Error: 'Must have defined a valid name for hit'

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Error: 'Must have defined a valid name for hit'

Dana Price
I'm getting loads of the below error in my maker logs.. is this
something I can rectify?

--Next Contig--

Processing run.log file...
#---------------------------------------------------------------------
Now retrying the contig!!
SeqID: ConsensusfromContig38211
Length: 4176
Retry: 1!!
#---------------------------------------------------------------------



------------- EXCEPTION: Bio::Root::Exception -------------
MSG: Must have defined a valid name for Hit
STACK: Error::throw
STACK: Bio::Root::Root::throw /usr/local/share/perl/5.10.1/Bio/Root/
Root.pm:368
STACK: Bio::Search::Hit::GenericHit::new /usr/local/share/perl/5.10.1/
Bio/Search/Hit/GenericHit.pm:148
STACK: Bio::Search::Hit::PhatHit::Base::new /usr/local/maker/bin/../
lib/Bio/Search/Hit/PhatHit/Base.pm:126
STACK: Bio::Search::Hit::PhatHit::gff3::new /usr/local/maker/bin/../
lib/Bio/Search/Hit/PhatHit/gff3.pm:23
STACK: GFFDB::_load_hits /usr/local/maker/bin/../lib/GFFDB.pm:784
STACK: GFFDB::phathits_on_chunk /usr/local/maker/bin/../lib/GFFDB.pm:
520
STACK: Process::MpiChunk::_go /usr/local/maker/bin/../lib/Process/
MpiChunk.pm:1511
STACK: Process::MpiChunk::run /usr/local/maker/bin/../lib/Process/
MpiChunk.pm:253
STACK: Process::MpiTiers::run /usr/local/maker/bin/../lib/Process/
MpiTiers.pm:169
STACK: main::node_thread /usr/local/maker/bin/mpi_maker:896
STACK: /usr/local/maker/bin/mpi_maker:362
-----------------------------------------------------------

FATAL ERROR
ERROR: Failed while processing the chunk divide!!

ERROR: Chunk failed at level 16


Thanks!


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Re: Error: 'Must have defined a valid name for hit'

Carson Hinton Holt
Re: [maker-devel] Error: 'Must have defined a valid name for hit' It looks like you’re using the GFF3 pass-through option.  The cause of the error is likely an incorrectly formatted GFF3 file.

Try this online GFF3 file validator --> http://modencode.oicr.on.ca/cgi-bin/validate_gff3_online

Thanks,
Carson


On 11/6/10 1:10 PM, "Dana" <dana.price@...> wrote:

I'm getting loads of the below error in my maker logs.. is this
something I can rectify?

--Next Contig--

Processing run.log file...
#---------------------------------------------------------------------
Now retrying the contig!!
SeqID: ConsensusfromContig38211
Length: 4176
Retry: 1!!
#---------------------------------------------------------------------



------------- EXCEPTION: Bio::Root::Exception -------------
MSG: Must have defined a valid name for Hit
STACK: Error::throw
STACK: Bio::Root::Root::throw /usr/local/share/perl/5.10.1/Bio/Root/
Root.pm:368
STACK: Bio::Search::Hit::GenericHit::new /usr/local/share/perl/5.10.1/
Bio/Search/Hit/GenericHit.pm:148
STACK: Bio::Search::Hit::PhatHit::Base::new /usr/local/maker/bin/../
lib/Bio/Search/Hit/PhatHit/Base.pm:126
STACK: Bio::Search::Hit::PhatHit::gff3::new /usr/local/maker/bin/../
lib/Bio/Search/Hit/PhatHit/gff3.pm:23
STACK: GFFDB::_load_hits /usr/local/maker/bin/../lib/GFFDB.pm:784
STACK: GFFDB::phathits_on_chunk /usr/local/maker/bin/../lib/GFFDB.pm:
520
STACK: Process::MpiChunk::_go /usr/local/maker/bin/../lib/Process/
MpiChunk.pm:1511
STACK: Process::MpiChunk::run /usr/local/maker/bin/../lib/Process/
MpiChunk.pm:253
STACK: Process::MpiTiers::run /usr/local/maker/bin/../lib/Process/
MpiTiers.pm:169
STACK: main::node_thread /usr/local/maker/bin/mpi_maker:896
STACK: /usr/local/maker/bin/mpi_maker:362
-----------------------------------------------------------

FATAL ERROR
ERROR: Failed while processing the chunk divide!!

ERROR: Chunk failed at level 16


Thanks!


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maker-devel mailing list
maker-devel@...
http://box290.bluehost.com/mailman/listinfo/maker-devel_yandell-lab.org


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Re: Error: 'Must have defined a valid name for hit'

Dana Price
I fed it a .gff of hints constructed for augustus via blat alignment of rnaseq reads to my genome as constructed in http://augustus.gobics.de/binaries/readme.rnaseq.html and used it in est_gff:  That gff validation website does indeed find problems.  I've assembled those reads now and I'll use that EST dataset instead.  I upgraded to the latest maker beta and I'm now seeing the below:


Producing est2genome hint based annotations
Producing augustus hint based annotations
Processing ab-initio predictions
Argument "-" isn't numeric in numeric eq (==) at /usr/local/maker/bin/../lib/Bio/Search/Hit/PhatHit/Base.pm line 453.

------------- EXCEPTION: Bio::Root::Exception -------------
MSG: Can't get HSPs: data not collected.
STACK: Error::throw
STACK: Bio::Root::Root::throw /usr/local/share/perl/5.10.0/Bio/Root/Root.pm:368
STACK: Bio::Search::Hit::PhatHit::Base::hsps /usr/local/maker/bin/../lib/Bio/Search/Hit/PhatHit/Base.pm:519
STACK: Bio::Search::Hit::PhatHit::Base::strand /usr/local/maker/bin/../lib/Bio/Search/Hit/PhatHit/Base.pm:458
STACK: PhatHit_utils::sort_hits /usr/local/maker/bin/../lib/PhatHit_utils.pm:23
STACK: maker::auto_annotator::get_transcript_seq /usr/local/maker/bin/../lib/maker/audeleted:0 hits
to_annotator.pm:2310
STACK: maker::auto_annotator::load_transcript_struct /usr/local/maker/bin/../lib/maker/auto_annotator.pm:1593
STACK: maker::auto_annotator::group_transcripts /usr/local/maker/bin/../lib/maker/auto_annotator.pm:1888
STACK: maker::auto_annotator::annotate /usr/local/maker/bin/../lib/maker/auto_annotator.pm:704
STACK: Process::MpiChunk::_go /usr/local/maker/bin/../lib/Process/MpiChunk.pm:1949
STACK: Process::MpiChunk::run /usr/local/maker/bin/../lib/Process/MpiChunk.pm:253
STACK: Process::MpiTiers::run /usr/local/maker/bin/../lib/Process/MpiTiers.pm:169
STACK: /usr/local/maker/bin/mpi_maker:823
-----------------------------------------------------------

FATAL ERROR
ERROR: Failed while calculating annotations!!

ERROR: Chunk failed at level 18
!!
FAILED CONTIG:ConsensusfromContig1628


On Sat, Nov 6, 2010 at 9:19 PM, Carson Holt <[hidden email]> wrote:
It looks like you’re using the GFF3 pass-through option.  The cause of the error is likely an incorrectly formatted GFF3 file.

Try this online GFF3 file validator --> http://modencode.oicr.on.ca/cgi-bin/validate_gff3_online

Thanks,
Carson



On 11/6/10 1:10 PM, "Dana" <dana.price@...> wrote:

I'm getting loads of the below error in my maker logs.. is this
something I can rectify?

--Next Contig--

Processing run.log file...
#---------------------------------------------------------------------
Now retrying the contig!!
SeqID: ConsensusfromContig38211
Length: 4176
Retry: 1!!
#---------------------------------------------------------------------



------------- EXCEPTION: Bio::Root::Exception -------------
MSG: Must have defined a valid name for Hit
STACK: Error::throw
STACK: Bio::Root::Root::throw /usr/local/share/perl/5.10.1/Bio/Root/
Root.pm:368
STACK: Bio::Search::Hit::GenericHit::new /usr/local/share/perl/5.10.1/
Bio/Search/Hit/GenericHit.pm:148
STACK: Bio::Search::Hit::PhatHit::Base::new /usr/local/maker/bin/../
lib/Bio/Search/Hit/PhatHit/Base.pm:126
STACK: Bio::Search::Hit::PhatHit::gff3::new /usr/local/maker/bin/../
lib/Bio/Search/Hit/PhatHit/gff3.pm:23
STACK: GFFDB::_load_hits /usr/local/maker/bin/../lib/GFFDB.pm:784
STACK: GFFDB::phathits_on_chunk /usr/local/maker/bin/../lib/GFFDB.pm:
520
STACK: Process::MpiChunk::_go /usr/local/maker/bin/../lib/Process/
MpiChunk.pm:1511
STACK: Process::MpiChunk::run /usr/local/maker/bin/../lib/Process/
MpiChunk.pm:253
STACK: Process::MpiTiers::run /usr/local/maker/bin/../lib/Process/
MpiTiers.pm:169
STACK: main::node_thread /usr/local/maker/bin/mpi_maker:896
STACK: /usr/local/maker/bin/mpi_maker:362
-----------------------------------------------------------

FATAL ERROR
ERROR: Failed while processing the chunk divide!!

ERROR: Chunk failed at level 16


Thanks!


_______________________________________________
maker-devel mailing list
maker-devel@...
http://box290.bluehost.com/mailman/listinfo/maker-devel_yandell-lab.org




--
Dana Price
Laboratory Researcher in Bioinformatics
Rutgers, The State University
Bhattacharya Lab
http://dblab.rutgers.edu
[hidden email]

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Re: Error: 'Must have defined a valid name for hit'

Carson Hinton Holt
Re: [maker-devel] Error: 'Must have defined a valid name for hit' I have put MAKER 2.05 on the download page.  http://malachite.genetics.utah.edu/cgi-bin/yandell-lab/register.cgi

Try that.  It should solve the problem.

Thanks,
Carson


On 11/11/10 3:05 PM, "Dana Price" <dana.price@...> wrote:

I fed it a .gff of hints constructed for augustus via blat alignment of rnaseq reads to my genome as constructed in http://augustus.gobics.de/binaries/readme.rnaseq.html and used it in est_gff:  That gff validation website does indeed find problems.  I've assembled those reads now and I'll use that EST dataset instead.  I upgraded to the latest maker beta and I'm now seeing the below:


Producing est2genome hint based annotations
Producing augustus hint based annotations
Processing ab-initio predictions
Argument "-" isn't numeric in numeric eq (==) at /usr/local/maker/bin/../lib/Bio/Search/Hit/PhatHit/Base.pm line 453.

------------- EXCEPTION: Bio::Root::Exception -------------
MSG: Can't get HSPs: data not collected.
STACK: Error::throw
STACK: Bio::Root::Root::throw /usr/local/share/perl/5.10.0/Bio/Root/Root.pm:368
STACK: Bio::Search::Hit::PhatHit::Base::hsps /usr/local/maker/bin/../lib/Bio/Search/Hit/PhatHit/Base.pm:519
STACK: Bio::Search::Hit::PhatHit::Base::strand /usr/local/maker/bin/../lib/Bio/Search/Hit/PhatHit/Base.pm:458
STACK: PhatHit_utils::sort_hits /usr/local/maker/bin/../lib/PhatHit_utils.pm:23
STACK: maker::auto_annotator::get_transcript_seq /usr/local/maker/bin/../lib/maker/audeleted:0 hits
to_annotator.pm:2310 <http://to_annotator.pm:2310>
STACK: maker::auto_annotator::load_transcript_struct /usr/local/maker/bin/../lib/maker/auto_annotator.pm:1593 <http://auto_annotator.pm:1593>
STACK: maker::auto_annotator::group_transcripts /usr/local/maker/bin/../lib/maker/auto_annotator.pm:1888 <http://auto_annotator.pm:1888>
STACK: maker::auto_annotator::annotate /usr/local/maker/bin/../lib/maker/auto_annotator.pm:704 <http://auto_annotator.pm:704>
STACK: Process::MpiChunk::_go /usr/local/maker/bin/../lib/Process/MpiChunk.pm:1949
STACK: Process::MpiChunk::run /usr/local/maker/bin/../lib/Process/MpiChunk.pm:253
STACK: Process::MpiTiers::run /usr/local/maker/bin/../lib/Process/MpiTiers.pm:169
STACK: /usr/local/maker/bin/mpi_maker:823
-----------------------------------------------------------

FATAL ERROR
ERROR: Failed while calculating annotations!!

ERROR: Chunk failed at level 18
!!
FAILED CONTIG:ConsensusfromContig1628


On Sat, Nov 6, 2010 at 9:19 PM, Carson Holt <carson.holt@...> wrote:
It looks like you’re using the GFF3 pass-through option.  The cause of the error is likely an incorrectly formatted GFF3 file.

Try this online GFF3 file validator --> http://modencode.oicr.on.ca/cgi-bin/validate_gff3_online

Thanks,
Carson



On 11/6/10 1:10 PM, "Dana" <dana.price@... <http://dana.price@...> > wrote:

I'm getting loads of the below error in my maker logs.. is this
something I can rectify?

--Next Contig--

Processing run.log file...
#---------------------------------------------------------------------
Now retrying the contig!!
SeqID: ConsensusfromContig38211
Length: 4176
Retry: 1!!
#---------------------------------------------------------------------



------------- EXCEPTION: Bio::Root::Exception -------------
MSG: Must have defined a valid name for Hit
STACK: Error::throw
STACK: Bio::Root::Root::throw /usr/local/share/perl/5.10.1/Bio/Root/
Root.pm:368
STACK: Bio::Search::Hit::GenericHit::new /usr/local/share/perl/5.10.1/
Bio/Search/Hit/GenericHit.pm:148
STACK: Bio::Search::Hit::PhatHit::Base::new /usr/local/maker/bin/../
lib/Bio/Search/Hit/PhatHit/Base.pm:126
STACK: Bio::Search::Hit::PhatHit::gff3::new /usr/local/maker/bin/../
lib/Bio/Search/Hit/PhatHit/gff3.pm:23 <http://gff3.pm:23>
STACK: GFFDB::_load_hits /usr/local/maker/bin/../lib/GFFDB.pm:784
STACK: GFFDB::phathits_on_chunk /usr/local/maker/bin/../lib/GFFDB.pm:
520
STACK: Process::MpiChunk::_go /usr/local/maker/bin/../lib/Process/
MpiChunk.pm:1511
STACK: Process::MpiChunk::run /usr/local/maker/bin/../lib/Process/
MpiChunk.pm:253
STACK: Process::MpiTiers::run /usr/local/maker/bin/../lib/Process/
MpiTiers.pm:169
STACK: main::node_thread /usr/local/maker/bin/mpi_maker:896
STACK: /usr/local/maker/bin/mpi_maker:362
-----------------------------------------------------------

FATAL ERROR
ERROR: Failed while processing the chunk divide!!

ERROR: Chunk failed at level 16


Thanks!


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Re: Error: 'Must have defined a valid name for hit'

Carson Hinton Holt
In reply to this post by Dana Price
Re: [maker-devel] Error: 'Must have defined a valid name for hit' That is very odd as I am currently using this same file and script for viewing MAKER results
 at http://derringer.genetics.utah.edu/cgi-bin/MWAS/maker.cgi without issue.  I wonder if JBrowse has undergone any changes as my version is ~6 months old.

I’ll have to run a test with the current version of JBrowse.

Thanks,
Carson

On 11/15/10 2:55 PM, "Dana Price" <dana.price@...> wrote:

Great, thanks Carson.

Incidentally, when I move the genome.css that's provided with maker into place within my JBrowse tree and reload the page, all my tracks disappear when I drag them into the main frame.  I'm using maker2jbrowse to build my data/ directory for jbrowse.  Do I need to do anything else to fix this?

Thanks again.



On Mon, Nov 15, 2010 at 4:44 PM, Carson Holt <carson.holt@...> wrote:
I have put MAKER 2.05 on the download page.  http://malachite.genetics.utah.edu/cgi-bin/yandell-lab/register.cgi

Try that.  It should solve the problem.

Thanks,
Carson



On 11/11/10 3:05 PM, "Dana Price" <dana.price@... <http://dana.price@...> > wrote:

I fed it a .gff of hints constructed for augustus via blat alignment of rnaseq reads to my genome as constructed in http://augustus.gobics.de/binaries/readme.rnaseq.html and used it in est_gff:  That gff validation website does indeed find problems.  I've assembled those reads now and I'll use that EST dataset instead.  I upgraded to the latest maker beta and I'm now seeing the below:


Producing est2genome hint based annotations
Producing augustus hint based annotations
Processing ab-initio predictions
Argument "-" isn't numeric in numeric eq (==) at /usr/local/maker/bin/../lib/Bio/Search/Hit/PhatHit/Base.pm line 453.

------------- EXCEPTION: Bio::Root::Exception -------------
MSG: Can't get HSPs: data not collected.
STACK: Error::throw
STACK: Bio::Root::Root::throw /usr/local/share/perl/5.10.0/Bio/Root/Root.pm:368
STACK: Bio::Search::Hit::PhatHit::Base::hsps /usr/local/maker/bin/../lib/Bio/Search/Hit/PhatHit/Base.pm:519
STACK: Bio::Search::Hit::PhatHit::Base::strand /usr/local/maker/bin/../lib/Bio/Search/Hit/PhatHit/Base.pm:458
STACK: PhatHit_utils::sort_hits /usr/local/maker/bin/../lib/PhatHit_utils.pm:23
STACK: maker::auto_annotator::get_transcript_seq /usr/local/maker/bin/../lib/maker/audeleted:0 hits
to_annotator.pm:2310 <http://to_annotator.pm:2310>  <http://to_annotator.pm:2310>
STACK: maker::auto_annotator::load_transcript_struct /usr/local/maker/bin/../lib/maker/auto_annotator.pm:1593 <http://auto_annotator.pm:1593>  <http://auto_annotator.pm:1593>
STACK: maker::auto_annotator::group_transcripts /usr/local/maker/bin/../lib/maker/auto_annotator.pm:1888 <http://auto_annotator.pm:1888>  <http://auto_annotator.pm:1888>
STACK: maker::auto_annotator::annotate /usr/local/maker/bin/../lib/maker/auto_annotator.pm:704 <http://auto_annotator.pm:704>  <http://auto_annotator.pm:704>
STACK: Process::MpiChunk::_go /usr/local/maker/bin/../lib/Process/MpiChunk.pm:1949
STACK: Process::MpiChunk::run /usr/local/maker/bin/../lib/Process/MpiChunk.pm:253
STACK: Process::MpiTiers::run /usr/local/maker/bin/../lib/Process/MpiTiers.pm:169
STACK: /usr/local/maker/bin/mpi_maker:823
-----------------------------------------------------------

FATAL ERROR
ERROR: Failed while calculating annotations!!

ERROR: Chunk failed at level 18
!!
FAILED CONTIG:ConsensusfromContig1628


On Sat, Nov 6, 2010 at 9:19 PM, Carson Holt <carson.holt@... <http://carson.holt@...> > wrote:
It looks like you’re using the GFF3 pass-through option.  The cause of the error is likely an incorrectly formatted GFF3 file.

Try this online GFF3 file validator --> http://modencode.oicr.on.ca/cgi-bin/validate_gff3_online

Thanks,
Carson



On 11/6/10 1:10 PM, "Dana" <dana.price@... <http://dana.price@...>  <http://dana.price@...> > wrote:

I'm getting loads of the below error in my maker logs.. is this
something I can rectify?

--Next Contig--

Processing run.log file...
#---------------------------------------------------------------------
Now retrying the contig!!
SeqID: ConsensusfromContig38211
Length: 4176
Retry: 1!!
#---------------------------------------------------------------------



------------- EXCEPTION: Bio::Root::Exception -------------
MSG: Must have defined a valid name for Hit
STACK: Error::throw
STACK: Bio::Root::Root::throw /usr/local/share/perl/5.10.1/Bio/Root/
Root.pm:368
STACK: Bio::Search::Hit::GenericHit::new /usr/local/share/perl/5.10.1/
Bio/Search/Hit/GenericHit.pm:148
STACK: Bio::Search::Hit::PhatHit::Base::new /usr/local/maker/bin/../
lib/Bio/Search/Hit/PhatHit/Base.pm:126
STACK: Bio::Search::Hit::PhatHit::gff3::new /usr/local/maker/bin/../
lib/Bio/Search/Hit/PhatHit/gff3.pm:23 <http://gff3.pm:23>  <http://gff3.pm:23>
STACK: GFFDB::_load_hits /usr/local/maker/bin/../lib/GFFDB.pm:784
STACK: GFFDB::phathits_on_chunk /usr/local/maker/bin/../lib/GFFDB.pm:
520
STACK: Process::MpiChunk::_go /usr/local/maker/bin/../lib/Process/
MpiChunk.pm:1511
STACK: Process::MpiChunk::run /usr/local/maker/bin/../lib/Process/
MpiChunk.pm:253
STACK: Process::MpiTiers::run /usr/local/maker/bin/../lib/Process/
MpiTiers.pm:169
STACK: main::node_thread /usr/local/maker/bin/mpi_maker:896
STACK: /usr/local/maker/bin/mpi_maker:362
-----------------------------------------------------------

FATAL ERROR
ERROR: Failed while processing the chunk divide!!

ERROR: Chunk failed at level 16


Thanks!


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Re: Error: 'Must have defined a valid name for hit'

Carson Hinton Holt
In reply to this post by Dana Price
Re: [maker-devel] Error: 'Must have defined a valid name for hit' Ok.  I’ve verified that this is a version issue.  JBrowse documentation notes that JBrowse version 1.1 JSON files (and as a result genome.css) are not compatible with the files from older versions of JBrowse and vice-versa.

I’ve made corrections to the genome.css file attached to be 1.1 compatible.  I tested the file, and colors display appropriately.  Note that this file will not work on pre-1.1 JBrowse.  I will start bundling this file with MAKER, and will note the version dependency.

Thanks,
Carson


On 11/15/10 2:55 PM, "Dana Price" <dana.price@...> wrote:

Great, thanks Carson.

Incidentally, when I move the genome.css that's provided with maker into place within my JBrowse tree and reload the page, all my tracks disappear when I drag them into the main frame.  I'm using maker2jbrowse to build my data/ directory for jbrowse.  Do I need to do anything else to fix this?

Thanks again.



On Mon, Nov 15, 2010 at 4:44 PM, Carson Holt <carson.holt@...> wrote:
I have put MAKER 2.05 on the download page.  http://malachite.genetics.utah.edu/cgi-bin/yandell-lab/register.cgi

Try that.  It should solve the problem.

Thanks,
Carson



On 11/11/10 3:05 PM, "Dana Price" <dana.price@... <http://dana.price@...> > wrote:

I fed it a .gff of hints constructed for augustus via blat alignment of rnaseq reads to my genome as constructed in http://augustus.gobics.de/binaries/readme.rnaseq.html and used it in est_gff:  That gff validation website does indeed find problems.  I've assembled those reads now and I'll use that EST dataset instead.  I upgraded to the latest maker beta and I'm now seeing the below:


Producing est2genome hint based annotations
Producing augustus hint based annotations
Processing ab-initio predictions
Argument "-" isn't numeric in numeric eq (==) at /usr/local/maker/bin/../lib/Bio/Search/Hit/PhatHit/Base.pm line 453.

------------- EXCEPTION: Bio::Root::Exception -------------
MSG: Can't get HSPs: data not collected.
STACK: Error::throw
STACK: Bio::Root::Root::throw /usr/local/share/perl/5.10.0/Bio/Root/Root.pm:368
STACK: Bio::Search::Hit::PhatHit::Base::hsps /usr/local/maker/bin/../lib/Bio/Search/Hit/PhatHit/Base.pm:519
STACK: Bio::Search::Hit::PhatHit::Base::strand /usr/local/maker/bin/../lib/Bio/Search/Hit/PhatHit/Base.pm:458
STACK: PhatHit_utils::sort_hits /usr/local/maker/bin/../lib/PhatHit_utils.pm:23
STACK: maker::auto_annotator::get_transcript_seq /usr/local/maker/bin/../lib/maker/audeleted:0 hits
to_annotator.pm:2310 <http://to_annotator.pm:2310>  <http://to_annotator.pm:2310>
STACK: maker::auto_annotator::load_transcript_struct /usr/local/maker/bin/../lib/maker/auto_annotator.pm:1593 <http://auto_annotator.pm:1593>  <http://auto_annotator.pm:1593>
STACK: maker::auto_annotator::group_transcripts /usr/local/maker/bin/../lib/maker/auto_annotator.pm:1888 <http://auto_annotator.pm:1888>  <http://auto_annotator.pm:1888>
STACK: maker::auto_annotator::annotate /usr/local/maker/bin/../lib/maker/auto_annotator.pm:704 <http://auto_annotator.pm:704>  <http://auto_annotator.pm:704>
STACK: Process::MpiChunk::_go /usr/local/maker/bin/../lib/Process/MpiChunk.pm:1949
STACK: Process::MpiChunk::run /usr/local/maker/bin/../lib/Process/MpiChunk.pm:253
STACK: Process::MpiTiers::run /usr/local/maker/bin/../lib/Process/MpiTiers.pm:169
STACK: /usr/local/maker/bin/mpi_maker:823
-----------------------------------------------------------

FATAL ERROR
ERROR: Failed while calculating annotations!!

ERROR: Chunk failed at level 18
!!
FAILED CONTIG:ConsensusfromContig1628


On Sat, Nov 6, 2010 at 9:19 PM, Carson Holt <carson.holt@... <http://carson.holt@...> > wrote:
It looks like you’re using the GFF3 pass-through option.  The cause of the error is likely an incorrectly formatted GFF3 file.

Try this online GFF3 file validator --> http://modencode.oicr.on.ca/cgi-bin/validate_gff3_online

Thanks,
Carson



On 11/6/10 1:10 PM, "Dana" <dana.price@... <http://dana.price@...>  <http://dana.price@...> > wrote:

I'm getting loads of the below error in my maker logs.. is this
something I can rectify?

--Next Contig--

Processing run.log file...
#---------------------------------------------------------------------
Now retrying the contig!!
SeqID: ConsensusfromContig38211
Length: 4176
Retry: 1!!
#---------------------------------------------------------------------



------------- EXCEPTION: Bio::Root::Exception -------------
MSG: Must have defined a valid name for Hit
STACK: Error::throw
STACK: Bio::Root::Root::throw /usr/local/share/perl/5.10.1/Bio/Root/
Root.pm:368
STACK: Bio::Search::Hit::GenericHit::new /usr/local/share/perl/5.10.1/
Bio/Search/Hit/GenericHit.pm:148
STACK: Bio::Search::Hit::PhatHit::Base::new /usr/local/maker/bin/../
lib/Bio/Search/Hit/PhatHit/Base.pm:126
STACK: Bio::Search::Hit::PhatHit::gff3::new /usr/local/maker/bin/../
lib/Bio/Search/Hit/PhatHit/gff3.pm:23 <http://gff3.pm:23>  <http://gff3.pm:23>
STACK: GFFDB::_load_hits /usr/local/maker/bin/../lib/GFFDB.pm:784
STACK: GFFDB::phathits_on_chunk /usr/local/maker/bin/../lib/GFFDB.pm:
520
STACK: Process::MpiChunk::_go /usr/local/maker/bin/../lib/Process/
MpiChunk.pm:1511
STACK: Process::MpiChunk::run /usr/local/maker/bin/../lib/Process/
MpiChunk.pm:253
STACK: Process::MpiTiers::run /usr/local/maker/bin/../lib/Process/
MpiTiers.pm:169
STACK: main::node_thread /usr/local/maker/bin/mpi_maker:896
STACK: /usr/local/maker/bin/mpi_maker:362
-----------------------------------------------------------

FATAL ERROR
ERROR: Failed while processing the chunk divide!!

ERROR: Chunk failed at level 16


Thanks!


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