/local/annotation/maker2.31/bin/../perl/lib/MAKER/ConfigData.pm<br>
1.32 POSIX /usr/lib/perl/5.18/POSIX.pm<br> 0.01 Parallel::Application::MPI /usr/local/annotation/maker2.31/bin/../perl/lib/Parallel/Application/MPI.pm<br> 0.02 Perl::Unsafe::Signals /usr/local/lib/perl/5.18.1/Perl/Unsafe/Signals.pm<br>
UNKNOWN PhatHit_utils /usr/local/annotation/maker2.31/bin/../lib/PhatHit_utils.pm<br> UNKNOWN PostData /usr/local/annotation/maker2.31/bin/../lib/PostData.pm<br> 1.0 Proc::ProcessTable_simple /usr/local/annotation/maker2.31/bin/../lib/Proc/ProcessTable_simple.pm<br>
1.0 Proc::Signal /usr/local/annotation/maker2.31/bin/../lib/Proc/Signal.pm<br> UNKNOWN Process::MpiChunk /usr/local/annotation/maker2.31/bin/../lib/Process/MpiChunk.pm<br> UNKNOWN Process::MpiTiers /usr/local/annotation/maker2.31/bin/../lib/Process/MpiTiers.pm<br>
1.38 Scalar::Util /usr/local/lib/perl/5.18.1/Scalar/Util.pm<br> 1.02 SelectSaver /usr/share/perl/5.18/SelectSaver.pm<br> UNKNOWN Shadower /usr/local/annotation/maker2.31/bin/../lib/Shadower.pm<br>
UNKNOWN SimpleCluster /usr/local/annotation/maker2.31/bin/../lib/SimpleCluster.pm<br> 2.009 Socket /usr/lib/perl/5.18/Socket.pm<br> UNKNOWN SpaceBase /usr/local/annotation/maker2.31/bin/../lib/SpaceBase.pm<br>
2.45 Storable /usr/local/lib/perl/5.18.1/Storable.pm<br> 1.07 Symbol /usr/share/perl/5.18/Symbol.pm<br> 1.17 Sys::Hostname /usr/lib/perl/5.18/Sys/Hostname.pm<br> 0.21 Sys::SigAction /usr/local/share/perl/5.18.1/Sys/SigAction.pm<br>
UNKNOWN Sys::SigAction::Alarm /usr/local/share/perl/5.18.1/Sys/SigAction/Alarm.pm<br> 4.02 Term::ANSIColor /usr/share/perl/5.18/Term/ANSIColor.pm<br> 4.2 Tie::Handle /usr/share/perl/5.18/Tie/Handle.pm<br>
1.04 Tie::Hash /usr/share/perl/5.18/Tie/Hash.pm<br> 4.3 Tie::StdHandle /usr/share/perl/5.18/Tie/StdHandle.pm<br> 1.9726 Time::HiRes /usr/local/lib/perl/5.18.1/Time/HiRes.pm<br> 1.2300 Time::Local /usr/share/perl/5.18/Time/Local.pm<br>
1.60 URI /usr/share/perl5/URI.pm<br> 3.31 URI::Escape /usr/share/perl5/URI/Escape.pm<br> UNKNOWN Widget /usr/local/annotation/maker2.31/bin/../lib/Widget.pm<br> UNKNOWN Widget::RepeatMasker /usr/local/annotation/maker2.31/bin/../lib/Widget/RepeatMasker.pm<br>
UNKNOWN Widget::augustus /usr/local/annotation/maker2.31/bin/../lib/Widget/<a href="http://augustus.pm" target="_blank">augustus.pm</a><br> UNKNOWN Widget::blastn /usr/local/annotation/maker2.31/bin/../lib/Widget/<a href="http://blastn.pm" target="_blank">blastn.pm</a><br>
UNKNOWN Widget::blastx /usr/local/annotation/maker2.31/bin/../lib/Widget/<a href="http://blastx.pm" target="_blank">blastx.pm</a><br> UNKNOWN Widget::exonerate /usr/local/annotation/maker2.31/bin/../lib/Widget/<a href="http://exonerate.pm" target="_blank">exonerate.pm</a><br>
UNKNOWN Widget::exonerate::cdna2genome /usr/local/annotation/maker2.31/bin/../lib/Widget/exonerate/<a href="http://cdna2genome.pm" target="_blank">cdna2genome.pm</a><br> UNKNOWN Widget::exonerate::est2genome /usr/local/annotation/maker2.31/bin/../lib/Widget/exonerate/<a href="http://est2genome.pm" target="_blank">est2genome.pm</a><br>
UNKNOWN Widget::exonerate::protein2genome /usr/local/annotation/maker2.31/bin/../lib/Widget/exonerate/<a href="http://protein2genome.pm" target="_blank">protein2genome.pm</a><br> UNKNOWN Widget::fgenesh /usr/local/annotation/maker2.31/bin/../lib/Widget/<a href="http://fgenesh.pm" target="_blank">fgenesh.pm</a><br>
UNKNOWN Widget::formater /usr/local/annotation/maker2.31/bin/../lib/Widget/<a href="http://formater.pm" target="_blank">formater.pm</a><br> UNKNOWN Widget::genemark /usr/local/annotation/maker2.31/bin/../lib/Widget/<a href="http://genemark.pm" target="_blank">genemark.pm</a><br>
UNKNOWN Widget::snap /usr/local/annotation/maker2.31/bin/../lib/Widget/<a href="http://snap.pm" target="_blank">snap.pm</a><br> UNKNOWN Widget::snoscan /usr/local/annotation/maker2.31/bin/../lib/Widget/<a href="http://snoscan.pm" target="_blank">snoscan.pm</a><br>
UNKNOWN Widget::tblastx /usr/local/annotation/maker2.31/bin/../lib/Widget/<a href="http://tblastx.pm" target="_blank">tblastx.pm</a><br> UNKNOWN Widget::trnascan /usr/local/annotation/maker2.31/bin/../lib/Widget/<a href="http://trnascan.pm" target="_blank">trnascan.pm</a><br>
0.16 XSLoader /usr/share/perl/5.18/XSLoader.pm<br> 0.21 attributes /usr/lib/perl/5.18/<a href="http://attributes.pm" target="_blank">attributes.pm</a><br> 2.18 base /usr/share/perl/5.18/<a href="http://base.pm" target="_blank">base.pm</a><br>
1.04 bytes /usr/share/perl/5.18/<a href="http://bytes.pm" target="_blank">bytes.pm</a><br> UNKNOWN clean /usr/local/annotation/maker2.31/bin/../lib/<a href="http://clean.pm" target="_blank">clean.pm</a><br>
UNKNOWN cluster /usr/local/annotation/maker2.31/bin/../lib/<a href="http://cluster.pm" target="_blank">cluster.pm</a><br>
UNKNOWN compare /usr/local/annotation/maker2.31/bin/../lib/<a href="http://compare.pm" target="_blank">compare.pm</a><br> 1.27 constant /usr/share/perl/5.18/<a href="http://constant.pm" target="_blank">constant.pm</a><br>
UNKNOWN ds_utility /usr/local/annotation/maker2.31/bin/../lib/<a href="http://ds_utility.pm" target="_blank">ds_utility.pm</a><br>
UNKNOWN exonerate::splice_info /usr/local/annotation/maker2.31/bin/../lib/exonerate/<a href="http://splice_info.pm" target="_blank">splice_info.pm</a><br> 0.34 forks /usr/local/lib/perl/5.18.1/<a href="http://forks.pm" target="_blank">forks.pm</a><br>
2.08001 forks::Devel::Symdump /usr/local/lib/perl/5.18.1/forks/Devel/Symdump.pm<br> 0.34 forks::shared /usr/local/lib/perl/5.18.1/forks/<a href="http://shared.pm" target="_blank">shared.pm</a><br> 0.34 forks::signals /usr/local/lib/perl/5.18.1/forks/<a href="http://signals.pm" target="_blank">signals.pm</a><br>
1.00 integer /usr/share/perl/5.18/<a href="http://integer.pm" target="_blank">integer.pm</a><br> 0.63 lib /usr/lib/perl/5.18/<a href="http://lib.pm" target="_blank">lib.pm</a><br> 1.02 locale /usr/share/perl/5.18/<a href="http://locale.pm" target="_blank">locale.pm</a><br>
UNKNOWN maker::auto_annotator /usr/local/annotation/maker2.31/bin/../lib/maker/<a href="http://auto_annotator.pm" target="_blank">auto_annotator.pm</a><br> UNKNOWN maker::join /usr/local/annotation/maker2.31/bin/../lib/maker/<a href="http://join.pm" target="_blank">join.pm</a><br>
UNKNOWN maker::quality_index /usr/local/annotation/maker2.31/bin/../lib/maker/<a href="http://quality_index.pm" target="_blank">quality_index.pm</a><br> UNKNOWN maker::sens_spec /usr/local/annotation/maker2.31/bin/../lib/maker/<a href="http://sens_spec.pm" target="_blank">sens_spec.pm</a><br>
1.22 overload /usr/share/perl/5.18/<a href="http://overload.pm" target="_blank">overload.pm</a><br> 0.02 overloading /usr/share/perl/5.18/<a href="http://overloading.pm" target="_blank">overloading.pm</a><br>
0.225 parent /usr/share/perl/5.18/<a href="http://parent.pm" target="_blank">parent.pm</a><br>
UNKNOWN polisher /usr/local/annotation/maker2.31/bin/../lib/<a href="http://polisher.pm" target="_blank">polisher.pm</a><br> UNKNOWN polisher::exonerate /usr/local/annotation/maker2.31/bin/../lib/polisher/<a href="http://exonerate.pm" target="_blank">exonerate.pm</a><br>
UNKNOWN polisher::exonerate::altest /usr/local/annotation/maker2.31/bin/../lib/polisher/exonerate/<a href="http://altest.pm" target="_blank">altest.pm</a><br> UNKNOWN polisher::exonerate::est /usr/local/annotation/maker2.31/bin/../lib/polisher/exonerate/<a href="http://est.pm" target="_blank">est.pm</a><br>
UNKNOWN polisher::exonerate::protein /usr/local/annotation/maker2.31/bin/../lib/polisher/exonerate/<a href="http://protein.pm" target="_blank">protein.pm</a><br> UNKNOWN repeat_mask_seq /usr/local/annotation/maker2.31/bin/../lib/<a href="http://repeat_mask_seq.pm" target="_blank">repeat_mask_seq.pm</a><br>
0.1 runlog /usr/local/annotation/maker2.31/bin/../lib/<a href="http://runlog.pm" target="_blank">runlog.pm</a><br> UNKNOWN shadow_AED /usr/local/annotation/maker2.31/bin/../lib/shadow_AED.pm<br> 1.07 sigtrap /usr/share/perl/5.18/<a href="http://sigtrap.pm" target="_blank">sigtrap.pm</a><br>
1.07 strict /usr/share/perl/5.18/<a href="http://strict.pm" target="_blank">strict.pm</a><br> 1.77 threads /usr/local/lib/perl/5.18.1/<a href="http://forks.pm" target="_blank">forks.pm</a><br> 1.33 threads::shared /usr/local/lib/perl/5.18.1/forks/<a href="http://shared.pm" target="_blank">shared.pm</a><br>
1.03 vars /usr/share/perl/5.18/<a href="http://vars.pm" target="_blank">vars.pm</a><br> 1.18 warnings /usr/share/perl/5.18/<a href="http://warnings.pm" target="_blank">warnings.pm</a><br> 1.02 warnings::register /usr/share/perl/5.18/warnings/<a href="http://register.pm" target="_blank">register.pm</a><br>
STATUS: Parsing control files...<br>Calling GI::load_control_files at /usr/local/annotation/maker2.31/bin/maker line 452.<br>Calling GI::new_instance_temp at /usr/local/annotation/maker2.31/bin/maker line 463.<br>Calling GI::mount_check at /usr/local/annotation/maker2.31/bin/maker line 465.<br>
Calling GI::set_global_temp at /usr/local/annotation/maker2.31/bin/maker line 483.<br>STATUS: Processing and indexing input FASTA files...<br>Calling GI::s_abs_path at /usr/local/annotation/maker2.31/bin/maker line 519.<br>
Calling GI::s_abs_path at /usr/local/annotation/maker2.31/bin/maker line 519.<br>Calling GI::s_abs_path at /usr/local/annotation/maker2.31/bin/maker line 519.<br>Calling GI::s_abs_path at /usr/local/annotation/maker2.31/bin/maker line 519.<br>
Calling GI::s_abs_path at /usr/local/annotation/maker2.31/bin/maker line 519.<br>Calling List::Util::shuffle at /usr/local/annotation/maker2.31/bin/maker line 529.<br>Calling GI::split_db at /usr/local/annotation/maker2.31/bin/maker line 536.<br>
Calling File::Path::rmtree at /usr/local/annotation/maker2.31/bin/maker line 537.<br>Calling Iterator::Any::new at /usr/local/annotation/maker2.31/bin/maker line 537.<br>Calling Iterator::Any::nextDef at /usr/local/annotation/maker2.31/bin/maker line 537.<br>
Calling Iterator::Any::new at /usr/local/annotation/maker2.31/bin/maker line 537.<br>Calling mkdir at /usr/local/annotation/maker2.31/bin/maker line 537.<br>Calling Iterator::Any::nextFastaRef at /usr/local/annotation/maker2.31/bin/maker line 537.<br>
Calling system at /usr/local/annotation/maker2.31/bin/maker line 537.<br>Calling File::NFSLock::unlock at /usr/local/annotation/maker2.31/bin/maker line 537.<br>Calling GI::build_fasta_index at /usr/local/annotation/maker2.31/bin/maker line 538.<br>
Calling FastaDB::new at /usr/local/annotation/maker2.31/bin/maker line 539.<br>Calling File::NFSLock::new at /usr/local/annotation/maker2.31/bin/../lib/Error.pm line 415.<br>Calling out to BioPerl Bio::DB::Fasta::new at /usr/local/annotation/maker2.31/bin/../lib/Error.pm line 415.<br>
Calling out to BioPerl Bio::DB::Fasta::new at /usr/local/annotation/maker2.31/bin/../lib/Error.pm line 415.<br>Calling out to BioPerl get_PrimarySeq_stream at /usr/local/annotation/maker2.31/bin/../lib/GI.pm line 1894.<br>
Calling GI::split_db at /usr/local/annotation/maker2.31/bin/maker line 536.<br>Calling File::Path::rmtree at /usr/local/annotation/maker2.31/bin/maker line 537.<br>Calling Iterator::Any::new at /usr/local/annotation/maker2.31/bin/maker line 537.<br>
Calling Iterator::Any::nextDef at /usr/local/annotation/maker2.31/bin/maker line 537.<br>Calling Iterator::Any::new at /usr/local/annotation/maker2.31/bin/maker line 537.<br>Calling mkdir at /usr/local/annotation/maker2.31/bin/maker line 537.<br>
Calling Iterator::Any::nextFastaRef at /usr/local/annotation/maker2.31/bin/maker line 537.<br>Calling system at /usr/local/annotation/maker2.31/bin/maker line 537.<br>Calling File::NFSLock::unlock at /usr/local/annotation/maker2.31/bin/maker line 537.<br>
Calling GI::build_fasta_index at /usr/local/annotation/maker2.31/bin/maker line 538.<br>Calling FastaDB::new at /usr/local/annotation/maker2.31/bin/maker line 539.<br>Calling File::NFSLock::new at /usr/local/annotation/maker2.31/bin/../lib/Error.pm line 415.<br>
Calling out to BioPerl Bio::DB::Fasta::new at /usr/local/annotation/maker2.31/bin/../lib/Error.pm line 415.<br>Calling out to BioPerl Bio::DB::Fasta::new at /usr/local/annotation/maker2.31/bin/../lib/Error.pm line 415.<br>
Calling out to BioPerl get_PrimarySeq_stream at /usr/local/annotation/maker2.31/bin/../lib/GI.pm line 1894.<br>Calling GI::split_db at /usr/local/annotation/maker2.31/bin/maker line 536.<br>Calling File::Path::rmtree at /usr/local/annotation/maker2.31/bin/maker line 537.<br>
Calling Iterator::Any::new at /usr/local/annotation/maker2.31/bin/maker line 537.<br>Calling Iterator::Any::nextDef at /usr/local/annotation/maker2.31/bin/maker line 537.<br>Calling Iterator::Any::new at /usr/local/annotation/maker2.31/bin/maker line 537.<br>
Calling mkdir at /usr/local/annotation/maker2.31/bin/maker line 537.<br>Calling Iterator::Any::nextFastaRef at /usr/local/annotation/maker2.31/bin/maker line 537.<br>Calling system at /usr/local/annotation/maker2.31/bin/maker line 537.<br>
Calling File::NFSLock::unlock at /usr/local/annotation/maker2.31/bin/maker line 537.<br>Calling GI::build_fasta_index at /usr/local/annotation/maker2.31/bin/maker line 538.<br>Calling FastaDB::new at /usr/local/annotation/maker2.31/bin/maker line 539.<br>
Calling File::NFSLock::new at /usr/local/annotation/maker2.31/bin/../lib/Error.pm line 415.<br>Calling out to BioPerl Bio::DB::Fasta::new at /usr/local/annotation/maker2.31/bin/../lib/Error.pm line 415.<br>Calling out to BioPerl Bio::DB::Fasta::new at /usr/local/annotation/maker2.31/bin/../lib/Error.pm line 415.<br>
Calling out to BioPerl get_PrimarySeq_stream at /usr/local/annotation/maker2.31/bin/../lib/GI.pm line 1894.<br>Calling GI::split_db at /usr/local/annotation/maker2.31/bin/maker line 536.<br>Calling File::Path::rmtree at /usr/local/annotation/maker2.31/bin/maker line 537.<br>
Calling Iterator::Any::new at /usr/local/annotation/maker2.31/bin/maker line 537.<br>Calling Iterator::Any::nextDef at /usr/local/annotation/maker2.31/bin/maker line 537.<br>Calling Iterator::Any::new at /usr/local/annotation/maker2.31/bin/maker line 537.<br>
Calling mkdir at /usr/local/annotation/maker2.31/bin/maker line 537.<br>Calling Iterator::Any::nextFastaRef at /usr/local/annotation/maker2.31/bin/maker line 537.<br>Calling system at /usr/local/annotation/maker2.31/bin/maker line 537.<br>
Calling File::NFSLock::unlock at /usr/local/annotation/maker2.31/bin/maker line 537.<br>Calling GI::build_fasta_index at /usr/local/annotation/maker2.31/bin/maker line 538.<br>Calling FastaDB::new at /usr/local/annotation/maker2.31/bin/maker line 539.<br>
Calling File::NFSLock::new at /usr/local/annotation/maker2.31/bin/../lib/Error.pm line 415.<br>Calling out to BioPerl Bio::DB::Fasta::new at /usr/local/annotation/maker2.31/bin/../lib/Error.pm line 415.<br>Calling out to BioPerl Bio::DB::Fasta::new at /usr/local/annotation/maker2.31/bin/../lib/Error.pm line 415.<br>
Calling out to BioPerl get_PrimarySeq_stream at /usr/local/annotation/maker2.31/bin/../lib/GI.pm line 1894.<br>Calling File::NFSLock::new at /usr/local/annotation/maker2.31/bin/../lib/Error.pm line 415.<br>Calling out to BioPerl Bio::DB::Fasta::new at /usr/local/annotation/maker2.31/bin/../lib/Error.pm line 415.<br>
Calling out to BioPerl Bio::DB::Fasta::new at /usr/local/annotation/maker2.31/bin/../lib/Error.pm line 415.<br>Calling out to BioPerl get_PrimarySeq_stream at /usr/local/annotation/maker2.31/bin/../lib/GI.pm line 1894.<br>
Calling File::NFSLock::new at /usr/local/annotation/maker2.31/bin/../lib/Error.pm line 415.<br>Calling out to BioPerl Bio::DB::Fasta::new at /usr/local/annotation/maker2.31/bin/../lib/Error.pm line 415.<br>Calling out to BioPerl Bio::DB::Fasta::new at /usr/local/annotation/maker2.31/bin/../lib/Error.pm line 415.<br>
Calling out to BioPerl get_PrimarySeq_stream at /usr/local/annotation/maker2.31/bin/../lib/GI.pm line 1894.<br>Calling File::NFSLock::new at /usr/local/annotation/maker2.31/bin/../lib/Error.pm line 415.<br>Calling out to BioPerl Bio::DB::Fasta::new at /usr/local/annotation/maker2.31/bin/../lib/Error.pm line 415.<br>
Calling out to BioPerl Bio::DB::Fasta::new at /usr/local/annotation/maker2.31/bin/../lib/Error.pm line 415.<br>Calling out to BioPerl get_PrimarySeq_stream at /usr/local/annotation/maker2.31/bin/../lib/GI.pm line 1894.<br>
Calling File::NFSLock::new at /usr/local/annotation/maker2.31/bin/../lib/Error.pm line 415.<br>Calling out to BioPerl Bio::DB::Fasta::new at /usr/local/annotation/maker2.31/bin/../lib/Error.pm line 415.<br>Calling out to BioPerl Bio::DB::Fasta::new at /usr/local/annotation/maker2.31/bin/../lib/Error.pm line 415.<br>
Calling out to BioPerl get_PrimarySeq_stream at /usr/local/annotation/maker2.31/bin/../lib/GI.pm line 1894.<br>Calling File::NFSLock::new at /usr/local/annotation/maker2.31/bin/../lib/Error.pm line 415.<br>Calling out to BioPerl Bio::DB::Fasta::new at /usr/local/annotation/maker2.31/bin/../lib/Error.pm line 415.<br>
Calling out to BioPerl Bio::DB::Fasta::new at /usr/local/annotation/maker2.31/bin/../lib/Error.pm line 415.<br>Calling out to BioPerl get_PrimarySeq_stream at /usr/local/annotation/maker2.31/bin/../lib/GI.pm line 1894.<br>
Calling File::NFSLock::new at /usr/local/annotation/maker2.31/bin/../lib/Error.pm line 415.<br>Calling out to BioPerl Bio::DB::Fasta::new at /usr/local/annotation/maker2.31/bin/../lib/Error.pm line 415.<br>Calling out to BioPerl Bio::DB::Fasta::new at /usr/local/annotation/maker2.31/bin/../lib/Error.pm line 415.<br>
Calling out to BioPerl get_PrimarySeq_stream at /usr/local/annotation/maker2.31/bin/../lib/GI.pm line 1894.<br>Calling File::NFSLock::new at /usr/local/annotation/maker2.31/bin/../lib/Error.pm line 415.<br>Calling out to BioPerl Bio::DB::Fasta::new at /usr/local/annotation/maker2.31/bin/../lib/Error.pm line 415.<br>
Calling out to BioPerl Bio::DB::Fasta::new at /usr/local/annotation/maker2.31/bin/../lib/Error.pm line 415.<br>Calling out to BioPerl get_PrimarySeq_stream at /usr/local/annotation/maker2.31/bin/../lib/GI.pm line 1894.<br>
Calling File::NFSLock::new at /usr/local/annotation/maker2.31/bin/../lib/Error.pm line 415.<br>Calling out to BioPerl Bio::DB::Fasta::new at /usr/local/annotation/maker2.31/bin/../lib/Error.pm line 415.<br>Calling out to BioPerl Bio::DB::Fasta::new at /usr/local/annotation/maker2.31/bin/../lib/Error.pm line 415.<br>
Calling out to BioPerl get_PrimarySeq_stream at /usr/local/annotation/maker2.31/bin/../lib/GI.pm line 1894.<br>Calling File::NFSLock::new at /usr/local/annotation/maker2.31/bin/../lib/Error.pm line 415.<br>Calling out to BioPerl Bio::DB::Fasta::new at /usr/local/annotation/maker2.31/bin/../lib/Error.pm line 415.<br>
Calling out to BioPerl Bio::DB::Fasta::new at /usr/local/annotation/maker2.31/bin/../lib/Error.pm line 415.<br>Calling out to BioPerl get_PrimarySeq_stream at /usr/local/annotation/maker2.31/bin/../lib/GI.pm line 1894.<br>
Calling GI::create_blastdb at /usr/local/annotation/maker2.31/bin/maker line 574.<br>Calling File::Path::rmtree at /usr/local/annotation/maker2.31/bin/maker line 575.<br>Calling Iterator::Any::new at /usr/local/annotation/maker2.31/bin/maker line 575.<br>
Calling Iterator::Any::nextDef at /usr/local/annotation/maker2.31/bin/maker line 575.<br>Calling Iterator::Any::new at /usr/local/annotation/maker2.31/bin/maker line 575.<br>Calling File::Path::rmtree at /usr/local/annotation/maker2.31/bin/maker line 575.<br>
Calling Iterator::Any::new at /usr/local/annotation/maker2.31/bin/maker line 575.<br>Calling Iterator::Any::nextDef at /usr/local/annotation/maker2.31/bin/maker line 575.<br>Calling Iterator::Any::new at /usr/local/annotation/maker2.31/bin/maker line 575.<br>
Calling GI::build_fasta_index at /usr/local/annotation/maker2.31/bin/maker line 622.<br>Calling FastaDB::new at /usr/local/annotation/maker2.31/bin/maker line 623.<br>Calling out to BioPerl Bio::DB::Fasta::new at /usr/local/annotation/maker2.31/bin/../lib/Error.pm line 415.<br>
Calling out to BioPerl get_PrimarySeq_stream at /usr/local/annotation/maker2.31/bin/../lib/GI.pm line 1894.<br>STATUS: Setting up database for any GFF3 input...<br>Calling GFFDB::new at /usr/local/annotation/maker2.31/bin/maker line 629.<br>
Calling GFFDB::next_build at /usr/local/annotation/maker2.31/bin/maker line 631.<br>Calling ds_utility::new at /usr/local/annotation/maker2.31/bin/maker line 635.<br>A data structure will be created for you at:<br>/home/cdantec/cutQuality/assembly/HR/path/to/Maker/test/dpp_contig.maker.output/dpp_contig_datastore<br><br>To access files for individual sequences use the datastore index:<br>/home/cdantec/cutQuality/assembly/HR/path/to/Maker/test/dpp_contig.maker.output/dpp_contig_master_datastore_index.log<br><br>Calling Datastore::MD5::new at /usr/local/annotation/maker2.31/bin/maker line 636.<br>
Calling Iterator::Fasta::new at /usr/local/annotation/maker2.31/bin/maker line 639.<br>Calling Iterator::Fasta::skip_file at /usr/local/annotation/maker2.31/bin/maker line 641.<br>Calling Iterator::Fasta::step at /usr/local/annotation/maker2.31/bin/maker line 643.<br>
STATUS: Now running MAKER...<br>examining contents of the fasta file and run log<br>Calling Datastore::MD5::mkdir at /usr/local/annotation/maker2.31/bin/../lib/Process/MpiChunk.pm line 439.<br>Calling Datastore::MD5::id_to_dir at /usr/local/annotation/maker2.31/bin/../lib/Process/MpiChunk.pm line 439.<br>
Calling Datastore::MD5::mkdir at /usr/local/annotation/maker2.31/bin/../lib/Process/MpiChunk.pm line 439.<br>Calling uri_escape at /usr/local/annotation/maker2.31/bin/../lib/Process/MpiChunk.pm line 439.<br>Calling File::Path::mkpath at /usr/local/annotation/maker2.31/bin/../lib/Process/MpiChunk.pm line 439.<br><br><br><br>--Next Contig--<br><br>#---------------------------------------------------------------------<br>Now starting the contig!!<br>SeqID: contig-dpp-500-500<br>Length: 32156<br>#---------------------------------------------------------------------<br><br><br>Calling FastaDB::new at /usr/local/annotation/maker2.31/bin/../lib/Process/MpiChunk.pm line 462.<br>Calling out to BioPerl get_PrimarySeq_stream at /usr/local/annotation/maker2.31/bin/../lib/GI.pm line 1894.<br>setting up GFF3 output and fasta chunks<br>
doing repeat masking<br>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.<br>
Can't call method "do" on an undefined value at /usr/local/annotation/maker2.31/bin/../lib/GFFDB.pm line 108.<br>--> rank=NA, hostname=belem<br>ERROR: Failed while doing repeat masking<br>ERROR: Chunk failed at level:0, tier_type:1<br>
FAILED CONTIG:contig-dpp-500-500<br><br>ERROR: Chunk failed at level:2, tier_type:0<br>FAILED CONTIG:contig-dpp-500-500<br><br>examining contents of the fasta file and run log<br>Calling Datastore::MD5::mkdir at /usr/local/annotation/maker2.31/bin/../lib/Process/MpiChunk.pm line 439.<br>
Calling Datastore::MD5::id_to_dir at /usr/local/annotation/maker2.31/bin/../lib/Process/MpiChunk.pm line 439.<br>Calling Datastore::MD5::mkdir at /usr/local/annotation/maker2.31/bin/../lib/Process/MpiChunk.pm line 439.<br>
Calling uri_escape at /usr/local/annotation/maker2.31/bin/../lib/Process/MpiChunk.pm line 439.<br>Calling File::Path::mkpath at /usr/local/annotation/maker2.31/bin/../lib/Process/MpiChunk.pm line 439.<br><br><br><br>--Next Contig--<br><br>Processing run.log file...<br>#---------------------------------------------------------------------<br>Now retrying the contig!!<br>SeqID: contig-dpp-500-500<br>Length: 32156<br>Tries: 2!!<br>#---------------------------------------------------------------------<br><br><br>Calling FastaDB::new at /usr/local/annotation/maker2.31/bin/../lib/Process/MpiChunk.pm line 462.<br>Calling out to BioPerl get_PrimarySeq_stream at /usr/local/annotation/maker2.31/bin/../lib/GI.pm line 1894.<br>setting up GFF3 output and fasta chunks<br>
doing repeat masking<br>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.<br>
Can't call method "do" on an undefined value at /usr/local/annotation/maker2.31/bin/../lib/GFFDB.pm line 108.<br>--> rank=NA, hostname=belem<br>ERROR: Failed while doing repeat masking<br>ERROR: Chunk failed at level:0, tier_type:1<br>
FAILED CONTIG:contig-dpp-500-500<br><br>ERROR: Chunk failed at level:2, tier_type:0<br>FAILED CONTIG:contig-dpp-500-500<br><br>examining contents of the fasta file and run log<br>Calling Datastore::MD5::mkdir at /usr/local/annotation/maker2.31/bin/../lib/Process/MpiChunk.pm line 439.<br>
Calling Datastore::MD5::id_to_dir at /usr/local/annotation/maker2.31/bin/../lib/Process/MpiChunk.pm line 439.<br>Calling Datastore::MD5::mkdir at /usr/local/annotation/maker2.31/bin/../lib/Process/MpiChunk.pm line 439.<br>
Calling uri_escape at /usr/local/annotation/maker2.31/bin/../lib/Process/MpiChunk.pm line 439.<br>Calling File::Path::mkpath at /usr/local/annotation/maker2.31/bin/../lib/Process/MpiChunk.pm line 439.<br><br><br><br>--Next Contig--<br><br>Processing run.log file...<br><br><br>Maker is now finished!!!<br><br></div>Many thanks for you help<br><br></div>Christelle<br><div><div><br></div></div></div><div class="gmail_extra"><br><br><div class="gmail_quote">
2014-03-19 14:01 GMT+01:00 Carson Holt <span dir="ltr"><<a href="mailto:carsonhh@gmail.com" target="_blank">carsonhh@gmail.com</a>></span>:<br><blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex"><div style="font-size:14px;font-family:Calibri,sans-serif;word-wrap:break-word"><div>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.</div><div><br></div><div>Thanks,</div><div>Carson</div><div><br></div><div><br></div><span><div style="border-right:medium none;padding-right:0in;padding-left:0in;padding-top:3pt;text-align:left;font-size:11pt;border-bottom:medium none;font-family:Calibri;border-top:#b5c4df 1pt solid;padding-bottom:0in;border-left:medium none"><span style="font-weight:bold">From: </span> Chris Bioinfo <<a href="mailto:chrisbioinfo@gmail.com" target="_blank">chrisbioinfo@gmail.com</a>><br><span style="font-weight:bold">Date: </span> Wednesday, March 19, 2014 at 5:09 AM<br><span style="font-weight:bold">To: </span> <<a href="mailto:maker-devel@yandell-lab.org" target="_blank">maker-devel@yandell-lab.org</a>><br><span style="font-weight:bold">Subject: </span> [maker-devel] Annotation with maker2<br></div><div><div><div><br></div><div dir="ltr"><div><div><div>Hello,<br><br></div>I'm installing/using maker2 for the first time and I have an error by using it.<br><br></div>I certainly missing something, but I don't know what.<br><br></div>I compile maker with no error message and I have all these directories after compilation: <br><div><div><div><div>bin data GMOD INSTALL lib LICENSE MWAS perl README src<br><br></div><div>Nevertheless when I try maker2 on the test data (dpp_contig.fasta) I have this error:<br><br></div><div>STATUS: Now running MAKER...<br>
examining contents of the fasta file and run log<br><br><br><br>--Next Contig--<br><br>#---------------------------------------------------------------------<br>Now starting the contig!!<br>SeqID: contig-dpp-500-500<br>Length: 32156<br>
#---------------------------------------------------------------------<br><br><br>setting up GFF3 output and fasta chunks<br>doing repeat masking<br>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<br><br>Can't call method "do" on an undefined value at /usr/local/annotation/maker2.31/bin/../lib/GFFDB.pm <br>--> rank=NA, hostname=belem<br>ERROR: Failed while doing repeat masking<br>ERROR: Chunk failed at level:0, tier_type:1<br>
FAILED CONTIG:contig-dpp-500-500<br>...<br><br></div><div>ideas?<br></div><div><br></div><div>Best,<br><br></div><div>Christelle<br></div><div><br></div></div></div></div></div></div></div>
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