[maker-devel] Cthe EST pass error.

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[maker-devel] Cthe EST pass error.

Daniel Quest
All,

I am attempting a re-annotation of Clostridium thermocellum ATCC 27405
as a proof of concept for using Maker.  This genome has many miscalled
genes and other errors and is important for bio-energy.  We have 454
RNASeq data that we wish to use in the re-annotation process.  I
constructed the maker_opts file and made the following modifications:

genome:cthe.fna #genome sequence file in fasta format
est: exampleEST.fasta #non-redundant set of assembled ESTs in fasta
format (classic EST analysis)
organism_type: prokaryotic #eukaryotic or prokaryotic. Default is eukaryotic
predictor: pred_gff #prediction methods for annotations (seperate
multiple values by ',')
pred_gff: prodigal.gff #ab-initio predictions from an external gff3 file

after running maker, I received the following errors:

indexing was interrupted, so unlinking
/home/gmod/Cthe/cthe.maker.output/mpi_blastdb/exampleEST.mpi.10/exampleEST.mpi.10.0.fasta.index
at /usr/local/share/perl/5.10.0/Bio/DB/Fasta.pm line 1053.

------------- EXCEPTION: Bio::Root::Exception -------------
MSG: Each line of the fasta entry must be the same length except the last.
    Line above #3 'GCTCAGCCGGGACGATGAGC..' is 61 != 8 chars.
STACK: Error::throw
STACK: Bio::Root::Root::throw /usr/local/share/perl/5.10.0/Bio/Root/Root.pm:368
STACK: Bio::DB::Fasta::calculate_offsets
/usr/local/share/perl/5.10.0/Bio/DB/Fasta.pm:770
STACK: Bio::DB::Fasta::index_file
/usr/local/share/perl/5.10.0/Bio/DB/Fasta.pm:680
STACK: Bio::DB::Fasta::new /usr/local/share/perl/5.10.0/Bio/DB/Fasta.pm:491
STACK: FastaDB::new /home/gmod/Documents/Software/maker/bin/../lib/FastaDB.pm:54
STACK: GI::build_fasta_index
/home/gmod/Documents/Software/maker/bin/../lib/GI.pm:1206
STACK: GI::build_all_indexes
/home/gmod/Documents/Software/maker/bin/../lib/GI.pm:1223
STACK: GI::load_control_files
/home/gmod/Documents/Software/maker/bin/../lib/GI.pm:3259
STACK: /home/gmod/Documents/Software/maker/bin/maker:240
-----------------------------------------------------------

FATAL ERROR

I have attached the exampleEST.fasta file...  Any ideas on why this happens?

Thanks so much
-Daniel

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Re: [maker-devel] Cthe EST pass error.

Jason Stajich-4
you need to just reformat your FASTA file so that line lengths are consistent.
 
Run the tool from Sean Eddy's toolkit (HMMER)
sreformat fasta ESTDB > newDB
mv newDB ESTDB

or you can do this with bioperl
bp_sreformat -if fasta -of fasta -i ESTDB -o newESTDB
mv newESTDB ESTDB

-jason
Daniel Quest wrote, On 5/18/10 8:21 AM:
All,

I am attempting a re-annotation of Clostridium thermocellum ATCC 27405
as a proof of concept for using Maker.  This genome has many miscalled
genes and other errors and is important for bio-energy.  We have 454
RNASeq data that we wish to use in the re-annotation process.  I
constructed the maker_opts file and made the following modifications:

genome:cthe.fna #genome sequence file in fasta format
est: exampleEST.fasta #non-redundant set of assembled ESTs in fasta
format (classic EST analysis)
organism_type: prokaryotic #eukaryotic or prokaryotic. Default is eukaryotic
predictor: pred_gff #prediction methods for annotations (seperate
multiple values by ',')
pred_gff: prodigal.gff #ab-initio predictions from an external gff3 file

after running maker, I received the following errors:

indexing was interrupted, so unlinking
/home/gmod/Cthe/cthe.maker.output/mpi_blastdb/exampleEST.mpi.10/exampleEST.mpi.10.0.fasta.index
at /usr/local/share/perl/5.10.0/Bio/DB/Fasta.pm line 1053.

------------- EXCEPTION: Bio::Root::Exception -------------
MSG: Each line of the fasta entry must be the same length except the last.
    Line above #3 'GCTCAGCCGGGACGATGAGC..' is 61 != 8 chars.
STACK: Error::throw
STACK: Bio::Root::Root::throw /usr/local/share/perl/5.10.0/Bio/Root/Root.pm:368
STACK: Bio::DB::Fasta::calculate_offsets
/usr/local/share/perl/5.10.0/Bio/DB/Fasta.pm:770
STACK: Bio::DB::Fasta::index_file
/usr/local/share/perl/5.10.0/Bio/DB/Fasta.pm:680
STACK: Bio::DB::Fasta::new /usr/local/share/perl/5.10.0/Bio/DB/Fasta.pm:491
STACK: FastaDB::new /home/gmod/Documents/Software/maker/bin/../lib/FastaDB.pm:54
STACK: GI::build_fasta_index
/home/gmod/Documents/Software/maker/bin/../lib/GI.pm:1206
STACK: GI::build_all_indexes
/home/gmod/Documents/Software/maker/bin/../lib/GI.pm:1223
STACK: GI::load_control_files
/home/gmod/Documents/Software/maker/bin/../lib/GI.pm:3259
STACK: /home/gmod/Documents/Software/maker/bin/maker:240
-----------------------------------------------------------

FATAL ERROR

I have attached the exampleEST.fasta file...  Any ideas on why this happens?

Thanks so much
-Daniel
  

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Re: [maker-devel] Cthe EST pass error.

Carson Hinton Holt
In reply to this post by Daniel Quest
Re: [maker-devel] Cthe EST pass error. Hi Daniel,

I have some questions about your installation.  Your fasta file looks fine, so the error should not be happening, but is which makes me wonder about something else.

Are you using wublast, NCBI blast, or NCBI blast+?

Thanks,
Carson


On 5/18/10 9:21 AM, "Daniel Quest" <daniel.quest@...> wrote:

All,

I am attempting a re-annotation of Clostridium thermocellum ATCC 27405
as a proof of concept for using Maker.  This genome has many miscalled
genes and other errors and is important for bio-energy.  We have 454
RNASeq data that we wish to use in the re-annotation process.  I
constructed the maker_opts file and made the following modifications:

genome:cthe.fna #genome sequence file in fasta format
est: exampleEST.fasta #non-redundant set of assembled ESTs in fasta
format (classic EST analysis)
organism_type: prokaryotic #eukaryotic or prokaryotic. Default is eukaryotic
predictor: pred_gff #prediction methods for annotations (seperate
multiple values by ',')
pred_gff: prodigal.gff #ab-initio predictions from an external gff3 file

after running maker, I received the following errors:

indexing was interrupted, so unlinking
/home/gmod/Cthe/cthe.maker.output/mpi_blastdb/exampleEST.mpi.10/exampleEST.mpi.10.0.fasta.index
at /usr/local/share/perl/5.10.0/Bio/DB/Fasta.pm line 1053.

------------- EXCEPTION: Bio::Root::Exception -------------
MSG: Each line of the fasta entry must be the same length except the last.
    Line above #3 'GCTCAGCCGGGACGATGAGC..' is 61 != 8 chars.
STACK: Error::throw
STACK: Bio::Root::Root::throw /usr/local/share/perl/5.10.0/Bio/Root/Root.pm:368
STACK: Bio::DB::Fasta::calculate_offsets
/usr/local/share/perl/5.10.0/Bio/DB/Fasta.pm:770
STACK: Bio::DB::Fasta::index_file
/usr/local/share/perl/5.10.0/Bio/DB/Fasta.pm:680
STACK: Bio::DB::Fasta::new /usr/local/share/perl/5.10.0/Bio/DB/Fasta.pm:491
STACK: FastaDB::new /home/gmod/Documents/Software/maker/bin/../lib/FastaDB.pm:54
STACK: GI::build_fasta_index
/home/gmod/Documents/Software/maker/bin/../lib/GI.pm:1206
STACK: GI::build_all_indexes
/home/gmod/Documents/Software/maker/bin/../lib/GI.pm:1223
STACK: GI::load_control_files
/home/gmod/Documents/Software/maker/bin/../lib/GI.pm:3259
STACK: /home/gmod/Documents/Software/maker/bin/maker:240
-----------------------------------------------------------

FATAL ERROR

I have attached the exampleEST.fasta file...  Any ideas on why this happens?

Thanks so much
-Daniel


_______________________________________________
maker-devel mailing list
[hidden email]
http://box290.bluehost.com/mailman/listinfo/maker-devel_yandell-lab.org