[maker-devel] maker-devel Digest, Vol 45, Issue 15

Fri Mar 2 00:26:51 MST 2012

Hi

About this problem I solve it removing ab-blast from the path. I'm now using ncbi+. Now I have another one. I read the articles on Maker to better understand the procedures. But I'm having some doubts. My data are:

EST from my organism J
genome sequence from organism A
EST from organism R (annotated)

My organism is closer to R than to A (but there isn't genome sequence for organism R). Should I run my EST against A or should I train maker with A and R and then use the result on my organism? If so, how can I do it? It isn't clear on your article.
Thanks for all your help.

Joana

-----Original Message-----
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Sent: terça-feira, 28 de Fevereiro de 2012 19:00
To: maker-devel at yandell-lab.org
Subject: maker-devel Digest, Vol 45, Issue 15

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Today's Topics:

   1. maker run error (Maria Joana F. B. A. Guimar?es)
   2. Re: maker run error (Carson Holt)

----------------------------------------------------------------------

Message: 1
Date: Tue, 28 Feb 2012 10:25:24 -0000
From: Maria Joana F. B. A. Guimar?es 	<joana.guimaraes at inrb.pt>
To: <maker-devel at yandell-lab.org>
Subject: [maker-devel] maker run error
Message-ID:
	<F5B5DE3EA7B4FD48A549687F860198325F5483 at INRBMSMXBE.INRB.PT>
Content-Type: text/plain; charset="iso-8859-1"

Hi 

I managed to install MAKER and everything looks OK. I'm trying to run maker with the examples but it keeps giving me this error:

bioinf at linux-hdoc:~/Desktop/TEMP> maker

STATUS: Parsing control files...

STATUS: Processing and indexing input FASTA files...

STATUS: Setting up database for any GFF3 input...

A data structure will be created for you at:

/home/bioinf/Desktop/TEMP/dpp_contig.maker.output/dpp_contig_datastore

To access files for individual sequences use the datastore index:

/home/bioinf/Desktop/TEMP/dpp_contig.maker.output/dpp_contig_master_datastore_index.log

STATUS: Now running MAKER...

--Next Contig--

#---------------------------------------------------------------------

Now starting the contig!!

SeqID: contig-dpp-500-500

Length: 32156

#---------------------------------------------------------------------

running  repeat masker.

#--------- command -------------#

Widget::RepeatMasker:

cd /tmp/maker_eiYoLm; /home/bioinf/maker/exe/RepeatMasker/RepeatMasker /home/bioinf/Desktop/TEMP/dpp_contig.maker.output/dpp_contig_datastore/05/1F/contig-dpp-500-500//theVoid.contig-dpp-500-500/contig-dpp-500-500.0.all.rb -species all -dir /home/bioinf/Desktop/TEMP/dpp_contig.maker.output/dpp_contig_datastore/05/1F/contig-dpp-500-500//theVoid.contig-dpp-500-500 -pa 1

#-------------------------------#

processing output: 

cycle 1 

cycle 2 

cycle 3 

cycle 4 

cycle 5 

cycle 6 

cycle 7 

cycle 8 

cycle 9 

cycle 10 

Generating output... 

masking

done

formating database...

#--------- command -------------#

Widget::formater:

/home/bioinf/maker/bin/../exe/blast/bin/makeblastdb -dbtype prot -in /tmp/maker_eiYoLm/te_proteins%2Efasta.mpi.10.0

#-------------------------------#

running  blast search.

#--------- command -------------#

Widget::blastx:

/home/bioinf/maker/bin/../exe/ab-blast/blastx -db /tmp/maker_eiYoLm/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_eiYoLm/rank0/contig-dpp-500-500.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/bioinf/Desktop/TEMP/dpp_contig.maker.output/dpp_contig_datastore/05/1F/contig-dpp-500-500//theVoid.contig-dpp-500-500/contig-dpp-500-500.0.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner

#-------------------------------#

FATAL:  Argument 1 ("-db") is not recognized or is improperly formed.

EXIT CODE 5

FATAL:  Argument 1 ("-db") is not recognized or is improperly formed.

EXIT CODE 5

ERROR: BLASTX failed

ERROR: Failed while doing blastx repeats

ERROR: Chunk failed at level:1, tier_type:1

FAILED CONTIG:contig-dpp-500-500

ERROR: Chunk failed at level:2, tier_type:0

FAILED CONTIG:contig-dpp-500-500

--Next Contig--

Processing run.log file...

MAKER WARNING: The file dpp_contig.maker.output/dpp_contig_datastore/05/1F/contig-dpp-500-500//theVoid.contig-dpp-500-500/contig-dpp-500-500.0.te_proteins%2Efasta.repeatrunner

did not finish on the last run and must be erased

#---------------------------------------------------------------------

Now retrying the contig!!

SeqID: contig-dpp-500-500

Length: 32156

Tries: 2!!

#---------------------------------------------------------------------

re reading repeat masker report.

/home/bioinf/Desktop/TEMP/dpp_contig.maker.output/dpp_contig_datastore/05/1F/contig-dpp-500-500//theVoid.contig-dpp-500-500/contig-dpp-500-500.0.all.rb.out

running  blast search.

#--------- command -------------#

Widget::blastx:

/home/bioinf/maker/bin/../exe/ab-blast/blastx -db /tmp/maker_eiYoLm/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_eiYoLm/rank0/contig-dpp-500-500.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/bioinf/Desktop/TEMP/dpp_contig.maker.output/dpp_contig_datastore/05/1F/contig-dpp-500-500//theVoid.contig-dpp-500-500/contig-dpp-500-500.0.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner

#-------------------------------#

FATAL:  Argument 1 ("-db") is not recognized or is improperly formed.

EXIT CODE 5

FATAL:  Argument 1 ("-db") is not recognized or is improperly formed.

EXIT CODE 5

ERROR: BLASTX failed

ERROR: Failed while doing blastx repeats

ERROR: Chunk failed at level:1, tier_type:1

FAILED CONTIG:contig-dpp-500-500

ERROR: Chunk failed at level:2, tier_type:0

FAILED CONTIG:contig-dpp-500-500

--Next Contig--

Processing run.log file...

MAKER WARNING: The file dpp_contig.maker.output/dpp_contig_datastore/05/1F/contig-dpp-500-500//theVoid.contig-dpp-500-500/contig-dpp-500-500.0.te_proteins%2Efasta.repeatrunner

did not finish on the last run and must be erased

Maker is now finished!!!

bioinf at linux-hdoc:~/Desktop/TEMP> 

Can you please help me?
Thanks

Joana
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Message: 2
Date: Tue, 28 Feb 2012 07:48:09 -0500
From: Carson Holt <carsonhh at gmail.com>
To: "Maria Joana F. B. A. =?ISO-8859-1?B?R3VpbWFy42Vz?="
	<joana.guimaraes at inrb.pt>, <maker-devel at yandell-lab.org>
Subject: Re: [maker-devel] maker run error
Message-ID: <CB7236CE.88F9%carsonhh at gmail.com>
Content-Type: text/plain; charset="iso-8859-1"

You're using ABBlast.  MAKER doesn't support it yet.  Maybe now would be a
good time to do it though.  It would take about 10 hours to implement and
test.  I could probably look into it this weekend.

Thanks,
Carson

From:  "Maria Joana F. B. A. Guimar?es" <joana.guimaraes at inrb.pt>
Date:  Tue, 28 Feb 2012 10:25:24 -0000
To:  <maker-devel at yandell-lab.org>
Subject:  [maker-devel] maker run error

maker run error
Hi

I managed to install MAKER and everything looks OK. I'm trying to run maker
with the examples but it keeps giving me this error:

bioinf at linux-hdoc:~/Desktop/TEMP> maker

STATUS: Parsing control files...

STATUS: Processing and indexing input FASTA files...

STATUS: Setting up database for any GFF3 input...

A data structure will be created for you at:

/home/bioinf/Desktop/TEMP/dpp_contig.maker.output/dpp_contig_datastore

To access files for individual sequences use the datastore index:

/home/bioinf/Desktop/TEMP/dpp_contig.maker.output/dpp_contig_master_datastor
e_index.log

STATUS: Now running MAKER...

--Next Contig--

#---------------------------------------------------------------------

Now starting the contig!!

SeqID: contig-dpp-500-500

Length: 32156

#---------------------------------------------------------------------

running  repeat masker.

#--------- command -------------#

Widget::RepeatMasker:

cd /tmp/maker_eiYoLm; /home/bioinf/maker/exe/RepeatMasker/RepeatMasker
/home/bioinf/Desktop/TEMP/dpp_contig.maker.output/dpp_contig_datastore/05/1F
/contig-dpp-500-500//theVoid.contig-dpp-500-500/contig-dpp-500-500.0.all.rb
-species all -dir 
/home/bioinf/Desktop/TEMP/dpp_contig.maker.output/dpp_contig_datastore/05/1F
/contig-dpp-500-500//theVoid.contig-dpp-500-500 -pa 1

#-------------------------------#

processing output:

cycle 1

cycle 2

cycle 3

cycle 4

cycle 5

cycle 6

cycle 7

cycle 8

cycle 9

cycle 10

Generating output...

masking

done

formating database...

#--------- command -------------#

Widget::formater:

/home/bioinf/maker/bin/../exe/blast/bin/makeblastdb -dbtype prot -in
/tmp/maker_eiYoLm/te_proteins%2Efasta.mpi.10.0

#-------------------------------#

running  blast search.

#--------- command -------------#

Widget::blastx:

/home/bioinf/maker/bin/../exe/ab-blast/blastx -db
/tmp/maker_eiYoLm/te_proteins%2Efasta.mpi.10.0 -query
/tmp/maker_eiYoLm/rank0/contig-dpp-500-500.0 -num_alignments 10000
-num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000
-num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out
/home/bioinf/Desktop/TEMP/dpp_contig.maker.output/dpp_contig_datastore/05/1F
/contig-dpp-500-500//theVoid.contig-dpp-500-500/contig-dpp-500-500.0.te_prot
eins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner

#-------------------------------#

FATAL:  Argument 1 ("-db") is not recognized or is improperly formed.

EXIT CODE 5

FATAL:  Argument 1 ("-db") is not recognized or is improperly formed.

EXIT CODE 5

ERROR: BLASTX failed

ERROR: Failed while doing blastx repeats

ERROR: Chunk failed at level:1, tier_type:1

FAILED CONTIG:contig-dpp-500-500

ERROR: Chunk failed at level:2, tier_type:0

FAILED CONTIG:contig-dpp-500-500

--Next Contig--

Processing run.log file...

MAKER WARNING: The file
dpp_contig.maker.output/dpp_contig_datastore/05/1F/contig-dpp-500-500//theVo
id.contig-dpp-500-500/contig-dpp-500-500.0.te_proteins%2Efasta.repeatrunner

did not finish on the last run and must be erased

#---------------------------------------------------------------------

Now retrying the contig!!

SeqID: contig-dpp-500-500

Length: 32156

Tries: 2!!

#---------------------------------------------------------------------

re reading repeat masker report.

/home/bioinf/Desktop/TEMP/dpp_contig.maker.output/dpp_contig_datastore/05/1F
/contig-dpp-500-500//theVoid.contig-dpp-500-500/contig-dpp-500-500.0.all.rb.
out

running  blast search.

#--------- command -------------#

Widget::blastx:

/home/bioinf/maker/bin/../exe/ab-blast/blastx -db
/tmp/maker_eiYoLm/te_proteins%2Efasta.mpi.10.0 -query
/tmp/maker_eiYoLm/rank0/contig-dpp-500-500.0 -num_alignments 10000
-num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000
-num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out
/home/bioinf/Desktop/TEMP/dpp_contig.maker.output/dpp_contig_datastore/05/1F
/contig-dpp-500-500//theVoid.contig-dpp-500-500/contig-dpp-500-500.0.te_prot
eins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner

#-------------------------------#

FATAL:  Argument 1 ("-db") is not recognized or is improperly formed.

EXIT CODE 5

FATAL:  Argument 1 ("-db") is not recognized or is improperly formed.

EXIT CODE 5

ERROR: BLASTX failed

ERROR: Failed while doing blastx repeats

ERROR: Chunk failed at level:1, tier_type:1

FAILED CONTIG:contig-dpp-500-500

ERROR: Chunk failed at level:2, tier_type:0

FAILED CONTIG:contig-dpp-500-500

--Next Contig--

Processing run.log file...

MAKER WARNING: The file
dpp_contig.maker.output/dpp_contig_datastore/05/1F/contig-dpp-500-500//theVo
id.contig-dpp-500-500/contig-dpp-500-500.0.te_proteins%2Efasta.repeatrunner

did not finish on the last run and must be erased

Maker is now finished!!!

bioinf at linux-hdoc:~/Desktop/TEMP>

Can you please help me?
Thanks

Joana
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