Maker vs blast

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Maker vs blast

filipegoncalo
Hi,

I am trying to use Maker, but it is being quite complicated when it turns into blast usage. As far as i see maker is not running blast...
I've tested Maker using a small sample .fasta file, this is what i observe on the screen:

"
#---------------------------------------------------------------------
Now starting the contig!!
SeqID: gi|219944660|gb|CP001349.1|
Length: 1050
#---------------------------------------------------------------------


running  genemark.
#--------- command -------------#
Widget::genemark:
/usr/bin/perl /usr/local/maker/maker/bin/../lib/Widget/genemark/gmhmm_wrap -m /usr/local/maker/genemark_suite_linux/blast_hmm_heuristic.mod -g /usr/local/maker/genemark_suite_linux/gmhmmp -p /usr/local/maker/genemark_suite_linux/probuild -o /home/fgoncalo/Desktop/testeblast.maker.output/testeblast_datastore/F5/62/gi%7C219944660%7Cgb%7CCP001349.1%7C//theVoid.gi%7C219944660%7Cgb%7CCP001349.1%7C/gi%7C219944660%7Cgb%7CCP001349%2E1%7C.all.blast_hmm_heuristic%2Emod.genemark /home/fgoncalo/Desktop/testeblast.maker.output/testeblast_datastore/F5/62/gi%7C219944660%7Cgb%7CCP001349.1%7C//theVoid.gi%7C219944660%7Cgb%7CCP001349.1%7C/query.fasta
#-------------------------------#
cleaning blastn...
cleaning tblastx...
cleaning blastx...
Preparing evidence for hint based annotation
 in cluster:shadow cluster...
    i_size:0 j_size:0
 sorting hits in shadow cluster...
... finished.
 in cluster:shadow cluster...
    i_size:0 j_size:0
 sorting hits in shadow cluster...
... finished.
Processing transcripts into genes
Choosing best annotations


Maker is now finished!!!
"

My log file is:

"
SHARED_ID 58f036856a1c4773870dd4e5860fbbcb
CTL_OPTIONS genome_gff
CTL_OPTIONS other_gff
CTL_OPTIONS est
CTL_OPTIONS est_reads
CTL_OPTIONS altest
CTL_OPTIONS est_gff
CTL_OPTIONS altest_gff
CTL_OPTIONS protein
CTL_OPTIONS protein_gff
CTL_OPTIONS model_org
CTL_OPTIONS repeat_protein
CTL_OPTIONS rmlib
CTL_OPTIONS rm_gff
CTL_OPTIONS organism_type prokaryotic
CTL_OPTIONS predictor genemark
CTL_OPTIONS est2genome 0
CTL_OPTIONS snaphmm
CTL_OPTIONS gmhmm /usr/local/maker/genemark_suite_linux/blast_hmm_heuristic.mod
CTL_OPTIONS augustus_species
CTL_OPTIONS fgenesh_par_file
CTL_OPTIONS model_gff
CTL_OPTIONS pred_gff
CTL_OPTIONS max_dna_len 100000
CTL_OPTIONS split_hit 0
CTL_OPTIONS pred_flank 200
CTL_OPTIONS min_protein 0
CTL_OPTIONS AED_threshold 1
CTL_OPTIONS single_exon 1
CTL_OPTIONS single_length 250
CTL_OPTIONS keep_preds 0
CTL_OPTIONS map_forward 0
CTL_OPTIONS est_forward 0
CTL_OPTIONS alt_splice 0
CTL_OPTIONS always_complete 0
CTL_OPTIONS alt_peptide C
CTL_OPTIONS evaluate 0
CTL_OPTIONS blast_type ncbi
CTL_OPTIONS softmask 1
CTL_OPTIONS pcov_blastn 0.8
CTL_OPTIONS pid_blastn 0.85
CTL_OPTIONS eval_blastn 1e-10
CTL_OPTIONS bit_blastn 40
CTL_OPTIONS pcov_rm_blastx 0.5
CTL_OPTIONS pid_rm_blastx 0.4
CTL_OPTIONS eval_rm_blastx 1e-06
CTL_OPTIONS bit_rm_blastx 30
CTL_OPTIONS pcov_blastx 0.5
CTL_OPTIONS pid_blastx 0.4
CTL_OPTIONS eval_blastx 1e-06
CTL_OPTIONS bit_blastx 30
CTL_OPTIONS pcov_tblastx 0.8
CTL_OPTIONS pid_tblastx 0.85
CTL_OPTIONS eval_tblastx 1e-10
CTL_OPTIONS bit_tblastx 40
CTL_OPTIONS ep_score_limit 20
CTL_OPTIONS en_score_limit 20
CTL_OPTIONS enable_fathom 0
CTL_OPTIONS unmask 0
CTL_OPTIONS model_pass 0
CTL_OPTIONS est_pass 0
CTL_OPTIONS altest_pass 0
CTL_OPTIONS protein_pass 0
CTL_OPTIONS rm_pass 0
CTL_OPTIONS other_pass 0
CTL_OPTIONS pred_pass 0
CTL_OPTIONS run genemark
STARTED testeblast.maker.output/testeblast_datastore/F5/62/gi%7C219944660%7Cgb%7CCP001349.1%7C//theVoid.gi%7C219944660%7Cgb%7CCP001349.1%7C/gi%7C219944660%7Cgb%7CCP001349%2E1%7C.all.blast_hmm_heuristic%2Emod.genemark
FINISHED testeblast.maker.output/testeblast_datastore/F5/62/gi%7C219944660%7Cgb%7CCP001349.1%7C//theVoid.gi%7C219944660%7Cgb%7CCP001349.1%7C/gi%7C219944660%7Cgb%7CCP001349%2E1%7C.all.blast_hmm_heuristic%2Emod.genemark
"
Does anyone have any idea about what is going wrong?
Sorry for bothering,

My regards,
Filipe

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Re: Maker vs blast

Jason Stajich-4
Fid you define the protein= PROTEINFILE 

Which is the FASTA database for it to do the searches against?
I don't see it in your pasted logfile.

Could be something like this:
maker_opts.ctl:protein=swissprot.fa #protein sequence file in fasta format

On Jun 28, 2011, at 2:21 AM, Filipe Bregieiro wrote:

Hi,

I am trying to use Maker, but it is being quite complicated when it turns into blast usage. As far as i see maker is not running blast...
I've tested Maker using a small sample .fasta file, this is what i observe on the screen:

"
#---------------------------------------------------------------------
Now starting the contig!!
SeqID: gi|219944660|gb|CP001349.1|
Length: 1050
#---------------------------------------------------------------------


running  genemark.
#--------- command -------------#
Widget::genemark:
/usr/bin/perl /usr/local/maker/maker/bin/../lib/Widget/genemark/gmhmm_wrap -m /usr/local/maker/genemark_suite_linux/blast_hmm_heuristic.mod -g /usr/local/maker/genemark_suite_linux/gmhmmp -p /usr/local/maker/genemark_suite_linux/probuild -o /home/fgoncalo/Desktop/testeblast.maker.output/testeblast_datastore/F5/62/gi%7C219944660%7Cgb%7CCP001349.1%7C//theVoid.gi%7C219944660%7Cgb%7CCP001349.1%7C/gi%7C219944660%7Cgb%7CCP001349%2E1%7C.all.blast_hmm_heuristic%2Emod.genemark /home/fgoncalo/Desktop/testeblast.maker.output/testeblast_datastore/F5/62/gi%7C219944660%7Cgb%7CCP001349.1%7C//theVoid.gi%7C219944660%7Cgb%7CCP001349.1%7C/query.fasta
#-------------------------------#
cleaning blastn...
cleaning tblastx...
cleaning blastx...
Preparing evidence for hint based annotation
 in cluster:shadow cluster...
    i_size:0 j_size:0
 sorting hits in shadow cluster...
... finished.
 in cluster:shadow cluster...
    i_size:0 j_size:0
 sorting hits in shadow cluster...
... finished.
Processing transcripts into genes
Choosing best annotations


Maker is now finished!!!
"

My log file is:

"
SHARED_ID 58f036856a1c4773870dd4e5860fbbcb
CTL_OPTIONS genome_gff
CTL_OPTIONS other_gff
CTL_OPTIONS est
CTL_OPTIONS est_reads
CTL_OPTIONS altest
CTL_OPTIONS est_gff
CTL_OPTIONS altest_gff
CTL_OPTIONS protein
CTL_OPTIONS protein_gff
CTL_OPTIONS model_org
CTL_OPTIONS repeat_protein
CTL_OPTIONS rmlib
CTL_OPTIONS rm_gff
CTL_OPTIONS organism_type prokaryotic
CTL_OPTIONS predictor genemark
CTL_OPTIONS est2genome 0
CTL_OPTIONS snaphmm
CTL_OPTIONS gmhmm /usr/local/maker/genemark_suite_linux/blast_hmm_heuristic.mod
CTL_OPTIONS augustus_species
CTL_OPTIONS fgenesh_par_file
CTL_OPTIONS model_gff
CTL_OPTIONS pred_gff
CTL_OPTIONS max_dna_len 100000
CTL_OPTIONS split_hit 0
CTL_OPTIONS pred_flank 200
CTL_OPTIONS min_protein 0
CTL_OPTIONS AED_threshold 1
CTL_OPTIONS single_exon 1
CTL_OPTIONS single_length 250
CTL_OPTIONS keep_preds 0
CTL_OPTIONS map_forward 0
CTL_OPTIONS est_forward 0
CTL_OPTIONS alt_splice 0
CTL_OPTIONS always_complete 0
CTL_OPTIONS alt_peptide C
CTL_OPTIONS evaluate 0
CTL_OPTIONS blast_type ncbi
CTL_OPTIONS softmask 1
CTL_OPTIONS pcov_blastn 0.8
CTL_OPTIONS pid_blastn 0.85
CTL_OPTIONS eval_blastn 1e-10
CTL_OPTIONS bit_blastn 40
CTL_OPTIONS pcov_rm_blastx 0.5
CTL_OPTIONS pid_rm_blastx 0.4
CTL_OPTIONS eval_rm_blastx 1e-06
CTL_OPTIONS bit_rm_blastx 30
CTL_OPTIONS pcov_blastx 0.5
CTL_OPTIONS pid_blastx 0.4
CTL_OPTIONS eval_blastx 1e-06
CTL_OPTIONS bit_blastx 30
CTL_OPTIONS pcov_tblastx 0.8
CTL_OPTIONS pid_tblastx 0.85
CTL_OPTIONS eval_tblastx 1e-10
CTL_OPTIONS bit_tblastx 40
CTL_OPTIONS ep_score_limit 20
CTL_OPTIONS en_score_limit 20
CTL_OPTIONS enable_fathom 0
CTL_OPTIONS unmask 0
CTL_OPTIONS model_pass 0
CTL_OPTIONS est_pass 0
CTL_OPTIONS altest_pass 0
CTL_OPTIONS protein_pass 0
CTL_OPTIONS rm_pass 0
CTL_OPTIONS other_pass 0
CTL_OPTIONS pred_pass 0
CTL_OPTIONS run genemark
STARTED testeblast.maker.output/testeblast_datastore/F5/62/gi%7C219944660%7Cgb%7CCP001349.1%7C//theVoid.gi%7C219944660%7Cgb%7CCP001349.1%7C/gi%7C219944660%7Cgb%7CCP001349%2E1%7C.all.blast_hmm_heuristic%2Emod.genemark
FINISHED testeblast.maker.output/testeblast_datastore/F5/62/gi%7C219944660%7Cgb%7CCP001349.1%7C//theVoid.gi%7C219944660%7Cgb%7CCP001349.1%7C/gi%7C219944660%7Cgb%7CCP001349%2E1%7C.all.blast_hmm_heuristic%2Emod.genemark
"
Does anyone have any idea about what is going wrong?
Sorry for bothering,

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


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Re: Maker vs blast

Carson Hinton Holt
In reply to this post by filipegoncalo
Re: [maker-devel] Maker vs blast You. Likely have not provided an EST or protein fasta file.

--Carson


On 6/28/11 3:21 AM, "Filipe Bregieiro" <filipegoncalo.duarte@...> wrote:

Hi,

I am trying to use Maker, but it is being quite complicated when it turns into blast usage. As far as i see maker is not running blast...
I've tested Maker using a small sample .fasta file, this is what i observe on the screen:

"
#---------------------------------------------------------------------
Now starting the contig!!
SeqID: gi|219944660|gb|CP001349.1|
Length: 1050
#---------------------------------------------------------------------


running  genemark.
#--------- command -------------#
Widget::genemark:
/usr/bin/perl /usr/local/maker/maker/bin/../lib/Widget/genemark/gmhmm_wrap -m /usr/local/maker/genemark_suite_linux/blast_hmm_heuristic.mod -g /usr/local/maker/genemark_suite_linux/gmhmmp -p /usr/local/maker/genemark_suite_linux/probuild -o /home/fgoncalo/Desktop/testeblast.maker.output/testeblast_datastore/F5/62/gi%7C219944660%7Cgb%7CCP001349.1%7C//theVoid.gi%7C219944660%7Cgb%7CCP001349.1%7C/gi%7C219944660%7Cgb%7CCP001349%2E1%7C.all.blast_hmm_heuristic%2Emod.genemark /home/fgoncalo/Desktop/testeblast.maker.output/testeblast_datastore/F5/62/gi%7C219944660%7Cgb%7CCP001349.1%7C//theVoid.gi%7C219944660%7Cgb%7CCP001349.1%7C/query.fasta
#-------------------------------#
cleaning blastn...
cleaning tblastx...
cleaning blastx...
Preparing evidence for hint based annotation
 in cluster:shadow cluster...
    i_size:0 j_size:0
 sorting hits in shadow cluster...
... finished.
 in cluster:shadow cluster...
    i_size:0 j_size:0
 sorting hits in shadow cluster...
... finished.
Processing transcripts into genes
Choosing best annotations


Maker is now finished!!!
"

My log file is:

"
SHARED_ID 58f036856a1c4773870dd4e5860fbbcb
CTL_OPTIONS genome_gff
CTL_OPTIONS other_gff
CTL_OPTIONS est
CTL_OPTIONS est_reads
CTL_OPTIONS altest
CTL_OPTIONS est_gff
CTL_OPTIONS altest_gff
CTL_OPTIONS protein
CTL_OPTIONS protein_gff
CTL_OPTIONS model_org
CTL_OPTIONS repeat_protein
CTL_OPTIONS rmlib
CTL_OPTIONS rm_gff
CTL_OPTIONS organism_type prokaryotic
CTL_OPTIONS predictor genemark
CTL_OPTIONS est2genome 0
CTL_OPTIONS snaphmm
CTL_OPTIONS gmhmm /usr/local/maker/genemark_suite_linux/blast_hmm_heuristic.mod
CTL_OPTIONS augustus_species
CTL_OPTIONS fgenesh_par_file
CTL_OPTIONS model_gff
CTL_OPTIONS pred_gff
CTL_OPTIONS max_dna_len 100000
CTL_OPTIONS split_hit 0
CTL_OPTIONS pred_flank 200
CTL_OPTIONS min_protein 0
CTL_OPTIONS AED_threshold 1
CTL_OPTIONS single_exon 1
CTL_OPTIONS single_length 250
CTL_OPTIONS keep_preds 0
CTL_OPTIONS map_forward 0
CTL_OPTIONS est_forward 0
CTL_OPTIONS alt_splice 0
CTL_OPTIONS always_complete 0
CTL_OPTIONS alt_peptide C
CTL_OPTIONS evaluate 0
CTL_OPTIONS blast_type ncbi
CTL_OPTIONS softmask 1
CTL_OPTIONS pcov_blastn 0.8
CTL_OPTIONS pid_blastn 0.85
CTL_OPTIONS eval_blastn 1e-10
CTL_OPTIONS bit_blastn 40
CTL_OPTIONS pcov_rm_blastx 0.5
CTL_OPTIONS pid_rm_blastx 0.4
CTL_OPTIONS eval_rm_blastx 1e-06
CTL_OPTIONS bit_rm_blastx 30
CTL_OPTIONS pcov_blastx 0.5
CTL_OPTIONS pid_blastx 0.4
CTL_OPTIONS eval_blastx 1e-06
CTL_OPTIONS bit_blastx 30
CTL_OPTIONS pcov_tblastx 0.8
CTL_OPTIONS pid_tblastx 0.85
CTL_OPTIONS eval_tblastx 1e-10
CTL_OPTIONS bit_tblastx 40
CTL_OPTIONS ep_score_limit 20
CTL_OPTIONS en_score_limit 20
CTL_OPTIONS enable_fathom 0
CTL_OPTIONS unmask 0
CTL_OPTIONS model_pass 0
CTL_OPTIONS est_pass 0
CTL_OPTIONS altest_pass 0
CTL_OPTIONS protein_pass 0
CTL_OPTIONS rm_pass 0
CTL_OPTIONS other_pass 0
CTL_OPTIONS pred_pass 0
CTL_OPTIONS run genemark
STARTED testeblast.maker.output/testeblast_datastore/F5/62/gi%7C219944660%7Cgb%7CCP001349.1%7C//theVoid.gi%7C219944660%7Cgb%7CCP001349.1%7C/gi%7C219944660%7Cgb%7CCP001349%2E1%7C.all.blast_hmm_heuristic%2Emod.genemark
FINISHED testeblast.maker.output/testeblast_datastore/F5/62/gi%7C219944660%7Cgb%7CCP001349.1%7C//theVoid.gi%7C219944660%7Cgb%7CCP001349.1%7C/gi%7C219944660%7Cgb%7CCP001349%2E1%7C.all.blast_hmm_heuristic%2Emod.genemark
"
Does anyone have any idea about what is going wrong?
Sorry for bothering,

My regards,
Filipe


Carson Holt
Graduate Student
Yandell Lab
http:/www.yandell-lab.org/
Eccles Institute of Human Genetics
University of Utah

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