From ianmisner at my.uri.edu  Thu Mar  1 16:25:06 2012
From: ianmisner at my.uri.edu (Ian Misner)
Date: Thu, 1 Mar 2012 17:25:06 -0500
Subject: [maker-devel] Rerunning Maker
Message-ID: <13A73C28-9CEF-4416-911E-2ACEE445533A@my.uri.edu>

Hello,

I have run maker 2.03 on a genome that we assembled a while back.  Now we have a new genome assembly.  Is there a way to rerun maker with the new assembly without losing all of the annotations I've done on the v2.03 predicted proteins?  I see the genome_gff option but all the contig numbers will have changed with the new assembly so that will not work.  The EST data will be the same as before.  From my original run I used a related species for protein homology, this time would I use the predicted set I have been working with?  Worst case scenario I need a way to link the old proteins with the new ones which I could do with BLAST post Maker but I'm hoping there is a better way.  Any help with this would be greatly appreciated.  


Cheers
Ian

*************************************
Mr. Ian Misner
PhD. Candidate
Department of Biological Sciences
University of Rhode Island
120 Flagg Road
Kingston, RI 02881
Office: CBLS 260
Ph: 1-401-874-9726
fax (401) 874-2065
ianmisner at my.uri.edu
http://cels.uri.edu/bio/lanelab/  










From joana.guimaraes at inrb.pt  Fri Mar  2 01:26:51 2012
From: joana.guimaraes at inrb.pt (=?iso-8859-1?Q?Maria_Joana_F=2E_B=2E_A=2E_Guimar=E3es?=)
Date: Fri, 2 Mar 2012 07:26:51 -0000
Subject: [maker-devel] maker-devel Digest, Vol 45, Issue 15
In-Reply-To: <mailman.3.1330455604.20855.maker-devel_yandell-lab.org@box290.bluehost.com>
References: <mailman.3.1330455604.20855.maker-devel_yandell-lab.org@box290.bluehost.com>
Message-ID: <F5B5DE3EA7B4FD48A549687F860198320100510E@INRBMSMXBE.INRB.PT>

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-----
From: maker-devel-bounces at yandell-lab.org [mailto:maker-devel-bounces at yandell-lab.org] On Behalf Of maker-devel-request at yandell-lab.org
Sent: ter?a-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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End of maker-devel Digest, Vol 45, Issue 15
*******************************************



From carsonhh at gmail.com  Fri Mar  2 09:39:47 2012
From: carsonhh at gmail.com (Carson Holt)
Date: Fri, 02 Mar 2012 10:39:47 -0500
Subject: [maker-devel] Rerunning Maker
In-Reply-To: <13A73C28-9CEF-4416-911E-2ACEE445533A@my.uri.edu>
Message-ID: <CB764CB4.8AF8%carsonhh@gmail.com>

There is a way to do this and it sounds harder than it really is.

Previously there was a tool that came with MAKER called map2assembly that
is no longer included with the distribution (certain changes to the MAKER
libraries broke it beyond repair).  The replacement for this tool is still
somewhat under development, so is not documented but is included with the
distribution and works far better (and faster) than map2assembly.

The new tool is internal to MAKER and called by setting several flags in
the control files before running a regular MAKER job.

To map genes forward do this:
1. Supply your old transcript file to the est= option in MAKER.
2. Set est2genome=1
3. Set single_exon=1
4. Set single_length=1
5. Turn all repeat masking options off (either delete values in control
files or use -R flag on the command line)
6. Set est_forward=1 (this is not in the maker_opts.ctl file.  You will
have to add it manually.
7. Don't run any gene predictors and don't provide any other evidence
files (we only want MAKER to map things forward)
8. Now run MAKER (remember to supply the -R flag from the command line if
you didn't delete masking options from thew control files)

MAKER will now map the old gene models to the new assembly (with names)
generating a new GFF3 file that can be used as input to future MAKER runs.

Some things to know about the process.  You can set the minimum accepted
coverage and identity to use when mapping the genes forward using the
blastn filters in the maker_bopts.ctl file.  Some genes may not map
forward and will be lost.  Some will map to multiple locations, so review
your GFF3 results file.  Also the est_forward option accepts hints via a
tag (maker_coor=) in the fasta headers.  For example, if you add the
following flag to fasta headers for the input transcript file -->
	>gene1-RA  maker_coor=chr1;
Then MAKER will only try and map that transcript to the new genomes contig
labelled chr1.  Or you can do -->
	>gene1-RA  maker_coor=chr1:2000-200000;
Then MAKER will restrict the alignment to somewhere within a given region
(could be the first half of the chromosome for example).


In future releases of MAKER, everything will be simplified.  The
est_forward will always be in the control files and will accept a file
name.  MAKER will then do all the work upstream including setting flags
and sorting out multiple location alignments as part of it's normal run
(not as an independent run as is done in what I described).

Thanks,
Carson


On 12-03-01 5:25 PM, "Ian Misner" <ianmisner at my.uri.edu> wrote:

>Hello,
>
>I have run maker 2.03 on a genome that we assembled a while back.  Now we
>have a new genome assembly.  Is there a way to rerun maker with the new
>assembly without losing all of the annotations I've done on the v2.03
>predicted proteins?  I see the genome_gff option but all the contig
>numbers will have changed with the new assembly so that will not work.
>The EST data will be the same as before.  From my original run I used a
>related species for protein homology, this time would I use the predicted
>set I have been working with?  Worst case scenario I need a way to link
>the old proteins with the new ones which I could do with BLAST post Maker
>but I'm hoping there is a better way.  Any help with this would be
>greatly appreciated.
>
>
>Cheers
>Ian
>
>*************************************
>Mr. Ian Misner
>PhD. Candidate
>Department of Biological Sciences
>University of Rhode Island
>120 Flagg Road
>Kingston, RI 02881
>Office: CBLS 260
>Ph: 1-401-874-9726
>fax (401) 874-2065
>ianmisner at my.uri.edu
>http://cels.uri.edu/bio/lanelab/
>
>
>
>
>
>
>
>
>_______________________________________________
>maker-devel mailing list
>maker-devel at box290.bluehost.com
>http://box290.bluehost.com/mailman/listinfo/maker-devel_yandell-lab.org





From carsonhh at gmail.com  Fri Mar  2 10:05:49 2012
From: carsonhh at gmail.com (Carson Holt)
Date: Fri, 02 Mar 2012 11:05:49 -0500
Subject: [maker-devel] maker-devel Digest, Vol 45, Issue 15
In-Reply-To: <F5B5DE3EA7B4FD48A549687F860198320100510E@INRBMSMXBE.INRB.PT>
Message-ID: <CB76559D.8B38%carsonhh@gmail.com>

There is more than one way to train your predictors.  If you have protein
sequence, you can run MAKER with the protein2genome=1 option set which
will generate preliminary gene models based on protein homology alone, and
those results can be used to train SNAP and augustus.  You can also train
SNAP independently using CEGMA - a program from the same group as SNAP.
It finds a small set of core genes that should be in all eukaryotic
genomes.

For me this is more of a question of speed.  Using ESTs that are not from
the same organism has caveats.  If the organisms are very closely related
(example: chimp and human), you can do a direct alignment in nucleotide
space.  But if they are not (example: human and mouse), you can use
MAKER's alt_est option and MAKER will align in translated space using
TBLASTX.  TBLASTX is mind numbingly slow, taking about 20x longer than a
direct EST alignment, and should be avoided when possible.

So to summarize, if you have ESTs from your organism, use those first.  If
not, then use proteins. Finally use alternate organism ESTs if that's all
you have. Of course you can also supply all three, but I normally only do
that for the final run.  I limit the dataset for the training rounds.

After using MAKER's results for training SNAP/augustus etc., just supply
MAKER with the resulting training HMM and run again in the same directory.
 Why in the same directory?  So that you can keep the evidence files you
used on the first run.  MAKER will see that the only thing that changed
was the HMM (so it won't have to rerun any of the alignments).  It will
just add the predictions, interpret them in light of the evidence, and
produce new output.  So the first run is slow, and the second is fast
(because MAKER takes advantage of archived BLAST, RepeatMasker, and
Exonerate results).

Thanks,
Carson



On 12-03-02 2:26 AM, "Maria Joana F. B. A. Guimar?es"
<joana.guimaraes at inrb.pt> wrote:

>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-----
>From: maker-devel-bounces at yandell-lab.org
>[mailto:maker-devel-bounces at yandell-lab.org] On Behalf Of
>maker-devel-request at yandell-lab.org
>Sent: ter?a-feira, 28 de Fevereiro de 2012 19:00
>To: maker-devel at yandell-lab.org
>Subject: maker-devel Digest, Vol 45, Issue 15
>
>Send maker-devel mailing list submissions to
>	maker-devel at yandell-lab.org
>
>To subscribe or unsubscribe via the World Wide Web, visit
>	http://box290.bluehost.com/mailman/listinfo/maker-devel_yandell-lab.org
>
>or, via email, send a message with subject or body 'help' to
>	maker-devel-request at yandell-lab.org
>
>You can reach the person managing the list at
>	maker-devel-owner at yandell-lab.org
>
>When replying, please edit your Subject line so it is more specific
>than "Re: Contents of maker-devel digest..."
>
>
>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_datast
>ore_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.repeat
>runner
>
>#-------------------------------#
>
>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//the
>Void.contig-dpp-500-500/contig-dpp-500-500.0.te_proteins%2Efasta.repeatrun
>ner
>
>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.repeat
>runner
>
>#-------------------------------#
>
>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//the
>Void.contig-dpp-500-500/contig-dpp-500-500.0.te_proteins%2Efasta.repeatrun
>ner
>
>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
>-------------- next part --------------
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><http://box290.bluehost.com/pipermail/maker-devel_yandell-lab.org/attachme
>nts/20120228/8e6a3106/attachment-0001.html>
>
>------------------------------
>
>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_datast
>or
>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.r
>b
>-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_pr
>ot
>eins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunn
>er
>
>#-------------------------------#
>
>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//the
>Vo
>id.contig-dpp-500-500/contig-dpp-500-500.0.te_proteins%2Efasta.repeatrunne
>r
>
>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.r
>b.
>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_pr
>ot
>eins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunn
>er
>
>#-------------------------------#
>
>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//the
>Vo
>id.contig-dpp-500-500/contig-dpp-500-500.0.te_proteins%2Efasta.repeatrunne
>r
>
>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
>_______________________________________________ maker-devel mailing list
>maker-devel at box290.bluehost.com
>http://box290.bluehost.com/mailman/listinfo/maker-devel_yandell-lab.org
>
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>
>------------------------------
>
>_______________________________________________
>maker-devel mailing list
>maker-devel at box290.bluehost.com
>http://box290.bluehost.com/mailman/listinfo/maker-devel_yandell-lab.org
>
>
>End of maker-devel Digest, Vol 45, Issue 15
>*******************************************
>
>_______________________________________________
>maker-devel mailing list
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>http://box290.bluehost.com/mailman/listinfo/maker-devel_yandell-lab.org





From njauxiongjie at gmail.com  Fri Mar  2 20:38:50 2012
From: njauxiongjie at gmail.com (Jie)
Date: Fri, 2 Mar 2012 18:38:50 -0800 (PST)
Subject: [maker-devel] question about augustus hints file
Message-ID: <078f6ced-b08d-4a1e-8fe4-c63a2ac68392@qr9g2000pbc.googlegroups.com>

Hi, all

I have aligned my EST to my genome and want to use the EST alignment
as hints of augustus. The command I run like your README file in
AUGUSTUS, and like bellow:

blat -minIdentity=92 genome.fa cdna.fa cdna.psl
blat2hints.pl --in=cdna.psl --out=hints.E.gff

but when I feed the hint file to augustus, it appeared some error like
bellow:
augustus: ERROR        FeatureCollection::esource: invalid source key:
E

How can I solve this problem?



From thomas.hackl at uni-wuerzburg.de  Wed Mar  7 02:31:39 2012
From: thomas.hackl at uni-wuerzburg.de (Thomas Hackl)
Date: Wed, 07 Mar 2012 09:31:39 +0100
Subject: [maker-devel] maker 2.22/2.23: Segmentation fault while processing
	FASTA input
Message-ID: <4F571CEB.7070707@uni-wuerzburg.de>

Hello,

we want to use a current release of maker (2.22, 2.23) but the program 
terminates with a seg fault while processing the input FASTA files. 
maker 2.15 , which we have been using for quite some time, runs 
perfectly with identical data and setup.

Please contact me if you need specifics on hardware, OS or anything else.

Best regards
Thomas

-- 
Thomas Hackl
Julius-Maximilians-Universit?t
Department of Bioinformatics
97074 W?rzburg, Germany
Fon:  +49 931 - 31 86883
Mail: thomas.hackl at uni-wuerzburg.de




From Carson.Holt at oicr.on.ca  Wed Mar  7 16:45:06 2012
From: Carson.Holt at oicr.on.ca (Carson Holt)
Date: Wed, 7 Mar 2012 22:45:06 +0000
Subject: [maker-devel] maker 2.22/2.23: Segmentation fault while
 processing FASTA input
In-Reply-To: <4F571CEB.7070707@uni-wuerzburg.de>
Message-ID: <CB7D4D49.8FCD%carson.holt@oicr.on.ca>

There should be no new hardware requirement.  But there is always a chance
that there is an issue with one of the perl modules being used.  I assume
the failure is happening when using maker serially and you are not using
MPI.

Could you reinstall the following perl modules, and try again.  If you are
using CPAN, do a 'force install' to force it to reinstall.

Modules:
*Storable
*Inline::C
*forks
*forks::shared

Also try reinstalling the latest version of BioPerl.

The fact that this is a seg fault suggests that something is happemning at
the C level (just outside of Perl).  Those area all the modules MAKER uses
that will call back to the C level.  BioPerl has a fasta indexing module
that is also making calls outside of Perl, and the fact it fails at that
point makes it a suspect.

Let me know what happens.  I can always generate an alternate MAKER
executable for you to run with additional status messages that may help
identify exactly which module is being called right before the failure.

Thanks,
Carson



On 12-03-07 3:31 AM, "Thomas Hackl" <thomas.hackl at uni-wuerzburg.de> wrote:

>Hello,
>
>we want to use a current release of maker (2.22, 2.23) but the program
>terminates with a seg fault while processing the input FASTA files.
>maker 2.15 , which we have been using for quite some time, runs
>perfectly with identical data and setup.
>
>Please contact me if you need specifics on hardware, OS or anything else.
>
>Best regards
>Thomas
>
>-- 
>Thomas Hackl
>Julius-Maximilians-Universit?t
>Department of Bioinformatics
>97074 W?rzburg, Germany
>Fon:  +49 931 - 31 86883
>Mail: thomas.hackl at uni-wuerzburg.de
>
>
>_______________________________________________
>maker-devel mailing list
>maker-devel at box290.bluehost.com
>http://box290.bluehost.com/mailman/listinfo/maker-devel_yandell-lab.org




From ianmisner at my.uri.edu  Thu Mar  8 08:15:05 2012
From: ianmisner at my.uri.edu (Ian Misner)
Date: Thu, 8 Mar 2012 09:15:05 -0500
Subject: [maker-devel] Error: Chunk failed at level
Message-ID: <6F68BCEE-BD5B-4059-BA87-188BA8585105@my.uri.edu>

Hello,

I've run maker with RM, SNAP, and gmhmm on my novel genome and I've some very large contigs that haven't annotated any proteins.  I have looked through the output from the run and of the 74 contigs that failed I only have three errors.

They are Chunk failed at level 3, 8, & 16

What are those errors?  How can I get the annotations for these failed runs to work?  I have the entire output if you would need to see that file.  In my opts ctl file I set it to retry failed contigs 2 times and do a fresh run each time.  All 74 contigs failed all 3 attempts to run.  Any help would be much appreciated.

Cheers
Ian


*************************************
Mr. Ian Misner
PhD. Candidate
Department of Biological Sciences
University of Rhode Island
120 Flagg Road
Kingston, RI 02881
Office: CBLS 260
Ph: 1-401-874-9726
fax (401) 874-2065
ianmisner at my.uri.edu
http://cels.uri.edu/bio/lanelab/  










From jason.stajich at gmail.com  Thu Mar  8 19:58:32 2012
From: jason.stajich at gmail.com (Jason Stajich)
Date: Thu, 8 Mar 2012 17:58:32 -0800
Subject: [maker-devel] Error: Chunk failed at level
In-Reply-To: <6F68BCEE-BD5B-4059-BA87-188BA8585105@my.uri.edu>
References: <6F68BCEE-BD5B-4059-BA87-188BA8585105@my.uri.edu>
Message-ID: <8CA12776-E69F-4868-B9CE-278062F83D32@gmail.com>

Hi Ian - 

Do you get any gene models if you run RM or SNAP on these directly?  I can't tell if this means there is no overlap between your different prediction sets or if you didn't get ab initio predictions?

Jason
On Mar 8, 2012, at 6:15 AM, Ian Misner wrote:

> Hello,
> 
> I've run maker with RM, SNAP, and gmhmm on my novel genome and I've some very large contigs that haven't annotated any proteins.  I have looked through the output from the run and of the 74 contigs that failed I only have three errors.
> 
> They are Chunk failed at level 3, 8, & 16
> 
> What are those errors?  How can I get the annotations for these failed runs to work?  I have the entire output if you would need to see that file.  In my opts ctl file I set it to retry failed contigs 2 times and do a fresh run each time.  All 74 contigs failed all 3 attempts to run.  Any help would be much appreciated.
> 
> Cheers
> Ian
> 
> 
> *************************************
> Mr. Ian Misner
> PhD. Candidate
> Department of Biological Sciences
> University of Rhode Island
> 120 Flagg Road
> Kingston, RI 02881
> Office: CBLS 260
> Ph: 1-401-874-9726
> fax (401) 874-2065
> ianmisner at my.uri.edu
> http://cels.uri.edu/bio/lanelab/  
> 
> 
> 
> 
> 
> 
> 
> 
> _______________________________________________
> maker-devel mailing list
> maker-devel at box290.bluehost.com
> http://box290.bluehost.com/mailman/listinfo/maker-devel_yandell-lab.org

Jason Stajich
jason.stajich at gmail.com
jason at bioperl.org

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From carsonhh at gmail.com  Fri Mar  9 13:02:58 2012
From: carsonhh at gmail.com (Carson Holt)
Date: Fri, 09 Mar 2012 14:02:58 -0500
Subject: [maker-devel] Error: Chunk failed at level
In-Reply-To: <6F68BCEE-BD5B-4059-BA87-188BA8585105@my.uri.edu>
Message-ID: <CB7FBDE5.90EB%carsonhh@gmail.com>

Those are the very last messages in a series of error handlers.  Look
further up the report, the errors triggering the handler should be further
back.  If your'e running parallel,  the other errors may be way back up
the report.  Also which version of MAKER are you using?

You can send my any failed contigs, the maker control files and any other
datasets/files you are using if you want me to take a look as well.

Thanks,
Carson



On 12-03-08 9:15 AM, "Ian Misner" <ianmisner at my.uri.edu> wrote:

>Hello,
>
>I've run maker with RM, SNAP, and gmhmm on my novel genome and I've some
>very large contigs that haven't annotated any proteins.  I have looked
>through the output from the run and of the 74 contigs that failed I only
>have three errors.
>
>They are Chunk failed at level 3, 8, & 16
>
>What are those errors?  How can I get the annotations for these failed
>runs to work?  I have the entire output if you would need to see that
>file.  In my opts ctl file I set it to retry failed contigs 2 times and
>do a fresh run each time.  All 74 contigs failed all 3 attempts to run.
>Any help would be much appreciated.
>
>Cheers
>Ian
>
>
>*************************************
>Mr. Ian Misner
>PhD. Candidate
>Department of Biological Sciences
>University of Rhode Island
>120 Flagg Road
>Kingston, RI 02881
>Office: CBLS 260
>Ph: 1-401-874-9726
>fax (401) 874-2065
>ianmisner at my.uri.edu
>http://cels.uri.edu/bio/lanelab/
>
>
>
>
>
>
>
>
>_______________________________________________
>maker-devel mailing list
>maker-devel at box290.bluehost.com
>http://box290.bluehost.com/mailman/listinfo/maker-devel_yandell-lab.org





From thomas.hackl at uni-wuerzburg.de  Tue Mar 13 04:41:40 2012
From: thomas.hackl at uni-wuerzburg.de (Thomas Hackl)
Date: Tue, 13 Mar 2012 10:41:40 +0100
Subject: [maker-devel] maker 2.22/2.23: Segmentation fault while
 processing FASTA input
In-Reply-To: <CB7D4D49.8FCD%carson.holt@oicr.on.ca>
References: <CB7D4D49.8FCD%carson.holt@oicr.on.ca>
Message-ID: <4F5F1654.1060100@uni-wuerzburg.de>

Hello,

We reinstalled the packages you suggested

forks is up to date (0.34).
forks::shared is up to date (0.34).
Inline::C is up to date (0.50).
Storable is up to date (2.30).

as well as BioPerl.

The problem is still the same.

With MPI it terminates with this message:

STATUS: Parsing control files...
STATUS: Processing and indexing input FASTA files...
===================================================================================== 


=   BAD TERMINATION OF ONE OF YOUR APPLICATION PROCESSES
=   EXIT CODE: 11
=   CLEANING UP REMAINING PROCESSES
=   YOU CAN IGNORE THE BELOW CLEANUP MESSAGES
===================================================================================== 

APPLICATION TERMINATED WITH THE EXIT STRING: Segmentation fault (signal 11)

which I presume is also the same problem.

I am with you that the error is caused somewhere on the C level. If the 
indexing step
is handled by non-maker modules exclusively, than the fact that the 2.15 
version works,
suggests that you are using different modules/methods in the current 
releases?

In any case, I think a version with verbose status messages might help 
to localize the
source of the problem.

Regards
Thomas

Am 07.03.2012 23:45, schrieb Carson Holt:
> There should be no new hardware requirement.  But there is always a chance
> that there is an issue with one of the perl modules being used.  I assume
> the failure is happening when using maker serially and you are not using
> MPI.
>
> Could you reinstall the following perl modules, and try again.  If you are
> using CPAN, do a 'force install' to force it to reinstall.
>
> Modules:
> *Storable
> *Inline::C
> *forks
> *forks::shared
>
> Also try reinstalling the latest version of BioPerl.
>
> The fact that this is a seg fault suggests that something is happemning at
> the C level (just outside of Perl).  Those area all the modules MAKER uses
> that will call back to the C level.  BioPerl has a fasta indexing module
> that is also making calls outside of Perl, and the fact it fails at that
> point makes it a suspect.
>
> Let me know what happens.  I can always generate an alternate MAKER
> executable for you to run with additional status messages that may help
> identify exactly which module is being called right before the failure.
>
> Thanks,
> Carson
>
>
>
> On 12-03-07 3:31 AM, "Thomas Hackl"<thomas.hackl at uni-wuerzburg.de>  wrote:
>
>> Hello,
>>
>> we want to use a current release of maker (2.22, 2.23) but the program
>> terminates with a seg fault while processing the input FASTA files.
>> maker 2.15 , which we have been using for quite some time, runs
>> perfectly with identical data and setup.
>>
>> Please contact me if you need specifics on hardware, OS or anything else.
>>
>> Best regards
>> Thomas
>>
>> -- 
>> Thomas Hackl
>> Julius-Maximilians-Universit?t
>> Department of Bioinformatics
>> 97074 W?rzburg, Germany
>> Fon:  +49 931 - 31 86883
>> Mail: thomas.hackl at uni-wuerzburg.de
>>
>>
>> _______________________________________________
>> maker-devel mailing list
>> maker-devel at box290.bluehost.com
>> http://box290.bluehost.com/mailman/listinfo/maker-devel_yandell-lab.org


-- 
Thomas Hackl
Julius-Maximilians-Universit?t
Department of Bioinformatics
97074 W?rzburg, Germany
Fon:  +49 931 - 31 86883
Mail: thomas.hackl at uni-wuerzburg.de




From carsonhh at gmail.com  Tue Mar 13 07:34:16 2012
From: carsonhh at gmail.com (Carson Holt)
Date: Tue, 13 Mar 2012 08:34:16 -0400
Subject: [maker-devel] maker 2.22/2.23: Segmentation fault while
 processing FASTA input
In-Reply-To: <4F5F1654.1060100@uni-wuerzburg.de>
Message-ID: <CB84B674.9207%carsonhh@gmail.com>

I've put together a new MAKER executable (mostly finished), and I will get
it to you soon.  This should help focus in on the exact module causing the
issue.

Thanks,
Carson



On 12-03-13 5:41 AM, "Thomas Hackl" <thomas.hackl at uni-wuerzburg.de> wrote:

>Hello,
>
>We reinstalled the packages you suggested
>
>forks is up to date (0.34).
>forks::shared is up to date (0.34).
>Inline::C is up to date (0.50).
>Storable is up to date (2.30).
>
>as well as BioPerl.
>
>The problem is still the same.
>
>With MPI it terminates with this message:
>
>STATUS: Parsing control files...
>STATUS: Processing and indexing input FASTA files...
>==========================================================================
>=========== 
>
>
>=   BAD TERMINATION OF ONE OF YOUR APPLICATION PROCESSES
>=   EXIT CODE: 11
>=   CLEANING UP REMAINING PROCESSES
>=   YOU CAN IGNORE THE BELOW CLEANUP MESSAGES
>==========================================================================
>=========== 
>
>APPLICATION TERMINATED WITH THE EXIT STRING: Segmentation fault (signal
>11)
>
>which I presume is also the same problem.
>
>I am with you that the error is caused somewhere on the C level. If the
>indexing step
>is handled by non-maker modules exclusively, than the fact that the 2.15
>version works,
>suggests that you are using different modules/methods in the current
>releases?
>
>In any case, I think a version with verbose status messages might help
>to localize the
>source of the problem.
>
>Regards
>Thomas
>
>Am 07.03.2012 23:45, schrieb Carson Holt:
>> There should be no new hardware requirement.  But there is always a
>>chance
>> that there is an issue with one of the perl modules being used.  I
>>assume
>> the failure is happening when using maker serially and you are not using
>> MPI.
>>
>> Could you reinstall the following perl modules, and try again.  If you
>>are
>> using CPAN, do a 'force install' to force it to reinstall.
>>
>> Modules:
>> *Storable
>> *Inline::C
>> *forks
>> *forks::shared
>>
>> Also try reinstalling the latest version of BioPerl.
>>
>> The fact that this is a seg fault suggests that something is happemning
>>at
>> the C level (just outside of Perl).  Those area all the modules MAKER
>>uses
>> that will call back to the C level.  BioPerl has a fasta indexing module
>> that is also making calls outside of Perl, and the fact it fails at that
>> point makes it a suspect.
>>
>> Let me know what happens.  I can always generate an alternate MAKER
>> executable for you to run with additional status messages that may help
>> identify exactly which module is being called right before the failure.
>>
>> Thanks,
>> Carson
>>
>>
>>
>> On 12-03-07 3:31 AM, "Thomas Hackl"<thomas.hackl at uni-wuerzburg.de>
>>wrote:
>>
>>> Hello,
>>>
>>> we want to use a current release of maker (2.22, 2.23) but the program
>>> terminates with a seg fault while processing the input FASTA files.
>>> maker 2.15 , which we have been using for quite some time, runs
>>> perfectly with identical data and setup.
>>>
>>> Please contact me if you need specifics on hardware, OS or anything
>>>else.
>>>
>>> Best regards
>>> Thomas
>>>
>>> -- 
>>> Thomas Hackl
>>> Julius-Maximilians-Universit?t
>>> Department of Bioinformatics
>>> 97074 W?rzburg, Germany
>>> Fon:  +49 931 - 31 86883
>>> Mail: thomas.hackl at uni-wuerzburg.de
>>>
>>>
>>> _______________________________________________
>>> maker-devel mailing list
>>> maker-devel at box290.bluehost.com
>>> http://box290.bluehost.com/mailman/listinfo/maker-devel_yandell-lab.org
>
>
>-- 
>Thomas Hackl
>Julius-Maximilians-Universit?t
>Department of Bioinformatics
>97074 W?rzburg, Germany
>Fon:  +49 931 - 31 86883
>Mail: thomas.hackl at uni-wuerzburg.de
>
>
>_______________________________________________
>maker-devel mailing list
>maker-devel at box290.bluehost.com
>http://box290.bluehost.com/mailman/listinfo/maker-devel_yandell-lab.org





From barry.moore at genetics.utah.edu  Tue Mar 13 16:37:13 2012
From: barry.moore at genetics.utah.edu (Barry Moore)
Date: Tue, 13 Mar 2012 15:37:13 -0600
Subject: [maker-devel] maker 2.22/2.23: Segmentation fault while
	processing FASTA input
In-Reply-To: <4F5F1654.1060100@uni-wuerzburg.de>
References: <CB7D4D49.8FCD%carson.holt@oicr.on.ca>
	<4F5F1654.1060100@uni-wuerzburg.de>
Message-ID: <33E794D7-81C6-4315-BE02-A92B8C82EB67@genetics.utah.edu>

You might also try a short perl script outside of MAKER to exercise Bio::DB::Fasta (which I believe is the module MAKER uses for Fasta indexing - correct Carson?).

Something like this should work to force indexing:

use Bio::DB::Fasta;
my $db      = Bio::DB::Fasta->new('/path/to/fasta/files');
my $seq      = $db->seq($seqid, $start, $end);

Point it at your fasta directory or file.

B

On Mar 13, 2012, at 3:41 AM, Thomas Hackl wrote:

> Hello,
> 
> We reinstalled the packages you suggested
> 
> forks is up to date (0.34).
> forks::shared is up to date (0.34).
> Inline::C is up to date (0.50).
> Storable is up to date (2.30).
> 
> as well as BioPerl.
> 
> The problem is still the same.
> 
> With MPI it terminates with this message:
> 
> STATUS: Parsing control files...
> STATUS: Processing and indexing input FASTA files...
> ===================================================================================== 
> 
> =   BAD TERMINATION OF ONE OF YOUR APPLICATION PROCESSES
> =   EXIT CODE: 11
> =   CLEANING UP REMAINING PROCESSES
> =   YOU CAN IGNORE THE BELOW CLEANUP MESSAGES
> ===================================================================================== 
> APPLICATION TERMINATED WITH THE EXIT STRING: Segmentation fault (signal 11)
> 
> which I presume is also the same problem.
> 
> I am with you that the error is caused somewhere on the C level. If the indexing step
> is handled by non-maker modules exclusively, than the fact that the 2.15 version works,
> suggests that you are using different modules/methods in the current releases?
> 
> In any case, I think a version with verbose status messages might help to localize the
> source of the problem.
> 
> Regards
> Thomas
> 
> Am 07.03.2012 23:45, schrieb Carson Holt:
>> There should be no new hardware requirement.  But there is always a chance
>> that there is an issue with one of the perl modules being used.  I assume
>> the failure is happening when using maker serially and you are not using
>> MPI.
>> 
>> Could you reinstall the following perl modules, and try again.  If you are
>> using CPAN, do a 'force install' to force it to reinstall.
>> 
>> Modules:
>> *Storable
>> *Inline::C
>> *forks
>> *forks::shared
>> 
>> Also try reinstalling the latest version of BioPerl.
>> 
>> The fact that this is a seg fault suggests that something is happemning at
>> the C level (just outside of Perl).  Those area all the modules MAKER uses
>> that will call back to the C level.  BioPerl has a fasta indexing module
>> that is also making calls outside of Perl, and the fact it fails at that
>> point makes it a suspect.
>> 
>> Let me know what happens.  I can always generate an alternate MAKER
>> executable for you to run with additional status messages that may help
>> identify exactly which module is being called right before the failure.
>> 
>> Thanks,
>> Carson
>> 
>> 
>> 
>> On 12-03-07 3:31 AM, "Thomas Hackl"<thomas.hackl at uni-wuerzburg.de>  wrote:
>> 
>>> Hello,
>>> 
>>> we want to use a current release of maker (2.22, 2.23) but the program
>>> terminates with a seg fault while processing the input FASTA files.
>>> maker 2.15 , which we have been using for quite some time, runs
>>> perfectly with identical data and setup.
>>> 
>>> Please contact me if you need specifics on hardware, OS or anything else.
>>> 
>>> Best regards
>>> Thomas
>>> 
>>> -- 
>>> Thomas Hackl
>>> Julius-Maximilians-Universit?t
>>> Department of Bioinformatics
>>> 97074 W?rzburg, Germany
>>> Fon:  +49 931 - 31 86883
>>> Mail: thomas.hackl at uni-wuerzburg.de
>>> 
>>> 
>>> _______________________________________________
>>> maker-devel mailing list
>>> maker-devel at box290.bluehost.com
>>> http://box290.bluehost.com/mailman/listinfo/maker-devel_yandell-lab.org
> 
> 
> -- 
> Thomas Hackl
> Julius-Maximilians-Universit?t
> Department of Bioinformatics
> 97074 W?rzburg, Germany
> Fon:  +49 931 - 31 86883
> Mail: thomas.hackl at uni-wuerzburg.de
> 
> 
> _______________________________________________
> maker-devel mailing list
> maker-devel at box290.bluehost.com
> http://box290.bluehost.com/mailman/listinfo/maker-devel_yandell-lab.org

Barry Moore
Research Scientist
Dept. of Human Genetics
University of Utah
Salt Lake City, UT 84112
--------------------------------------------
(801) 585-3543




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From felix.bemm at uni-wuerzburg.de  Wed Mar 14 00:57:58 2012
From: felix.bemm at uni-wuerzburg.de (Felix Bemm)
Date: Wed, 14 Mar 2012 06:57:58 +0100
Subject: [maker-devel] maker 2.22/2.23: Segmentation fault while
 processing FASTA input
In-Reply-To: <33E794D7-81C6-4315-BE02-A92B8C82EB67@genetics.utah.edu>
References: <CB7D4D49.8FCD%carson.holt@oicr.on.ca>
	<4F5F1654.1060100@uni-wuerzburg.de>
	<33E794D7-81C6-4315-BE02-A92B8C82EB67@genetics.utah.edu>
Message-ID: <4F603366.3090501@uni-wuerzburg.de>

Hi,

Thomas and I are colleagues and dealing with the same problem here. I 
wrote some test code that forced the indexing and it work fine. We are 
using most of the bioperl seqio and db modules in combination with other 
tools and don't experience the same problem there at the moment.

Regards
Felix

Am 13.03.2012 22:37, schrieb Barry Moore:
> You might also try a short perl script outside of MAKER to exercise
> Bio::DB::Fasta (which I believe is the module MAKER uses for Fasta
> indexing - correct Carson?).
>
> Something like this should work to force indexing:
>
> useBio::DB::Fasta;
> my $db = Bio::DB::Fasta->new('/path/to/fasta/files');
> my$seq=$db->seq($seqid, $start, $end);
>
> Point it at your fasta directory or file.
>
> B
>
> On Mar 13, 2012, at 3:41 AM, Thomas Hackl wrote:
>
>> Hello,
>>
>> We reinstalled the packages you suggested
>>
>> forks is up to date (0.34).
>> forks::shared is up to date (0.34).
>> Inline::C is up to date (0.50).
>> Storable is up to date (2.30).
>>
>> as well as BioPerl.
>>
>> The problem is still the same.
>>
>> With MPI it terminates with this message:
>>
>> STATUS: Parsing control files...
>> STATUS: Processing and indexing input FASTA files...
>> =====================================================================================
>>
>>
>> = BAD TERMINATION OF ONE OF YOUR APPLICATION PROCESSES
>> = EXIT CODE: 11
>> = CLEANING UP REMAINING PROCESSES
>> = YOU CAN IGNORE THE BELOW CLEANUP MESSAGES
>> =====================================================================================
>>
>> APPLICATION TERMINATED WITH THE EXIT STRING: Segmentation fault
>> (signal 11)
>>
>> which I presume is also the same problem.
>>
>> I am with you that the error is caused somewhere on the C level. If
>> the indexing step
>> is handled by non-maker modules exclusively, than the fact that the
>> 2.15 version works,
>> suggests that you are using different modules/methods in the current
>> releases?
>>
>> In any case, I think a version with verbose status messages might help
>> to localize the
>> source of the problem.
>>
>> Regards
>> Thomas
>>
>> Am 07.03.2012 23:45, schrieb Carson Holt:
>>> There should be no new hardware requirement. But there is always a chance
>>> that there is an issue with one of the perl modules being used. I assume
>>> the failure is happening when using maker serially and you are not using
>>> MPI.
>>>
>>> Could you reinstall the following perl modules, and try again. If you are
>>> using CPAN, do a 'force install' to force it to reinstall.
>>>
>>> Modules:
>>> *Storable
>>> *Inline::C
>>> *forks
>>> *forks::shared
>>>
>>> Also try reinstalling the latest version of BioPerl.
>>>
>>> The fact that this is a seg fault suggests that something is
>>> happemning at
>>> the C level (just outside of Perl). Those area all the modules MAKER uses
>>> that will call back to the C level. BioPerl has a fasta indexing module
>>> that is also making calls outside of Perl, and the fact it fails at that
>>> point makes it a suspect.
>>>
>>> Let me know what happens. I can always generate an alternate MAKER
>>> executable for you to run with additional status messages that may help
>>> identify exactly which module is being called right before the failure.
>>>
>>> Thanks,
>>> Carson
>>>
>>>
>>>
>>> On 12-03-07 3:31 AM, "Thomas Hackl"<thomas.hackl at uni-wuerzburg.de
>>> <mailto:thomas.hackl at uni-wuerzburg.de>> wrote:
>>>
>>>> Hello,
>>>>
>>>> we want to use a current release of maker (2.22, 2.23) but the program
>>>> terminates with a seg fault while processing the input FASTA files.
>>>> maker 2.15 , which we have been using for quite some time, runs
>>>> perfectly with identical data and setup.
>>>>
>>>> Please contact me if you need specifics on hardware, OS or anything
>>>> else.
>>>>
>>>> Best regards
>>>> Thomas
>>>>
>>>> --
>>>> Thomas Hackl
>>>> Julius-Maximilians-Universit?t
>>>> Department of Bioinformatics
>>>> 97074 W?rzburg, Germany
>>>> Fon: +49 931 - 31 86883
>>>> Mail: thomas.hackl at uni-wuerzburg.de
>>>> <mailto:thomas.hackl at uni-wuerzburg.de>
>>>>
>>>>
>>>> _______________________________________________
>>>> maker-devel mailing list
>>>> maker-devel at box290.bluehost.com <mailto:maker-devel at box290.bluehost.com>
>>>> http://box290.bluehost.com/mailman/listinfo/maker-devel_yandell-lab.org
>>
>>
>> --
>> Thomas Hackl
>> Julius-Maximilians-Universit?t
>> Department of Bioinformatics
>> 97074 W?rzburg, Germany
>> Fon: +49 931 - 31 86883
>> Mail: thomas.hackl at uni-wuerzburg.de <mailto:thomas.hackl at uni-wuerzburg.de>
>>
>>
>> _______________________________________________
>> maker-devel mailing list
>> maker-devel at box290.bluehost.com <mailto:maker-devel at box290.bluehost.com>
>> http://box290.bluehost.com/mailman/listinfo/maker-devel_yandell-lab.org
>
> Barry Moore
> Research Scientist
> Dept. of Human Genetics
> University of Utah
> Salt Lake City, UT 84112
> --------------------------------------------
> (801) 585-3543
>
>
>
>
>
>
> _______________________________________________
> maker-devel mailing list
> maker-devel at box290.bluehost.com
> http://box290.bluehost.com/mailman/listinfo/maker-devel_yandell-lab.org



From darkbring_05 at yahoo.com  Wed Mar 14 00:21:46 2012
From: darkbring_05 at yahoo.com (asdsa sdadsad)
Date: Tue, 13 Mar 2012 22:21:46 -0700 (PDT)
Subject: [maker-devel] maker gff3 to genbank tbl
Message-ID: <1331702506.55291.YahooMailNeo@web124906.mail.ne1.yahoo.com>

Dear MAKER experts,

i hope that you can share your expertise regarding, conversion of?maker gff3 to genbank tbl or gbk. im trying to produce a working genbank tbl, i tried converting to chado using maker2chado and ?gmodtools genbanksubmit writer. but so far it doesnt end well. most probably due to xml configuration(which im really loss, especially defining the "goldenpath") .is there any other way to produce the tbl from maker output??

thanks :)

Joe Wilders
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From joe.wilders at gmail.com  Wed Mar 14 00:31:48 2012
From: joe.wilders at gmail.com (Joe Wilders)
Date: Tue, 13 Mar 2012 22:31:48 -0700 (PDT)
Subject: [maker-devel] maker gff3 to genbank tbl/gbk
Message-ID: <214404c1-206e-474c-b01c-24b6cde2b91e@y17g2000yqg.googlegroups.com>

Dear MAKER experts,

i hope that you can share your expertise regarding, conversion of
maker gff3 to genbank tbl or gbk. im trying to produce a working
genbank tbl, i tried converting to chado using maker2chado and
gmodtools genbanksubmit writer. but so far it doesnt end well. most
probably due to xml configuration(which im really loss, especially
defining the "goldenpath") .is there any other way to produce the tbl
from maker output?

thanks :)

Joe Wilders



From carsonhh at gmail.com  Sun Mar 18 17:21:03 2012
From: carsonhh at gmail.com (Carson Holt)
Date: Sun, 18 Mar 2012 18:21:03 -0400
Subject: [maker-devel] maker gff3 to genbank tbl/gbk
In-Reply-To: <214404c1-206e-474c-b01c-24b6cde2b91e@y17g2000yqg.googlegroups.com>
Message-ID: <CB8BD6ED.935C%carsonhh@gmail.com>

Try using Apollo.  You can open up GFF3 files and them save them as
GenBank format.  That might be sufficient.

Alternatively.  I've attached a script that can convert SNAP's ZFF format
to GeneBank.  You could then use the maker2zff that comes with MAKER to
convert results to ZFF and then this script to get GenBank format.

Thanks,
Carson

On 12-03-14 1:31 AM, "Joe Wilders" <joe.wilders at gmail.com> wrote:

>Dear MAKER experts,
>
>i hope that you can share your expertise regarding, conversion of
>maker gff3 to genbank tbl or gbk. im trying to produce a working
>genbank tbl, i tried converting to chado using maker2chado and
>gmodtools genbanksubmit writer. but so far it doesnt end well. most
>probably due to xml configuration(which im really loss, especially
>defining the "goldenpath") .is there any other way to produce the tbl
>from maker output?
>
>thanks :)
>
>Joe Wilders
>
>_______________________________________________
>maker-devel mailing list
>maker-devel at box290.bluehost.com
>http://box290.bluehost.com/mailman/listinfo/maker-devel_yandell-lab.org

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From joe.wilders at gmail.com  Sun Mar 18 20:53:37 2012
From: joe.wilders at gmail.com (Joe Wilders)
Date: Mon, 19 Mar 2012 09:53:37 +0800
Subject: [maker-devel] maker gff3 to genbank tbl/gbk
In-Reply-To: <CB8BD6ED.935C%carsonhh@gmail.com>
References: <214404c1-206e-474c-b01c-24b6cde2b91e@y17g2000yqg.googlegroups.com>
	<CB8BD6ED.935C%carsonhh@gmail.com>
Message-ID: <CAGYDdgYv8=qMqsz_Vk0d8Y=iNLYW8siJrB0gEDz+m6Qr40qVpA@mail.gmail.com>

Hi Carson,
Thank you very much for your suggestion, will try that up and let you know.

by the way i did found this in one of the revisions at the svn
http://malachite.genetics.utah.edu/projects/maker/browser/bin/gff3_2_gbk?rev=217
,
i wonder why it gets pulled out on the later revision..


On Mon, Mar 19, 2012 at 6:21 AM, Carson Holt <carsonhh at gmail.com> wrote:

> Try using Apollo.  You can open up GFF3 files and them save them as
> GenBank format.  That might be sufficient.
>
> Alternatively.  I've attached a script that can convert SNAP's ZFF format
> to GeneBank.  You could then use the maker2zff that comes with MAKER to
> convert results to ZFF and then this script to get GenBank format.
>
> Thanks,
> Carson
>
> On 12-03-14 1:31 AM, "Joe Wilders" <joe.wilders at gmail.com> wrote:
>
> >Dear MAKER experts,
> >
> >i hope that you can share your expertise regarding, conversion of
> >maker gff3 to genbank tbl or gbk. im trying to produce a working
> >genbank tbl, i tried converting to chado using maker2chado and
> >gmodtools genbanksubmit writer. but so far it doesnt end well. most
> >probably due to xml configuration(which im really loss, especially
> >defining the "goldenpath") .is there any other way to produce the tbl
> >from maker output?
> >
> >thanks :)
> >
> >Joe Wilders
> >
> >_______________________________________________
> >maker-devel mailing list
> >maker-devel at box290.bluehost.com
> >http://box290.bluehost.com/mailman/listinfo/maker-devel_yandell-lab.org
>
>
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From carsonhh at gmail.com  Mon Mar 19 00:27:00 2012
From: carsonhh at gmail.com (Carson Holt)
Date: Mon, 19 Mar 2012 01:27:00 -0400
Subject: [maker-devel] maker gff3 to genbank tbl/gbk
In-Reply-To: <CAGYDdgYv8=qMqsz_Vk0d8Y=iNLYW8siJrB0gEDz+m6Qr40qVpA@mail.gmail.com>
Message-ID: <CB8C38D3.944D%carsonhh@gmail.com>

A lot of the early code in the SVN suppository, contains one-off scripts.
This one looks a lot like one of my old scripts.  If I remember, I was
trying to get GenBank format for Augustus training.  I started with just a
quick BioPerl based conversion, but the script didn't produce the right
types in GenBank format.  I found another way to do what I wanted (i.e.
someone gave me a different script that worked well enough), and I just
abandoned that script.

Thanks,
Carson


From:  Joe Wilders <joe.wilders at gmail.com>
Date:  Mon, 19 Mar 2012 09:53:37 +0800
To:  Carson Holt <carsonhh at gmail.com>
Cc:  <maker-devel at yandell-lab.org>
Subject:  Re: [maker-devel] maker gff3 to genbank tbl/gbk


Hi Carson,
Thank you very much for your suggestion, will try that up and let you know.

by the way i did found this in one of the revisions at the svn
http://malachite.genetics.utah.edu/projects/maker/browser/bin/gff3_2_gbk?rev
=217 , i wonder why it gets pulled out on the later revision..


On Mon, Mar 19, 2012 at 6:21 AM, Carson Holt <carsonhh at gmail.com> wrote:
> Try using Apollo.  You can open up GFF3 files and them save them as
> GenBank format.  That might be sufficient.
> 
> Alternatively.  I've attached a script that can convert SNAP's ZFF format
> to GeneBank.  You could then use the maker2zff that comes with MAKER to
> convert results to ZFF and then this script to get GenBank format.
> 
> Thanks,
> Carson
> 
> On 12-03-14 1:31 AM, "Joe Wilders" <joe.wilders at gmail.com> wrote:
> 
>> >Dear MAKER experts,
>> >
>> >i hope that you can share your expertise regarding, conversion of
>> >maker gff3 to genbank tbl or gbk. im trying to produce a working
>> >genbank tbl, i tried converting to chado using maker2chado and
>> >gmodtools genbanksubmit writer. but so far it doesnt end well. most
>> >probably due to xml configuration(which im really loss, especially
>> >defining the "goldenpath") .is there any other way to produce the tbl
>> >from maker output?
>> >
>> >thanks :)
>> >
>> >Joe Wilders
>> >
>> >_______________________________________________
>> >maker-devel mailing list
>> >maker-devel at box290.bluehost.com
>> >http://box290.bluehost.com/mailman/listinfo/maker-devel_yandell-lab.org
> 



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From dinatal at uwindsor.ca  Tue Mar 20 11:55:34 2012
From: dinatal at uwindsor.ca (claudia)
Date: Tue, 20 Mar 2012 12:55:34 -0400
Subject: [maker-devel] loading scaffold features into chado
Message-ID: <4F68B686.6050800@uwindsor.ca>

To whom it may concern,

I have 2 concerns, the first is:  regarding representing scaffold 
features in chado and gbrowse. I noticed that the Sequence ontology uses 
the term supercontig and so if my assembly generated scaffolds entitled 
"scaffold" should I change the names to supercontigs so that chado 
recognizes the terms?

Corresponding to my first question, Maker does not know that the contigs 
are actually scaffold/supercontigs when annotating and so Maker will 
still call the "type" feature or column 3 in the GFF3, a 'contig', how 
can Maker be implemented to change this naming convention before 
annotation, or after?

Consequently, I am having problems pulling up gene features in Gbrowse 
when doing a generic gene search, and I must provide the maker generated 
unique-gene_id in the gbrowse search bar or the known sequence id i.e 
'scaffold001', which is not useful for someone who does not have this 
information.
---- I do not have this problem when my seq_id, and 'type' feature id 
match in the true case of 'contigs'. I can do a generic gene search in 
gbrowse with the term 'maker' and gbrowse will provide me all the 
associated maker generated gene calls.

Thank you for any guidance resolving these concerns,
Claudia



-- 
Claudia DiNatale
Master's Candidate
The Crosby Lab
University of Windsor
519-253-3000 ext: 4755




From carsonhh at gmail.com  Tue Mar 20 12:13:35 2012
From: carsonhh at gmail.com (Carson Holt)
Date: Tue, 20 Mar 2012 13:13:35 -0400
Subject: [maker-devel] loading scaffold features into chado
In-Reply-To: <4F68B686.6050800@uwindsor.ca>
Message-ID: <CB8E2F50.97C7%carsonhh@gmail.com>


>I have 2 concerns, the first is:  regarding representing scaffold
>features in chado and gbrowse. I noticed that the Sequence ontology uses
>the term supercontig and so if my assembly generated scaffolds entitled
>"scaffold" should I change the names to supercontigs so that chado
>recognizes the terms?

Yes.  You must use valid SO terms.  It is a requirement of GFF3, and Chado
will enforce this requirement on loading a GFF3 file (note Chado will even
go as far as to check the validity of the Ontology_term= attribute in GFF3
if you use it).  You can decide to use contig or supercontig as your
sequence feature.  It doesn?t really matter unless you are placing both
into the database as separate features (i.e. You have a supercontig as the
parent feature and then you enter contigs individually as children of the
supercontig).


>
>Corresponding to my first question, Maker does not know that the contigs
>are actually scaffold/supercontigs when annotating and so Maker will
>still call the "type" feature or column 3 in the GFF3, a 'contig', how
>can Maker be implemented to change this naming convention before
>annotation, or after?

Not really important unless you plan on making contigs children of the
supercontig.  But you can always do a search and replace. -->
cat file.gff | perl -ane 's/\tcontig\t/\tsupercontig\t/s; print $_' >
new_file.gff


>
>Consequently, I am having problems pulling up gene features in Gbrowse
>when doing a generic gene search, and I must provide the maker generated
>unique-gene_id in the gbrowse search bar or the known sequence id i.e
>'scaffold001', which is not useful for someone who does not have this
>information.
>---- I do not have this problem when my seq_id, and 'type' feature id
>match in the true case of 'contigs'. I can do a generic gene search in
>gbrowse with the term 'maker' and gbrowse will provide me all the
>associated maker generated gene calls.

See "Adjusting GBrowse Name Searches" in the GBrowse tutorial -->
http://gmod.org/gbrowse2/tutorial/tutorial.html#naming


Thanks,
Carson











>
>Thank you for any guidance resolving these concerns,
>Claudia
>
>
>
>-- 
>Claudia DiNatale
>Master's Candidate
>The Crosby Lab
>University of Windsor
>519-253-3000 ext: 4755
>
>
>_______________________________________________
>maker-devel mailing list
>maker-devel at box290.bluehost.com
>http://box290.bluehost.com/mailman/listinfo/maker-devel_yandell-lab.org





From scott at scottcain.net  Tue Mar 20 12:25:04 2012
From: scott at scottcain.net (Scott Cain)
Date: Tue, 20 Mar 2012 13:25:04 -0400
Subject: [maker-devel] loading scaffold features into chado
In-Reply-To: <CB8E2F50.97C7%carsonhh@gmail.com>
References: <4F68B686.6050800@uwindsor.ca> <CB8E2F50.97C7%carsonhh@gmail.com>
Message-ID: <CA+JTaoy00sX+3Pdyrw=Apus09Lppg9YNQsr8k4uoYXHmK24Euw@mail.gmail.com>

Hi Claudia,

I agree with everything that Carson wrote, except about name
searching--it's a little trickier in Chado.  What you probably want to
do is implement full text searching.  See:

  http://gmod.org/wiki/Chado_Full_Text_Search

for more information on setting it up and maintaining it.

Scott


On Tue, Mar 20, 2012 at 1:13 PM, Carson Holt <carsonhh at gmail.com> wrote:
>
>>I have 2 concerns, the first is: ?regarding representing scaffold
>>features in chado and gbrowse. I noticed that the Sequence ontology uses
>>the term supercontig and so if my assembly generated scaffolds entitled
>>"scaffold" should I change the names to supercontigs so that chado
>>recognizes the terms?
>
> Yes. ?You must use valid SO terms. ?It is a requirement of GFF3, and Chado
> will enforce this requirement on loading a GFF3 file (note Chado will even
> go as far as to check the validity of the Ontology_term= attribute in GFF3
> if you use it). ?You can decide to use contig or supercontig as your
> sequence feature. ?It doesn?t really matter unless you are placing both
> into the database as separate features (i.e. You have a supercontig as the
> parent feature and then you enter contigs individually as children of the
> supercontig).
>
>
>>
>>Corresponding to my first question, Maker does not know that the contigs
>>are actually scaffold/supercontigs when annotating and so Maker will
>>still call the "type" feature or column 3 in the GFF3, a 'contig', how
>>can Maker be implemented to change this naming convention before
>>annotation, or after?
>
> Not really important unless you plan on making contigs children of the
> supercontig. ?But you can always do a search and replace. -->
> cat file.gff | perl -ane 's/\tcontig\t/\tsupercontig\t/s; print $_' >
> new_file.gff
>
>
>>
>>Consequently, I am having problems pulling up gene features in Gbrowse
>>when doing a generic gene search, and I must provide the maker generated
>>unique-gene_id in the gbrowse search bar or the known sequence id i.e
>>'scaffold001', which is not useful for someone who does not have this
>>information.
>>---- I do not have this problem when my seq_id, and 'type' feature id
>>match in the true case of 'contigs'. I can do a generic gene search in
>>gbrowse with the term 'maker' and gbrowse will provide me all the
>>associated maker generated gene calls.
>
> See "Adjusting GBrowse Name Searches" in the GBrowse tutorial -->
> http://gmod.org/gbrowse2/tutorial/tutorial.html#naming
>
>
> Thanks,
> Carson
>
>
>
>
>
>
>
>
>
>
>
>>
>>Thank you for any guidance resolving these concerns,
>>Claudia
>>
>>
>>
>>--
>>Claudia DiNatale
>>Master's Candidate
>>The Crosby Lab
>>University of Windsor
>>519-253-3000 ext: 4755
>>
>>
>>_______________________________________________
>>maker-devel mailing list
>>maker-devel at box290.bluehost.com
>>http://box290.bluehost.com/mailman/listinfo/maker-devel_yandell-lab.org
>
>
>
> _______________________________________________
> maker-devel mailing list
> maker-devel at box290.bluehost.com
> http://box290.bluehost.com/mailman/listinfo/maker-devel_yandell-lab.org



-- 
------------------------------------------------------------------------
Scott Cain, Ph. D.? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ?? scott at scottcain dot net
GMOD Coordinator (http://gmod.org/)? ? ? ? ? ? ? ? ? ?? 216-392-3087
Ontario Institute for Cancer Research



From carsonhh at gmail.com  Tue Mar 20 12:27:10 2012
From: carsonhh at gmail.com (Carson Holt)
Date: Tue, 20 Mar 2012 13:27:10 -0400
Subject: [maker-devel] loading scaffold features into chado
In-Reply-To: <CA+JTaoy00sX+3Pdyrw=Apus09Lppg9YNQsr8k4uoYXHmK24Euw@mail.gmail.com>
Message-ID: <CB8E3600.97EA%carsonhh@gmail.com>

Yes. thank you Scott.  My answer would work for GBrowse NOT Chado :-)

--Carson



On 12-03-20 1:25 PM, "Scott Cain" <scott at scottcain.net> wrote:

>Hi Claudia,
>
>I agree with everything that Carson wrote, except about name
>searching--it's a little trickier in Chado.  What you probably want to
>do is implement full text searching.  See:
>
>  http://gmod.org/wiki/Chado_Full_Text_Search
>
>for more information on setting it up and maintaining it.
>
>Scott
>
>
>On Tue, Mar 20, 2012 at 1:13 PM, Carson Holt <carsonhh at gmail.com> wrote:
>>
>>>I have 2 concerns, the first is:  regarding representing scaffold
>>>features in chado and gbrowse. I noticed that the Sequence ontology uses
>>>the term supercontig and so if my assembly generated scaffolds entitled
>>>"scaffold" should I change the names to supercontigs so that chado
>>>recognizes the terms?
>>
>> Yes.  You must use valid SO terms.  It is a requirement of GFF3, and
>>Chado
>> will enforce this requirement on loading a GFF3 file (note Chado will
>>even
>> go as far as to check the validity of the Ontology_term= attribute in
>>GFF3
>> if you use it).  You can decide to use contig or supercontig as your
>> sequence feature.  It doesn?t really matter unless you are placing both
>> into the database as separate features (i.e. You have a supercontig as
>>the
>> parent feature and then you enter contigs individually as children of
>>the
>> supercontig).
>>
>>
>>>
>>>Corresponding to my first question, Maker does not know that the contigs
>>>are actually scaffold/supercontigs when annotating and so Maker will
>>>still call the "type" feature or column 3 in the GFF3, a 'contig', how
>>>can Maker be implemented to change this naming convention before
>>>annotation, or after?
>>
>> Not really important unless you plan on making contigs children of the
>> supercontig.  But you can always do a search and replace. -->
>> cat file.gff | perl -ane 's/\tcontig\t/\tsupercontig\t/s; print $_' >
>> new_file.gff
>>
>>
>>>
>>>Consequently, I am having problems pulling up gene features in Gbrowse
>>>when doing a generic gene search, and I must provide the maker generated
>>>unique-gene_id in the gbrowse search bar or the known sequence id i.e
>>>'scaffold001', which is not useful for someone who does not have this
>>>information.
>>>---- I do not have this problem when my seq_id, and 'type' feature id
>>>match in the true case of 'contigs'. I can do a generic gene search in
>>>gbrowse with the term 'maker' and gbrowse will provide me all the
>>>associated maker generated gene calls.
>>
>> See "Adjusting GBrowse Name Searches" in the GBrowse tutorial -->
>> http://gmod.org/gbrowse2/tutorial/tutorial.html#naming
>>
>>
>> Thanks,
>> Carson
>>
>>
>>
>>
>>
>>
>>
>>
>>
>>
>>
>>>
>>>Thank you for any guidance resolving these concerns,
>>>Claudia
>>>
>>>
>>>
>>>--
>>>Claudia DiNatale
>>>Master's Candidate
>>>The Crosby Lab
>>>University of Windsor
>>>519-253-3000 ext: 4755
>>>
>>>
>>>_______________________________________________
>>>maker-devel mailing list
>>>maker-devel at box290.bluehost.com
>>>http://box290.bluehost.com/mailman/listinfo/maker-devel_yandell-lab.org
>>
>>
>>
>> _______________________________________________
>> maker-devel mailing list
>> maker-devel at box290.bluehost.com
>> http://box290.bluehost.com/mailman/listinfo/maker-devel_yandell-lab.org
>
>
>
>-- 
>------------------------------------------------------------------------
>Scott Cain, Ph. D.                                   scott at scottcain
>dot net
>GMOD Coordinator (http://gmod.org/)                     216-392-3087
>Ontario Institute for Cancer Research





From dinatal at uwindsor.ca  Tue Mar 20 13:03:27 2012
From: dinatal at uwindsor.ca (claudia)
Date: Tue, 20 Mar 2012 14:03:27 -0400
Subject: [maker-devel] loading scaffold features into chado
In-Reply-To: <CA+JTaoy00sX+3Pdyrw=Apus09Lppg9YNQsr8k4uoYXHmK24Euw@mail.gmail.com>
References: <4F68B686.6050800@uwindsor.ca> <CB8E2F50.97C7%carsonhh@gmail.com>
	<CA+JTaoy00sX+3Pdyrw=Apus09Lppg9YNQsr8k4uoYXHmK24Euw@mail.gmail.com>
Message-ID: <4F68C66F.2010902@uwindsor.ca>

Hi,

  I have enabled full text searching and I still have this problem, 
another reason for concern... So I wondered if in fact I changed all the 
ID's in the GFF3 file to supercontigs, then perhaps Chado would better 
link all the terms, annotations, and fasta files.... Although, i realize 
that the seq_id ( column 1) shouldn't need to be specific since the 
'type' term would take care of designating the feature type, no?

Claudia



On 20/03/2012 1:25 PM, Scott Cain wrote:
> Hi Claudia,
>
> I agree with everything that Carson wrote, except about name
> searching--it's a little trickier in Chado.  What you probably want to
> do is implement full text searching.  See:
>
>    http://gmod.org/wiki/Chado_Full_Text_Search
>
> for more information on setting it up and maintaining it.
>
> Scott
>
>
> On Tue, Mar 20, 2012 at 1:13 PM, Carson Holt<carsonhh at gmail.com>  wrote:
>>> I have 2 concerns, the first is:  regarding representing scaffold
>>> features in chado and gbrowse. I noticed that the Sequence ontology uses
>>> the term supercontig and so if my assembly generated scaffolds entitled
>>> "scaffold" should I change the names to supercontigs so that chado
>>> recognizes the terms?
>> Yes.  You must use valid SO terms.  It is a requirement of GFF3, and Chado
>> will enforce this requirement on loading a GFF3 file (note Chado will even
>> go as far as to check the validity of the Ontology_term= attribute in GFF3
>> if you use it).  You can decide to use contig or supercontig as your
>> sequence feature.  It doesn?t really matter unless you are placing both
>> into the database as separate features (i.e. You have a supercontig as the
>> parent feature and then you enter contigs individually as children of the
>> supercontig).
>>
>>
>>> Corresponding to my first question, Maker does not know that the contigs
>>> are actually scaffold/supercontigs when annotating and so Maker will
>>> still call the "type" feature or column 3 in the GFF3, a 'contig', how
>>> can Maker be implemented to change this naming convention before
>>> annotation, or after?
>> Not really important unless you plan on making contigs children of the
>> supercontig.  But you can always do a search and replace. -->
>> cat file.gff | perl -ane 's/\tcontig\t/\tsupercontig\t/s; print $_'>
>> new_file.gff
>>
>>
>>> Consequently, I am having problems pulling up gene features in Gbrowse
>>> when doing a generic gene search, and I must provide the maker generated
>>> unique-gene_id in the gbrowse search bar or the known sequence id i.e
>>> 'scaffold001', which is not useful for someone who does not have this
>>> information.
>>> ---- I do not have this problem when my seq_id, and 'type' feature id
>>> match in the true case of 'contigs'. I can do a generic gene search in
>>> gbrowse with the term 'maker' and gbrowse will provide me all the
>>> associated maker generated gene calls.
>> See "Adjusting GBrowse Name Searches" in the GBrowse tutorial -->
>> http://gmod.org/gbrowse2/tutorial/tutorial.html#naming
>>
>>
>> Thanks,
>> Carson
>>
>>
>>
>>
>>
>>
>>
>>
>>
>>
>>
>>> Thank you for any guidance resolving these concerns,
>>> Claudia
>>>
>>>
>>>
>>> --
>>> Claudia DiNatale
>>> Master's Candidate
>>> The Crosby Lab
>>> University of Windsor
>>> 519-253-3000 ext: 4755
>>>
>>>
>>> _______________________________________________
>>> maker-devel mailing list
>>> maker-devel at box290.bluehost.com
>>> http://box290.bluehost.com/mailman/listinfo/maker-devel_yandell-lab.org
>>
>>
>> _______________________________________________
>> maker-devel mailing list
>> maker-devel at box290.bluehost.com
>> http://box290.bluehost.com/mailman/listinfo/maker-devel_yandell-lab.org
>
>


-- 
Claudia DiNatale
Master's Candidate
The Crosby Lab
University of Windsor
519-253-3000 ext: 4755




From scott at scottcain.net  Tue Mar 20 14:50:55 2012
From: scott at scottcain.net (Scott Cain)
Date: Tue, 20 Mar 2012 15:50:55 -0400
Subject: [maker-devel] loading scaffold features into chado
In-Reply-To: <4F68C66F.2010902@uwindsor.ca>
References: <4F68B686.6050800@uwindsor.ca> <CB8E2F50.97C7%carsonhh@gmail.com>
	<CA+JTaoy00sX+3Pdyrw=Apus09Lppg9YNQsr8k4uoYXHmK24Euw@mail.gmail.com>
	<4F68C66F.2010902@uwindsor.ca>
Message-ID: <FFACED63-40D9-4810-9927-0E4984BA8465@scottcain.net>

Hi Claudia,

Can you post a sample of the gff that shows what you are looking for and not finding?

Scott


Sent from my iPad

On Mar 20, 2012, at 2:03 PM, claudia <dinatal at uwindsor.ca> wrote:

> Hi,
> 
> I have enabled full text searching and I still have this problem, another reason for concern... So I wondered if in fact I changed all the ID's in the GFF3 file to supercontigs, then perhaps Chado would better link all the terms, annotations, and fasta files.... Although, i realize that the seq_id ( column 1) shouldn't need to be specific since the 'type' term would take care of designating the feature type, no?
> 
> Claudia
> 
> 
> 
> On 20/03/2012 1:25 PM, Scott Cain wrote:
>> Hi Claudia,
>> 
>> I agree with everything that Carson wrote, except about name
>> searching--it's a little trickier in Chado.  What you probably want to
>> do is implement full text searching.  See:
>> 
>>   http://gmod.org/wiki/Chado_Full_Text_Search
>> 
>> for more information on setting it up and maintaining it.
>> 
>> Scott
>> 
>> 
>> On Tue, Mar 20, 2012 at 1:13 PM, Carson Holt<carsonhh at gmail.com>  wrote:
>>>> I have 2 concerns, the first is:  regarding representing scaffold
>>>> features in chado and gbrowse. I noticed that the Sequence ontology uses
>>>> the term supercontig and so if my assembly generated scaffolds entitled
>>>> "scaffold" should I change the names to supercontigs so that chado
>>>> recognizes the terms?
>>> Yes.  You must use valid SO terms.  It is a requirement of GFF3, and Chado
>>> will enforce this requirement on loading a GFF3 file (note Chado will even
>>> go as far as to check the validity of the Ontology_term= attribute in GFF3
>>> if you use it).  You can decide to use contig or supercontig as your
>>> sequence feature.  It doesn?t really matter unless you are placing both
>>> into the database as separate features (i.e. You have a supercontig as the
>>> parent feature and then you enter contigs individually as children of the
>>> supercontig).
>>> 
>>> 
>>>> Corresponding to my first question, Maker does not know that the contigs
>>>> are actually scaffold/supercontigs when annotating and so Maker will
>>>> still call the "type" feature or column 3 in the GFF3, a 'contig', how
>>>> can Maker be implemented to change this naming convention before
>>>> annotation, or after?
>>> Not really important unless you plan on making contigs children of the
>>> supercontig.  But you can always do a search and replace. -->
>>> cat file.gff | perl -ane 's/\tcontig\t/\tsupercontig\t/s; print $_'>
>>> new_file.gff
>>> 
>>> 
>>>> Consequently, I am having problems pulling up gene features in Gbrowse
>>>> when doing a generic gene search, and I must provide the maker generated
>>>> unique-gene_id in the gbrowse search bar or the known sequence id i.e
>>>> 'scaffold001', which is not useful for someone who does not have this
>>>> information.
>>>> ---- I do not have this problem when my seq_id, and 'type' feature id
>>>> match in the true case of 'contigs'. I can do a generic gene search in
>>>> gbrowse with the term 'maker' and gbrowse will provide me all the
>>>> associated maker generated gene calls.
>>> See "Adjusting GBrowse Name Searches" in the GBrowse tutorial -->
>>> http://gmod.org/gbrowse2/tutorial/tutorial.html#naming
>>> 
>>> 
>>> Thanks,
>>> Carson
>>> 
>>> 
>>> 
>>> 
>>> 
>>> 
>>> 
>>> 
>>> 
>>> 
>>> 
>>>> Thank you for any guidance resolving these concerns,
>>>> Claudia
>>>> 
>>>> 
>>>> 
>>>> --
>>>> Claudia DiNatale
>>>> Master's Candidate
>>>> The Crosby Lab
>>>> University of Windsor
>>>> 519-253-3000 ext: 4755
>>>> 
>>>> 
>>>> _______________________________________________
>>>> maker-devel mailing list
>>>> maker-devel at box290.bluehost.com
>>>> http://box290.bluehost.com/mailman/listinfo/maker-devel_yandell-lab.org
>>> 
>>> 
>>> _______________________________________________
>>> maker-devel mailing list
>>> maker-devel at box290.bluehost.com
>>> http://box290.bluehost.com/mailman/listinfo/maker-devel_yandell-lab.org
>> 
>> 
> 
> 
> -- 
> Claudia DiNatale
> Master's Candidate
> The Crosby Lab
> University of Windsor
> 519-253-3000 ext: 4755
> 



From thomas.hackl at uni-wuerzburg.de  Tue Mar 20 13:16:03 2012
From: thomas.hackl at uni-wuerzburg.de (Thomas Hackl)
Date: Tue, 20 Mar 2012 19:16:03 +0100
Subject: [maker-devel] maker 2.22/2.23: Segmentation fault while
 processing FASTA input
In-Reply-To: <CB8CD562.94D0%carsonhh@gmail.com>
References: <CB8CD562.94D0%carsonhh@gmail.com>
Message-ID: <4F68C963.3040108@uni-wuerzburg.de>

Hi,

I installed and ran the debug version of maker. Without -debug it 
results in the expected segmentation fault. With -debug it paradoxically 
finishes without the error.

I screened the debug log anyway but could not find anything that helped 
me to localize the problem. I attached a condensed version (sort | uniq) 
of the log.
Any ideas are appreciated.

Regards
Thomas



Am 19.03.2012 17:24, schrieb Carson Holt:
> Ok.  I finished the special debug version over the weekend.  Run with
> -debug set as a command line flag.  Capture and return the STDERR on
> failure.  It will list all modules used, the versions, and when they are
> called so we can see what happens right before failure.
>
> http://yandell-lab.org/research/maker_debug.tgz
>
>
> Thanks,
> Carson
>
>
>
> On 12-03-14 1:57 AM, "Felix Bemm"<felix.bemm at uni-wuerzburg.de>  wrote:
>
>> Hi,
>>
>> Thomas and I are colleagues and dealing with the same problem here. I
>> wrote some test code that forced the indexing and it work fine. We are
>> using most of the bioperl seqio and db modules in combination with other
>> tools and don't experience the same problem there at the moment.
>>
>> Regards
>> Felix
>>
>> Am 13.03.2012 22:37, schrieb Barry Moore:
>>> You might also try a short perl script outside of MAKER to exercise
>>> Bio::DB::Fasta (which I believe is the module MAKER uses for Fasta
>>> indexing - correct Carson?).
>>>
>>> Something like this should work to force indexing:
>>>
>>> useBio::DB::Fasta;
>>> my $db = Bio::DB::Fasta->new('/path/to/fasta/files');
>>> my$seq=$db->seq($seqid, $start, $end);
>>>
>>> Point it at your fasta directory or file.
>>>
>>> B
>>>
>>> On Mar 13, 2012, at 3:41 AM, Thomas Hackl wrote:
>>>
>>>> Hello,
>>>>
>>>> We reinstalled the packages you suggested
>>>>
>>>> forks is up to date (0.34).
>>>> forks::shared is up to date (0.34).
>>>> Inline::C is up to date (0.50).
>>>> Storable is up to date (2.30).
>>>>
>>>> as well as BioPerl.
>>>>
>>>> The problem is still the same.
>>>>
>>>> With MPI it terminates with this message:
>>>>
>>>> STATUS: Parsing control files...
>>>> STATUS: Processing and indexing input FASTA files...
>>>>
>>>> ========================================================================
>>>> =============
>>>>
>>>>
>>>> = BAD TERMINATION OF ONE OF YOUR APPLICATION PROCESSES
>>>> = EXIT CODE: 11
>>>> = CLEANING UP REMAINING PROCESSES
>>>> = YOU CAN IGNORE THE BELOW CLEANUP MESSAGES
>>>>
>>>> ========================================================================
>>>> =============
>>>>
>>>> APPLICATION TERMINATED WITH THE EXIT STRING: Segmentation fault
>>>> (signal 11)
>>>>
>>>> which I presume is also the same problem.
>>>>
>>>> I am with you that the error is caused somewhere on the C level. If
>>>> the indexing step
>>>> is handled by non-maker modules exclusively, than the fact that the
>>>> 2.15 version works,
>>>> suggests that you are using different modules/methods in the current
>>>> releases?
>>>>
>>>> In any case, I think a version with verbose status messages might help
>>>> to localize the
>>>> source of the problem.
>>>>
>>>> Regards
>>>> Thomas
>>>>
>>>> Am 07.03.2012 23:45, schrieb Carson Holt:
>>>>> There should be no new hardware requirement. But there is always a
>>>>> chance
>>>>> that there is an issue with one of the perl modules being used. I
>>>>> assume
>>>>> the failure is happening when using maker serially and you are not
>>>>> using
>>>>> MPI.
>>>>>
>>>>> Could you reinstall the following perl modules, and try again. If you
>>>>> are
>>>>> using CPAN, do a 'force install' to force it to reinstall.
>>>>>
>>>>> Modules:
>>>>> *Storable
>>>>> *Inline::C
>>>>> *forks
>>>>> *forks::shared
>>>>>
>>>>> Also try reinstalling the latest version of BioPerl.
>>>>>
>>>>> The fact that this is a seg fault suggests that something is
>>>>> happemning at
>>>>> the C level (just outside of Perl). Those area all the modules MAKER
>>>>> uses
>>>>> that will call back to the C level. BioPerl has a fasta indexing
>>>>> module
>>>>> that is also making calls outside of Perl, and the fact it fails at
>>>>> that
>>>>> point makes it a suspect.
>>>>>
>>>>> Let me know what happens. I can always generate an alternate MAKER
>>>>> executable for you to run with additional status messages that may
>>>>> help
>>>>> identify exactly which module is being called right before the
>>>>> failure.
>>>>>
>>>>> Thanks,
>>>>> Carson
>>>>>
>>>>>
>>>>>
>>>>> On 12-03-07 3:31 AM, "Thomas Hackl"<thomas.hackl at uni-wuerzburg.de
>>>>> <mailto:thomas.hackl at uni-wuerzburg.de>>  wrote:
>>>>>
>>>>>> Hello,
>>>>>>
>>>>>> we want to use a current release of maker (2.22, 2.23) but the
>>>>>> program
>>>>>> terminates with a seg fault while processing the input FASTA files.
>>>>>> maker 2.15 , which we have been using for quite some time, runs
>>>>>> perfectly with identical data and setup.
>>>>>>
>>>>>> Please contact me if you need specifics on hardware, OS or anything
>>>>>> else.
>>>>>>
>>>>>> Best regards
>>>>>> Thomas
>>>>>>
>>>>>> --
>>>>>> Thomas Hackl
>>>>>> Julius-Maximilians-Universit?t
>>>>>> Department of Bioinformatics
>>>>>> 97074 W?rzburg, Germany
>>>>>> Fon: +49 931 - 31 86883
>>>>>> Mail: thomas.hackl at uni-wuerzburg.de
>>>>>> <mailto:thomas.hackl at uni-wuerzburg.de>
>>>>>>
>>>>>>
>>>>>> _______________________________________________
>>>>>> maker-devel mailing list
>>>>>> maker-devel at box290.bluehost.com
>>>>>> <mailto:maker-devel at box290.bluehost.com>
>>>>>>
>>>>>> http://box290.bluehost.com/mailman/listinfo/maker-devel_yandell-lab.or
>>>>>> g
>>>>
>>>> --
>>>> Thomas Hackl
>>>> Julius-Maximilians-Universit?t
>>>> Department of Bioinformatics
>>>> 97074 W?rzburg, Germany
>>>> Fon: +49 931 - 31 86883
>>>> Mail: thomas.hackl at uni-wuerzburg.de
>>>> <mailto:thomas.hackl at uni-wuerzburg.de>
>>>>
>>>>
>>>> _______________________________________________
>>>> maker-devel mailing list
>>>> maker-devel at box290.bluehost.com
>>>> <mailto:maker-devel at box290.bluehost.com>
>>>> http://box290.bluehost.com/mailman/listinfo/maker-devel_yandell-lab.org
>>> Barry Moore
>>> Research Scientist
>>> Dept. of Human Genetics
>>> University of Utah
>>> Salt Lake City, UT 84112
>>> --------------------------------------------
>>> (801) 585-3543
>>>
>>>
>>>
>>>
>>>
>>>
>>> _______________________________________________
>>> maker-devel mailing list
>>> maker-devel at box290.bluehost.com
>>> http://box290.bluehost.com/mailman/listinfo/maker-devel_yandell-lab.org
>> _______________________________________________
>> maker-devel mailing list
>> maker-devel at box290.bluehost.com
>> http://box290.bluehost.com/mailman/listinfo/maker-devel_yandell-lab.org

-- 
Thomas Hackl
Julius-Maximilians-Universit?t
Department of Bioinformatics
97074 W?rzburg, Germany
Fon:  +49 931 - 31 86883
Mail: thomas.hackl at uni-wuerzburg.de

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From scott at scottcain.net  Wed Mar 21 15:59:19 2012
From: scott at scottcain.net (Scott Cain)
Date: Wed, 21 Mar 2012 16:59:19 -0400
Subject: [maker-devel] loading scaffold features into chado
In-Reply-To: <4F6A290E.8000306@uwindsor.ca>
References: <4F68B686.6050800@uwindsor.ca> <CB8E2F50.97C7%carsonhh@gmail.com>
	<CA+JTaoy00sX+3Pdyrw=Apus09Lppg9YNQsr8k4uoYXHmK24Euw@mail.gmail.com>
	<4F68C66F.2010902@uwindsor.ca>
	<FFACED63-40D9-4810-9927-0E4984BA8465@scottcain.net>
	<web-60068456@uwindsor.ca>
	<CA+JTaoxshG4M+awmuw93=JkwqtisgFSw6igZE+_2tCFaN-ocrw@mail.gmail.com>
	<4F6A03D2.5010503@uwindsor.ca>
	<CA+JTaoyMT6_uxYG_b28j-PCJfiOeL6FUqgLRj1FNvwR7XZUOkA@mail.gmail.com>
	<4F6A290E.8000306@uwindsor.ca>
Message-ID: <CA+JTaowKA=wFW8A91wpOMZLAe+phkFdHdppO1ume+30sWN9T9g@mail.gmail.com>

Hi Claudia,

I wanted to bring this back to the mailing lists, so I cc'ed them here.

First, with the fasta loading issue: what command are you using to
load the fasta sequences?  It works for me whether the fasta is at the
bottom of the GFF file or if it is a separate fasta file (as long as I
supply the --fastafile flag to the loader).

About the searching problem: when I turn on full text searching (which
means both running gmod_chado_fts_prep.pl and adding "-fulltext 1" to
the db_args in the gbrowse config file), I can search for "cnot1" and
find both a gene and an mRNA (of course, they are really the same
feature, but GBrowse doesn't know that).  Also, searching for "maker"
works, but in a real database, this will not be an effective query,
since the number of results returned are limited, and presumably there
will be lots of features resulting from a query like that.  Please
remind me, is that what you wanted to do?

Scott




On Wed, Mar 21, 2012 at 3:16 PM, claudia <dinatal at uwindsor.ca> wrote:
> Hi Scott,
>
> ?Wanted to give you a quick heads up that the bulk loader seems to be
> loading my fasta files now after deleting the ' ##FASTA' header ( the first
> line of the file now looks like this >scaffold0001)...
> Never had this problem before, it seems the bulk loader wanted to see a '>'
> symbol in front of the first line...
>
> -- when I say seems, I will let you know if it finishes, as it currently
> ?states " Loading sequences ( if any)" ... and I never made it this far
> before :)
>
> Claudia
>
>
>
> On 21/03/2012 12:53 PM, Scott Cain wrote:
>>
>> Hi Claudia,
>>
>> I imagine one scaffold and gene models would be good--the problem is
>> finding genes, right?
>>
>> Also, with loading fasta: were the corresponding features from the GFF
>> file already loaded? ?If so, that should have worked, and if it didn't
>> it implies a bug. ?If not, that's why.
>>
>> Scott
>>
>>
>> On Wed, Mar 21, 2012 at 12:37 PM, claudia<dinatal at uwindsor.ca> ?wrote:
>>>
>>> Hi Scott,
>>> ?So would one scaffold with Maker gene models suffice? Do you want the
>>> analysis as well?
>>>
>>> --along those same lines, I did try and load the original sequence
>>> (fasta)
>>> file first that I ran the Pipeline on and chado seems to refuse the files
>>> saying they don't contain the appropriate feature '>' in the header which
>>> in
>>> fact they do i.e> ?scaffold00001 ... So not sure what is wrong with the
>>> fasta that chado doesn't want to load even if it is embedded in the GFF3,
>>> the bulk loader or maker2chado return errors stating 'feature not
>>> found'...
>>>
>>>
>>> Claudia
>>>
>>>
>>>
>>> On 21/03/2012 12:20 PM, Scott Cain wrote:
>>>>
>>>> Hi Claudia,
>>>>
>>>> I was hoping to get actual files that I could do testing on, not
>>>> pictures of files :-)
>>>>
>>>> Scott
>>>>
>>>>
>>>> On Tue, Mar 20, 2012 at 4:15 PM, Dinatale C<dinatal at uwindsor.ca>
>>>> ?wrote:
>>>>>
>>>>> Hi,
>>>>>
>>>>> Attached: ?I have samples of the contig file ( I extracted the contig
>>>>> features first to load prior to the gene models) the fasta of the
>>>>> sequences
>>>>> is in the footer of the gff3 file.
>>>>>
>>>>> --so basically, based on experience with contig annotations, I should
>>>>> be
>>>>> able to type in 'maker' in to the gbrowse search bar, and recieve all
>>>>> the
>>>>> maker gene annotations, but I don't. I must specifiy the exact ID i.e "
>>>>> maker-scaffold11323-augustus-gene...." or 'scaffold11323'
>>>>>
>>>>> --so I wonder if it has to do with the fasta files being named as
>>>>> 'scaffolds' and perhaps causing a problem with chado recognizing that
>>>>> they
>>>>> are linked to the gene annotations due to scaffold not being a SOFA
>>>>> type
>>>>> term, if in fact the sequences must be submitted to the database first?
>>>>>
>>>>>
>>>>> Thanks in advance,
>>>>>
>>>>> Claudia
>>>>>
>>>>> On Tue, 20 Mar 2012 15:50:55 -0400 Scott Cain wrote:
>>>>>>
>>>>>> Hi Claudia,
>>>>>>
>>>>>> Can you post a sample of the gff that shows what you are looking for
>>>>>> and
>>>>>> not finding?
>>>>>>
>>>>>> Scott
>>>>>>
>>>>>>
>>>>>> Sent from my iPad
>>>>>>
>>>>>> On Mar 20, 2012, at 2:03 PM, claudia wrote:
>>>>>>
>>>>>>> Hi,
>>>>>>>
>>>>>>> I have enabled full text searching and I still have this problem,
>>>>>>> another reason for
>>>>>>
>>>>>> concern... So I wondered if in fact I changed all the ID's in the GFF3
>>>>>> file to supercontigs,
>>>>>> then perhaps Chado would better link all the terms, annotations, and
>>>>>> fasta
>>>>>> files....
>>>>>> Although, i realize that the seq_id ( column 1) shouldn't need to be
>>>>>> specific since the
>>>>>> 'type' term would take care of designating the feature type, no?
>>>>>>>
>>>>>>> Claudia
>>>>>>>
>>>>>>>
>>>>>>>
>>>>>>> On 20/03/2012 1:25 PM, Scott Cain wrote:
>>>>>>>>
>>>>>>>> Hi Claudia,
>>>>>>>>
>>>>>>>> I agree with everything that Carson wrote, except about name
>>>>>>>> searching--it's a little trickier in Chado. What you probably want
>>>>>>>> to
>>>>>>>> do is implement full text searching. See:
>>>>>>>>
>>>>>>>> http://gmod.org/wiki/Chado_Full_Text_Search
>>>>>>>>
>>>>>>>> for more information on setting it up and maintaining it.
>>>>>>>>
>>>>>>>> Scott
>>>>>>>>
>>>>>>>>
>>>>>>>> On Tue, Mar 20, 2012 at 1:13 PM, Carson Holt wrote:
>>>>>>>>>>
>>>>>>>>>> I have 2 concerns, the first is: regarding representing scaffold
>>>>>>>>>> features in chado and gbrowse. I noticed that the Sequence
>>>>>>>>>> ontology
>>>>>>>>>> uses
>>>>>>>>>> the term supercontig and so if my assembly generated scaffolds
>>>>>>>>>> entitled
>>>>>>>>>> "scaffold" should I change the names to supercontigs so that chado
>>>>>>>>>> recognizes the terms?
>>>>>>>>>
>>>>>>>>> Yes. You must use valid SO terms. It is a requirement of GFF3, and
>>>>>>>>> Chado
>>>>>>>>> will enforce this requirement on loading a GFF3 file (note Chado
>>>>>>>>> will
>>>>>>>>> even
>>>>>>>>> go as far as to check the validity of the Ontology_term= attribute
>>>>>>>>> in
>>>>>>>>> GFF3
>>>>>>>>> if you use it). You can decide to use contig or supercontig as your
>>>>>>>>> sequence feature. It doesn?t really matter unless you are placing
>>>>>>>>>
>>>>>>>>> both
>>>>>>>>> into the database as separate features (i.e. You have a supercontig
>>>>>>>>> as
>>>>>>>>> the
>>>>>>>>> parent feature and then you enter contigs individually as children
>>>>>>>>> of
>>>>>>>>> the
>>>>>>>>> supercontig).
>>>>>>>>>
>>>>>>>>>
>>>>>>>>>> Corresponding to my first question, Maker does not know that the
>>>>>>>>>> contigs
>>>>>>>>>> are actually scaffold/supercontigs when annotating and so Maker
>>>>>>>>>> will
>>>>>>>>>> still call the "type" feature or column 3 in the GFF3, a 'contig',
>>>>>>>>>> how
>>>>>>>>>> can Maker be implemented to change this naming convention before
>>>>>>>>>> annotation, or after?
>>>>>>>>>
>>>>>>>>> Not really important unless you plan on making contigs children of
>>>>>>>>> the
>>>>>>>>> supercontig. But you can always do a search and replace. -->
>>>>>>>>> cat file.gff | perl -ane 's/\tcontig\t/\tsupercontig\t/s; print
>>>>>>>>> $_'>
>>>>>>>>> new_file.gff
>>>>>>>>>
>>>>>>>>>
>>>>>>>>>> Consequently, I am having problems pulling up gene features in
>>>>>>>>>> Gbrowse
>>>>>>>>>> when doing a generic gene search, and I must provide the maker
>>>>>>>>>> generated
>>>>>>>>>> unique-gene_id in the gbrowse search bar or the known sequence id
>>>>>>>>>> i.e
>>>>>>>>>> 'scaffold001', which is not useful for someone who does not have
>>>>>>>>>> this
>>>>>>>>>> information.
>>>>>>>>>> ---- I do not have this problem when my seq_id, and 'type' feature
>>>>>>>>>> id
>>>>>>>>>> match in the true case of 'contigs'. I can do a generic gene
>>>>>>>>>> search
>>>>>>>>>> in
>>>>>>>>>> gbrowse with the term 'maker' and gbrowse will provide me all the
>>>>>>>>>> associated maker generated gene calls.
>>>>>>>>>
>>>>>>>>> See "Adjusting GBrowse Name Searches" in the GBrowse tutorial -->
>>>>>>>>> http://gmod.org/gbrowse2/tutorial/tutorial.html#naming
>>>>>>>>>
>>>>>>>>>
>>>>>>>>> Thanks,
>>>>>>>>> Carson
>>>>>>>>>
>>>>>>>>>
>>>>>>>>>
>>>>>>>>>
>>>>>>>>>
>>>>>>>>>
>>>>>>>>>
>>>>>>>>>
>>>>>>>>>
>>>>>>>>>
>>>>>>>>>
>>>>>>>>>> Thank you for any guidance resolving these concerns,
>>>>>>>>>> Claudia
>>>>>>>>>>
>>>>>>>>>>
>>>>>>>>>>
>>>>>>>>>> --
>>>>>>>>>> Claudia DiNatale
>>>>>>>>>> Master's Candidate
>>>>>>>>>> The Crosby Lab
>>>>>>>>>> University of Windsor
>>>>>>>>>> 519-253-3000 ext: 4755
>>>>>>>>>>
>>>>>>>>>>
>>>>>>>>>> _______________________________________________
>>>>>>>>>> maker-devel mailing list
>>>>>>>>>> maker-devel at box290.bluehost.com
>>>>>>>>>>
>>>>>>>>>>
>>>>>>>>>>
>>>>>>>>>> http://box290.bluehost.com/mailman/listinfo/maker-devel_yandell-lab.org
>>>>>>>>>
>>>>>>>>>
>>>>>>>>> _______________________________________________
>>>>>>>>> maker-devel mailing list
>>>>>>>>> maker-devel at box290.bluehost.com
>>>>>>>>>
>>>>>>>>>
>>>>>>>>>
>>>>>>>>> http://box290.bluehost.com/mailman/listinfo/maker-devel_yandell-lab.org
>>>>>>>>
>>>>>>>>
>>>>>>> --
>>>>>>> Claudia DiNatale
>>>>>>> Master's Candidate
>>>>>>> The Crosby Lab
>>>>>>> University of Windsor
>>>>>>> 519-253-3000 ext: 4755
>>>>>>>
>>>>
>>>
>>> --
>>> Claudia DiNatale
>>> Master's Candidate
>>> The Crosby Lab
>>> University of Windsor
>>> 519-253-3000 ext: 4755
>>>
>>
>>
>
>
> --
> Claudia DiNatale
> Master's Candidate
> The Crosby Lab
> University of Windsor
> 519-253-3000 ext: 4755
>



-- 
------------------------------------------------------------------------
Scott Cain, Ph. D.? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ?? scott at scottcain dot net
GMOD Coordinator (http://gmod.org/)? ? ? ? ? ? ? ? ? ?? 216-392-3087
Ontario Institute for Cancer Research



From dinatal at uwindsor.ca  Wed Mar 21 16:14:54 2012
From: dinatal at uwindsor.ca (claudia)
Date: Wed, 21 Mar 2012 17:14:54 -0400
Subject: [maker-devel] loading scaffold features into chado
In-Reply-To: <CA+JTaowKA=wFW8A91wpOMZLAe+phkFdHdppO1ume+30sWN9T9g@mail.gmail.com>
References: <4F68B686.6050800@uwindsor.ca> <CB8E2F50.97C7%carsonhh@gmail.com>
	<CA+JTaoy00sX+3Pdyrw=Apus09Lppg9YNQsr8k4uoYXHmK24Euw@mail.gmail.com>
	<4F68C66F.2010902@uwindsor.ca>
	<FFACED63-40D9-4810-9927-0E4984BA8465@scottcain.net>
	<web-60068456@uwindsor.ca>
	<CA+JTaoxshG4M+awmuw93=JkwqtisgFSw6igZE+_2tCFaN-ocrw@mail.gmail.com>
	<4F6A03D2.5010503@uwindsor.ca>
	<CA+JTaoyMT6_uxYG_b28j-PCJfiOeL6FUqgLRj1FNvwR7XZUOkA@mail.gmail.com>
	<4F6A290E.8000306@uwindsor.ca>
	<CA+JTaowKA=wFW8A91wpOMZLAe+phkFdHdppO1ume+30sWN9T9g@mail.gmail.com>
Message-ID: <4F6A44CE.3010100@uwindsor.ca>

Hi Scott,
  I tried both maker2chado and gmod_bulk_load_gff.pl with fasta embedded 
or not... If the fastafile was seperate I used the command --fastafile 
and if it was embedded, it was simply --gfffile with the other 
appropriate commands for loading gene models not analysis ( i.e no 
exon).  It finally resulted that, as I mentioned, when I changed the 
header in the fasta file, the fasta loaded fine with the bulk-loader and 
using the --fastafile command..

Next, my gene models loaded fine with the bulk loader, so the db was 
populated. I turned on full-text searching by running the scripts, and 
stating -full text 1 in the conf file...
So it seems, I can do as you mentioned, query specific genes i.e cnot1, 
or with specific IDs or scaffold IDs, but what I really wanted is to be 
able to do generic gene searches using the 'maker' search, as done with 
my other databases, so that someone without knowledge of the contents of 
the database will recieve gene information. This I still can't do, but 
can be done with prior db's I set up that contained contig annotation 
vs. scaffolds, and I found was very useful returning all maker generated 
gene models.  With that, I thought the problem was with the nomenclature 
being used across annotations, scaffolds etc..

Claudia

On 21/03/2012 4:59 PM, Scott Cain wrote:
> Hi Claudia,
>
> I wanted to bring this back to the mailing lists, so I cc'ed them here.
>
> First, with the fasta loading issue: what command are you using to
> load the fasta sequences?  It works for me whether the fasta is at the
> bottom of the GFF file or if it is a separate fasta file (as long as I
> supply the --fastafile flag to the loader).
>
> About the searching problem: when I turn on full text searching (which
> means both running gmod_chado_fts_prep.pl and adding "-fulltext 1" to
> the db_args in the gbrowse config file), I can search for "cnot1" and
> find both a gene and an mRNA (of course, they are really the same
> feature, but GBrowse doesn't know that).  Also, searching for "maker"
> works, but in a real database, this will not be an effective query,
> since the number of results returned are limited, and presumably there
> will be lots of features resulting from a query like that.  Please
> remind me, is that what you wanted to do?
>
> Scott
>
>
>
>
> On Wed, Mar 21, 2012 at 3:16 PM, claudia<dinatal at uwindsor.ca>  wrote:
>> Hi Scott,
>>
>>   Wanted to give you a quick heads up that the bulk loader seems to be
>> loading my fasta files now after deleting the ' ##FASTA' header ( the first
>> line of the file now looks like this>scaffold0001)...
>> Never had this problem before, it seems the bulk loader wanted to see a '>'
>> symbol in front of the first line...
>>
>> -- when I say seems, I will let you know if it finishes, as it currently
>>   states " Loading sequences ( if any)" ... and I never made it this far
>> before :)
>>
>> Claudia
>>
>>
>>
>> On 21/03/2012 12:53 PM, Scott Cain wrote:
>>> Hi Claudia,
>>>
>>> I imagine one scaffold and gene models would be good--the problem is
>>> finding genes, right?
>>>
>>> Also, with loading fasta: were the corresponding features from the GFF
>>> file already loaded?  If so, that should have worked, and if it didn't
>>> it implies a bug.  If not, that's why.
>>>
>>> Scott
>>>
>>>
>>> On Wed, Mar 21, 2012 at 12:37 PM, claudia<dinatal at uwindsor.ca>    wrote:
>>>> Hi Scott,
>>>>   So would one scaffold with Maker gene models suffice? Do you want the
>>>> analysis as well?
>>>>
>>>> --along those same lines, I did try and load the original sequence
>>>> (fasta)
>>>> file first that I ran the Pipeline on and chado seems to refuse the files
>>>> saying they don't contain the appropriate feature '>' in the header which
>>>> in
>>>> fact they do i.e>    scaffold00001 ... So not sure what is wrong with the
>>>> fasta that chado doesn't want to load even if it is embedded in the GFF3,
>>>> the bulk loader or maker2chado return errors stating 'feature not
>>>> found'...
>>>>
>>>>
>>>> Claudia
>>>>
>>>>
>>>>
>>>> On 21/03/2012 12:20 PM, Scott Cain wrote:
>>>>> Hi Claudia,
>>>>>
>>>>> I was hoping to get actual files that I could do testing on, not
>>>>> pictures of files :-)
>>>>>
>>>>> Scott
>>>>>
>>>>>
>>>>> On Tue, Mar 20, 2012 at 4:15 PM, Dinatale C<dinatal at uwindsor.ca>
>>>>>   wrote:
>>>>>> Hi,
>>>>>>
>>>>>> Attached:  I have samples of the contig file ( I extracted the contig
>>>>>> features first to load prior to the gene models) the fasta of the
>>>>>> sequences
>>>>>> is in the footer of the gff3 file.
>>>>>>
>>>>>> --so basically, based on experience with contig annotations, I should
>>>>>> be
>>>>>> able to type in 'maker' in to the gbrowse search bar, and recieve all
>>>>>> the
>>>>>> maker gene annotations, but I don't. I must specifiy the exact ID i.e "
>>>>>> maker-scaffold11323-augustus-gene...." or 'scaffold11323'
>>>>>>
>>>>>> --so I wonder if it has to do with the fasta files being named as
>>>>>> 'scaffolds' and perhaps causing a problem with chado recognizing that
>>>>>> they
>>>>>> are linked to the gene annotations due to scaffold not being a SOFA
>>>>>> type
>>>>>> term, if in fact the sequences must be submitted to the database first?
>>>>>>
>>>>>>
>>>>>> Thanks in advance,
>>>>>>
>>>>>> Claudia
>>>>>>
>>>>>> On Tue, 20 Mar 2012 15:50:55 -0400 Scott Cain wrote:
>>>>>>> Hi Claudia,
>>>>>>>
>>>>>>> Can you post a sample of the gff that shows what you are looking for
>>>>>>> and
>>>>>>> not finding?
>>>>>>>
>>>>>>> Scott
>>>>>>>
>>>>>>>
>>>>>>> Sent from my iPad
>>>>>>>
>>>>>>> On Mar 20, 2012, at 2:03 PM, claudia wrote:
>>>>>>>
>>>>>>>> Hi,
>>>>>>>>
>>>>>>>> I have enabled full text searching and I still have this problem,
>>>>>>>> another reason for
>>>>>>> concern... So I wondered if in fact I changed all the ID's in the GFF3
>>>>>>> file to supercontigs,
>>>>>>> then perhaps Chado would better link all the terms, annotations, and
>>>>>>> fasta
>>>>>>> files....
>>>>>>> Although, i realize that the seq_id ( column 1) shouldn't need to be
>>>>>>> specific since the
>>>>>>> 'type' term would take care of designating the feature type, no?
>>>>>>>> Claudia
>>>>>>>>
>>>>>>>>
>>>>>>>>
>>>>>>>> On 20/03/2012 1:25 PM, Scott Cain wrote:
>>>>>>>>> Hi Claudia,
>>>>>>>>>
>>>>>>>>> I agree with everything that Carson wrote, except about name
>>>>>>>>> searching--it's a little trickier in Chado. What you probably want
>>>>>>>>> to
>>>>>>>>> do is implement full text searching. See:
>>>>>>>>>
>>>>>>>>> http://gmod.org/wiki/Chado_Full_Text_Search
>>>>>>>>>
>>>>>>>>> for more information on setting it up and maintaining it.
>>>>>>>>>
>>>>>>>>> Scott
>>>>>>>>>
>>>>>>>>>
>>>>>>>>> On Tue, Mar 20, 2012 at 1:13 PM, Carson Holt wrote:
>>>>>>>>>>> I have 2 concerns, the first is: regarding representing scaffold
>>>>>>>>>>> features in chado and gbrowse. I noticed that the Sequence
>>>>>>>>>>> ontology
>>>>>>>>>>> uses
>>>>>>>>>>> the term supercontig and so if my assembly generated scaffolds
>>>>>>>>>>> entitled
>>>>>>>>>>> "scaffold" should I change the names to supercontigs so that chado
>>>>>>>>>>> recognizes the terms?
>>>>>>>>>> Yes. You must use valid SO terms. It is a requirement of GFF3, and
>>>>>>>>>> Chado
>>>>>>>>>> will enforce this requirement on loading a GFF3 file (note Chado
>>>>>>>>>> will
>>>>>>>>>> even
>>>>>>>>>> go as far as to check the validity of the Ontology_term= attribute
>>>>>>>>>> in
>>>>>>>>>> GFF3
>>>>>>>>>> if you use it). You can decide to use contig or supercontig as your
>>>>>>>>>> sequence feature. It doesn?t really matter unless you are placing
>>>>>>>>>>
>>>>>>>>>> both
>>>>>>>>>> into the database as separate features (i.e. You have a supercontig
>>>>>>>>>> as
>>>>>>>>>> the
>>>>>>>>>> parent feature and then you enter contigs individually as children
>>>>>>>>>> of
>>>>>>>>>> the
>>>>>>>>>> supercontig).
>>>>>>>>>>
>>>>>>>>>>
>>>>>>>>>>> Corresponding to my first question, Maker does not know that the
>>>>>>>>>>> contigs
>>>>>>>>>>> are actually scaffold/supercontigs when annotating and so Maker
>>>>>>>>>>> will
>>>>>>>>>>> still call the "type" feature or column 3 in the GFF3, a 'contig',
>>>>>>>>>>> how
>>>>>>>>>>> can Maker be implemented to change this naming convention before
>>>>>>>>>>> annotation, or after?
>>>>>>>>>> Not really important unless you plan on making contigs children of
>>>>>>>>>> the
>>>>>>>>>> supercontig. But you can always do a search and replace. -->
>>>>>>>>>> cat file.gff | perl -ane 's/\tcontig\t/\tsupercontig\t/s; print
>>>>>>>>>> $_'>
>>>>>>>>>> new_file.gff
>>>>>>>>>>
>>>>>>>>>>
>>>>>>>>>>> Consequently, I am having problems pulling up gene features in
>>>>>>>>>>> Gbrowse
>>>>>>>>>>> when doing a generic gene search, and I must provide the maker
>>>>>>>>>>> generated
>>>>>>>>>>> unique-gene_id in the gbrowse search bar or the known sequence id
>>>>>>>>>>> i.e
>>>>>>>>>>> 'scaffold001', which is not useful for someone who does not have
>>>>>>>>>>> this
>>>>>>>>>>> information.
>>>>>>>>>>> ---- I do not have this problem when my seq_id, and 'type' feature
>>>>>>>>>>> id
>>>>>>>>>>> match in the true case of 'contigs'. I can do a generic gene
>>>>>>>>>>> search
>>>>>>>>>>> in
>>>>>>>>>>> gbrowse with the term 'maker' and gbrowse will provide me all the
>>>>>>>>>>> associated maker generated gene calls.
>>>>>>>>>> See "Adjusting GBrowse Name Searches" in the GBrowse tutorial -->
>>>>>>>>>> http://gmod.org/gbrowse2/tutorial/tutorial.html#naming
>>>>>>>>>>
>>>>>>>>>>
>>>>>>>>>> Thanks,
>>>>>>>>>> Carson
>>>>>>>>>>
>>>>>>>>>>
>>>>>>>>>>
>>>>>>>>>>
>>>>>>>>>>
>>>>>>>>>>
>>>>>>>>>>
>>>>>>>>>>
>>>>>>>>>>
>>>>>>>>>>
>>>>>>>>>>
>>>>>>>>>>> Thank you for any guidance resolving these concerns,
>>>>>>>>>>> Claudia
>>>>>>>>>>>
>>>>>>>>>>>
>>>>>>>>>>>
>>>>>>>>>>> --
>>>>>>>>>>> Claudia DiNatale
>>>>>>>>>>> Master's Candidate
>>>>>>>>>>> The Crosby Lab
>>>>>>>>>>> University of Windsor
>>>>>>>>>>> 519-253-3000 ext: 4755
>>>>>>>>>>>
>>>>>>>>>>>
>>>>>>>>>>> _______________________________________________
>>>>>>>>>>> maker-devel mailing list
>>>>>>>>>>> maker-devel at box290.bluehost.com
>>>>>>>>>>>
>>>>>>>>>>>
>>>>>>>>>>>
>>>>>>>>>>> http://box290.bluehost.com/mailman/listinfo/maker-devel_yandell-lab.org
>>>>>>>>>>
>>>>>>>>>> _______________________________________________
>>>>>>>>>> maker-devel mailing list
>>>>>>>>>> maker-devel at box290.bluehost.com
>>>>>>>>>>
>>>>>>>>>>
>>>>>>>>>>
>>>>>>>>>> http://box290.bluehost.com/mailman/listinfo/maker-devel_yandell-lab.org
>>>>>>>>>
>>>>>>>> --
>>>>>>>> Claudia DiNatale
>>>>>>>> Master's Candidate
>>>>>>>> The Crosby Lab
>>>>>>>> University of Windsor
>>>>>>>> 519-253-3000 ext: 4755
>>>>>>>>
>>>> --
>>>> Claudia DiNatale
>>>> Master's Candidate
>>>> The Crosby Lab
>>>> University of Windsor
>>>> 519-253-3000 ext: 4755
>>>>
>>>
>>
>> --
>> Claudia DiNatale
>> Master's Candidate
>> The Crosby Lab
>> University of Windsor
>> 519-253-3000 ext: 4755
>>
>
>


-- 
Claudia DiNatale
Master's Candidate
The Crosby Lab
University of Windsor
519-253-3000 ext: 4755




From carsonhh at gmail.com  Wed Mar 21 17:05:32 2012
From: carsonhh at gmail.com (Carson Holt)
Date: Wed, 21 Mar 2012 18:05:32 -0400
Subject: [maker-devel] maker 2.22/2.23: Segmentation fault while
 processing FASTA input
In-Reply-To: <4F68C963.3040108@uni-wuerzburg.de>
Message-ID: <CB8FC294.9902%carsonhh@gmail.com>

That is likely the strangest result I could imagine?  The --debug option
really only cause MAKER to print status messages everywhere and nothing
else, so there must be something else going on between the tests.


One things I did notice from the error log though -->
0.49	Inline	/home/s187512/perl/lib/perl5/site_perl/5.12.1/Inline.pm
	UNKNOWN	Inline::denter	/home/s187512/perl/lib/perl5/site_perl/5.12.1/Inlin
e/denter.pm


These are both being loaded from perl 5.12.1 (you are using 5.14.1).  That
can cause issues since I know the first one is executed at the C level and
I wouldn't be surprised if the same is true on the second one.



I also saw this -->
Can't locate package GDBM_File for @AnyDBM_File::ISA at
/storage/tmp/software/perl-5.14.1/lib/5.14.1/x86_64-linux-thread-multi/DB_F
ile.pm line 293.
Can't locate package NDBM_File for @AnyDBM_File::ISA at
/storage/tmp/software/perl-5.14.1/lib/5.14.1/x86_64-linux-thread-multi/DB_F
ile.pm line 293.
Can't locate package SDBM_File for @AnyDBM_File::ISA at
/storage/tmp/software/perl-5.14.1/lib/5.14.1/x86_64-linux-thread-multi/DB_F
ile.pm line 293.



This appears could be related to Bio::DB::Fasta (which would make sense
with the timing of the seg fault).  This is line 405 in the BEGIN
statement for Bio::DB::Fasta
-->  @AnyDBM_File::ISA = qw(DB_File GDBM_File NDBM_File SDBM_File)

I'm not sure what to do about those?  Are you able to install GDBM_File,
NDBM_File, or SDBM_File by themselves?  They really should just be
optional?  I know I don't have NDBM_File, and I don't get an error.
DB_File is part of the perl distribution, but can be updated via CPAN.
Perhaps that would be good to do.  It may just be that DB_file is broken
and falling back to the other modules doesn?t work because you don't have
them.  There is also the chance that the issue is really with Berkley_DB.
DB_File accesses Berkley_DB and it wants version 1.x, but will work with
2.x and 3.x.  You may need to even go as far as building a new Berkley_DB.

Well that's enough to try for now.

Thanks,
Carson


On 12-03-20 2:16 PM, "Thomas Hackl" <thomas.hackl at uni-wuerzburg.de> wrote:

>Hi,
>
>I installed and ran the debug version of maker. Without -debug it
>results in the expected segmentation fault. With -debug it paradoxically
>finishes without the error.
>
>I screened the debug log anyway but could not find anything that helped
>me to localize the problem. I attached a condensed version (sort | uniq)
>of the log.
>Any ideas are appreciated.
>
>Regards
>Thomas
>
>
>
>Am 19.03.2012 17:24, schrieb Carson Holt:
>> Ok.  I finished the special debug version over the weekend.  Run with
>> -debug set as a command line flag.  Capture and return the STDERR on
>> failure.  It will list all modules used, the versions, and when they are
>> called so we can see what happens right before failure.
>>
>> http://yandell-lab.org/research/maker_debug.tgz
>>
>>
>> Thanks,
>> Carson
>>
>>
>>
>> On 12-03-14 1:57 AM, "Felix Bemm"<felix.bemm at uni-wuerzburg.de>  wrote:
>>
>>> Hi,
>>>
>>> Thomas and I are colleagues and dealing with the same problem here. I
>>> wrote some test code that forced the indexing and it work fine. We are
>>> using most of the bioperl seqio and db modules in combination with
>>>other
>>> tools and don't experience the same problem there at the moment.
>>>
>>> Regards
>>> Felix
>>>
>>> Am 13.03.2012 22:37, schrieb Barry Moore:
>>>> You might also try a short perl script outside of MAKER to exercise
>>>> Bio::DB::Fasta (which I believe is the module MAKER uses for Fasta
>>>> indexing - correct Carson?).
>>>>
>>>> Something like this should work to force indexing:
>>>>
>>>> useBio::DB::Fasta;
>>>> my $db = Bio::DB::Fasta->new('/path/to/fasta/files');
>>>> my$seq=$db->seq($seqid, $start, $end);
>>>>
>>>> Point it at your fasta directory or file.
>>>>
>>>> B
>>>>
>>>> On Mar 13, 2012, at 3:41 AM, Thomas Hackl wrote:
>>>>
>>>>> Hello,
>>>>>
>>>>> We reinstalled the packages you suggested
>>>>>
>>>>> forks is up to date (0.34).
>>>>> forks::shared is up to date (0.34).
>>>>> Inline::C is up to date (0.50).
>>>>> Storable is up to date (2.30).
>>>>>
>>>>> as well as BioPerl.
>>>>>
>>>>> The problem is still the same.
>>>>>
>>>>> With MPI it terminates with this message:
>>>>>
>>>>> STATUS: Parsing control files...
>>>>> STATUS: Processing and indexing input FASTA files...
>>>>>
>>>>> 
>>>>>======================================================================
>>>>>==
>>>>> =============
>>>>>
>>>>>
>>>>> = BAD TERMINATION OF ONE OF YOUR APPLICATION PROCESSES
>>>>> = EXIT CODE: 11
>>>>> = CLEANING UP REMAINING PROCESSES
>>>>> = YOU CAN IGNORE THE BELOW CLEANUP MESSAGES
>>>>>
>>>>> 
>>>>>======================================================================
>>>>>==
>>>>> =============
>>>>>
>>>>> APPLICATION TERMINATED WITH THE EXIT STRING: Segmentation fault
>>>>> (signal 11)
>>>>>
>>>>> which I presume is also the same problem.
>>>>>
>>>>> I am with you that the error is caused somewhere on the C level. If
>>>>> the indexing step
>>>>> is handled by non-maker modules exclusively, than the fact that the
>>>>> 2.15 version works,
>>>>> suggests that you are using different modules/methods in the current
>>>>> releases?
>>>>>
>>>>> In any case, I think a version with verbose status messages might
>>>>>help
>>>>> to localize the
>>>>> source of the problem.
>>>>>
>>>>> Regards
>>>>> Thomas
>>>>>
>>>>> Am 07.03.2012 23:45, schrieb Carson Holt:
>>>>>> There should be no new hardware requirement. But there is always a
>>>>>> chance
>>>>>> that there is an issue with one of the perl modules being used. I
>>>>>> assume
>>>>>> the failure is happening when using maker serially and you are not
>>>>>> using
>>>>>> MPI.
>>>>>>
>>>>>> Could you reinstall the following perl modules, and try again. If
>>>>>>you
>>>>>> are
>>>>>> using CPAN, do a 'force install' to force it to reinstall.
>>>>>>
>>>>>> Modules:
>>>>>> *Storable
>>>>>> *Inline::C
>>>>>> *forks
>>>>>> *forks::shared
>>>>>>
>>>>>> Also try reinstalling the latest version of BioPerl.
>>>>>>
>>>>>> The fact that this is a seg fault suggests that something is
>>>>>> happemning at
>>>>>> the C level (just outside of Perl). Those area all the modules MAKER
>>>>>> uses
>>>>>> that will call back to the C level. BioPerl has a fasta indexing
>>>>>> module
>>>>>> that is also making calls outside of Perl, and the fact it fails at
>>>>>> that
>>>>>> point makes it a suspect.
>>>>>>
>>>>>> Let me know what happens. I can always generate an alternate MAKER
>>>>>> executable for you to run with additional status messages that may
>>>>>> help
>>>>>> identify exactly which module is being called right before the
>>>>>> failure.
>>>>>>
>>>>>> Thanks,
>>>>>> Carson
>>>>>>
>>>>>>
>>>>>>
>>>>>> On 12-03-07 3:31 AM, "Thomas Hackl"<thomas.hackl at uni-wuerzburg.de
>>>>>> <mailto:thomas.hackl at uni-wuerzburg.de>>  wrote:
>>>>>>
>>>>>>> Hello,
>>>>>>>
>>>>>>> we want to use a current release of maker (2.22, 2.23) but the
>>>>>>> program
>>>>>>> terminates with a seg fault while processing the input FASTA files.
>>>>>>> maker 2.15 , which we have been using for quite some time, runs
>>>>>>> perfectly with identical data and setup.
>>>>>>>
>>>>>>> Please contact me if you need specifics on hardware, OS or anything
>>>>>>> else.
>>>>>>>
>>>>>>> Best regards
>>>>>>> Thomas
>>>>>>>
>>>>>>> --
>>>>>>> Thomas Hackl
>>>>>>> Julius-Maximilians-Universit?t
>>>>>>> Department of Bioinformatics
>>>>>>> 97074 W?rzburg, Germany
>>>>>>> Fon: +49 931 - 31 86883
>>>>>>> Mail: thomas.hackl at uni-wuerzburg.de
>>>>>>> <mailto:thomas.hackl at uni-wuerzburg.de>
>>>>>>>
>>>>>>>
>>>>>>> _______________________________________________
>>>>>>> maker-devel mailing list
>>>>>>> maker-devel at box290.bluehost.com
>>>>>>> <mailto:maker-devel at box290.bluehost.com>
>>>>>>>
>>>>>>> 
>>>>>>>http://box290.bluehost.com/mailman/listinfo/maker-devel_yandell-lab.
>>>>>>>or
>>>>>>> g
>>>>>
>>>>> --
>>>>> Thomas Hackl
>>>>> Julius-Maximilians-Universit?t
>>>>> Department of Bioinformatics
>>>>> 97074 W?rzburg, Germany
>>>>> Fon: +49 931 - 31 86883
>>>>> Mail: thomas.hackl at uni-wuerzburg.de
>>>>> <mailto:thomas.hackl at uni-wuerzburg.de>
>>>>>
>>>>>
>>>>> _______________________________________________
>>>>> maker-devel mailing list
>>>>> maker-devel at box290.bluehost.com
>>>>> <mailto:maker-devel at box290.bluehost.com>
>>>>> 
>>>>>http://box290.bluehost.com/mailman/listinfo/maker-devel_yandell-lab.or
>>>>>g
>>>> Barry Moore
>>>> Research Scientist
>>>> Dept. of Human Genetics
>>>> University of Utah
>>>> Salt Lake City, UT 84112
>>>> --------------------------------------------
>>>> (801) 585-3543
>>>>
>>>>
>>>>
>>>>
>>>>
>>>>
>>>> _______________________________________________
>>>> maker-devel mailing list
>>>> maker-devel at box290.bluehost.com
>>>> 
>>>>http://box290.bluehost.com/mailman/listinfo/maker-devel_yandell-lab.org
>>> _______________________________________________
>>> maker-devel mailing list
>>> maker-devel at box290.bluehost.com
>>> http://box290.bluehost.com/mailman/listinfo/maker-devel_yandell-lab.org
>
>-- 
>Thomas Hackl
>Julius-Maximilians-Universit?t
>Department of Bioinformatics
>97074 W?rzburg, Germany
>Fon:  +49 931 - 31 86883
>Mail: thomas.hackl at uni-wuerzburg.de
>
>_______________________________________________
>maker-devel mailing list
>maker-devel at box290.bluehost.com
>http://box290.bluehost.com/mailman/listinfo/maker-devel_yandell-lab.org





From seoanezonjic at hotmail.com  Thu Mar 22 04:38:39 2012
From: seoanezonjic at hotmail.com (Seoane Zonjic)
Date: Thu, 22 Mar 2012 02:38:39 -0700 (PDT)
Subject: [maker-devel] Error: Can't call method "num_hsps" on unblessed
	reference
Message-ID: <16b63903-4205-4064-ab30-efe67b37f7fa@b18g2000vbz.googlegroups.com>

Hi!
First, sorry for my poor english. I updated Maker at last release and
I have triying it with a set of contigs. With one of contigs, Maker
give me this error:

Processing transcripts into genes
Calculating annotation quality statistics
Can't call method "num_hsps" on unblessed referenceERROR: Failed while
adding statistics to annotations
ERROR: Chunk failed at level:3, tier_type:3
FAILED CONTIG:contig_4_0

ERROR: Chunk failed at level:7, tier_type:0
FAILED CONTIG:contig_4_0

At first, I thought that problem were the length of contig (125Kb). I
cut the the sequence in parts of 10Kb but a part again give me the
same error. I have worked with the debugger version of maker (I took
it of post of segmentation fault).
The input fasta (the part that failed me) and all logs are in this
link:
http://dl.dropbox.com/u/54903225/log.tar.gz
Other contigs of same set,  bigger or equal, work fine without
problem. There are something in this sequence that broken the Maker
run.
Thanks in advance



From carsonhh at gmail.com  Thu Mar 22 09:36:37 2012
From: carsonhh at gmail.com (Carson Holt)
Date: Thu, 22 Mar 2012 10:36:37 -0400
Subject: [maker-devel] Error: Can't call method "num_hsps" on unblessed
 reference
In-Reply-To: <16b63903-4205-4064-ab30-efe67b37f7fa@b18g2000vbz.googlegroups.com>
Message-ID: <CB90B0FA.9946%carsonhh@gmail.com>

Could you make a tarball of this directory and send it to me exactly as is
 --> 
/export/home_users/home/cvi_114_uma/pedro/testmaker/Spliced2.maker.output/S
pliced2_datastore/72/86/contig_4_0/

Thanks,
Carson


On 12-03-22 5:38 AM, "Seoane Zonjic" <seoanezonjic at hotmail.com> wrote:

>Hi!
>First, sorry for my poor english. I updated Maker at last release and
>I have triying it with a set of contigs. With one of contigs, Maker
>give me this error:
>
>Processing transcripts into genes
>Calculating annotation quality statistics
>Can't call method "num_hsps" on unblessed referenceERROR: Failed while
>adding statistics to annotations
>ERROR: Chunk failed at level:3, tier_type:3
>FAILED CONTIG:contig_4_0
>
>ERROR: Chunk failed at level:7, tier_type:0
>FAILED CONTIG:contig_4_0
>
>At first, I thought that problem were the length of contig (125Kb). I
>cut the the sequence in parts of 10Kb but a part again give me the
>same error. I have worked with the debugger version of maker (I took
>it of post of segmentation fault).
>The input fasta (the part that failed me) and all logs are in this
>link:
>http://dl.dropbox.com/u/54903225/log.tar.gz
>Other contigs of same set,  bigger or equal, work fine without
>problem. There are something in this sequence that broken the Maker
>run.
>Thanks in advance
>
>_______________________________________________
>maker-devel mailing list
>maker-devel at box290.bluehost.com
>http://box290.bluehost.com/mailman/listinfo/maker-devel_yandell-lab.org





From thomas.hackl at uni-wuerzburg.de  Mon Mar 26 05:51:48 2012
From: thomas.hackl at uni-wuerzburg.de (Thomas Hackl)
Date: Mon, 26 Mar 2012 12:51:48 +0200
Subject: [maker-devel] maker 2.22/2.23: Segmentation fault while
 processing FASTA input
In-Reply-To: <CB8FC294.9902%carsonhh@gmail.com>
References: <CB8FC294.9902%carsonhh@gmail.com>
Message-ID: <4F704A44.2080707@uni-wuerzburg.de>

Hi,

I was finally able to "fix" the Problem. I tried everything you 
suggested, nice catch on my screwed up Perl lib path btw, but I could 
neither install GDBM_File or NDBM_File nor Berkley_DB separately. In the 
end I simply removed the  ISA relations to the modules in question from 
the source code and now it seems to works fine...

sed -i 's/qw(DB_File GDBM_File NDBM_File SDBM_File)/qw(DB_File)/'

So thanks a lot for your prompt and comprehensive response, the debug 
executables and the help with the messages.

Regards
Thomas



Am 21.03.2012 23:05, schrieb Carson Holt:
> That is likely the strangest result I could imagine?  The --debug option
> really only cause MAKER to print status messages everywhere and nothing
> else, so there must be something else going on between the tests.
>
>
> One things I did notice from the error log though -->
> 0.49	Inline	/home/s187512/perl/lib/perl5/site_perl/5.12.1/Inline.pm
> 	UNKNOWN	Inline::denter	/home/s187512/perl/lib/perl5/site_perl/5.12.1/Inlin
> e/denter.pm
>
>
> These are both being loaded from perl 5.12.1 (you are using 5.14.1).  That
> can cause issues since I know the first one is executed at the C level and
> I wouldn't be surprised if the same is true on the second one.
>
>
>
> I also saw this -->
> Can't locate package GDBM_File for @AnyDBM_File::ISA at
> /storage/tmp/software/perl-5.14.1/lib/5.14.1/x86_64-linux-thread-multi/DB_F
> ile.pm line 293.
> Can't locate package NDBM_File for @AnyDBM_File::ISA at
> /storage/tmp/software/perl-5.14.1/lib/5.14.1/x86_64-linux-thread-multi/DB_F
> ile.pm line 293.
> Can't locate package SDBM_File for @AnyDBM_File::ISA at
> /storage/tmp/software/perl-5.14.1/lib/5.14.1/x86_64-linux-thread-multi/DB_F
> ile.pm line 293.
>
>
>
> This appears could be related to Bio::DB::Fasta (which would make sense
> with the timing of the seg fault).  This is line 405 in the BEGIN
> statement for Bio::DB::Fasta
> -->   @AnyDBM_File::ISA = qw(DB_File GDBM_File NDBM_File SDBM_File)
>
> I'm not sure what to do about those?  Are you able to install GDBM_File,
> NDBM_File, or SDBM_File by themselves?  They really should just be
> optional?  I know I don't have NDBM_File, and I don't get an error.
> DB_File is part of the perl distribution, but can be updated via CPAN.
> Perhaps that would be good to do.  It may just be that DB_file is broken
> and falling back to the other modules doesn?t work because you don't have
> them.  There is also the chance that the issue is really with Berkley_DB.
> DB_File accesses Berkley_DB and it wants version 1.x, but will work with
> 2.x and 3.x.  You may need to even go as far as building a new Berkley_DB.
>
> Well that's enough to try for now.
>
> Thanks,
> Carson
>
>
> On 12-03-20 2:16 PM, "Thomas Hackl"<thomas.hackl at uni-wuerzburg.de>  wrote:
>
>> Hi,
>>
>> I installed and ran the debug version of maker. Without -debug it
>> results in the expected segmentation fault. With -debug it paradoxically
>> finishes without the error.
>>
>> I screened the debug log anyway but could not find anything that helped
>> me to localize the problem. I attached a condensed version (sort | uniq)
>> of the log.
>> Any ideas are appreciated.
>>
>> Regards
>> Thomas
>>
>>
>>
>> Am 19.03.2012 17:24, schrieb Carson Holt:
>>> Ok.  I finished the special debug version over the weekend.  Run with
>>> -debug set as a command line flag.  Capture and return the STDERR on
>>> failure.  It will list all modules used, the versions, and when they are
>>> called so we can see what happens right before failure.
>>>
>>> http://yandell-lab.org/research/maker_debug.tgz
>>>
>>>
>>> Thanks,
>>> Carson
>>>
>>>
>>>
>>> On 12-03-14 1:57 AM, "Felix Bemm"<felix.bemm at uni-wuerzburg.de>   wrote:
>>>
>>>> Hi,
>>>>
>>>> Thomas and I are colleagues and dealing with the same problem here. I
>>>> wrote some test code that forced the indexing and it work fine. We are
>>>> using most of the bioperl seqio and db modules in combination with
>>>> other
>>>> tools and don't experience the same problem there at the moment.
>>>>
>>>> Regards
>>>> Felix
>>>>
>>>> Am 13.03.2012 22:37, schrieb Barry Moore:
>>>>> You might also try a short perl script outside of MAKER to exercise
>>>>> Bio::DB::Fasta (which I believe is the module MAKER uses for Fasta
>>>>> indexing - correct Carson?).
>>>>>
>>>>> Something like this should work to force indexing:
>>>>>
>>>>> useBio::DB::Fasta;
>>>>> my $db = Bio::DB::Fasta->new('/path/to/fasta/files');
>>>>> my$seq=$db->seq($seqid, $start, $end);
>>>>>
>>>>> Point it at your fasta directory or file.
>>>>>
>>>>> B
>>>>>
>>>>> On Mar 13, 2012, at 3:41 AM, Thomas Hackl wrote:
>>>>>
>>>>>> Hello,
>>>>>>
>>>>>> We reinstalled the packages you suggested
>>>>>>
>>>>>> forks is up to date (0.34).
>>>>>> forks::shared is up to date (0.34).
>>>>>> Inline::C is up to date (0.50).
>>>>>> Storable is up to date (2.30).
>>>>>>
>>>>>> as well as BioPerl.
>>>>>>
>>>>>> The problem is still the same.
>>>>>>
>>>>>> With MPI it terminates with this message:
>>>>>>
>>>>>> STATUS: Parsing control files...
>>>>>> STATUS: Processing and indexing input FASTA files...
>>>>>>
>>>>>>
>>>>>> ======================================================================
>>>>>> ==
>>>>>> =============
>>>>>>
>>>>>>
>>>>>> = BAD TERMINATION OF ONE OF YOUR APPLICATION PROCESSES
>>>>>> = EXIT CODE: 11
>>>>>> = CLEANING UP REMAINING PROCESSES
>>>>>> = YOU CAN IGNORE THE BELOW CLEANUP MESSAGES
>>>>>>
>>>>>>
>>>>>> ======================================================================
>>>>>> ==
>>>>>> =============
>>>>>>
>>>>>> APPLICATION TERMINATED WITH THE EXIT STRING: Segmentation fault
>>>>>> (signal 11)
>>>>>>
>>>>>> which I presume is also the same problem.
>>>>>>
>>>>>> I am with you that the error is caused somewhere on the C level. If
>>>>>> the indexing step
>>>>>> is handled by non-maker modules exclusively, than the fact that the
>>>>>> 2.15 version works,
>>>>>> suggests that you are using different modules/methods in the current
>>>>>> releases?
>>>>>>
>>>>>> In any case, I think a version with verbose status messages might
>>>>>> help
>>>>>> to localize the
>>>>>> source of the problem.
>>>>>>
>>>>>> Regards
>>>>>> Thomas
>>>>>>
>>>>>> Am 07.03.2012 23:45, schrieb Carson Holt:
>>>>>>> There should be no new hardware requirement. But there is always a
>>>>>>> chance
>>>>>>> that there is an issue with one of the perl modules being used. I
>>>>>>> assume
>>>>>>> the failure is happening when using maker serially and you are not
>>>>>>> using
>>>>>>> MPI.
>>>>>>>
>>>>>>> Could you reinstall the following perl modules, and try again. If
>>>>>>> you
>>>>>>> are
>>>>>>> using CPAN, do a 'force install' to force it to reinstall.
>>>>>>>
>>>>>>> Modules:
>>>>>>> *Storable
>>>>>>> *Inline::C
>>>>>>> *forks
>>>>>>> *forks::shared
>>>>>>>
>>>>>>> Also try reinstalling the latest version of BioPerl.
>>>>>>>
>>>>>>> The fact that this is a seg fault suggests that something is
>>>>>>> happemning at
>>>>>>> the C level (just outside of Perl). Those area all the modules MAKER
>>>>>>> uses
>>>>>>> that will call back to the C level. BioPerl has a fasta indexing
>>>>>>> module
>>>>>>> that is also making calls outside of Perl, and the fact it fails at
>>>>>>> that
>>>>>>> point makes it a suspect.
>>>>>>>
>>>>>>> Let me know what happens. I can always generate an alternate MAKER
>>>>>>> executable for you to run with additional status messages that may
>>>>>>> help
>>>>>>> identify exactly which module is being called right before the
>>>>>>> failure.
>>>>>>>
>>>>>>> Thanks,
>>>>>>> Carson
>>>>>>>
>>>>>>>
>>>>>>>
>>>>>>> On 12-03-07 3:31 AM, "Thomas Hackl"<thomas.hackl at uni-wuerzburg.de
>>>>>>> <mailto:thomas.hackl at uni-wuerzburg.de>>   wrote:
>>>>>>>
>>>>>>>> Hello,
>>>>>>>>
>>>>>>>> we want to use a current release of maker (2.22, 2.23) but the
>>>>>>>> program
>>>>>>>> terminates with a seg fault while processing the input FASTA files.
>>>>>>>> maker 2.15 , which we have been using for quite some time, runs
>>>>>>>> perfectly with identical data and setup.
>>>>>>>>
>>>>>>>> Please contact me if you need specifics on hardware, OS or anything
>>>>>>>> else.
>>>>>>>>
>>>>>>>> Best regards
>>>>>>>> Thomas
>>>>>>>>
>>>>>>>> --
>>>>>>>> Thomas Hackl
>>>>>>>> Julius-Maximilians-Universit?t
>>>>>>>> Department of Bioinformatics
>>>>>>>> 97074 W?rzburg, Germany
>>>>>>>> Fon: +49 931 - 31 86883
>>>>>>>> Mail: thomas.hackl at uni-wuerzburg.de
>>>>>>>> <mailto:thomas.hackl at uni-wuerzburg.de>
>>>>>>>>
>>>>>>>>
>>>>>>>> _______________________________________________
>>>>>>>> maker-devel mailing list
>>>>>>>> maker-devel at box290.bluehost.com
>>>>>>>> <mailto:maker-devel at box290.bluehost.com>
>>>>>>>>
>>>>>>>>
>>>>>>>> http://box290.bluehost.com/mailman/listinfo/maker-devel_yandell-lab.
>>>>>>>> or
>>>>>>>> g
>>>>>> --
>>>>>> Thomas Hackl
>>>>>> Julius-Maximilians-Universit?t
>>>>>> Department of Bioinformatics
>>>>>> 97074 W?rzburg, Germany
>>>>>> Fon: +49 931 - 31 86883
>>>>>> Mail: thomas.hackl at uni-wuerzburg.de
>>>>>> <mailto:thomas.hackl at uni-wuerzburg.de>
>>>>>>
>>>>>>
>>>>>> _______________________________________________
>>>>>> maker-devel mailing list
>>>>>> maker-devel at box290.bluehost.com
>>>>>> <mailto:maker-devel at box290.bluehost.com>
>>>>>>
>>>>>> http://box290.bluehost.com/mailman/listinfo/maker-devel_yandell-lab.or
>>>>>> g
>>>>> Barry Moore
>>>>> Research Scientist
>>>>> Dept. of Human Genetics
>>>>> University of Utah
>>>>> Salt Lake City, UT 84112
>>>>> --------------------------------------------
>>>>> (801) 585-3543
>>>>>
>>>>>
>>>>>
>>>>>
>>>>>
>>>>>
>>>>> _______________________________________________
>>>>> maker-devel mailing list
>>>>> maker-devel at box290.bluehost.com
>>>>>
>>>>> http://box290.bluehost.com/mailman/listinfo/maker-devel_yandell-lab.org
>>>> _______________________________________________
>>>> maker-devel mailing list
>>>> maker-devel at box290.bluehost.com
>>>> http://box290.bluehost.com/mailman/listinfo/maker-devel_yandell-lab.org
>> --
>> Thomas Hackl
>> Julius-Maximilians-Universit?t
>> Department of Bioinformatics
>> 97074 W?rzburg, Germany
>> Fon:  +49 931 - 31 86883
>> Mail: thomas.hackl at uni-wuerzburg.de
>>
>> _______________________________________________
>> maker-devel mailing list
>> maker-devel at box290.bluehost.com
>> http://box290.bluehost.com/mailman/listinfo/maker-devel_yandell-lab.org


-- 
Thomas Hackl
Julius-Maximilians-Universit?t
Department of Bioinformatics
97074 W?rzburg, Germany
Fon:  +49 931 - 31 86883
Mail: thomas.hackl at uni-wuerzburg.de




From carsonhh at gmail.com  Mon Mar 26 08:01:52 2012
From: carsonhh at gmail.com (Carson Holt)
Date: Mon, 26 Mar 2012 09:01:52 -0400
Subject: [maker-devel] maker 2.22/2.23: Segmentation fault while
 processing FASTA input
In-Reply-To: <4F704A44.2080707@uni-wuerzburg.de>
Message-ID: <CB95E04E.9E8B%carsonhh@gmail.com>

Well, if that works, I'd call it a success.  Just be careful with any
future updates to BioPerl.  Since the root cause of the problem may still
be there.

Thanks,
Carson




On 12-03-26 6:51 AM, "Thomas Hackl" <thomas.hackl at uni-wuerzburg.de> wrote:

>Hi,
>
>I was finally able to "fix" the Problem. I tried everything you
>suggested, nice catch on my screwed up Perl lib path btw, but I could
>neither install GDBM_File or NDBM_File nor Berkley_DB separately. In the
>end I simply removed the  ISA relations to the modules in question from
>the source code and now it seems to works fine...
>
>sed -i 's/qw(DB_File GDBM_File NDBM_File SDBM_File)/qw(DB_File)/'
>
>So thanks a lot for your prompt and comprehensive response, the debug
>executables and the help with the messages.
>
>Regards
>Thomas
>
>
>
>Am 21.03.2012 23:05, schrieb Carson Holt:
>> That is likely the strangest result I could imagine?  The --debug option
>> really only cause MAKER to print status messages everywhere and nothing
>> else, so there must be something else going on between the tests.
>>
>>
>> One things I did notice from the error log though -->
>> 0.49	Inline	/home/s187512/perl/lib/perl5/site_perl/5.12.1/Inline.pm
>> 
>>	UNKNOWN	Inline::denter	/home/s187512/perl/lib/perl5/site_perl/5.12.1/Inl
>>in
>> e/denter.pm
>>
>>
>> These are both being loaded from perl 5.12.1 (you are using 5.14.1).
>>That
>> can cause issues since I know the first one is executed at the C level
>>and
>> I wouldn't be surprised if the same is true on the second one.
>>
>>
>>
>> I also saw this -->
>> Can't locate package GDBM_File for @AnyDBM_File::ISA at
>> 
>>/storage/tmp/software/perl-5.14.1/lib/5.14.1/x86_64-linux-thread-multi/DB
>>_F
>> ile.pm line 293.
>> Can't locate package NDBM_File for @AnyDBM_File::ISA at
>> 
>>/storage/tmp/software/perl-5.14.1/lib/5.14.1/x86_64-linux-thread-multi/DB
>>_F
>> ile.pm line 293.
>> Can't locate package SDBM_File for @AnyDBM_File::ISA at
>> 
>>/storage/tmp/software/perl-5.14.1/lib/5.14.1/x86_64-linux-thread-multi/DB
>>_F
>> ile.pm line 293.
>>
>>
>>
>> This appears could be related to Bio::DB::Fasta (which would make sense
>> with the timing of the seg fault).  This is line 405 in the BEGIN
>> statement for Bio::DB::Fasta
>> -->   @AnyDBM_File::ISA = qw(DB_File GDBM_File NDBM_File SDBM_File)
>>
>> I'm not sure what to do about those?  Are you able to install GDBM_File,
>> NDBM_File, or SDBM_File by themselves?  They really should just be
>> optional?  I know I don't have NDBM_File, and I don't get an error.
>> DB_File is part of the perl distribution, but can be updated via CPAN.
>> Perhaps that would be good to do.  It may just be that DB_file is broken
>> and falling back to the other modules doesn?t work because you don't
>>have
>> them.  There is also the chance that the issue is really with
>>Berkley_DB.
>> DB_File accesses Berkley_DB and it wants version 1.x, but will work with
>> 2.x and 3.x.  You may need to even go as far as building a new
>>Berkley_DB.
>>
>> Well that's enough to try for now.
>>
>> Thanks,
>> Carson
>>
>>
>> On 12-03-20 2:16 PM, "Thomas Hackl"<thomas.hackl at uni-wuerzburg.de>
>>wrote:
>>
>>> Hi,
>>>
>>> I installed and ran the debug version of maker. Without -debug it
>>> results in the expected segmentation fault. With -debug it
>>>paradoxically
>>> finishes without the error.
>>>
>>> I screened the debug log anyway but could not find anything that helped
>>> me to localize the problem. I attached a condensed version (sort |
>>>uniq)
>>> of the log.
>>> Any ideas are appreciated.
>>>
>>> Regards
>>> Thomas
>>>
>>>
>>>
>>> Am 19.03.2012 17:24, schrieb Carson Holt:
>>>> Ok.  I finished the special debug version over the weekend.  Run with
>>>> -debug set as a command line flag.  Capture and return the STDERR on
>>>> failure.  It will list all modules used, the versions, and when they
>>>>are
>>>> called so we can see what happens right before failure.
>>>>
>>>> http://yandell-lab.org/research/maker_debug.tgz
>>>>
>>>>
>>>> Thanks,
>>>> Carson
>>>>
>>>>
>>>>
>>>> On 12-03-14 1:57 AM, "Felix Bemm"<felix.bemm at uni-wuerzburg.de>
>>>>wrote:
>>>>
>>>>> Hi,
>>>>>
>>>>> Thomas and I are colleagues and dealing with the same problem here. I
>>>>> wrote some test code that forced the indexing and it work fine. We
>>>>>are
>>>>> using most of the bioperl seqio and db modules in combination with
>>>>> other
>>>>> tools and don't experience the same problem there at the moment.
>>>>>
>>>>> Regards
>>>>> Felix
>>>>>
>>>>> Am 13.03.2012 22:37, schrieb Barry Moore:
>>>>>> You might also try a short perl script outside of MAKER to exercise
>>>>>> Bio::DB::Fasta (which I believe is the module MAKER uses for Fasta
>>>>>> indexing - correct Carson?).
>>>>>>
>>>>>> Something like this should work to force indexing:
>>>>>>
>>>>>> useBio::DB::Fasta;
>>>>>> my $db = Bio::DB::Fasta->new('/path/to/fasta/files');
>>>>>> my$seq=$db->seq($seqid, $start, $end);
>>>>>>
>>>>>> Point it at your fasta directory or file.
>>>>>>
>>>>>> B
>>>>>>
>>>>>> On Mar 13, 2012, at 3:41 AM, Thomas Hackl wrote:
>>>>>>
>>>>>>> Hello,
>>>>>>>
>>>>>>> We reinstalled the packages you suggested
>>>>>>>
>>>>>>> forks is up to date (0.34).
>>>>>>> forks::shared is up to date (0.34).
>>>>>>> Inline::C is up to date (0.50).
>>>>>>> Storable is up to date (2.30).
>>>>>>>
>>>>>>> as well as BioPerl.
>>>>>>>
>>>>>>> The problem is still the same.
>>>>>>>
>>>>>>> With MPI it terminates with this message:
>>>>>>>
>>>>>>> STATUS: Parsing control files...
>>>>>>> STATUS: Processing and indexing input FASTA files...
>>>>>>>
>>>>>>>
>>>>>>> 
>>>>>>>====================================================================
>>>>>>>==
>>>>>>> ==
>>>>>>> =============
>>>>>>>
>>>>>>>
>>>>>>> = BAD TERMINATION OF ONE OF YOUR APPLICATION PROCESSES
>>>>>>> = EXIT CODE: 11
>>>>>>> = CLEANING UP REMAINING PROCESSES
>>>>>>> = YOU CAN IGNORE THE BELOW CLEANUP MESSAGES
>>>>>>>
>>>>>>>
>>>>>>> 
>>>>>>>====================================================================
>>>>>>>==
>>>>>>> ==
>>>>>>> =============
>>>>>>>
>>>>>>> APPLICATION TERMINATED WITH THE EXIT STRING: Segmentation fault
>>>>>>> (signal 11)
>>>>>>>
>>>>>>> which I presume is also the same problem.
>>>>>>>
>>>>>>> I am with you that the error is caused somewhere on the C level. If
>>>>>>> the indexing step
>>>>>>> is handled by non-maker modules exclusively, than the fact that the
>>>>>>> 2.15 version works,
>>>>>>> suggests that you are using different modules/methods in the
>>>>>>>current
>>>>>>> releases?
>>>>>>>
>>>>>>> In any case, I think a version with verbose status messages might
>>>>>>> help
>>>>>>> to localize the
>>>>>>> source of the problem.
>>>>>>>
>>>>>>> Regards
>>>>>>> Thomas
>>>>>>>
>>>>>>> Am 07.03.2012 23:45, schrieb Carson Holt:
>>>>>>>> There should be no new hardware requirement. But there is always a
>>>>>>>> chance
>>>>>>>> that there is an issue with one of the perl modules being used. I
>>>>>>>> assume
>>>>>>>> the failure is happening when using maker serially and you are not
>>>>>>>> using
>>>>>>>> MPI.
>>>>>>>>
>>>>>>>> Could you reinstall the following perl modules, and try again. If
>>>>>>>> you
>>>>>>>> are
>>>>>>>> using CPAN, do a 'force install' to force it to reinstall.
>>>>>>>>
>>>>>>>> Modules:
>>>>>>>> *Storable
>>>>>>>> *Inline::C
>>>>>>>> *forks
>>>>>>>> *forks::shared
>>>>>>>>
>>>>>>>> Also try reinstalling the latest version of BioPerl.
>>>>>>>>
>>>>>>>> The fact that this is a seg fault suggests that something is
>>>>>>>> happemning at
>>>>>>>> the C level (just outside of Perl). Those area all the modules
>>>>>>>>MAKER
>>>>>>>> uses
>>>>>>>> that will call back to the C level. BioPerl has a fasta indexing
>>>>>>>> module
>>>>>>>> that is also making calls outside of Perl, and the fact it fails
>>>>>>>>at
>>>>>>>> that
>>>>>>>> point makes it a suspect.
>>>>>>>>
>>>>>>>> Let me know what happens. I can always generate an alternate MAKER
>>>>>>>> executable for you to run with additional status messages that may
>>>>>>>> help
>>>>>>>> identify exactly which module is being called right before the
>>>>>>>> failure.
>>>>>>>>
>>>>>>>> Thanks,
>>>>>>>> Carson
>>>>>>>>
>>>>>>>>
>>>>>>>>
>>>>>>>> On 12-03-07 3:31 AM, "Thomas Hackl"<thomas.hackl at uni-wuerzburg.de
>>>>>>>> <mailto:thomas.hackl at uni-wuerzburg.de>>   wrote:
>>>>>>>>
>>>>>>>>> Hello,
>>>>>>>>>
>>>>>>>>> we want to use a current release of maker (2.22, 2.23) but the
>>>>>>>>> program
>>>>>>>>> terminates with a seg fault while processing the input FASTA
>>>>>>>>>files.
>>>>>>>>> maker 2.15 , which we have been using for quite some time, runs
>>>>>>>>> perfectly with identical data and setup.
>>>>>>>>>
>>>>>>>>> Please contact me if you need specifics on hardware, OS or
>>>>>>>>>anything
>>>>>>>>> else.
>>>>>>>>>
>>>>>>>>> Best regards
>>>>>>>>> Thomas
>>>>>>>>>
>>>>>>>>> --
>>>>>>>>> Thomas Hackl
>>>>>>>>> Julius-Maximilians-Universit?t
>>>>>>>>> Department of Bioinformatics
>>>>>>>>> 97074 W?rzburg, Germany
>>>>>>>>> Fon: +49 931 - 31 86883
>>>>>>>>> Mail: thomas.hackl at uni-wuerzburg.de
>>>>>>>>> <mailto:thomas.hackl at uni-wuerzburg.de>
>>>>>>>>>
>>>>>>>>>
>>>>>>>>> _______________________________________________
>>>>>>>>> maker-devel mailing list
>>>>>>>>> maker-devel at box290.bluehost.com
>>>>>>>>> <mailto:maker-devel at box290.bluehost.com>
>>>>>>>>>
>>>>>>>>>
>>>>>>>>> 
>>>>>>>>>http://box290.bluehost.com/mailman/listinfo/maker-devel_yandell-la
>>>>>>>>>b.
>>>>>>>>> or
>>>>>>>>> g
>>>>>>> --
>>>>>>> Thomas Hackl
>>>>>>> Julius-Maximilians-Universit?t
>>>>>>> Department of Bioinformatics
>>>>>>> 97074 W?rzburg, Germany
>>>>>>> Fon: +49 931 - 31 86883
>>>>>>> Mail: thomas.hackl at uni-wuerzburg.de
>>>>>>> <mailto:thomas.hackl at uni-wuerzburg.de>
>>>>>>>
>>>>>>>
>>>>>>> _______________________________________________
>>>>>>> maker-devel mailing list
>>>>>>> maker-devel at box290.bluehost.com
>>>>>>> <mailto:maker-devel at box290.bluehost.com>
>>>>>>>
>>>>>>> 
>>>>>>>http://box290.bluehost.com/mailman/listinfo/maker-devel_yandell-lab.
>>>>>>>or
>>>>>>> g
>>>>>> Barry Moore
>>>>>> Research Scientist
>>>>>> Dept. of Human Genetics
>>>>>> University of Utah
>>>>>> Salt Lake City, UT 84112
>>>>>> --------------------------------------------
>>>>>> (801) 585-3543
>>>>>>
>>>>>>
>>>>>>
>>>>>>
>>>>>>
>>>>>>
>>>>>> _______________________________________________
>>>>>> maker-devel mailing list
>>>>>> maker-devel at box290.bluehost.com
>>>>>>
>>>>>> 
>>>>>>http://box290.bluehost.com/mailman/listinfo/maker-devel_yandell-lab.o
>>>>>>rg
>>>>> _______________________________________________
>>>>> maker-devel mailing list
>>>>> maker-devel at box290.bluehost.com
>>>>> 
>>>>>http://box290.bluehost.com/mailman/listinfo/maker-devel_yandell-lab.or
>>>>>g
>>> --
>>> Thomas Hackl
>>> Julius-Maximilians-Universit?t
>>> Department of Bioinformatics
>>> 97074 W?rzburg, Germany
>>> Fon:  +49 931 - 31 86883
>>> Mail: thomas.hackl at uni-wuerzburg.de
>>>
>>> _______________________________________________
>>> maker-devel mailing list
>>> maker-devel at box290.bluehost.com
>>> http://box290.bluehost.com/mailman/listinfo/maker-devel_yandell-lab.org
>
>
>-- 
>Thomas Hackl
>Julius-Maximilians-Universit?t
>Department of Bioinformatics
>97074 W?rzburg, Germany
>Fon:  +49 931 - 31 86883
>Mail: thomas.hackl at uni-wuerzburg.de
>
>
>_______________________________________________
>maker-devel mailing list
>maker-devel at box290.bluehost.com
>http://box290.bluehost.com/mailman/listinfo/maker-devel_yandell-lab.org





From daniel.fer.u at gmail.com  Sun Mar 25 21:53:25 2012
From: daniel.fer.u at gmail.com (=?UTF-8?Q?Daniel_Fern=C3=A1ndez?=)
Date: Sun, 25 Mar 2012 19:53:25 -0700 (PDT)
Subject: [maker-devel] Problem with RMBlast installation
Message-ID: <8109224.101.1332730405163.JavaMail.geo-discussion-forums@ynlx41>

Hi,

I trying to install MAKER, I don't have WU-Blast, I have Blast+ so in the 
README file tell me that I need RMBlast, but I don't know what file I have 
to choose, rmblast-1.2-ncbi-blast-2.2.23+-src.tar.gz or rmblast-1.2-ncbi-blast-2.2.23+-x64-linux.tar.gz 
(I have Linux 64-bit) in each version the README file is the same, and 
there tell me how I can install it, but the instructions is only for rmblast-1.2-ncbi-blast-2.2.23+-src, 
well, when I try to install it, I type this 
$./configure --with-mt --prefix=/usr/local/bioinfo/repeatmasker/rmblast 
--without-debug
This show me error, and I type make and this show stop.

Can you help me please?

This show me when I type $./configure --with-mt 
--prefix=/usr/local/bioinfo/repeatmasker/rmblast --without-debug
-----------------------------------------------------------------------------------------------------------------------------------------------
configure: loading site script ./src/build-system/config.site
configure: loading cache config.cache
checking build system type... x86_64-unknown-linux-gnu
checking host system type... x86_64-unknown-linux-gnu
checking for a BSD-compatible install... /usr/bin/install -c
checking for gcc... gcc
checking for C compiler default output file name... a.out
checking whether the C compiler works... yes
checking whether we are cross compiling... no
checking for suffix of executables... 
checking for suffix of object files... o
checking whether we are using the GNU C compiler... yes
checking whether gcc accepts -g... yes
checking for gcc option to accept ANSI C... none needed
checking for g++... no
checking for c++... no
checking for gpp... no
checking for aCC... no
checking for CC... no
checking for cxx... no
checking for cc++... no
checking for cl... no
checking for FCC... no
checking for KCC... no
checking for RCC... no
checking for xlC_r... no
checking for xlC... no
checking whether we are using the GNU C++ compiler... no
checking whether g++ accepts -g... no
adjusted C   compiler: /usr/bin/gcc 
./src/build-system/configure: line 4404: type: g++: not found
dirname: missing operand
Try `dirname --help' for more information.
configure: error: Do not know how to build MT-safe with compiler g++ 
./src/build-system/configure: line 4187: g++: command not found
-----------------------------------------------------------------------------------------------------------------------------------
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From jason.stajich at gmail.com  Mon Mar 26 10:33:55 2012
From: jason.stajich at gmail.com (Jason Stajich)
Date: Mon, 26 Mar 2012 08:33:55 -0700
Subject: [maker-devel] Problem with RMBlast installation
In-Reply-To: <8109224.101.1332730405163.JavaMail.geo-discussion-forums@ynlx41>
References: <8109224.101.1332730405163.JavaMail.geo-discussion-forums@ynlx41>
Message-ID: <7A26C949-4ED3-4CEF-8455-2D3A85B35A2B@gmail.com>

Hi Daniel -

Just download, unpackage the precompiled ( rmblast-1.2-ncbi-blast-2.2.23+-x64-linux.tar.gz ) version and tell RepeatMasker where the exes are when you configure RepeatMasker.  RMBlast is for RepeatMasker.
 
For running BLAST in MAKAER would install NCBI-BLAST+ if you don't have wu-blast --- ftp://ftp.ncbi.nih.gov/blast/executables/blast+/LATEST - I believe current maker supports BLAST+, BLAST, and WU-BLAST so you have your pick.

Jason
On Mar 25, 2012, at 7:53 PM, Daniel Fern?ndez wrote:

> Hi,
> 
> I trying to install MAKER, I don't have WU-Blast, I have Blast+ so in the README file tell me that I need RMBlast, but I don't know what file I have to choose, rmblast-1.2-ncbi-blast-2.2.23+-src.tar.gz or rmblast-1.2-ncbi-blast-2.2.23+-x64-linux.tar.gz (I have Linux 64-bit) in each version the README file is the same, and there tell me how I can install it, but the instructions is only for rmblast-1.2-ncbi-blast-2.2.23+-src, well, when I try to install it, I type this 
> $./configure --with-mt --prefix=/usr/local/bioinfo/repeatmasker/rmblast --without-debug
> This show me error, and I type make and this show stop.
> 
> Can you help me please?
> 
> This show me when I type $./configure --with-mt --prefix=/usr/local/bioinfo/repeatmasker/rmblast --without-debug
> -----------------------------------------------------------------------------------------------------------------------------------------------
> configure: loading site script ./src/build-system/config.site
> configure: loading cache config.cache
> checking build system type... x86_64-unknown-linux-gnu
> checking host system type... x86_64-unknown-linux-gnu
> checking for a BSD-compatible install... /usr/bin/install -c
> checking for gcc... gcc
> checking for C compiler default output file name... a.out
> checking whether the C compiler works... yes
> checking whether we are cross compiling... no
> checking for suffix of executables... 
> checking for suffix of object files... o
> checking whether we are using the GNU C compiler... yes
> checking whether gcc accepts -g... yes
> checking for gcc option to accept ANSI C... none needed
> checking for g++... no
> checking for c++... no
> checking for gpp... no
> checking for aCC... no
> checking for CC... no
> checking for cxx... no
> checking for cc++... no
> checking for cl... no
> checking for FCC... no
> checking for KCC... no
> checking for RCC... no
> checking for xlC_r... no
> checking for xlC... no
> checking whether we are using the GNU C++ compiler... no
> checking whether g++ accepts -g... no
> adjusted C   compiler: /usr/bin/gcc 
> ./src/build-system/configure: line 4404: type: g++: not found
> dirname: missing operand
> Try `dirname --help' for more information.
> configure: error: Do not know how to build MT-safe with compiler g++ ./src/build-system/configure: line 4187: g++: command not found
> -----------------------------------------------------------------------------------------------------------------------------------
> _______________________________________________
> maker-devel mailing list
> maker-devel at box290.bluehost.com
> http://box290.bluehost.com/mailman/listinfo/maker-devel_yandell-lab.org

Jason Stajich
jason.stajich at gmail.com
jason at bioperl.org

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From eernst at cshl.edu  Mon Mar 26 11:29:45 2012
From: eernst at cshl.edu (Evan)
Date: Mon, 26 Mar 2012 09:29:45 -0700 (PDT)
Subject: [maker-devel] Can't call method "start" on an undefined value
Message-ID: <31251549.92.1332779385632.JavaMail.geo-discussion-forums@vbbfy7>

Hi,

I'm running maker 2.24-beta. At least 10-15% of scaffolds are failing with 
the following error:

Preparing evidence for hint based annotation
cleaning clusters....
total clusters:1 now processing 0
in cluster::shadow_cluster...
...finished clustering.
cleaning clusters....
total clusters:4 now processing 0
 ...processing 0 of 3
 ...processing 1 of 3
total clusters:4 now processing 0
 ...processing 0 of 2
total clusters:4 now processing 0
total clusters:4 now processing 0
Can't call method "start" on an undefined valueERROR: Failed while 
preparing evidence clusters for annotations
ERROR: Chunk failed at level:0, tier_type:3
FAILED CONTIG:scaffold93.1

ERROR: Chunk failed at level:7, tier_type:0
FAILED CONTIG:scaffold93.1

This occurs when running just a single maker instance. 

Thanks,
Evan
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From carsonhh at gmail.com  Mon Mar 26 12:22:15 2012
From: carsonhh at gmail.com (Carson Holt)
Date: Mon, 26 Mar 2012 13:22:15 -0400
Subject: [maker-devel] maker 2.22-beta: identical names and sequences
 repeated in maker.all.proteins fasta - attached FASTA, gff3
In-Reply-To: <407831381.989320.1332781349591.JavaMail.root@ksu-sfpop-mailstore03>
Message-ID: <CB961AC7.9EF5%carsonhh@gmail.com>

Thanks for the file.  I now see that the issue is caused by repeated model
entries in the maker_gff file (example from the following lines in the
input GFF3).


scaffold09875   maker   mRNA    255     1019    .       +       .
ID=maker-scaffold09875-est_gff_Cufflinks-gene-0.0-mRNA-1;Parent=maker-scaff
old09875-est_gff_Cufflinks-gene-0.0;
scaffold09875   model_gff:maker match   255     1019    .       +       .
     
ID=scaffold09875:hit:419759:0_0;Name=maker-scaffold09875-est_gff_Cufflinks-
gene-0.0-mRNA-1;


During recent MAKER updates, it was requested that MAKER add model_gff
features used from a previous run as a reference annotation, so you can
still see it even when it is not chosen on the second round.  However this
has an unexpected effect on multiple reruns using maker output as the new
input because both entries get interpreted as model_gff, they both then
end up in the results of a rerun (duplicated each round).

I've fixed this in the developers release (be a couple of days till it
hits the download page as a beta release), but in the mean time just
remove the model_gff:maker entries from the input fasta and it will work
as expected.

To do that use this command -->
   grep -v "model_gff:maker"
Msex05162011.genome.all.maker-2.22-15Feb2012.gff3 >
filtered_Msex05162011.genome.all.maker-2.22-15Feb2012.gff3


Then put filtered_Msex05162011.genome.all.maker-2.22-15Feb2012.gff3 as
your maker_gff file.

I also recommend that you delete and .db extension files from the maker
output directory (there will be only one there).  That will make extra
sure that the GFF3 file index gets rebuilt to the new file.

Note:  I also noticed that Msex05162011.genome.cegma.gff is not in GFF3
format (it is in ZFF format).  It would work for training SNAP but will
not work with MAKER.

Thanks,
Carson





On 12-03-26 1:02 PM, "Sanjay Chellapilla" wrote:

>
>
>----- Original Message -----
>> Since you are using it as input.  I'll need to see this file.
>> 
>> 
>>/home/sanjay/manduca_sexta/maker/maker-runs-2.22/Msex05162011.genome.all.
>>ma
>> ker-2.22-15Feb2012.gff3
>> 
>> Thanks,
>> Carson
>> 
>> 
>> 
>> On 12-03-26 12:42 PM, "Sanjay Chellapilla"
>> wrote:
>> 
>> >Attached
>> >"Msex-maker-2.22-identical-repeated-proteins-input-files.tar.bz2"
>> >containing 3 files
>> >
>> >maker-2.22_opts.ctl.28Feb2012
>> >est_gff = baylor_cufflinks_transcripts_gtf_no_G14G15.gff3
>> >model_gff = Msex05162011.genome.cegma.gff
>> >
>> >The maker_gff (Msex05162011.genome.all.maker-2.22-15Feb2012.gff3) is
>> >633MB so I didn't include it in this message. Please let me know if
>> >you'd want to see it - I'll send it separately.
>> >
>> >Thank you,
>> >Sanjay.
>> >
>> >----- Original Message -----
>> >> Could you send me the file you are passing to the est_gff,
>> >> model_gff,
>> >> or
>> >> maker_gff options.
>> >> 
>> >> Also could you send me your MAKER control files?
>> >> 
>> >> Thanks,
>> >> Carson
>> >> 
>> >> 
>> >> 
>> >> 
>> >> On 12-03-14 1:26 PM, "Sanjay Chellapilla"
>> >> wrote:
>> >> 
>> >> >Hi Carson,
>> >> >
>> >> >Sorry I forgot to attach files showing the issue. Attached zip
>> >> >containing one such maker proteins fasta file and corresponding
>> >> >maker gff3 for scaffold00126 having identical repeated sequence
>> >> >">maker-scaffold00126-est_gff_Cufflinks-gene-2.0-mRNA-1".
>> >> >
>> >> >Thank you.
>> >> >
>> >> >----- Forwarded Message -----
>> >> >> Hi Carson,
>> >> >> 
>> >> >> I ran maker-2.22-beta a total of 3 times with the same
>> >> >> evidence,
>> >> >> to annotate the Manduca.sexta genome, each time using
>> >> >> maker-gff3
>> >> >> for the re-annotation run and gene-predictors SNAP, Augustus
>> >> >> trained
>> >> >> on maker-gff3 from the previous run. At the end of the third
>> >> >> run,
>> >> >> I used fasta_merge script to obtain the various fasta files.
>> >> >> I notice that some sequences are repeated in the maker.all
>> >> >> transcripts/proteins fasta files. I found 34 repeated out of
>> >> >> 16128 transcripts/proteins, so there are actually only 16094
>> >> >> unique
>> >> >> sequences. Could this be related to the "repeated genes" issue
>> >> >> from the strange cufflinks cuffmerge gff3 that's used as input
>> >> >> to maker - we discussed this back in January when we first came
>> >> >> across and I had sent you a portion of the gff3 where we saw
>> >> >> this,
>> >> >> and then you recommended trying maker-2.22-beta where this was
>> >> >> fixed
>> >> >> ?
>> >> >> Naturally this also causes repeated short-IDs created using the
>> >> >> maker_map_ids, map_fasta_ids, map_gff_ids scripts.
>> >> >> 
>> >> >> Thanks,
>> >> >> Sanjay.





From carsonhh at gmail.com  Mon Mar 26 14:08:48 2012
From: carsonhh at gmail.com (Carson Holt)
Date: Mon, 26 Mar 2012 15:08:48 -0400
Subject: [maker-devel] FW: Can't call method "start" on an undefined value
In-Reply-To: <CB963617.9F28%carsonhh@gmail.com>
Message-ID: <CB9636EF.9F37%carsonhh@gmail.com>

Ok.  This is fixed (along with a few other things), and is available for
download as MAKER 2.25.

Thanks,
Carson



From:  Evan <eernst at cshl.edu>
Date:  Mon, 26 Mar 2012 09:29:45 -0700 (PDT)
To:  <maker-devel at googlegroups.com>
Subject:  [maker-devel] Can't call method "start" on an undefined value

Hi,

I'm running maker 2.24-beta. At least 10-15% of scaffolds are failing with
the following error:

Preparing evidence for hint based annotation
cleaning clusters....
total clusters:1 now processing 0
in cluster::shadow_cluster...
...finished clustering.
cleaning clusters....
total clusters:4 now processing 0
 ...processing 0 of 3
 ...processing 1 of 3
total clusters:4 now processing 0
 ...processing 0 of 2
total clusters:4 now processing 0
total clusters:4 now processing 0
Can't call method "start" on an undefined valueERROR: Failed while preparing
evidence clusters for annotations
ERROR: Chunk failed at level:0, tier_type:3
FAILED CONTIG:scaffold93.1

ERROR: Chunk failed at level:7, tier_type:0
FAILED CONTIG:scaffold93.1

This occurs when running just a single maker instance.

Thanks,
Evan
_______________________________________________ maker-devel mailing list
maker-devel at box290.bluehost.comhttp://box290.bluehost.com/mailman/listinfo/m
aker-devel_yandell-lab.org


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From carsonhh at gmail.com  Mon Mar 26 15:17:36 2012
From: carsonhh at gmail.com (Carson Holt)
Date: Mon, 26 Mar 2012 16:17:36 -0400
Subject: [maker-devel] Can't call method "start" on an undefined value
In-Reply-To: <CAOqGFX-wEA2weUPSZRrpXBd+gV8nHAEsR9ST-YA96u+q+RvgyA@mail.gmail.com>
Message-ID: <CB964686.9FBB%carsonhh@gmail.com>

 //= is a feature of perl versions 5.10 and above.

You must have an older version of perl.
Just change it to ||= and it will work for older versions.  I'll make that
change to the release as well to make it work with older perl.

Thanks,
Carson




From:  Evan Ernst <eernst at cshl.edu>
Date:  Mon, 26 Mar 2012 16:13:19 -0400
To:  Carson Holt <carsonhh at gmail.com>
Cc:  <maker-devel at googlegroups.com>
Subject:  Re: [maker-devel] Can't call method "start" on an undefined value

Hi Carson,

Line 242 of maker is causing a compilation failure in the version I
downloaded:

241 -> eval "\$ver = \$${name}::VERSION";
242 -> $ver //= 'UNKNOWN';
243 -> $ver = 'UNKNOWN' if($ver =~ /^\-1\,/);

Thanks,
Evan

On Mon, Mar 26, 2012 at 3:06 PM, Evan Ernst <eernst at cshl.edu> wrote:
> Fantastic. Thanks for your help.
> 
> Best,
> Evan
> 
> 
> On Mon, Mar 26, 2012 at 3:05 PM, Carson Holt <carsonhh at gmail.com> wrote:
>> Ok.  This is fixed (along with a few other things), and is available for
>> download as MAKER 2.25.
>> 
>> Thanks,
>> Carson
>> 
>> 
>> 
>> From:  Evan <eernst at cshl.edu>
>> Date:  Mon, 26 Mar 2012 09:29:45 -0700 (PDT)
>> To:  <maker-devel at googlegroups.com>
>> Subject:  [maker-devel] Can't call method "start" on an undefined value
>> 
>> Hi,
>> 
>> I'm running maker 2.24-beta. At least 10-15% of scaffolds are failing with
>> the following error:
>> 
>> Preparing evidence for hint based annotation
>> cleaning clusters....
>> total clusters:1 now processing 0
>> in cluster::shadow_cluster...
>> ...finished clustering.
>> cleaning clusters....
>> total clusters:4 now processing 0
>>  ...processing 0 of 3
>>  ...processing 1 of 3
>> total clusters:4 now processing 0
>>  ...processing 0 of 2
>> total clusters:4 now processing 0
>> total clusters:4 now processing 0
>> Can't call method "start" on an undefined valueERROR: Failed while preparing
>> evidence clusters for annotations
>> ERROR: Chunk failed at level:0, tier_type:3
>> FAILED CONTIG:scaffold93.1
>> 
>> ERROR: Chunk failed at level:7, tier_type:0
>> FAILED CONTIG:scaffold93.1
>> 
>> This occurs when running just a single maker instance.
>> 
>> Thanks,
>> Evan
>> _______________________________________________ maker-devel mailing list
>> maker-devel at box290.bluehost.comhttp://box290.bluehost.com/mailman/listinfo/ma
>> ker-devel_yandell-lab.org
> 
> 
> 
> -- 
> Evan Ernst
> Martienssen Lab
> 
> Delbruck #216
> Cold Spring Harbor Laboratory
> 1 Bungtown Rd.
> Cold Spring Harbor, NY 11724
> 



-- 
Evan Ernst
Martienssen Lab

Delbruck #216
Cold Spring Harbor Laboratory
1 Bungtown Rd.
Cold Spring Harbor, NY 11724



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From daniel.fer.u at gmail.com  Mon Mar 26 21:39:43 2012
From: daniel.fer.u at gmail.com (=?UTF-8?Q?Daniel_Fern=C3=A1ndez?=)
Date: Mon, 26 Mar 2012 19:39:43 -0700 (PDT)
Subject: [maker-devel] Problem with RMBlast installation
In-Reply-To: <7A26C949-4ED3-4CEF-8455-2D3A85B35A2B@gmail.com>
References: <8109224.101.1332730405163.JavaMail.geo-discussion-forums@ynlx41>
	<7A26C949-4ED3-4CEF-8455-2D3A85B35A2B@gmail.com>
Message-ID: <3452112.702.1332815983251.JavaMail.geo-discussion-forums@ynne2>

Ok, I unpack this file, I have 3 directories (bin include lib) and the 
readme file, you tell me add this to my $PATH, but I  add to my path all 
executables (bin), but the other 2 directories? I don't think that I have 
to add to my path, is different to Blast+, in blast+ I only copy the 
executables to my path, the other directories are only data

The bin directory have many executables like blast+, if I add all to my 
path, so I will have many duplicate executables, does this not cause a 
conflict?

On Monday, March 26, 2012 10:33:55 AM UTC-5, Jason Stajich wrote:
>
> Hi Daniel -
>
> Just download, unpackage the precompiled ( rmblast-1.2-ncbi-blast-2.2.23+-x64-linux.tar.gz 
> ) version and tell RepeatMasker where the exes are when you configure 
> RepeatMasker.  RMBlast is for RepeatMasker.
>  
> For running BLAST in MAKAER would install NCBI-BLAST+ if you don't have 
> wu-blast --- ftp://ftp.ncbi.nih.gov/blast/executables/blast+/LATEST - I 
> believe current maker supports BLAST+, BLAST, and WU-BLAST so you have your 
> pick.
>
> Jason
> On Mar 25, 2012, at 7:53 PM, Daniel Fern?ndez wrote:
>
> Hi,
>
> I trying to install MAKER, I don't have WU-Blast, I have Blast+ so in the 
> README file tell me that I need RMBlast, but I don't know what file I have 
> to choose, rmblast-1.2-ncbi-blast-2.2.23+-src.tar.gz or rmblast-1.2-ncbi-blast-2.2.23+-x64-linux.tar.gz 
> (I have Linux 64-bit) in each version the README file is the same, and 
> there tell me how I can install it, but the instructions is only for rmblast-1.2-ncbi-blast-2.2.23+-src, 
> well, when I try to install it, I type this 
> $./configure --with-mt --prefix=/usr/local/bioinfo/repeatmasker/rmblast 
> --without-debug
> This show me error, and I type make and this show stop.
>
> Can you help me please?
>
> This show me when I type $./configure --with-mt 
> --prefix=/usr/local/bioinfo/repeatmasker/rmblast --without-debug
>
> -----------------------------------------------------------------------------------------------------------------------------------------------
> configure: loading site script ./src/build-system/config.site
> configure: loading cache config.cache
> checking build system type... x86_64-unknown-linux-gnu
> checking host system type... x86_64-unknown-linux-gnu
> checking for a BSD-compatible install... /usr/bin/install -c
> checking for gcc... gcc
> checking for C compiler default output file name... a.out
> checking whether the C compiler works... yes
> checking whether we are cross compiling... no
> checking for suffix of executables... 
> checking for suffix of object files... o
> checking whether we are using the GNU C compiler... yes
> checking whether gcc accepts -g... yes
> checking for gcc option to accept ANSI C... none needed
> checking for g++... no
> checking for c++... no
> checking for gpp... no
> checking for aCC... no
> checking for CC... no
> checking for cxx... no
> checking for cc++... no
> checking for cl... no
> checking for FCC... no
> checking for KCC... no
> checking for RCC... no
> checking for xlC_r... no
> checking for xlC... no
> checking whether we are using the GNU C++ compiler... no
> checking whether g++ accepts -g... no
> adjusted C   compiler: /usr/bin/gcc 
> ./src/build-system/configure: line 4404: type: g++: not found
> dirname: missing operand
> Try `dirname --help' for more information.
> configure: error: Do not know how to build MT-safe with compiler g++ 
> ./src/build-system/configure: line 4187: g++: command not found
>
> -----------------------------------------------------------------------------------------------------------------------------------
> _______________________________________________
> maker-devel mailing list
> maker-devel at box290.bluehost.com
> http://box290.bluehost.com/mailman/listinfo/maker-devel_yandell-lab.org
>
>
> Jason Stajich
> jason.stajich at gmail.com
> jason at bioperl.org
>  
>
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From carsonhh at gmail.com  Mon Mar 26 21:47:37 2012
From: carsonhh at gmail.com (Carson Holt)
Date: Mon, 26 Mar 2012 22:47:37 -0400
Subject: [maker-devel] Problem with RMBlast installation
In-Reply-To: <3452112.702.1332815983251.JavaMail.geo-discussion-forums@ynne2>
Message-ID: <CB96A177.A1BD%carsonhh@gmail.com>

You only need to add the directory location for executables you plan on
calling yourself from the command line.  You don't need to add RMBlast to
the PATH for example because you should never use it directly.  RepeatMasker
knows where it is once configured, and you want to use NCBI's BLAST.

Thanks,
Carson

From:  Daniel Fern?ndez <daniel.fer.u at gmail.com>
Date:  Mon, 26 Mar 2012 19:39:43 -0700 (PDT)
To:  <maker-devel at googlegroups.com>
Cc:  "maker-devel at yandell-lab.org List" <maker-devel at yandell-lab.org>,
Daniel Fern?ndez <daniel.fer.u at gmail.com>
Subject:  Re: [maker-devel] Problem with RMBlast installation

Ok, I unpack this file, I have 3 directories (bin include lib) and the
readme file, you tell me add this to my $PATH, but I  add to my path all
executables (bin), but the other 2 directories? I don't think that I have to
add to my path, is different to Blast+, in blast+ I only copy the
executables to my path, the other directories are only data

The bin directory have many executables like blast+, if I add all to my
path, so I will have many duplicate executables, does this not cause a
conflict?

On Monday, March 26, 2012 10:33:55 AM UTC-5, Jason Stajich wrote:
> Hi Daniel -
> 
> Just download, unpackage the precompiled (
> rmblast-1.2-ncbi-blast-2.2.23+-x64-linux.tar.gz ) version and tell
> RepeatMasker where the exes are when you configure RepeatMasker.  RMBlast is
> for RepeatMasker.
>  
> For running BLAST in MAKAER would install NCBI-BLAST+ if you don't have
> wu-blast --- ftp://ftp.ncbi.nih.gov/blast/executables/blast+/LATEST - I
> believe current maker supports BLAST+, BLAST, and WU-BLAST so you have your
> pick.
> 
> Jason
> On Mar 25, 2012, at 7:53 PM, Daniel Fern?ndez wrote:
> 
>> Hi,
>> 
>> I trying to install MAKER, I don't have WU-Blast, I have Blast+ so in the
>> README file tell me that I need RMBlast, but I don't know what file I have to
>> choose, rmblast-1.2-ncbi-blast-2.2.23+-src.tar.gz or
>> rmblast-1.2-ncbi-blast-2.2.23+-x64-linux.tar.gz (I have Linux 64-bit) in each
>> version the README file is the same, and there tell me how I can install it,
>> but the instructions is only for rmblast-1.2-ncbi-blast-2.2.23+-src, well,
>> when I try to install it, I type this
>> $./configure --with-mt --prefix=/usr/local/bioinfo/repeatmasker/rmblast
>> --without-debug
>> This show me error, and I type make and this show stop.
>> 
>> Can you help me please?
>> 
>> This show me when I type $./configure --with-mt
>> --prefix=/usr/local/bioinfo/repeatmasker/rmblast --without-debug
>> -----------------------------------------------------------------------------
>> ------------------------------------------------------------------
>> configure: loading site script ./src/build-system/config.site
>> configure: loading cache config.cache
>> checking build system type... x86_64-unknown-linux-gnu
>> checking host system type... x86_64-unknown-linux-gnu
>> checking for a BSD-compatible install... /usr/bin/install -c
>> checking for gcc... gcc
>> checking for C compiler default output file name... a.out
>> checking whether the C compiler works... yes
>> checking whether we are cross compiling... no
>> checking for suffix of executables...
>> checking for suffix of object files... o
>> checking whether we are using the GNU C compiler... yes
>> checking whether gcc accepts -g... yes
>> checking for gcc option to accept ANSI C... none needed
>> checking for g++... no
>> checking for c++... no
>> checking for gpp... no
>> checking for aCC... no
>> checking for CC... no
>> checking for cxx... no
>> checking for cc++... no
>> checking for cl... no
>> checking for FCC... no
>> checking for KCC... no
>> checking for RCC... no
>> checking for xlC_r... no
>> checking for xlC... no
>> checking whether we are using the GNU C++ compiler... no
>> checking whether g++ accepts -g... no
>> adjusted C   compiler: /usr/bin/gcc
>> ./src/build-system/configure: line 4404: type: g++: not found
>> dirname: missing operand
>> Try `dirname --help' for more information.
>> configure: error: Do not know how to build MT-safe with compiler g++
>> ./src/build-system/configure: line 4187: g++: command not found
>> -----------------------------------------------------------------------------
>> ------------------------------------------------------
>> _______________________________________________
>> maker-devel mailing list
>> maker-devel at box290.bluehost.com
>> http://box290.bluehost.com/mailman/listinfo/maker-devel_yandell-lab.org
> 
> Jason Stajich
> jason.stajich at gmail.com
> jason at bioperl.org
> 
_______________________________________________ maker-devel mailing list
maker-devel at box290.bluehost.com
http://box290.bluehost.com/mailman/listinfo/maker-devel_yandell-lab.org

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From tr at ncgr.org  Wed Mar 28 13:34:39 2012
From: tr at ncgr.org (Thiru Ramaraj)
Date: Wed, 28 Mar 2012 12:34:39 -0600
Subject: [maker-devel] maker_functional_gff
Message-ID: <4F7359BF.5020900@ncgr.org>

Hi All,

I am in the process of using maker_functional_gff script th generate 
functional gff file. I was wondering if NCBI BLAST tab delimited output 
will work as it is or there any formatting needed to be  more like a 
WUBLAST output.

Any thoughts would be greatly appreciated.

Thanks,
-Thiru



From carsonhh at gmail.com  Thu Mar 29 09:58:18 2012
From: carsonhh at gmail.com (Carson Holt)
Date: Thu, 29 Mar 2012 10:58:18 -0400
Subject: [maker-devel] maker_functional_gff
In-Reply-To: <4F7359BF.5020900@ncgr.org>
Message-ID: <CB99EE84.A2F7%carsonhh@gmail.com>

It should work with NCBI BLAST as long as it is the optional tab delimited
format, and not the standard raw format report.

The report must be generated from UniProt/Swiss-prot formatted fasta files.

Here is an example of the header format for the fasta file -->
>sp|P18560|1101L_ASFB7 Protein MGF 110-1L OS=African swine fever virus
>(strain Badajoz 1971 Vero-adapted) GN=BA71V-008 PE=3 SV=1

This ia a description of what maker_functional_gff is looked for
>transcript_ID  Description  OS=species  GN=gene_name
>PE=any_text_from_this_point_on_is_ignored

Thanks,
Carson




On 12-03-28 2:34 PM, "Thiru Ramaraj" <tr at ncgr.org> wrote:

>Hi All,
>
>I am in the process of using maker_functional_gff script th generate
>functional gff file. I was wondering if NCBI BLAST tab delimited output
>will work as it is or there any formatting needed to be  more like a
>WUBLAST output.
>
>Any thoughts would be greatly appreciated.
>
>Thanks,
>-Thiru
>
>_______________________________________________
>maker-devel mailing list
>maker-devel at box290.bluehost.com
>http://box290.bluehost.com/mailman/listinfo/maker-devel_yandell-lab.org





From barry.utah at gmail.com  Thu Mar 29 14:29:48 2012
From: barry.utah at gmail.com (Barry Moore)
Date: Thu, 29 Mar 2012 13:29:48 -0600
Subject: [maker-devel] GFF3 Specification
Message-ID: <C8A5B771-CCB5-4629-9F02-CF2437493F39@genetics.utah.edu>

Hi All,

There has been active discussion on the song-devel mailing list over the past 12 months about various ambiguities and unresolved issues with the GFF3 specification.  The SO group is initiating a process to resolve these issues so that GFF3 can continue to serve it's role of unifying genome annotations in a format that promotes collaboration between genome projects and comparison of datasets across a wide variety of genomes.  With the rapid acceleration of genome sequencing, a simple, standard format for genome annotation and comparative genomics is more critical than ever.

Several issues have been raised, and they range from simple requests for clarification to more fundamental questions about the structure of the specification.  We can't address all of these issues in one update to the spec, so we've started the ball rolling with three steps:

Incorporate all the minor changes into a GFF3 1.21 candidate spec (http://www.sequenceontology.org/resources/gff3_1.21.html).
Organize remaining unresolved issues onto a wiki page and start working through those issues one by one (http://www.sequenceontology.org/wiki/index.php?title=GFF3_Developement).
Develop a set of wiki pages to describe 'GFF3 Best Practices' and existing community usage (http://www.sequenceontology.org/wiki/index.php?title=GFF3_best_practices).

We will work through the unresolved issues one at a time - soliciting feedback from the community, and clarify/update the GFF3 spec in a backwards compatible way with existing tools and datasets, adding documenting wiki pages as needed.

We welcome and encourage feedback from the genomics community and gratefully acknowledge those who have been active in the discussion thus far.  Please have a look at the pages described above and join the conversation.  The best place for discussion of all things GFF3 is the SO mailing list (song-devel at lists.sourceforge.net).  Please feel free to re-post this message to relevant mailing lists so that all interested parties can be involved.

On behalf of the SO developers - Thanks.

Barry Moore
Research Scientist
Dept. of Human Genetics
University of Utah
Salt Lake City, UT 84112
--------------------------------------------
(801) 585-3543




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From ianmisner at my.uri.edu  Thu Mar  1 15:25:06 2012
From: ianmisner at my.uri.edu (Ian Misner)
Date: Thu, 1 Mar 2012 17:25:06 -0500
Subject: [maker-devel] Rerunning Maker
Message-ID: <13A73C28-9CEF-4416-911E-2ACEE445533A@my.uri.edu>

Hello,

I have run maker 2.03 on a genome that we assembled a while back.  Now we have a new genome assembly.  Is there a way to rerun maker with the new assembly without losing all of the annotations I've done on the v2.03 predicted proteins?  I see the genome_gff option but all the contig numbers will have changed with the new assembly so that will not work.  The EST data will be the same as before.  From my original run I used a related species for protein homology, this time would I use the predicted set I have been working with?  Worst case scenario I need a way to link the old proteins with the new ones which I could do with BLAST post Maker but I'm hoping there is a better way.  Any help with this would be greatly appreciated.  


Cheers
Ian

*************************************
Mr. Ian Misner
PhD. Candidate
Department of Biological Sciences
University of Rhode Island
120 Flagg Road
Kingston, RI 02881
Office: CBLS 260
Ph: 1-401-874-9726
fax (401) 874-2065
ianmisner at my.uri.edu
http://cels.uri.edu/bio/lanelab/  










From joana.guimaraes at inrb.pt  Fri Mar  2 00:26:51 2012
From: joana.guimaraes at inrb.pt (=?iso-8859-1?Q?Maria_Joana_F=2E_B=2E_A=2E_Guimar=E3es?=)
Date: Fri, 2 Mar 2012 07:26:51 -0000
Subject: [maker-devel] maker-devel Digest, Vol 45, Issue 15
In-Reply-To: <mailman.3.1330455604.20855.maker-devel_yandell-lab.org@box290.bluehost.com>
References: <mailman.3.1330455604.20855.maker-devel_yandell-lab.org@box290.bluehost.com>
Message-ID: <F5B5DE3EA7B4FD48A549687F860198320100510E@INRBMSMXBE.INRB.PT>

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-----
From: maker-devel-bounces at yandell-lab.org [mailto:maker-devel-bounces at yandell-lab.org] On Behalf Of maker-devel-request at yandell-lab.org
Sent: ter?a-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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End of maker-devel Digest, Vol 45, Issue 15
*******************************************



From carsonhh at gmail.com  Fri Mar  2 08:39:47 2012
From: carsonhh at gmail.com (Carson Holt)
Date: Fri, 02 Mar 2012 10:39:47 -0500
Subject: [maker-devel] Rerunning Maker
In-Reply-To: <13A73C28-9CEF-4416-911E-2ACEE445533A@my.uri.edu>
Message-ID: <CB764CB4.8AF8%carsonhh@gmail.com>

There is a way to do this and it sounds harder than it really is.

Previously there was a tool that came with MAKER called map2assembly that
is no longer included with the distribution (certain changes to the MAKER
libraries broke it beyond repair).  The replacement for this tool is still
somewhat under development, so is not documented but is included with the
distribution and works far better (and faster) than map2assembly.

The new tool is internal to MAKER and called by setting several flags in
the control files before running a regular MAKER job.

To map genes forward do this:
1. Supply your old transcript file to the est= option in MAKER.
2. Set est2genome=1
3. Set single_exon=1
4. Set single_length=1
5. Turn all repeat masking options off (either delete values in control
files or use -R flag on the command line)
6. Set est_forward=1 (this is not in the maker_opts.ctl file.  You will
have to add it manually.
7. Don't run any gene predictors and don't provide any other evidence
files (we only want MAKER to map things forward)
8. Now run MAKER (remember to supply the -R flag from the command line if
you didn't delete masking options from thew control files)

MAKER will now map the old gene models to the new assembly (with names)
generating a new GFF3 file that can be used as input to future MAKER runs.

Some things to know about the process.  You can set the minimum accepted
coverage and identity to use when mapping the genes forward using the
blastn filters in the maker_bopts.ctl file.  Some genes may not map
forward and will be lost.  Some will map to multiple locations, so review
your GFF3 results file.  Also the est_forward option accepts hints via a
tag (maker_coor=) in the fasta headers.  For example, if you add the
following flag to fasta headers for the input transcript file -->
	>gene1-RA  maker_coor=chr1;
Then MAKER will only try and map that transcript to the new genomes contig
labelled chr1.  Or you can do -->
	>gene1-RA  maker_coor=chr1:2000-200000;
Then MAKER will restrict the alignment to somewhere within a given region
(could be the first half of the chromosome for example).


In future releases of MAKER, everything will be simplified.  The
est_forward will always be in the control files and will accept a file
name.  MAKER will then do all the work upstream including setting flags
and sorting out multiple location alignments as part of it's normal run
(not as an independent run as is done in what I described).

Thanks,
Carson


On 12-03-01 5:25 PM, "Ian Misner" <ianmisner at my.uri.edu> wrote:

>Hello,
>
>I have run maker 2.03 on a genome that we assembled a while back.  Now we
>have a new genome assembly.  Is there a way to rerun maker with the new
>assembly without losing all of the annotations I've done on the v2.03
>predicted proteins?  I see the genome_gff option but all the contig
>numbers will have changed with the new assembly so that will not work.
>The EST data will be the same as before.  From my original run I used a
>related species for protein homology, this time would I use the predicted
>set I have been working with?  Worst case scenario I need a way to link
>the old proteins with the new ones which I could do with BLAST post Maker
>but I'm hoping there is a better way.  Any help with this would be
>greatly appreciated.
>
>
>Cheers
>Ian
>
>*************************************
>Mr. Ian Misner
>PhD. Candidate
>Department of Biological Sciences
>University of Rhode Island
>120 Flagg Road
>Kingston, RI 02881
>Office: CBLS 260
>Ph: 1-401-874-9726
>fax (401) 874-2065
>ianmisner at my.uri.edu
>http://cels.uri.edu/bio/lanelab/
>
>
>
>
>
>
>
>
>_______________________________________________
>maker-devel mailing list
>maker-devel at box290.bluehost.com
>http://box290.bluehost.com/mailman/listinfo/maker-devel_yandell-lab.org





From carsonhh at gmail.com  Fri Mar  2 09:05:49 2012
From: carsonhh at gmail.com (Carson Holt)
Date: Fri, 02 Mar 2012 11:05:49 -0500
Subject: [maker-devel] maker-devel Digest, Vol 45, Issue 15
In-Reply-To: <F5B5DE3EA7B4FD48A549687F860198320100510E@INRBMSMXBE.INRB.PT>
Message-ID: <CB76559D.8B38%carsonhh@gmail.com>

There is more than one way to train your predictors.  If you have protein
sequence, you can run MAKER with the protein2genome=1 option set which
will generate preliminary gene models based on protein homology alone, and
those results can be used to train SNAP and augustus.  You can also train
SNAP independently using CEGMA - a program from the same group as SNAP.
It finds a small set of core genes that should be in all eukaryotic
genomes.

For me this is more of a question of speed.  Using ESTs that are not from
the same organism has caveats.  If the organisms are very closely related
(example: chimp and human), you can do a direct alignment in nucleotide
space.  But if they are not (example: human and mouse), you can use
MAKER's alt_est option and MAKER will align in translated space using
TBLASTX.  TBLASTX is mind numbingly slow, taking about 20x longer than a
direct EST alignment, and should be avoided when possible.

So to summarize, if you have ESTs from your organism, use those first.  If
not, then use proteins. Finally use alternate organism ESTs if that's all
you have. Of course you can also supply all three, but I normally only do
that for the final run.  I limit the dataset for the training rounds.

After using MAKER's results for training SNAP/augustus etc., just supply
MAKER with the resulting training HMM and run again in the same directory.
 Why in the same directory?  So that you can keep the evidence files you
used on the first run.  MAKER will see that the only thing that changed
was the HMM (so it won't have to rerun any of the alignments).  It will
just add the predictions, interpret them in light of the evidence, and
produce new output.  So the first run is slow, and the second is fast
(because MAKER takes advantage of archived BLAST, RepeatMasker, and
Exonerate results).

Thanks,
Carson



On 12-03-02 2:26 AM, "Maria Joana F. B. A. Guimar?es"
<joana.guimaraes at inrb.pt> wrote:

>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-----
>From: maker-devel-bounces at yandell-lab.org
>[mailto:maker-devel-bounces at yandell-lab.org] On Behalf Of
>maker-devel-request at yandell-lab.org
>Sent: ter?a-feira, 28 de Fevereiro de 2012 19:00
>To: maker-devel at yandell-lab.org
>Subject: maker-devel Digest, Vol 45, Issue 15
>
>Send maker-devel mailing list submissions to
>	maker-devel at yandell-lab.org
>
>To subscribe or unsubscribe via the World Wide Web, visit
>	http://box290.bluehost.com/mailman/listinfo/maker-devel_yandell-lab.org
>
>or, via email, send a message with subject or body 'help' to
>	maker-devel-request at yandell-lab.org
>
>You can reach the person managing the list at
>	maker-devel-owner at yandell-lab.org
>
>When replying, please edit your Subject line so it is more specific
>than "Re: Contents of maker-devel digest..."
>
>
>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_datast
>ore_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.repeat
>runner
>
>#-------------------------------#
>
>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//the
>Void.contig-dpp-500-500/contig-dpp-500-500.0.te_proteins%2Efasta.repeatrun
>ner
>
>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.repeat
>runner
>
>#-------------------------------#
>
>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//the
>Void.contig-dpp-500-500/contig-dpp-500-500.0.te_proteins%2Efasta.repeatrun
>ner
>
>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
>-------------- next part --------------
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>nts/20120228/8e6a3106/attachment-0001.html>
>
>------------------------------
>
>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_datast
>or
>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.r
>b
>-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_pr
>ot
>eins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunn
>er
>
>#-------------------------------#
>
>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//the
>Vo
>id.contig-dpp-500-500/contig-dpp-500-500.0.te_proteins%2Efasta.repeatrunne
>r
>
>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.r
>b.
>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_pr
>ot
>eins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunn
>er
>
>#-------------------------------#
>
>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//the
>Vo
>id.contig-dpp-500-500/contig-dpp-500-500.0.te_proteins%2Efasta.repeatrunne
>r
>
>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
>_______________________________________________ maker-devel mailing list
>maker-devel at box290.bluehost.com
>http://box290.bluehost.com/mailman/listinfo/maker-devel_yandell-lab.org
>
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>
>------------------------------
>
>_______________________________________________
>maker-devel mailing list
>maker-devel at box290.bluehost.com
>http://box290.bluehost.com/mailman/listinfo/maker-devel_yandell-lab.org
>
>
>End of maker-devel Digest, Vol 45, Issue 15
>*******************************************
>
>_______________________________________________
>maker-devel mailing list
>maker-devel at box290.bluehost.com
>http://box290.bluehost.com/mailman/listinfo/maker-devel_yandell-lab.org





From njauxiongjie at gmail.com  Fri Mar  2 19:38:50 2012
From: njauxiongjie at gmail.com (Jie)
Date: Fri, 2 Mar 2012 18:38:50 -0800 (PST)
Subject: [maker-devel] question about augustus hints file
Message-ID: <078f6ced-b08d-4a1e-8fe4-c63a2ac68392@qr9g2000pbc.googlegroups.com>

Hi, all

I have aligned my EST to my genome and want to use the EST alignment
as hints of augustus. The command I run like your README file in
AUGUSTUS, and like bellow:

blat -minIdentity=92 genome.fa cdna.fa cdna.psl
blat2hints.pl --in=cdna.psl --out=hints.E.gff

but when I feed the hint file to augustus, it appeared some error like
bellow:
augustus: ERROR        FeatureCollection::esource: invalid source key:
E

How can I solve this problem?



From thomas.hackl at uni-wuerzburg.de  Wed Mar  7 01:31:39 2012
From: thomas.hackl at uni-wuerzburg.de (Thomas Hackl)
Date: Wed, 07 Mar 2012 09:31:39 +0100
Subject: [maker-devel] maker 2.22/2.23: Segmentation fault while processing
	FASTA input
Message-ID: <4F571CEB.7070707@uni-wuerzburg.de>

Hello,

we want to use a current release of maker (2.22, 2.23) but the program 
terminates with a seg fault while processing the input FASTA files. 
maker 2.15 , which we have been using for quite some time, runs 
perfectly with identical data and setup.

Please contact me if you need specifics on hardware, OS or anything else.

Best regards
Thomas

-- 
Thomas Hackl
Julius-Maximilians-Universit?t
Department of Bioinformatics
97074 W?rzburg, Germany
Fon:  +49 931 - 31 86883
Mail: thomas.hackl at uni-wuerzburg.de




From Carson.Holt at oicr.on.ca  Wed Mar  7 15:45:06 2012
From: Carson.Holt at oicr.on.ca (Carson Holt)
Date: Wed, 7 Mar 2012 22:45:06 +0000
Subject: [maker-devel] maker 2.22/2.23: Segmentation fault while
 processing FASTA input
In-Reply-To: <4F571CEB.7070707@uni-wuerzburg.de>
Message-ID: <CB7D4D49.8FCD%carson.holt@oicr.on.ca>

There should be no new hardware requirement.  But there is always a chance
that there is an issue with one of the perl modules being used.  I assume
the failure is happening when using maker serially and you are not using
MPI.

Could you reinstall the following perl modules, and try again.  If you are
using CPAN, do a 'force install' to force it to reinstall.

Modules:
*Storable
*Inline::C
*forks
*forks::shared

Also try reinstalling the latest version of BioPerl.

The fact that this is a seg fault suggests that something is happemning at
the C level (just outside of Perl).  Those area all the modules MAKER uses
that will call back to the C level.  BioPerl has a fasta indexing module
that is also making calls outside of Perl, and the fact it fails at that
point makes it a suspect.

Let me know what happens.  I can always generate an alternate MAKER
executable for you to run with additional status messages that may help
identify exactly which module is being called right before the failure.

Thanks,
Carson



On 12-03-07 3:31 AM, "Thomas Hackl" <thomas.hackl at uni-wuerzburg.de> wrote:

>Hello,
>
>we want to use a current release of maker (2.22, 2.23) but the program
>terminates with a seg fault while processing the input FASTA files.
>maker 2.15 , which we have been using for quite some time, runs
>perfectly with identical data and setup.
>
>Please contact me if you need specifics on hardware, OS or anything else.
>
>Best regards
>Thomas
>
>-- 
>Thomas Hackl
>Julius-Maximilians-Universit?t
>Department of Bioinformatics
>97074 W?rzburg, Germany
>Fon:  +49 931 - 31 86883
>Mail: thomas.hackl at uni-wuerzburg.de
>
>
>_______________________________________________
>maker-devel mailing list
>maker-devel at box290.bluehost.com
>http://box290.bluehost.com/mailman/listinfo/maker-devel_yandell-lab.org




From ianmisner at my.uri.edu  Thu Mar  8 07:15:05 2012
From: ianmisner at my.uri.edu (Ian Misner)
Date: Thu, 8 Mar 2012 09:15:05 -0500
Subject: [maker-devel] Error: Chunk failed at level
Message-ID: <6F68BCEE-BD5B-4059-BA87-188BA8585105@my.uri.edu>

Hello,

I've run maker with RM, SNAP, and gmhmm on my novel genome and I've some very large contigs that haven't annotated any proteins.  I have looked through the output from the run and of the 74 contigs that failed I only have three errors.

They are Chunk failed at level 3, 8, & 16

What are those errors?  How can I get the annotations for these failed runs to work?  I have the entire output if you would need to see that file.  In my opts ctl file I set it to retry failed contigs 2 times and do a fresh run each time.  All 74 contigs failed all 3 attempts to run.  Any help would be much appreciated.

Cheers
Ian


*************************************
Mr. Ian Misner
PhD. Candidate
Department of Biological Sciences
University of Rhode Island
120 Flagg Road
Kingston, RI 02881
Office: CBLS 260
Ph: 1-401-874-9726
fax (401) 874-2065
ianmisner at my.uri.edu
http://cels.uri.edu/bio/lanelab/  










From jason.stajich at gmail.com  Thu Mar  8 18:58:32 2012
From: jason.stajich at gmail.com (Jason Stajich)
Date: Thu, 8 Mar 2012 17:58:32 -0800
Subject: [maker-devel] Error: Chunk failed at level
In-Reply-To: <6F68BCEE-BD5B-4059-BA87-188BA8585105@my.uri.edu>
References: <6F68BCEE-BD5B-4059-BA87-188BA8585105@my.uri.edu>
Message-ID: <8CA12776-E69F-4868-B9CE-278062F83D32@gmail.com>

Hi Ian - 

Do you get any gene models if you run RM or SNAP on these directly?  I can't tell if this means there is no overlap between your different prediction sets or if you didn't get ab initio predictions?

Jason
On Mar 8, 2012, at 6:15 AM, Ian Misner wrote:

> Hello,
> 
> I've run maker with RM, SNAP, and gmhmm on my novel genome and I've some very large contigs that haven't annotated any proteins.  I have looked through the output from the run and of the 74 contigs that failed I only have three errors.
> 
> They are Chunk failed at level 3, 8, & 16
> 
> What are those errors?  How can I get the annotations for these failed runs to work?  I have the entire output if you would need to see that file.  In my opts ctl file I set it to retry failed contigs 2 times and do a fresh run each time.  All 74 contigs failed all 3 attempts to run.  Any help would be much appreciated.
> 
> Cheers
> Ian
> 
> 
> *************************************
> Mr. Ian Misner
> PhD. Candidate
> Department of Biological Sciences
> University of Rhode Island
> 120 Flagg Road
> Kingston, RI 02881
> Office: CBLS 260
> Ph: 1-401-874-9726
> fax (401) 874-2065
> ianmisner at my.uri.edu
> http://cels.uri.edu/bio/lanelab/  
> 
> 
> 
> 
> 
> 
> 
> 
> _______________________________________________
> maker-devel mailing list
> maker-devel at box290.bluehost.com
> http://box290.bluehost.com/mailman/listinfo/maker-devel_yandell-lab.org

Jason Stajich
jason.stajich at gmail.com
jason at bioperl.org

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From carsonhh at gmail.com  Fri Mar  9 12:02:58 2012
From: carsonhh at gmail.com (Carson Holt)
Date: Fri, 09 Mar 2012 14:02:58 -0500
Subject: [maker-devel] Error: Chunk failed at level
In-Reply-To: <6F68BCEE-BD5B-4059-BA87-188BA8585105@my.uri.edu>
Message-ID: <CB7FBDE5.90EB%carsonhh@gmail.com>

Those are the very last messages in a series of error handlers.  Look
further up the report, the errors triggering the handler should be further
back.  If your'e running parallel,  the other errors may be way back up
the report.  Also which version of MAKER are you using?

You can send my any failed contigs, the maker control files and any other
datasets/files you are using if you want me to take a look as well.

Thanks,
Carson



On 12-03-08 9:15 AM, "Ian Misner" <ianmisner at my.uri.edu> wrote:

>Hello,
>
>I've run maker with RM, SNAP, and gmhmm on my novel genome and I've some
>very large contigs that haven't annotated any proteins.  I have looked
>through the output from the run and of the 74 contigs that failed I only
>have three errors.
>
>They are Chunk failed at level 3, 8, & 16
>
>What are those errors?  How can I get the annotations for these failed
>runs to work?  I have the entire output if you would need to see that
>file.  In my opts ctl file I set it to retry failed contigs 2 times and
>do a fresh run each time.  All 74 contigs failed all 3 attempts to run.
>Any help would be much appreciated.
>
>Cheers
>Ian
>
>
>*************************************
>Mr. Ian Misner
>PhD. Candidate
>Department of Biological Sciences
>University of Rhode Island
>120 Flagg Road
>Kingston, RI 02881
>Office: CBLS 260
>Ph: 1-401-874-9726
>fax (401) 874-2065
>ianmisner at my.uri.edu
>http://cels.uri.edu/bio/lanelab/
>
>
>
>
>
>
>
>
>_______________________________________________
>maker-devel mailing list
>maker-devel at box290.bluehost.com
>http://box290.bluehost.com/mailman/listinfo/maker-devel_yandell-lab.org





From thomas.hackl at uni-wuerzburg.de  Tue Mar 13 03:41:40 2012
From: thomas.hackl at uni-wuerzburg.de (Thomas Hackl)
Date: Tue, 13 Mar 2012 10:41:40 +0100
Subject: [maker-devel] maker 2.22/2.23: Segmentation fault while
 processing FASTA input
In-Reply-To: <CB7D4D49.8FCD%carson.holt@oicr.on.ca>
References: <CB7D4D49.8FCD%carson.holt@oicr.on.ca>
Message-ID: <4F5F1654.1060100@uni-wuerzburg.de>

Hello,

We reinstalled the packages you suggested

forks is up to date (0.34).
forks::shared is up to date (0.34).
Inline::C is up to date (0.50).
Storable is up to date (2.30).

as well as BioPerl.

The problem is still the same.

With MPI it terminates with this message:

STATUS: Parsing control files...
STATUS: Processing and indexing input FASTA files...
===================================================================================== 


=   BAD TERMINATION OF ONE OF YOUR APPLICATION PROCESSES
=   EXIT CODE: 11
=   CLEANING UP REMAINING PROCESSES
=   YOU CAN IGNORE THE BELOW CLEANUP MESSAGES
===================================================================================== 

APPLICATION TERMINATED WITH THE EXIT STRING: Segmentation fault (signal 11)

which I presume is also the same problem.

I am with you that the error is caused somewhere on the C level. If the 
indexing step
is handled by non-maker modules exclusively, than the fact that the 2.15 
version works,
suggests that you are using different modules/methods in the current 
releases?

In any case, I think a version with verbose status messages might help 
to localize the
source of the problem.

Regards
Thomas

Am 07.03.2012 23:45, schrieb Carson Holt:
> There should be no new hardware requirement.  But there is always a chance
> that there is an issue with one of the perl modules being used.  I assume
> the failure is happening when using maker serially and you are not using
> MPI.
>
> Could you reinstall the following perl modules, and try again.  If you are
> using CPAN, do a 'force install' to force it to reinstall.
>
> Modules:
> *Storable
> *Inline::C
> *forks
> *forks::shared
>
> Also try reinstalling the latest version of BioPerl.
>
> The fact that this is a seg fault suggests that something is happemning at
> the C level (just outside of Perl).  Those area all the modules MAKER uses
> that will call back to the C level.  BioPerl has a fasta indexing module
> that is also making calls outside of Perl, and the fact it fails at that
> point makes it a suspect.
>
> Let me know what happens.  I can always generate an alternate MAKER
> executable for you to run with additional status messages that may help
> identify exactly which module is being called right before the failure.
>
> Thanks,
> Carson
>
>
>
> On 12-03-07 3:31 AM, "Thomas Hackl"<thomas.hackl at uni-wuerzburg.de>  wrote:
>
>> Hello,
>>
>> we want to use a current release of maker (2.22, 2.23) but the program
>> terminates with a seg fault while processing the input FASTA files.
>> maker 2.15 , which we have been using for quite some time, runs
>> perfectly with identical data and setup.
>>
>> Please contact me if you need specifics on hardware, OS or anything else.
>>
>> Best regards
>> Thomas
>>
>> -- 
>> Thomas Hackl
>> Julius-Maximilians-Universit?t
>> Department of Bioinformatics
>> 97074 W?rzburg, Germany
>> Fon:  +49 931 - 31 86883
>> Mail: thomas.hackl at uni-wuerzburg.de
>>
>>
>> _______________________________________________
>> maker-devel mailing list
>> maker-devel at box290.bluehost.com
>> http://box290.bluehost.com/mailman/listinfo/maker-devel_yandell-lab.org


-- 
Thomas Hackl
Julius-Maximilians-Universit?t
Department of Bioinformatics
97074 W?rzburg, Germany
Fon:  +49 931 - 31 86883
Mail: thomas.hackl at uni-wuerzburg.de




From carsonhh at gmail.com  Tue Mar 13 06:34:16 2012
From: carsonhh at gmail.com (Carson Holt)
Date: Tue, 13 Mar 2012 08:34:16 -0400
Subject: [maker-devel] maker 2.22/2.23: Segmentation fault while
 processing FASTA input
In-Reply-To: <4F5F1654.1060100@uni-wuerzburg.de>
Message-ID: <CB84B674.9207%carsonhh@gmail.com>

I've put together a new MAKER executable (mostly finished), and I will get
it to you soon.  This should help focus in on the exact module causing the
issue.

Thanks,
Carson



On 12-03-13 5:41 AM, "Thomas Hackl" <thomas.hackl at uni-wuerzburg.de> wrote:

>Hello,
>
>We reinstalled the packages you suggested
>
>forks is up to date (0.34).
>forks::shared is up to date (0.34).
>Inline::C is up to date (0.50).
>Storable is up to date (2.30).
>
>as well as BioPerl.
>
>The problem is still the same.
>
>With MPI it terminates with this message:
>
>STATUS: Parsing control files...
>STATUS: Processing and indexing input FASTA files...
>==========================================================================
>=========== 
>
>
>=   BAD TERMINATION OF ONE OF YOUR APPLICATION PROCESSES
>=   EXIT CODE: 11
>=   CLEANING UP REMAINING PROCESSES
>=   YOU CAN IGNORE THE BELOW CLEANUP MESSAGES
>==========================================================================
>=========== 
>
>APPLICATION TERMINATED WITH THE EXIT STRING: Segmentation fault (signal
>11)
>
>which I presume is also the same problem.
>
>I am with you that the error is caused somewhere on the C level. If the
>indexing step
>is handled by non-maker modules exclusively, than the fact that the 2.15
>version works,
>suggests that you are using different modules/methods in the current
>releases?
>
>In any case, I think a version with verbose status messages might help
>to localize the
>source of the problem.
>
>Regards
>Thomas
>
>Am 07.03.2012 23:45, schrieb Carson Holt:
>> There should be no new hardware requirement.  But there is always a
>>chance
>> that there is an issue with one of the perl modules being used.  I
>>assume
>> the failure is happening when using maker serially and you are not using
>> MPI.
>>
>> Could you reinstall the following perl modules, and try again.  If you
>>are
>> using CPAN, do a 'force install' to force it to reinstall.
>>
>> Modules:
>> *Storable
>> *Inline::C
>> *forks
>> *forks::shared
>>
>> Also try reinstalling the latest version of BioPerl.
>>
>> The fact that this is a seg fault suggests that something is happemning
>>at
>> the C level (just outside of Perl).  Those area all the modules MAKER
>>uses
>> that will call back to the C level.  BioPerl has a fasta indexing module
>> that is also making calls outside of Perl, and the fact it fails at that
>> point makes it a suspect.
>>
>> Let me know what happens.  I can always generate an alternate MAKER
>> executable for you to run with additional status messages that may help
>> identify exactly which module is being called right before the failure.
>>
>> Thanks,
>> Carson
>>
>>
>>
>> On 12-03-07 3:31 AM, "Thomas Hackl"<thomas.hackl at uni-wuerzburg.de>
>>wrote:
>>
>>> Hello,
>>>
>>> we want to use a current release of maker (2.22, 2.23) but the program
>>> terminates with a seg fault while processing the input FASTA files.
>>> maker 2.15 , which we have been using for quite some time, runs
>>> perfectly with identical data and setup.
>>>
>>> Please contact me if you need specifics on hardware, OS or anything
>>>else.
>>>
>>> Best regards
>>> Thomas
>>>
>>> -- 
>>> Thomas Hackl
>>> Julius-Maximilians-Universit?t
>>> Department of Bioinformatics
>>> 97074 W?rzburg, Germany
>>> Fon:  +49 931 - 31 86883
>>> Mail: thomas.hackl at uni-wuerzburg.de
>>>
>>>
>>> _______________________________________________
>>> maker-devel mailing list
>>> maker-devel at box290.bluehost.com
>>> http://box290.bluehost.com/mailman/listinfo/maker-devel_yandell-lab.org
>
>
>-- 
>Thomas Hackl
>Julius-Maximilians-Universit?t
>Department of Bioinformatics
>97074 W?rzburg, Germany
>Fon:  +49 931 - 31 86883
>Mail: thomas.hackl at uni-wuerzburg.de
>
>
>_______________________________________________
>maker-devel mailing list
>maker-devel at box290.bluehost.com
>http://box290.bluehost.com/mailman/listinfo/maker-devel_yandell-lab.org





From barry.moore at genetics.utah.edu  Tue Mar 13 15:37:13 2012
From: barry.moore at genetics.utah.edu (Barry Moore)
Date: Tue, 13 Mar 2012 15:37:13 -0600
Subject: [maker-devel] maker 2.22/2.23: Segmentation fault while
	processing FASTA input
In-Reply-To: <4F5F1654.1060100@uni-wuerzburg.de>
References: <CB7D4D49.8FCD%carson.holt@oicr.on.ca>
	<4F5F1654.1060100@uni-wuerzburg.de>
Message-ID: <33E794D7-81C6-4315-BE02-A92B8C82EB67@genetics.utah.edu>

You might also try a short perl script outside of MAKER to exercise Bio::DB::Fasta (which I believe is the module MAKER uses for Fasta indexing - correct Carson?).

Something like this should work to force indexing:

use Bio::DB::Fasta;
my $db      = Bio::DB::Fasta->new('/path/to/fasta/files');
my $seq      = $db->seq($seqid, $start, $end);

Point it at your fasta directory or file.

B

On Mar 13, 2012, at 3:41 AM, Thomas Hackl wrote:

> Hello,
> 
> We reinstalled the packages you suggested
> 
> forks is up to date (0.34).
> forks::shared is up to date (0.34).
> Inline::C is up to date (0.50).
> Storable is up to date (2.30).
> 
> as well as BioPerl.
> 
> The problem is still the same.
> 
> With MPI it terminates with this message:
> 
> STATUS: Parsing control files...
> STATUS: Processing and indexing input FASTA files...
> ===================================================================================== 
> 
> =   BAD TERMINATION OF ONE OF YOUR APPLICATION PROCESSES
> =   EXIT CODE: 11
> =   CLEANING UP REMAINING PROCESSES
> =   YOU CAN IGNORE THE BELOW CLEANUP MESSAGES
> ===================================================================================== 
> APPLICATION TERMINATED WITH THE EXIT STRING: Segmentation fault (signal 11)
> 
> which I presume is also the same problem.
> 
> I am with you that the error is caused somewhere on the C level. If the indexing step
> is handled by non-maker modules exclusively, than the fact that the 2.15 version works,
> suggests that you are using different modules/methods in the current releases?
> 
> In any case, I think a version with verbose status messages might help to localize the
> source of the problem.
> 
> Regards
> Thomas
> 
> Am 07.03.2012 23:45, schrieb Carson Holt:
>> There should be no new hardware requirement.  But there is always a chance
>> that there is an issue with one of the perl modules being used.  I assume
>> the failure is happening when using maker serially and you are not using
>> MPI.
>> 
>> Could you reinstall the following perl modules, and try again.  If you are
>> using CPAN, do a 'force install' to force it to reinstall.
>> 
>> Modules:
>> *Storable
>> *Inline::C
>> *forks
>> *forks::shared
>> 
>> Also try reinstalling the latest version of BioPerl.
>> 
>> The fact that this is a seg fault suggests that something is happemning at
>> the C level (just outside of Perl).  Those area all the modules MAKER uses
>> that will call back to the C level.  BioPerl has a fasta indexing module
>> that is also making calls outside of Perl, and the fact it fails at that
>> point makes it a suspect.
>> 
>> Let me know what happens.  I can always generate an alternate MAKER
>> executable for you to run with additional status messages that may help
>> identify exactly which module is being called right before the failure.
>> 
>> Thanks,
>> Carson
>> 
>> 
>> 
>> On 12-03-07 3:31 AM, "Thomas Hackl"<thomas.hackl at uni-wuerzburg.de>  wrote:
>> 
>>> Hello,
>>> 
>>> we want to use a current release of maker (2.22, 2.23) but the program
>>> terminates with a seg fault while processing the input FASTA files.
>>> maker 2.15 , which we have been using for quite some time, runs
>>> perfectly with identical data and setup.
>>> 
>>> Please contact me if you need specifics on hardware, OS or anything else.
>>> 
>>> Best regards
>>> Thomas
>>> 
>>> -- 
>>> Thomas Hackl
>>> Julius-Maximilians-Universit?t
>>> Department of Bioinformatics
>>> 97074 W?rzburg, Germany
>>> Fon:  +49 931 - 31 86883
>>> Mail: thomas.hackl at uni-wuerzburg.de
>>> 
>>> 
>>> _______________________________________________
>>> maker-devel mailing list
>>> maker-devel at box290.bluehost.com
>>> http://box290.bluehost.com/mailman/listinfo/maker-devel_yandell-lab.org
> 
> 
> -- 
> Thomas Hackl
> Julius-Maximilians-Universit?t
> Department of Bioinformatics
> 97074 W?rzburg, Germany
> Fon:  +49 931 - 31 86883
> Mail: thomas.hackl at uni-wuerzburg.de
> 
> 
> _______________________________________________
> maker-devel mailing list
> maker-devel at box290.bluehost.com
> http://box290.bluehost.com/mailman/listinfo/maker-devel_yandell-lab.org

Barry Moore
Research Scientist
Dept. of Human Genetics
University of Utah
Salt Lake City, UT 84112
--------------------------------------------
(801) 585-3543




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From felix.bemm at uni-wuerzburg.de  Tue Mar 13 23:57:58 2012
From: felix.bemm at uni-wuerzburg.de (Felix Bemm)
Date: Wed, 14 Mar 2012 06:57:58 +0100
Subject: [maker-devel] maker 2.22/2.23: Segmentation fault while
 processing FASTA input
In-Reply-To: <33E794D7-81C6-4315-BE02-A92B8C82EB67@genetics.utah.edu>
References: <CB7D4D49.8FCD%carson.holt@oicr.on.ca>
	<4F5F1654.1060100@uni-wuerzburg.de>
	<33E794D7-81C6-4315-BE02-A92B8C82EB67@genetics.utah.edu>
Message-ID: <4F603366.3090501@uni-wuerzburg.de>

Hi,

Thomas and I are colleagues and dealing with the same problem here. I 
wrote some test code that forced the indexing and it work fine. We are 
using most of the bioperl seqio and db modules in combination with other 
tools and don't experience the same problem there at the moment.

Regards
Felix

Am 13.03.2012 22:37, schrieb Barry Moore:
> You might also try a short perl script outside of MAKER to exercise
> Bio::DB::Fasta (which I believe is the module MAKER uses for Fasta
> indexing - correct Carson?).
>
> Something like this should work to force indexing:
>
> useBio::DB::Fasta;
> my $db = Bio::DB::Fasta->new('/path/to/fasta/files');
> my$seq=$db->seq($seqid, $start, $end);
>
> Point it at your fasta directory or file.
>
> B
>
> On Mar 13, 2012, at 3:41 AM, Thomas Hackl wrote:
>
>> Hello,
>>
>> We reinstalled the packages you suggested
>>
>> forks is up to date (0.34).
>> forks::shared is up to date (0.34).
>> Inline::C is up to date (0.50).
>> Storable is up to date (2.30).
>>
>> as well as BioPerl.
>>
>> The problem is still the same.
>>
>> With MPI it terminates with this message:
>>
>> STATUS: Parsing control files...
>> STATUS: Processing and indexing input FASTA files...
>> =====================================================================================
>>
>>
>> = BAD TERMINATION OF ONE OF YOUR APPLICATION PROCESSES
>> = EXIT CODE: 11
>> = CLEANING UP REMAINING PROCESSES
>> = YOU CAN IGNORE THE BELOW CLEANUP MESSAGES
>> =====================================================================================
>>
>> APPLICATION TERMINATED WITH THE EXIT STRING: Segmentation fault
>> (signal 11)
>>
>> which I presume is also the same problem.
>>
>> I am with you that the error is caused somewhere on the C level. If
>> the indexing step
>> is handled by non-maker modules exclusively, than the fact that the
>> 2.15 version works,
>> suggests that you are using different modules/methods in the current
>> releases?
>>
>> In any case, I think a version with verbose status messages might help
>> to localize the
>> source of the problem.
>>
>> Regards
>> Thomas
>>
>> Am 07.03.2012 23:45, schrieb Carson Holt:
>>> There should be no new hardware requirement. But there is always a chance
>>> that there is an issue with one of the perl modules being used. I assume
>>> the failure is happening when using maker serially and you are not using
>>> MPI.
>>>
>>> Could you reinstall the following perl modules, and try again. If you are
>>> using CPAN, do a 'force install' to force it to reinstall.
>>>
>>> Modules:
>>> *Storable
>>> *Inline::C
>>> *forks
>>> *forks::shared
>>>
>>> Also try reinstalling the latest version of BioPerl.
>>>
>>> The fact that this is a seg fault suggests that something is
>>> happemning at
>>> the C level (just outside of Perl). Those area all the modules MAKER uses
>>> that will call back to the C level. BioPerl has a fasta indexing module
>>> that is also making calls outside of Perl, and the fact it fails at that
>>> point makes it a suspect.
>>>
>>> Let me know what happens. I can always generate an alternate MAKER
>>> executable for you to run with additional status messages that may help
>>> identify exactly which module is being called right before the failure.
>>>
>>> Thanks,
>>> Carson
>>>
>>>
>>>
>>> On 12-03-07 3:31 AM, "Thomas Hackl"<thomas.hackl at uni-wuerzburg.de
>>> <mailto:thomas.hackl at uni-wuerzburg.de>> wrote:
>>>
>>>> Hello,
>>>>
>>>> we want to use a current release of maker (2.22, 2.23) but the program
>>>> terminates with a seg fault while processing the input FASTA files.
>>>> maker 2.15 , which we have been using for quite some time, runs
>>>> perfectly with identical data and setup.
>>>>
>>>> Please contact me if you need specifics on hardware, OS or anything
>>>> else.
>>>>
>>>> Best regards
>>>> Thomas
>>>>
>>>> --
>>>> Thomas Hackl
>>>> Julius-Maximilians-Universit?t
>>>> Department of Bioinformatics
>>>> 97074 W?rzburg, Germany
>>>> Fon: +49 931 - 31 86883
>>>> Mail: thomas.hackl at uni-wuerzburg.de
>>>> <mailto:thomas.hackl at uni-wuerzburg.de>
>>>>
>>>>
>>>> _______________________________________________
>>>> maker-devel mailing list
>>>> maker-devel at box290.bluehost.com <mailto:maker-devel at box290.bluehost.com>
>>>> http://box290.bluehost.com/mailman/listinfo/maker-devel_yandell-lab.org
>>
>>
>> --
>> Thomas Hackl
>> Julius-Maximilians-Universit?t
>> Department of Bioinformatics
>> 97074 W?rzburg, Germany
>> Fon: +49 931 - 31 86883
>> Mail: thomas.hackl at uni-wuerzburg.de <mailto:thomas.hackl at uni-wuerzburg.de>
>>
>>
>> _______________________________________________
>> maker-devel mailing list
>> maker-devel at box290.bluehost.com <mailto:maker-devel at box290.bluehost.com>
>> http://box290.bluehost.com/mailman/listinfo/maker-devel_yandell-lab.org
>
> Barry Moore
> Research Scientist
> Dept. of Human Genetics
> University of Utah
> Salt Lake City, UT 84112
> --------------------------------------------
> (801) 585-3543
>
>
>
>
>
>
> _______________________________________________
> maker-devel mailing list
> maker-devel at box290.bluehost.com
> http://box290.bluehost.com/mailman/listinfo/maker-devel_yandell-lab.org



From darkbring_05 at yahoo.com  Tue Mar 13 23:21:46 2012
From: darkbring_05 at yahoo.com (asdsa sdadsad)
Date: Tue, 13 Mar 2012 22:21:46 -0700 (PDT)
Subject: [maker-devel] maker gff3 to genbank tbl
Message-ID: <1331702506.55291.YahooMailNeo@web124906.mail.ne1.yahoo.com>

Dear MAKER experts,

i hope that you can share your expertise regarding, conversion of?maker gff3 to genbank tbl or gbk. im trying to produce a working genbank tbl, i tried converting to chado using maker2chado and ?gmodtools genbanksubmit writer. but so far it doesnt end well. most probably due to xml configuration(which im really loss, especially defining the "goldenpath") .is there any other way to produce the tbl from maker output??

thanks :)

Joe Wilders
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From joe.wilders at gmail.com  Tue Mar 13 23:31:48 2012
From: joe.wilders at gmail.com (Joe Wilders)
Date: Tue, 13 Mar 2012 22:31:48 -0700 (PDT)
Subject: [maker-devel] maker gff3 to genbank tbl/gbk
Message-ID: <214404c1-206e-474c-b01c-24b6cde2b91e@y17g2000yqg.googlegroups.com>

Dear MAKER experts,

i hope that you can share your expertise regarding, conversion of
maker gff3 to genbank tbl or gbk. im trying to produce a working
genbank tbl, i tried converting to chado using maker2chado and
gmodtools genbanksubmit writer. but so far it doesnt end well. most
probably due to xml configuration(which im really loss, especially
defining the "goldenpath") .is there any other way to produce the tbl
from maker output?

thanks :)

Joe Wilders



From carsonhh at gmail.com  Sun Mar 18 16:21:03 2012
From: carsonhh at gmail.com (Carson Holt)
Date: Sun, 18 Mar 2012 18:21:03 -0400
Subject: [maker-devel] maker gff3 to genbank tbl/gbk
In-Reply-To: <214404c1-206e-474c-b01c-24b6cde2b91e@y17g2000yqg.googlegroups.com>
Message-ID: <CB8BD6ED.935C%carsonhh@gmail.com>

Try using Apollo.  You can open up GFF3 files and them save them as
GenBank format.  That might be sufficient.

Alternatively.  I've attached a script that can convert SNAP's ZFF format
to GeneBank.  You could then use the maker2zff that comes with MAKER to
convert results to ZFF and then this script to get GenBank format.

Thanks,
Carson

On 12-03-14 1:31 AM, "Joe Wilders" <joe.wilders at gmail.com> wrote:

>Dear MAKER experts,
>
>i hope that you can share your expertise regarding, conversion of
>maker gff3 to genbank tbl or gbk. im trying to produce a working
>genbank tbl, i tried converting to chado using maker2chado and
>gmodtools genbanksubmit writer. but so far it doesnt end well. most
>probably due to xml configuration(which im really loss, especially
>defining the "goldenpath") .is there any other way to produce the tbl
>from maker output?
>
>thanks :)
>
>Joe Wilders
>
>_______________________________________________
>maker-devel mailing list
>maker-devel at box290.bluehost.com
>http://box290.bluehost.com/mailman/listinfo/maker-devel_yandell-lab.org

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From joe.wilders at gmail.com  Sun Mar 18 19:53:37 2012
From: joe.wilders at gmail.com (Joe Wilders)
Date: Mon, 19 Mar 2012 09:53:37 +0800
Subject: [maker-devel] maker gff3 to genbank tbl/gbk
In-Reply-To: <CB8BD6ED.935C%carsonhh@gmail.com>
References: <214404c1-206e-474c-b01c-24b6cde2b91e@y17g2000yqg.googlegroups.com>
	<CB8BD6ED.935C%carsonhh@gmail.com>
Message-ID: <CAGYDdgYv8=qMqsz_Vk0d8Y=iNLYW8siJrB0gEDz+m6Qr40qVpA@mail.gmail.com>

Hi Carson,
Thank you very much for your suggestion, will try that up and let you know.

by the way i did found this in one of the revisions at the svn
http://malachite.genetics.utah.edu/projects/maker/browser/bin/gff3_2_gbk?rev=217
,
i wonder why it gets pulled out on the later revision..


On Mon, Mar 19, 2012 at 6:21 AM, Carson Holt <carsonhh at gmail.com> wrote:

> Try using Apollo.  You can open up GFF3 files and them save them as
> GenBank format.  That might be sufficient.
>
> Alternatively.  I've attached a script that can convert SNAP's ZFF format
> to GeneBank.  You could then use the maker2zff that comes with MAKER to
> convert results to ZFF and then this script to get GenBank format.
>
> Thanks,
> Carson
>
> On 12-03-14 1:31 AM, "Joe Wilders" <joe.wilders at gmail.com> wrote:
>
> >Dear MAKER experts,
> >
> >i hope that you can share your expertise regarding, conversion of
> >maker gff3 to genbank tbl or gbk. im trying to produce a working
> >genbank tbl, i tried converting to chado using maker2chado and
> >gmodtools genbanksubmit writer. but so far it doesnt end well. most
> >probably due to xml configuration(which im really loss, especially
> >defining the "goldenpath") .is there any other way to produce the tbl
> >from maker output?
> >
> >thanks :)
> >
> >Joe Wilders
> >
> >_______________________________________________
> >maker-devel mailing list
> >maker-devel at box290.bluehost.com
> >http://box290.bluehost.com/mailman/listinfo/maker-devel_yandell-lab.org
>
>
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From carsonhh at gmail.com  Sun Mar 18 23:27:00 2012
From: carsonhh at gmail.com (Carson Holt)
Date: Mon, 19 Mar 2012 01:27:00 -0400
Subject: [maker-devel] maker gff3 to genbank tbl/gbk
In-Reply-To: <CAGYDdgYv8=qMqsz_Vk0d8Y=iNLYW8siJrB0gEDz+m6Qr40qVpA@mail.gmail.com>
Message-ID: <CB8C38D3.944D%carsonhh@gmail.com>

A lot of the early code in the SVN suppository, contains one-off scripts.
This one looks a lot like one of my old scripts.  If I remember, I was
trying to get GenBank format for Augustus training.  I started with just a
quick BioPerl based conversion, but the script didn't produce the right
types in GenBank format.  I found another way to do what I wanted (i.e.
someone gave me a different script that worked well enough), and I just
abandoned that script.

Thanks,
Carson


From:  Joe Wilders <joe.wilders at gmail.com>
Date:  Mon, 19 Mar 2012 09:53:37 +0800
To:  Carson Holt <carsonhh at gmail.com>
Cc:  <maker-devel at yandell-lab.org>
Subject:  Re: [maker-devel] maker gff3 to genbank tbl/gbk


Hi Carson,
Thank you very much for your suggestion, will try that up and let you know.

by the way i did found this in one of the revisions at the svn
http://malachite.genetics.utah.edu/projects/maker/browser/bin/gff3_2_gbk?rev
=217 , i wonder why it gets pulled out on the later revision..


On Mon, Mar 19, 2012 at 6:21 AM, Carson Holt <carsonhh at gmail.com> wrote:
> Try using Apollo.  You can open up GFF3 files and them save them as
> GenBank format.  That might be sufficient.
> 
> Alternatively.  I've attached a script that can convert SNAP's ZFF format
> to GeneBank.  You could then use the maker2zff that comes with MAKER to
> convert results to ZFF and then this script to get GenBank format.
> 
> Thanks,
> Carson
> 
> On 12-03-14 1:31 AM, "Joe Wilders" <joe.wilders at gmail.com> wrote:
> 
>> >Dear MAKER experts,
>> >
>> >i hope that you can share your expertise regarding, conversion of
>> >maker gff3 to genbank tbl or gbk. im trying to produce a working
>> >genbank tbl, i tried converting to chado using maker2chado and
>> >gmodtools genbanksubmit writer. but so far it doesnt end well. most
>> >probably due to xml configuration(which im really loss, especially
>> >defining the "goldenpath") .is there any other way to produce the tbl
>> >from maker output?
>> >
>> >thanks :)
>> >
>> >Joe Wilders
>> >
>> >_______________________________________________
>> >maker-devel mailing list
>> >maker-devel at box290.bluehost.com
>> >http://box290.bluehost.com/mailman/listinfo/maker-devel_yandell-lab.org
> 



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From dinatal at uwindsor.ca  Tue Mar 20 10:55:34 2012
From: dinatal at uwindsor.ca (claudia)
Date: Tue, 20 Mar 2012 12:55:34 -0400
Subject: [maker-devel] loading scaffold features into chado
Message-ID: <4F68B686.6050800@uwindsor.ca>

To whom it may concern,

I have 2 concerns, the first is:  regarding representing scaffold 
features in chado and gbrowse. I noticed that the Sequence ontology uses 
the term supercontig and so if my assembly generated scaffolds entitled 
"scaffold" should I change the names to supercontigs so that chado 
recognizes the terms?

Corresponding to my first question, Maker does not know that the contigs 
are actually scaffold/supercontigs when annotating and so Maker will 
still call the "type" feature or column 3 in the GFF3, a 'contig', how 
can Maker be implemented to change this naming convention before 
annotation, or after?

Consequently, I am having problems pulling up gene features in Gbrowse 
when doing a generic gene search, and I must provide the maker generated 
unique-gene_id in the gbrowse search bar or the known sequence id i.e 
'scaffold001', which is not useful for someone who does not have this 
information.
---- I do not have this problem when my seq_id, and 'type' feature id 
match in the true case of 'contigs'. I can do a generic gene search in 
gbrowse with the term 'maker' and gbrowse will provide me all the 
associated maker generated gene calls.

Thank you for any guidance resolving these concerns,
Claudia



-- 
Claudia DiNatale
Master's Candidate
The Crosby Lab
University of Windsor
519-253-3000 ext: 4755




From carsonhh at gmail.com  Tue Mar 20 11:13:35 2012
From: carsonhh at gmail.com (Carson Holt)
Date: Tue, 20 Mar 2012 13:13:35 -0400
Subject: [maker-devel] loading scaffold features into chado
In-Reply-To: <4F68B686.6050800@uwindsor.ca>
Message-ID: <CB8E2F50.97C7%carsonhh@gmail.com>


>I have 2 concerns, the first is:  regarding representing scaffold
>features in chado and gbrowse. I noticed that the Sequence ontology uses
>the term supercontig and so if my assembly generated scaffolds entitled
>"scaffold" should I change the names to supercontigs so that chado
>recognizes the terms?

Yes.  You must use valid SO terms.  It is a requirement of GFF3, and Chado
will enforce this requirement on loading a GFF3 file (note Chado will even
go as far as to check the validity of the Ontology_term= attribute in GFF3
if you use it).  You can decide to use contig or supercontig as your
sequence feature.  It doesn?t really matter unless you are placing both
into the database as separate features (i.e. You have a supercontig as the
parent feature and then you enter contigs individually as children of the
supercontig).


>
>Corresponding to my first question, Maker does not know that the contigs
>are actually scaffold/supercontigs when annotating and so Maker will
>still call the "type" feature or column 3 in the GFF3, a 'contig', how
>can Maker be implemented to change this naming convention before
>annotation, or after?

Not really important unless you plan on making contigs children of the
supercontig.  But you can always do a search and replace. -->
cat file.gff | perl -ane 's/\tcontig\t/\tsupercontig\t/s; print $_' >
new_file.gff


>
>Consequently, I am having problems pulling up gene features in Gbrowse
>when doing a generic gene search, and I must provide the maker generated
>unique-gene_id in the gbrowse search bar or the known sequence id i.e
>'scaffold001', which is not useful for someone who does not have this
>information.
>---- I do not have this problem when my seq_id, and 'type' feature id
>match in the true case of 'contigs'. I can do a generic gene search in
>gbrowse with the term 'maker' and gbrowse will provide me all the
>associated maker generated gene calls.

See "Adjusting GBrowse Name Searches" in the GBrowse tutorial -->
http://gmod.org/gbrowse2/tutorial/tutorial.html#naming


Thanks,
Carson











>
>Thank you for any guidance resolving these concerns,
>Claudia
>
>
>
>-- 
>Claudia DiNatale
>Master's Candidate
>The Crosby Lab
>University of Windsor
>519-253-3000 ext: 4755
>
>
>_______________________________________________
>maker-devel mailing list
>maker-devel at box290.bluehost.com
>http://box290.bluehost.com/mailman/listinfo/maker-devel_yandell-lab.org





From scott at scottcain.net  Tue Mar 20 11:25:04 2012
From: scott at scottcain.net (Scott Cain)
Date: Tue, 20 Mar 2012 13:25:04 -0400
Subject: [maker-devel] loading scaffold features into chado
In-Reply-To: <CB8E2F50.97C7%carsonhh@gmail.com>
References: <4F68B686.6050800@uwindsor.ca> <CB8E2F50.97C7%carsonhh@gmail.com>
Message-ID: <CA+JTaoy00sX+3Pdyrw=Apus09Lppg9YNQsr8k4uoYXHmK24Euw@mail.gmail.com>

Hi Claudia,

I agree with everything that Carson wrote, except about name
searching--it's a little trickier in Chado.  What you probably want to
do is implement full text searching.  See:

  http://gmod.org/wiki/Chado_Full_Text_Search

for more information on setting it up and maintaining it.

Scott


On Tue, Mar 20, 2012 at 1:13 PM, Carson Holt <carsonhh at gmail.com> wrote:
>
>>I have 2 concerns, the first is: ?regarding representing scaffold
>>features in chado and gbrowse. I noticed that the Sequence ontology uses
>>the term supercontig and so if my assembly generated scaffolds entitled
>>"scaffold" should I change the names to supercontigs so that chado
>>recognizes the terms?
>
> Yes. ?You must use valid SO terms. ?It is a requirement of GFF3, and Chado
> will enforce this requirement on loading a GFF3 file (note Chado will even
> go as far as to check the validity of the Ontology_term= attribute in GFF3
> if you use it). ?You can decide to use contig or supercontig as your
> sequence feature. ?It doesn?t really matter unless you are placing both
> into the database as separate features (i.e. You have a supercontig as the
> parent feature and then you enter contigs individually as children of the
> supercontig).
>
>
>>
>>Corresponding to my first question, Maker does not know that the contigs
>>are actually scaffold/supercontigs when annotating and so Maker will
>>still call the "type" feature or column 3 in the GFF3, a 'contig', how
>>can Maker be implemented to change this naming convention before
>>annotation, or after?
>
> Not really important unless you plan on making contigs children of the
> supercontig. ?But you can always do a search and replace. -->
> cat file.gff | perl -ane 's/\tcontig\t/\tsupercontig\t/s; print $_' >
> new_file.gff
>
>
>>
>>Consequently, I am having problems pulling up gene features in Gbrowse
>>when doing a generic gene search, and I must provide the maker generated
>>unique-gene_id in the gbrowse search bar or the known sequence id i.e
>>'scaffold001', which is not useful for someone who does not have this
>>information.
>>---- I do not have this problem when my seq_id, and 'type' feature id
>>match in the true case of 'contigs'. I can do a generic gene search in
>>gbrowse with the term 'maker' and gbrowse will provide me all the
>>associated maker generated gene calls.
>
> See "Adjusting GBrowse Name Searches" in the GBrowse tutorial -->
> http://gmod.org/gbrowse2/tutorial/tutorial.html#naming
>
>
> Thanks,
> Carson
>
>
>
>
>
>
>
>
>
>
>
>>
>>Thank you for any guidance resolving these concerns,
>>Claudia
>>
>>
>>
>>--
>>Claudia DiNatale
>>Master's Candidate
>>The Crosby Lab
>>University of Windsor
>>519-253-3000 ext: 4755
>>
>>
>>_______________________________________________
>>maker-devel mailing list
>>maker-devel at box290.bluehost.com
>>http://box290.bluehost.com/mailman/listinfo/maker-devel_yandell-lab.org
>
>
>
> _______________________________________________
> maker-devel mailing list
> maker-devel at box290.bluehost.com
> http://box290.bluehost.com/mailman/listinfo/maker-devel_yandell-lab.org



-- 
------------------------------------------------------------------------
Scott Cain, Ph. D.? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ?? scott at scottcain dot net
GMOD Coordinator (http://gmod.org/)? ? ? ? ? ? ? ? ? ?? 216-392-3087
Ontario Institute for Cancer Research



From carsonhh at gmail.com  Tue Mar 20 11:27:10 2012
From: carsonhh at gmail.com (Carson Holt)
Date: Tue, 20 Mar 2012 13:27:10 -0400
Subject: [maker-devel] loading scaffold features into chado
In-Reply-To: <CA+JTaoy00sX+3Pdyrw=Apus09Lppg9YNQsr8k4uoYXHmK24Euw@mail.gmail.com>
Message-ID: <CB8E3600.97EA%carsonhh@gmail.com>

Yes. thank you Scott.  My answer would work for GBrowse NOT Chado :-)

--Carson



On 12-03-20 1:25 PM, "Scott Cain" <scott at scottcain.net> wrote:

>Hi Claudia,
>
>I agree with everything that Carson wrote, except about name
>searching--it's a little trickier in Chado.  What you probably want to
>do is implement full text searching.  See:
>
>  http://gmod.org/wiki/Chado_Full_Text_Search
>
>for more information on setting it up and maintaining it.
>
>Scott
>
>
>On Tue, Mar 20, 2012 at 1:13 PM, Carson Holt <carsonhh at gmail.com> wrote:
>>
>>>I have 2 concerns, the first is:  regarding representing scaffold
>>>features in chado and gbrowse. I noticed that the Sequence ontology uses
>>>the term supercontig and so if my assembly generated scaffolds entitled
>>>"scaffold" should I change the names to supercontigs so that chado
>>>recognizes the terms?
>>
>> Yes.  You must use valid SO terms.  It is a requirement of GFF3, and
>>Chado
>> will enforce this requirement on loading a GFF3 file (note Chado will
>>even
>> go as far as to check the validity of the Ontology_term= attribute in
>>GFF3
>> if you use it).  You can decide to use contig or supercontig as your
>> sequence feature.  It doesn?t really matter unless you are placing both
>> into the database as separate features (i.e. You have a supercontig as
>>the
>> parent feature and then you enter contigs individually as children of
>>the
>> supercontig).
>>
>>
>>>
>>>Corresponding to my first question, Maker does not know that the contigs
>>>are actually scaffold/supercontigs when annotating and so Maker will
>>>still call the "type" feature or column 3 in the GFF3, a 'contig', how
>>>can Maker be implemented to change this naming convention before
>>>annotation, or after?
>>
>> Not really important unless you plan on making contigs children of the
>> supercontig.  But you can always do a search and replace. -->
>> cat file.gff | perl -ane 's/\tcontig\t/\tsupercontig\t/s; print $_' >
>> new_file.gff
>>
>>
>>>
>>>Consequently, I am having problems pulling up gene features in Gbrowse
>>>when doing a generic gene search, and I must provide the maker generated
>>>unique-gene_id in the gbrowse search bar or the known sequence id i.e
>>>'scaffold001', which is not useful for someone who does not have this
>>>information.
>>>---- I do not have this problem when my seq_id, and 'type' feature id
>>>match in the true case of 'contigs'. I can do a generic gene search in
>>>gbrowse with the term 'maker' and gbrowse will provide me all the
>>>associated maker generated gene calls.
>>
>> See "Adjusting GBrowse Name Searches" in the GBrowse tutorial -->
>> http://gmod.org/gbrowse2/tutorial/tutorial.html#naming
>>
>>
>> Thanks,
>> Carson
>>
>>
>>
>>
>>
>>
>>
>>
>>
>>
>>
>>>
>>>Thank you for any guidance resolving these concerns,
>>>Claudia
>>>
>>>
>>>
>>>--
>>>Claudia DiNatale
>>>Master's Candidate
>>>The Crosby Lab
>>>University of Windsor
>>>519-253-3000 ext: 4755
>>>
>>>
>>>_______________________________________________
>>>maker-devel mailing list
>>>maker-devel at box290.bluehost.com
>>>http://box290.bluehost.com/mailman/listinfo/maker-devel_yandell-lab.org
>>
>>
>>
>> _______________________________________________
>> maker-devel mailing list
>> maker-devel at box290.bluehost.com
>> http://box290.bluehost.com/mailman/listinfo/maker-devel_yandell-lab.org
>
>
>
>-- 
>------------------------------------------------------------------------
>Scott Cain, Ph. D.                                   scott at scottcain
>dot net
>GMOD Coordinator (http://gmod.org/)                     216-392-3087
>Ontario Institute for Cancer Research





From dinatal at uwindsor.ca  Tue Mar 20 12:03:27 2012
From: dinatal at uwindsor.ca (claudia)
Date: Tue, 20 Mar 2012 14:03:27 -0400
Subject: [maker-devel] loading scaffold features into chado
In-Reply-To: <CA+JTaoy00sX+3Pdyrw=Apus09Lppg9YNQsr8k4uoYXHmK24Euw@mail.gmail.com>
References: <4F68B686.6050800@uwindsor.ca> <CB8E2F50.97C7%carsonhh@gmail.com>
	<CA+JTaoy00sX+3Pdyrw=Apus09Lppg9YNQsr8k4uoYXHmK24Euw@mail.gmail.com>
Message-ID: <4F68C66F.2010902@uwindsor.ca>

Hi,

  I have enabled full text searching and I still have this problem, 
another reason for concern... So I wondered if in fact I changed all the 
ID's in the GFF3 file to supercontigs, then perhaps Chado would better 
link all the terms, annotations, and fasta files.... Although, i realize 
that the seq_id ( column 1) shouldn't need to be specific since the 
'type' term would take care of designating the feature type, no?

Claudia



On 20/03/2012 1:25 PM, Scott Cain wrote:
> Hi Claudia,
>
> I agree with everything that Carson wrote, except about name
> searching--it's a little trickier in Chado.  What you probably want to
> do is implement full text searching.  See:
>
>    http://gmod.org/wiki/Chado_Full_Text_Search
>
> for more information on setting it up and maintaining it.
>
> Scott
>
>
> On Tue, Mar 20, 2012 at 1:13 PM, Carson Holt<carsonhh at gmail.com>  wrote:
>>> I have 2 concerns, the first is:  regarding representing scaffold
>>> features in chado and gbrowse. I noticed that the Sequence ontology uses
>>> the term supercontig and so if my assembly generated scaffolds entitled
>>> "scaffold" should I change the names to supercontigs so that chado
>>> recognizes the terms?
>> Yes.  You must use valid SO terms.  It is a requirement of GFF3, and Chado
>> will enforce this requirement on loading a GFF3 file (note Chado will even
>> go as far as to check the validity of the Ontology_term= attribute in GFF3
>> if you use it).  You can decide to use contig or supercontig as your
>> sequence feature.  It doesn?t really matter unless you are placing both
>> into the database as separate features (i.e. You have a supercontig as the
>> parent feature and then you enter contigs individually as children of the
>> supercontig).
>>
>>
>>> Corresponding to my first question, Maker does not know that the contigs
>>> are actually scaffold/supercontigs when annotating and so Maker will
>>> still call the "type" feature or column 3 in the GFF3, a 'contig', how
>>> can Maker be implemented to change this naming convention before
>>> annotation, or after?
>> Not really important unless you plan on making contigs children of the
>> supercontig.  But you can always do a search and replace. -->
>> cat file.gff | perl -ane 's/\tcontig\t/\tsupercontig\t/s; print $_'>
>> new_file.gff
>>
>>
>>> Consequently, I am having problems pulling up gene features in Gbrowse
>>> when doing a generic gene search, and I must provide the maker generated
>>> unique-gene_id in the gbrowse search bar or the known sequence id i.e
>>> 'scaffold001', which is not useful for someone who does not have this
>>> information.
>>> ---- I do not have this problem when my seq_id, and 'type' feature id
>>> match in the true case of 'contigs'. I can do a generic gene search in
>>> gbrowse with the term 'maker' and gbrowse will provide me all the
>>> associated maker generated gene calls.
>> See "Adjusting GBrowse Name Searches" in the GBrowse tutorial -->
>> http://gmod.org/gbrowse2/tutorial/tutorial.html#naming
>>
>>
>> Thanks,
>> Carson
>>
>>
>>
>>
>>
>>
>>
>>
>>
>>
>>
>>> Thank you for any guidance resolving these concerns,
>>> Claudia
>>>
>>>
>>>
>>> --
>>> Claudia DiNatale
>>> Master's Candidate
>>> The Crosby Lab
>>> University of Windsor
>>> 519-253-3000 ext: 4755
>>>
>>>
>>> _______________________________________________
>>> maker-devel mailing list
>>> maker-devel at box290.bluehost.com
>>> http://box290.bluehost.com/mailman/listinfo/maker-devel_yandell-lab.org
>>
>>
>> _______________________________________________
>> maker-devel mailing list
>> maker-devel at box290.bluehost.com
>> http://box290.bluehost.com/mailman/listinfo/maker-devel_yandell-lab.org
>
>


-- 
Claudia DiNatale
Master's Candidate
The Crosby Lab
University of Windsor
519-253-3000 ext: 4755




From scott at scottcain.net  Tue Mar 20 13:50:55 2012
From: scott at scottcain.net (Scott Cain)
Date: Tue, 20 Mar 2012 15:50:55 -0400
Subject: [maker-devel] loading scaffold features into chado
In-Reply-To: <4F68C66F.2010902@uwindsor.ca>
References: <4F68B686.6050800@uwindsor.ca> <CB8E2F50.97C7%carsonhh@gmail.com>
	<CA+JTaoy00sX+3Pdyrw=Apus09Lppg9YNQsr8k4uoYXHmK24Euw@mail.gmail.com>
	<4F68C66F.2010902@uwindsor.ca>
Message-ID: <FFACED63-40D9-4810-9927-0E4984BA8465@scottcain.net>

Hi Claudia,

Can you post a sample of the gff that shows what you are looking for and not finding?

Scott


Sent from my iPad

On Mar 20, 2012, at 2:03 PM, claudia <dinatal at uwindsor.ca> wrote:

> Hi,
> 
> I have enabled full text searching and I still have this problem, another reason for concern... So I wondered if in fact I changed all the ID's in the GFF3 file to supercontigs, then perhaps Chado would better link all the terms, annotations, and fasta files.... Although, i realize that the seq_id ( column 1) shouldn't need to be specific since the 'type' term would take care of designating the feature type, no?
> 
> Claudia
> 
> 
> 
> On 20/03/2012 1:25 PM, Scott Cain wrote:
>> Hi Claudia,
>> 
>> I agree with everything that Carson wrote, except about name
>> searching--it's a little trickier in Chado.  What you probably want to
>> do is implement full text searching.  See:
>> 
>>   http://gmod.org/wiki/Chado_Full_Text_Search
>> 
>> for more information on setting it up and maintaining it.
>> 
>> Scott
>> 
>> 
>> On Tue, Mar 20, 2012 at 1:13 PM, Carson Holt<carsonhh at gmail.com>  wrote:
>>>> I have 2 concerns, the first is:  regarding representing scaffold
>>>> features in chado and gbrowse. I noticed that the Sequence ontology uses
>>>> the term supercontig and so if my assembly generated scaffolds entitled
>>>> "scaffold" should I change the names to supercontigs so that chado
>>>> recognizes the terms?
>>> Yes.  You must use valid SO terms.  It is a requirement of GFF3, and Chado
>>> will enforce this requirement on loading a GFF3 file (note Chado will even
>>> go as far as to check the validity of the Ontology_term= attribute in GFF3
>>> if you use it).  You can decide to use contig or supercontig as your
>>> sequence feature.  It doesn?t really matter unless you are placing both
>>> into the database as separate features (i.e. You have a supercontig as the
>>> parent feature and then you enter contigs individually as children of the
>>> supercontig).
>>> 
>>> 
>>>> Corresponding to my first question, Maker does not know that the contigs
>>>> are actually scaffold/supercontigs when annotating and so Maker will
>>>> still call the "type" feature or column 3 in the GFF3, a 'contig', how
>>>> can Maker be implemented to change this naming convention before
>>>> annotation, or after?
>>> Not really important unless you plan on making contigs children of the
>>> supercontig.  But you can always do a search and replace. -->
>>> cat file.gff | perl -ane 's/\tcontig\t/\tsupercontig\t/s; print $_'>
>>> new_file.gff
>>> 
>>> 
>>>> Consequently, I am having problems pulling up gene features in Gbrowse
>>>> when doing a generic gene search, and I must provide the maker generated
>>>> unique-gene_id in the gbrowse search bar or the known sequence id i.e
>>>> 'scaffold001', which is not useful for someone who does not have this
>>>> information.
>>>> ---- I do not have this problem when my seq_id, and 'type' feature id
>>>> match in the true case of 'contigs'. I can do a generic gene search in
>>>> gbrowse with the term 'maker' and gbrowse will provide me all the
>>>> associated maker generated gene calls.
>>> See "Adjusting GBrowse Name Searches" in the GBrowse tutorial -->
>>> http://gmod.org/gbrowse2/tutorial/tutorial.html#naming
>>> 
>>> 
>>> Thanks,
>>> Carson
>>> 
>>> 
>>> 
>>> 
>>> 
>>> 
>>> 
>>> 
>>> 
>>> 
>>> 
>>>> Thank you for any guidance resolving these concerns,
>>>> Claudia
>>>> 
>>>> 
>>>> 
>>>> --
>>>> Claudia DiNatale
>>>> Master's Candidate
>>>> The Crosby Lab
>>>> University of Windsor
>>>> 519-253-3000 ext: 4755
>>>> 
>>>> 
>>>> _______________________________________________
>>>> maker-devel mailing list
>>>> maker-devel at box290.bluehost.com
>>>> http://box290.bluehost.com/mailman/listinfo/maker-devel_yandell-lab.org
>>> 
>>> 
>>> _______________________________________________
>>> maker-devel mailing list
>>> maker-devel at box290.bluehost.com
>>> http://box290.bluehost.com/mailman/listinfo/maker-devel_yandell-lab.org
>> 
>> 
> 
> 
> -- 
> Claudia DiNatale
> Master's Candidate
> The Crosby Lab
> University of Windsor
> 519-253-3000 ext: 4755
> 



From thomas.hackl at uni-wuerzburg.de  Tue Mar 20 12:16:03 2012
From: thomas.hackl at uni-wuerzburg.de (Thomas Hackl)
Date: Tue, 20 Mar 2012 19:16:03 +0100
Subject: [maker-devel] maker 2.22/2.23: Segmentation fault while
 processing FASTA input
In-Reply-To: <CB8CD562.94D0%carsonhh@gmail.com>
References: <CB8CD562.94D0%carsonhh@gmail.com>
Message-ID: <4F68C963.3040108@uni-wuerzburg.de>

Hi,

I installed and ran the debug version of maker. Without -debug it 
results in the expected segmentation fault. With -debug it paradoxically 
finishes without the error.

I screened the debug log anyway but could not find anything that helped 
me to localize the problem. I attached a condensed version (sort | uniq) 
of the log.
Any ideas are appreciated.

Regards
Thomas



Am 19.03.2012 17:24, schrieb Carson Holt:
> Ok.  I finished the special debug version over the weekend.  Run with
> -debug set as a command line flag.  Capture and return the STDERR on
> failure.  It will list all modules used, the versions, and when they are
> called so we can see what happens right before failure.
>
> http://yandell-lab.org/research/maker_debug.tgz
>
>
> Thanks,
> Carson
>
>
>
> On 12-03-14 1:57 AM, "Felix Bemm"<felix.bemm at uni-wuerzburg.de>  wrote:
>
>> Hi,
>>
>> Thomas and I are colleagues and dealing with the same problem here. I
>> wrote some test code that forced the indexing and it work fine. We are
>> using most of the bioperl seqio and db modules in combination with other
>> tools and don't experience the same problem there at the moment.
>>
>> Regards
>> Felix
>>
>> Am 13.03.2012 22:37, schrieb Barry Moore:
>>> You might also try a short perl script outside of MAKER to exercise
>>> Bio::DB::Fasta (which I believe is the module MAKER uses for Fasta
>>> indexing - correct Carson?).
>>>
>>> Something like this should work to force indexing:
>>>
>>> useBio::DB::Fasta;
>>> my $db = Bio::DB::Fasta->new('/path/to/fasta/files');
>>> my$seq=$db->seq($seqid, $start, $end);
>>>
>>> Point it at your fasta directory or file.
>>>
>>> B
>>>
>>> On Mar 13, 2012, at 3:41 AM, Thomas Hackl wrote:
>>>
>>>> Hello,
>>>>
>>>> We reinstalled the packages you suggested
>>>>
>>>> forks is up to date (0.34).
>>>> forks::shared is up to date (0.34).
>>>> Inline::C is up to date (0.50).
>>>> Storable is up to date (2.30).
>>>>
>>>> as well as BioPerl.
>>>>
>>>> The problem is still the same.
>>>>
>>>> With MPI it terminates with this message:
>>>>
>>>> STATUS: Parsing control files...
>>>> STATUS: Processing and indexing input FASTA files...
>>>>
>>>> ========================================================================
>>>> =============
>>>>
>>>>
>>>> = BAD TERMINATION OF ONE OF YOUR APPLICATION PROCESSES
>>>> = EXIT CODE: 11
>>>> = CLEANING UP REMAINING PROCESSES
>>>> = YOU CAN IGNORE THE BELOW CLEANUP MESSAGES
>>>>
>>>> ========================================================================
>>>> =============
>>>>
>>>> APPLICATION TERMINATED WITH THE EXIT STRING: Segmentation fault
>>>> (signal 11)
>>>>
>>>> which I presume is also the same problem.
>>>>
>>>> I am with you that the error is caused somewhere on the C level. If
>>>> the indexing step
>>>> is handled by non-maker modules exclusively, than the fact that the
>>>> 2.15 version works,
>>>> suggests that you are using different modules/methods in the current
>>>> releases?
>>>>
>>>> In any case, I think a version with verbose status messages might help
>>>> to localize the
>>>> source of the problem.
>>>>
>>>> Regards
>>>> Thomas
>>>>
>>>> Am 07.03.2012 23:45, schrieb Carson Holt:
>>>>> There should be no new hardware requirement. But there is always a
>>>>> chance
>>>>> that there is an issue with one of the perl modules being used. I
>>>>> assume
>>>>> the failure is happening when using maker serially and you are not
>>>>> using
>>>>> MPI.
>>>>>
>>>>> Could you reinstall the following perl modules, and try again. If you
>>>>> are
>>>>> using CPAN, do a 'force install' to force it to reinstall.
>>>>>
>>>>> Modules:
>>>>> *Storable
>>>>> *Inline::C
>>>>> *forks
>>>>> *forks::shared
>>>>>
>>>>> Also try reinstalling the latest version of BioPerl.
>>>>>
>>>>> The fact that this is a seg fault suggests that something is
>>>>> happemning at
>>>>> the C level (just outside of Perl). Those area all the modules MAKER
>>>>> uses
>>>>> that will call back to the C level. BioPerl has a fasta indexing
>>>>> module
>>>>> that is also making calls outside of Perl, and the fact it fails at
>>>>> that
>>>>> point makes it a suspect.
>>>>>
>>>>> Let me know what happens. I can always generate an alternate MAKER
>>>>> executable for you to run with additional status messages that may
>>>>> help
>>>>> identify exactly which module is being called right before the
>>>>> failure.
>>>>>
>>>>> Thanks,
>>>>> Carson
>>>>>
>>>>>
>>>>>
>>>>> On 12-03-07 3:31 AM, "Thomas Hackl"<thomas.hackl at uni-wuerzburg.de
>>>>> <mailto:thomas.hackl at uni-wuerzburg.de>>  wrote:
>>>>>
>>>>>> Hello,
>>>>>>
>>>>>> we want to use a current release of maker (2.22, 2.23) but the
>>>>>> program
>>>>>> terminates with a seg fault while processing the input FASTA files.
>>>>>> maker 2.15 , which we have been using for quite some time, runs
>>>>>> perfectly with identical data and setup.
>>>>>>
>>>>>> Please contact me if you need specifics on hardware, OS or anything
>>>>>> else.
>>>>>>
>>>>>> Best regards
>>>>>> Thomas
>>>>>>
>>>>>> --
>>>>>> Thomas Hackl
>>>>>> Julius-Maximilians-Universit?t
>>>>>> Department of Bioinformatics
>>>>>> 97074 W?rzburg, Germany
>>>>>> Fon: +49 931 - 31 86883
>>>>>> Mail: thomas.hackl at uni-wuerzburg.de
>>>>>> <mailto:thomas.hackl at uni-wuerzburg.de>
>>>>>>
>>>>>>
>>>>>> _______________________________________________
>>>>>> maker-devel mailing list
>>>>>> maker-devel at box290.bluehost.com
>>>>>> <mailto:maker-devel at box290.bluehost.com>
>>>>>>
>>>>>> http://box290.bluehost.com/mailman/listinfo/maker-devel_yandell-lab.or
>>>>>> g
>>>>
>>>> --
>>>> Thomas Hackl
>>>> Julius-Maximilians-Universit?t
>>>> Department of Bioinformatics
>>>> 97074 W?rzburg, Germany
>>>> Fon: +49 931 - 31 86883
>>>> Mail: thomas.hackl at uni-wuerzburg.de
>>>> <mailto:thomas.hackl at uni-wuerzburg.de>
>>>>
>>>>
>>>> _______________________________________________
>>>> maker-devel mailing list
>>>> maker-devel at box290.bluehost.com
>>>> <mailto:maker-devel at box290.bluehost.com>
>>>> http://box290.bluehost.com/mailman/listinfo/maker-devel_yandell-lab.org
>>> Barry Moore
>>> Research Scientist
>>> Dept. of Human Genetics
>>> University of Utah
>>> Salt Lake City, UT 84112
>>> --------------------------------------------
>>> (801) 585-3543
>>>
>>>
>>>
>>>
>>>
>>>
>>> _______________________________________________
>>> maker-devel mailing list
>>> maker-devel at box290.bluehost.com
>>> http://box290.bluehost.com/mailman/listinfo/maker-devel_yandell-lab.org
>> _______________________________________________
>> maker-devel mailing list
>> maker-devel at box290.bluehost.com
>> http://box290.bluehost.com/mailman/listinfo/maker-devel_yandell-lab.org

-- 
Thomas Hackl
Julius-Maximilians-Universit?t
Department of Bioinformatics
97074 W?rzburg, Germany
Fon:  +49 931 - 31 86883
Mail: thomas.hackl at uni-wuerzburg.de

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From scott at scottcain.net  Wed Mar 21 14:59:19 2012
From: scott at scottcain.net (Scott Cain)
Date: Wed, 21 Mar 2012 16:59:19 -0400
Subject: [maker-devel] loading scaffold features into chado
In-Reply-To: <4F6A290E.8000306@uwindsor.ca>
References: <4F68B686.6050800@uwindsor.ca> <CB8E2F50.97C7%carsonhh@gmail.com>
	<CA+JTaoy00sX+3Pdyrw=Apus09Lppg9YNQsr8k4uoYXHmK24Euw@mail.gmail.com>
	<4F68C66F.2010902@uwindsor.ca>
	<FFACED63-40D9-4810-9927-0E4984BA8465@scottcain.net>
	<web-60068456@uwindsor.ca>
	<CA+JTaoxshG4M+awmuw93=JkwqtisgFSw6igZE+_2tCFaN-ocrw@mail.gmail.com>
	<4F6A03D2.5010503@uwindsor.ca>
	<CA+JTaoyMT6_uxYG_b28j-PCJfiOeL6FUqgLRj1FNvwR7XZUOkA@mail.gmail.com>
	<4F6A290E.8000306@uwindsor.ca>
Message-ID: <CA+JTaowKA=wFW8A91wpOMZLAe+phkFdHdppO1ume+30sWN9T9g@mail.gmail.com>

Hi Claudia,

I wanted to bring this back to the mailing lists, so I cc'ed them here.

First, with the fasta loading issue: what command are you using to
load the fasta sequences?  It works for me whether the fasta is at the
bottom of the GFF file or if it is a separate fasta file (as long as I
supply the --fastafile flag to the loader).

About the searching problem: when I turn on full text searching (which
means both running gmod_chado_fts_prep.pl and adding "-fulltext 1" to
the db_args in the gbrowse config file), I can search for "cnot1" and
find both a gene and an mRNA (of course, they are really the same
feature, but GBrowse doesn't know that).  Also, searching for "maker"
works, but in a real database, this will not be an effective query,
since the number of results returned are limited, and presumably there
will be lots of features resulting from a query like that.  Please
remind me, is that what you wanted to do?

Scott




On Wed, Mar 21, 2012 at 3:16 PM, claudia <dinatal at uwindsor.ca> wrote:
> Hi Scott,
>
> ?Wanted to give you a quick heads up that the bulk loader seems to be
> loading my fasta files now after deleting the ' ##FASTA' header ( the first
> line of the file now looks like this >scaffold0001)...
> Never had this problem before, it seems the bulk loader wanted to see a '>'
> symbol in front of the first line...
>
> -- when I say seems, I will let you know if it finishes, as it currently
> ?states " Loading sequences ( if any)" ... and I never made it this far
> before :)
>
> Claudia
>
>
>
> On 21/03/2012 12:53 PM, Scott Cain wrote:
>>
>> Hi Claudia,
>>
>> I imagine one scaffold and gene models would be good--the problem is
>> finding genes, right?
>>
>> Also, with loading fasta: were the corresponding features from the GFF
>> file already loaded? ?If so, that should have worked, and if it didn't
>> it implies a bug. ?If not, that's why.
>>
>> Scott
>>
>>
>> On Wed, Mar 21, 2012 at 12:37 PM, claudia<dinatal at uwindsor.ca> ?wrote:
>>>
>>> Hi Scott,
>>> ?So would one scaffold with Maker gene models suffice? Do you want the
>>> analysis as well?
>>>
>>> --along those same lines, I did try and load the original sequence
>>> (fasta)
>>> file first that I ran the Pipeline on and chado seems to refuse the files
>>> saying they don't contain the appropriate feature '>' in the header which
>>> in
>>> fact they do i.e> ?scaffold00001 ... So not sure what is wrong with the
>>> fasta that chado doesn't want to load even if it is embedded in the GFF3,
>>> the bulk loader or maker2chado return errors stating 'feature not
>>> found'...
>>>
>>>
>>> Claudia
>>>
>>>
>>>
>>> On 21/03/2012 12:20 PM, Scott Cain wrote:
>>>>
>>>> Hi Claudia,
>>>>
>>>> I was hoping to get actual files that I could do testing on, not
>>>> pictures of files :-)
>>>>
>>>> Scott
>>>>
>>>>
>>>> On Tue, Mar 20, 2012 at 4:15 PM, Dinatale C<dinatal at uwindsor.ca>
>>>> ?wrote:
>>>>>
>>>>> Hi,
>>>>>
>>>>> Attached: ?I have samples of the contig file ( I extracted the contig
>>>>> features first to load prior to the gene models) the fasta of the
>>>>> sequences
>>>>> is in the footer of the gff3 file.
>>>>>
>>>>> --so basically, based on experience with contig annotations, I should
>>>>> be
>>>>> able to type in 'maker' in to the gbrowse search bar, and recieve all
>>>>> the
>>>>> maker gene annotations, but I don't. I must specifiy the exact ID i.e "
>>>>> maker-scaffold11323-augustus-gene...." or 'scaffold11323'
>>>>>
>>>>> --so I wonder if it has to do with the fasta files being named as
>>>>> 'scaffolds' and perhaps causing a problem with chado recognizing that
>>>>> they
>>>>> are linked to the gene annotations due to scaffold not being a SOFA
>>>>> type
>>>>> term, if in fact the sequences must be submitted to the database first?
>>>>>
>>>>>
>>>>> Thanks in advance,
>>>>>
>>>>> Claudia
>>>>>
>>>>> On Tue, 20 Mar 2012 15:50:55 -0400 Scott Cain wrote:
>>>>>>
>>>>>> Hi Claudia,
>>>>>>
>>>>>> Can you post a sample of the gff that shows what you are looking for
>>>>>> and
>>>>>> not finding?
>>>>>>
>>>>>> Scott
>>>>>>
>>>>>>
>>>>>> Sent from my iPad
>>>>>>
>>>>>> On Mar 20, 2012, at 2:03 PM, claudia wrote:
>>>>>>
>>>>>>> Hi,
>>>>>>>
>>>>>>> I have enabled full text searching and I still have this problem,
>>>>>>> another reason for
>>>>>>
>>>>>> concern... So I wondered if in fact I changed all the ID's in the GFF3
>>>>>> file to supercontigs,
>>>>>> then perhaps Chado would better link all the terms, annotations, and
>>>>>> fasta
>>>>>> files....
>>>>>> Although, i realize that the seq_id ( column 1) shouldn't need to be
>>>>>> specific since the
>>>>>> 'type' term would take care of designating the feature type, no?
>>>>>>>
>>>>>>> Claudia
>>>>>>>
>>>>>>>
>>>>>>>
>>>>>>> On 20/03/2012 1:25 PM, Scott Cain wrote:
>>>>>>>>
>>>>>>>> Hi Claudia,
>>>>>>>>
>>>>>>>> I agree with everything that Carson wrote, except about name
>>>>>>>> searching--it's a little trickier in Chado. What you probably want
>>>>>>>> to
>>>>>>>> do is implement full text searching. See:
>>>>>>>>
>>>>>>>> http://gmod.org/wiki/Chado_Full_Text_Search
>>>>>>>>
>>>>>>>> for more information on setting it up and maintaining it.
>>>>>>>>
>>>>>>>> Scott
>>>>>>>>
>>>>>>>>
>>>>>>>> On Tue, Mar 20, 2012 at 1:13 PM, Carson Holt wrote:
>>>>>>>>>>
>>>>>>>>>> I have 2 concerns, the first is: regarding representing scaffold
>>>>>>>>>> features in chado and gbrowse. I noticed that the Sequence
>>>>>>>>>> ontology
>>>>>>>>>> uses
>>>>>>>>>> the term supercontig and so if my assembly generated scaffolds
>>>>>>>>>> entitled
>>>>>>>>>> "scaffold" should I change the names to supercontigs so that chado
>>>>>>>>>> recognizes the terms?
>>>>>>>>>
>>>>>>>>> Yes. You must use valid SO terms. It is a requirement of GFF3, and
>>>>>>>>> Chado
>>>>>>>>> will enforce this requirement on loading a GFF3 file (note Chado
>>>>>>>>> will
>>>>>>>>> even
>>>>>>>>> go as far as to check the validity of the Ontology_term= attribute
>>>>>>>>> in
>>>>>>>>> GFF3
>>>>>>>>> if you use it). You can decide to use contig or supercontig as your
>>>>>>>>> sequence feature. It doesn?t really matter unless you are placing
>>>>>>>>>
>>>>>>>>> both
>>>>>>>>> into the database as separate features (i.e. You have a supercontig
>>>>>>>>> as
>>>>>>>>> the
>>>>>>>>> parent feature and then you enter contigs individually as children
>>>>>>>>> of
>>>>>>>>> the
>>>>>>>>> supercontig).
>>>>>>>>>
>>>>>>>>>
>>>>>>>>>> Corresponding to my first question, Maker does not know that the
>>>>>>>>>> contigs
>>>>>>>>>> are actually scaffold/supercontigs when annotating and so Maker
>>>>>>>>>> will
>>>>>>>>>> still call the "type" feature or column 3 in the GFF3, a 'contig',
>>>>>>>>>> how
>>>>>>>>>> can Maker be implemented to change this naming convention before
>>>>>>>>>> annotation, or after?
>>>>>>>>>
>>>>>>>>> Not really important unless you plan on making contigs children of
>>>>>>>>> the
>>>>>>>>> supercontig. But you can always do a search and replace. -->
>>>>>>>>> cat file.gff | perl -ane 's/\tcontig\t/\tsupercontig\t/s; print
>>>>>>>>> $_'>
>>>>>>>>> new_file.gff
>>>>>>>>>
>>>>>>>>>
>>>>>>>>>> Consequently, I am having problems pulling up gene features in
>>>>>>>>>> Gbrowse
>>>>>>>>>> when doing a generic gene search, and I must provide the maker
>>>>>>>>>> generated
>>>>>>>>>> unique-gene_id in the gbrowse search bar or the known sequence id
>>>>>>>>>> i.e
>>>>>>>>>> 'scaffold001', which is not useful for someone who does not have
>>>>>>>>>> this
>>>>>>>>>> information.
>>>>>>>>>> ---- I do not have this problem when my seq_id, and 'type' feature
>>>>>>>>>> id
>>>>>>>>>> match in the true case of 'contigs'. I can do a generic gene
>>>>>>>>>> search
>>>>>>>>>> in
>>>>>>>>>> gbrowse with the term 'maker' and gbrowse will provide me all the
>>>>>>>>>> associated maker generated gene calls.
>>>>>>>>>
>>>>>>>>> See "Adjusting GBrowse Name Searches" in the GBrowse tutorial -->
>>>>>>>>> http://gmod.org/gbrowse2/tutorial/tutorial.html#naming
>>>>>>>>>
>>>>>>>>>
>>>>>>>>> Thanks,
>>>>>>>>> Carson
>>>>>>>>>
>>>>>>>>>
>>>>>>>>>
>>>>>>>>>
>>>>>>>>>
>>>>>>>>>
>>>>>>>>>
>>>>>>>>>
>>>>>>>>>
>>>>>>>>>
>>>>>>>>>
>>>>>>>>>> Thank you for any guidance resolving these concerns,
>>>>>>>>>> Claudia
>>>>>>>>>>
>>>>>>>>>>
>>>>>>>>>>
>>>>>>>>>> --
>>>>>>>>>> Claudia DiNatale
>>>>>>>>>> Master's Candidate
>>>>>>>>>> The Crosby Lab
>>>>>>>>>> University of Windsor
>>>>>>>>>> 519-253-3000 ext: 4755
>>>>>>>>>>
>>>>>>>>>>
>>>>>>>>>> _______________________________________________
>>>>>>>>>> maker-devel mailing list
>>>>>>>>>> maker-devel at box290.bluehost.com
>>>>>>>>>>
>>>>>>>>>>
>>>>>>>>>>
>>>>>>>>>> http://box290.bluehost.com/mailman/listinfo/maker-devel_yandell-lab.org
>>>>>>>>>
>>>>>>>>>
>>>>>>>>> _______________________________________________
>>>>>>>>> maker-devel mailing list
>>>>>>>>> maker-devel at box290.bluehost.com
>>>>>>>>>
>>>>>>>>>
>>>>>>>>>
>>>>>>>>> http://box290.bluehost.com/mailman/listinfo/maker-devel_yandell-lab.org
>>>>>>>>
>>>>>>>>
>>>>>>> --
>>>>>>> Claudia DiNatale
>>>>>>> Master's Candidate
>>>>>>> The Crosby Lab
>>>>>>> University of Windsor
>>>>>>> 519-253-3000 ext: 4755
>>>>>>>
>>>>
>>>
>>> --
>>> Claudia DiNatale
>>> Master's Candidate
>>> The Crosby Lab
>>> University of Windsor
>>> 519-253-3000 ext: 4755
>>>
>>
>>
>
>
> --
> Claudia DiNatale
> Master's Candidate
> The Crosby Lab
> University of Windsor
> 519-253-3000 ext: 4755
>



-- 
------------------------------------------------------------------------
Scott Cain, Ph. D.? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ?? scott at scottcain dot net
GMOD Coordinator (http://gmod.org/)? ? ? ? ? ? ? ? ? ?? 216-392-3087
Ontario Institute for Cancer Research



From dinatal at uwindsor.ca  Wed Mar 21 15:14:54 2012
From: dinatal at uwindsor.ca (claudia)
Date: Wed, 21 Mar 2012 17:14:54 -0400
Subject: [maker-devel] loading scaffold features into chado
In-Reply-To: <CA+JTaowKA=wFW8A91wpOMZLAe+phkFdHdppO1ume+30sWN9T9g@mail.gmail.com>
References: <4F68B686.6050800@uwindsor.ca> <CB8E2F50.97C7%carsonhh@gmail.com>
	<CA+JTaoy00sX+3Pdyrw=Apus09Lppg9YNQsr8k4uoYXHmK24Euw@mail.gmail.com>
	<4F68C66F.2010902@uwindsor.ca>
	<FFACED63-40D9-4810-9927-0E4984BA8465@scottcain.net>
	<web-60068456@uwindsor.ca>
	<CA+JTaoxshG4M+awmuw93=JkwqtisgFSw6igZE+_2tCFaN-ocrw@mail.gmail.com>
	<4F6A03D2.5010503@uwindsor.ca>
	<CA+JTaoyMT6_uxYG_b28j-PCJfiOeL6FUqgLRj1FNvwR7XZUOkA@mail.gmail.com>
	<4F6A290E.8000306@uwindsor.ca>
	<CA+JTaowKA=wFW8A91wpOMZLAe+phkFdHdppO1ume+30sWN9T9g@mail.gmail.com>
Message-ID: <4F6A44CE.3010100@uwindsor.ca>

Hi Scott,
  I tried both maker2chado and gmod_bulk_load_gff.pl with fasta embedded 
or not... If the fastafile was seperate I used the command --fastafile 
and if it was embedded, it was simply --gfffile with the other 
appropriate commands for loading gene models not analysis ( i.e no 
exon).  It finally resulted that, as I mentioned, when I changed the 
header in the fasta file, the fasta loaded fine with the bulk-loader and 
using the --fastafile command..

Next, my gene models loaded fine with the bulk loader, so the db was 
populated. I turned on full-text searching by running the scripts, and 
stating -full text 1 in the conf file...
So it seems, I can do as you mentioned, query specific genes i.e cnot1, 
or with specific IDs or scaffold IDs, but what I really wanted is to be 
able to do generic gene searches using the 'maker' search, as done with 
my other databases, so that someone without knowledge of the contents of 
the database will recieve gene information. This I still can't do, but 
can be done with prior db's I set up that contained contig annotation 
vs. scaffolds, and I found was very useful returning all maker generated 
gene models.  With that, I thought the problem was with the nomenclature 
being used across annotations, scaffolds etc..

Claudia

On 21/03/2012 4:59 PM, Scott Cain wrote:
> Hi Claudia,
>
> I wanted to bring this back to the mailing lists, so I cc'ed them here.
>
> First, with the fasta loading issue: what command are you using to
> load the fasta sequences?  It works for me whether the fasta is at the
> bottom of the GFF file or if it is a separate fasta file (as long as I
> supply the --fastafile flag to the loader).
>
> About the searching problem: when I turn on full text searching (which
> means both running gmod_chado_fts_prep.pl and adding "-fulltext 1" to
> the db_args in the gbrowse config file), I can search for "cnot1" and
> find both a gene and an mRNA (of course, they are really the same
> feature, but GBrowse doesn't know that).  Also, searching for "maker"
> works, but in a real database, this will not be an effective query,
> since the number of results returned are limited, and presumably there
> will be lots of features resulting from a query like that.  Please
> remind me, is that what you wanted to do?
>
> Scott
>
>
>
>
> On Wed, Mar 21, 2012 at 3:16 PM, claudia<dinatal at uwindsor.ca>  wrote:
>> Hi Scott,
>>
>>   Wanted to give you a quick heads up that the bulk loader seems to be
>> loading my fasta files now after deleting the ' ##FASTA' header ( the first
>> line of the file now looks like this>scaffold0001)...
>> Never had this problem before, it seems the bulk loader wanted to see a '>'
>> symbol in front of the first line...
>>
>> -- when I say seems, I will let you know if it finishes, as it currently
>>   states " Loading sequences ( if any)" ... and I never made it this far
>> before :)
>>
>> Claudia
>>
>>
>>
>> On 21/03/2012 12:53 PM, Scott Cain wrote:
>>> Hi Claudia,
>>>
>>> I imagine one scaffold and gene models would be good--the problem is
>>> finding genes, right?
>>>
>>> Also, with loading fasta: were the corresponding features from the GFF
>>> file already loaded?  If so, that should have worked, and if it didn't
>>> it implies a bug.  If not, that's why.
>>>
>>> Scott
>>>
>>>
>>> On Wed, Mar 21, 2012 at 12:37 PM, claudia<dinatal at uwindsor.ca>    wrote:
>>>> Hi Scott,
>>>>   So would one scaffold with Maker gene models suffice? Do you want the
>>>> analysis as well?
>>>>
>>>> --along those same lines, I did try and load the original sequence
>>>> (fasta)
>>>> file first that I ran the Pipeline on and chado seems to refuse the files
>>>> saying they don't contain the appropriate feature '>' in the header which
>>>> in
>>>> fact they do i.e>    scaffold00001 ... So not sure what is wrong with the
>>>> fasta that chado doesn't want to load even if it is embedded in the GFF3,
>>>> the bulk loader or maker2chado return errors stating 'feature not
>>>> found'...
>>>>
>>>>
>>>> Claudia
>>>>
>>>>
>>>>
>>>> On 21/03/2012 12:20 PM, Scott Cain wrote:
>>>>> Hi Claudia,
>>>>>
>>>>> I was hoping to get actual files that I could do testing on, not
>>>>> pictures of files :-)
>>>>>
>>>>> Scott
>>>>>
>>>>>
>>>>> On Tue, Mar 20, 2012 at 4:15 PM, Dinatale C<dinatal at uwindsor.ca>
>>>>>   wrote:
>>>>>> Hi,
>>>>>>
>>>>>> Attached:  I have samples of the contig file ( I extracted the contig
>>>>>> features first to load prior to the gene models) the fasta of the
>>>>>> sequences
>>>>>> is in the footer of the gff3 file.
>>>>>>
>>>>>> --so basically, based on experience with contig annotations, I should
>>>>>> be
>>>>>> able to type in 'maker' in to the gbrowse search bar, and recieve all
>>>>>> the
>>>>>> maker gene annotations, but I don't. I must specifiy the exact ID i.e "
>>>>>> maker-scaffold11323-augustus-gene...." or 'scaffold11323'
>>>>>>
>>>>>> --so I wonder if it has to do with the fasta files being named as
>>>>>> 'scaffolds' and perhaps causing a problem with chado recognizing that
>>>>>> they
>>>>>> are linked to the gene annotations due to scaffold not being a SOFA
>>>>>> type
>>>>>> term, if in fact the sequences must be submitted to the database first?
>>>>>>
>>>>>>
>>>>>> Thanks in advance,
>>>>>>
>>>>>> Claudia
>>>>>>
>>>>>> On Tue, 20 Mar 2012 15:50:55 -0400 Scott Cain wrote:
>>>>>>> Hi Claudia,
>>>>>>>
>>>>>>> Can you post a sample of the gff that shows what you are looking for
>>>>>>> and
>>>>>>> not finding?
>>>>>>>
>>>>>>> Scott
>>>>>>>
>>>>>>>
>>>>>>> Sent from my iPad
>>>>>>>
>>>>>>> On Mar 20, 2012, at 2:03 PM, claudia wrote:
>>>>>>>
>>>>>>>> Hi,
>>>>>>>>
>>>>>>>> I have enabled full text searching and I still have this problem,
>>>>>>>> another reason for
>>>>>>> concern... So I wondered if in fact I changed all the ID's in the GFF3
>>>>>>> file to supercontigs,
>>>>>>> then perhaps Chado would better link all the terms, annotations, and
>>>>>>> fasta
>>>>>>> files....
>>>>>>> Although, i realize that the seq_id ( column 1) shouldn't need to be
>>>>>>> specific since the
>>>>>>> 'type' term would take care of designating the feature type, no?
>>>>>>>> Claudia
>>>>>>>>
>>>>>>>>
>>>>>>>>
>>>>>>>> On 20/03/2012 1:25 PM, Scott Cain wrote:
>>>>>>>>> Hi Claudia,
>>>>>>>>>
>>>>>>>>> I agree with everything that Carson wrote, except about name
>>>>>>>>> searching--it's a little trickier in Chado. What you probably want
>>>>>>>>> to
>>>>>>>>> do is implement full text searching. See:
>>>>>>>>>
>>>>>>>>> http://gmod.org/wiki/Chado_Full_Text_Search
>>>>>>>>>
>>>>>>>>> for more information on setting it up and maintaining it.
>>>>>>>>>
>>>>>>>>> Scott
>>>>>>>>>
>>>>>>>>>
>>>>>>>>> On Tue, Mar 20, 2012 at 1:13 PM, Carson Holt wrote:
>>>>>>>>>>> I have 2 concerns, the first is: regarding representing scaffold
>>>>>>>>>>> features in chado and gbrowse. I noticed that the Sequence
>>>>>>>>>>> ontology
>>>>>>>>>>> uses
>>>>>>>>>>> the term supercontig and so if my assembly generated scaffolds
>>>>>>>>>>> entitled
>>>>>>>>>>> "scaffold" should I change the names to supercontigs so that chado
>>>>>>>>>>> recognizes the terms?
>>>>>>>>>> Yes. You must use valid SO terms. It is a requirement of GFF3, and
>>>>>>>>>> Chado
>>>>>>>>>> will enforce this requirement on loading a GFF3 file (note Chado
>>>>>>>>>> will
>>>>>>>>>> even
>>>>>>>>>> go as far as to check the validity of the Ontology_term= attribute
>>>>>>>>>> in
>>>>>>>>>> GFF3
>>>>>>>>>> if you use it). You can decide to use contig or supercontig as your
>>>>>>>>>> sequence feature. It doesn?t really matter unless you are placing
>>>>>>>>>>
>>>>>>>>>> both
>>>>>>>>>> into the database as separate features (i.e. You have a supercontig
>>>>>>>>>> as
>>>>>>>>>> the
>>>>>>>>>> parent feature and then you enter contigs individually as children
>>>>>>>>>> of
>>>>>>>>>> the
>>>>>>>>>> supercontig).
>>>>>>>>>>
>>>>>>>>>>
>>>>>>>>>>> Corresponding to my first question, Maker does not know that the
>>>>>>>>>>> contigs
>>>>>>>>>>> are actually scaffold/supercontigs when annotating and so Maker
>>>>>>>>>>> will
>>>>>>>>>>> still call the "type" feature or column 3 in the GFF3, a 'contig',
>>>>>>>>>>> how
>>>>>>>>>>> can Maker be implemented to change this naming convention before
>>>>>>>>>>> annotation, or after?
>>>>>>>>>> Not really important unless you plan on making contigs children of
>>>>>>>>>> the
>>>>>>>>>> supercontig. But you can always do a search and replace. -->
>>>>>>>>>> cat file.gff | perl -ane 's/\tcontig\t/\tsupercontig\t/s; print
>>>>>>>>>> $_'>
>>>>>>>>>> new_file.gff
>>>>>>>>>>
>>>>>>>>>>
>>>>>>>>>>> Consequently, I am having problems pulling up gene features in
>>>>>>>>>>> Gbrowse
>>>>>>>>>>> when doing a generic gene search, and I must provide the maker
>>>>>>>>>>> generated
>>>>>>>>>>> unique-gene_id in the gbrowse search bar or the known sequence id
>>>>>>>>>>> i.e
>>>>>>>>>>> 'scaffold001', which is not useful for someone who does not have
>>>>>>>>>>> this
>>>>>>>>>>> information.
>>>>>>>>>>> ---- I do not have this problem when my seq_id, and 'type' feature
>>>>>>>>>>> id
>>>>>>>>>>> match in the true case of 'contigs'. I can do a generic gene
>>>>>>>>>>> search
>>>>>>>>>>> in
>>>>>>>>>>> gbrowse with the term 'maker' and gbrowse will provide me all the
>>>>>>>>>>> associated maker generated gene calls.
>>>>>>>>>> See "Adjusting GBrowse Name Searches" in the GBrowse tutorial -->
>>>>>>>>>> http://gmod.org/gbrowse2/tutorial/tutorial.html#naming
>>>>>>>>>>
>>>>>>>>>>
>>>>>>>>>> Thanks,
>>>>>>>>>> Carson
>>>>>>>>>>
>>>>>>>>>>
>>>>>>>>>>
>>>>>>>>>>
>>>>>>>>>>
>>>>>>>>>>
>>>>>>>>>>
>>>>>>>>>>
>>>>>>>>>>
>>>>>>>>>>
>>>>>>>>>>
>>>>>>>>>>> Thank you for any guidance resolving these concerns,
>>>>>>>>>>> Claudia
>>>>>>>>>>>
>>>>>>>>>>>
>>>>>>>>>>>
>>>>>>>>>>> --
>>>>>>>>>>> Claudia DiNatale
>>>>>>>>>>> Master's Candidate
>>>>>>>>>>> The Crosby Lab
>>>>>>>>>>> University of Windsor
>>>>>>>>>>> 519-253-3000 ext: 4755
>>>>>>>>>>>
>>>>>>>>>>>
>>>>>>>>>>> _______________________________________________
>>>>>>>>>>> maker-devel mailing list
>>>>>>>>>>> maker-devel at box290.bluehost.com
>>>>>>>>>>>
>>>>>>>>>>>
>>>>>>>>>>>
>>>>>>>>>>> http://box290.bluehost.com/mailman/listinfo/maker-devel_yandell-lab.org
>>>>>>>>>>
>>>>>>>>>> _______________________________________________
>>>>>>>>>> maker-devel mailing list
>>>>>>>>>> maker-devel at box290.bluehost.com
>>>>>>>>>>
>>>>>>>>>>
>>>>>>>>>>
>>>>>>>>>> http://box290.bluehost.com/mailman/listinfo/maker-devel_yandell-lab.org
>>>>>>>>>
>>>>>>>> --
>>>>>>>> Claudia DiNatale
>>>>>>>> Master's Candidate
>>>>>>>> The Crosby Lab
>>>>>>>> University of Windsor
>>>>>>>> 519-253-3000 ext: 4755
>>>>>>>>
>>>> --
>>>> Claudia DiNatale
>>>> Master's Candidate
>>>> The Crosby Lab
>>>> University of Windsor
>>>> 519-253-3000 ext: 4755
>>>>
>>>
>>
>> --
>> Claudia DiNatale
>> Master's Candidate
>> The Crosby Lab
>> University of Windsor
>> 519-253-3000 ext: 4755
>>
>
>


-- 
Claudia DiNatale
Master's Candidate
The Crosby Lab
University of Windsor
519-253-3000 ext: 4755




From carsonhh at gmail.com  Wed Mar 21 16:05:32 2012
From: carsonhh at gmail.com (Carson Holt)
Date: Wed, 21 Mar 2012 18:05:32 -0400
Subject: [maker-devel] maker 2.22/2.23: Segmentation fault while
 processing FASTA input
In-Reply-To: <4F68C963.3040108@uni-wuerzburg.de>
Message-ID: <CB8FC294.9902%carsonhh@gmail.com>

That is likely the strangest result I could imagine?  The --debug option
really only cause MAKER to print status messages everywhere and nothing
else, so there must be something else going on between the tests.


One things I did notice from the error log though -->
0.49	Inline	/home/s187512/perl/lib/perl5/site_perl/5.12.1/Inline.pm
	UNKNOWN	Inline::denter	/home/s187512/perl/lib/perl5/site_perl/5.12.1/Inlin
e/denter.pm


These are both being loaded from perl 5.12.1 (you are using 5.14.1).  That
can cause issues since I know the first one is executed at the C level and
I wouldn't be surprised if the same is true on the second one.



I also saw this -->
Can't locate package GDBM_File for @AnyDBM_File::ISA at
/storage/tmp/software/perl-5.14.1/lib/5.14.1/x86_64-linux-thread-multi/DB_F
ile.pm line 293.
Can't locate package NDBM_File for @AnyDBM_File::ISA at
/storage/tmp/software/perl-5.14.1/lib/5.14.1/x86_64-linux-thread-multi/DB_F
ile.pm line 293.
Can't locate package SDBM_File for @AnyDBM_File::ISA at
/storage/tmp/software/perl-5.14.1/lib/5.14.1/x86_64-linux-thread-multi/DB_F
ile.pm line 293.



This appears could be related to Bio::DB::Fasta (which would make sense
with the timing of the seg fault).  This is line 405 in the BEGIN
statement for Bio::DB::Fasta
-->  @AnyDBM_File::ISA = qw(DB_File GDBM_File NDBM_File SDBM_File)

I'm not sure what to do about those?  Are you able to install GDBM_File,
NDBM_File, or SDBM_File by themselves?  They really should just be
optional?  I know I don't have NDBM_File, and I don't get an error.
DB_File is part of the perl distribution, but can be updated via CPAN.
Perhaps that would be good to do.  It may just be that DB_file is broken
and falling back to the other modules doesn?t work because you don't have
them.  There is also the chance that the issue is really with Berkley_DB.
DB_File accesses Berkley_DB and it wants version 1.x, but will work with
2.x and 3.x.  You may need to even go as far as building a new Berkley_DB.

Well that's enough to try for now.

Thanks,
Carson


On 12-03-20 2:16 PM, "Thomas Hackl" <thomas.hackl at uni-wuerzburg.de> wrote:

>Hi,
>
>I installed and ran the debug version of maker. Without -debug it
>results in the expected segmentation fault. With -debug it paradoxically
>finishes without the error.
>
>I screened the debug log anyway but could not find anything that helped
>me to localize the problem. I attached a condensed version (sort | uniq)
>of the log.
>Any ideas are appreciated.
>
>Regards
>Thomas
>
>
>
>Am 19.03.2012 17:24, schrieb Carson Holt:
>> Ok.  I finished the special debug version over the weekend.  Run with
>> -debug set as a command line flag.  Capture and return the STDERR on
>> failure.  It will list all modules used, the versions, and when they are
>> called so we can see what happens right before failure.
>>
>> http://yandell-lab.org/research/maker_debug.tgz
>>
>>
>> Thanks,
>> Carson
>>
>>
>>
>> On 12-03-14 1:57 AM, "Felix Bemm"<felix.bemm at uni-wuerzburg.de>  wrote:
>>
>>> Hi,
>>>
>>> Thomas and I are colleagues and dealing with the same problem here. I
>>> wrote some test code that forced the indexing and it work fine. We are
>>> using most of the bioperl seqio and db modules in combination with
>>>other
>>> tools and don't experience the same problem there at the moment.
>>>
>>> Regards
>>> Felix
>>>
>>> Am 13.03.2012 22:37, schrieb Barry Moore:
>>>> You might also try a short perl script outside of MAKER to exercise
>>>> Bio::DB::Fasta (which I believe is the module MAKER uses for Fasta
>>>> indexing - correct Carson?).
>>>>
>>>> Something like this should work to force indexing:
>>>>
>>>> useBio::DB::Fasta;
>>>> my $db = Bio::DB::Fasta->new('/path/to/fasta/files');
>>>> my$seq=$db->seq($seqid, $start, $end);
>>>>
>>>> Point it at your fasta directory or file.
>>>>
>>>> B
>>>>
>>>> On Mar 13, 2012, at 3:41 AM, Thomas Hackl wrote:
>>>>
>>>>> Hello,
>>>>>
>>>>> We reinstalled the packages you suggested
>>>>>
>>>>> forks is up to date (0.34).
>>>>> forks::shared is up to date (0.34).
>>>>> Inline::C is up to date (0.50).
>>>>> Storable is up to date (2.30).
>>>>>
>>>>> as well as BioPerl.
>>>>>
>>>>> The problem is still the same.
>>>>>
>>>>> With MPI it terminates with this message:
>>>>>
>>>>> STATUS: Parsing control files...
>>>>> STATUS: Processing and indexing input FASTA files...
>>>>>
>>>>> 
>>>>>======================================================================
>>>>>==
>>>>> =============
>>>>>
>>>>>
>>>>> = BAD TERMINATION OF ONE OF YOUR APPLICATION PROCESSES
>>>>> = EXIT CODE: 11
>>>>> = CLEANING UP REMAINING PROCESSES
>>>>> = YOU CAN IGNORE THE BELOW CLEANUP MESSAGES
>>>>>
>>>>> 
>>>>>======================================================================
>>>>>==
>>>>> =============
>>>>>
>>>>> APPLICATION TERMINATED WITH THE EXIT STRING: Segmentation fault
>>>>> (signal 11)
>>>>>
>>>>> which I presume is also the same problem.
>>>>>
>>>>> I am with you that the error is caused somewhere on the C level. If
>>>>> the indexing step
>>>>> is handled by non-maker modules exclusively, than the fact that the
>>>>> 2.15 version works,
>>>>> suggests that you are using different modules/methods in the current
>>>>> releases?
>>>>>
>>>>> In any case, I think a version with verbose status messages might
>>>>>help
>>>>> to localize the
>>>>> source of the problem.
>>>>>
>>>>> Regards
>>>>> Thomas
>>>>>
>>>>> Am 07.03.2012 23:45, schrieb Carson Holt:
>>>>>> There should be no new hardware requirement. But there is always a
>>>>>> chance
>>>>>> that there is an issue with one of the perl modules being used. I
>>>>>> assume
>>>>>> the failure is happening when using maker serially and you are not
>>>>>> using
>>>>>> MPI.
>>>>>>
>>>>>> Could you reinstall the following perl modules, and try again. If
>>>>>>you
>>>>>> are
>>>>>> using CPAN, do a 'force install' to force it to reinstall.
>>>>>>
>>>>>> Modules:
>>>>>> *Storable
>>>>>> *Inline::C
>>>>>> *forks
>>>>>> *forks::shared
>>>>>>
>>>>>> Also try reinstalling the latest version of BioPerl.
>>>>>>
>>>>>> The fact that this is a seg fault suggests that something is
>>>>>> happemning at
>>>>>> the C level (just outside of Perl). Those area all the modules MAKER
>>>>>> uses
>>>>>> that will call back to the C level. BioPerl has a fasta indexing
>>>>>> module
>>>>>> that is also making calls outside of Perl, and the fact it fails at
>>>>>> that
>>>>>> point makes it a suspect.
>>>>>>
>>>>>> Let me know what happens. I can always generate an alternate MAKER
>>>>>> executable for you to run with additional status messages that may
>>>>>> help
>>>>>> identify exactly which module is being called right before the
>>>>>> failure.
>>>>>>
>>>>>> Thanks,
>>>>>> Carson
>>>>>>
>>>>>>
>>>>>>
>>>>>> On 12-03-07 3:31 AM, "Thomas Hackl"<thomas.hackl at uni-wuerzburg.de
>>>>>> <mailto:thomas.hackl at uni-wuerzburg.de>>  wrote:
>>>>>>
>>>>>>> Hello,
>>>>>>>
>>>>>>> we want to use a current release of maker (2.22, 2.23) but the
>>>>>>> program
>>>>>>> terminates with a seg fault while processing the input FASTA files.
>>>>>>> maker 2.15 , which we have been using for quite some time, runs
>>>>>>> perfectly with identical data and setup.
>>>>>>>
>>>>>>> Please contact me if you need specifics on hardware, OS or anything
>>>>>>> else.
>>>>>>>
>>>>>>> Best regards
>>>>>>> Thomas
>>>>>>>
>>>>>>> --
>>>>>>> Thomas Hackl
>>>>>>> Julius-Maximilians-Universit?t
>>>>>>> Department of Bioinformatics
>>>>>>> 97074 W?rzburg, Germany
>>>>>>> Fon: +49 931 - 31 86883
>>>>>>> Mail: thomas.hackl at uni-wuerzburg.de
>>>>>>> <mailto:thomas.hackl at uni-wuerzburg.de>
>>>>>>>
>>>>>>>
>>>>>>> _______________________________________________
>>>>>>> maker-devel mailing list
>>>>>>> maker-devel at box290.bluehost.com
>>>>>>> <mailto:maker-devel at box290.bluehost.com>
>>>>>>>
>>>>>>> 
>>>>>>>http://box290.bluehost.com/mailman/listinfo/maker-devel_yandell-lab.
>>>>>>>or
>>>>>>> g
>>>>>
>>>>> --
>>>>> Thomas Hackl
>>>>> Julius-Maximilians-Universit?t
>>>>> Department of Bioinformatics
>>>>> 97074 W?rzburg, Germany
>>>>> Fon: +49 931 - 31 86883
>>>>> Mail: thomas.hackl at uni-wuerzburg.de
>>>>> <mailto:thomas.hackl at uni-wuerzburg.de>
>>>>>
>>>>>
>>>>> _______________________________________________
>>>>> maker-devel mailing list
>>>>> maker-devel at box290.bluehost.com
>>>>> <mailto:maker-devel at box290.bluehost.com>
>>>>> 
>>>>>http://box290.bluehost.com/mailman/listinfo/maker-devel_yandell-lab.or
>>>>>g
>>>> Barry Moore
>>>> Research Scientist
>>>> Dept. of Human Genetics
>>>> University of Utah
>>>> Salt Lake City, UT 84112
>>>> --------------------------------------------
>>>> (801) 585-3543
>>>>
>>>>
>>>>
>>>>
>>>>
>>>>
>>>> _______________________________________________
>>>> maker-devel mailing list
>>>> maker-devel at box290.bluehost.com
>>>> 
>>>>http://box290.bluehost.com/mailman/listinfo/maker-devel_yandell-lab.org
>>> _______________________________________________
>>> maker-devel mailing list
>>> maker-devel at box290.bluehost.com
>>> http://box290.bluehost.com/mailman/listinfo/maker-devel_yandell-lab.org
>
>-- 
>Thomas Hackl
>Julius-Maximilians-Universit?t
>Department of Bioinformatics
>97074 W?rzburg, Germany
>Fon:  +49 931 - 31 86883
>Mail: thomas.hackl at uni-wuerzburg.de
>
>_______________________________________________
>maker-devel mailing list
>maker-devel at box290.bluehost.com
>http://box290.bluehost.com/mailman/listinfo/maker-devel_yandell-lab.org





From seoanezonjic at hotmail.com  Thu Mar 22 03:38:39 2012
From: seoanezonjic at hotmail.com (Seoane Zonjic)
Date: Thu, 22 Mar 2012 02:38:39 -0700 (PDT)
Subject: [maker-devel] Error: Can't call method "num_hsps" on unblessed
	reference
Message-ID: <16b63903-4205-4064-ab30-efe67b37f7fa@b18g2000vbz.googlegroups.com>

Hi!
First, sorry for my poor english. I updated Maker at last release and
I have triying it with a set of contigs. With one of contigs, Maker
give me this error:

Processing transcripts into genes
Calculating annotation quality statistics
Can't call method "num_hsps" on unblessed referenceERROR: Failed while
adding statistics to annotations
ERROR: Chunk failed at level:3, tier_type:3
FAILED CONTIG:contig_4_0

ERROR: Chunk failed at level:7, tier_type:0
FAILED CONTIG:contig_4_0

At first, I thought that problem were the length of contig (125Kb). I
cut the the sequence in parts of 10Kb but a part again give me the
same error. I have worked with the debugger version of maker (I took
it of post of segmentation fault).
The input fasta (the part that failed me) and all logs are in this
link:
http://dl.dropbox.com/u/54903225/log.tar.gz
Other contigs of same set,  bigger or equal, work fine without
problem. There are something in this sequence that broken the Maker
run.
Thanks in advance



From carsonhh at gmail.com  Thu Mar 22 08:36:37 2012
From: carsonhh at gmail.com (Carson Holt)
Date: Thu, 22 Mar 2012 10:36:37 -0400
Subject: [maker-devel] Error: Can't call method "num_hsps" on unblessed
 reference
In-Reply-To: <16b63903-4205-4064-ab30-efe67b37f7fa@b18g2000vbz.googlegroups.com>
Message-ID: <CB90B0FA.9946%carsonhh@gmail.com>

Could you make a tarball of this directory and send it to me exactly as is
 --> 
/export/home_users/home/cvi_114_uma/pedro/testmaker/Spliced2.maker.output/S
pliced2_datastore/72/86/contig_4_0/

Thanks,
Carson


On 12-03-22 5:38 AM, "Seoane Zonjic" <seoanezonjic at hotmail.com> wrote:

>Hi!
>First, sorry for my poor english. I updated Maker at last release and
>I have triying it with a set of contigs. With one of contigs, Maker
>give me this error:
>
>Processing transcripts into genes
>Calculating annotation quality statistics
>Can't call method "num_hsps" on unblessed referenceERROR: Failed while
>adding statistics to annotations
>ERROR: Chunk failed at level:3, tier_type:3
>FAILED CONTIG:contig_4_0
>
>ERROR: Chunk failed at level:7, tier_type:0
>FAILED CONTIG:contig_4_0
>
>At first, I thought that problem were the length of contig (125Kb). I
>cut the the sequence in parts of 10Kb but a part again give me the
>same error. I have worked with the debugger version of maker (I took
>it of post of segmentation fault).
>The input fasta (the part that failed me) and all logs are in this
>link:
>http://dl.dropbox.com/u/54903225/log.tar.gz
>Other contigs of same set,  bigger or equal, work fine without
>problem. There are something in this sequence that broken the Maker
>run.
>Thanks in advance
>
>_______________________________________________
>maker-devel mailing list
>maker-devel at box290.bluehost.com
>http://box290.bluehost.com/mailman/listinfo/maker-devel_yandell-lab.org





From thomas.hackl at uni-wuerzburg.de  Mon Mar 26 04:51:48 2012
From: thomas.hackl at uni-wuerzburg.de (Thomas Hackl)
Date: Mon, 26 Mar 2012 12:51:48 +0200
Subject: [maker-devel] maker 2.22/2.23: Segmentation fault while
 processing FASTA input
In-Reply-To: <CB8FC294.9902%carsonhh@gmail.com>
References: <CB8FC294.9902%carsonhh@gmail.com>
Message-ID: <4F704A44.2080707@uni-wuerzburg.de>

Hi,

I was finally able to "fix" the Problem. I tried everything you 
suggested, nice catch on my screwed up Perl lib path btw, but I could 
neither install GDBM_File or NDBM_File nor Berkley_DB separately. In the 
end I simply removed the  ISA relations to the modules in question from 
the source code and now it seems to works fine...

sed -i 's/qw(DB_File GDBM_File NDBM_File SDBM_File)/qw(DB_File)/'

So thanks a lot for your prompt and comprehensive response, the debug 
executables and the help with the messages.

Regards
Thomas



Am 21.03.2012 23:05, schrieb Carson Holt:
> That is likely the strangest result I could imagine?  The --debug option
> really only cause MAKER to print status messages everywhere and nothing
> else, so there must be something else going on between the tests.
>
>
> One things I did notice from the error log though -->
> 0.49	Inline	/home/s187512/perl/lib/perl5/site_perl/5.12.1/Inline.pm
> 	UNKNOWN	Inline::denter	/home/s187512/perl/lib/perl5/site_perl/5.12.1/Inlin
> e/denter.pm
>
>
> These are both being loaded from perl 5.12.1 (you are using 5.14.1).  That
> can cause issues since I know the first one is executed at the C level and
> I wouldn't be surprised if the same is true on the second one.
>
>
>
> I also saw this -->
> Can't locate package GDBM_File for @AnyDBM_File::ISA at
> /storage/tmp/software/perl-5.14.1/lib/5.14.1/x86_64-linux-thread-multi/DB_F
> ile.pm line 293.
> Can't locate package NDBM_File for @AnyDBM_File::ISA at
> /storage/tmp/software/perl-5.14.1/lib/5.14.1/x86_64-linux-thread-multi/DB_F
> ile.pm line 293.
> Can't locate package SDBM_File for @AnyDBM_File::ISA at
> /storage/tmp/software/perl-5.14.1/lib/5.14.1/x86_64-linux-thread-multi/DB_F
> ile.pm line 293.
>
>
>
> This appears could be related to Bio::DB::Fasta (which would make sense
> with the timing of the seg fault).  This is line 405 in the BEGIN
> statement for Bio::DB::Fasta
> -->   @AnyDBM_File::ISA = qw(DB_File GDBM_File NDBM_File SDBM_File)
>
> I'm not sure what to do about those?  Are you able to install GDBM_File,
> NDBM_File, or SDBM_File by themselves?  They really should just be
> optional?  I know I don't have NDBM_File, and I don't get an error.
> DB_File is part of the perl distribution, but can be updated via CPAN.
> Perhaps that would be good to do.  It may just be that DB_file is broken
> and falling back to the other modules doesn?t work because you don't have
> them.  There is also the chance that the issue is really with Berkley_DB.
> DB_File accesses Berkley_DB and it wants version 1.x, but will work with
> 2.x and 3.x.  You may need to even go as far as building a new Berkley_DB.
>
> Well that's enough to try for now.
>
> Thanks,
> Carson
>
>
> On 12-03-20 2:16 PM, "Thomas Hackl"<thomas.hackl at uni-wuerzburg.de>  wrote:
>
>> Hi,
>>
>> I installed and ran the debug version of maker. Without -debug it
>> results in the expected segmentation fault. With -debug it paradoxically
>> finishes without the error.
>>
>> I screened the debug log anyway but could not find anything that helped
>> me to localize the problem. I attached a condensed version (sort | uniq)
>> of the log.
>> Any ideas are appreciated.
>>
>> Regards
>> Thomas
>>
>>
>>
>> Am 19.03.2012 17:24, schrieb Carson Holt:
>>> Ok.  I finished the special debug version over the weekend.  Run with
>>> -debug set as a command line flag.  Capture and return the STDERR on
>>> failure.  It will list all modules used, the versions, and when they are
>>> called so we can see what happens right before failure.
>>>
>>> http://yandell-lab.org/research/maker_debug.tgz
>>>
>>>
>>> Thanks,
>>> Carson
>>>
>>>
>>>
>>> On 12-03-14 1:57 AM, "Felix Bemm"<felix.bemm at uni-wuerzburg.de>   wrote:
>>>
>>>> Hi,
>>>>
>>>> Thomas and I are colleagues and dealing with the same problem here. I
>>>> wrote some test code that forced the indexing and it work fine. We are
>>>> using most of the bioperl seqio and db modules in combination with
>>>> other
>>>> tools and don't experience the same problem there at the moment.
>>>>
>>>> Regards
>>>> Felix
>>>>
>>>> Am 13.03.2012 22:37, schrieb Barry Moore:
>>>>> You might also try a short perl script outside of MAKER to exercise
>>>>> Bio::DB::Fasta (which I believe is the module MAKER uses for Fasta
>>>>> indexing - correct Carson?).
>>>>>
>>>>> Something like this should work to force indexing:
>>>>>
>>>>> useBio::DB::Fasta;
>>>>> my $db = Bio::DB::Fasta->new('/path/to/fasta/files');
>>>>> my$seq=$db->seq($seqid, $start, $end);
>>>>>
>>>>> Point it at your fasta directory or file.
>>>>>
>>>>> B
>>>>>
>>>>> On Mar 13, 2012, at 3:41 AM, Thomas Hackl wrote:
>>>>>
>>>>>> Hello,
>>>>>>
>>>>>> We reinstalled the packages you suggested
>>>>>>
>>>>>> forks is up to date (0.34).
>>>>>> forks::shared is up to date (0.34).
>>>>>> Inline::C is up to date (0.50).
>>>>>> Storable is up to date (2.30).
>>>>>>
>>>>>> as well as BioPerl.
>>>>>>
>>>>>> The problem is still the same.
>>>>>>
>>>>>> With MPI it terminates with this message:
>>>>>>
>>>>>> STATUS: Parsing control files...
>>>>>> STATUS: Processing and indexing input FASTA files...
>>>>>>
>>>>>>
>>>>>> ======================================================================
>>>>>> ==
>>>>>> =============
>>>>>>
>>>>>>
>>>>>> = BAD TERMINATION OF ONE OF YOUR APPLICATION PROCESSES
>>>>>> = EXIT CODE: 11
>>>>>> = CLEANING UP REMAINING PROCESSES
>>>>>> = YOU CAN IGNORE THE BELOW CLEANUP MESSAGES
>>>>>>
>>>>>>
>>>>>> ======================================================================
>>>>>> ==
>>>>>> =============
>>>>>>
>>>>>> APPLICATION TERMINATED WITH THE EXIT STRING: Segmentation fault
>>>>>> (signal 11)
>>>>>>
>>>>>> which I presume is also the same problem.
>>>>>>
>>>>>> I am with you that the error is caused somewhere on the C level. If
>>>>>> the indexing step
>>>>>> is handled by non-maker modules exclusively, than the fact that the
>>>>>> 2.15 version works,
>>>>>> suggests that you are using different modules/methods in the current
>>>>>> releases?
>>>>>>
>>>>>> In any case, I think a version with verbose status messages might
>>>>>> help
>>>>>> to localize the
>>>>>> source of the problem.
>>>>>>
>>>>>> Regards
>>>>>> Thomas
>>>>>>
>>>>>> Am 07.03.2012 23:45, schrieb Carson Holt:
>>>>>>> There should be no new hardware requirement. But there is always a
>>>>>>> chance
>>>>>>> that there is an issue with one of the perl modules being used. I
>>>>>>> assume
>>>>>>> the failure is happening when using maker serially and you are not
>>>>>>> using
>>>>>>> MPI.
>>>>>>>
>>>>>>> Could you reinstall the following perl modules, and try again. If
>>>>>>> you
>>>>>>> are
>>>>>>> using CPAN, do a 'force install' to force it to reinstall.
>>>>>>>
>>>>>>> Modules:
>>>>>>> *Storable
>>>>>>> *Inline::C
>>>>>>> *forks
>>>>>>> *forks::shared
>>>>>>>
>>>>>>> Also try reinstalling the latest version of BioPerl.
>>>>>>>
>>>>>>> The fact that this is a seg fault suggests that something is
>>>>>>> happemning at
>>>>>>> the C level (just outside of Perl). Those area all the modules MAKER
>>>>>>> uses
>>>>>>> that will call back to the C level. BioPerl has a fasta indexing
>>>>>>> module
>>>>>>> that is also making calls outside of Perl, and the fact it fails at
>>>>>>> that
>>>>>>> point makes it a suspect.
>>>>>>>
>>>>>>> Let me know what happens. I can always generate an alternate MAKER
>>>>>>> executable for you to run with additional status messages that may
>>>>>>> help
>>>>>>> identify exactly which module is being called right before the
>>>>>>> failure.
>>>>>>>
>>>>>>> Thanks,
>>>>>>> Carson
>>>>>>>
>>>>>>>
>>>>>>>
>>>>>>> On 12-03-07 3:31 AM, "Thomas Hackl"<thomas.hackl at uni-wuerzburg.de
>>>>>>> <mailto:thomas.hackl at uni-wuerzburg.de>>   wrote:
>>>>>>>
>>>>>>>> Hello,
>>>>>>>>
>>>>>>>> we want to use a current release of maker (2.22, 2.23) but the
>>>>>>>> program
>>>>>>>> terminates with a seg fault while processing the input FASTA files.
>>>>>>>> maker 2.15 , which we have been using for quite some time, runs
>>>>>>>> perfectly with identical data and setup.
>>>>>>>>
>>>>>>>> Please contact me if you need specifics on hardware, OS or anything
>>>>>>>> else.
>>>>>>>>
>>>>>>>> Best regards
>>>>>>>> Thomas
>>>>>>>>
>>>>>>>> --
>>>>>>>> Thomas Hackl
>>>>>>>> Julius-Maximilians-Universit?t
>>>>>>>> Department of Bioinformatics
>>>>>>>> 97074 W?rzburg, Germany
>>>>>>>> Fon: +49 931 - 31 86883
>>>>>>>> Mail: thomas.hackl at uni-wuerzburg.de
>>>>>>>> <mailto:thomas.hackl at uni-wuerzburg.de>
>>>>>>>>
>>>>>>>>
>>>>>>>> _______________________________________________
>>>>>>>> maker-devel mailing list
>>>>>>>> maker-devel at box290.bluehost.com
>>>>>>>> <mailto:maker-devel at box290.bluehost.com>
>>>>>>>>
>>>>>>>>
>>>>>>>> http://box290.bluehost.com/mailman/listinfo/maker-devel_yandell-lab.
>>>>>>>> or
>>>>>>>> g
>>>>>> --
>>>>>> Thomas Hackl
>>>>>> Julius-Maximilians-Universit?t
>>>>>> Department of Bioinformatics
>>>>>> 97074 W?rzburg, Germany
>>>>>> Fon: +49 931 - 31 86883
>>>>>> Mail: thomas.hackl at uni-wuerzburg.de
>>>>>> <mailto:thomas.hackl at uni-wuerzburg.de>
>>>>>>
>>>>>>
>>>>>> _______________________________________________
>>>>>> maker-devel mailing list
>>>>>> maker-devel at box290.bluehost.com
>>>>>> <mailto:maker-devel at box290.bluehost.com>
>>>>>>
>>>>>> http://box290.bluehost.com/mailman/listinfo/maker-devel_yandell-lab.or
>>>>>> g
>>>>> Barry Moore
>>>>> Research Scientist
>>>>> Dept. of Human Genetics
>>>>> University of Utah
>>>>> Salt Lake City, UT 84112
>>>>> --------------------------------------------
>>>>> (801) 585-3543
>>>>>
>>>>>
>>>>>
>>>>>
>>>>>
>>>>>
>>>>> _______________________________________________
>>>>> maker-devel mailing list
>>>>> maker-devel at box290.bluehost.com
>>>>>
>>>>> http://box290.bluehost.com/mailman/listinfo/maker-devel_yandell-lab.org
>>>> _______________________________________________
>>>> maker-devel mailing list
>>>> maker-devel at box290.bluehost.com
>>>> http://box290.bluehost.com/mailman/listinfo/maker-devel_yandell-lab.org
>> --
>> Thomas Hackl
>> Julius-Maximilians-Universit?t
>> Department of Bioinformatics
>> 97074 W?rzburg, Germany
>> Fon:  +49 931 - 31 86883
>> Mail: thomas.hackl at uni-wuerzburg.de
>>
>> _______________________________________________
>> maker-devel mailing list
>> maker-devel at box290.bluehost.com
>> http://box290.bluehost.com/mailman/listinfo/maker-devel_yandell-lab.org


-- 
Thomas Hackl
Julius-Maximilians-Universit?t
Department of Bioinformatics
97074 W?rzburg, Germany
Fon:  +49 931 - 31 86883
Mail: thomas.hackl at uni-wuerzburg.de




From carsonhh at gmail.com  Mon Mar 26 07:01:52 2012
From: carsonhh at gmail.com (Carson Holt)
Date: Mon, 26 Mar 2012 09:01:52 -0400
Subject: [maker-devel] maker 2.22/2.23: Segmentation fault while
 processing FASTA input
In-Reply-To: <4F704A44.2080707@uni-wuerzburg.de>
Message-ID: <CB95E04E.9E8B%carsonhh@gmail.com>

Well, if that works, I'd call it a success.  Just be careful with any
future updates to BioPerl.  Since the root cause of the problem may still
be there.

Thanks,
Carson




On 12-03-26 6:51 AM, "Thomas Hackl" <thomas.hackl at uni-wuerzburg.de> wrote:

>Hi,
>
>I was finally able to "fix" the Problem. I tried everything you
>suggested, nice catch on my screwed up Perl lib path btw, but I could
>neither install GDBM_File or NDBM_File nor Berkley_DB separately. In the
>end I simply removed the  ISA relations to the modules in question from
>the source code and now it seems to works fine...
>
>sed -i 's/qw(DB_File GDBM_File NDBM_File SDBM_File)/qw(DB_File)/'
>
>So thanks a lot for your prompt and comprehensive response, the debug
>executables and the help with the messages.
>
>Regards
>Thomas
>
>
>
>Am 21.03.2012 23:05, schrieb Carson Holt:
>> That is likely the strangest result I could imagine?  The --debug option
>> really only cause MAKER to print status messages everywhere and nothing
>> else, so there must be something else going on between the tests.
>>
>>
>> One things I did notice from the error log though -->
>> 0.49	Inline	/home/s187512/perl/lib/perl5/site_perl/5.12.1/Inline.pm
>> 
>>	UNKNOWN	Inline::denter	/home/s187512/perl/lib/perl5/site_perl/5.12.1/Inl
>>in
>> e/denter.pm
>>
>>
>> These are both being loaded from perl 5.12.1 (you are using 5.14.1).
>>That
>> can cause issues since I know the first one is executed at the C level
>>and
>> I wouldn't be surprised if the same is true on the second one.
>>
>>
>>
>> I also saw this -->
>> Can't locate package GDBM_File for @AnyDBM_File::ISA at
>> 
>>/storage/tmp/software/perl-5.14.1/lib/5.14.1/x86_64-linux-thread-multi/DB
>>_F
>> ile.pm line 293.
>> Can't locate package NDBM_File for @AnyDBM_File::ISA at
>> 
>>/storage/tmp/software/perl-5.14.1/lib/5.14.1/x86_64-linux-thread-multi/DB
>>_F
>> ile.pm line 293.
>> Can't locate package SDBM_File for @AnyDBM_File::ISA at
>> 
>>/storage/tmp/software/perl-5.14.1/lib/5.14.1/x86_64-linux-thread-multi/DB
>>_F
>> ile.pm line 293.
>>
>>
>>
>> This appears could be related to Bio::DB::Fasta (which would make sense
>> with the timing of the seg fault).  This is line 405 in the BEGIN
>> statement for Bio::DB::Fasta
>> -->   @AnyDBM_File::ISA = qw(DB_File GDBM_File NDBM_File SDBM_File)
>>
>> I'm not sure what to do about those?  Are you able to install GDBM_File,
>> NDBM_File, or SDBM_File by themselves?  They really should just be
>> optional?  I know I don't have NDBM_File, and I don't get an error.
>> DB_File is part of the perl distribution, but can be updated via CPAN.
>> Perhaps that would be good to do.  It may just be that DB_file is broken
>> and falling back to the other modules doesn?t work because you don't
>>have
>> them.  There is also the chance that the issue is really with
>>Berkley_DB.
>> DB_File accesses Berkley_DB and it wants version 1.x, but will work with
>> 2.x and 3.x.  You may need to even go as far as building a new
>>Berkley_DB.
>>
>> Well that's enough to try for now.
>>
>> Thanks,
>> Carson
>>
>>
>> On 12-03-20 2:16 PM, "Thomas Hackl"<thomas.hackl at uni-wuerzburg.de>
>>wrote:
>>
>>> Hi,
>>>
>>> I installed and ran the debug version of maker. Without -debug it
>>> results in the expected segmentation fault. With -debug it
>>>paradoxically
>>> finishes without the error.
>>>
>>> I screened the debug log anyway but could not find anything that helped
>>> me to localize the problem. I attached a condensed version (sort |
>>>uniq)
>>> of the log.
>>> Any ideas are appreciated.
>>>
>>> Regards
>>> Thomas
>>>
>>>
>>>
>>> Am 19.03.2012 17:24, schrieb Carson Holt:
>>>> Ok.  I finished the special debug version over the weekend.  Run with
>>>> -debug set as a command line flag.  Capture and return the STDERR on
>>>> failure.  It will list all modules used, the versions, and when they
>>>>are
>>>> called so we can see what happens right before failure.
>>>>
>>>> http://yandell-lab.org/research/maker_debug.tgz
>>>>
>>>>
>>>> Thanks,
>>>> Carson
>>>>
>>>>
>>>>
>>>> On 12-03-14 1:57 AM, "Felix Bemm"<felix.bemm at uni-wuerzburg.de>
>>>>wrote:
>>>>
>>>>> Hi,
>>>>>
>>>>> Thomas and I are colleagues and dealing with the same problem here. I
>>>>> wrote some test code that forced the indexing and it work fine. We
>>>>>are
>>>>> using most of the bioperl seqio and db modules in combination with
>>>>> other
>>>>> tools and don't experience the same problem there at the moment.
>>>>>
>>>>> Regards
>>>>> Felix
>>>>>
>>>>> Am 13.03.2012 22:37, schrieb Barry Moore:
>>>>>> You might also try a short perl script outside of MAKER to exercise
>>>>>> Bio::DB::Fasta (which I believe is the module MAKER uses for Fasta
>>>>>> indexing - correct Carson?).
>>>>>>
>>>>>> Something like this should work to force indexing:
>>>>>>
>>>>>> useBio::DB::Fasta;
>>>>>> my $db = Bio::DB::Fasta->new('/path/to/fasta/files');
>>>>>> my$seq=$db->seq($seqid, $start, $end);
>>>>>>
>>>>>> Point it at your fasta directory or file.
>>>>>>
>>>>>> B
>>>>>>
>>>>>> On Mar 13, 2012, at 3:41 AM, Thomas Hackl wrote:
>>>>>>
>>>>>>> Hello,
>>>>>>>
>>>>>>> We reinstalled the packages you suggested
>>>>>>>
>>>>>>> forks is up to date (0.34).
>>>>>>> forks::shared is up to date (0.34).
>>>>>>> Inline::C is up to date (0.50).
>>>>>>> Storable is up to date (2.30).
>>>>>>>
>>>>>>> as well as BioPerl.
>>>>>>>
>>>>>>> The problem is still the same.
>>>>>>>
>>>>>>> With MPI it terminates with this message:
>>>>>>>
>>>>>>> STATUS: Parsing control files...
>>>>>>> STATUS: Processing and indexing input FASTA files...
>>>>>>>
>>>>>>>
>>>>>>> 
>>>>>>>====================================================================
>>>>>>>==
>>>>>>> ==
>>>>>>> =============
>>>>>>>
>>>>>>>
>>>>>>> = BAD TERMINATION OF ONE OF YOUR APPLICATION PROCESSES
>>>>>>> = EXIT CODE: 11
>>>>>>> = CLEANING UP REMAINING PROCESSES
>>>>>>> = YOU CAN IGNORE THE BELOW CLEANUP MESSAGES
>>>>>>>
>>>>>>>
>>>>>>> 
>>>>>>>====================================================================
>>>>>>>==
>>>>>>> ==
>>>>>>> =============
>>>>>>>
>>>>>>> APPLICATION TERMINATED WITH THE EXIT STRING: Segmentation fault
>>>>>>> (signal 11)
>>>>>>>
>>>>>>> which I presume is also the same problem.
>>>>>>>
>>>>>>> I am with you that the error is caused somewhere on the C level. If
>>>>>>> the indexing step
>>>>>>> is handled by non-maker modules exclusively, than the fact that the
>>>>>>> 2.15 version works,
>>>>>>> suggests that you are using different modules/methods in the
>>>>>>>current
>>>>>>> releases?
>>>>>>>
>>>>>>> In any case, I think a version with verbose status messages might
>>>>>>> help
>>>>>>> to localize the
>>>>>>> source of the problem.
>>>>>>>
>>>>>>> Regards
>>>>>>> Thomas
>>>>>>>
>>>>>>> Am 07.03.2012 23:45, schrieb Carson Holt:
>>>>>>>> There should be no new hardware requirement. But there is always a
>>>>>>>> chance
>>>>>>>> that there is an issue with one of the perl modules being used. I
>>>>>>>> assume
>>>>>>>> the failure is happening when using maker serially and you are not
>>>>>>>> using
>>>>>>>> MPI.
>>>>>>>>
>>>>>>>> Could you reinstall the following perl modules, and try again. If
>>>>>>>> you
>>>>>>>> are
>>>>>>>> using CPAN, do a 'force install' to force it to reinstall.
>>>>>>>>
>>>>>>>> Modules:
>>>>>>>> *Storable
>>>>>>>> *Inline::C
>>>>>>>> *forks
>>>>>>>> *forks::shared
>>>>>>>>
>>>>>>>> Also try reinstalling the latest version of BioPerl.
>>>>>>>>
>>>>>>>> The fact that this is a seg fault suggests that something is
>>>>>>>> happemning at
>>>>>>>> the C level (just outside of Perl). Those area all the modules
>>>>>>>>MAKER
>>>>>>>> uses
>>>>>>>> that will call back to the C level. BioPerl has a fasta indexing
>>>>>>>> module
>>>>>>>> that is also making calls outside of Perl, and the fact it fails
>>>>>>>>at
>>>>>>>> that
>>>>>>>> point makes it a suspect.
>>>>>>>>
>>>>>>>> Let me know what happens. I can always generate an alternate MAKER
>>>>>>>> executable for you to run with additional status messages that may
>>>>>>>> help
>>>>>>>> identify exactly which module is being called right before the
>>>>>>>> failure.
>>>>>>>>
>>>>>>>> Thanks,
>>>>>>>> Carson
>>>>>>>>
>>>>>>>>
>>>>>>>>
>>>>>>>> On 12-03-07 3:31 AM, "Thomas Hackl"<thomas.hackl at uni-wuerzburg.de
>>>>>>>> <mailto:thomas.hackl at uni-wuerzburg.de>>   wrote:
>>>>>>>>
>>>>>>>>> Hello,
>>>>>>>>>
>>>>>>>>> we want to use a current release of maker (2.22, 2.23) but the
>>>>>>>>> program
>>>>>>>>> terminates with a seg fault while processing the input FASTA
>>>>>>>>>files.
>>>>>>>>> maker 2.15 , which we have been using for quite some time, runs
>>>>>>>>> perfectly with identical data and setup.
>>>>>>>>>
>>>>>>>>> Please contact me if you need specifics on hardware, OS or
>>>>>>>>>anything
>>>>>>>>> else.
>>>>>>>>>
>>>>>>>>> Best regards
>>>>>>>>> Thomas
>>>>>>>>>
>>>>>>>>> --
>>>>>>>>> Thomas Hackl
>>>>>>>>> Julius-Maximilians-Universit?t
>>>>>>>>> Department of Bioinformatics
>>>>>>>>> 97074 W?rzburg, Germany
>>>>>>>>> Fon: +49 931 - 31 86883
>>>>>>>>> Mail: thomas.hackl at uni-wuerzburg.de
>>>>>>>>> <mailto:thomas.hackl at uni-wuerzburg.de>
>>>>>>>>>
>>>>>>>>>
>>>>>>>>> _______________________________________________
>>>>>>>>> maker-devel mailing list
>>>>>>>>> maker-devel at box290.bluehost.com
>>>>>>>>> <mailto:maker-devel at box290.bluehost.com>
>>>>>>>>>
>>>>>>>>>
>>>>>>>>> 
>>>>>>>>>http://box290.bluehost.com/mailman/listinfo/maker-devel_yandell-la
>>>>>>>>>b.
>>>>>>>>> or
>>>>>>>>> g
>>>>>>> --
>>>>>>> Thomas Hackl
>>>>>>> Julius-Maximilians-Universit?t
>>>>>>> Department of Bioinformatics
>>>>>>> 97074 W?rzburg, Germany
>>>>>>> Fon: +49 931 - 31 86883
>>>>>>> Mail: thomas.hackl at uni-wuerzburg.de
>>>>>>> <mailto:thomas.hackl at uni-wuerzburg.de>
>>>>>>>
>>>>>>>
>>>>>>> _______________________________________________
>>>>>>> maker-devel mailing list
>>>>>>> maker-devel at box290.bluehost.com
>>>>>>> <mailto:maker-devel at box290.bluehost.com>
>>>>>>>
>>>>>>> 
>>>>>>>http://box290.bluehost.com/mailman/listinfo/maker-devel_yandell-lab.
>>>>>>>or
>>>>>>> g
>>>>>> Barry Moore
>>>>>> Research Scientist
>>>>>> Dept. of Human Genetics
>>>>>> University of Utah
>>>>>> Salt Lake City, UT 84112
>>>>>> --------------------------------------------
>>>>>> (801) 585-3543
>>>>>>
>>>>>>
>>>>>>
>>>>>>
>>>>>>
>>>>>>
>>>>>> _______________________________________________
>>>>>> maker-devel mailing list
>>>>>> maker-devel at box290.bluehost.com
>>>>>>
>>>>>> 
>>>>>>http://box290.bluehost.com/mailman/listinfo/maker-devel_yandell-lab.o
>>>>>>rg
>>>>> _______________________________________________
>>>>> maker-devel mailing list
>>>>> maker-devel at box290.bluehost.com
>>>>> 
>>>>>http://box290.bluehost.com/mailman/listinfo/maker-devel_yandell-lab.or
>>>>>g
>>> --
>>> Thomas Hackl
>>> Julius-Maximilians-Universit?t
>>> Department of Bioinformatics
>>> 97074 W?rzburg, Germany
>>> Fon:  +49 931 - 31 86883
>>> Mail: thomas.hackl at uni-wuerzburg.de
>>>
>>> _______________________________________________
>>> maker-devel mailing list
>>> maker-devel at box290.bluehost.com
>>> http://box290.bluehost.com/mailman/listinfo/maker-devel_yandell-lab.org
>
>
>-- 
>Thomas Hackl
>Julius-Maximilians-Universit?t
>Department of Bioinformatics
>97074 W?rzburg, Germany
>Fon:  +49 931 - 31 86883
>Mail: thomas.hackl at uni-wuerzburg.de
>
>
>_______________________________________________
>maker-devel mailing list
>maker-devel at box290.bluehost.com
>http://box290.bluehost.com/mailman/listinfo/maker-devel_yandell-lab.org





From daniel.fer.u at gmail.com  Sun Mar 25 20:53:25 2012
From: daniel.fer.u at gmail.com (=?UTF-8?Q?Daniel_Fern=C3=A1ndez?=)
Date: Sun, 25 Mar 2012 19:53:25 -0700 (PDT)
Subject: [maker-devel] Problem with RMBlast installation
Message-ID: <8109224.101.1332730405163.JavaMail.geo-discussion-forums@ynlx41>

Hi,

I trying to install MAKER, I don't have WU-Blast, I have Blast+ so in the 
README file tell me that I need RMBlast, but I don't know what file I have 
to choose, rmblast-1.2-ncbi-blast-2.2.23+-src.tar.gz or rmblast-1.2-ncbi-blast-2.2.23+-x64-linux.tar.gz 
(I have Linux 64-bit) in each version the README file is the same, and 
there tell me how I can install it, but the instructions is only for rmblast-1.2-ncbi-blast-2.2.23+-src, 
well, when I try to install it, I type this 
$./configure --with-mt --prefix=/usr/local/bioinfo/repeatmasker/rmblast 
--without-debug
This show me error, and I type make and this show stop.

Can you help me please?

This show me when I type $./configure --with-mt 
--prefix=/usr/local/bioinfo/repeatmasker/rmblast --without-debug
-----------------------------------------------------------------------------------------------------------------------------------------------
configure: loading site script ./src/build-system/config.site
configure: loading cache config.cache
checking build system type... x86_64-unknown-linux-gnu
checking host system type... x86_64-unknown-linux-gnu
checking for a BSD-compatible install... /usr/bin/install -c
checking for gcc... gcc
checking for C compiler default output file name... a.out
checking whether the C compiler works... yes
checking whether we are cross compiling... no
checking for suffix of executables... 
checking for suffix of object files... o
checking whether we are using the GNU C compiler... yes
checking whether gcc accepts -g... yes
checking for gcc option to accept ANSI C... none needed
checking for g++... no
checking for c++... no
checking for gpp... no
checking for aCC... no
checking for CC... no
checking for cxx... no
checking for cc++... no
checking for cl... no
checking for FCC... no
checking for KCC... no
checking for RCC... no
checking for xlC_r... no
checking for xlC... no
checking whether we are using the GNU C++ compiler... no
checking whether g++ accepts -g... no
adjusted C   compiler: /usr/bin/gcc 
./src/build-system/configure: line 4404: type: g++: not found
dirname: missing operand
Try `dirname --help' for more information.
configure: error: Do not know how to build MT-safe with compiler g++ 
./src/build-system/configure: line 4187: g++: command not found
-----------------------------------------------------------------------------------------------------------------------------------
-------------- next part --------------
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From jason.stajich at gmail.com  Mon Mar 26 09:33:55 2012
From: jason.stajich at gmail.com (Jason Stajich)
Date: Mon, 26 Mar 2012 08:33:55 -0700
Subject: [maker-devel] Problem with RMBlast installation
In-Reply-To: <8109224.101.1332730405163.JavaMail.geo-discussion-forums@ynlx41>
References: <8109224.101.1332730405163.JavaMail.geo-discussion-forums@ynlx41>
Message-ID: <7A26C949-4ED3-4CEF-8455-2D3A85B35A2B@gmail.com>

Hi Daniel -

Just download, unpackage the precompiled ( rmblast-1.2-ncbi-blast-2.2.23+-x64-linux.tar.gz ) version and tell RepeatMasker where the exes are when you configure RepeatMasker.  RMBlast is for RepeatMasker.
 
For running BLAST in MAKAER would install NCBI-BLAST+ if you don't have wu-blast --- ftp://ftp.ncbi.nih.gov/blast/executables/blast+/LATEST - I believe current maker supports BLAST+, BLAST, and WU-BLAST so you have your pick.

Jason
On Mar 25, 2012, at 7:53 PM, Daniel Fern?ndez wrote:

> Hi,
> 
> I trying to install MAKER, I don't have WU-Blast, I have Blast+ so in the README file tell me that I need RMBlast, but I don't know what file I have to choose, rmblast-1.2-ncbi-blast-2.2.23+-src.tar.gz or rmblast-1.2-ncbi-blast-2.2.23+-x64-linux.tar.gz (I have Linux 64-bit) in each version the README file is the same, and there tell me how I can install it, but the instructions is only for rmblast-1.2-ncbi-blast-2.2.23+-src, well, when I try to install it, I type this 
> $./configure --with-mt --prefix=/usr/local/bioinfo/repeatmasker/rmblast --without-debug
> This show me error, and I type make and this show stop.
> 
> Can you help me please?
> 
> This show me when I type $./configure --with-mt --prefix=/usr/local/bioinfo/repeatmasker/rmblast --without-debug
> -----------------------------------------------------------------------------------------------------------------------------------------------
> configure: loading site script ./src/build-system/config.site
> configure: loading cache config.cache
> checking build system type... x86_64-unknown-linux-gnu
> checking host system type... x86_64-unknown-linux-gnu
> checking for a BSD-compatible install... /usr/bin/install -c
> checking for gcc... gcc
> checking for C compiler default output file name... a.out
> checking whether the C compiler works... yes
> checking whether we are cross compiling... no
> checking for suffix of executables... 
> checking for suffix of object files... o
> checking whether we are using the GNU C compiler... yes
> checking whether gcc accepts -g... yes
> checking for gcc option to accept ANSI C... none needed
> checking for g++... no
> checking for c++... no
> checking for gpp... no
> checking for aCC... no
> checking for CC... no
> checking for cxx... no
> checking for cc++... no
> checking for cl... no
> checking for FCC... no
> checking for KCC... no
> checking for RCC... no
> checking for xlC_r... no
> checking for xlC... no
> checking whether we are using the GNU C++ compiler... no
> checking whether g++ accepts -g... no
> adjusted C   compiler: /usr/bin/gcc 
> ./src/build-system/configure: line 4404: type: g++: not found
> dirname: missing operand
> Try `dirname --help' for more information.
> configure: error: Do not know how to build MT-safe with compiler g++ ./src/build-system/configure: line 4187: g++: command not found
> -----------------------------------------------------------------------------------------------------------------------------------
> _______________________________________________
> maker-devel mailing list
> maker-devel at box290.bluehost.com
> http://box290.bluehost.com/mailman/listinfo/maker-devel_yandell-lab.org

Jason Stajich
jason.stajich at gmail.com
jason at bioperl.org

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From eernst at cshl.edu  Mon Mar 26 10:29:45 2012
From: eernst at cshl.edu (Evan)
Date: Mon, 26 Mar 2012 09:29:45 -0700 (PDT)
Subject: [maker-devel] Can't call method "start" on an undefined value
Message-ID: <31251549.92.1332779385632.JavaMail.geo-discussion-forums@vbbfy7>

Hi,

I'm running maker 2.24-beta. At least 10-15% of scaffolds are failing with 
the following error:

Preparing evidence for hint based annotation
cleaning clusters....
total clusters:1 now processing 0
in cluster::shadow_cluster...
...finished clustering.
cleaning clusters....
total clusters:4 now processing 0
 ...processing 0 of 3
 ...processing 1 of 3
total clusters:4 now processing 0
 ...processing 0 of 2
total clusters:4 now processing 0
total clusters:4 now processing 0
Can't call method "start" on an undefined valueERROR: Failed while 
preparing evidence clusters for annotations
ERROR: Chunk failed at level:0, tier_type:3
FAILED CONTIG:scaffold93.1

ERROR: Chunk failed at level:7, tier_type:0
FAILED CONTIG:scaffold93.1

This occurs when running just a single maker instance. 

Thanks,
Evan
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From carsonhh at gmail.com  Mon Mar 26 11:22:15 2012
From: carsonhh at gmail.com (Carson Holt)
Date: Mon, 26 Mar 2012 13:22:15 -0400
Subject: [maker-devel] maker 2.22-beta: identical names and sequences
 repeated in maker.all.proteins fasta - attached FASTA, gff3
In-Reply-To: <407831381.989320.1332781349591.JavaMail.root@ksu-sfpop-mailstore03>
Message-ID: <CB961AC7.9EF5%carsonhh@gmail.com>

Thanks for the file.  I now see that the issue is caused by repeated model
entries in the maker_gff file (example from the following lines in the
input GFF3).


scaffold09875   maker   mRNA    255     1019    .       +       .
ID=maker-scaffold09875-est_gff_Cufflinks-gene-0.0-mRNA-1;Parent=maker-scaff
old09875-est_gff_Cufflinks-gene-0.0;
scaffold09875   model_gff:maker match   255     1019    .       +       .
     
ID=scaffold09875:hit:419759:0_0;Name=maker-scaffold09875-est_gff_Cufflinks-
gene-0.0-mRNA-1;


During recent MAKER updates, it was requested that MAKER add model_gff
features used from a previous run as a reference annotation, so you can
still see it even when it is not chosen on the second round.  However this
has an unexpected effect on multiple reruns using maker output as the new
input because both entries get interpreted as model_gff, they both then
end up in the results of a rerun (duplicated each round).

I've fixed this in the developers release (be a couple of days till it
hits the download page as a beta release), but in the mean time just
remove the model_gff:maker entries from the input fasta and it will work
as expected.

To do that use this command -->
   grep -v "model_gff:maker"
Msex05162011.genome.all.maker-2.22-15Feb2012.gff3 >
filtered_Msex05162011.genome.all.maker-2.22-15Feb2012.gff3


Then put filtered_Msex05162011.genome.all.maker-2.22-15Feb2012.gff3 as
your maker_gff file.

I also recommend that you delete and .db extension files from the maker
output directory (there will be only one there).  That will make extra
sure that the GFF3 file index gets rebuilt to the new file.

Note:  I also noticed that Msex05162011.genome.cegma.gff is not in GFF3
format (it is in ZFF format).  It would work for training SNAP but will
not work with MAKER.

Thanks,
Carson





On 12-03-26 1:02 PM, "Sanjay Chellapilla" wrote:

>
>
>----- Original Message -----
>> Since you are using it as input.  I'll need to see this file.
>> 
>> 
>>/home/sanjay/manduca_sexta/maker/maker-runs-2.22/Msex05162011.genome.all.
>>ma
>> ker-2.22-15Feb2012.gff3
>> 
>> Thanks,
>> Carson
>> 
>> 
>> 
>> On 12-03-26 12:42 PM, "Sanjay Chellapilla"
>> wrote:
>> 
>> >Attached
>> >"Msex-maker-2.22-identical-repeated-proteins-input-files.tar.bz2"
>> >containing 3 files
>> >
>> >maker-2.22_opts.ctl.28Feb2012
>> >est_gff = baylor_cufflinks_transcripts_gtf_no_G14G15.gff3
>> >model_gff = Msex05162011.genome.cegma.gff
>> >
>> >The maker_gff (Msex05162011.genome.all.maker-2.22-15Feb2012.gff3) is
>> >633MB so I didn't include it in this message. Please let me know if
>> >you'd want to see it - I'll send it separately.
>> >
>> >Thank you,
>> >Sanjay.
>> >
>> >----- Original Message -----
>> >> Could you send me the file you are passing to the est_gff,
>> >> model_gff,
>> >> or
>> >> maker_gff options.
>> >> 
>> >> Also could you send me your MAKER control files?
>> >> 
>> >> Thanks,
>> >> Carson
>> >> 
>> >> 
>> >> 
>> >> 
>> >> On 12-03-14 1:26 PM, "Sanjay Chellapilla"
>> >> wrote:
>> >> 
>> >> >Hi Carson,
>> >> >
>> >> >Sorry I forgot to attach files showing the issue. Attached zip
>> >> >containing one such maker proteins fasta file and corresponding
>> >> >maker gff3 for scaffold00126 having identical repeated sequence
>> >> >">maker-scaffold00126-est_gff_Cufflinks-gene-2.0-mRNA-1".
>> >> >
>> >> >Thank you.
>> >> >
>> >> >----- Forwarded Message -----
>> >> >> Hi Carson,
>> >> >> 
>> >> >> I ran maker-2.22-beta a total of 3 times with the same
>> >> >> evidence,
>> >> >> to annotate the Manduca.sexta genome, each time using
>> >> >> maker-gff3
>> >> >> for the re-annotation run and gene-predictors SNAP, Augustus
>> >> >> trained
>> >> >> on maker-gff3 from the previous run. At the end of the third
>> >> >> run,
>> >> >> I used fasta_merge script to obtain the various fasta files.
>> >> >> I notice that some sequences are repeated in the maker.all
>> >> >> transcripts/proteins fasta files. I found 34 repeated out of
>> >> >> 16128 transcripts/proteins, so there are actually only 16094
>> >> >> unique
>> >> >> sequences. Could this be related to the "repeated genes" issue
>> >> >> from the strange cufflinks cuffmerge gff3 that's used as input
>> >> >> to maker - we discussed this back in January when we first came
>> >> >> across and I had sent you a portion of the gff3 where we saw
>> >> >> this,
>> >> >> and then you recommended trying maker-2.22-beta where this was
>> >> >> fixed
>> >> >> ?
>> >> >> Naturally this also causes repeated short-IDs created using the
>> >> >> maker_map_ids, map_fasta_ids, map_gff_ids scripts.
>> >> >> 
>> >> >> Thanks,
>> >> >> Sanjay.





From carsonhh at gmail.com  Mon Mar 26 13:08:48 2012
From: carsonhh at gmail.com (Carson Holt)
Date: Mon, 26 Mar 2012 15:08:48 -0400
Subject: [maker-devel] FW: Can't call method "start" on an undefined value
In-Reply-To: <CB963617.9F28%carsonhh@gmail.com>
Message-ID: <CB9636EF.9F37%carsonhh@gmail.com>

Ok.  This is fixed (along with a few other things), and is available for
download as MAKER 2.25.

Thanks,
Carson



From:  Evan <eernst at cshl.edu>
Date:  Mon, 26 Mar 2012 09:29:45 -0700 (PDT)
To:  <maker-devel at googlegroups.com>
Subject:  [maker-devel] Can't call method "start" on an undefined value

Hi,

I'm running maker 2.24-beta. At least 10-15% of scaffolds are failing with
the following error:

Preparing evidence for hint based annotation
cleaning clusters....
total clusters:1 now processing 0
in cluster::shadow_cluster...
...finished clustering.
cleaning clusters....
total clusters:4 now processing 0
 ...processing 0 of 3
 ...processing 1 of 3
total clusters:4 now processing 0
 ...processing 0 of 2
total clusters:4 now processing 0
total clusters:4 now processing 0
Can't call method "start" on an undefined valueERROR: Failed while preparing
evidence clusters for annotations
ERROR: Chunk failed at level:0, tier_type:3
FAILED CONTIG:scaffold93.1

ERROR: Chunk failed at level:7, tier_type:0
FAILED CONTIG:scaffold93.1

This occurs when running just a single maker instance.

Thanks,
Evan
_______________________________________________ maker-devel mailing list
maker-devel at box290.bluehost.comhttp://box290.bluehost.com/mailman/listinfo/m
aker-devel_yandell-lab.org


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From carsonhh at gmail.com  Mon Mar 26 14:17:36 2012
From: carsonhh at gmail.com (Carson Holt)
Date: Mon, 26 Mar 2012 16:17:36 -0400
Subject: [maker-devel] Can't call method "start" on an undefined value
In-Reply-To: <CAOqGFX-wEA2weUPSZRrpXBd+gV8nHAEsR9ST-YA96u+q+RvgyA@mail.gmail.com>
Message-ID: <CB964686.9FBB%carsonhh@gmail.com>

 //= is a feature of perl versions 5.10 and above.

You must have an older version of perl.
Just change it to ||= and it will work for older versions.  I'll make that
change to the release as well to make it work with older perl.

Thanks,
Carson




From:  Evan Ernst <eernst at cshl.edu>
Date:  Mon, 26 Mar 2012 16:13:19 -0400
To:  Carson Holt <carsonhh at gmail.com>
Cc:  <maker-devel at googlegroups.com>
Subject:  Re: [maker-devel] Can't call method "start" on an undefined value

Hi Carson,

Line 242 of maker is causing a compilation failure in the version I
downloaded:

241 -> eval "\$ver = \$${name}::VERSION";
242 -> $ver //= 'UNKNOWN';
243 -> $ver = 'UNKNOWN' if($ver =~ /^\-1\,/);

Thanks,
Evan

On Mon, Mar 26, 2012 at 3:06 PM, Evan Ernst <eernst at cshl.edu> wrote:
> Fantastic. Thanks for your help.
> 
> Best,
> Evan
> 
> 
> On Mon, Mar 26, 2012 at 3:05 PM, Carson Holt <carsonhh at gmail.com> wrote:
>> Ok.  This is fixed (along with a few other things), and is available for
>> download as MAKER 2.25.
>> 
>> Thanks,
>> Carson
>> 
>> 
>> 
>> From:  Evan <eernst at cshl.edu>
>> Date:  Mon, 26 Mar 2012 09:29:45 -0700 (PDT)
>> To:  <maker-devel at googlegroups.com>
>> Subject:  [maker-devel] Can't call method "start" on an undefined value
>> 
>> Hi,
>> 
>> I'm running maker 2.24-beta. At least 10-15% of scaffolds are failing with
>> the following error:
>> 
>> Preparing evidence for hint based annotation
>> cleaning clusters....
>> total clusters:1 now processing 0
>> in cluster::shadow_cluster...
>> ...finished clustering.
>> cleaning clusters....
>> total clusters:4 now processing 0
>>  ...processing 0 of 3
>>  ...processing 1 of 3
>> total clusters:4 now processing 0
>>  ...processing 0 of 2
>> total clusters:4 now processing 0
>> total clusters:4 now processing 0
>> Can't call method "start" on an undefined valueERROR: Failed while preparing
>> evidence clusters for annotations
>> ERROR: Chunk failed at level:0, tier_type:3
>> FAILED CONTIG:scaffold93.1
>> 
>> ERROR: Chunk failed at level:7, tier_type:0
>> FAILED CONTIG:scaffold93.1
>> 
>> This occurs when running just a single maker instance.
>> 
>> Thanks,
>> Evan
>> _______________________________________________ maker-devel mailing list
>> maker-devel at box290.bluehost.comhttp://box290.bluehost.com/mailman/listinfo/ma
>> ker-devel_yandell-lab.org
> 
> 
> 
> -- 
> Evan Ernst
> Martienssen Lab
> 
> Delbruck #216
> Cold Spring Harbor Laboratory
> 1 Bungtown Rd.
> Cold Spring Harbor, NY 11724
> 



-- 
Evan Ernst
Martienssen Lab

Delbruck #216
Cold Spring Harbor Laboratory
1 Bungtown Rd.
Cold Spring Harbor, NY 11724



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From daniel.fer.u at gmail.com  Mon Mar 26 20:39:43 2012
From: daniel.fer.u at gmail.com (=?UTF-8?Q?Daniel_Fern=C3=A1ndez?=)
Date: Mon, 26 Mar 2012 19:39:43 -0700 (PDT)
Subject: [maker-devel] Problem with RMBlast installation
In-Reply-To: <7A26C949-4ED3-4CEF-8455-2D3A85B35A2B@gmail.com>
References: <8109224.101.1332730405163.JavaMail.geo-discussion-forums@ynlx41>
	<7A26C949-4ED3-4CEF-8455-2D3A85B35A2B@gmail.com>
Message-ID: <3452112.702.1332815983251.JavaMail.geo-discussion-forums@ynne2>

Ok, I unpack this file, I have 3 directories (bin include lib) and the 
readme file, you tell me add this to my $PATH, but I  add to my path all 
executables (bin), but the other 2 directories? I don't think that I have 
to add to my path, is different to Blast+, in blast+ I only copy the 
executables to my path, the other directories are only data

The bin directory have many executables like blast+, if I add all to my 
path, so I will have many duplicate executables, does this not cause a 
conflict?

On Monday, March 26, 2012 10:33:55 AM UTC-5, Jason Stajich wrote:
>
> Hi Daniel -
>
> Just download, unpackage the precompiled ( rmblast-1.2-ncbi-blast-2.2.23+-x64-linux.tar.gz 
> ) version and tell RepeatMasker where the exes are when you configure 
> RepeatMasker.  RMBlast is for RepeatMasker.
>  
> For running BLAST in MAKAER would install NCBI-BLAST+ if you don't have 
> wu-blast --- ftp://ftp.ncbi.nih.gov/blast/executables/blast+/LATEST - I 
> believe current maker supports BLAST+, BLAST, and WU-BLAST so you have your 
> pick.
>
> Jason
> On Mar 25, 2012, at 7:53 PM, Daniel Fern?ndez wrote:
>
> Hi,
>
> I trying to install MAKER, I don't have WU-Blast, I have Blast+ so in the 
> README file tell me that I need RMBlast, but I don't know what file I have 
> to choose, rmblast-1.2-ncbi-blast-2.2.23+-src.tar.gz or rmblast-1.2-ncbi-blast-2.2.23+-x64-linux.tar.gz 
> (I have Linux 64-bit) in each version the README file is the same, and 
> there tell me how I can install it, but the instructions is only for rmblast-1.2-ncbi-blast-2.2.23+-src, 
> well, when I try to install it, I type this 
> $./configure --with-mt --prefix=/usr/local/bioinfo/repeatmasker/rmblast 
> --without-debug
> This show me error, and I type make and this show stop.
>
> Can you help me please?
>
> This show me when I type $./configure --with-mt 
> --prefix=/usr/local/bioinfo/repeatmasker/rmblast --without-debug
>
> -----------------------------------------------------------------------------------------------------------------------------------------------
> configure: loading site script ./src/build-system/config.site
> configure: loading cache config.cache
> checking build system type... x86_64-unknown-linux-gnu
> checking host system type... x86_64-unknown-linux-gnu
> checking for a BSD-compatible install... /usr/bin/install -c
> checking for gcc... gcc
> checking for C compiler default output file name... a.out
> checking whether the C compiler works... yes
> checking whether we are cross compiling... no
> checking for suffix of executables... 
> checking for suffix of object files... o
> checking whether we are using the GNU C compiler... yes
> checking whether gcc accepts -g... yes
> checking for gcc option to accept ANSI C... none needed
> checking for g++... no
> checking for c++... no
> checking for gpp... no
> checking for aCC... no
> checking for CC... no
> checking for cxx... no
> checking for cc++... no
> checking for cl... no
> checking for FCC... no
> checking for KCC... no
> checking for RCC... no
> checking for xlC_r... no
> checking for xlC... no
> checking whether we are using the GNU C++ compiler... no
> checking whether g++ accepts -g... no
> adjusted C   compiler: /usr/bin/gcc 
> ./src/build-system/configure: line 4404: type: g++: not found
> dirname: missing operand
> Try `dirname --help' for more information.
> configure: error: Do not know how to build MT-safe with compiler g++ 
> ./src/build-system/configure: line 4187: g++: command not found
>
> -----------------------------------------------------------------------------------------------------------------------------------
> _______________________________________________
> maker-devel mailing list
> maker-devel at box290.bluehost.com
> http://box290.bluehost.com/mailman/listinfo/maker-devel_yandell-lab.org
>
>
> Jason Stajich
> jason.stajich at gmail.com
> jason at bioperl.org
>  
>
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From carsonhh at gmail.com  Mon Mar 26 20:47:37 2012
From: carsonhh at gmail.com (Carson Holt)
Date: Mon, 26 Mar 2012 22:47:37 -0400
Subject: [maker-devel] Problem with RMBlast installation
In-Reply-To: <3452112.702.1332815983251.JavaMail.geo-discussion-forums@ynne2>
Message-ID: <CB96A177.A1BD%carsonhh@gmail.com>

You only need to add the directory location for executables you plan on
calling yourself from the command line.  You don't need to add RMBlast to
the PATH for example because you should never use it directly.  RepeatMasker
knows where it is once configured, and you want to use NCBI's BLAST.

Thanks,
Carson

From:  Daniel Fern?ndez <daniel.fer.u at gmail.com>
Date:  Mon, 26 Mar 2012 19:39:43 -0700 (PDT)
To:  <maker-devel at googlegroups.com>
Cc:  "maker-devel at yandell-lab.org List" <maker-devel at yandell-lab.org>,
Daniel Fern?ndez <daniel.fer.u at gmail.com>
Subject:  Re: [maker-devel] Problem with RMBlast installation

Ok, I unpack this file, I have 3 directories (bin include lib) and the
readme file, you tell me add this to my $PATH, but I  add to my path all
executables (bin), but the other 2 directories? I don't think that I have to
add to my path, is different to Blast+, in blast+ I only copy the
executables to my path, the other directories are only data

The bin directory have many executables like blast+, if I add all to my
path, so I will have many duplicate executables, does this not cause a
conflict?

On Monday, March 26, 2012 10:33:55 AM UTC-5, Jason Stajich wrote:
> Hi Daniel -
> 
> Just download, unpackage the precompiled (
> rmblast-1.2-ncbi-blast-2.2.23+-x64-linux.tar.gz ) version and tell
> RepeatMasker where the exes are when you configure RepeatMasker.  RMBlast is
> for RepeatMasker.
>  
> For running BLAST in MAKAER would install NCBI-BLAST+ if you don't have
> wu-blast --- ftp://ftp.ncbi.nih.gov/blast/executables/blast+/LATEST - I
> believe current maker supports BLAST+, BLAST, and WU-BLAST so you have your
> pick.
> 
> Jason
> On Mar 25, 2012, at 7:53 PM, Daniel Fern?ndez wrote:
> 
>> Hi,
>> 
>> I trying to install MAKER, I don't have WU-Blast, I have Blast+ so in the
>> README file tell me that I need RMBlast, but I don't know what file I have to
>> choose, rmblast-1.2-ncbi-blast-2.2.23+-src.tar.gz or
>> rmblast-1.2-ncbi-blast-2.2.23+-x64-linux.tar.gz (I have Linux 64-bit) in each
>> version the README file is the same, and there tell me how I can install it,
>> but the instructions is only for rmblast-1.2-ncbi-blast-2.2.23+-src, well,
>> when I try to install it, I type this
>> $./configure --with-mt --prefix=/usr/local/bioinfo/repeatmasker/rmblast
>> --without-debug
>> This show me error, and I type make and this show stop.
>> 
>> Can you help me please?
>> 
>> This show me when I type $./configure --with-mt
>> --prefix=/usr/local/bioinfo/repeatmasker/rmblast --without-debug
>> -----------------------------------------------------------------------------
>> ------------------------------------------------------------------
>> configure: loading site script ./src/build-system/config.site
>> configure: loading cache config.cache
>> checking build system type... x86_64-unknown-linux-gnu
>> checking host system type... x86_64-unknown-linux-gnu
>> checking for a BSD-compatible install... /usr/bin/install -c
>> checking for gcc... gcc
>> checking for C compiler default output file name... a.out
>> checking whether the C compiler works... yes
>> checking whether we are cross compiling... no
>> checking for suffix of executables...
>> checking for suffix of object files... o
>> checking whether we are using the GNU C compiler... yes
>> checking whether gcc accepts -g... yes
>> checking for gcc option to accept ANSI C... none needed
>> checking for g++... no
>> checking for c++... no
>> checking for gpp... no
>> checking for aCC... no
>> checking for CC... no
>> checking for cxx... no
>> checking for cc++... no
>> checking for cl... no
>> checking for FCC... no
>> checking for KCC... no
>> checking for RCC... no
>> checking for xlC_r... no
>> checking for xlC... no
>> checking whether we are using the GNU C++ compiler... no
>> checking whether g++ accepts -g... no
>> adjusted C   compiler: /usr/bin/gcc
>> ./src/build-system/configure: line 4404: type: g++: not found
>> dirname: missing operand
>> Try `dirname --help' for more information.
>> configure: error: Do not know how to build MT-safe with compiler g++
>> ./src/build-system/configure: line 4187: g++: command not found
>> -----------------------------------------------------------------------------
>> ------------------------------------------------------
>> _______________________________________________
>> maker-devel mailing list
>> maker-devel at box290.bluehost.com
>> http://box290.bluehost.com/mailman/listinfo/maker-devel_yandell-lab.org
> 
> Jason Stajich
> jason.stajich at gmail.com
> jason at bioperl.org
> 
_______________________________________________ maker-devel mailing list
maker-devel at box290.bluehost.com
http://box290.bluehost.com/mailman/listinfo/maker-devel_yandell-lab.org

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From tr at ncgr.org  Wed Mar 28 12:34:39 2012
From: tr at ncgr.org (Thiru Ramaraj)
Date: Wed, 28 Mar 2012 12:34:39 -0600
Subject: [maker-devel] maker_functional_gff
Message-ID: <4F7359BF.5020900@ncgr.org>

Hi All,

I am in the process of using maker_functional_gff script th generate 
functional gff file. I was wondering if NCBI BLAST tab delimited output 
will work as it is or there any formatting needed to be  more like a 
WUBLAST output.

Any thoughts would be greatly appreciated.

Thanks,
-Thiru



From carsonhh at gmail.com  Thu Mar 29 08:58:18 2012
From: carsonhh at gmail.com (Carson Holt)
Date: Thu, 29 Mar 2012 10:58:18 -0400
Subject: [maker-devel] maker_functional_gff
In-Reply-To: <4F7359BF.5020900@ncgr.org>
Message-ID: <CB99EE84.A2F7%carsonhh@gmail.com>

It should work with NCBI BLAST as long as it is the optional tab delimited
format, and not the standard raw format report.

The report must be generated from UniProt/Swiss-prot formatted fasta files.

Here is an example of the header format for the fasta file -->
>sp|P18560|1101L_ASFB7 Protein MGF 110-1L OS=African swine fever virus
>(strain Badajoz 1971 Vero-adapted) GN=BA71V-008 PE=3 SV=1

This ia a description of what maker_functional_gff is looked for
>transcript_ID  Description  OS=species  GN=gene_name
>PE=any_text_from_this_point_on_is_ignored

Thanks,
Carson




On 12-03-28 2:34 PM, "Thiru Ramaraj" <tr at ncgr.org> wrote:

>Hi All,
>
>I am in the process of using maker_functional_gff script th generate
>functional gff file. I was wondering if NCBI BLAST tab delimited output
>will work as it is or there any formatting needed to be  more like a
>WUBLAST output.
>
>Any thoughts would be greatly appreciated.
>
>Thanks,
>-Thiru
>
>_______________________________________________
>maker-devel mailing list
>maker-devel at box290.bluehost.com
>http://box290.bluehost.com/mailman/listinfo/maker-devel_yandell-lab.org





From barry.utah at gmail.com  Thu Mar 29 13:29:48 2012
From: barry.utah at gmail.com (Barry Moore)
Date: Thu, 29 Mar 2012 13:29:48 -0600
Subject: [maker-devel] GFF3 Specification
Message-ID: <C8A5B771-CCB5-4629-9F02-CF2437493F39@genetics.utah.edu>

Hi All,

There has been active discussion on the song-devel mailing list over the past 12 months about various ambiguities and unresolved issues with the GFF3 specification.  The SO group is initiating a process to resolve these issues so that GFF3 can continue to serve it's role of unifying genome annotations in a format that promotes collaboration between genome projects and comparison of datasets across a wide variety of genomes.  With the rapid acceleration of genome sequencing, a simple, standard format for genome annotation and comparative genomics is more critical than ever.

Several issues have been raised, and they range from simple requests for clarification to more fundamental questions about the structure of the specification.  We can't address all of these issues in one update to the spec, so we've started the ball rolling with three steps:

Incorporate all the minor changes into a GFF3 1.21 candidate spec (http://www.sequenceontology.org/resources/gff3_1.21.html).
Organize remaining unresolved issues onto a wiki page and start working through those issues one by one (http://www.sequenceontology.org/wiki/index.php?title=GFF3_Developement).
Develop a set of wiki pages to describe 'GFF3 Best Practices' and existing community usage (http://www.sequenceontology.org/wiki/index.php?title=GFF3_best_practices).

We will work through the unresolved issues one at a time - soliciting feedback from the community, and clarify/update the GFF3 spec in a backwards compatible way with existing tools and datasets, adding documenting wiki pages as needed.

We welcome and encourage feedback from the genomics community and gratefully acknowledge those who have been active in the discussion thus far.  Please have a look at the pages described above and join the conversation.  The best place for discussion of all things GFF3 is the SO mailing list (song-devel at lists.sourceforge.net).  Please feel free to re-post this message to relevant mailing lists so that all interested parties can be involved.

On behalf of the SO developers - Thanks.

Barry Moore
Research Scientist
Dept. of Human Genetics
University of Utah
Salt Lake City, UT 84112
--------------------------------------------
(801) 585-3543




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From ianmisner at my.uri.edu  Thu Mar  1 15:25:06 2012
From: ianmisner at my.uri.edu (Ian Misner)
Date: Thu, 1 Mar 2012 17:25:06 -0500
Subject: [maker-devel] Rerunning Maker
Message-ID: <13A73C28-9CEF-4416-911E-2ACEE445533A@my.uri.edu>

Hello,

I have run maker 2.03 on a genome that we assembled a while back.  Now we have a new genome assembly.  Is there a way to rerun maker with the new assembly without losing all of the annotations I've done on the v2.03 predicted proteins?  I see the genome_gff option but all the contig numbers will have changed with the new assembly so that will not work.  The EST data will be the same as before.  From my original run I used a related species for protein homology, this time would I use the predicted set I have been working with?  Worst case scenario I need a way to link the old proteins with the new ones which I could do with BLAST post Maker but I'm hoping there is a better way.  Any help with this would be greatly appreciated.  


Cheers
Ian

*************************************
Mr. Ian Misner
PhD. Candidate
Department of Biological Sciences
University of Rhode Island
120 Flagg Road
Kingston, RI 02881
Office: CBLS 260
Ph: 1-401-874-9726
fax (401) 874-2065
ianmisner at my.uri.edu
http://cels.uri.edu/bio/lanelab/  










From joana.guimaraes at inrb.pt  Fri Mar  2 00:26:51 2012
From: joana.guimaraes at inrb.pt (=?iso-8859-1?Q?Maria_Joana_F=2E_B=2E_A=2E_Guimar=E3es?=)
Date: Fri, 2 Mar 2012 07:26:51 -0000
Subject: [maker-devel] maker-devel Digest, Vol 45, Issue 15
In-Reply-To: <mailman.3.1330455604.20855.maker-devel_yandell-lab.org@box290.bluehost.com>
References: <mailman.3.1330455604.20855.maker-devel_yandell-lab.org@box290.bluehost.com>
Message-ID: <F5B5DE3EA7B4FD48A549687F860198320100510E@INRBMSMXBE.INRB.PT>

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: ter?a-feira, 28 de Fevereiro de 2012 19:00
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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
_______________________________________________ maker-devel mailing list
maker-devel at box290.bluehost.com
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End of maker-devel Digest, Vol 45, Issue 15
*******************************************



From carsonhh at gmail.com  Fri Mar  2 08:39:47 2012
From: carsonhh at gmail.com (Carson Holt)
Date: Fri, 02 Mar 2012 10:39:47 -0500
Subject: [maker-devel] Rerunning Maker
In-Reply-To: <13A73C28-9CEF-4416-911E-2ACEE445533A@my.uri.edu>
Message-ID: <CB764CB4.8AF8%carsonhh@gmail.com>

There is a way to do this and it sounds harder than it really is.

Previously there was a tool that came with MAKER called map2assembly that
is no longer included with the distribution (certain changes to the MAKER
libraries broke it beyond repair).  The replacement for this tool is still
somewhat under development, so is not documented but is included with the
distribution and works far better (and faster) than map2assembly.

The new tool is internal to MAKER and called by setting several flags in
the control files before running a regular MAKER job.

To map genes forward do this:
1. Supply your old transcript file to the est= option in MAKER.
2. Set est2genome=1
3. Set single_exon=1
4. Set single_length=1
5. Turn all repeat masking options off (either delete values in control
files or use -R flag on the command line)
6. Set est_forward=1 (this is not in the maker_opts.ctl file.  You will
have to add it manually.
7. Don't run any gene predictors and don't provide any other evidence
files (we only want MAKER to map things forward)
8. Now run MAKER (remember to supply the -R flag from the command line if
you didn't delete masking options from thew control files)

MAKER will now map the old gene models to the new assembly (with names)
generating a new GFF3 file that can be used as input to future MAKER runs.

Some things to know about the process.  You can set the minimum accepted
coverage and identity to use when mapping the genes forward using the
blastn filters in the maker_bopts.ctl file.  Some genes may not map
forward and will be lost.  Some will map to multiple locations, so review
your GFF3 results file.  Also the est_forward option accepts hints via a
tag (maker_coor=) in the fasta headers.  For example, if you add the
following flag to fasta headers for the input transcript file -->
	>gene1-RA  maker_coor=chr1;
Then MAKER will only try and map that transcript to the new genomes contig
labelled chr1.  Or you can do -->
	>gene1-RA  maker_coor=chr1:2000-200000;
Then MAKER will restrict the alignment to somewhere within a given region
(could be the first half of the chromosome for example).


In future releases of MAKER, everything will be simplified.  The
est_forward will always be in the control files and will accept a file
name.  MAKER will then do all the work upstream including setting flags
and sorting out multiple location alignments as part of it's normal run
(not as an independent run as is done in what I described).

Thanks,
Carson


On 12-03-01 5:25 PM, "Ian Misner" <ianmisner at my.uri.edu> wrote:

>Hello,
>
>I have run maker 2.03 on a genome that we assembled a while back.  Now we
>have a new genome assembly.  Is there a way to rerun maker with the new
>assembly without losing all of the annotations I've done on the v2.03
>predicted proteins?  I see the genome_gff option but all the contig
>numbers will have changed with the new assembly so that will not work.
>The EST data will be the same as before.  From my original run I used a
>related species for protein homology, this time would I use the predicted
>set I have been working with?  Worst case scenario I need a way to link
>the old proteins with the new ones which I could do with BLAST post Maker
>but I'm hoping there is a better way.  Any help with this would be
>greatly appreciated.
>
>
>Cheers
>Ian
>
>*************************************
>Mr. Ian Misner
>PhD. Candidate
>Department of Biological Sciences
>University of Rhode Island
>120 Flagg Road
>Kingston, RI 02881
>Office: CBLS 260
>Ph: 1-401-874-9726
>fax (401) 874-2065
>ianmisner at my.uri.edu
>http://cels.uri.edu/bio/lanelab/
>
>
>
>
>
>
>
>
>_______________________________________________
>maker-devel mailing list
>maker-devel at box290.bluehost.com
>http://box290.bluehost.com/mailman/listinfo/maker-devel_yandell-lab.org





From carsonhh at gmail.com  Fri Mar  2 09:05:49 2012
From: carsonhh at gmail.com (Carson Holt)
Date: Fri, 02 Mar 2012 11:05:49 -0500
Subject: [maker-devel] maker-devel Digest, Vol 45, Issue 15
In-Reply-To: <F5B5DE3EA7B4FD48A549687F860198320100510E@INRBMSMXBE.INRB.PT>
Message-ID: <CB76559D.8B38%carsonhh@gmail.com>

There is more than one way to train your predictors.  If you have protein
sequence, you can run MAKER with the protein2genome=1 option set which
will generate preliminary gene models based on protein homology alone, and
those results can be used to train SNAP and augustus.  You can also train
SNAP independently using CEGMA - a program from the same group as SNAP.
It finds a small set of core genes that should be in all eukaryotic
genomes.

For me this is more of a question of speed.  Using ESTs that are not from
the same organism has caveats.  If the organisms are very closely related
(example: chimp and human), you can do a direct alignment in nucleotide
space.  But if they are not (example: human and mouse), you can use
MAKER's alt_est option and MAKER will align in translated space using
TBLASTX.  TBLASTX is mind numbingly slow, taking about 20x longer than a
direct EST alignment, and should be avoided when possible.

So to summarize, if you have ESTs from your organism, use those first.  If
not, then use proteins. Finally use alternate organism ESTs if that's all
you have. Of course you can also supply all three, but I normally only do
that for the final run.  I limit the dataset for the training rounds.

After using MAKER's results for training SNAP/augustus etc., just supply
MAKER with the resulting training HMM and run again in the same directory.
 Why in the same directory?  So that you can keep the evidence files you
used on the first run.  MAKER will see that the only thing that changed
was the HMM (so it won't have to rerun any of the alignments).  It will
just add the predictions, interpret them in light of the evidence, and
produce new output.  So the first run is slow, and the second is fast
(because MAKER takes advantage of archived BLAST, RepeatMasker, and
Exonerate results).

Thanks,
Carson



On 12-03-02 2:26 AM, "Maria Joana F. B. A. Guimar?es"
<joana.guimaraes at inrb.pt> wrote:

>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-----
>From: maker-devel-bounces at yandell-lab.org
>[mailto:maker-devel-bounces at yandell-lab.org] On Behalf Of
>maker-devel-request at yandell-lab.org
>Sent: ter?a-feira, 28 de Fevereiro de 2012 19:00
>To: maker-devel at yandell-lab.org
>Subject: maker-devel Digest, Vol 45, Issue 15
>
>Send maker-devel mailing list submissions to
>	maker-devel at yandell-lab.org
>
>To subscribe or unsubscribe via the World Wide Web, visit
>	http://box290.bluehost.com/mailman/listinfo/maker-devel_yandell-lab.org
>
>or, via email, send a message with subject or body 'help' to
>	maker-devel-request at yandell-lab.org
>
>You can reach the person managing the list at
>	maker-devel-owner at yandell-lab.org
>
>When replying, please edit your Subject line so it is more specific
>than "Re: Contents of maker-devel digest..."
>
>
>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_datast
>ore_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.repeat
>runner
>
>#-------------------------------#
>
>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//the
>Void.contig-dpp-500-500/contig-dpp-500-500.0.te_proteins%2Efasta.repeatrun
>ner
>
>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.repeat
>runner
>
>#-------------------------------#
>
>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//the
>Void.contig-dpp-500-500/contig-dpp-500-500.0.te_proteins%2Efasta.repeatrun
>ner
>
>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
>-------------- next part --------------
>An HTML attachment was scrubbed...
>URL: 
><http://box290.bluehost.com/pipermail/maker-devel_yandell-lab.org/attachme
>nts/20120228/8e6a3106/attachment-0001.html>
>
>------------------------------
>
>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_datast
>or
>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.r
>b
>-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_pr
>ot
>eins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunn
>er
>
>#-------------------------------#
>
>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//the
>Vo
>id.contig-dpp-500-500/contig-dpp-500-500.0.te_proteins%2Efasta.repeatrunne
>r
>
>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.r
>b.
>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_pr
>ot
>eins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunn
>er
>
>#-------------------------------#
>
>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//the
>Vo
>id.contig-dpp-500-500/contig-dpp-500-500.0.te_proteins%2Efasta.repeatrunne
>r
>
>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
>_______________________________________________ maker-devel mailing list
>maker-devel at box290.bluehost.com
>http://box290.bluehost.com/mailman/listinfo/maker-devel_yandell-lab.org
>
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><http://box290.bluehost.com/pipermail/maker-devel_yandell-lab.org/attachme
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>
>------------------------------
>
>_______________________________________________
>maker-devel mailing list
>maker-devel at box290.bluehost.com
>http://box290.bluehost.com/mailman/listinfo/maker-devel_yandell-lab.org
>
>
>End of maker-devel Digest, Vol 45, Issue 15
>*******************************************
>
>_______________________________________________
>maker-devel mailing list
>maker-devel at box290.bluehost.com
>http://box290.bluehost.com/mailman/listinfo/maker-devel_yandell-lab.org





From njauxiongjie at gmail.com  Fri Mar  2 19:38:50 2012
From: njauxiongjie at gmail.com (Jie)
Date: Fri, 2 Mar 2012 18:38:50 -0800 (PST)
Subject: [maker-devel] question about augustus hints file
Message-ID: <078f6ced-b08d-4a1e-8fe4-c63a2ac68392@qr9g2000pbc.googlegroups.com>

Hi, all

I have aligned my EST to my genome and want to use the EST alignment
as hints of augustus. The command I run like your README file in
AUGUSTUS, and like bellow:

blat -minIdentity=92 genome.fa cdna.fa cdna.psl
blat2hints.pl --in=cdna.psl --out=hints.E.gff

but when I feed the hint file to augustus, it appeared some error like
bellow:
augustus: ERROR        FeatureCollection::esource: invalid source key:
E

How can I solve this problem?



From thomas.hackl at uni-wuerzburg.de  Wed Mar  7 01:31:39 2012
From: thomas.hackl at uni-wuerzburg.de (Thomas Hackl)
Date: Wed, 07 Mar 2012 09:31:39 +0100
Subject: [maker-devel] maker 2.22/2.23: Segmentation fault while processing
	FASTA input
Message-ID: <4F571CEB.7070707@uni-wuerzburg.de>

Hello,

we want to use a current release of maker (2.22, 2.23) but the program 
terminates with a seg fault while processing the input FASTA files. 
maker 2.15 , which we have been using for quite some time, runs 
perfectly with identical data and setup.

Please contact me if you need specifics on hardware, OS or anything else.

Best regards
Thomas

-- 
Thomas Hackl
Julius-Maximilians-Universit?t
Department of Bioinformatics
97074 W?rzburg, Germany
Fon:  +49 931 - 31 86883
Mail: thomas.hackl at uni-wuerzburg.de




From Carson.Holt at oicr.on.ca  Wed Mar  7 15:45:06 2012
From: Carson.Holt at oicr.on.ca (Carson Holt)
Date: Wed, 7 Mar 2012 22:45:06 +0000
Subject: [maker-devel] maker 2.22/2.23: Segmentation fault while
 processing FASTA input
In-Reply-To: <4F571CEB.7070707@uni-wuerzburg.de>
Message-ID: <CB7D4D49.8FCD%carson.holt@oicr.on.ca>

There should be no new hardware requirement.  But there is always a chance
that there is an issue with one of the perl modules being used.  I assume
the failure is happening when using maker serially and you are not using
MPI.

Could you reinstall the following perl modules, and try again.  If you are
using CPAN, do a 'force install' to force it to reinstall.

Modules:
*Storable
*Inline::C
*forks
*forks::shared

Also try reinstalling the latest version of BioPerl.

The fact that this is a seg fault suggests that something is happemning at
the C level (just outside of Perl).  Those area all the modules MAKER uses
that will call back to the C level.  BioPerl has a fasta indexing module
that is also making calls outside of Perl, and the fact it fails at that
point makes it a suspect.

Let me know what happens.  I can always generate an alternate MAKER
executable for you to run with additional status messages that may help
identify exactly which module is being called right before the failure.

Thanks,
Carson



On 12-03-07 3:31 AM, "Thomas Hackl" <thomas.hackl at uni-wuerzburg.de> wrote:

>Hello,
>
>we want to use a current release of maker (2.22, 2.23) but the program
>terminates with a seg fault while processing the input FASTA files.
>maker 2.15 , which we have been using for quite some time, runs
>perfectly with identical data and setup.
>
>Please contact me if you need specifics on hardware, OS or anything else.
>
>Best regards
>Thomas
>
>-- 
>Thomas Hackl
>Julius-Maximilians-Universit?t
>Department of Bioinformatics
>97074 W?rzburg, Germany
>Fon:  +49 931 - 31 86883
>Mail: thomas.hackl at uni-wuerzburg.de
>
>
>_______________________________________________
>maker-devel mailing list
>maker-devel at box290.bluehost.com
>http://box290.bluehost.com/mailman/listinfo/maker-devel_yandell-lab.org




From ianmisner at my.uri.edu  Thu Mar  8 07:15:05 2012
From: ianmisner at my.uri.edu (Ian Misner)
Date: Thu, 8 Mar 2012 09:15:05 -0500
Subject: [maker-devel] Error: Chunk failed at level
Message-ID: <6F68BCEE-BD5B-4059-BA87-188BA8585105@my.uri.edu>

Hello,

I've run maker with RM, SNAP, and gmhmm on my novel genome and I've some very large contigs that haven't annotated any proteins.  I have looked through the output from the run and of the 74 contigs that failed I only have three errors.

They are Chunk failed at level 3, 8, & 16

What are those errors?  How can I get the annotations for these failed runs to work?  I have the entire output if you would need to see that file.  In my opts ctl file I set it to retry failed contigs 2 times and do a fresh run each time.  All 74 contigs failed all 3 attempts to run.  Any help would be much appreciated.

Cheers
Ian


*************************************
Mr. Ian Misner
PhD. Candidate
Department of Biological Sciences
University of Rhode Island
120 Flagg Road
Kingston, RI 02881
Office: CBLS 260
Ph: 1-401-874-9726
fax (401) 874-2065
ianmisner at my.uri.edu
http://cels.uri.edu/bio/lanelab/  










From jason.stajich at gmail.com  Thu Mar  8 18:58:32 2012
From: jason.stajich at gmail.com (Jason Stajich)
Date: Thu, 8 Mar 2012 17:58:32 -0800
Subject: [maker-devel] Error: Chunk failed at level
In-Reply-To: <6F68BCEE-BD5B-4059-BA87-188BA8585105@my.uri.edu>
References: <6F68BCEE-BD5B-4059-BA87-188BA8585105@my.uri.edu>
Message-ID: <8CA12776-E69F-4868-B9CE-278062F83D32@gmail.com>

Hi Ian - 

Do you get any gene models if you run RM or SNAP on these directly?  I can't tell if this means there is no overlap between your different prediction sets or if you didn't get ab initio predictions?

Jason
On Mar 8, 2012, at 6:15 AM, Ian Misner wrote:

> Hello,
> 
> I've run maker with RM, SNAP, and gmhmm on my novel genome and I've some very large contigs that haven't annotated any proteins.  I have looked through the output from the run and of the 74 contigs that failed I only have three errors.
> 
> They are Chunk failed at level 3, 8, & 16
> 
> What are those errors?  How can I get the annotations for these failed runs to work?  I have the entire output if you would need to see that file.  In my opts ctl file I set it to retry failed contigs 2 times and do a fresh run each time.  All 74 contigs failed all 3 attempts to run.  Any help would be much appreciated.
> 
> Cheers
> Ian
> 
> 
> *************************************
> Mr. Ian Misner
> PhD. Candidate
> Department of Biological Sciences
> University of Rhode Island
> 120 Flagg Road
> Kingston, RI 02881
> Office: CBLS 260
> Ph: 1-401-874-9726
> fax (401) 874-2065
> ianmisner at my.uri.edu
> http://cels.uri.edu/bio/lanelab/  
> 
> 
> 
> 
> 
> 
> 
> 
> _______________________________________________
> maker-devel mailing list
> maker-devel at box290.bluehost.com
> http://box290.bluehost.com/mailman/listinfo/maker-devel_yandell-lab.org

Jason Stajich
jason.stajich at gmail.com
jason at bioperl.org

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From carsonhh at gmail.com  Fri Mar  9 12:02:58 2012
From: carsonhh at gmail.com (Carson Holt)
Date: Fri, 09 Mar 2012 14:02:58 -0500
Subject: [maker-devel] Error: Chunk failed at level
In-Reply-To: <6F68BCEE-BD5B-4059-BA87-188BA8585105@my.uri.edu>
Message-ID: <CB7FBDE5.90EB%carsonhh@gmail.com>

Those are the very last messages in a series of error handlers.  Look
further up the report, the errors triggering the handler should be further
back.  If your'e running parallel,  the other errors may be way back up
the report.  Also which version of MAKER are you using?

You can send my any failed contigs, the maker control files and any other
datasets/files you are using if you want me to take a look as well.

Thanks,
Carson



On 12-03-08 9:15 AM, "Ian Misner" <ianmisner at my.uri.edu> wrote:

>Hello,
>
>I've run maker with RM, SNAP, and gmhmm on my novel genome and I've some
>very large contigs that haven't annotated any proteins.  I have looked
>through the output from the run and of the 74 contigs that failed I only
>have three errors.
>
>They are Chunk failed at level 3, 8, & 16
>
>What are those errors?  How can I get the annotations for these failed
>runs to work?  I have the entire output if you would need to see that
>file.  In my opts ctl file I set it to retry failed contigs 2 times and
>do a fresh run each time.  All 74 contigs failed all 3 attempts to run.
>Any help would be much appreciated.
>
>Cheers
>Ian
>
>
>*************************************
>Mr. Ian Misner
>PhD. Candidate
>Department of Biological Sciences
>University of Rhode Island
>120 Flagg Road
>Kingston, RI 02881
>Office: CBLS 260
>Ph: 1-401-874-9726
>fax (401) 874-2065
>ianmisner at my.uri.edu
>http://cels.uri.edu/bio/lanelab/
>
>
>
>
>
>
>
>
>_______________________________________________
>maker-devel mailing list
>maker-devel at box290.bluehost.com
>http://box290.bluehost.com/mailman/listinfo/maker-devel_yandell-lab.org





From thomas.hackl at uni-wuerzburg.de  Tue Mar 13 03:41:40 2012
From: thomas.hackl at uni-wuerzburg.de (Thomas Hackl)
Date: Tue, 13 Mar 2012 10:41:40 +0100
Subject: [maker-devel] maker 2.22/2.23: Segmentation fault while
 processing FASTA input
In-Reply-To: <CB7D4D49.8FCD%carson.holt@oicr.on.ca>
References: <CB7D4D49.8FCD%carson.holt@oicr.on.ca>
Message-ID: <4F5F1654.1060100@uni-wuerzburg.de>

Hello,

We reinstalled the packages you suggested

forks is up to date (0.34).
forks::shared is up to date (0.34).
Inline::C is up to date (0.50).
Storable is up to date (2.30).

as well as BioPerl.

The problem is still the same.

With MPI it terminates with this message:

STATUS: Parsing control files...
STATUS: Processing and indexing input FASTA files...
===================================================================================== 


=   BAD TERMINATION OF ONE OF YOUR APPLICATION PROCESSES
=   EXIT CODE: 11
=   CLEANING UP REMAINING PROCESSES
=   YOU CAN IGNORE THE BELOW CLEANUP MESSAGES
===================================================================================== 

APPLICATION TERMINATED WITH THE EXIT STRING: Segmentation fault (signal 11)

which I presume is also the same problem.

I am with you that the error is caused somewhere on the C level. If the 
indexing step
is handled by non-maker modules exclusively, than the fact that the 2.15 
version works,
suggests that you are using different modules/methods in the current 
releases?

In any case, I think a version with verbose status messages might help 
to localize the
source of the problem.

Regards
Thomas

Am 07.03.2012 23:45, schrieb Carson Holt:
> There should be no new hardware requirement.  But there is always a chance
> that there is an issue with one of the perl modules being used.  I assume
> the failure is happening when using maker serially and you are not using
> MPI.
>
> Could you reinstall the following perl modules, and try again.  If you are
> using CPAN, do a 'force install' to force it to reinstall.
>
> Modules:
> *Storable
> *Inline::C
> *forks
> *forks::shared
>
> Also try reinstalling the latest version of BioPerl.
>
> The fact that this is a seg fault suggests that something is happemning at
> the C level (just outside of Perl).  Those area all the modules MAKER uses
> that will call back to the C level.  BioPerl has a fasta indexing module
> that is also making calls outside of Perl, and the fact it fails at that
> point makes it a suspect.
>
> Let me know what happens.  I can always generate an alternate MAKER
> executable for you to run with additional status messages that may help
> identify exactly which module is being called right before the failure.
>
> Thanks,
> Carson
>
>
>
> On 12-03-07 3:31 AM, "Thomas Hackl"<thomas.hackl at uni-wuerzburg.de>  wrote:
>
>> Hello,
>>
>> we want to use a current release of maker (2.22, 2.23) but the program
>> terminates with a seg fault while processing the input FASTA files.
>> maker 2.15 , which we have been using for quite some time, runs
>> perfectly with identical data and setup.
>>
>> Please contact me if you need specifics on hardware, OS or anything else.
>>
>> Best regards
>> Thomas
>>
>> -- 
>> Thomas Hackl
>> Julius-Maximilians-Universit?t
>> Department of Bioinformatics
>> 97074 W?rzburg, Germany
>> Fon:  +49 931 - 31 86883
>> Mail: thomas.hackl at uni-wuerzburg.de
>>
>>
>> _______________________________________________
>> maker-devel mailing list
>> maker-devel at box290.bluehost.com
>> http://box290.bluehost.com/mailman/listinfo/maker-devel_yandell-lab.org


-- 
Thomas Hackl
Julius-Maximilians-Universit?t
Department of Bioinformatics
97074 W?rzburg, Germany
Fon:  +49 931 - 31 86883
Mail: thomas.hackl at uni-wuerzburg.de




From carsonhh at gmail.com  Tue Mar 13 06:34:16 2012
From: carsonhh at gmail.com (Carson Holt)
Date: Tue, 13 Mar 2012 08:34:16 -0400
Subject: [maker-devel] maker 2.22/2.23: Segmentation fault while
 processing FASTA input
In-Reply-To: <4F5F1654.1060100@uni-wuerzburg.de>
Message-ID: <CB84B674.9207%carsonhh@gmail.com>

I've put together a new MAKER executable (mostly finished), and I will get
it to you soon.  This should help focus in on the exact module causing the
issue.

Thanks,
Carson



On 12-03-13 5:41 AM, "Thomas Hackl" <thomas.hackl at uni-wuerzburg.de> wrote:

>Hello,
>
>We reinstalled the packages you suggested
>
>forks is up to date (0.34).
>forks::shared is up to date (0.34).
>Inline::C is up to date (0.50).
>Storable is up to date (2.30).
>
>as well as BioPerl.
>
>The problem is still the same.
>
>With MPI it terminates with this message:
>
>STATUS: Parsing control files...
>STATUS: Processing and indexing input FASTA files...
>==========================================================================
>=========== 
>
>
>=   BAD TERMINATION OF ONE OF YOUR APPLICATION PROCESSES
>=   EXIT CODE: 11
>=   CLEANING UP REMAINING PROCESSES
>=   YOU CAN IGNORE THE BELOW CLEANUP MESSAGES
>==========================================================================
>=========== 
>
>APPLICATION TERMINATED WITH THE EXIT STRING: Segmentation fault (signal
>11)
>
>which I presume is also the same problem.
>
>I am with you that the error is caused somewhere on the C level. If the
>indexing step
>is handled by non-maker modules exclusively, than the fact that the 2.15
>version works,
>suggests that you are using different modules/methods in the current
>releases?
>
>In any case, I think a version with verbose status messages might help
>to localize the
>source of the problem.
>
>Regards
>Thomas
>
>Am 07.03.2012 23:45, schrieb Carson Holt:
>> There should be no new hardware requirement.  But there is always a
>>chance
>> that there is an issue with one of the perl modules being used.  I
>>assume
>> the failure is happening when using maker serially and you are not using
>> MPI.
>>
>> Could you reinstall the following perl modules, and try again.  If you
>>are
>> using CPAN, do a 'force install' to force it to reinstall.
>>
>> Modules:
>> *Storable
>> *Inline::C
>> *forks
>> *forks::shared
>>
>> Also try reinstalling the latest version of BioPerl.
>>
>> The fact that this is a seg fault suggests that something is happemning
>>at
>> the C level (just outside of Perl).  Those area all the modules MAKER
>>uses
>> that will call back to the C level.  BioPerl has a fasta indexing module
>> that is also making calls outside of Perl, and the fact it fails at that
>> point makes it a suspect.
>>
>> Let me know what happens.  I can always generate an alternate MAKER
>> executable for you to run with additional status messages that may help
>> identify exactly which module is being called right before the failure.
>>
>> Thanks,
>> Carson
>>
>>
>>
>> On 12-03-07 3:31 AM, "Thomas Hackl"<thomas.hackl at uni-wuerzburg.de>
>>wrote:
>>
>>> Hello,
>>>
>>> we want to use a current release of maker (2.22, 2.23) but the program
>>> terminates with a seg fault while processing the input FASTA files.
>>> maker 2.15 , which we have been using for quite some time, runs
>>> perfectly with identical data and setup.
>>>
>>> Please contact me if you need specifics on hardware, OS or anything
>>>else.
>>>
>>> Best regards
>>> Thomas
>>>
>>> -- 
>>> Thomas Hackl
>>> Julius-Maximilians-Universit?t
>>> Department of Bioinformatics
>>> 97074 W?rzburg, Germany
>>> Fon:  +49 931 - 31 86883
>>> Mail: thomas.hackl at uni-wuerzburg.de
>>>
>>>
>>> _______________________________________________
>>> maker-devel mailing list
>>> maker-devel at box290.bluehost.com
>>> http://box290.bluehost.com/mailman/listinfo/maker-devel_yandell-lab.org
>
>
>-- 
>Thomas Hackl
>Julius-Maximilians-Universit?t
>Department of Bioinformatics
>97074 W?rzburg, Germany
>Fon:  +49 931 - 31 86883
>Mail: thomas.hackl at uni-wuerzburg.de
>
>
>_______________________________________________
>maker-devel mailing list
>maker-devel at box290.bluehost.com
>http://box290.bluehost.com/mailman/listinfo/maker-devel_yandell-lab.org





From barry.moore at genetics.utah.edu  Tue Mar 13 15:37:13 2012
From: barry.moore at genetics.utah.edu (Barry Moore)
Date: Tue, 13 Mar 2012 15:37:13 -0600
Subject: [maker-devel] maker 2.22/2.23: Segmentation fault while
	processing FASTA input
In-Reply-To: <4F5F1654.1060100@uni-wuerzburg.de>
References: <CB7D4D49.8FCD%carson.holt@oicr.on.ca>
	<4F5F1654.1060100@uni-wuerzburg.de>
Message-ID: <33E794D7-81C6-4315-BE02-A92B8C82EB67@genetics.utah.edu>

You might also try a short perl script outside of MAKER to exercise Bio::DB::Fasta (which I believe is the module MAKER uses for Fasta indexing - correct Carson?).

Something like this should work to force indexing:

use Bio::DB::Fasta;
my $db      = Bio::DB::Fasta->new('/path/to/fasta/files');
my $seq      = $db->seq($seqid, $start, $end);

Point it at your fasta directory or file.

B

On Mar 13, 2012, at 3:41 AM, Thomas Hackl wrote:

> Hello,
> 
> We reinstalled the packages you suggested
> 
> forks is up to date (0.34).
> forks::shared is up to date (0.34).
> Inline::C is up to date (0.50).
> Storable is up to date (2.30).
> 
> as well as BioPerl.
> 
> The problem is still the same.
> 
> With MPI it terminates with this message:
> 
> STATUS: Parsing control files...
> STATUS: Processing and indexing input FASTA files...
> ===================================================================================== 
> 
> =   BAD TERMINATION OF ONE OF YOUR APPLICATION PROCESSES
> =   EXIT CODE: 11
> =   CLEANING UP REMAINING PROCESSES
> =   YOU CAN IGNORE THE BELOW CLEANUP MESSAGES
> ===================================================================================== 
> APPLICATION TERMINATED WITH THE EXIT STRING: Segmentation fault (signal 11)
> 
> which I presume is also the same problem.
> 
> I am with you that the error is caused somewhere on the C level. If the indexing step
> is handled by non-maker modules exclusively, than the fact that the 2.15 version works,
> suggests that you are using different modules/methods in the current releases?
> 
> In any case, I think a version with verbose status messages might help to localize the
> source of the problem.
> 
> Regards
> Thomas
> 
> Am 07.03.2012 23:45, schrieb Carson Holt:
>> There should be no new hardware requirement.  But there is always a chance
>> that there is an issue with one of the perl modules being used.  I assume
>> the failure is happening when using maker serially and you are not using
>> MPI.
>> 
>> Could you reinstall the following perl modules, and try again.  If you are
>> using CPAN, do a 'force install' to force it to reinstall.
>> 
>> Modules:
>> *Storable
>> *Inline::C
>> *forks
>> *forks::shared
>> 
>> Also try reinstalling the latest version of BioPerl.
>> 
>> The fact that this is a seg fault suggests that something is happemning at
>> the C level (just outside of Perl).  Those area all the modules MAKER uses
>> that will call back to the C level.  BioPerl has a fasta indexing module
>> that is also making calls outside of Perl, and the fact it fails at that
>> point makes it a suspect.
>> 
>> Let me know what happens.  I can always generate an alternate MAKER
>> executable for you to run with additional status messages that may help
>> identify exactly which module is being called right before the failure.
>> 
>> Thanks,
>> Carson
>> 
>> 
>> 
>> On 12-03-07 3:31 AM, "Thomas Hackl"<thomas.hackl at uni-wuerzburg.de>  wrote:
>> 
>>> Hello,
>>> 
>>> we want to use a current release of maker (2.22, 2.23) but the program
>>> terminates with a seg fault while processing the input FASTA files.
>>> maker 2.15 , which we have been using for quite some time, runs
>>> perfectly with identical data and setup.
>>> 
>>> Please contact me if you need specifics on hardware, OS or anything else.
>>> 
>>> Best regards
>>> Thomas
>>> 
>>> -- 
>>> Thomas Hackl
>>> Julius-Maximilians-Universit?t
>>> Department of Bioinformatics
>>> 97074 W?rzburg, Germany
>>> Fon:  +49 931 - 31 86883
>>> Mail: thomas.hackl at uni-wuerzburg.de
>>> 
>>> 
>>> _______________________________________________
>>> maker-devel mailing list
>>> maker-devel at box290.bluehost.com
>>> http://box290.bluehost.com/mailman/listinfo/maker-devel_yandell-lab.org
> 
> 
> -- 
> Thomas Hackl
> Julius-Maximilians-Universit?t
> Department of Bioinformatics
> 97074 W?rzburg, Germany
> Fon:  +49 931 - 31 86883
> Mail: thomas.hackl at uni-wuerzburg.de
> 
> 
> _______________________________________________
> maker-devel mailing list
> maker-devel at box290.bluehost.com
> http://box290.bluehost.com/mailman/listinfo/maker-devel_yandell-lab.org

Barry Moore
Research Scientist
Dept. of Human Genetics
University of Utah
Salt Lake City, UT 84112
--------------------------------------------
(801) 585-3543




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From felix.bemm at uni-wuerzburg.de  Tue Mar 13 23:57:58 2012
From: felix.bemm at uni-wuerzburg.de (Felix Bemm)
Date: Wed, 14 Mar 2012 06:57:58 +0100
Subject: [maker-devel] maker 2.22/2.23: Segmentation fault while
 processing FASTA input
In-Reply-To: <33E794D7-81C6-4315-BE02-A92B8C82EB67@genetics.utah.edu>
References: <CB7D4D49.8FCD%carson.holt@oicr.on.ca>
	<4F5F1654.1060100@uni-wuerzburg.de>
	<33E794D7-81C6-4315-BE02-A92B8C82EB67@genetics.utah.edu>
Message-ID: <4F603366.3090501@uni-wuerzburg.de>

Hi,

Thomas and I are colleagues and dealing with the same problem here. I 
wrote some test code that forced the indexing and it work fine. We are 
using most of the bioperl seqio and db modules in combination with other 
tools and don't experience the same problem there at the moment.

Regards
Felix

Am 13.03.2012 22:37, schrieb Barry Moore:
> You might also try a short perl script outside of MAKER to exercise
> Bio::DB::Fasta (which I believe is the module MAKER uses for Fasta
> indexing - correct Carson?).
>
> Something like this should work to force indexing:
>
> useBio::DB::Fasta;
> my $db = Bio::DB::Fasta->new('/path/to/fasta/files');
> my$seq=$db->seq($seqid, $start, $end);
>
> Point it at your fasta directory or file.
>
> B
>
> On Mar 13, 2012, at 3:41 AM, Thomas Hackl wrote:
>
>> Hello,
>>
>> We reinstalled the packages you suggested
>>
>> forks is up to date (0.34).
>> forks::shared is up to date (0.34).
>> Inline::C is up to date (0.50).
>> Storable is up to date (2.30).
>>
>> as well as BioPerl.
>>
>> The problem is still the same.
>>
>> With MPI it terminates with this message:
>>
>> STATUS: Parsing control files...
>> STATUS: Processing and indexing input FASTA files...
>> =====================================================================================
>>
>>
>> = BAD TERMINATION OF ONE OF YOUR APPLICATION PROCESSES
>> = EXIT CODE: 11
>> = CLEANING UP REMAINING PROCESSES
>> = YOU CAN IGNORE THE BELOW CLEANUP MESSAGES
>> =====================================================================================
>>
>> APPLICATION TERMINATED WITH THE EXIT STRING: Segmentation fault
>> (signal 11)
>>
>> which I presume is also the same problem.
>>
>> I am with you that the error is caused somewhere on the C level. If
>> the indexing step
>> is handled by non-maker modules exclusively, than the fact that the
>> 2.15 version works,
>> suggests that you are using different modules/methods in the current
>> releases?
>>
>> In any case, I think a version with verbose status messages might help
>> to localize the
>> source of the problem.
>>
>> Regards
>> Thomas
>>
>> Am 07.03.2012 23:45, schrieb Carson Holt:
>>> There should be no new hardware requirement. But there is always a chance
>>> that there is an issue with one of the perl modules being used. I assume
>>> the failure is happening when using maker serially and you are not using
>>> MPI.
>>>
>>> Could you reinstall the following perl modules, and try again. If you are
>>> using CPAN, do a 'force install' to force it to reinstall.
>>>
>>> Modules:
>>> *Storable
>>> *Inline::C
>>> *forks
>>> *forks::shared
>>>
>>> Also try reinstalling the latest version of BioPerl.
>>>
>>> The fact that this is a seg fault suggests that something is
>>> happemning at
>>> the C level (just outside of Perl). Those area all the modules MAKER uses
>>> that will call back to the C level. BioPerl has a fasta indexing module
>>> that is also making calls outside of Perl, and the fact it fails at that
>>> point makes it a suspect.
>>>
>>> Let me know what happens. I can always generate an alternate MAKER
>>> executable for you to run with additional status messages that may help
>>> identify exactly which module is being called right before the failure.
>>>
>>> Thanks,
>>> Carson
>>>
>>>
>>>
>>> On 12-03-07 3:31 AM, "Thomas Hackl"<thomas.hackl at uni-wuerzburg.de
>>> <mailto:thomas.hackl at uni-wuerzburg.de>> wrote:
>>>
>>>> Hello,
>>>>
>>>> we want to use a current release of maker (2.22, 2.23) but the program
>>>> terminates with a seg fault while processing the input FASTA files.
>>>> maker 2.15 , which we have been using for quite some time, runs
>>>> perfectly with identical data and setup.
>>>>
>>>> Please contact me if you need specifics on hardware, OS or anything
>>>> else.
>>>>
>>>> Best regards
>>>> Thomas
>>>>
>>>> --
>>>> Thomas Hackl
>>>> Julius-Maximilians-Universit?t
>>>> Department of Bioinformatics
>>>> 97074 W?rzburg, Germany
>>>> Fon: +49 931 - 31 86883
>>>> Mail: thomas.hackl at uni-wuerzburg.de
>>>> <mailto:thomas.hackl at uni-wuerzburg.de>
>>>>
>>>>
>>>> _______________________________________________
>>>> maker-devel mailing list
>>>> maker-devel at box290.bluehost.com <mailto:maker-devel at box290.bluehost.com>
>>>> http://box290.bluehost.com/mailman/listinfo/maker-devel_yandell-lab.org
>>
>>
>> --
>> Thomas Hackl
>> Julius-Maximilians-Universit?t
>> Department of Bioinformatics
>> 97074 W?rzburg, Germany
>> Fon: +49 931 - 31 86883
>> Mail: thomas.hackl at uni-wuerzburg.de <mailto:thomas.hackl at uni-wuerzburg.de>
>>
>>
>> _______________________________________________
>> maker-devel mailing list
>> maker-devel at box290.bluehost.com <mailto:maker-devel at box290.bluehost.com>
>> http://box290.bluehost.com/mailman/listinfo/maker-devel_yandell-lab.org
>
> Barry Moore
> Research Scientist
> Dept. of Human Genetics
> University of Utah
> Salt Lake City, UT 84112
> --------------------------------------------
> (801) 585-3543
>
>
>
>
>
>
> _______________________________________________
> maker-devel mailing list
> maker-devel at box290.bluehost.com
> http://box290.bluehost.com/mailman/listinfo/maker-devel_yandell-lab.org



From darkbring_05 at yahoo.com  Tue Mar 13 23:21:46 2012
From: darkbring_05 at yahoo.com (asdsa sdadsad)
Date: Tue, 13 Mar 2012 22:21:46 -0700 (PDT)
Subject: [maker-devel] maker gff3 to genbank tbl
Message-ID: <1331702506.55291.YahooMailNeo@web124906.mail.ne1.yahoo.com>

Dear MAKER experts,

i hope that you can share your expertise regarding, conversion of?maker gff3 to genbank tbl or gbk. im trying to produce a working genbank tbl, i tried converting to chado using maker2chado and ?gmodtools genbanksubmit writer. but so far it doesnt end well. most probably due to xml configuration(which im really loss, especially defining the "goldenpath") .is there any other way to produce the tbl from maker output??

thanks :)

Joe Wilders
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From joe.wilders at gmail.com  Tue Mar 13 23:31:48 2012
From: joe.wilders at gmail.com (Joe Wilders)
Date: Tue, 13 Mar 2012 22:31:48 -0700 (PDT)
Subject: [maker-devel] maker gff3 to genbank tbl/gbk
Message-ID: <214404c1-206e-474c-b01c-24b6cde2b91e@y17g2000yqg.googlegroups.com>

Dear MAKER experts,

i hope that you can share your expertise regarding, conversion of
maker gff3 to genbank tbl or gbk. im trying to produce a working
genbank tbl, i tried converting to chado using maker2chado and
gmodtools genbanksubmit writer. but so far it doesnt end well. most
probably due to xml configuration(which im really loss, especially
defining the "goldenpath") .is there any other way to produce the tbl
from maker output?

thanks :)

Joe Wilders



From carsonhh at gmail.com  Sun Mar 18 16:21:03 2012
From: carsonhh at gmail.com (Carson Holt)
Date: Sun, 18 Mar 2012 18:21:03 -0400
Subject: [maker-devel] maker gff3 to genbank tbl/gbk
In-Reply-To: <214404c1-206e-474c-b01c-24b6cde2b91e@y17g2000yqg.googlegroups.com>
Message-ID: <CB8BD6ED.935C%carsonhh@gmail.com>

Try using Apollo.  You can open up GFF3 files and them save them as
GenBank format.  That might be sufficient.

Alternatively.  I've attached a script that can convert SNAP's ZFF format
to GeneBank.  You could then use the maker2zff that comes with MAKER to
convert results to ZFF and then this script to get GenBank format.

Thanks,
Carson

On 12-03-14 1:31 AM, "Joe Wilders" <joe.wilders at gmail.com> wrote:

>Dear MAKER experts,
>
>i hope that you can share your expertise regarding, conversion of
>maker gff3 to genbank tbl or gbk. im trying to produce a working
>genbank tbl, i tried converting to chado using maker2chado and
>gmodtools genbanksubmit writer. but so far it doesnt end well. most
>probably due to xml configuration(which im really loss, especially
>defining the "goldenpath") .is there any other way to produce the tbl
>from maker output?
>
>thanks :)
>
>Joe Wilders
>
>_______________________________________________
>maker-devel mailing list
>maker-devel at box290.bluehost.com
>http://box290.bluehost.com/mailman/listinfo/maker-devel_yandell-lab.org

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From joe.wilders at gmail.com  Sun Mar 18 19:53:37 2012
From: joe.wilders at gmail.com (Joe Wilders)
Date: Mon, 19 Mar 2012 09:53:37 +0800
Subject: [maker-devel] maker gff3 to genbank tbl/gbk
In-Reply-To: <CB8BD6ED.935C%carsonhh@gmail.com>
References: <214404c1-206e-474c-b01c-24b6cde2b91e@y17g2000yqg.googlegroups.com>
	<CB8BD6ED.935C%carsonhh@gmail.com>
Message-ID: <CAGYDdgYv8=qMqsz_Vk0d8Y=iNLYW8siJrB0gEDz+m6Qr40qVpA@mail.gmail.com>

Hi Carson,
Thank you very much for your suggestion, will try that up and let you know.

by the way i did found this in one of the revisions at the svn
http://malachite.genetics.utah.edu/projects/maker/browser/bin/gff3_2_gbk?rev=217
,
i wonder why it gets pulled out on the later revision..


On Mon, Mar 19, 2012 at 6:21 AM, Carson Holt <carsonhh at gmail.com> wrote:

> Try using Apollo.  You can open up GFF3 files and them save them as
> GenBank format.  That might be sufficient.
>
> Alternatively.  I've attached a script that can convert SNAP's ZFF format
> to GeneBank.  You could then use the maker2zff that comes with MAKER to
> convert results to ZFF and then this script to get GenBank format.
>
> Thanks,
> Carson
>
> On 12-03-14 1:31 AM, "Joe Wilders" <joe.wilders at gmail.com> wrote:
>
> >Dear MAKER experts,
> >
> >i hope that you can share your expertise regarding, conversion of
> >maker gff3 to genbank tbl or gbk. im trying to produce a working
> >genbank tbl, i tried converting to chado using maker2chado and
> >gmodtools genbanksubmit writer. but so far it doesnt end well. most
> >probably due to xml configuration(which im really loss, especially
> >defining the "goldenpath") .is there any other way to produce the tbl
> >from maker output?
> >
> >thanks :)
> >
> >Joe Wilders
> >
> >_______________________________________________
> >maker-devel mailing list
> >maker-devel at box290.bluehost.com
> >http://box290.bluehost.com/mailman/listinfo/maker-devel_yandell-lab.org
>
>
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From carsonhh at gmail.com  Sun Mar 18 23:27:00 2012
From: carsonhh at gmail.com (Carson Holt)
Date: Mon, 19 Mar 2012 01:27:00 -0400
Subject: [maker-devel] maker gff3 to genbank tbl/gbk
In-Reply-To: <CAGYDdgYv8=qMqsz_Vk0d8Y=iNLYW8siJrB0gEDz+m6Qr40qVpA@mail.gmail.com>
Message-ID: <CB8C38D3.944D%carsonhh@gmail.com>

A lot of the early code in the SVN suppository, contains one-off scripts.
This one looks a lot like one of my old scripts.  If I remember, I was
trying to get GenBank format for Augustus training.  I started with just a
quick BioPerl based conversion, but the script didn't produce the right
types in GenBank format.  I found another way to do what I wanted (i.e.
someone gave me a different script that worked well enough), and I just
abandoned that script.

Thanks,
Carson


From:  Joe Wilders <joe.wilders at gmail.com>
Date:  Mon, 19 Mar 2012 09:53:37 +0800
To:  Carson Holt <carsonhh at gmail.com>
Cc:  <maker-devel at yandell-lab.org>
Subject:  Re: [maker-devel] maker gff3 to genbank tbl/gbk


Hi Carson,
Thank you very much for your suggestion, will try that up and let you know.

by the way i did found this in one of the revisions at the svn
http://malachite.genetics.utah.edu/projects/maker/browser/bin/gff3_2_gbk?rev
=217 , i wonder why it gets pulled out on the later revision..


On Mon, Mar 19, 2012 at 6:21 AM, Carson Holt <carsonhh at gmail.com> wrote:
> Try using Apollo.  You can open up GFF3 files and them save them as
> GenBank format.  That might be sufficient.
> 
> Alternatively.  I've attached a script that can convert SNAP's ZFF format
> to GeneBank.  You could then use the maker2zff that comes with MAKER to
> convert results to ZFF and then this script to get GenBank format.
> 
> Thanks,
> Carson
> 
> On 12-03-14 1:31 AM, "Joe Wilders" <joe.wilders at gmail.com> wrote:
> 
>> >Dear MAKER experts,
>> >
>> >i hope that you can share your expertise regarding, conversion of
>> >maker gff3 to genbank tbl or gbk. im trying to produce a working
>> >genbank tbl, i tried converting to chado using maker2chado and
>> >gmodtools genbanksubmit writer. but so far it doesnt end well. most
>> >probably due to xml configuration(which im really loss, especially
>> >defining the "goldenpath") .is there any other way to produce the tbl
>> >from maker output?
>> >
>> >thanks :)
>> >
>> >Joe Wilders
>> >
>> >_______________________________________________
>> >maker-devel mailing list
>> >maker-devel at box290.bluehost.com
>> >http://box290.bluehost.com/mailman/listinfo/maker-devel_yandell-lab.org
> 



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From dinatal at uwindsor.ca  Tue Mar 20 10:55:34 2012
From: dinatal at uwindsor.ca (claudia)
Date: Tue, 20 Mar 2012 12:55:34 -0400
Subject: [maker-devel] loading scaffold features into chado
Message-ID: <4F68B686.6050800@uwindsor.ca>

To whom it may concern,

I have 2 concerns, the first is:  regarding representing scaffold 
features in chado and gbrowse. I noticed that the Sequence ontology uses 
the term supercontig and so if my assembly generated scaffolds entitled 
"scaffold" should I change the names to supercontigs so that chado 
recognizes the terms?

Corresponding to my first question, Maker does not know that the contigs 
are actually scaffold/supercontigs when annotating and so Maker will 
still call the "type" feature or column 3 in the GFF3, a 'contig', how 
can Maker be implemented to change this naming convention before 
annotation, or after?

Consequently, I am having problems pulling up gene features in Gbrowse 
when doing a generic gene search, and I must provide the maker generated 
unique-gene_id in the gbrowse search bar or the known sequence id i.e 
'scaffold001', which is not useful for someone who does not have this 
information.
---- I do not have this problem when my seq_id, and 'type' feature id 
match in the true case of 'contigs'. I can do a generic gene search in 
gbrowse with the term 'maker' and gbrowse will provide me all the 
associated maker generated gene calls.

Thank you for any guidance resolving these concerns,
Claudia



-- 
Claudia DiNatale
Master's Candidate
The Crosby Lab
University of Windsor
519-253-3000 ext: 4755




From carsonhh at gmail.com  Tue Mar 20 11:13:35 2012
From: carsonhh at gmail.com (Carson Holt)
Date: Tue, 20 Mar 2012 13:13:35 -0400
Subject: [maker-devel] loading scaffold features into chado
In-Reply-To: <4F68B686.6050800@uwindsor.ca>
Message-ID: <CB8E2F50.97C7%carsonhh@gmail.com>


>I have 2 concerns, the first is:  regarding representing scaffold
>features in chado and gbrowse. I noticed that the Sequence ontology uses
>the term supercontig and so if my assembly generated scaffolds entitled
>"scaffold" should I change the names to supercontigs so that chado
>recognizes the terms?

Yes.  You must use valid SO terms.  It is a requirement of GFF3, and Chado
will enforce this requirement on loading a GFF3 file (note Chado will even
go as far as to check the validity of the Ontology_term= attribute in GFF3
if you use it).  You can decide to use contig or supercontig as your
sequence feature.  It doesn?t really matter unless you are placing both
into the database as separate features (i.e. You have a supercontig as the
parent feature and then you enter contigs individually as children of the
supercontig).


>
>Corresponding to my first question, Maker does not know that the contigs
>are actually scaffold/supercontigs when annotating and so Maker will
>still call the "type" feature or column 3 in the GFF3, a 'contig', how
>can Maker be implemented to change this naming convention before
>annotation, or after?

Not really important unless you plan on making contigs children of the
supercontig.  But you can always do a search and replace. -->
cat file.gff | perl -ane 's/\tcontig\t/\tsupercontig\t/s; print $_' >
new_file.gff


>
>Consequently, I am having problems pulling up gene features in Gbrowse
>when doing a generic gene search, and I must provide the maker generated
>unique-gene_id in the gbrowse search bar or the known sequence id i.e
>'scaffold001', which is not useful for someone who does not have this
>information.
>---- I do not have this problem when my seq_id, and 'type' feature id
>match in the true case of 'contigs'. I can do a generic gene search in
>gbrowse with the term 'maker' and gbrowse will provide me all the
>associated maker generated gene calls.

See "Adjusting GBrowse Name Searches" in the GBrowse tutorial -->
http://gmod.org/gbrowse2/tutorial/tutorial.html#naming


Thanks,
Carson











>
>Thank you for any guidance resolving these concerns,
>Claudia
>
>
>
>-- 
>Claudia DiNatale
>Master's Candidate
>The Crosby Lab
>University of Windsor
>519-253-3000 ext: 4755
>
>
>_______________________________________________
>maker-devel mailing list
>maker-devel at box290.bluehost.com
>http://box290.bluehost.com/mailman/listinfo/maker-devel_yandell-lab.org





From scott at scottcain.net  Tue Mar 20 11:25:04 2012
From: scott at scottcain.net (Scott Cain)
Date: Tue, 20 Mar 2012 13:25:04 -0400
Subject: [maker-devel] loading scaffold features into chado
In-Reply-To: <CB8E2F50.97C7%carsonhh@gmail.com>
References: <4F68B686.6050800@uwindsor.ca> <CB8E2F50.97C7%carsonhh@gmail.com>
Message-ID: <CA+JTaoy00sX+3Pdyrw=Apus09Lppg9YNQsr8k4uoYXHmK24Euw@mail.gmail.com>

Hi Claudia,

I agree with everything that Carson wrote, except about name
searching--it's a little trickier in Chado.  What you probably want to
do is implement full text searching.  See:

  http://gmod.org/wiki/Chado_Full_Text_Search

for more information on setting it up and maintaining it.

Scott


On Tue, Mar 20, 2012 at 1:13 PM, Carson Holt <carsonhh at gmail.com> wrote:
>
>>I have 2 concerns, the first is: ?regarding representing scaffold
>>features in chado and gbrowse. I noticed that the Sequence ontology uses
>>the term supercontig and so if my assembly generated scaffolds entitled
>>"scaffold" should I change the names to supercontigs so that chado
>>recognizes the terms?
>
> Yes. ?You must use valid SO terms. ?It is a requirement of GFF3, and Chado
> will enforce this requirement on loading a GFF3 file (note Chado will even
> go as far as to check the validity of the Ontology_term= attribute in GFF3
> if you use it). ?You can decide to use contig or supercontig as your
> sequence feature. ?It doesn?t really matter unless you are placing both
> into the database as separate features (i.e. You have a supercontig as the
> parent feature and then you enter contigs individually as children of the
> supercontig).
>
>
>>
>>Corresponding to my first question, Maker does not know that the contigs
>>are actually scaffold/supercontigs when annotating and so Maker will
>>still call the "type" feature or column 3 in the GFF3, a 'contig', how
>>can Maker be implemented to change this naming convention before
>>annotation, or after?
>
> Not really important unless you plan on making contigs children of the
> supercontig. ?But you can always do a search and replace. -->
> cat file.gff | perl -ane 's/\tcontig\t/\tsupercontig\t/s; print $_' >
> new_file.gff
>
>
>>
>>Consequently, I am having problems pulling up gene features in Gbrowse
>>when doing a generic gene search, and I must provide the maker generated
>>unique-gene_id in the gbrowse search bar or the known sequence id i.e
>>'scaffold001', which is not useful for someone who does not have this
>>information.
>>---- I do not have this problem when my seq_id, and 'type' feature id
>>match in the true case of 'contigs'. I can do a generic gene search in
>>gbrowse with the term 'maker' and gbrowse will provide me all the
>>associated maker generated gene calls.
>
> See "Adjusting GBrowse Name Searches" in the GBrowse tutorial -->
> http://gmod.org/gbrowse2/tutorial/tutorial.html#naming
>
>
> Thanks,
> Carson
>
>
>
>
>
>
>
>
>
>
>
>>
>>Thank you for any guidance resolving these concerns,
>>Claudia
>>
>>
>>
>>--
>>Claudia DiNatale
>>Master's Candidate
>>The Crosby Lab
>>University of Windsor
>>519-253-3000 ext: 4755
>>
>>
>>_______________________________________________
>>maker-devel mailing list
>>maker-devel at box290.bluehost.com
>>http://box290.bluehost.com/mailman/listinfo/maker-devel_yandell-lab.org
>
>
>
> _______________________________________________
> maker-devel mailing list
> maker-devel at box290.bluehost.com
> http://box290.bluehost.com/mailman/listinfo/maker-devel_yandell-lab.org



-- 
------------------------------------------------------------------------
Scott Cain, Ph. D.? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ?? scott at scottcain dot net
GMOD Coordinator (http://gmod.org/)? ? ? ? ? ? ? ? ? ?? 216-392-3087
Ontario Institute for Cancer Research



From carsonhh at gmail.com  Tue Mar 20 11:27:10 2012
From: carsonhh at gmail.com (Carson Holt)
Date: Tue, 20 Mar 2012 13:27:10 -0400
Subject: [maker-devel] loading scaffold features into chado
In-Reply-To: <CA+JTaoy00sX+3Pdyrw=Apus09Lppg9YNQsr8k4uoYXHmK24Euw@mail.gmail.com>
Message-ID: <CB8E3600.97EA%carsonhh@gmail.com>

Yes. thank you Scott.  My answer would work for GBrowse NOT Chado :-)

--Carson



On 12-03-20 1:25 PM, "Scott Cain" <scott at scottcain.net> wrote:

>Hi Claudia,
>
>I agree with everything that Carson wrote, except about name
>searching--it's a little trickier in Chado.  What you probably want to
>do is implement full text searching.  See:
>
>  http://gmod.org/wiki/Chado_Full_Text_Search
>
>for more information on setting it up and maintaining it.
>
>Scott
>
>
>On Tue, Mar 20, 2012 at 1:13 PM, Carson Holt <carsonhh at gmail.com> wrote:
>>
>>>I have 2 concerns, the first is:  regarding representing scaffold
>>>features in chado and gbrowse. I noticed that the Sequence ontology uses
>>>the term supercontig and so if my assembly generated scaffolds entitled
>>>"scaffold" should I change the names to supercontigs so that chado
>>>recognizes the terms?
>>
>> Yes.  You must use valid SO terms.  It is a requirement of GFF3, and
>>Chado
>> will enforce this requirement on loading a GFF3 file (note Chado will
>>even
>> go as far as to check the validity of the Ontology_term= attribute in
>>GFF3
>> if you use it).  You can decide to use contig or supercontig as your
>> sequence feature.  It doesn?t really matter unless you are placing both
>> into the database as separate features (i.e. You have a supercontig as
>>the
>> parent feature and then you enter contigs individually as children of
>>the
>> supercontig).
>>
>>
>>>
>>>Corresponding to my first question, Maker does not know that the contigs
>>>are actually scaffold/supercontigs when annotating and so Maker will
>>>still call the "type" feature or column 3 in the GFF3, a 'contig', how
>>>can Maker be implemented to change this naming convention before
>>>annotation, or after?
>>
>> Not really important unless you plan on making contigs children of the
>> supercontig.  But you can always do a search and replace. -->
>> cat file.gff | perl -ane 's/\tcontig\t/\tsupercontig\t/s; print $_' >
>> new_file.gff
>>
>>
>>>
>>>Consequently, I am having problems pulling up gene features in Gbrowse
>>>when doing a generic gene search, and I must provide the maker generated
>>>unique-gene_id in the gbrowse search bar or the known sequence id i.e
>>>'scaffold001', which is not useful for someone who does not have this
>>>information.
>>>---- I do not have this problem when my seq_id, and 'type' feature id
>>>match in the true case of 'contigs'. I can do a generic gene search in
>>>gbrowse with the term 'maker' and gbrowse will provide me all the
>>>associated maker generated gene calls.
>>
>> See "Adjusting GBrowse Name Searches" in the GBrowse tutorial -->
>> http://gmod.org/gbrowse2/tutorial/tutorial.html#naming
>>
>>
>> Thanks,
>> Carson
>>
>>
>>
>>
>>
>>
>>
>>
>>
>>
>>
>>>
>>>Thank you for any guidance resolving these concerns,
>>>Claudia
>>>
>>>
>>>
>>>--
>>>Claudia DiNatale
>>>Master's Candidate
>>>The Crosby Lab
>>>University of Windsor
>>>519-253-3000 ext: 4755
>>>
>>>
>>>_______________________________________________
>>>maker-devel mailing list
>>>maker-devel at box290.bluehost.com
>>>http://box290.bluehost.com/mailman/listinfo/maker-devel_yandell-lab.org
>>
>>
>>
>> _______________________________________________
>> maker-devel mailing list
>> maker-devel at box290.bluehost.com
>> http://box290.bluehost.com/mailman/listinfo/maker-devel_yandell-lab.org
>
>
>
>-- 
>------------------------------------------------------------------------
>Scott Cain, Ph. D.                                   scott at scottcain
>dot net
>GMOD Coordinator (http://gmod.org/)                     216-392-3087
>Ontario Institute for Cancer Research





From dinatal at uwindsor.ca  Tue Mar 20 12:03:27 2012
From: dinatal at uwindsor.ca (claudia)
Date: Tue, 20 Mar 2012 14:03:27 -0400
Subject: [maker-devel] loading scaffold features into chado
In-Reply-To: <CA+JTaoy00sX+3Pdyrw=Apus09Lppg9YNQsr8k4uoYXHmK24Euw@mail.gmail.com>
References: <4F68B686.6050800@uwindsor.ca> <CB8E2F50.97C7%carsonhh@gmail.com>
	<CA+JTaoy00sX+3Pdyrw=Apus09Lppg9YNQsr8k4uoYXHmK24Euw@mail.gmail.com>
Message-ID: <4F68C66F.2010902@uwindsor.ca>

Hi,

  I have enabled full text searching and I still have this problem, 
another reason for concern... So I wondered if in fact I changed all the 
ID's in the GFF3 file to supercontigs, then perhaps Chado would better 
link all the terms, annotations, and fasta files.... Although, i realize 
that the seq_id ( column 1) shouldn't need to be specific since the 
'type' term would take care of designating the feature type, no?

Claudia



On 20/03/2012 1:25 PM, Scott Cain wrote:
> Hi Claudia,
>
> I agree with everything that Carson wrote, except about name
> searching--it's a little trickier in Chado.  What you probably want to
> do is implement full text searching.  See:
>
>    http://gmod.org/wiki/Chado_Full_Text_Search
>
> for more information on setting it up and maintaining it.
>
> Scott
>
>
> On Tue, Mar 20, 2012 at 1:13 PM, Carson Holt<carsonhh at gmail.com>  wrote:
>>> I have 2 concerns, the first is:  regarding representing scaffold
>>> features in chado and gbrowse. I noticed that the Sequence ontology uses
>>> the term supercontig and so if my assembly generated scaffolds entitled
>>> "scaffold" should I change the names to supercontigs so that chado
>>> recognizes the terms?
>> Yes.  You must use valid SO terms.  It is a requirement of GFF3, and Chado
>> will enforce this requirement on loading a GFF3 file (note Chado will even
>> go as far as to check the validity of the Ontology_term= attribute in GFF3
>> if you use it).  You can decide to use contig or supercontig as your
>> sequence feature.  It doesn?t really matter unless you are placing both
>> into the database as separate features (i.e. You have a supercontig as the
>> parent feature and then you enter contigs individually as children of the
>> supercontig).
>>
>>
>>> Corresponding to my first question, Maker does not know that the contigs
>>> are actually scaffold/supercontigs when annotating and so Maker will
>>> still call the "type" feature or column 3 in the GFF3, a 'contig', how
>>> can Maker be implemented to change this naming convention before
>>> annotation, or after?
>> Not really important unless you plan on making contigs children of the
>> supercontig.  But you can always do a search and replace. -->
>> cat file.gff | perl -ane 's/\tcontig\t/\tsupercontig\t/s; print $_'>
>> new_file.gff
>>
>>
>>> Consequently, I am having problems pulling up gene features in Gbrowse
>>> when doing a generic gene search, and I must provide the maker generated
>>> unique-gene_id in the gbrowse search bar or the known sequence id i.e
>>> 'scaffold001', which is not useful for someone who does not have this
>>> information.
>>> ---- I do not have this problem when my seq_id, and 'type' feature id
>>> match in the true case of 'contigs'. I can do a generic gene search in
>>> gbrowse with the term 'maker' and gbrowse will provide me all the
>>> associated maker generated gene calls.
>> See "Adjusting GBrowse Name Searches" in the GBrowse tutorial -->
>> http://gmod.org/gbrowse2/tutorial/tutorial.html#naming
>>
>>
>> Thanks,
>> Carson
>>
>>
>>
>>
>>
>>
>>
>>
>>
>>
>>
>>> Thank you for any guidance resolving these concerns,
>>> Claudia
>>>
>>>
>>>
>>> --
>>> Claudia DiNatale
>>> Master's Candidate
>>> The Crosby Lab
>>> University of Windsor
>>> 519-253-3000 ext: 4755
>>>
>>>
>>> _______________________________________________
>>> maker-devel mailing list
>>> maker-devel at box290.bluehost.com
>>> http://box290.bluehost.com/mailman/listinfo/maker-devel_yandell-lab.org
>>
>>
>> _______________________________________________
>> maker-devel mailing list
>> maker-devel at box290.bluehost.com
>> http://box290.bluehost.com/mailman/listinfo/maker-devel_yandell-lab.org
>
>


-- 
Claudia DiNatale
Master's Candidate
The Crosby Lab
University of Windsor
519-253-3000 ext: 4755




From scott at scottcain.net  Tue Mar 20 13:50:55 2012
From: scott at scottcain.net (Scott Cain)
Date: Tue, 20 Mar 2012 15:50:55 -0400
Subject: [maker-devel] loading scaffold features into chado
In-Reply-To: <4F68C66F.2010902@uwindsor.ca>
References: <4F68B686.6050800@uwindsor.ca> <CB8E2F50.97C7%carsonhh@gmail.com>
	<CA+JTaoy00sX+3Pdyrw=Apus09Lppg9YNQsr8k4uoYXHmK24Euw@mail.gmail.com>
	<4F68C66F.2010902@uwindsor.ca>
Message-ID: <FFACED63-40D9-4810-9927-0E4984BA8465@scottcain.net>

Hi Claudia,

Can you post a sample of the gff that shows what you are looking for and not finding?

Scott


Sent from my iPad

On Mar 20, 2012, at 2:03 PM, claudia <dinatal at uwindsor.ca> wrote:

> Hi,
> 
> I have enabled full text searching and I still have this problem, another reason for concern... So I wondered if in fact I changed all the ID's in the GFF3 file to supercontigs, then perhaps Chado would better link all the terms, annotations, and fasta files.... Although, i realize that the seq_id ( column 1) shouldn't need to be specific since the 'type' term would take care of designating the feature type, no?
> 
> Claudia
> 
> 
> 
> On 20/03/2012 1:25 PM, Scott Cain wrote:
>> Hi Claudia,
>> 
>> I agree with everything that Carson wrote, except about name
>> searching--it's a little trickier in Chado.  What you probably want to
>> do is implement full text searching.  See:
>> 
>>   http://gmod.org/wiki/Chado_Full_Text_Search
>> 
>> for more information on setting it up and maintaining it.
>> 
>> Scott
>> 
>> 
>> On Tue, Mar 20, 2012 at 1:13 PM, Carson Holt<carsonhh at gmail.com>  wrote:
>>>> I have 2 concerns, the first is:  regarding representing scaffold
>>>> features in chado and gbrowse. I noticed that the Sequence ontology uses
>>>> the term supercontig and so if my assembly generated scaffolds entitled
>>>> "scaffold" should I change the names to supercontigs so that chado
>>>> recognizes the terms?
>>> Yes.  You must use valid SO terms.  It is a requirement of GFF3, and Chado
>>> will enforce this requirement on loading a GFF3 file (note Chado will even
>>> go as far as to check the validity of the Ontology_term= attribute in GFF3
>>> if you use it).  You can decide to use contig or supercontig as your
>>> sequence feature.  It doesn?t really matter unless you are placing both
>>> into the database as separate features (i.e. You have a supercontig as the
>>> parent feature and then you enter contigs individually as children of the
>>> supercontig).
>>> 
>>> 
>>>> Corresponding to my first question, Maker does not know that the contigs
>>>> are actually scaffold/supercontigs when annotating and so Maker will
>>>> still call the "type" feature or column 3 in the GFF3, a 'contig', how
>>>> can Maker be implemented to change this naming convention before
>>>> annotation, or after?
>>> Not really important unless you plan on making contigs children of the
>>> supercontig.  But you can always do a search and replace. -->
>>> cat file.gff | perl -ane 's/\tcontig\t/\tsupercontig\t/s; print $_'>
>>> new_file.gff
>>> 
>>> 
>>>> Consequently, I am having problems pulling up gene features in Gbrowse
>>>> when doing a generic gene search, and I must provide the maker generated
>>>> unique-gene_id in the gbrowse search bar or the known sequence id i.e
>>>> 'scaffold001', which is not useful for someone who does not have this
>>>> information.
>>>> ---- I do not have this problem when my seq_id, and 'type' feature id
>>>> match in the true case of 'contigs'. I can do a generic gene search in
>>>> gbrowse with the term 'maker' and gbrowse will provide me all the
>>>> associated maker generated gene calls.
>>> See "Adjusting GBrowse Name Searches" in the GBrowse tutorial -->
>>> http://gmod.org/gbrowse2/tutorial/tutorial.html#naming
>>> 
>>> 
>>> Thanks,
>>> Carson
>>> 
>>> 
>>> 
>>> 
>>> 
>>> 
>>> 
>>> 
>>> 
>>> 
>>> 
>>>> Thank you for any guidance resolving these concerns,
>>>> Claudia
>>>> 
>>>> 
>>>> 
>>>> --
>>>> Claudia DiNatale
>>>> Master's Candidate
>>>> The Crosby Lab
>>>> University of Windsor
>>>> 519-253-3000 ext: 4755
>>>> 
>>>> 
>>>> _______________________________________________
>>>> maker-devel mailing list
>>>> maker-devel at box290.bluehost.com
>>>> http://box290.bluehost.com/mailman/listinfo/maker-devel_yandell-lab.org
>>> 
>>> 
>>> _______________________________________________
>>> maker-devel mailing list
>>> maker-devel at box290.bluehost.com
>>> http://box290.bluehost.com/mailman/listinfo/maker-devel_yandell-lab.org
>> 
>> 
> 
> 
> -- 
> Claudia DiNatale
> Master's Candidate
> The Crosby Lab
> University of Windsor
> 519-253-3000 ext: 4755
> 



From thomas.hackl at uni-wuerzburg.de  Tue Mar 20 12:16:03 2012
From: thomas.hackl at uni-wuerzburg.de (Thomas Hackl)
Date: Tue, 20 Mar 2012 19:16:03 +0100
Subject: [maker-devel] maker 2.22/2.23: Segmentation fault while
 processing FASTA input
In-Reply-To: <CB8CD562.94D0%carsonhh@gmail.com>
References: <CB8CD562.94D0%carsonhh@gmail.com>
Message-ID: <4F68C963.3040108@uni-wuerzburg.de>

Hi,

I installed and ran the debug version of maker. Without -debug it 
results in the expected segmentation fault. With -debug it paradoxically 
finishes without the error.

I screened the debug log anyway but could not find anything that helped 
me to localize the problem. I attached a condensed version (sort | uniq) 
of the log.
Any ideas are appreciated.

Regards
Thomas



Am 19.03.2012 17:24, schrieb Carson Holt:
> Ok.  I finished the special debug version over the weekend.  Run with
> -debug set as a command line flag.  Capture and return the STDERR on
> failure.  It will list all modules used, the versions, and when they are
> called so we can see what happens right before failure.
>
> http://yandell-lab.org/research/maker_debug.tgz
>
>
> Thanks,
> Carson
>
>
>
> On 12-03-14 1:57 AM, "Felix Bemm"<felix.bemm at uni-wuerzburg.de>  wrote:
>
>> Hi,
>>
>> Thomas and I are colleagues and dealing with the same problem here. I
>> wrote some test code that forced the indexing and it work fine. We are
>> using most of the bioperl seqio and db modules in combination with other
>> tools and don't experience the same problem there at the moment.
>>
>> Regards
>> Felix
>>
>> Am 13.03.2012 22:37, schrieb Barry Moore:
>>> You might also try a short perl script outside of MAKER to exercise
>>> Bio::DB::Fasta (which I believe is the module MAKER uses for Fasta
>>> indexing - correct Carson?).
>>>
>>> Something like this should work to force indexing:
>>>
>>> useBio::DB::Fasta;
>>> my $db = Bio::DB::Fasta->new('/path/to/fasta/files');
>>> my$seq=$db->seq($seqid, $start, $end);
>>>
>>> Point it at your fasta directory or file.
>>>
>>> B
>>>
>>> On Mar 13, 2012, at 3:41 AM, Thomas Hackl wrote:
>>>
>>>> Hello,
>>>>
>>>> We reinstalled the packages you suggested
>>>>
>>>> forks is up to date (0.34).
>>>> forks::shared is up to date (0.34).
>>>> Inline::C is up to date (0.50).
>>>> Storable is up to date (2.30).
>>>>
>>>> as well as BioPerl.
>>>>
>>>> The problem is still the same.
>>>>
>>>> With MPI it terminates with this message:
>>>>
>>>> STATUS: Parsing control files...
>>>> STATUS: Processing and indexing input FASTA files...
>>>>
>>>> ========================================================================
>>>> =============
>>>>
>>>>
>>>> = BAD TERMINATION OF ONE OF YOUR APPLICATION PROCESSES
>>>> = EXIT CODE: 11
>>>> = CLEANING UP REMAINING PROCESSES
>>>> = YOU CAN IGNORE THE BELOW CLEANUP MESSAGES
>>>>
>>>> ========================================================================
>>>> =============
>>>>
>>>> APPLICATION TERMINATED WITH THE EXIT STRING: Segmentation fault
>>>> (signal 11)
>>>>
>>>> which I presume is also the same problem.
>>>>
>>>> I am with you that the error is caused somewhere on the C level. If
>>>> the indexing step
>>>> is handled by non-maker modules exclusively, than the fact that the
>>>> 2.15 version works,
>>>> suggests that you are using different modules/methods in the current
>>>> releases?
>>>>
>>>> In any case, I think a version with verbose status messages might help
>>>> to localize the
>>>> source of the problem.
>>>>
>>>> Regards
>>>> Thomas
>>>>
>>>> Am 07.03.2012 23:45, schrieb Carson Holt:
>>>>> There should be no new hardware requirement. But there is always a
>>>>> chance
>>>>> that there is an issue with one of the perl modules being used. I
>>>>> assume
>>>>> the failure is happening when using maker serially and you are not
>>>>> using
>>>>> MPI.
>>>>>
>>>>> Could you reinstall the following perl modules, and try again. If you
>>>>> are
>>>>> using CPAN, do a 'force install' to force it to reinstall.
>>>>>
>>>>> Modules:
>>>>> *Storable
>>>>> *Inline::C
>>>>> *forks
>>>>> *forks::shared
>>>>>
>>>>> Also try reinstalling the latest version of BioPerl.
>>>>>
>>>>> The fact that this is a seg fault suggests that something is
>>>>> happemning at
>>>>> the C level (just outside of Perl). Those area all the modules MAKER
>>>>> uses
>>>>> that will call back to the C level. BioPerl has a fasta indexing
>>>>> module
>>>>> that is also making calls outside of Perl, and the fact it fails at
>>>>> that
>>>>> point makes it a suspect.
>>>>>
>>>>> Let me know what happens. I can always generate an alternate MAKER
>>>>> executable for you to run with additional status messages that may
>>>>> help
>>>>> identify exactly which module is being called right before the
>>>>> failure.
>>>>>
>>>>> Thanks,
>>>>> Carson
>>>>>
>>>>>
>>>>>
>>>>> On 12-03-07 3:31 AM, "Thomas Hackl"<thomas.hackl at uni-wuerzburg.de
>>>>> <mailto:thomas.hackl at uni-wuerzburg.de>>  wrote:
>>>>>
>>>>>> Hello,
>>>>>>
>>>>>> we want to use a current release of maker (2.22, 2.23) but the
>>>>>> program
>>>>>> terminates with a seg fault while processing the input FASTA files.
>>>>>> maker 2.15 , which we have been using for quite some time, runs
>>>>>> perfectly with identical data and setup.
>>>>>>
>>>>>> Please contact me if you need specifics on hardware, OS or anything
>>>>>> else.
>>>>>>
>>>>>> Best regards
>>>>>> Thomas
>>>>>>
>>>>>> --
>>>>>> Thomas Hackl
>>>>>> Julius-Maximilians-Universit?t
>>>>>> Department of Bioinformatics
>>>>>> 97074 W?rzburg, Germany
>>>>>> Fon: +49 931 - 31 86883
>>>>>> Mail: thomas.hackl at uni-wuerzburg.de
>>>>>> <mailto:thomas.hackl at uni-wuerzburg.de>
>>>>>>
>>>>>>
>>>>>> _______________________________________________
>>>>>> maker-devel mailing list
>>>>>> maker-devel at box290.bluehost.com
>>>>>> <mailto:maker-devel at box290.bluehost.com>
>>>>>>
>>>>>> http://box290.bluehost.com/mailman/listinfo/maker-devel_yandell-lab.or
>>>>>> g
>>>>
>>>> --
>>>> Thomas Hackl
>>>> Julius-Maximilians-Universit?t
>>>> Department of Bioinformatics
>>>> 97074 W?rzburg, Germany
>>>> Fon: +49 931 - 31 86883
>>>> Mail: thomas.hackl at uni-wuerzburg.de
>>>> <mailto:thomas.hackl at uni-wuerzburg.de>
>>>>
>>>>
>>>> _______________________________________________
>>>> maker-devel mailing list
>>>> maker-devel at box290.bluehost.com
>>>> <mailto:maker-devel at box290.bluehost.com>
>>>> http://box290.bluehost.com/mailman/listinfo/maker-devel_yandell-lab.org
>>> Barry Moore
>>> Research Scientist
>>> Dept. of Human Genetics
>>> University of Utah
>>> Salt Lake City, UT 84112
>>> --------------------------------------------
>>> (801) 585-3543
>>>
>>>
>>>
>>>
>>>
>>>
>>> _______________________________________________
>>> maker-devel mailing list
>>> maker-devel at box290.bluehost.com
>>> http://box290.bluehost.com/mailman/listinfo/maker-devel_yandell-lab.org
>> _______________________________________________
>> maker-devel mailing list
>> maker-devel at box290.bluehost.com
>> http://box290.bluehost.com/mailman/listinfo/maker-devel_yandell-lab.org

-- 
Thomas Hackl
Julius-Maximilians-Universit?t
Department of Bioinformatics
97074 W?rzburg, Germany
Fon:  +49 931 - 31 86883
Mail: thomas.hackl at uni-wuerzburg.de

-------------- next part --------------

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	0.01	Bio::Search::Hit::PhatHit::Base	/storage/tmp/software/maker-2.24-debug/bin/../lib/Bio/Search/Hit/PhatHit/Base.pm
	0.01	Bio::Search::Hit::PhatHit::blastn	/storage/tmp/software/maker-2.24-debug/bin/../lib/Bio/Search/Hit/PhatHit/blastn.pm
	0.01	Bio::Search::Hit::PhatHit::blastx	/storage/tmp/software/maker-2.24-debug/bin/../lib/Bio/Search/Hit/PhatHit/blastx.pm
	0.01	Bio::Search::Hit::PhatHit::tblastx	/storage/tmp/software/maker-2.24-debug/bin/../lib/Bio/Search/Hit/PhatHit/tblastx.pm
	0.01	Bio::Search::HSP::PhatHSP::Base	/storage/tmp/software/maker-2.24-debug/bin/../lib/Bio/Search/HSP/PhatHSP/Base.pm
	0.01	Bio::Search::HSP::PhatHSP::blastn	/storage/tmp/software/maker-2.24-debug/bin/../lib/Bio/Search/HSP/PhatHSP/blastn.pm
	0.01	Bio::Search::HSP::PhatHSP::blastx	/storage/tmp/software/maker-2.24-debug/bin/../lib/Bio/Search/HSP/PhatHSP/blastx.pm
	0.01	Bio::Search::HSP::PhatHSP::tblastx	/storage/tmp/software/maker-2.24-debug/bin/../lib/Bio/Search/HSP/PhatHSP/tblastx.pm
	0.01	CGL::Annotation::Feature::Contig	/storage/tmp/software/maker-2.24-debug/bin/../lib/CGL/Annotation/Feature/Contig.pm
	0.01	CGL::Annotation::Feature::Exon	/storage/tmp/software/maker-2.24-debug/bin/../lib/CGL/Annotation/Feature/Exon.pm
	0.01	CGL::Annotation::Feature::Gene	/storage/tmp/software/maker-2.24-debug/bin/../lib/CGL/Annotation/Feature/Gene.pm
	0.01	CGL::Annotation::Feature::Intron	/storage/tmp/software/maker-2.24-debug/bin/../lib/CGL/Annotation/Feature/Intron.pm
	0.01	CGL::Annotation::FeatureLocation	/storage/tmp/software/maker-2.24-debug/bin/../lib/CGL/Annotation/FeatureLocation.pm
	0.01	CGL::Annotation::Feature::Protein	/storage/tmp/software/maker-2.24-debug/bin/../lib/CGL/Annotation/Feature/Protein.pm
	0.01	CGL::Annotation::FeatureRelationship	/storage/tmp/software/maker-2.24-debug/bin/../lib/CGL/Annotation/FeatureRelationship.pm
	0.01	CGL::Annotation::Feature::Sequence_variant	/storage/tmp/software/maker-2.24-debug/bin/../lib/CGL/Annotation/Feature/Sequence_variant.pm
	0.01	CGL::Annotation::Feature	/storage/tmp/software/maker-2.24-debug/bin/../lib/CGL/Annotation/Feature.pm
	0.01	CGL::Annotation::Feature::Transcript	/storage/tmp/software/maker-2.24-debug/bin/../lib/CGL/Annotation/Feature/Transcript.pm
	0.01	CGL::Annotation::Iterator	/storage/tmp/software/maker-2.24-debug/bin/../lib/CGL/Annotation/Iterator.pm
	0.01	CGL::Annotation	/storage/tmp/software/maker-2.24-debug/bin/../lib/CGL/Annotation.pm
	0.01	CGL::Annotation::Trace	/storage/tmp/software/maker-2.24-debug/bin/../lib/CGL/Annotation/Trace.pm
	0.01	CGL::Clone	/storage/tmp/software/maker-2.24-debug/bin/../lib/CGL/Clone.pm
	0.01	CGL::Ontology::NodeRelationship	/storage/tmp/software/maker-2.24-debug/bin/../lib/CGL/Ontology/NodeRelationship.pm
	0.01	CGL::Ontology::Node	/storage/tmp/software/maker-2.24-debug/bin/../lib/CGL/Ontology/Node.pm
	0.01	CGL::Ontology::Ontology	/storage/tmp/software/maker-2.24-debug/bin/../lib/CGL/Ontology/Ontology.pm
	0.01	CGL::Ontology::Parser::OBO	/storage/tmp/software/maker-2.24-debug/bin/../lib/CGL/Ontology/Parser/OBO.pm
	0.01	CGL::Ontology::SO	/storage/tmp/software/maker-2.24-debug/bin/../lib/CGL/Ontology/SO.pm
	0.01	CGL::Ontology::Trace	/storage/tmp/software/maker-2.24-debug/bin/../lib/CGL/Ontology/Trace.pm
	0.01	CGL::Revcomp	/storage/tmp/software/maker-2.24-debug/bin/../lib/CGL/Revcomp.pm
	0.01	CGL::TranslationMachine	/storage/tmp/software/maker-2.24-debug/bin/../lib/CGL/TranslationMachine.pm
	0.01	Datastore::MD5	/storage/tmp/software/maker-2.24-debug/bin/../lib/Datastore/MD5.pm
	0.01	Parallel::Application::MPI	/storage/tmp/software/maker-2.24-debug/bin/../perl/lib/Parallel/Application/MPI.pm
	0.02	Perl::Unsafe::Signals	/storage/tmp/software/perl-5.14.1/lib/site_perl/5.14.1/x86_64-linux-thread-multi/Perl/Unsafe/Signals.pm
	0.02	Proc::ProcessTable::Process	/storage/tmp/software/perl-5.14.1/lib/site_perl/5.14.1/x86_64-linux-thread-multi/Proc/ProcessTable/Process.pm
	0.04	Acme::Damn	/storage/tmp/software/perl-5.14.1/lib/site_perl/5.14.1/x86_64-linux-thread-multi/Acme/Damn.pm
	0.11	Datastore::Base	/storage/tmp/software/maker-2.24-debug/bin/../lib/Datastore/Base.pm
	0.13	XSLoader	/storage/tmp/software/perl-5.14.1/lib/5.14.1/XSLoader.pm
	0.14	attributes	/storage/tmp/software/perl-5.14.1/lib/5.14.1/x86_64-linux-thread-multi/attributes.pm
	0.15	Sys::SigAction	/storage/tmp/software/perl-5.14.1/lib/site_perl/5.14.1/Sys/SigAction.pm
	0.17015	Error	/storage/tmp/software/maker-2.24-debug/bin/../lib/Error.pm
	0.1	runlog	/storage/tmp/software/maker-2.24-debug/bin/../lib/runlog.pm
	0.22	File::Temp	/storage/tmp/software/perl-5.14.1/lib/5.14.1/File/Temp.pm
	0.32	List::MoreUtils	/storage/tmp/software/perl-5.14.1/lib/site_perl/5.14.1/x86_64-linux-thread-multi/List/MoreUtils.pm
	0.34	forks::shared	/storage/tmp/software/perl-5.14.1/lib/site_perl/5.14.1/x86_64-linux-thread-multi/forks/shared.pm
	0.34	forks::signals	/storage/tmp/software/perl-5.14.1/lib/site_perl/5.14.1/x86_64-linux-thread-multi/forks/signals.pm
	0.34	forks	/storage/tmp/software/perl-5.14.1/lib/site_perl/5.14.1/x86_64-linux-thread-multi/forks.pm
	0.45	Proc::ProcessTable	/storage/tmp/software/perl-5.14.1/lib/site_perl/5.14.1/x86_64-linux-thread-multi/Proc/ProcessTable.pm
	0.49	Inline	/home/s187512/perl/lib/perl5/site_perl/5.12.1/Inline.pm
	0.63	Class::Struct	/storage/tmp/software/perl-5.14.1/lib/5.14.1/Class/Struct.pm
	0.63	lib	/storage/tmp/software/perl-5.14.1/lib/5.14.1/x86_64-linux-thread-multi/lib.pm
	1.006001	Bio::DB::Fasta	/storage/tmp/software/perl-5.14.1/lib/site_perl/5.14.1/Bio/DB/Fasta.pm
	1.006001	Bio::DB::RandomAccessI	/storage/tmp/software/perl-5.14.1/lib/site_perl/5.14.1/Bio/DB/RandomAccessI.pm
	1.006001	Bio::DB::SeqI	/storage/tmp/software/perl-5.14.1/lib/site_perl/5.14.1/Bio/DB/SeqI.pm
	1.006001	Bio::Root::Exception	/storage/tmp/software/perl-5.14.1/lib/site_perl/5.14.1/Bio/Root/Exception.pm
	1.006001	Bio::Root::RootI	/storage/tmp/software/perl-5.14.1/lib/site_perl/5.14.1/Bio/Root/RootI.pm
	1.006001	Bio::Root::Version	/storage/tmp/software/perl-5.14.1/lib/site_perl/5.14.1/Bio/Root/Version.pm
	1.006001	Bio::Search::Hit::GenericHit	/storage/tmp/software/perl-5.14.1/lib/site_perl/5.14.1/Bio/Search/Hit/GenericHit.pm
	1.006001	Bio::Search::Hit::PhatHit::repeatmasker	/storage/tmp/software/maker-2.24-debug/bin/../lib/Bio/Search/Hit/PhatHit/repeatmasker.pm
	1.006001	Bio::Search::SearchUtils	/storage/tmp/software/perl-5.14.1/lib/site_perl/5.14.1/Bio/Search/SearchUtils.pm
	1.00	AnyDBM_File	/storage/tmp/software/perl-5.14.1/lib/5.14.1/AnyDBM_File.pm
	1.00	integer	/storage/tmp/software/perl-5.14.1/lib/5.14.1/integer.pm
	1.00	locale	/storage/tmp/software/perl-5.14.1/lib/5.14.1/locale.pm
	1.02	SelectSaver	/storage/tmp/software/perl-5.14.1/lib/5.14.1/SelectSaver.pm
	1.02	vars	/storage/tmp/software/perl-5.14.1/lib/5.14.1/vars.pm
	1.02	warnings::register	/storage/tmp/software/perl-5.14.1/lib/5.14.1/warnings/register.pm
	1.04	bytes	/storage/tmp/software/perl-5.14.1/lib/5.14.1/bytes.pm
	1.04	strict	/storage/tmp/software/perl-5.14.1/lib/5.14.1/strict.pm
	1.04	Tie::Hash	/storage/tmp/software/perl-5.14.1/lib/5.14.1/Tie/Hash.pm
	1.05	sigtrap	/storage/tmp/software/perl-5.14.1/lib/5.14.1/sigtrap.pm
	1.07	Symbol	/storage/tmp/software/perl-5.14.1/lib/5.14.1/Symbol.pm
	1.09	File::Which	/storage/tmp/software/maker-2.24-debug/bin/../lib/File/Which.pm
	1.09	IPC::Open3	/storage/tmp/software/perl-5.14.1/lib/5.14.1/IPC/Open3.pm
	1.0	Proc::Signal	/storage/tmp/software/maker-2.24-debug/bin/../lib/Proc/Signal.pm
	1.11	Fcntl	/storage/tmp/software/perl-5.14.1/lib/5.14.1/x86_64-linux-thread-multi/Fcntl.pm
	1.12	File::Glob	/storage/tmp/software/perl-5.14.1/lib/5.14.1/x86_64-linux-thread-multi/File/Glob.pm
	1.12	warnings	/storage/tmp/software/perl-5.14.1/lib/5.14.1/warnings.pm
	1.13	DynaLoader	/storage/tmp/software/perl-5.14.1/lib/5.14.1/x86_64-linux-thread-multi/DynaLoader.pm
	1.13	Errno	/storage/tmp/software/perl-5.14.1/lib/5.14.1/x86_64-linux-thread-multi/Errno.pm
	1.13	overload	/storage/tmp/software/perl-5.14.1/lib/5.14.1/overload.pm
	1.15	IO::File	/storage/tmp/software/perl-5.14.1/lib/5.14.1/x86_64-linux-thread-multi/IO/File.pm
	1.16	Digest::base	/storage/tmp/software/perl-5.14.1/lib/5.14.1/Digest/base.pm
	1.16	Sys::Hostname	/storage/tmp/software/perl-5.14.1/lib/5.14.1/x86_64-linux-thread-multi/Sys/Hostname.pm
	1.19	File::Find	/storage/tmp/software/perl-5.14.1/lib/5.14.1/File/Find.pm
	1.1	IO::Seekable	/storage/tmp/software/perl-5.14.1/lib/5.14.1/x86_64-linux-thread-multi/IO/Seekable.pm
	1.2000	Time::Local	/storage/tmp/software/perl-5.14.1/lib/5.14.1/Time/Local.pm
	1.20	Carp	/storage/tmp/software/perl-5.14.1/lib/5.14.1/Carp.pm
	1.20	feature	/storage/tmp/software/perl-5.14.1/lib/5.14.1/feature.pm
	1.20	File::NFSLock	/storage/tmp/software/maker-2.24-debug/bin/../lib/File/NFSLock.pm
	1.20	IO::Select	/storage/tmp/software/perl-5.14.1/lib/5.14.1/x86_64-linux-thread-multi/IO/Select.pm
	1.21	constant	/storage/tmp/software/perl-5.14.1/lib/5.14.1/constant.pm
	1.23	IO::Socket::UNIX	/storage/tmp/software/perl-5.14.1/lib/5.14.1/x86_64-linux-thread-multi/IO/Socket/UNIX.pm
	1.23	List::Util	/storage/tmp/software/perl-5.14.1/lib/5.14.1/x86_64-linux-thread-multi/List/Util.pm
	1.23	Scalar::Util	/storage/tmp/software/perl-5.14.1/lib/5.14.1/x86_64-linux-thread-multi/Scalar/Util.pm
	1.24	POSIX	/storage/tmp/software/perl-5.14.1/lib/5.14.1/x86_64-linux-thread-multi/POSIX.pm
	1.25_04	IO	/storage/tmp/software/perl-5.14.1/lib/5.14.1/x86_64-linux-thread-multi/IO.pm
	1.31	IO::Handle	/storage/tmp/software/perl-5.14.1/lib/5.14.1/x86_64-linux-thread-multi/IO/Handle.pm
	1.31	IO::Socket::INET	/storage/tmp/software/perl-5.14.1/lib/5.14.1/x86_64-linux-thread-multi/IO/Socket/INET.pm
	1.32	IO::Socket	/storage/tmp/software/perl-5.14.1/lib/5.14.1/x86_64-linux-thread-multi/IO/Socket.pm
	1.33	DBD::SQLite	/storage/tmp/software/perl-5.14.1/lib/site_perl/5.14.1/x86_64-linux-thread-multi/DBD/SQLite.pm
	1.33	threads::shared	/storage/tmp/software/perl-5.14.1/lib/site_perl/5.14.1/x86_64-linux-thread-multi/forks/shared.pm
	1.50	FindBin	/storage/tmp/software/perl-5.14.1/lib/5.14.1/FindBin.pm
	1.58	URI	/storage/tmp/software/perl-5.14.1/lib/site_perl/5.14.1/URI.pm
	1.616	DBI	/storage/tmp/software/perl-5.14.1/lib/site_perl/5.14.1/x86_64-linux-thread-multi/DBI.pm
	1.77	threads	/storage/tmp/software/perl-5.14.1/lib/site_perl/5.14.1/x86_64-linux-thread-multi/forks.pm
	1.822	DB_File	/storage/tmp/software/perl-5.14.1/lib/5.14.1/x86_64-linux-thread-multi/DB_File.pm
	1.94	Socket	/storage/tmp/software/perl-5.14.1/lib/5.14.1/x86_64-linux-thread-multi/Socket.pm
	1.972101	Time::HiRes	/storage/tmp/software/perl-5.14.1/lib/5.14.1/x86_64-linux-thread-multi/Time/HiRes.pm
	2.02	FileHandle	/storage/tmp/software/perl-5.14.1/lib/5.14.1/FileHandle.pm
	2.08001	forks::Devel::Symdump	/storage/tmp/software/perl-5.14.1/lib/site_perl/5.14.1/x86_64-linux-thread-multi/forks/Devel/Symdump.pm
	2.08_01	File::Path	/storage/tmp/software/perl-5.14.1/lib/5.14.1/File/Path.pm
	2.131	Data::Dumper	/storage/tmp/software/perl-5.14.1/lib/5.14.1/x86_64-linux-thread-multi/Data/Dumper.pm
	2.16	base	/storage/tmp/software/perl-5.14.1/lib/5.14.1/base.pm
	2.21	File::Copy	/storage/tmp/software/perl-5.14.1/lib/5.14.1/File/Copy.pm
	2.30	Storable	/storage/tmp/software/perl-5.14.1/lib/5.14.1/x86_64-linux-thread-multi/Storable.pm
	2.38	Getopt::Long	/storage/tmp/software/perl-5.14.1/lib/5.14.1/Getopt/Long.pm
	2.51	Digest::MD5	/storage/tmp/software/perl-5.14.1/lib/5.14.1/x86_64-linux-thread-multi/Digest/MD5.pm
	2.82	File::Basename	/storage/tmp/software/perl-5.14.1/lib/5.14.1/File/Basename.pm
	3.00	Term::ANSIColor	/storage/tmp/software/perl-5.14.1/lib/5.14.1/Term/ANSIColor.pm
	3.30	URI::Escape	/storage/tmp/software/perl-5.14.1/lib/site_perl/5.14.1/URI/Escape.pm
	3.33	File::Spec	/storage/tmp/software/perl-5.14.1/lib/5.14.1/x86_64-linux-thread-multi/File/Spec.pm
	3.33	File::Spec::Unix	/storage/tmp/software/perl-5.14.1/lib/5.14.1/x86_64-linux-thread-multi/File/Spec/Unix.pm
	3.36	Cwd	/storage/tmp/software/perl-5.14.1/lib/5.14.1/x86_64-linux-thread-multi/Cwd.pm
	4.2	Tie::Handle	/storage/tmp/software/perl-5.14.1/lib/5.14.1/Tie/Handle.pm
	4.2	Tie::StdHandle	/storage/tmp/software/perl-5.14.1/lib/5.14.1/Tie/StdHandle.pm
	5.64_03	Exporter::Heavy	/storage/tmp/software/perl-5.14.1/lib/5.14.1/Exporter/Heavy.pm
	5.64_03	Exporter	/storage/tmp/software/perl-5.14.1/lib/5.14.1/Exporter.pm
	5.71	AutoLoader	/storage/tmp/software/perl-5.14.1/lib/5.14.1/AutoLoader.pm
	6.00	HTTP::Date	/storage/tmp/software/perl-5.14.1/lib/site_perl/5.14.1/HTTP/Date.pm
	6.00	HTTP::Headers	/storage/tmp/software/perl-5.14.1/lib/site_perl/5.14.1/HTTP/Headers.pm
	6.00	HTTP::Request	/storage/tmp/software/perl-5.14.1/lib/site_perl/5.14.1/HTTP/Request.pm
	6.00	HTTP::Status	/storage/tmp/software/perl-5.14.1/lib/site_perl/5.14.1/HTTP/Status.pm
	6.00	LWP::Protocol	/storage/tmp/software/perl-5.14.1/lib/site_perl/5.14.1/LWP/Protocol.pm
	6.01	HTTP::Response	/storage/tmp/software/perl-5.14.1/lib/site_perl/5.14.1/HTTP/Response.pm
	6.02	HTTP::Message	/storage/tmp/software/perl-5.14.1/lib/site_perl/5.14.1/HTTP/Message.pm
	6.02	LWP	/storage/tmp/software/perl-5.14.1/lib/site_perl/5.14.1/LWP.pm
	6.02	LWP::UserAgent	/storage/tmp/software/perl-5.14.1/lib/site_perl/5.14.1/LWP/UserAgent.pm
	7.1	Bit::Vector	/storage/tmp/software/perl-5.14.1/lib/site_perl/5.14.1/x86_64-linux-thread-multi/Bit/Vector.pm
A data structure will be created for you at:
Calculating annotation quality statistics
Calling Datastore::MD5::id_to_dir at /storage/tmp/software/maker-2.24-debug/bin/../lib/Process/MpiChunk.pm line 428
Calling Datastore::MD5::mkdir at /storage/tmp/software/maker-2.24-debug/bin/../lib/Process/MpiChunk.pm line 428
Calling Datastore::MD5::new at /storage/tmp/software/maker-2.24-debug/bin/maker line 536
Calling ds_utility::new at /storage/tmp/software/maker-2.24-debug/bin/maker line 535
Calling FastaDB::add_to_global_index at /storage/tmp/software/maker-2.24-debug/bin/maker line 523
Calling FastaDB::makeid from BioPerl Bio::DB::Fasta hook at /storage/tmp/software/perl-5.14.1/lib/site_perl/5.14.1/Bio/DB/Fasta.pm line 760
Calling FastaDB::new at /storage/tmp/software/maker-2.24-debug/bin/../lib/Process/MpiChunk.pm line 1066
Calling FastaDB::new at /storage/tmp/software/maker-2.24-debug/bin/../lib/Process/MpiChunk.pm line 1067
Calling FastaDB::new at /storage/tmp/software/maker-2.24-debug/bin/../lib/Process/MpiChunk.pm line 1515
Calling FastaDB::new at /storage/tmp/software/maker-2.24-debug/bin/../lib/Process/MpiChunk.pm line 1636
Calling FastaDB::new at /storage/tmp/software/maker-2.24-debug/bin/../lib/Process/MpiChunk.pm line 2460
Calling FastaDB::new at /storage/tmp/software/maker-2.24-debug/bin/../lib/Process/MpiChunk.pm line 2573
Calling FastaDB::new at /storage/tmp/software/maker-2.24-debug/bin/../lib/Process/MpiChunk.pm line 449
Calling FastaDB::new at /storage/tmp/software/maker-2.24-debug/bin/../lib/Widget/augustus.pm line 417
Calling FastaDB::new at /storage/tmp/software/maker-2.24-debug/bin/maker line 432
Calling FastaDB::new at /storage/tmp/software/maker-2.24-debug/bin/maker line 522
Calling Fasta::def2SeqID at /storage/tmp/software/maker-2.24-debug/bin/maker line 430
Calling Fasta::fasta2seqRef at /storage/tmp/software/maker-2.24-debug/bin/maker line 430
Calling Fasta::getDef at /storage/tmp/software/maker-2.24-debug/bin/maker line 430
Calling Fasta::seq2fastaRef at /storage/tmp/software/maker-2.24-debug/bin/maker line 430
Calling File::NFSLock::maintain at /storage/tmp/software/maker-2.24-debug/bin/../lib/GI.pm line 1670
Calling File::NFSLock::new at /storage/tmp/software/maker-2.24-debug/bin/../lib/GI.pm line 1670
Calling File::NFSLock::new at /storage/tmp/software/maker-2.24-debug/bin/maker line 430
Calling File::NFSLock::new at /storage/tmp/software/maker-2.24-debug/bin/maker line 468
Calling File::NFSLock::unlock at /storage/tmp/software/maker-2.24-debug/bin/maker line 430
Calling File::NFSLock::unlock at /storage/tmp/software/maker-2.24-debug/bin/maker line 468
Calling File::Path::mkpath at /storage/tmp/software/maker-2.24-debug/bin/../lib/Process/MpiChunk.pm line 428
Calling File::Path::rmtree at /storage/tmp/software/maker-2.24-debug/bin/maker line 430
Calling GFFDB::new at /storage/tmp/software/maker-2.24-debug/bin/maker line 529
Calling GFFDB::next_build at /storage/tmp/software/maker-2.24-debug/bin/maker line 531
Calling GI::build_fasta_index at /storage/tmp/software/maker-2.24-debug/bin/maker line 431
Calling GI::build_fasta_index at /storage/tmp/software/maker-2.24-debug/bin/maker line 521
Calling GI::create_blastdb at /storage/tmp/software/maker-2.24-debug/bin/maker line 467
Calling GI::load_control_files at /storage/tmp/software/maker-2.24-debug/bin/maker line 346
Calling GI::mount_check at /storage/tmp/software/maker-2.24-debug/bin/maker line 359
Calling GI::new_instance_temp at /storage/tmp/software/maker-2.24-debug/bin/maker line 357
Calling GI::s_abs_path at /storage/tmp/software/maker-2.24-debug/bin/maker line 412
Calling GI::set_global_temp at /storage/tmp/software/maker-2.24-debug/bin/maker line 377
Calling GI::split_db at /storage/tmp/software/maker-2.24-debug/bin/maker line 429
Calling Iterator::Any::new at /storage/tmp/software/maker-2.24-debug/bin/maker line 430
Calling Iterator::Any::nextDef at /storage/tmp/software/maker-2.24-debug/bin/maker line 430
Calling Iterator::Any::nextFastaRef at /storage/tmp/software/maker-2.24-debug/bin/maker line 430
Calling Iterator::Fasta::new at /storage/tmp/software/maker-2.24-debug/bin/maker line 539
Calling Iterator::Fasta::skip_file at /storage/tmp/software/maker-2.24-debug/bin/maker line 541
Calling Iterator::Fasta::step at /storage/tmp/software/maker-2.24-debug/bin/maker line 543
Calling List::Util::shuffle at /storage/tmp/software/maker-2.24-debug/bin/maker line 422
Calling mkdir at /storage/tmp/software/maker-2.24-debug/bin/maker line 430
Calling out to BioPerl Bio::DB::Fasta::_close_index at /storage/tmp/software/maker-2.24-debug/bin/../lib/Process/MpiChunk.pm line 1066
Calling out to BioPerl Bio::DB::Fasta::new at /storage/tmp/software/maker-2.24-debug/bin/../lib/Error.pm line 339
Calling out to BioPerl get_PrimarySeq_stream at /storage/tmp/software/maker-2.24-debug/bin/../lib/GI.pm line 1670
Calling out to FastaSeq::convert at /storage/tmp/software/maker-2.24-debug/bin/../lib/GI.pm line 1413
Calling system at /storage/tmp/software/maker-2.24-debug/bin/maker line 430
Calling uri_escape at /storage/tmp/software/maker-2.24-debug/bin/../lib/Process/MpiChunk.pm line 428
Can't locate package GDBM_File for @AnyDBM_File::ISA at /storage/tmp/software/perl-5.14.1/lib/5.14.1/x86_64-linux-thread-multi/DB_File.pm line 293.
Can't locate package NDBM_File for @AnyDBM_File::ISA at /storage/tmp/software/perl-5.14.1/lib/5.14.1/x86_64-linux-thread-multi/DB_File.pm line 293.
Can't locate package SDBM_File for @AnyDBM_File::ISA at /storage/tmp/software/perl-5.14.1/lib/5.14.1/x86_64-linux-thread-multi/DB_File.pm line 293.
cd /tmp/maker_mOO8LA; /storage/tmp/software/repeatmasker-3.3.0/RepeatMasker /storage/tmp/jobs/dmuscipula/experiments/SLAx/maker/SLAx_merged_02_03.maker.output/SLAx_merged_02_03_datastore/AB/FC/MblContig1//theVoid.MblContig1/MblContig1.0.all.rb -species all -dir /storage/tmp/jobs/dmuscipula/experiments/SLAx/maker/SLAx_merged_02_03.maker.output/SLAx_merged_02_03_datastore/AB/FC/MblContig1//theVoid.MblContig1 -pa 1
Choosing best annotations
cleaning blastn...
cleaning blastx...
cleaning clusters....
#--------- command -------------#
cycle 1 
cycle 10 
cycle 2 
cycle 3 
cycle 4 
cycle 5 
cycle 6 
cycle 7 
cycle 8 
cycle 9 
deleted:0 genes
deleted:0 hits
done
...finished clustering.
formating database...
Generating output... 
in cluster::shadow_cluster...
Length: 3612
Maker is now finished!!!
Making transcripts
masking
****MODULE VERSION INFO
--Next Contig--
Now starting the contig!!
Preparing evidence for hint based annotation
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processing output: 
Processing transcripts into genes
running  augustus.
running  blast search.
running  est2genome search.
running  exonerate search.
running  repeat masker.
SeqID: MblContig1
STATUS: Now running MAKER...
STATUS: Parsing control files...
STATUS: Processing and indexing input FASTA files...
STATUS: Setting up database for any GFF3 input...
/storage/tmp/jobs/dmuscipula/experiments/SLAx/maker/SLAx_merged_02_03.maker.output/SLAx_merged_02_03_datastore
/storage/tmp/jobs/dmuscipula/experiments/SLAx/maker/SLAx_merged_02_03.maker.output/SLAx_merged_02_03_master_datastore_index.log
/storage/tmp/software/augustus-2.5.5/bin/augustus --species=arabidopsis --strand=backward --UTR=off --hintsfile=/storage/tmp/jobs/dmuscipula/experiments/SLAx/maker/SLAx_merged_02_03.maker.output/SLAx_merged_02_03_datastore/AB/FC/MblContig1//theVoid.MblContig1/2_0.1976-3065.arabidopsis.auto_annotator.xdef.augustus --extrinsicCfgFile=/storage/tmp/software/augustus/config//extrinsic/extrinsic.MPE.cfg /storage/tmp/jobs/dmuscipula/experiments/SLAx/maker/SLAx_merged_02_03.maker.output/SLAx_merged_02_03_datastore/AB/FC/MblContig1//theVoid.MblContig1/2_0.1976-3065.arabidopsis.auto_annotator.augustus.fasta > /storage/tmp/jobs/dmuscipula/experiments/SLAx/maker/SLAx_merged_02_03.maker.output/SLAx_merged_02_03_datastore/AB/FC/MblContig1//theVoid.MblContig1/2_0.1976-3065.arabidopsis.auto_annotator.augustus
/storage/tmp/software/augustus-2.5.5/bin/augustus --species=arabidopsis --strand=forward --UTR=off --hintsfile=/storage/tmp/jobs/dmuscipula/experiments/SLAx/maker/SLAx_merged_02_03.maker.output/SLAx_merged_02_03_datastore/AB/FC/MblContig1//theVoid.MblContig1/1_0.0-3612.arabidopsis.auto_annotator.xdef.augustus --extrinsicCfgFile=/storage/tmp/software/augustus/config//extrinsic/extrinsic.MPE.cfg /storage/tmp/jobs/dmuscipula/experiments/SLAx/maker/SLAx_merged_02_03.maker.output/SLAx_merged_02_03_datastore/AB/FC/MblContig1//theVoid.MblContig1/1_0.0-3612.arabidopsis.auto_annotator.augustus.fasta > /storage/tmp/jobs/dmuscipula/experiments/SLAx/maker/SLAx_merged_02_03.maker.output/SLAx_merged_02_03_datastore/AB/FC/MblContig1//theVoid.MblContig1/1_0.0-3612.arabidopsis.auto_annotator.augustus
/storage/tmp/software/augustus-2.5.5/bin/augustus --species=arabidopsis --UTR=off /storage/tmp/jobs/dmuscipula/experiments/SLAx/maker/SLAx_merged_02_03.maker.output/SLAx_merged_02_03_datastore/AB/FC/MblContig1//theVoid.MblContig1/query.masked.fasta > /storage/tmp/jobs/dmuscipula/experiments/SLAx/maker/SLAx_merged_02_03.maker.output/SLAx_merged_02_03_datastore/AB/FC/MblContig1//theVoid.MblContig1/MblContig1.masked.all.arabidopsis.augustus
/storage/tmp/software/blast/bin/blastn -db /tmp/maker_mOO8LA/DM_Tra02%2Emerged%2Efasta.mpi.10.0 -query /tmp/maker_mOO8LA/rank0/MblContig1.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-10 -word_size 28 -reward 1 -penalty -5 -gapopen 5 -gapextend 5 -dbsize 1000 -searchsp 500000000 -num_threads 1 -lcase_masking -dust yes -soft_masking true -show_gis -out /storage/tmp/jobs/dmuscipula/experiments/SLAx/maker/SLAx_merged_02_03.maker.output/SLAx_merged_02_03_datastore/AB/FC/MblContig1//theVoid.MblContig1/MblContig1.0.DM_Tra02%2Emerged%2Efasta.blastn.temp_dir/DM_Tra02%2Emerged%2Efasta.mpi.10.0.blastn
/storage/tmp/software/blast/bin/blastn -db /tmp/maker_mOO8LA/DM_Tra02%2Emerged%2Efasta.mpi.10.1 -query /tmp/maker_mOO8LA/rank0/MblContig1.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-10 -word_size 28 -reward 1 -penalty -5 -gapopen 5 -gapextend 5 -dbsize 1000 -searchsp 500000000 -num_threads 1 -lcase_masking -dust yes -soft_masking true -show_gis -out /storage/tmp/jobs/dmuscipula/experiments/SLAx/maker/SLAx_merged_02_03.maker.output/SLAx_merged_02_03_datastore/AB/FC/MblContig1//theVoid.MblContig1/MblContig1.0.DM_Tra02%2Emerged%2Efasta.blastn.temp_dir/DM_Tra02%2Emerged%2Efasta.mpi.10.1.blastn
/storage/tmp/software/blast/bin/blastn -db /tmp/maker_mOO8LA/DM_Tra02%2Emerged%2Efasta.mpi.10.2 -query /tmp/maker_mOO8LA/rank0/MblContig1.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-10 -word_size 28 -reward 1 -penalty -5 -gapopen 5 -gapextend 5 -dbsize 1000 -searchsp 500000000 -num_threads 1 -lcase_masking -dust yes -soft_masking true -show_gis -out /storage/tmp/jobs/dmuscipula/experiments/SLAx/maker/SLAx_merged_02_03.maker.output/SLAx_merged_02_03_datastore/AB/FC/MblContig1//theVoid.MblContig1/MblContig1.0.DM_Tra02%2Emerged%2Efasta.blastn.temp_dir/DM_Tra02%2Emerged%2Efasta.mpi.10.2.blastn
/storage/tmp/software/blast/bin/blastn -db /tmp/maker_mOO8LA/DM_Tra02%2Emerged%2Efasta.mpi.10.3 -query /tmp/maker_mOO8LA/rank0/MblContig1.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-10 -word_size 28 -reward 1 -penalty -5 -gapopen 5 -gapextend 5 -dbsize 1000 -searchsp 500000000 -num_threads 1 -lcase_masking -dust yes -soft_masking true -show_gis -out /storage/tmp/jobs/dmuscipula/experiments/SLAx/maker/SLAx_merged_02_03.maker.output/SLAx_merged_02_03_datastore/AB/FC/MblContig1//theVoid.MblContig1/MblContig1.0.DM_Tra02%2Emerged%2Efasta.blastn.temp_dir/DM_Tra02%2Emerged%2Efasta.mpi.10.3.blastn
/storage/tmp/software/blast/bin/blastn -db /tmp/maker_mOO8LA/DM_Tra02%2Emerged%2Efasta.mpi.10.4 -query /tmp/maker_mOO8LA/rank0/MblContig1.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-10 -word_size 28 -reward 1 -penalty -5 -gapopen 5 -gapextend 5 -dbsize 1000 -searchsp 500000000 -num_threads 1 -lcase_masking -dust yes -soft_masking true -show_gis -out /storage/tmp/jobs/dmuscipula/experiments/SLAx/maker/SLAx_merged_02_03.maker.output/SLAx_merged_02_03_datastore/AB/FC/MblContig1//theVoid.MblContig1/MblContig1.0.DM_Tra02%2Emerged%2Efasta.blastn.temp_dir/DM_Tra02%2Emerged%2Efasta.mpi.10.4.blastn
/storage/tmp/software/blast/bin/blastn -db /tmp/maker_mOO8LA/DM_Tra02%2Emerged%2Efasta.mpi.10.5 -query /tmp/maker_mOO8LA/rank0/MblContig1.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-10 -word_size 28 -reward 1 -penalty -5 -gapopen 5 -gapextend 5 -dbsize 1000 -searchsp 500000000 -num_threads 1 -lcase_masking -dust yes -soft_masking true -show_gis -out /storage/tmp/jobs/dmuscipula/experiments/SLAx/maker/SLAx_merged_02_03.maker.output/SLAx_merged_02_03_datastore/AB/FC/MblContig1//theVoid.MblContig1/MblContig1.0.DM_Tra02%2Emerged%2Efasta.blastn.temp_dir/DM_Tra02%2Emerged%2Efasta.mpi.10.5.blastn
/storage/tmp/software/blast/bin/blastn -db /tmp/maker_mOO8LA/DM_Tra02%2Emerged%2Efasta.mpi.10.6 -query /tmp/maker_mOO8LA/rank0/MblContig1.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-10 -word_size 28 -reward 1 -penalty -5 -gapopen 5 -gapextend 5 -dbsize 1000 -searchsp 500000000 -num_threads 1 -lcase_masking -dust yes -soft_masking true -show_gis -out /storage/tmp/jobs/dmuscipula/experiments/SLAx/maker/SLAx_merged_02_03.maker.output/SLAx_merged_02_03_datastore/AB/FC/MblContig1//theVoid.MblContig1/MblContig1.0.DM_Tra02%2Emerged%2Efasta.blastn.temp_dir/DM_Tra02%2Emerged%2Efasta.mpi.10.6.blastn
/storage/tmp/software/blast/bin/blastn -db /tmp/maker_mOO8LA/DM_Tra02%2Emerged%2Efasta.mpi.10.7 -query /tmp/maker_mOO8LA/rank0/MblContig1.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-10 -word_size 28 -reward 1 -penalty -5 -gapopen 5 -gapextend 5 -dbsize 1000 -searchsp 500000000 -num_threads 1 -lcase_masking -dust yes -soft_masking true -show_gis -out /storage/tmp/jobs/dmuscipula/experiments/SLAx/maker/SLAx_merged_02_03.maker.output/SLAx_merged_02_03_datastore/AB/FC/MblContig1//theVoid.MblContig1/MblContig1.0.DM_Tra02%2Emerged%2Efasta.blastn.temp_dir/DM_Tra02%2Emerged%2Efasta.mpi.10.7.blastn
/storage/tmp/software/blast/bin/blastn -db /tmp/maker_mOO8LA/DM_Tra02%2Emerged%2Efasta.mpi.10.8 -query /tmp/maker_mOO8LA/rank0/MblContig1.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-10 -word_size 28 -reward 1 -penalty -5 -gapopen 5 -gapextend 5 -dbsize 1000 -searchsp 500000000 -num_threads 1 -lcase_masking -dust yes -soft_masking true -show_gis -out /storage/tmp/jobs/dmuscipula/experiments/SLAx/maker/SLAx_merged_02_03.maker.output/SLAx_merged_02_03_datastore/AB/FC/MblContig1//theVoid.MblContig1/MblContig1.0.DM_Tra02%2Emerged%2Efasta.blastn.temp_dir/DM_Tra02%2Emerged%2Efasta.mpi.10.8.blastn
/storage/tmp/software/blast/bin/blastn -db /tmp/maker_mOO8LA/DM_Tra02%2Emerged%2Efasta.mpi.10.9 -query /tmp/maker_mOO8LA/rank0/MblContig1.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-10 -word_size 28 -reward 1 -penalty -5 -gapopen 5 -gapextend 5 -dbsize 1000 -searchsp 500000000 -num_threads 1 -lcase_masking -dust yes -soft_masking true -show_gis -out /storage/tmp/jobs/dmuscipula/experiments/SLAx/maker/SLAx_merged_02_03.maker.output/SLAx_merged_02_03_datastore/AB/FC/MblContig1//theVoid.MblContig1/MblContig1.0.DM_Tra02%2Emerged%2Efasta.blastn.temp_dir/DM_Tra02%2Emerged%2Efasta.mpi.10.9.blastn
/storage/tmp/software/blast/bin/blastx -db /tmp/maker_mOO8LA/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_mOO8LA/rank0/MblContig1.0 -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 /storage/tmp/jobs/dmuscipula/experiments/SLAx/maker/SLAx_merged_02_03.maker.output/SLAx_merged_02_03_datastore/AB/FC/MblContig1//theVoid.MblContig1/MblContig1.0.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
/storage/tmp/software/blast/bin/blastx -db /tmp/maker_mOO8LA/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_mOO8LA/rank0/MblContig1.0 -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 /storage/tmp/jobs/dmuscipula/experiments/SLAx/maker/SLAx_merged_02_03.maker.output/SLAx_merged_02_03_datastore/AB/FC/MblContig1//theVoid.MblContig1/MblContig1.0.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
/storage/tmp/software/blast/bin/blastx -db /tmp/maker_mOO8LA/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_mOO8LA/rank0/MblContig1.0 -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 /storage/tmp/jobs/dmuscipula/experiments/SLAx/maker/SLAx_merged_02_03.maker.output/SLAx_merged_02_03_datastore/AB/FC/MblContig1//theVoid.MblContig1/MblContig1.0.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
/storage/tmp/software/blast/bin/blastx -db /tmp/maker_mOO8LA/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_mOO8LA/rank0/MblContig1.0 -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 /storage/tmp/jobs/dmuscipula/experiments/SLAx/maker/SLAx_merged_02_03.maker.output/SLAx_merged_02_03_datastore/AB/FC/MblContig1//theVoid.MblContig1/MblContig1.0.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
/storage/tmp/software/blast/bin/blastx -db /tmp/maker_mOO8LA/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_mOO8LA/rank0/MblContig1.0 -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 /storage/tmp/jobs/dmuscipula/experiments/SLAx/maker/SLAx_merged_02_03.maker.output/SLAx_merged_02_03_datastore/AB/FC/MblContig1//theVoid.MblContig1/MblContig1.0.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
/storage/tmp/software/blast/bin/blastx -db /tmp/maker_mOO8LA/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_mOO8LA/rank0/MblContig1.0 -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 /storage/tmp/jobs/dmuscipula/experiments/SLAx/maker/SLAx_merged_02_03.maker.output/SLAx_merged_02_03_datastore/AB/FC/MblContig1//theVoid.MblContig1/MblContig1.0.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
/storage/tmp/software/blast/bin/blastx -db /tmp/maker_mOO8LA/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_mOO8LA/rank0/MblContig1.0 -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 /storage/tmp/jobs/dmuscipula/experiments/SLAx/maker/SLAx_merged_02_03.maker.output/SLAx_merged_02_03_datastore/AB/FC/MblContig1//theVoid.MblContig1/MblContig1.0.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
/storage/tmp/software/blast/bin/blastx -db /tmp/maker_mOO8LA/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_mOO8LA/rank0/MblContig1.0 -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 /storage/tmp/jobs/dmuscipula/experiments/SLAx/maker/SLAx_merged_02_03.maker.output/SLAx_merged_02_03_datastore/AB/FC/MblContig1//theVoid.MblContig1/MblContig1.0.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
/storage/tmp/software/blast/bin/blastx -db /tmp/maker_mOO8LA/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_mOO8LA/rank0/MblContig1.0 -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 /storage/tmp/jobs/dmuscipula/experiments/SLAx/maker/SLAx_merged_02_03.maker.output/SLAx_merged_02_03_datastore/AB/FC/MblContig1//theVoid.MblContig1/MblContig1.0.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
/storage/tmp/software/blast/bin/blastx -db /tmp/maker_mOO8LA/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_mOO8LA/rank0/MblContig1.0 -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 /storage/tmp/jobs/dmuscipula/experiments/SLAx/maker/SLAx_merged_02_03.maker.output/SLAx_merged_02_03_datastore/AB/FC/MblContig1//theVoid.MblContig1/MblContig1.0.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
/storage/tmp/software/blast/bin/blastx -db /tmp/maker_mOO8LA/uniprotkb_viridiplantae%2Efasta.mpi.10.0 -query /tmp/maker_mOO8LA/rank0/MblContig1.0 -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 /storage/tmp/jobs/dmuscipula/experiments/SLAx/maker/SLAx_merged_02_03.maker.output/SLAx_merged_02_03_datastore/AB/FC/MblContig1//theVoid.MblContig1/MblContig1.0.uniprotkb_viridiplantae%2Efasta.blastx.temp_dir/uniprotkb_viridiplantae%2Efasta.mpi.10.0.blastx
/storage/tmp/software/blast/bin/blastx -db /tmp/maker_mOO8LA/uniprotkb_viridiplantae%2Efasta.mpi.10.1 -query /tmp/maker_mOO8LA/rank0/MblContig1.0 -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 /storage/tmp/jobs/dmuscipula/experiments/SLAx/maker/SLAx_merged_02_03.maker.output/SLAx_merged_02_03_datastore/AB/FC/MblContig1//theVoid.MblContig1/MblContig1.0.uniprotkb_viridiplantae%2Efasta.blastx.temp_dir/uniprotkb_viridiplantae%2Efasta.mpi.10.1.blastx
/storage/tmp/software/blast/bin/blastx -db /tmp/maker_mOO8LA/uniprotkb_viridiplantae%2Efasta.mpi.10.2 -query /tmp/maker_mOO8LA/rank0/MblContig1.0 -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 /storage/tmp/jobs/dmuscipula/experiments/SLAx/maker/SLAx_merged_02_03.maker.output/SLAx_merged_02_03_datastore/AB/FC/MblContig1//theVoid.MblContig1/MblContig1.0.uniprotkb_viridiplantae%2Efasta.blastx.temp_dir/uniprotkb_viridiplantae%2Efasta.mpi.10.2.blastx
/storage/tmp/software/blast/bin/blastx -db /tmp/maker_mOO8LA/uniprotkb_viridiplantae%2Efasta.mpi.10.3 -query /tmp/maker_mOO8LA/rank0/MblContig1.0 -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 /storage/tmp/jobs/dmuscipula/experiments/SLAx/maker/SLAx_merged_02_03.maker.output/SLAx_merged_02_03_datastore/AB/FC/MblContig1//theVoid.MblContig1/MblContig1.0.uniprotkb_viridiplantae%2Efasta.blastx.temp_dir/uniprotkb_viridiplantae%2Efasta.mpi.10.3.blastx
/storage/tmp/software/blast/bin/blastx -db /tmp/maker_mOO8LA/uniprotkb_viridiplantae%2Efasta.mpi.10.4 -query /tmp/maker_mOO8LA/rank0/MblContig1.0 -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 /storage/tmp/jobs/dmuscipula/experiments/SLAx/maker/SLAx_merged_02_03.maker.output/SLAx_merged_02_03_datastore/AB/FC/MblContig1//theVoid.MblContig1/MblContig1.0.uniprotkb_viridiplantae%2Efasta.blastx.temp_dir/uniprotkb_viridiplantae%2Efasta.mpi.10.4.blastx
/storage/tmp/software/blast/bin/blastx -db /tmp/maker_mOO8LA/uniprotkb_viridiplantae%2Efasta.mpi.10.5 -query /tmp/maker_mOO8LA/rank0/MblContig1.0 -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 /storage/tmp/jobs/dmuscipula/experiments/SLAx/maker/SLAx_merged_02_03.maker.output/SLAx_merged_02_03_datastore/AB/FC/MblContig1//theVoid.MblContig1/MblContig1.0.uniprotkb_viridiplantae%2Efasta.blastx.temp_dir/uniprotkb_viridiplantae%2Efasta.mpi.10.5.blastx
/storage/tmp/software/blast/bin/blastx -db /tmp/maker_mOO8LA/uniprotkb_viridiplantae%2Efasta.mpi.10.6 -query /tmp/maker_mOO8LA/rank0/MblContig1.0 -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 /storage/tmp/jobs/dmuscipula/experiments/SLAx/maker/SLAx_merged_02_03.maker.output/SLAx_merged_02_03_datastore/AB/FC/MblContig1//theVoid.MblContig1/MblContig1.0.uniprotkb_viridiplantae%2Efasta.blastx.temp_dir/uniprotkb_viridiplantae%2Efasta.mpi.10.6.blastx
/storage/tmp/software/blast/bin/blastx -db /tmp/maker_mOO8LA/uniprotkb_viridiplantae%2Efasta.mpi.10.7 -query /tmp/maker_mOO8LA/rank0/MblContig1.0 -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 /storage/tmp/jobs/dmuscipula/experiments/SLAx/maker/SLAx_merged_02_03.maker.output/SLAx_merged_02_03_datastore/AB/FC/MblContig1//theVoid.MblContig1/MblContig1.0.uniprotkb_viridiplantae%2Efasta.blastx.temp_dir/uniprotkb_viridiplantae%2Efasta.mpi.10.7.blastx
/storage/tmp/software/blast/bin/blastx -db /tmp/maker_mOO8LA/uniprotkb_viridiplantae%2Efasta.mpi.10.8 -query /tmp/maker_mOO8LA/rank0/MblContig1.0 -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 /storage/tmp/jobs/dmuscipula/experiments/SLAx/maker/SLAx_merged_02_03.maker.output/SLAx_merged_02_03_datastore/AB/FC/MblContig1//theVoid.MblContig1/MblContig1.0.uniprotkb_viridiplantae%2Efasta.blastx.temp_dir/uniprotkb_viridiplantae%2Efasta.mpi.10.8.blastx
/storage/tmp/software/blast/bin/blastx -db /tmp/maker_mOO8LA/uniprotkb_viridiplantae%2Efasta.mpi.10.9 -query /tmp/maker_mOO8LA/rank0/MblContig1.0 -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 /storage/tmp/jobs/dmuscipula/experiments/SLAx/maker/SLAx_merged_02_03.maker.output/SLAx_merged_02_03_datastore/AB/FC/MblContig1//theVoid.MblContig1/MblContig1.0.uniprotkb_viridiplantae%2Efasta.blastx.temp_dir/uniprotkb_viridiplantae%2Efasta.mpi.10.9.blastx
/storage/tmp/software/blast/bin/makeblastdb -dbtype nucl -in /tmp/maker_mOO8LA/DM_Tra02%2Emerged%2Efasta.mpi.10.0
/storage/tmp/software/blast/bin/makeblastdb -dbtype nucl -in /tmp/maker_mOO8LA/DM_Tra02%2Emerged%2Efasta.mpi.10.1
/storage/tmp/software/blast/bin/makeblastdb -dbtype nucl -in /tmp/maker_mOO8LA/DM_Tra02%2Emerged%2Efasta.mpi.10.2
/storage/tmp/software/blast/bin/makeblastdb -dbtype nucl -in /tmp/maker_mOO8LA/DM_Tra02%2Emerged%2Efasta.mpi.10.3
/storage/tmp/software/blast/bin/makeblastdb -dbtype nucl -in /tmp/maker_mOO8LA/DM_Tra02%2Emerged%2Efasta.mpi.10.4
/storage/tmp/software/blast/bin/makeblastdb -dbtype nucl -in /tmp/maker_mOO8LA/DM_Tra02%2Emerged%2Efasta.mpi.10.5
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/storage/tmp/software/blast/bin/makeblastdb -dbtype nucl -in /tmp/maker_mOO8LA/DM_Tra02%2Emerged%2Efasta.mpi.10.8
/storage/tmp/software/blast/bin/makeblastdb -dbtype nucl -in /tmp/maker_mOO8LA/DM_Tra02%2Emerged%2Efasta.mpi.10.9
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/storage/tmp/software/blast/bin/makeblastdb -dbtype prot -in /tmp/maker_mOO8LA/te_proteins%2Efasta.mpi.10.5
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/storage/tmp/software/blast/bin/makeblastdb -dbtype prot -in /tmp/maker_mOO8LA/te_proteins%2Efasta.mpi.10.7
/storage/tmp/software/blast/bin/makeblastdb -dbtype prot -in /tmp/maker_mOO8LA/te_proteins%2Efasta.mpi.10.8
/storage/tmp/software/blast/bin/makeblastdb -dbtype prot -in /tmp/maker_mOO8LA/te_proteins%2Efasta.mpi.10.9
/storage/tmp/software/blast/bin/makeblastdb -dbtype prot -in /tmp/maker_mOO8LA/uniprotkb_viridiplantae%2Efasta.mpi.10.0
/storage/tmp/software/blast/bin/makeblastdb -dbtype prot -in /tmp/maker_mOO8LA/uniprotkb_viridiplantae%2Efasta.mpi.10.1
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/storage/tmp/software/blast/bin/makeblastdb -dbtype prot -in /tmp/maker_mOO8LA/uniprotkb_viridiplantae%2Efasta.mpi.10.5
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/storage/tmp/software/blast/bin/makeblastdb -dbtype prot -in /tmp/maker_mOO8LA/uniprotkb_viridiplantae%2Efasta.mpi.10.8
/storage/tmp/software/blast/bin/makeblastdb -dbtype prot -in /tmp/maker_mOO8LA/uniprotkb_viridiplantae%2Efasta.mpi.10.9
/storage/tmp/software/exonerate-2.2.0-x86_64/bin/exonerate  -q /storage/tmp/jobs/dmuscipula/experiments/SLAx/maker/SLAx_merged_02_03.maker.output/SLAx_merged_02_03_datastore/AB/FC/MblContig1//theVoid.MblContig1/DM_Tra02_c148766.for.2237-2794.0.fasta -t /storage/tmp/jobs/dmuscipula/experiments/SLAx/maker/SLAx_merged_02_03.maker.output/SLAx_merged_02_03_datastore/AB/FC/MblContig1//theVoid.MblContig1/MblContig1.2237-2794.0.fasta -Q dna -T dna --model est2genome  --minintron 20 --maxintron 10000 --showcigar --percent 20 > /storage/tmp/jobs/dmuscipula/experiments/SLAx/maker/SLAx_merged_02_03.maker.output/SLAx_merged_02_03_datastore/AB/FC/MblContig1//theVoid.MblContig1/MblContig1.2237-2794.DM_Tra02_c148766.est_exonerate.0
/storage/tmp/software/exonerate-2.2.0-x86_64/bin/exonerate  -q /storage/tmp/jobs/dmuscipula/experiments/SLAx/maker/SLAx_merged_02_03.maker.output/SLAx_merged_02_03_datastore/AB/FC/MblContig1//theVoid.MblContig1/DM_Tra02_c22210.for.2531-3447.0.fasta -t /storage/tmp/jobs/dmuscipula/experiments/SLAx/maker/SLAx_merged_02_03.maker.output/SLAx_merged_02_03_datastore/AB/FC/MblContig1//theVoid.MblContig1/MblContig1.2531-3447.0.fasta -Q dna -T dna --model est2genome  --minintron 20 --maxintron 10000 --showcigar --percent 20 > /storage/tmp/jobs/dmuscipula/experiments/SLAx/maker/SLAx_merged_02_03.maker.output/SLAx_merged_02_03_datastore/AB/FC/MblContig1//theVoid.MblContig1/MblContig1.2531-3447.DM_Tra02_c22210.est_exonerate.0
/storage/tmp/software/exonerate-2.2.0-x86_64/bin/exonerate  -q /storage/tmp/jobs/dmuscipula/experiments/SLAx/maker/SLAx_merged_02_03.maker.output/SLAx_merged_02_03_datastore/AB/FC/MblContig1//theVoid.MblContig1/DM_Tra02_c28558.for.1766-3612.0.fasta -t /storage/tmp/jobs/dmuscipula/experiments/SLAx/maker/SLAx_merged_02_03.maker.output/SLAx_merged_02_03_datastore/AB/FC/MblContig1//theVoid.MblContig1/MblContig1.1766-3612.0.fasta -Q dna -T dna --model est2genome  --minintron 20 --maxintron 10000 --showcigar --percent 20 > /storage/tmp/jobs/dmuscipula/experiments/SLAx/maker/SLAx_merged_02_03.maker.output/SLAx_merged_02_03_datastore/AB/FC/MblContig1//theVoid.MblContig1/MblContig1.1766-3612.DM_Tra02_c28558.est_exonerate.0
/storage/tmp/software/exonerate-2.2.0-x86_64/bin/exonerate  -q /storage/tmp/jobs/dmuscipula/experiments/SLAx/maker/SLAx_merged_02_03.maker.output/SLAx_merged_02_03_datastore/AB/FC/MblContig1//theVoid.MblContig1/DM_Tra02_c46480.for.1375-1980.0.fasta -t /storage/tmp/jobs/dmuscipula/experiments/SLAx/maker/SLAx_merged_02_03.maker.output/SLAx_merged_02_03_datastore/AB/FC/MblContig1//theVoid.MblContig1/MblContig1.1375-1980.0.fasta -Q dna -T dna --model est2genome  --minintron 20 --maxintron 10000 --showcigar --percent 20 > /storage/tmp/jobs/dmuscipula/experiments/SLAx/maker/SLAx_merged_02_03.maker.output/SLAx_merged_02_03_datastore/AB/FC/MblContig1//theVoid.MblContig1/MblContig1.1375-1980.DM_Tra02_c46480.est_exonerate.0
/storage/tmp/software/exonerate-2.2.0-x86_64/bin/exonerate  -q /storage/tmp/jobs/dmuscipula/experiments/SLAx/maker/SLAx_merged_02_03.maker.output/SLAx_merged_02_03_datastore/AB/FC/MblContig1//theVoid.MblContig1/DM_Tra02_rep_c103390.for.2176-2881.0.fasta -t /storage/tmp/jobs/dmuscipula/experiments/SLAx/maker/SLAx_merged_02_03.maker.output/SLAx_merged_02_03_datastore/AB/FC/MblContig1//theVoid.MblContig1/MblContig1.2176-2881.0.fasta -Q dna -T dna --model est2genome  --minintron 20 --maxintron 10000 --showcigar --percent 20 > /storage/tmp/jobs/dmuscipula/experiments/SLAx/maker/SLAx_merged_02_03.maker.output/SLAx_merged_02_03_datastore/AB/FC/MblContig1//theVoid.MblContig1/MblContig1.2176-2881.DM_Tra02_rep_c103390.est_exonerate.0
/storage/tmp/software/exonerate-2.2.0-x86_64/bin/exonerate  -q /storage/tmp/jobs/dmuscipula/experiments/SLAx/maker/SLAx_merged_02_03.maker.output/SLAx_merged_02_03_datastore/AB/FC/MblContig1//theVoid.MblContig1/DM_Tra02_rep_c150200.for.2198-2924.0.fasta -t /storage/tmp/jobs/dmuscipula/experiments/SLAx/maker/SLAx_merged_02_03.maker.output/SLAx_merged_02_03_datastore/AB/FC/MblContig1//theVoid.MblContig1/MblContig1.2198-2924.0.fasta -Q dna -T dna --model est2genome  --minintron 20 --maxintron 10000 --showcigar --percent 20 > /storage/tmp/jobs/dmuscipula/experiments/SLAx/maker/SLAx_merged_02_03.maker.output/SLAx_merged_02_03_datastore/AB/FC/MblContig1//theVoid.MblContig1/MblContig1.2198-2924.DM_Tra02_rep_c150200.est_exonerate.0
/storage/tmp/software/exonerate-2.2.0-x86_64/bin/exonerate  -q /storage/tmp/jobs/dmuscipula/experiments/SLAx/maker/SLAx_merged_02_03.maker.output/SLAx_merged_02_03_datastore/AB/FC/MblContig1//theVoid.MblContig1/DM_Tra02_rep_c152823.for.2191-2815.0.fasta -t /storage/tmp/jobs/dmuscipula/experiments/SLAx/maker/SLAx_merged_02_03.maker.output/SLAx_merged_02_03_datastore/AB/FC/MblContig1//theVoid.MblContig1/MblContig1.2191-2815.0.fasta -Q dna -T dna --model est2genome  --minintron 20 --maxintron 10000 --showcigar --percent 20 > /storage/tmp/jobs/dmuscipula/experiments/SLAx/maker/SLAx_merged_02_03.maker.output/SLAx_merged_02_03_datastore/AB/FC/MblContig1//theVoid.MblContig1/MblContig1.2191-2815.DM_Tra02_rep_c152823.est_exonerate.0
/storage/tmp/software/exonerate-2.2.0-x86_64/bin/exonerate  -q /storage/tmp/jobs/dmuscipula/experiments/SLAx/maker/SLAx_merged_02_03.maker.output/SLAx_merged_02_03_datastore/AB/FC/MblContig1//theVoid.MblContig1/DM_Tra02_rep_c152902.for.2182-2808.0.fasta -t /storage/tmp/jobs/dmuscipula/experiments/SLAx/maker/SLAx_merged_02_03.maker.output/SLAx_merged_02_03_datastore/AB/FC/MblContig1//theVoid.MblContig1/MblContig1.2182-2808.0.fasta -Q dna -T dna --model est2genome  --minintron 20 --maxintron 10000 --showcigar --percent 20 > /storage/tmp/jobs/dmuscipula/experiments/SLAx/maker/SLAx_merged_02_03.maker.output/SLAx_merged_02_03_datastore/AB/FC/MblContig1//theVoid.MblContig1/MblContig1.2182-2808.DM_Tra02_rep_c152902.est_exonerate.0
/storage/tmp/software/exonerate-2.2.0-x86_64/bin/exonerate  -q /storage/tmp/jobs/dmuscipula/experiments/SLAx/maker/SLAx_merged_02_03.maker.output/SLAx_merged_02_03_datastore/AB/FC/MblContig1//theVoid.MblContig1/DM_Tra02_rep_c59058.for.2219-2853.0.fasta -t /storage/tmp/jobs/dmuscipula/experiments/SLAx/maker/SLAx_merged_02_03.maker.output/SLAx_merged_02_03_datastore/AB/FC/MblContig1//theVoid.MblContig1/MblContig1.2219-2853.0.fasta -Q dna -T dna --model est2genome  --minintron 20 --maxintron 10000 --showcigar --percent 20 > /storage/tmp/jobs/dmuscipula/experiments/SLAx/maker/SLAx_merged_02_03.maker.output/SLAx_merged_02_03_datastore/AB/FC/MblContig1//theVoid.MblContig1/MblContig1.2219-2853.DM_Tra02_rep_c59058.est_exonerate.0
/storage/tmp/software/exonerate-2.2.0-x86_64/bin/exonerate  -q /storage/tmp/jobs/dmuscipula/experiments/SLAx/maker/SLAx_merged_02_03.maker.output/SLAx_merged_02_03_datastore/AB/FC/MblContig1//theVoid.MblContig1/DM_Tra02_rep_c62416.for.2337-2853.0.fasta -t /storage/tmp/jobs/dmuscipula/experiments/SLAx/maker/SLAx_merged_02_03.maker.output/SLAx_merged_02_03_datastore/AB/FC/MblContig1//theVoid.MblContig1/MblContig1.2337-2853.0.fasta -Q dna -T dna --model est2genome  --minintron 20 --maxintron 10000 --showcigar --percent 20 > /storage/tmp/jobs/dmuscipula/experiments/SLAx/maker/SLAx_merged_02_03.maker.output/SLAx_merged_02_03_datastore/AB/FC/MblContig1//theVoid.MblContig1/MblContig1.2337-2853.DM_Tra02_rep_c62416.est_exonerate.0
/storage/tmp/software/exonerate-2.2.0-x86_64/bin/exonerate  -q /storage/tmp/jobs/dmuscipula/experiments/SLAx/maker/SLAx_merged_02_03.maker.output/SLAx_merged_02_03_datastore/AB/FC/MblContig1//theVoid.MblContig1/DM_Tra02_rep_c64040.for.2253-2808.0.fasta -t /storage/tmp/jobs/dmuscipula/experiments/SLAx/maker/SLAx_merged_02_03.maker.output/SLAx_merged_02_03_datastore/AB/FC/MblContig1//theVoid.MblContig1/MblContig1.2253-2808.0.fasta -Q dna -T dna --model est2genome  --minintron 20 --maxintron 10000 --showcigar --percent 20 > /storage/tmp/jobs/dmuscipula/experiments/SLAx/maker/SLAx_merged_02_03.maker.output/SLAx_merged_02_03_datastore/AB/FC/MblContig1//theVoid.MblContig1/MblContig1.2253-2808.DM_Tra02_rep_c64040.est_exonerate.0
/storage/tmp/software/exonerate-2.2.0-x86_64/bin/exonerate  -q /storage/tmp/jobs/dmuscipula/experiments/SLAx/maker/SLAx_merged_02_03.maker.output/SLAx_merged_02_03_datastore/AB/FC/MblContig1//theVoid.MblContig1/DM_Tra02_rep_c85280.for.2222-2887.0.fasta -t /storage/tmp/jobs/dmuscipula/experiments/SLAx/maker/SLAx_merged_02_03.maker.output/SLAx_merged_02_03_datastore/AB/FC/MblContig1//theVoid.MblContig1/MblContig1.2222-2887.0.fasta -Q dna -T dna --model est2genome  --minintron 20 --maxintron 10000 --showcigar --percent 20 > /storage/tmp/jobs/dmuscipula/experiments/SLAx/maker/SLAx_merged_02_03.maker.output/SLAx_merged_02_03_datastore/AB/FC/MblContig1//theVoid.MblContig1/MblContig1.2222-2887.DM_Tra02_rep_c85280.est_exonerate.0
/storage/tmp/software/exonerate-2.2.0-x86_64/bin/exonerate  -q /storage/tmp/jobs/dmuscipula/experiments/SLAx/maker/SLAx_merged_02_03.maker.output/SLAx_merged_02_03_datastore/AB/FC/MblContig1//theVoid.MblContig1/DM_Tra02_rep_c85677.for.2174-2811.0.fasta -t /storage/tmp/jobs/dmuscipula/experiments/SLAx/maker/SLAx_merged_02_03.maker.output/SLAx_merged_02_03_datastore/AB/FC/MblContig1//theVoid.MblContig1/MblContig1.2174-2811.0.fasta -Q dna -T dna --model est2genome  --minintron 20 --maxintron 10000 --showcigar --percent 20 > /storage/tmp/jobs/dmuscipula/experiments/SLAx/maker/SLAx_merged_02_03.maker.output/SLAx_merged_02_03_datastore/AB/FC/MblContig1//theVoid.MblContig1/MblContig1.2174-2811.DM_Tra02_rep_c85677.est_exonerate.0
/storage/tmp/software/exonerate-2.2.0-x86_64/bin/exonerate  -q /storage/tmp/jobs/dmuscipula/experiments/SLAx/maker/SLAx_merged_02_03.maker.output/SLAx_merged_02_03_datastore/AB/FC/MblContig1//theVoid.MblContig1/DM_Tra02_rep_c86203.for.2191-2894.0.fasta -t /storage/tmp/jobs/dmuscipula/experiments/SLAx/maker/SLAx_merged_02_03.maker.output/SLAx_merged_02_03_datastore/AB/FC/MblContig1//theVoid.MblContig1/MblContig1.2191-2894.0.fasta -Q dna -T dna --model est2genome  --minintron 20 --maxintron 10000 --showcigar --percent 20 > /storage/tmp/jobs/dmuscipula/experiments/SLAx/maker/SLAx_merged_02_03.maker.output/SLAx_merged_02_03_datastore/AB/FC/MblContig1//theVoid.MblContig1/MblContig1.2191-2894.DM_Tra02_rep_c86203.est_exonerate.0
/storage/tmp/software/exonerate-2.2.0-x86_64/bin/exonerate  -q /storage/tmp/jobs/dmuscipula/experiments/SLAx/maker/SLAx_merged_02_03.maker.output/SLAx_merged_02_03_datastore/AB/FC/MblContig1//theVoid.MblContig1/DM_Tra02_rep_c88538.for.2176-2837.0.fasta -t /storage/tmp/jobs/dmuscipula/experiments/SLAx/maker/SLAx_merged_02_03.maker.output/SLAx_merged_02_03_datastore/AB/FC/MblContig1//theVoid.MblContig1/MblContig1.2176-2837.0.fasta -Q dna -T dna --model est2genome  --minintron 20 --maxintron 10000 --showcigar --percent 20 > /storage/tmp/jobs/dmuscipula/experiments/SLAx/maker/SLAx_merged_02_03.maker.output/SLAx_merged_02_03_datastore/AB/FC/MblContig1//theVoid.MblContig1/MblContig1.2176-2837.DM_Tra02_rep_c88538.est_exonerate.0
/storage/tmp/software/exonerate-2.2.0-x86_64/bin/exonerate  -q /storage/tmp/jobs/dmuscipula/experiments/SLAx/maker/SLAx_merged_02_03.maker.output/SLAx_merged_02_03_datastore/AB/FC/MblContig1//theVoid.MblContig1/DM_Tra02_rep_c94992.for.2269-2918.0.fasta -t /storage/tmp/jobs/dmuscipula/experiments/SLAx/maker/SLAx_merged_02_03.maker.output/SLAx_merged_02_03_datastore/AB/FC/MblContig1//theVoid.MblContig1/MblContig1.2269-2918.0.fasta -Q dna -T dna --model est2genome  --minintron 20 --maxintron 10000 --showcigar --percent 20 > /storage/tmp/jobs/dmuscipula/experiments/SLAx/maker/SLAx_merged_02_03.maker.output/SLAx_merged_02_03_datastore/AB/FC/MblContig1//theVoid.MblContig1/MblContig1.2269-2918.DM_Tra02_rep_c94992.est_exonerate.0
/storage/tmp/software/exonerate-2.2.0-x86_64/bin/exonerate  -q /storage/tmp/jobs/dmuscipula/experiments/SLAx/maker/SLAx_merged_02_03.maker.output/SLAx_merged_02_03_datastore/AB/FC/MblContig1//theVoid.MblContig1/NODE_1236506_length_398_cov_6%2E628141.for.1385-2206.0.fasta -t /storage/tmp/jobs/dmuscipula/experiments/SLAx/maker/SLAx_merged_02_03.maker.output/SLAx_merged_02_03_datastore/AB/FC/MblContig1//theVoid.MblContig1/MblContig1.1385-2206.0.fasta -Q dna -T dna --model est2genome  --minintron 20 --maxintron 10000 --showcigar --percent 20 > /storage/tmp/jobs/dmuscipula/experiments/SLAx/maker/SLAx_merged_02_03.maker.output/SLAx_merged_02_03_datastore/AB/FC/MblContig1//theVoid.MblContig1/MblContig1.1385-2206.NODE_1236506_length_398_cov_6%2E628141.est_exonerate.0
/storage/tmp/software/exonerate-2.2.0-x86_64/bin/exonerate  -q /storage/tmp/jobs/dmuscipula/experiments/SLAx/maker/SLAx_merged_02_03.maker.output/SLAx_merged_02_03_datastore/AB/FC/MblContig1//theVoid.MblContig1/NODE_139529_length_544_cov_11%2E053308.for.841-1808.0.fasta -t /storage/tmp/jobs/dmuscipula/experiments/SLAx/maker/SLAx_merged_02_03.maker.output/SLAx_merged_02_03_datastore/AB/FC/MblContig1//theVoid.MblContig1/MblContig1.841-1808.0.fasta -Q dna -T dna --model est2genome  --minintron 20 --maxintron 10000 --showcigar --percent 20 > /storage/tmp/jobs/dmuscipula/experiments/SLAx/maker/SLAx_merged_02_03.maker.output/SLAx_merged_02_03_datastore/AB/FC/MblContig1//theVoid.MblContig1/MblContig1.841-1808.NODE_139529_length_544_cov_11%2E053308.est_exonerate.0
/storage/tmp/software/exonerate-2.2.0-x86_64/bin/exonerate -q /storage/tmp/jobs/dmuscipula/experiments/SLAx/maker/SLAx_merged_02_03.maker.output/SLAx_merged_02_03_datastore/AB/FC/MblContig1//theVoid.MblContig1/SP%3ASLAC1_ARATH.for.1120-3518.0.fasta -t /storage/tmp/jobs/dmuscipula/experiments/SLAx/maker/SLAx_merged_02_03.maker.output/SLAx_merged_02_03_datastore/AB/FC/MblContig1//theVoid.MblContig1/MblContig1.1120-3518.0.fasta -Q protein -T dna -m protein2genome --softmasktarget  --percent 20 --showcigar  > /storage/tmp/jobs/dmuscipula/experiments/SLAx/maker/SLAx_merged_02_03.maker.output/SLAx_merged_02_03_datastore/AB/FC/MblContig1//theVoid.MblContig1/MblContig1.1120-3518.SP%3ASLAC1_ARATH.p_exonerate.0
/storage/tmp/software/exonerate-2.2.0-x86_64/bin/exonerate -q /storage/tmp/jobs/dmuscipula/experiments/SLAx/maker/SLAx_merged_02_03.maker.output/SLAx_merged_02_03_datastore/AB/FC/MblContig1//theVoid.MblContig1/SP%3ASLAH2_ARATH.for.248-3548.0.fasta -t /storage/tmp/jobs/dmuscipula/experiments/SLAx/maker/SLAx_merged_02_03.maker.output/SLAx_merged_02_03_datastore/AB/FC/MblContig1//theVoid.MblContig1/MblContig1.248-3548.0.fasta -Q protein -T dna -m protein2genome --softmasktarget  --percent 20 --showcigar  > /storage/tmp/jobs/dmuscipula/experiments/SLAx/maker/SLAx_merged_02_03.maker.output/SLAx_merged_02_03_datastore/AB/FC/MblContig1//theVoid.MblContig1/MblContig1.248-3548.SP%3ASLAH2_ARATH.p_exonerate.0
/storage/tmp/software/exonerate-2.2.0-x86_64/bin/exonerate -q /storage/tmp/jobs/dmuscipula/experiments/SLAx/maker/SLAx_merged_02_03.maker.output/SLAx_merged_02_03_datastore/AB/FC/MblContig1//theVoid.MblContig1/SP%3ASLAH3_ARATH.for.86-3612.0.fasta -t /storage/tmp/jobs/dmuscipula/experiments/SLAx/maker/SLAx_merged_02_03.maker.output/SLAx_merged_02_03_datastore/AB/FC/MblContig1//theVoid.MblContig1/MblContig1.86-3612.0.fasta -Q protein -T dna -m protein2genome --softmasktarget  --percent 20 --showcigar  > /storage/tmp/jobs/dmuscipula/experiments/SLAx/maker/SLAx_merged_02_03.maker.output/SLAx_merged_02_03_datastore/AB/FC/MblContig1//theVoid.MblContig1/MblContig1.86-3612.SP%3ASLAH3_ARATH.p_exonerate.0
/storage/tmp/software/exonerate-2.2.0-x86_64/bin/exonerate -q /storage/tmp/jobs/dmuscipula/experiments/SLAx/maker/SLAx_merged_02_03.maker.output/SLAx_merged_02_03_datastore/AB/FC/MblContig1//theVoid.MblContig1/TR%3AA2WMT8_ORYSI.for.1180-3500.0.fasta -t /storage/tmp/jobs/dmuscipula/experiments/SLAx/maker/SLAx_merged_02_03.maker.output/SLAx_merged_02_03_datastore/AB/FC/MblContig1//theVoid.MblContig1/MblContig1.1180-3500.0.fasta -Q protein -T dna -m protein2genome --softmasktarget  --percent 20 --showcigar  > /storage/tmp/jobs/dmuscipula/experiments/SLAx/maker/SLAx_merged_02_03.maker.output/SLAx_merged_02_03_datastore/AB/FC/MblContig1//theVoid.MblContig1/MblContig1.1180-3500.TR%3AA2WMT8_ORYSI.p_exonerate.0
/storage/tmp/software/exonerate-2.2.0-x86_64/bin/exonerate -q /storage/tmp/jobs/dmuscipula/experiments/SLAx/maker/SLAx_merged_02_03.maker.output/SLAx_merged_02_03_datastore/AB/FC/MblContig1//theVoid.MblContig1/TR%3AA2WQC0_ORYSI.for.1120-3536.0.fasta -t /storage/tmp/jobs/dmuscipula/experiments/SLAx/maker/SLAx_merged_02_03.maker.output/SLAx_merged_02_03_datastore/AB/FC/MblContig1//theVoid.MblContig1/MblContig1.1120-3536.0.fasta -Q protein -T dna -m protein2genome --softmasktarget  --percent 20 --showcigar  > /storage/tmp/jobs/dmuscipula/experiments/SLAx/maker/SLAx_merged_02_03.maker.output/SLAx_merged_02_03_datastore/AB/FC/MblContig1//theVoid.MblContig1/MblContig1.1120-3536.TR%3AA2WQC0_ORYSI.p_exonerate.0
/storage/tmp/software/exonerate-2.2.0-x86_64/bin/exonerate -q /storage/tmp/jobs/dmuscipula/experiments/SLAx/maker/SLAx_merged_02_03.maker.output/SLAx_merged_02_03_datastore/AB/FC/MblContig1//theVoid.MblContig1/TR%3AA2WSR8_ORYSI.for.110-3584.0.fasta -t /storage/tmp/jobs/dmuscipula/experiments/SLAx/maker/SLAx_merged_02_03.maker.output/SLAx_merged_02_03_datastore/AB/FC/MblContig1//theVoid.MblContig1/MblContig1.110-3584.0.fasta -Q protein -T dna -m protein2genome --softmasktarget  --percent 20 --showcigar  > /storage/tmp/jobs/dmuscipula/experiments/SLAx/maker/SLAx_merged_02_03.maker.output/SLAx_merged_02_03_datastore/AB/FC/MblContig1//theVoid.MblContig1/MblContig1.110-3584.TR%3AA2WSR8_ORYSI.p_exonerate.0
/storage/tmp/software/exonerate-2.2.0-x86_64/bin/exonerate -q /storage/tmp/jobs/dmuscipula/experiments/SLAx/maker/SLAx_merged_02_03.maker.output/SLAx_merged_02_03_datastore/AB/FC/MblContig1//theVoid.MblContig1/TR%3AA2XWN1_ORYSI.for.1120-3518.0.fasta -t /storage/tmp/jobs/dmuscipula/experiments/SLAx/maker/SLAx_merged_02_03.maker.output/SLAx_merged_02_03_datastore/AB/FC/MblContig1//theVoid.MblContig1/MblContig1.1120-3518.0.fasta -Q protein -T dna -m protein2genome --softmasktarget  --percent 20 --showcigar  > /storage/tmp/jobs/dmuscipula/experiments/SLAx/maker/SLAx_merged_02_03.maker.output/SLAx_merged_02_03_datastore/AB/FC/MblContig1//theVoid.MblContig1/MblContig1.1120-3518.TR%3AA2XWN1_ORYSI.p_exonerate.0
/storage/tmp/software/exonerate-2.2.0-x86_64/bin/exonerate -q /storage/tmp/jobs/dmuscipula/experiments/SLAx/maker/SLAx_merged_02_03.maker.output/SLAx_merged_02_03_datastore/AB/FC/MblContig1//theVoid.MblContig1/TR%3AA2Y1P3_ORYSI.for.1141-3521.0.fasta -t /storage/tmp/jobs/dmuscipula/experiments/SLAx/maker/SLAx_merged_02_03.maker.output/SLAx_merged_02_03_datastore/AB/FC/MblContig1//theVoid.MblContig1/MblContig1.1141-3521.0.fasta -Q protein -T dna -m protein2genome --softmasktarget  --percent 20 --showcigar  > /storage/tmp/jobs/dmuscipula/experiments/SLAx/maker/SLAx_merged_02_03.maker.output/SLAx_merged_02_03_datastore/AB/FC/MblContig1//theVoid.MblContig1/MblContig1.1141-3521.TR%3AA2Y1P3_ORYSI.p_exonerate.0
/storage/tmp/software/exonerate-2.2.0-x86_64/bin/exonerate -q /storage/tmp/jobs/dmuscipula/experiments/SLAx/maker/SLAx_merged_02_03.maker.output/SLAx_merged_02_03_datastore/AB/FC/MblContig1//theVoid.MblContig1/TR%3AA2Y7Z7_ORYSI.for.110-3569.0.fasta -t /storage/tmp/jobs/dmuscipula/experiments/SLAx/maker/SLAx_merged_02_03.maker.output/SLAx_merged_02_03_datastore/AB/FC/MblContig1//theVoid.MblContig1/MblContig1.110-3569.0.fasta -Q protein -T dna -m protein2genome --softmasktarget  --percent 20 --showcigar  > /storage/tmp/jobs/dmuscipula/experiments/SLAx/maker/SLAx_merged_02_03.maker.output/SLAx_merged_02_03_datastore/AB/FC/MblContig1//theVoid.MblContig1/MblContig1.110-3569.TR%3AA2Y7Z7_ORYSI.p_exonerate.0
/storage/tmp/software/exonerate-2.2.0-x86_64/bin/exonerate -q /storage/tmp/jobs/dmuscipula/experiments/SLAx/maker/SLAx_merged_02_03.maker.output/SLAx_merged_02_03_datastore/AB/FC/MblContig1//theVoid.MblContig1/TR%3AA2YIS4_ORYSI.for.1141-3539.0.fasta -t /storage/tmp/jobs/dmuscipula/experiments/SLAx/maker/SLAx_merged_02_03.maker.output/SLAx_merged_02_03_datastore/AB/FC/MblContig1//theVoid.MblContig1/MblContig1.1141-3539.0.fasta -Q protein -T dna -m protein2genome --softmasktarget  --percent 20 --showcigar  > /storage/tmp/jobs/dmuscipula/experiments/SLAx/maker/SLAx_merged_02_03.maker.output/SLAx_merged_02_03_datastore/AB/FC/MblContig1//theVoid.MblContig1/MblContig1.1141-3539.TR%3AA2YIS4_ORYSI.p_exonerate.0
/storage/tmp/software/exonerate-2.2.0-x86_64/bin/exonerate -q /storage/tmp/jobs/dmuscipula/experiments/SLAx/maker/SLAx_merged_02_03.maker.output/SLAx_merged_02_03_datastore/AB/FC/MblContig1//theVoid.MblContig1/TR%3AA2ZR94_ORYSJ.for.1180-3500.0.fasta -t /storage/tmp/jobs/dmuscipula/experiments/SLAx/maker/SLAx_merged_02_03.maker.output/SLAx_merged_02_03_datastore/AB/FC/MblContig1//theVoid.MblContig1/MblContig1.1180-3500.0.fasta -Q protein -T dna -m protein2genome --softmasktarget  --percent 20 --showcigar  > /storage/tmp/jobs/dmuscipula/experiments/SLAx/maker/SLAx_merged_02_03.maker.output/SLAx_merged_02_03_datastore/AB/FC/MblContig1//theVoid.MblContig1/MblContig1.1180-3500.TR%3AA2ZR94_ORYSJ.p_exonerate.0
/storage/tmp/software/exonerate-2.2.0-x86_64/bin/exonerate -q /storage/tmp/jobs/dmuscipula/experiments/SLAx/maker/SLAx_merged_02_03.maker.output/SLAx_merged_02_03_datastore/AB/FC/MblContig1//theVoid.MblContig1/TR%3AA3AWM0_ORYSJ.for.1120-2182.0.fasta -t /storage/tmp/jobs/dmuscipula/experiments/SLAx/maker/SLAx_merged_02_03.maker.output/SLAx_merged_02_03_datastore/AB/FC/MblContig1//theVoid.MblContig1/MblContig1.1120-2182.0.fasta -Q protein -T dna -m protein2genome --softmasktarget  --percent 20 --showcigar  > /storage/tmp/jobs/dmuscipula/experiments/SLAx/maker/SLAx_merged_02_03.maker.output/SLAx_merged_02_03_datastore/AB/FC/MblContig1//theVoid.MblContig1/MblContig1.1120-2182.TR%3AA3AWM0_ORYSJ.p_exonerate.0
/storage/tmp/software/exonerate-2.2.0-x86_64/bin/exonerate -q /storage/tmp/jobs/dmuscipula/experiments/SLAx/maker/SLAx_merged_02_03.maker.output/SLAx_merged_02_03_datastore/AB/FC/MblContig1//theVoid.MblContig1/TR%3AA5B4F4_VITVI.for.1174-3479.0.fasta -t /storage/tmp/jobs/dmuscipula/experiments/SLAx/maker/SLAx_merged_02_03.maker.output/SLAx_merged_02_03_datastore/AB/FC/MblContig1//theVoid.MblContig1/MblContig1.1174-3479.0.fasta -Q protein -T dna -m protein2genome --softmasktarget  --percent 20 --showcigar  > /storage/tmp/jobs/dmuscipula/experiments/SLAx/maker/SLAx_merged_02_03.maker.output/SLAx_merged_02_03_datastore/AB/FC/MblContig1//theVoid.MblContig1/MblContig1.1174-3479.TR%3AA5B4F4_VITVI.p_exonerate.0
/storage/tmp/software/exonerate-2.2.0-x86_64/bin/exonerate -q /storage/tmp/jobs/dmuscipula/experiments/SLAx/maker/SLAx_merged_02_03.maker.output/SLAx_merged_02_03_datastore/AB/FC/MblContig1//theVoid.MblContig1/TR%3AA9RQS2_PHYPA.for.1141-3515.0.fasta -t /storage/tmp/jobs/dmuscipula/experiments/SLAx/maker/SLAx_merged_02_03.maker.output/SLAx_merged_02_03_datastore/AB/FC/MblContig1//theVoid.MblContig1/MblContig1.1141-3515.0.fasta -Q protein -T dna -m protein2genome --softmasktarget  --percent 20 --showcigar  > /storage/tmp/jobs/dmuscipula/experiments/SLAx/maker/SLAx_merged_02_03.maker.output/SLAx_merged_02_03_datastore/AB/FC/MblContig1//theVoid.MblContig1/MblContig1.1141-3515.TR%3AA9RQS2_PHYPA.p_exonerate.0
/storage/tmp/software/exonerate-2.2.0-x86_64/bin/exonerate -q /storage/tmp/jobs/dmuscipula/experiments/SLAx/maker/SLAx_merged_02_03.maker.output/SLAx_merged_02_03_datastore/AB/FC/MblContig1//theVoid.MblContig1/TR%3AA9RU49_PHYPA.for.1120-3518.0.fasta -t /storage/tmp/jobs/dmuscipula/experiments/SLAx/maker/SLAx_merged_02_03.maker.output/SLAx_merged_02_03_datastore/AB/FC/MblContig1//theVoid.MblContig1/MblContig1.1120-3518.0.fasta -Q protein -T dna -m protein2genome --softmasktarget  --percent 20 --showcigar  > /storage/tmp/jobs/dmuscipula/experiments/SLAx/maker/SLAx_merged_02_03.maker.output/SLAx_merged_02_03_datastore/AB/FC/MblContig1//theVoid.MblContig1/MblContig1.1120-3518.TR%3AA9RU49_PHYPA.p_exonerate.0
/storage/tmp/software/exonerate-2.2.0-x86_64/bin/exonerate -q /storage/tmp/jobs/dmuscipula/experiments/SLAx/maker/SLAx_merged_02_03.maker.output/SLAx_merged_02_03_datastore/AB/FC/MblContig1//theVoid.MblContig1/TR%3AA9SH15_PHYPA.for.1141-3518.0.fasta -t /storage/tmp/jobs/dmuscipula/experiments/SLAx/maker/SLAx_merged_02_03.maker.output/SLAx_merged_02_03_datastore/AB/FC/MblContig1//theVoid.MblContig1/MblContig1.1141-3518.0.fasta -Q protein -T dna -m protein2genome --softmasktarget  --percent 20 --showcigar  > /storage/tmp/jobs/dmuscipula/experiments/SLAx/maker/SLAx_merged_02_03.maker.output/SLAx_merged_02_03_datastore/AB/FC/MblContig1//theVoid.MblContig1/MblContig1.1141-3518.TR%3AA9SH15_PHYPA.p_exonerate.0
/storage/tmp/software/exonerate-2.2.0-x86_64/bin/exonerate -q /storage/tmp/jobs/dmuscipula/experiments/SLAx/maker/SLAx_merged_02_03.maker.output/SLAx_merged_02_03_datastore/AB/FC/MblContig1//theVoid.MblContig1/TR%3AA9TDH3_PHYPA.for.1150-3590.0.fasta -t /storage/tmp/jobs/dmuscipula/experiments/SLAx/maker/SLAx_merged_02_03.maker.output/SLAx_merged_02_03_datastore/AB/FC/MblContig1//theVoid.MblContig1/MblContig1.1150-3590.0.fasta -Q protein -T dna -m protein2genome --softmasktarget  --percent 20 --showcigar  > /storage/tmp/jobs/dmuscipula/experiments/SLAx/maker/SLAx_merged_02_03.maker.output/SLAx_merged_02_03_datastore/AB/FC/MblContig1//theVoid.MblContig1/MblContig1.1150-3590.TR%3AA9TDH3_PHYPA.p_exonerate.0
/storage/tmp/software/exonerate-2.2.0-x86_64/bin/exonerate -q /storage/tmp/jobs/dmuscipula/experiments/SLAx/maker/SLAx_merged_02_03.maker.output/SLAx_merged_02_03_datastore/AB/FC/MblContig1//theVoid.MblContig1/TR%3AB6SQ55_MAIZE.for.1162-3500.0.fasta -t /storage/tmp/jobs/dmuscipula/experiments/SLAx/maker/SLAx_merged_02_03.maker.output/SLAx_merged_02_03_datastore/AB/FC/MblContig1//theVoid.MblContig1/MblContig1.1162-3500.0.fasta -Q protein -T dna -m protein2genome --softmasktarget  --percent 20 --showcigar  > /storage/tmp/jobs/dmuscipula/experiments/SLAx/maker/SLAx_merged_02_03.maker.output/SLAx_merged_02_03_datastore/AB/FC/MblContig1//theVoid.MblContig1/MblContig1.1162-3500.TR%3AB6SQ55_MAIZE.p_exonerate.0
/storage/tmp/software/exonerate-2.2.0-x86_64/bin/exonerate -q /storage/tmp/jobs/dmuscipula/experiments/SLAx/maker/SLAx_merged_02_03.maker.output/SLAx_merged_02_03_datastore/AB/FC/MblContig1//theVoid.MblContig1/TR%3AB6SWN8_MAIZE.for.1120-3551.0.fasta -t /storage/tmp/jobs/dmuscipula/experiments/SLAx/maker/SLAx_merged_02_03.maker.output/SLAx_merged_02_03_datastore/AB/FC/MblContig1//theVoid.MblContig1/MblContig1.1120-3551.0.fasta -Q protein -T dna -m protein2genome --softmasktarget  --percent 20 --showcigar  > /storage/tmp/jobs/dmuscipula/experiments/SLAx/maker/SLAx_merged_02_03.maker.output/SLAx_merged_02_03_datastore/AB/FC/MblContig1//theVoid.MblContig1/MblContig1.1120-3551.TR%3AB6SWN8_MAIZE.p_exonerate.0
/storage/tmp/software/exonerate-2.2.0-x86_64/bin/exonerate -q /storage/tmp/jobs/dmuscipula/experiments/SLAx/maker/SLAx_merged_02_03.maker.output/SLAx_merged_02_03_datastore/AB/FC/MblContig1//theVoid.MblContig1/TR%3AB8AAY8_ORYSI.for.1132-3551.0.fasta -t /storage/tmp/jobs/dmuscipula/experiments/SLAx/maker/SLAx_merged_02_03.maker.output/SLAx_merged_02_03_datastore/AB/FC/MblContig1//theVoid.MblContig1/MblContig1.1132-3551.0.fasta -Q protein -T dna -m protein2genome --softmasktarget  --percent 20 --showcigar  > /storage/tmp/jobs/dmuscipula/experiments/SLAx/maker/SLAx_merged_02_03.maker.output/SLAx_merged_02_03_datastore/AB/FC/MblContig1//theVoid.MblContig1/MblContig1.1132-3551.TR%3AB8AAY8_ORYSI.p_exonerate.0
/storage/tmp/software/exonerate-2.2.0-x86_64/bin/exonerate -q /storage/tmp/jobs/dmuscipula/experiments/SLAx/maker/SLAx_merged_02_03.maker.output/SLAx_merged_02_03_datastore/AB/FC/MblContig1//theVoid.MblContig1/TR%3AB8B7U9_ORYSI.for.2933-3539.0.fasta -t /storage/tmp/jobs/dmuscipula/experiments/SLAx/maker/SLAx_merged_02_03.maker.output/SLAx_merged_02_03_datastore/AB/FC/MblContig1//theVoid.MblContig1/MblContig1.2933-3539.0.fasta -Q protein -T dna -m protein2genome --softmasktarget  --percent 20 --showcigar  > /storage/tmp/jobs/dmuscipula/experiments/SLAx/maker/SLAx_merged_02_03.maker.output/SLAx_merged_02_03_datastore/AB/FC/MblContig1//theVoid.MblContig1/MblContig1.2933-3539.TR%3AB8B7U9_ORYSI.p_exonerate.0
/storage/tmp/software/exonerate-2.2.0-x86_64/bin/exonerate -q /storage/tmp/jobs/dmuscipula/experiments/SLAx/maker/SLAx_merged_02_03.maker.output/SLAx_merged_02_03_datastore/AB/FC/MblContig1//theVoid.MblContig1/TR%3AB9EU69_ORYSJ.for.1132-3575.0.fasta -t /storage/tmp/jobs/dmuscipula/experiments/SLAx/maker/SLAx_merged_02_03.maker.output/SLAx_merged_02_03_datastore/AB/FC/MblContig1//theVoid.MblContig1/MblContig1.1132-3575.0.fasta -Q protein -T dna -m protein2genome --softmasktarget  --percent 20 --showcigar  > /storage/tmp/jobs/dmuscipula/experiments/SLAx/maker/SLAx_merged_02_03.maker.output/SLAx_merged_02_03_datastore/AB/FC/MblContig1//theVoid.MblContig1/MblContig1.1132-3575.TR%3AB9EU69_ORYSJ.p_exonerate.0
/storage/tmp/software/exonerate-2.2.0-x86_64/bin/exonerate -q /storage/tmp/jobs/dmuscipula/experiments/SLAx/maker/SLAx_merged_02_03.maker.output/SLAx_merged_02_03_datastore/AB/FC/MblContig1//theVoid.MblContig1/TR%3AB9EY47_ORYSJ.for.110-3584.0.fasta -t /storage/tmp/jobs/dmuscipula/experiments/SLAx/maker/SLAx_merged_02_03.maker.output/SLAx_merged_02_03_datastore/AB/FC/MblContig1//theVoid.MblContig1/MblContig1.110-3584.0.fasta -Q protein -T dna -m protein2genome --softmasktarget  --percent 20 --showcigar  > /storage/tmp/jobs/dmuscipula/experiments/SLAx/maker/SLAx_merged_02_03.maker.output/SLAx_merged_02_03_datastore/AB/FC/MblContig1//theVoid.MblContig1/MblContig1.110-3584.TR%3AB9EY47_ORYSJ.p_exonerate.0
/storage/tmp/software/exonerate-2.2.0-x86_64/bin/exonerate -q /storage/tmp/jobs/dmuscipula/experiments/SLAx/maker/SLAx_merged_02_03.maker.output/SLAx_merged_02_03_datastore/AB/FC/MblContig1//theVoid.MblContig1/TR%3AB9F0C5_ORYSJ.for.1120-1777.0.fasta -t /storage/tmp/jobs/dmuscipula/experiments/SLAx/maker/SLAx_merged_02_03.maker.output/SLAx_merged_02_03_datastore/AB/FC/MblContig1//theVoid.MblContig1/MblContig1.1120-1777.0.fasta -Q protein -T dna -m protein2genome --softmasktarget  --percent 20 --showcigar  > /storage/tmp/jobs/dmuscipula/experiments/SLAx/maker/SLAx_merged_02_03.maker.output/SLAx_merged_02_03_datastore/AB/FC/MblContig1//theVoid.MblContig1/MblContig1.1120-1777.TR%3AB9F0C5_ORYSJ.p_exonerate.0
/storage/tmp/software/exonerate-2.2.0-x86_64/bin/exonerate -q /storage/tmp/jobs/dmuscipula/experiments/SLAx/maker/SLAx_merged_02_03.maker.output/SLAx_merged_02_03_datastore/AB/FC/MblContig1//theVoid.MblContig1/TR%3AB9FIR4_ORYSJ.for.110-3612.0.fasta -t /storage/tmp/jobs/dmuscipula/experiments/SLAx/maker/SLAx_merged_02_03.maker.output/SLAx_merged_02_03_datastore/AB/FC/MblContig1//theVoid.MblContig1/MblContig1.110-3612.0.fasta -Q protein -T dna -m protein2genome --softmasktarget  --percent 20 --showcigar  > /storage/tmp/jobs/dmuscipula/experiments/SLAx/maker/SLAx_merged_02_03.maker.output/SLAx_merged_02_03_datastore/AB/FC/MblContig1//theVoid.MblContig1/MblContig1.110-3612.TR%3AB9FIR4_ORYSJ.p_exonerate.0
/storage/tmp/software/exonerate-2.2.0-x86_64/bin/exonerate -q /storage/tmp/jobs/dmuscipula/experiments/SLAx/maker/SLAx_merged_02_03.maker.output/SLAx_merged_02_03_datastore/AB/FC/MblContig1//theVoid.MblContig1/TR%3AB9FVU2_ORYSJ.for.1141-2117.0.fasta -t /storage/tmp/jobs/dmuscipula/experiments/SLAx/maker/SLAx_merged_02_03.maker.output/SLAx_merged_02_03_datastore/AB/FC/MblContig1//theVoid.MblContig1/MblContig1.1141-2117.0.fasta -Q protein -T dna -m protein2genome --softmasktarget  --percent 20 --showcigar  > /storage/tmp/jobs/dmuscipula/experiments/SLAx/maker/SLAx_merged_02_03.maker.output/SLAx_merged_02_03_datastore/AB/FC/MblContig1//theVoid.MblContig1/MblContig1.1141-2117.TR%3AB9FVU2_ORYSJ.p_exonerate.0
/storage/tmp/software/exonerate-2.2.0-x86_64/bin/exonerate -q /storage/tmp/jobs/dmuscipula/experiments/SLAx/maker/SLAx_merged_02_03.maker.output/SLAx_merged_02_03_datastore/AB/FC/MblContig1//theVoid.MblContig1/TR%3AB9FVU3_ORYSJ.for.2894-3539.0.fasta -t /storage/tmp/jobs/dmuscipula/experiments/SLAx/maker/SLAx_merged_02_03.maker.output/SLAx_merged_02_03_datastore/AB/FC/MblContig1//theVoid.MblContig1/MblContig1.2894-3539.0.fasta -Q protein -T dna -m protein2genome --softmasktarget  --percent 20 --showcigar  > /storage/tmp/jobs/dmuscipula/experiments/SLAx/maker/SLAx_merged_02_03.maker.output/SLAx_merged_02_03_datastore/AB/FC/MblContig1//theVoid.MblContig1/MblContig1.2894-3539.TR%3AB9FVU3_ORYSJ.p_exonerate.0
/storage/tmp/software/exonerate-2.2.0-x86_64/bin/exonerate -q /storage/tmp/jobs/dmuscipula/experiments/SLAx/maker/SLAx_merged_02_03.maker.output/SLAx_merged_02_03_datastore/AB/FC/MblContig1//theVoid.MblContig1/TR%3AB9I506_POPTR.for.1822-3612.0.fasta -t /storage/tmp/jobs/dmuscipula/experiments/SLAx/maker/SLAx_merged_02_03.maker.output/SLAx_merged_02_03_datastore/AB/FC/MblContig1//theVoid.MblContig1/MblContig1.1822-3612.0.fasta -Q protein -T dna -m protein2genome --softmasktarget  --percent 20 --showcigar  > /storage/tmp/jobs/dmuscipula/experiments/SLAx/maker/SLAx_merged_02_03.maker.output/SLAx_merged_02_03_datastore/AB/FC/MblContig1//theVoid.MblContig1/MblContig1.1822-3612.TR%3AB9I506_POPTR.p_exonerate.0
/storage/tmp/software/exonerate-2.2.0-x86_64/bin/exonerate -q /storage/tmp/jobs/dmuscipula/experiments/SLAx/maker/SLAx_merged_02_03.maker.output/SLAx_merged_02_03_datastore/AB/FC/MblContig1//theVoid.MblContig1/TR%3AB9N343_POPTR.for.1564-3612.0.fasta -t /storage/tmp/jobs/dmuscipula/experiments/SLAx/maker/SLAx_merged_02_03.maker.output/SLAx_merged_02_03_datastore/AB/FC/MblContig1//theVoid.MblContig1/MblContig1.1564-3612.0.fasta -Q protein -T dna -m protein2genome --softmasktarget  --percent 20 --showcigar  > /storage/tmp/jobs/dmuscipula/experiments/SLAx/maker/SLAx_merged_02_03.maker.output/SLAx_merged_02_03_datastore/AB/FC/MblContig1//theVoid.MblContig1/MblContig1.1564-3612.TR%3AB9N343_POPTR.p_exonerate.0
/storage/tmp/software/exonerate-2.2.0-x86_64/bin/exonerate -q /storage/tmp/jobs/dmuscipula/experiments/SLAx/maker/SLAx_merged_02_03.maker.output/SLAx_merged_02_03_datastore/AB/FC/MblContig1//theVoid.MblContig1/TR%3AB9N344_POPTR.for.335-1648.0.fasta -t /storage/tmp/jobs/dmuscipula/experiments/SLAx/maker/SLAx_merged_02_03.maker.output/SLAx_merged_02_03_datastore/AB/FC/MblContig1//theVoid.MblContig1/MblContig1.335-1648.0.fasta -Q protein -T dna -m protein2genome --softmasktarget  --percent 20 --showcigar  > /storage/tmp/jobs/dmuscipula/experiments/SLAx/maker/SLAx_merged_02_03.maker.output/SLAx_merged_02_03_datastore/AB/FC/MblContig1//theVoid.MblContig1/MblContig1.335-1648.TR%3AB9N344_POPTR.p_exonerate.0
/storage/tmp/software/exonerate-2.2.0-x86_64/bin/exonerate -q /storage/tmp/jobs/dmuscipula/experiments/SLAx/maker/SLAx_merged_02_03.maker.output/SLAx_merged_02_03_datastore/AB/FC/MblContig1//theVoid.MblContig1/TR%3AB9RBW3_RICCO.for.1120-3612.0.fasta -t /storage/tmp/jobs/dmuscipula/experiments/SLAx/maker/SLAx_merged_02_03.maker.output/SLAx_merged_02_03_datastore/AB/FC/MblContig1//theVoid.MblContig1/MblContig1.1120-3612.0.fasta -Q protein -T dna -m protein2genome --softmasktarget  --percent 20 --showcigar  > /storage/tmp/jobs/dmuscipula/experiments/SLAx/maker/SLAx_merged_02_03.maker.output/SLAx_merged_02_03_datastore/AB/FC/MblContig1//theVoid.MblContig1/MblContig1.1120-3612.TR%3AB9RBW3_RICCO.p_exonerate.0
/storage/tmp/software/exonerate-2.2.0-x86_64/bin/exonerate -q /storage/tmp/jobs/dmuscipula/experiments/SLAx/maker/SLAx_merged_02_03.maker.output/SLAx_merged_02_03_datastore/AB/FC/MblContig1//theVoid.MblContig1/TR%3AB9RIQ3_RICCO.for.80-3612.0.fasta -t /storage/tmp/jobs/dmuscipula/experiments/SLAx/maker/SLAx_merged_02_03.maker.output/SLAx_merged_02_03_datastore/AB/FC/MblContig1//theVoid.MblContig1/MblContig1.80-3612.0.fasta -Q protein -T dna -m protein2genome --softmasktarget  --percent 20 --showcigar  > /storage/tmp/jobs/dmuscipula/experiments/SLAx/maker/SLAx_merged_02_03.maker.output/SLAx_merged_02_03_datastore/AB/FC/MblContig1//theVoid.MblContig1/MblContig1.80-3612.TR%3AB9RIQ3_RICCO.p_exonerate.0
/storage/tmp/software/exonerate-2.2.0-x86_64/bin/exonerate -q /storage/tmp/jobs/dmuscipula/experiments/SLAx/maker/SLAx_merged_02_03.maker.output/SLAx_merged_02_03_datastore/AB/FC/MblContig1//theVoid.MblContig1/TR%3AB9SFR4_RICCO.for.1720-3518.0.fasta -t /storage/tmp/jobs/dmuscipula/experiments/SLAx/maker/SLAx_merged_02_03.maker.output/SLAx_merged_02_03_datastore/AB/FC/MblContig1//theVoid.MblContig1/MblContig1.1720-3518.0.fasta -Q protein -T dna -m protein2genome --softmasktarget  --percent 20 --showcigar  > /storage/tmp/jobs/dmuscipula/experiments/SLAx/maker/SLAx_merged_02_03.maker.output/SLAx_merged_02_03_datastore/AB/FC/MblContig1//theVoid.MblContig1/MblContig1.1720-3518.TR%3AB9SFR4_RICCO.p_exonerate.0
/storage/tmp/software/exonerate-2.2.0-x86_64/bin/exonerate -q /storage/tmp/jobs/dmuscipula/experiments/SLAx/maker/SLAx_merged_02_03.maker.output/SLAx_merged_02_03_datastore/AB/FC/MblContig1//theVoid.MblContig1/TR%3AC5XJG5_SORBI.for.1180-3542.0.fasta -t /storage/tmp/jobs/dmuscipula/experiments/SLAx/maker/SLAx_merged_02_03.maker.output/SLAx_merged_02_03_datastore/AB/FC/MblContig1//theVoid.MblContig1/MblContig1.1180-3542.0.fasta -Q protein -T dna -m protein2genome --softmasktarget  --percent 20 --showcigar  > /storage/tmp/jobs/dmuscipula/experiments/SLAx/maker/SLAx_merged_02_03.maker.output/SLAx_merged_02_03_datastore/AB/FC/MblContig1//theVoid.MblContig1/MblContig1.1180-3542.TR%3AC5XJG5_SORBI.p_exonerate.0
/storage/tmp/software/exonerate-2.2.0-x86_64/bin/exonerate -q /storage/tmp/jobs/dmuscipula/experiments/SLAx/maker/SLAx_merged_02_03.maker.output/SLAx_merged_02_03_datastore/AB/FC/MblContig1//theVoid.MblContig1/TR%3AC5XK99_SORBI.for.1342-3518.0.fasta -t /storage/tmp/jobs/dmuscipula/experiments/SLAx/maker/SLAx_merged_02_03.maker.output/SLAx_merged_02_03_datastore/AB/FC/MblContig1//theVoid.MblContig1/MblContig1.1342-3518.0.fasta -Q protein -T dna -m protein2genome --softmasktarget  --percent 20 --showcigar  > /storage/tmp/jobs/dmuscipula/experiments/SLAx/maker/SLAx_merged_02_03.maker.output/SLAx_merged_02_03_datastore/AB/FC/MblContig1//theVoid.MblContig1/MblContig1.1342-3518.TR%3AC5XK99_SORBI.p_exonerate.0
/storage/tmp/software/exonerate-2.2.0-x86_64/bin/exonerate -q /storage/tmp/jobs/dmuscipula/experiments/SLAx/maker/SLAx_merged_02_03.maker.output/SLAx_merged_02_03_datastore/AB/FC/MblContig1//theVoid.MblContig1/TR%3AC5XR65_SORBI.for.110-3578.0.fasta -t /storage/tmp/jobs/dmuscipula/experiments/SLAx/maker/SLAx_merged_02_03.maker.output/SLAx_merged_02_03_datastore/AB/FC/MblContig1//theVoid.MblContig1/MblContig1.110-3578.0.fasta -Q protein -T dna -m protein2genome --softmasktarget  --percent 20 --showcigar  > /storage/tmp/jobs/dmuscipula/experiments/SLAx/maker/SLAx_merged_02_03.maker.output/SLAx_merged_02_03_datastore/AB/FC/MblContig1//theVoid.MblContig1/MblContig1.110-3578.TR%3AC5XR65_SORBI.p_exonerate.0
/storage/tmp/software/exonerate-2.2.0-x86_64/bin/exonerate -q /storage/tmp/jobs/dmuscipula/experiments/SLAx/maker/SLAx_merged_02_03.maker.output/SLAx_merged_02_03_datastore/AB/FC/MblContig1//theVoid.MblContig1/TR%3AC5Y2R5_SORBI.for.1159-3536.0.fasta -t /storage/tmp/jobs/dmuscipula/experiments/SLAx/maker/SLAx_merged_02_03.maker.output/SLAx_merged_02_03_datastore/AB/FC/MblContig1//theVoid.MblContig1/MblContig1.1159-3536.0.fasta -Q protein -T dna -m protein2genome --softmasktarget  --percent 20 --showcigar  > /storage/tmp/jobs/dmuscipula/experiments/SLAx/maker/SLAx_merged_02_03.maker.output/SLAx_merged_02_03_datastore/AB/FC/MblContig1//theVoid.MblContig1/MblContig1.1159-3536.TR%3AC5Y2R5_SORBI.p_exonerate.0
/storage/tmp/software/exonerate-2.2.0-x86_64/bin/exonerate -q /storage/tmp/jobs/dmuscipula/experiments/SLAx/maker/SLAx_merged_02_03.maker.output/SLAx_merged_02_03_datastore/AB/FC/MblContig1//theVoid.MblContig1/TR%3AC5YEF3_SORBI.for.1120-3518.0.fasta -t /storage/tmp/jobs/dmuscipula/experiments/SLAx/maker/SLAx_merged_02_03.maker.output/SLAx_merged_02_03_datastore/AB/FC/MblContig1//theVoid.MblContig1/MblContig1.1120-3518.0.fasta -Q protein -T dna -m protein2genome --softmasktarget  --percent 20 --showcigar  > /storage/tmp/jobs/dmuscipula/experiments/SLAx/maker/SLAx_merged_02_03.maker.output/SLAx_merged_02_03_datastore/AB/FC/MblContig1//theVoid.MblContig1/MblContig1.1120-3518.TR%3AC5YEF3_SORBI.p_exonerate.0
/storage/tmp/software/exonerate-2.2.0-x86_64/bin/exonerate -q /storage/tmp/jobs/dmuscipula/experiments/SLAx/maker/SLAx_merged_02_03.maker.output/SLAx_merged_02_03_datastore/AB/FC/MblContig1//theVoid.MblContig1/TR%3AC5YN44_SORBI.for.1120-3551.0.fasta -t /storage/tmp/jobs/dmuscipula/experiments/SLAx/maker/SLAx_merged_02_03.maker.output/SLAx_merged_02_03_datastore/AB/FC/MblContig1//theVoid.MblContig1/MblContig1.1120-3551.0.fasta -Q protein -T dna -m protein2genome --softmasktarget  --percent 20 --showcigar  > /storage/tmp/jobs/dmuscipula/experiments/SLAx/maker/SLAx_merged_02_03.maker.output/SLAx_merged_02_03_datastore/AB/FC/MblContig1//theVoid.MblContig1/MblContig1.1120-3551.TR%3AC5YN44_SORBI.p_exonerate.0
/storage/tmp/software/exonerate-2.2.0-x86_64/bin/exonerate -q /storage/tmp/jobs/dmuscipula/experiments/SLAx/maker/SLAx_merged_02_03.maker.output/SLAx_merged_02_03_datastore/AB/FC/MblContig1//theVoid.MblContig1/TR%3AC5YUS9_SORBI.for.1120-3536.0.fasta -t /storage/tmp/jobs/dmuscipula/experiments/SLAx/maker/SLAx_merged_02_03.maker.output/SLAx_merged_02_03_datastore/AB/FC/MblContig1//theVoid.MblContig1/MblContig1.1120-3536.0.fasta -Q protein -T dna -m protein2genome --softmasktarget  --percent 20 --showcigar  > /storage/tmp/jobs/dmuscipula/experiments/SLAx/maker/SLAx_merged_02_03.maker.output/SLAx_merged_02_03_datastore/AB/FC/MblContig1//theVoid.MblContig1/MblContig1.1120-3536.TR%3AC5YUS9_SORBI.p_exonerate.0
/storage/tmp/software/exonerate-2.2.0-x86_64/bin/exonerate -q /storage/tmp/jobs/dmuscipula/experiments/SLAx/maker/SLAx_merged_02_03.maker.output/SLAx_merged_02_03_datastore/AB/FC/MblContig1//theVoid.MblContig1/TR%3AC5YWJ1_SORBI.for.32-3527.0.fasta -t /storage/tmp/jobs/dmuscipula/experiments/SLAx/maker/SLAx_merged_02_03.maker.output/SLAx_merged_02_03_datastore/AB/FC/MblContig1//theVoid.MblContig1/MblContig1.32-3527.0.fasta -Q protein -T dna -m protein2genome --softmasktarget  --percent 20 --showcigar  > /storage/tmp/jobs/dmuscipula/experiments/SLAx/maker/SLAx_merged_02_03.maker.output/SLAx_merged_02_03_datastore/AB/FC/MblContig1//theVoid.MblContig1/MblContig1.32-3527.TR%3AC5YWJ1_SORBI.p_exonerate.0
/storage/tmp/software/exonerate-2.2.0-x86_64/bin/exonerate -q /storage/tmp/jobs/dmuscipula/experiments/SLAx/maker/SLAx_merged_02_03.maker.output/SLAx_merged_02_03_datastore/AB/FC/MblContig1//theVoid.MblContig1/TR%3AC5YWJ2_SORBI.for.41-3527.0.fasta -t /storage/tmp/jobs/dmuscipula/experiments/SLAx/maker/SLAx_merged_02_03.maker.output/SLAx_merged_02_03_datastore/AB/FC/MblContig1//theVoid.MblContig1/MblContig1.41-3527.0.fasta -Q protein -T dna -m protein2genome --softmasktarget  --percent 20 --showcigar  > /storage/tmp/jobs/dmuscipula/experiments/SLAx/maker/SLAx_merged_02_03.maker.output/SLAx_merged_02_03_datastore/AB/FC/MblContig1//theVoid.MblContig1/MblContig1.41-3527.TR%3AC5YWJ2_SORBI.p_exonerate.0
/storage/tmp/software/exonerate-2.2.0-x86_64/bin/exonerate -q /storage/tmp/jobs/dmuscipula/experiments/SLAx/maker/SLAx_merged_02_03.maker.output/SLAx_merged_02_03_datastore/AB/FC/MblContig1//theVoid.MblContig1/TR%3AC5YWJ3_SORBI.for.1120-3527.0.fasta -t /storage/tmp/jobs/dmuscipula/experiments/SLAx/maker/SLAx_merged_02_03.maker.output/SLAx_merged_02_03_datastore/AB/FC/MblContig1//theVoid.MblContig1/MblContig1.1120-3527.0.fasta -Q protein -T dna -m protein2genome --softmasktarget  --percent 20 --showcigar  > /storage/tmp/jobs/dmuscipula/experiments/SLAx/maker/SLAx_merged_02_03.maker.output/SLAx_merged_02_03_datastore/AB/FC/MblContig1//theVoid.MblContig1/MblContig1.1120-3527.TR%3AC5YWJ3_SORBI.p_exonerate.0
/storage/tmp/software/exonerate-2.2.0-x86_64/bin/exonerate -q /storage/tmp/jobs/dmuscipula/experiments/SLAx/maker/SLAx_merged_02_03.maker.output/SLAx_merged_02_03_datastore/AB/FC/MblContig1//theVoid.MblContig1/TR%3AC5YZG0_SORBI.for.365-3530.0.fasta -t /storage/tmp/jobs/dmuscipula/experiments/SLAx/maker/SLAx_merged_02_03.maker.output/SLAx_merged_02_03_datastore/AB/FC/MblContig1//theVoid.MblContig1/MblContig1.365-3530.0.fasta -Q protein -T dna -m protein2genome --softmasktarget  --percent 20 --showcigar  > /storage/tmp/jobs/dmuscipula/experiments/SLAx/maker/SLAx_merged_02_03.maker.output/SLAx_merged_02_03_datastore/AB/FC/MblContig1//theVoid.MblContig1/MblContig1.365-3530.TR%3AC5YZG0_SORBI.p_exonerate.0
/storage/tmp/software/exonerate-2.2.0-x86_64/bin/exonerate -q /storage/tmp/jobs/dmuscipula/experiments/SLAx/maker/SLAx_merged_02_03.maker.output/SLAx_merged_02_03_datastore/AB/FC/MblContig1//theVoid.MblContig1/TR%3AC7IXE7_ORYSJ.for.2897-3500.0.fasta -t /storage/tmp/jobs/dmuscipula/experiments/SLAx/maker/SLAx_merged_02_03.maker.output/SLAx_merged_02_03_datastore/AB/FC/MblContig1//theVoid.MblContig1/MblContig1.2897-3500.0.fasta -Q protein -T dna -m protein2genome --softmasktarget  --percent 20 --showcigar  > /storage/tmp/jobs/dmuscipula/experiments/SLAx/maker/SLAx_merged_02_03.maker.output/SLAx_merged_02_03_datastore/AB/FC/MblContig1//theVoid.MblContig1/MblContig1.2897-3500.TR%3AC7IXE7_ORYSJ.p_exonerate.0
/storage/tmp/software/exonerate-2.2.0-x86_64/bin/exonerate -q /storage/tmp/jobs/dmuscipula/experiments/SLAx/maker/SLAx_merged_02_03.maker.output/SLAx_merged_02_03_datastore/AB/FC/MblContig1//theVoid.MblContig1/TR%3AD2U834_9ROSI.for.1168-3536.0.fasta -t /storage/tmp/jobs/dmuscipula/experiments/SLAx/maker/SLAx_merged_02_03.maker.output/SLAx_merged_02_03_datastore/AB/FC/MblContig1//theVoid.MblContig1/MblContig1.1168-3536.0.fasta -Q protein -T dna -m protein2genome --softmasktarget  --percent 20 --showcigar  > /storage/tmp/jobs/dmuscipula/experiments/SLAx/maker/SLAx_merged_02_03.maker.output/SLAx_merged_02_03_datastore/AB/FC/MblContig1//theVoid.MblContig1/MblContig1.1168-3536.TR%3AD2U834_9ROSI.p_exonerate.0
/storage/tmp/software/exonerate-2.2.0-x86_64/bin/exonerate -q /storage/tmp/jobs/dmuscipula/experiments/SLAx/maker/SLAx_merged_02_03.maker.output/SLAx_merged_02_03_datastore/AB/FC/MblContig1//theVoid.MblContig1/TR%3AD7KND2_ARALL.for.1120-3518.0.fasta -t /storage/tmp/jobs/dmuscipula/experiments/SLAx/maker/SLAx_merged_02_03.maker.output/SLAx_merged_02_03_datastore/AB/FC/MblContig1//theVoid.MblContig1/MblContig1.1120-3518.0.fasta -Q protein -T dna -m protein2genome --softmasktarget  --percent 20 --showcigar  > /storage/tmp/jobs/dmuscipula/experiments/SLAx/maker/SLAx_merged_02_03.maker.output/SLAx_merged_02_03_datastore/AB/FC/MblContig1//theVoid.MblContig1/MblContig1.1120-3518.TR%3AD7KND2_ARALL.p_exonerate.0
/storage/tmp/software/exonerate-2.2.0-x86_64/bin/exonerate -q /storage/tmp/jobs/dmuscipula/experiments/SLAx/maker/SLAx_merged_02_03.maker.output/SLAx_merged_02_03_datastore/AB/FC/MblContig1//theVoid.MblContig1/TR%3AD7M2F7_ARALL.for.344-3612.0.fasta -t /storage/tmp/jobs/dmuscipula/experiments/SLAx/maker/SLAx_merged_02_03.maker.output/SLAx_merged_02_03_datastore/AB/FC/MblContig1//theVoid.MblContig1/MblContig1.344-3612.0.fasta -Q protein -T dna -m protein2genome --softmasktarget  --percent 20 --showcigar  > /storage/tmp/jobs/dmuscipula/experiments/SLAx/maker/SLAx_merged_02_03.maker.output/SLAx_merged_02_03_datastore/AB/FC/MblContig1//theVoid.MblContig1/MblContig1.344-3612.TR%3AD7M2F7_ARALL.p_exonerate.0
/storage/tmp/software/exonerate-2.2.0-x86_64/bin/exonerate -q /storage/tmp/jobs/dmuscipula/experiments/SLAx/maker/SLAx_merged_02_03.maker.output/SLAx_merged_02_03_datastore/AB/FC/MblContig1//theVoid.MblContig1/TR%3AD7MDP9_ARALL.for.236-3612.0.fasta -t /storage/tmp/jobs/dmuscipula/experiments/SLAx/maker/SLAx_merged_02_03.maker.output/SLAx_merged_02_03_datastore/AB/FC/MblContig1//theVoid.MblContig1/MblContig1.236-3612.0.fasta -Q protein -T dna -m protein2genome --softmasktarget  --percent 20 --showcigar  > /storage/tmp/jobs/dmuscipula/experiments/SLAx/maker/SLAx_merged_02_03.maker.output/SLAx_merged_02_03_datastore/AB/FC/MblContig1//theVoid.MblContig1/MblContig1.236-3612.TR%3AD7MDP9_ARALL.p_exonerate.0
/storage/tmp/software/exonerate-2.2.0-x86_64/bin/exonerate -q /storage/tmp/jobs/dmuscipula/experiments/SLAx/maker/SLAx_merged_02_03.maker.output/SLAx_merged_02_03_datastore/AB/FC/MblContig1//theVoid.MblContig1/TR%3AD7TWC1_VITVI.for.1120-3518.0.fasta -t /storage/tmp/jobs/dmuscipula/experiments/SLAx/maker/SLAx_merged_02_03.maker.output/SLAx_merged_02_03_datastore/AB/FC/MblContig1//theVoid.MblContig1/MblContig1.1120-3518.0.fasta -Q protein -T dna -m protein2genome --softmasktarget  --percent 20 --showcigar  > /storage/tmp/jobs/dmuscipula/experiments/SLAx/maker/SLAx_merged_02_03.maker.output/SLAx_merged_02_03_datastore/AB/FC/MblContig1//theVoid.MblContig1/MblContig1.1120-3518.TR%3AD7TWC1_VITVI.p_exonerate.0
/storage/tmp/software/exonerate-2.2.0-x86_64/bin/exonerate -q /storage/tmp/jobs/dmuscipula/experiments/SLAx/maker/SLAx_merged_02_03.maker.output/SLAx_merged_02_03_datastore/AB/FC/MblContig1//theVoid.MblContig1/TR%3AD8R497_SELML.for.1120-3518.0.fasta -t /storage/tmp/jobs/dmuscipula/experiments/SLAx/maker/SLAx_merged_02_03.maker.output/SLAx_merged_02_03_datastore/AB/FC/MblContig1//theVoid.MblContig1/MblContig1.1120-3518.0.fasta -Q protein -T dna -m protein2genome --softmasktarget  --percent 20 --showcigar  > /storage/tmp/jobs/dmuscipula/experiments/SLAx/maker/SLAx_merged_02_03.maker.output/SLAx_merged_02_03_datastore/AB/FC/MblContig1//theVoid.MblContig1/MblContig1.1120-3518.TR%3AD8R497_SELML.p_exonerate.0
/storage/tmp/software/exonerate-2.2.0-x86_64/bin/exonerate -q /storage/tmp/jobs/dmuscipula/experiments/SLAx/maker/SLAx_merged_02_03.maker.output/SLAx_merged_02_03_datastore/AB/FC/MblContig1//theVoid.MblContig1/TR%3AD8RQR2_SELML.for.1120-3518.0.fasta -t /storage/tmp/jobs/dmuscipula/experiments/SLAx/maker/SLAx_merged_02_03.maker.output/SLAx_merged_02_03_datastore/AB/FC/MblContig1//theVoid.MblContig1/MblContig1.1120-3518.0.fasta -Q protein -T dna -m protein2genome --softmasktarget  --percent 20 --showcigar  > /storage/tmp/jobs/dmuscipula/experiments/SLAx/maker/SLAx_merged_02_03.maker.output/SLAx_merged_02_03_datastore/AB/FC/MblContig1//theVoid.MblContig1/MblContig1.1120-3518.TR%3AD8RQR2_SELML.p_exonerate.0
/storage/tmp/software/exonerate-2.2.0-x86_64/bin/exonerate -q /storage/tmp/jobs/dmuscipula/experiments/SLAx/maker/SLAx_merged_02_03.maker.output/SLAx_merged_02_03_datastore/AB/FC/MblContig1//theVoid.MblContig1/TR%3AD8S028_SELML.for.1120-3518.0.fasta -t /storage/tmp/jobs/dmuscipula/experiments/SLAx/maker/SLAx_merged_02_03.maker.output/SLAx_merged_02_03_datastore/AB/FC/MblContig1//theVoid.MblContig1/MblContig1.1120-3518.0.fasta -Q protein -T dna -m protein2genome --softmasktarget  --percent 20 --showcigar  > /storage/tmp/jobs/dmuscipula/experiments/SLAx/maker/SLAx_merged_02_03.maker.output/SLAx_merged_02_03_datastore/AB/FC/MblContig1//theVoid.MblContig1/MblContig1.1120-3518.TR%3AD8S028_SELML.p_exonerate.0
/storage/tmp/software/exonerate-2.2.0-x86_64/bin/exonerate -q /storage/tmp/jobs/dmuscipula/experiments/SLAx/maker/SLAx_merged_02_03.maker.output/SLAx_merged_02_03_datastore/AB/FC/MblContig1//theVoid.MblContig1/TR%3AD8S5U7_SELML.for.1141-3521.0.fasta -t /storage/tmp/jobs/dmuscipula/experiments/SLAx/maker/SLAx_merged_02_03.maker.output/SLAx_merged_02_03_datastore/AB/FC/MblContig1//theVoid.MblContig1/MblContig1.1141-3521.0.fasta -Q protein -T dna -m protein2genome --softmasktarget  --percent 20 --showcigar  > /storage/tmp/jobs/dmuscipula/experiments/SLAx/maker/SLAx_merged_02_03.maker.output/SLAx_merged_02_03_datastore/AB/FC/MblContig1//theVoid.MblContig1/MblContig1.1141-3521.TR%3AD8S5U7_SELML.p_exonerate.0
/storage/tmp/software/exonerate-2.2.0-x86_64/bin/exonerate -q /storage/tmp/jobs/dmuscipula/experiments/SLAx/maker/SLAx_merged_02_03.maker.output/SLAx_merged_02_03_datastore/AB/FC/MblContig1//theVoid.MblContig1/TR%3AD8SMW1_SELML.for.1141-3521.0.fasta -t /storage/tmp/jobs/dmuscipula/experiments/SLAx/maker/SLAx_merged_02_03.maker.output/SLAx_merged_02_03_datastore/AB/FC/MblContig1//theVoid.MblContig1/MblContig1.1141-3521.0.fasta -Q protein -T dna -m protein2genome --softmasktarget  --percent 20 --showcigar  > /storage/tmp/jobs/dmuscipula/experiments/SLAx/maker/SLAx_merged_02_03.maker.output/SLAx_merged_02_03_datastore/AB/FC/MblContig1//theVoid.MblContig1/MblContig1.1141-3521.TR%3AD8SMW1_SELML.p_exonerate.0
/storage/tmp/software/exonerate-2.2.0-x86_64/bin/exonerate -q /storage/tmp/jobs/dmuscipula/experiments/SLAx/maker/SLAx_merged_02_03.maker.output/SLAx_merged_02_03_datastore/AB/FC/MblContig1//theVoid.MblContig1/TR%3AD8SQB3_SELML.for.1150-3521.0.fasta -t /storage/tmp/jobs/dmuscipula/experiments/SLAx/maker/SLAx_merged_02_03.maker.output/SLAx_merged_02_03_datastore/AB/FC/MblContig1//theVoid.MblContig1/MblContig1.1150-3521.0.fasta -Q protein -T dna -m protein2genome --softmasktarget  --percent 20 --showcigar  > /storage/tmp/jobs/dmuscipula/experiments/SLAx/maker/SLAx_merged_02_03.maker.output/SLAx_merged_02_03_datastore/AB/FC/MblContig1//theVoid.MblContig1/MblContig1.1150-3521.TR%3AD8SQB3_SELML.p_exonerate.0
/storage/tmp/software/exonerate-2.2.0-x86_64/bin/exonerate -q /storage/tmp/jobs/dmuscipula/experiments/SLAx/maker/SLAx_merged_02_03.maker.output/SLAx_merged_02_03_datastore/AB/FC/MblContig1//theVoid.MblContig1/TR%3AD8SUM0_SELML.for.1150-3542.0.fasta -t /storage/tmp/jobs/dmuscipula/experiments/SLAx/maker/SLAx_merged_02_03.maker.output/SLAx_merged_02_03_datastore/AB/FC/MblContig1//theVoid.MblContig1/MblContig1.1150-3542.0.fasta -Q protein -T dna -m protein2genome --softmasktarget  --percent 20 --showcigar  > /storage/tmp/jobs/dmuscipula/experiments/SLAx/maker/SLAx_merged_02_03.maker.output/SLAx_merged_02_03_datastore/AB/FC/MblContig1//theVoid.MblContig1/MblContig1.1150-3542.TR%3AD8SUM0_SELML.p_exonerate.0
/storage/tmp/software/exonerate-2.2.0-x86_64/bin/exonerate -q /storage/tmp/jobs/dmuscipula/experiments/SLAx/maker/SLAx_merged_02_03.maker.output/SLAx_merged_02_03_datastore/AB/FC/MblContig1//theVoid.MblContig1/TR%3AE0CUQ2_VITVI.for.1-3612.0.fasta -t /storage/tmp/jobs/dmuscipula/experiments/SLAx/maker/SLAx_merged_02_03.maker.output/SLAx_merged_02_03_datastore/AB/FC/MblContig1//theVoid.MblContig1/MblContig1.1-3612.0.fasta -Q protein -T dna -m protein2genome --softmasktarget  --percent 20 --showcigar  > /storage/tmp/jobs/dmuscipula/experiments/SLAx/maker/SLAx_merged_02_03.maker.output/SLAx_merged_02_03_datastore/AB/FC/MblContig1//theVoid.MblContig1/MblContig1.1-3612.TR%3AE0CUQ2_VITVI.p_exonerate.0
/storage/tmp/software/exonerate-2.2.0-x86_64/bin/exonerate -q /storage/tmp/jobs/dmuscipula/experiments/SLAx/maker/SLAx_merged_02_03.maker.output/SLAx_merged_02_03_datastore/AB/FC/MblContig1//theVoid.MblContig1/TR%3AE5FYR7_BRARC.for.1120-3521.0.fasta -t /storage/tmp/jobs/dmuscipula/experiments/SLAx/maker/SLAx_merged_02_03.maker.output/SLAx_merged_02_03_datastore/AB/FC/MblContig1//theVoid.MblContig1/MblContig1.1120-3521.0.fasta -Q protein -T dna -m protein2genome --softmasktarget  --percent 20 --showcigar  > /storage/tmp/jobs/dmuscipula/experiments/SLAx/maker/SLAx_merged_02_03.maker.output/SLAx_merged_02_03_datastore/AB/FC/MblContig1//theVoid.MblContig1/MblContig1.1120-3521.TR%3AE5FYR7_BRARC.p_exonerate.0
/storage/tmp/software/exonerate-2.2.0-x86_64/bin/exonerate -q /storage/tmp/jobs/dmuscipula/experiments/SLAx/maker/SLAx_merged_02_03.maker.output/SLAx_merged_02_03_datastore/AB/FC/MblContig1//theVoid.MblContig1/TR%3AE5GBD8_CUCME.for.119-3612.0.fasta -t /storage/tmp/jobs/dmuscipula/experiments/SLAx/maker/SLAx_merged_02_03.maker.output/SLAx_merged_02_03_datastore/AB/FC/MblContig1//theVoid.MblContig1/MblContig1.119-3612.0.fasta -Q protein -T dna -m protein2genome --softmasktarget  --percent 20 --showcigar  > /storage/tmp/jobs/dmuscipula/experiments/SLAx/maker/SLAx_merged_02_03.maker.output/SLAx_merged_02_03_datastore/AB/FC/MblContig1//theVoid.MblContig1/MblContig1.119-3612.TR%3AE5GBD8_CUCME.p_exonerate.0
/storage/tmp/software/exonerate-2.2.0-x86_64/bin/exonerate -q /storage/tmp/jobs/dmuscipula/experiments/SLAx/maker/SLAx_merged_02_03.maker.output/SLAx_merged_02_03_datastore/AB/FC/MblContig1//theVoid.MblContig1/TR%3AE6NU71_9ROSI.for.1180-3530.0.fasta -t /storage/tmp/jobs/dmuscipula/experiments/SLAx/maker/SLAx_merged_02_03.maker.output/SLAx_merged_02_03_datastore/AB/FC/MblContig1//theVoid.MblContig1/MblContig1.1180-3530.0.fasta -Q protein -T dna -m protein2genome --softmasktarget  --percent 20 --showcigar  > /storage/tmp/jobs/dmuscipula/experiments/SLAx/maker/SLAx_merged_02_03.maker.output/SLAx_merged_02_03_datastore/AB/FC/MblContig1//theVoid.MblContig1/MblContig1.1180-3530.TR%3AE6NU71_9ROSI.p_exonerate.0
/storage/tmp/software/exonerate-2.2.0-x86_64/bin/exonerate -q /storage/tmp/jobs/dmuscipula/experiments/SLAx/maker/SLAx_merged_02_03.maker.output/SLAx_merged_02_03_datastore/AB/FC/MblContig1//theVoid.MblContig1/TR%3AF2DB49_HORVD.for.110-3578.0.fasta -t /storage/tmp/jobs/dmuscipula/experiments/SLAx/maker/SLAx_merged_02_03.maker.output/SLAx_merged_02_03_datastore/AB/FC/MblContig1//theVoid.MblContig1/MblContig1.110-3578.0.fasta -Q protein -T dna -m protein2genome --softmasktarget  --percent 20 --showcigar  > /storage/tmp/jobs/dmuscipula/experiments/SLAx/maker/SLAx_merged_02_03.maker.output/SLAx_merged_02_03_datastore/AB/FC/MblContig1//theVoid.MblContig1/MblContig1.110-3578.TR%3AF2DB49_HORVD.p_exonerate.0
/storage/tmp/software/exonerate-2.2.0-x86_64/bin/exonerate -q /storage/tmp/jobs/dmuscipula/experiments/SLAx/maker/SLAx_merged_02_03.maker.output/SLAx_merged_02_03_datastore/AB/FC/MblContig1//theVoid.MblContig1/TR%3AF2DVZ2_HORVD.for.1120-3536.0.fasta -t /storage/tmp/jobs/dmuscipula/experiments/SLAx/maker/SLAx_merged_02_03.maker.output/SLAx_merged_02_03_datastore/AB/FC/MblContig1//theVoid.MblContig1/MblContig1.1120-3536.0.fasta -Q protein -T dna -m protein2genome --softmasktarget  --percent 20 --showcigar  > /storage/tmp/jobs/dmuscipula/experiments/SLAx/maker/SLAx_merged_02_03.maker.output/SLAx_merged_02_03_datastore/AB/FC/MblContig1//theVoid.MblContig1/MblContig1.1120-3536.TR%3AF2DVZ2_HORVD.p_exonerate.0
/storage/tmp/software/exonerate-2.2.0-x86_64/bin/exonerate -q /storage/tmp/jobs/dmuscipula/experiments/SLAx/maker/SLAx_merged_02_03.maker.output/SLAx_merged_02_03_datastore/AB/FC/MblContig1//theVoid.MblContig1/TR%3AF2EEJ5_HORVD.for.1120-3533.0.fasta -t /storage/tmp/jobs/dmuscipula/experiments/SLAx/maker/SLAx_merged_02_03.maker.output/SLAx_merged_02_03_datastore/AB/FC/MblContig1//theVoid.MblContig1/MblContig1.1120-3533.0.fasta -Q protein -T dna -m protein2genome --softmasktarget  --percent 20 --showcigar  > /storage/tmp/jobs/dmuscipula/experiments/SLAx/maker/SLAx_merged_02_03.maker.output/SLAx_merged_02_03_datastore/AB/FC/MblContig1//theVoid.MblContig1/MblContig1.1120-3533.TR%3AF2EEJ5_HORVD.p_exonerate.0
/storage/tmp/software/exonerate-2.2.0-x86_64/bin/exonerate -q /storage/tmp/jobs/dmuscipula/experiments/SLAx/maker/SLAx_merged_02_03.maker.output/SLAx_merged_02_03_datastore/AB/FC/MblContig1//theVoid.MblContig1/TR%3AF6GZQ2_VITVI.for.1180-2308.0.fasta -t /storage/tmp/jobs/dmuscipula/experiments/SLAx/maker/SLAx_merged_02_03.maker.output/SLAx_merged_02_03_datastore/AB/FC/MblContig1//theVoid.MblContig1/MblContig1.1180-2308.0.fasta -Q protein -T dna -m protein2genome --softmasktarget  --percent 20 --showcigar  > /storage/tmp/jobs/dmuscipula/experiments/SLAx/maker/SLAx_merged_02_03.maker.output/SLAx_merged_02_03_datastore/AB/FC/MblContig1//theVoid.MblContig1/MblContig1.1180-2308.TR%3AF6GZQ2_VITVI.p_exonerate.0
/storage/tmp/software/exonerate-2.2.0-x86_64/bin/exonerate -q /storage/tmp/jobs/dmuscipula/experiments/SLAx/maker/SLAx_merged_02_03.maker.output/SLAx_merged_02_03_datastore/AB/FC/MblContig1//theVoid.MblContig1/TR%3AF6GZQ3_VITVI.for.2897-3500.0.fasta -t /storage/tmp/jobs/dmuscipula/experiments/SLAx/maker/SLAx_merged_02_03.maker.output/SLAx_merged_02_03_datastore/AB/FC/MblContig1//theVoid.MblContig1/MblContig1.2897-3500.0.fasta -Q protein -T dna -m protein2genome --softmasktarget  --percent 20 --showcigar  > /storage/tmp/jobs/dmuscipula/experiments/SLAx/maker/SLAx_merged_02_03.maker.output/SLAx_merged_02_03_datastore/AB/FC/MblContig1//theVoid.MblContig1/MblContig1.2897-3500.TR%3AF6GZQ3_VITVI.p_exonerate.0
/storage/tmp/software/exonerate-2.2.0-x86_64/bin/exonerate -q /storage/tmp/jobs/dmuscipula/experiments/SLAx/maker/SLAx_merged_02_03.maker.output/SLAx_merged_02_03_datastore/AB/FC/MblContig1//theVoid.MblContig1/TR%3AF6H7H3_VITVI.for.1144-3500.0.fasta -t /storage/tmp/jobs/dmuscipula/experiments/SLAx/maker/SLAx_merged_02_03.maker.output/SLAx_merged_02_03_datastore/AB/FC/MblContig1//theVoid.MblContig1/MblContig1.1144-3500.0.fasta -Q protein -T dna -m protein2genome --softmasktarget  --percent 20 --showcigar  > /storage/tmp/jobs/dmuscipula/experiments/SLAx/maker/SLAx_merged_02_03.maker.output/SLAx_merged_02_03_datastore/AB/FC/MblContig1//theVoid.MblContig1/MblContig1.1144-3500.TR%3AF6H7H3_VITVI.p_exonerate.0
/storage/tmp/software/exonerate-2.2.0-x86_64/bin/exonerate -q /storage/tmp/jobs/dmuscipula/experiments/SLAx/maker/SLAx_merged_02_03.maker.output/SLAx_merged_02_03_datastore/AB/FC/MblContig1//theVoid.MblContig1/TR%3AF6HIC6_VITVI.for.1174-3479.0.fasta -t /storage/tmp/jobs/dmuscipula/experiments/SLAx/maker/SLAx_merged_02_03.maker.output/SLAx_merged_02_03_datastore/AB/FC/MblContig1//theVoid.MblContig1/MblContig1.1174-3479.0.fasta -Q protein -T dna -m protein2genome --softmasktarget  --percent 20 --showcigar  > /storage/tmp/jobs/dmuscipula/experiments/SLAx/maker/SLAx_merged_02_03.maker.output/SLAx_merged_02_03_datastore/AB/FC/MblContig1//theVoid.MblContig1/MblContig1.1174-3479.TR%3AF6HIC6_VITVI.p_exonerate.0
/storage/tmp/software/exonerate-2.2.0-x86_64/bin/exonerate -q /storage/tmp/jobs/dmuscipula/experiments/SLAx/maker/SLAx_merged_02_03.maker.output/SLAx_merged_02_03_datastore/AB/FC/MblContig1//theVoid.MblContig1/TR%3AG7JEQ3_MEDTR.for.1204-3467.0.fasta -t /storage/tmp/jobs/dmuscipula/experiments/SLAx/maker/SLAx_merged_02_03.maker.output/SLAx_merged_02_03_datastore/AB/FC/MblContig1//theVoid.MblContig1/MblContig1.1204-3467.0.fasta -Q protein -T dna -m protein2genome --softmasktarget  --percent 20 --showcigar  > /storage/tmp/jobs/dmuscipula/experiments/SLAx/maker/SLAx_merged_02_03.maker.output/SLAx_merged_02_03_datastore/AB/FC/MblContig1//theVoid.MblContig1/MblContig1.1204-3467.TR%3AG7JEQ3_MEDTR.p_exonerate.0
/storage/tmp/software/exonerate-2.2.0-x86_64/bin/exonerate -q /storage/tmp/jobs/dmuscipula/experiments/SLAx/maker/SLAx_merged_02_03.maker.output/SLAx_merged_02_03_datastore/AB/FC/MblContig1//theVoid.MblContig1/TR%3AG7JK66_MEDTR.for.1120-3518.0.fasta -t /storage/tmp/jobs/dmuscipula/experiments/SLAx/maker/SLAx_merged_02_03.maker.output/SLAx_merged_02_03_datastore/AB/FC/MblContig1//theVoid.MblContig1/MblContig1.1120-3518.0.fasta -Q protein -T dna -m protein2genome --softmasktarget  --percent 20 --showcigar  > /storage/tmp/jobs/dmuscipula/experiments/SLAx/maker/SLAx_merged_02_03.maker.output/SLAx_merged_02_03_datastore/AB/FC/MblContig1//theVoid.MblContig1/MblContig1.1120-3518.TR%3AG7JK66_MEDTR.p_exonerate.0
/storage/tmp/software/exonerate-2.2.0-x86_64/bin/exonerate -q /storage/tmp/jobs/dmuscipula/experiments/SLAx/maker/SLAx_merged_02_03.maker.output/SLAx_merged_02_03_datastore/AB/FC/MblContig1//theVoid.MblContig1/TR%3AG7KJM6_MEDTR.for.110-3612.0.fasta -t /storage/tmp/jobs/dmuscipula/experiments/SLAx/maker/SLAx_merged_02_03.maker.output/SLAx_merged_02_03_datastore/AB/FC/MblContig1//theVoid.MblContig1/MblContig1.110-3612.0.fasta -Q protein -T dna -m protein2genome --softmasktarget  --percent 20 --showcigar  > /storage/tmp/jobs/dmuscipula/experiments/SLAx/maker/SLAx_merged_02_03.maker.output/SLAx_merged_02_03_datastore/AB/FC/MblContig1//theVoid.MblContig1/MblContig1.110-3612.TR%3AG7KJM6_MEDTR.p_exonerate.0
/storage/tmp/software/exonerate-2.2.0-x86_64/bin/exonerate -q /storage/tmp/jobs/dmuscipula/experiments/SLAx/maker/SLAx_merged_02_03.maker.output/SLAx_merged_02_03_datastore/AB/FC/MblContig1//theVoid.MblContig1/TR%3AG7KK21_MEDTR.for.110-3612.0.fasta -t /storage/tmp/jobs/dmuscipula/experiments/SLAx/maker/SLAx_merged_02_03.maker.output/SLAx_merged_02_03_datastore/AB/FC/MblContig1//theVoid.MblContig1/MblContig1.110-3612.0.fasta -Q protein -T dna -m protein2genome --softmasktarget  --percent 20 --showcigar  > /storage/tmp/jobs/dmuscipula/experiments/SLAx/maker/SLAx_merged_02_03.maker.output/SLAx_merged_02_03_datastore/AB/FC/MblContig1//theVoid.MblContig1/MblContig1.110-3612.TR%3AG7KK21_MEDTR.p_exonerate.0
/storage/tmp/software/exonerate-2.2.0-x86_64/bin/exonerate -q /storage/tmp/jobs/dmuscipula/experiments/SLAx/maker/SLAx_merged_02_03.maker.output/SLAx_merged_02_03_datastore/AB/FC/MblContig1//theVoid.MblContig1/TR%3AG7KK46_MEDTR.for.1249-3612.0.fasta -t /storage/tmp/jobs/dmuscipula/experiments/SLAx/maker/SLAx_merged_02_03.maker.output/SLAx_merged_02_03_datastore/AB/FC/MblContig1//theVoid.MblContig1/MblContig1.1249-3612.0.fasta -Q protein -T dna -m protein2genome --softmasktarget  --percent 20 --showcigar  > /storage/tmp/jobs/dmuscipula/experiments/SLAx/maker/SLAx_merged_02_03.maker.output/SLAx_merged_02_03_datastore/AB/FC/MblContig1//theVoid.MblContig1/MblContig1.1249-3612.TR%3AG7KK46_MEDTR.p_exonerate.0
/storage/tmp/software/exonerate-2.2.0-x86_64/bin/exonerate -q /storage/tmp/jobs/dmuscipula/experiments/SLAx/maker/SLAx_merged_02_03.maker.output/SLAx_merged_02_03_datastore/AB/FC/MblContig1//theVoid.MblContig1/TR%3AQ0DFK6_ORYSJ.for.1129-3612.0.fasta -t /storage/tmp/jobs/dmuscipula/experiments/SLAx/maker/SLAx_merged_02_03.maker.output/SLAx_merged_02_03_datastore/AB/FC/MblContig1//theVoid.MblContig1/MblContig1.1129-3612.0.fasta -Q protein -T dna -m protein2genome --softmasktarget  --percent 20 --showcigar  > /storage/tmp/jobs/dmuscipula/experiments/SLAx/maker/SLAx_merged_02_03.maker.output/SLAx_merged_02_03_datastore/AB/FC/MblContig1//theVoid.MblContig1/MblContig1.1129-3612.TR%3AQ0DFK6_ORYSJ.p_exonerate.0
/storage/tmp/software/exonerate-2.2.0-x86_64/bin/exonerate -q /storage/tmp/jobs/dmuscipula/experiments/SLAx/maker/SLAx_merged_02_03.maker.output/SLAx_merged_02_03_datastore/AB/FC/MblContig1//theVoid.MblContig1/TR%3AQ0JL49_ORYSJ.for.110-2308.0.fasta -t /storage/tmp/jobs/dmuscipula/experiments/SLAx/maker/SLAx_merged_02_03.maker.output/SLAx_merged_02_03_datastore/AB/FC/MblContig1//theVoid.MblContig1/MblContig1.110-2308.0.fasta -Q protein -T dna -m protein2genome --softmasktarget  --percent 20 --showcigar  > /storage/tmp/jobs/dmuscipula/experiments/SLAx/maker/SLAx_merged_02_03.maker.output/SLAx_merged_02_03_datastore/AB/FC/MblContig1//theVoid.MblContig1/MblContig1.110-2308.TR%3AQ0JL49_ORYSJ.p_exonerate.0
/storage/tmp/software/exonerate-2.2.0-x86_64/bin/exonerate -q /storage/tmp/jobs/dmuscipula/experiments/SLAx/maker/SLAx_merged_02_03.maker.output/SLAx_merged_02_03_datastore/AB/FC/MblContig1//theVoid.MblContig1/TR%3AQ0JPE8_ORYSJ.for.1120-3551.0.fasta -t /storage/tmp/jobs/dmuscipula/experiments/SLAx/maker/SLAx_merged_02_03.maker.output/SLAx_merged_02_03_datastore/AB/FC/MblContig1//theVoid.MblContig1/MblContig1.1120-3551.0.fasta -Q protein -T dna -m protein2genome --softmasktarget  --percent 20 --showcigar  > /storage/tmp/jobs/dmuscipula/experiments/SLAx/maker/SLAx_merged_02_03.maker.output/SLAx_merged_02_03_datastore/AB/FC/MblContig1//theVoid.MblContig1/MblContig1.1120-3551.TR%3AQ0JPE8_ORYSJ.p_exonerate.0
/storage/tmp/software/exonerate-2.2.0-x86_64/bin/exonerate -q /storage/tmp/jobs/dmuscipula/experiments/SLAx/maker/SLAx_merged_02_03.maker.output/SLAx_merged_02_03_datastore/AB/FC/MblContig1//theVoid.MblContig1/TR%3AQ5NAK3_ORYSJ.for.1120-3551.0.fasta -t /storage/tmp/jobs/dmuscipula/experiments/SLAx/maker/SLAx_merged_02_03.maker.output/SLAx_merged_02_03_datastore/AB/FC/MblContig1//theVoid.MblContig1/MblContig1.1120-3551.0.fasta -Q protein -T dna -m protein2genome --softmasktarget  --percent 20 --showcigar  > /storage/tmp/jobs/dmuscipula/experiments/SLAx/maker/SLAx_merged_02_03.maker.output/SLAx_merged_02_03_datastore/AB/FC/MblContig1//theVoid.MblContig1/MblContig1.1120-3551.TR%3AQ5NAK3_ORYSJ.p_exonerate.0
/storage/tmp/software/exonerate-2.2.0-x86_64/bin/exonerate -q /storage/tmp/jobs/dmuscipula/experiments/SLAx/maker/SLAx_merged_02_03.maker.output/SLAx_merged_02_03_datastore/AB/FC/MblContig1//theVoid.MblContig1/TR%3AQ5NAK4_ORYSJ.for.1132-3551.0.fasta -t /storage/tmp/jobs/dmuscipula/experiments/SLAx/maker/SLAx_merged_02_03.maker.output/SLAx_merged_02_03_datastore/AB/FC/MblContig1//theVoid.MblContig1/MblContig1.1132-3551.0.fasta -Q protein -T dna -m protein2genome --softmasktarget  --percent 20 --showcigar  > /storage/tmp/jobs/dmuscipula/experiments/SLAx/maker/SLAx_merged_02_03.maker.output/SLAx_merged_02_03_datastore/AB/FC/MblContig1//theVoid.MblContig1/MblContig1.1132-3551.TR%3AQ5NAK4_ORYSJ.p_exonerate.0
/storage/tmp/software/exonerate-2.2.0-x86_64/bin/exonerate -q /storage/tmp/jobs/dmuscipula/experiments/SLAx/maker/SLAx_merged_02_03.maker.output/SLAx_merged_02_03_datastore/AB/FC/MblContig1//theVoid.MblContig1/TR%3AQ5ZE68_ORYSJ.for.110-3584.0.fasta -t /storage/tmp/jobs/dmuscipula/experiments/SLAx/maker/SLAx_merged_02_03.maker.output/SLAx_merged_02_03_datastore/AB/FC/MblContig1//theVoid.MblContig1/MblContig1.110-3584.0.fasta -Q protein -T dna -m protein2genome --softmasktarget  --percent 20 --showcigar  > /storage/tmp/jobs/dmuscipula/experiments/SLAx/maker/SLAx_merged_02_03.maker.output/SLAx_merged_02_03_datastore/AB/FC/MblContig1//theVoid.MblContig1/MblContig1.110-3584.TR%3AQ5ZE68_ORYSJ.p_exonerate.0
/storage/tmp/software/exonerate-2.2.0-x86_64/bin/exonerate -q /storage/tmp/jobs/dmuscipula/experiments/SLAx/maker/SLAx_merged_02_03.maker.output/SLAx_merged_02_03_datastore/AB/FC/MblContig1//theVoid.MblContig1/TR%3AQ6I589_ORYSJ.for.1210-3612.0.fasta -t /storage/tmp/jobs/dmuscipula/experiments/SLAx/maker/SLAx_merged_02_03.maker.output/SLAx_merged_02_03_datastore/AB/FC/MblContig1//theVoid.MblContig1/MblContig1.1210-3612.0.fasta -Q protein -T dna -m protein2genome --softmasktarget  --percent 20 --showcigar  > /storage/tmp/jobs/dmuscipula/experiments/SLAx/maker/SLAx_merged_02_03.maker.output/SLAx_merged_02_03_datastore/AB/FC/MblContig1//theVoid.MblContig1/MblContig1.1210-3612.TR%3AQ6I589_ORYSJ.p_exonerate.0
/storage/tmp/software/exonerate-2.2.0-x86_64/bin/exonerate -q /storage/tmp/jobs/dmuscipula/experiments/SLAx/maker/SLAx_merged_02_03.maker.output/SLAx_merged_02_03_datastore/AB/FC/MblContig1//theVoid.MblContig1/TR%3AQ6ZLB6_ORYSJ.for.1141-3539.0.fasta -t /storage/tmp/jobs/dmuscipula/experiments/SLAx/maker/SLAx_merged_02_03.maker.output/SLAx_merged_02_03_datastore/AB/FC/MblContig1//theVoid.MblContig1/MblContig1.1141-3539.0.fasta -Q protein -T dna -m protein2genome --softmasktarget  --percent 20 --showcigar  > /storage/tmp/jobs/dmuscipula/experiments/SLAx/maker/SLAx_merged_02_03.maker.output/SLAx_merged_02_03_datastore/AB/FC/MblContig1//theVoid.MblContig1/MblContig1.1141-3539.TR%3AQ6ZLB6_ORYSJ.p_exonerate.0
/storage/tmp/software/exonerate-2.2.0-x86_64/bin/exonerate -q /storage/tmp/jobs/dmuscipula/experiments/SLAx/maker/SLAx_merged_02_03.maker.output/SLAx_merged_02_03_datastore/AB/FC/MblContig1//theVoid.MblContig1/TR%3AQ75G55_ORYSJ.for.1141-3521.0.fasta -t /storage/tmp/jobs/dmuscipula/experiments/SLAx/maker/SLAx_merged_02_03.maker.output/SLAx_merged_02_03_datastore/AB/FC/MblContig1//theVoid.MblContig1/MblContig1.1141-3521.0.fasta -Q protein -T dna -m protein2genome --softmasktarget  --percent 20 --showcigar  > /storage/tmp/jobs/dmuscipula/experiments/SLAx/maker/SLAx_merged_02_03.maker.output/SLAx_merged_02_03_datastore/AB/FC/MblContig1//theVoid.MblContig1/MblContig1.1141-3521.TR%3AQ75G55_ORYSJ.p_exonerate.0
/storage/tmp/software/exonerate-2.2.0-x86_64/bin/exonerate -q /storage/tmp/jobs/dmuscipula/experiments/SLAx/maker/SLAx_merged_02_03.maker.output/SLAx_merged_02_03_datastore/AB/FC/MblContig1//theVoid.MblContig1/TR%3AQ7XTX7_ORYSJ.for.1120-3518.0.fasta -t /storage/tmp/jobs/dmuscipula/experiments/SLAx/maker/SLAx_merged_02_03.maker.output/SLAx_merged_02_03_datastore/AB/FC/MblContig1//theVoid.MblContig1/MblContig1.1120-3518.0.fasta -Q protein -T dna -m protein2genome --softmasktarget  --percent 20 --showcigar  > /storage/tmp/jobs/dmuscipula/experiments/SLAx/maker/SLAx_merged_02_03.maker.output/SLAx_merged_02_03_datastore/AB/FC/MblContig1//theVoid.MblContig1/MblContig1.1120-3518.TR%3AQ7XTX7_ORYSJ.p_exonerate.0
/storage/tmp/software/exonerate-2.2.0-x86_64/bin/exonerate -q /storage/tmp/jobs/dmuscipula/experiments/SLAx/maker/SLAx_merged_02_03.maker.output/SLAx_merged_02_03_datastore/AB/FC/MblContig1//theVoid.MblContig1/TR%3AQ8L4G8_ORYSJ.for.1120-3536.0.fasta -t /storage/tmp/jobs/dmuscipula/experiments/SLAx/maker/SLAx_merged_02_03.maker.output/SLAx_merged_02_03_datastore/AB/FC/MblContig1//theVoid.MblContig1/MblContig1.1120-3536.0.fasta -Q protein -T dna -m protein2genome --softmasktarget  --percent 20 --showcigar  > /storage/tmp/jobs/dmuscipula/experiments/SLAx/maker/SLAx_merged_02_03.maker.output/SLAx_merged_02_03_datastore/AB/FC/MblContig1//theVoid.MblContig1/MblContig1.1120-3536.TR%3AQ8L4G8_ORYSJ.p_exonerate.0
/storage/tmp/software/exonerate-2.2.0-x86_64/bin/exonerate -q /storage/tmp/jobs/dmuscipula/experiments/SLAx/maker/SLAx_merged_02_03.maker.output/SLAx_merged_02_03_datastore/AB/FC/MblContig1//theVoid.MblContig1/TR%3AQ9FTK9_ORYSJ.for.1180-3500.0.fasta -t /storage/tmp/jobs/dmuscipula/experiments/SLAx/maker/SLAx_merged_02_03.maker.output/SLAx_merged_02_03_datastore/AB/FC/MblContig1//theVoid.MblContig1/MblContig1.1180-3500.0.fasta -Q protein -T dna -m protein2genome --softmasktarget  --percent 20 --showcigar  > /storage/tmp/jobs/dmuscipula/experiments/SLAx/maker/SLAx_merged_02_03.maker.output/SLAx_merged_02_03_datastore/AB/FC/MblContig1//theVoid.MblContig1/MblContig1.1180-3500.TR%3AQ9FTK9_ORYSJ.p_exonerate.0
/storage/tmp/software/exonerate-2.2.0-x86_64/bin/exonerate -q /storage/tmp/jobs/dmuscipula/experiments/SLAx/maker/SLAx_merged_02_03.maker.output/SLAx_merged_02_03_datastore/AB/FC/MblContig1//theVoid.MblContig1/TR%3AQ9XHX8_ORYSJ.for.1180-2344.0.fasta -t /storage/tmp/jobs/dmuscipula/experiments/SLAx/maker/SLAx_merged_02_03.maker.output/SLAx_merged_02_03_datastore/AB/FC/MblContig1//theVoid.MblContig1/MblContig1.1180-2344.0.fasta -Q protein -T dna -m protein2genome --softmasktarget  --percent 20 --showcigar  > /storage/tmp/jobs/dmuscipula/experiments/SLAx/maker/SLAx_merged_02_03.maker.output/SLAx_merged_02_03_datastore/AB/FC/MblContig1//theVoid.MblContig1/MblContig1.1180-2344.TR%3AQ9XHX8_ORYSJ.p_exonerate.0
To access files for individual sequences use the datastore index:
total clusters:1 now processing 0
total clusters:2 now processing 0
	UNKNOWN	Bio::AnalysisParserI	/storage/tmp/software/perl-5.14.1/lib/site_perl/5.14.1/Bio/AnalysisParserI.pm
	UNKNOWN	Bio::AnnotatableI	/storage/tmp/software/perl-5.14.1/lib/site_perl/5.14.1/Bio/AnnotatableI.pm
	UNKNOWN	Bio::AnnotationCollectionI	/storage/tmp/software/perl-5.14.1/lib/site_perl/5.14.1/Bio/AnnotationCollectionI.pm
	UNKNOWN	Bio::Annotation::Collection	/storage/tmp/software/perl-5.14.1/lib/site_perl/5.14.1/Bio/Annotation/Collection.pm
	UNKNOWN	Bio::AnnotationI	/storage/tmp/software/perl-5.14.1/lib/site_perl/5.14.1/Bio/AnnotationI.pm
	UNKNOWN	Bio::Annotation::SimpleValue	/storage/tmp/software/perl-5.14.1/lib/site_perl/5.14.1/Bio/Annotation/SimpleValue.pm
	UNKNOWN	Bio::Annotation::TypeManager	/storage/tmp/software/perl-5.14.1/lib/site_perl/5.14.1/Bio/Annotation/TypeManager.pm
	UNKNOWN	Bio::DB::InMemoryCache	/storage/tmp/software/perl-5.14.1/lib/site_perl/5.14.1/Bio/DB/InMemoryCache.pm
	UNKNOWN	Bio::DescribableI	/storage/tmp/software/perl-5.14.1/lib/site_perl/5.14.1/Bio/DescribableI.pm
	UNKNOWN	Bio::Event::EventGeneratorI	/storage/tmp/software/perl-5.14.1/lib/site_perl/5.14.1/Bio/Event/EventGeneratorI.pm
	UNKNOWN	Bio::Event::EventHandlerI	/storage/tmp/software/perl-5.14.1/lib/site_perl/5.14.1/Bio/Event/EventHandlerI.pm
	UNKNOWN	Bio::Factory::ObjectFactoryI	/storage/tmp/software/perl-5.14.1/lib/site_perl/5.14.1/Bio/Factory/ObjectFactoryI.pm
	UNKNOWN	Bio::Factory::ObjectFactory	/storage/tmp/software/perl-5.14.1/lib/site_perl/5.14.1/Bio/Factory/ObjectFactory.pm
	UNKNOWN	Bio::Factory::SequenceFactoryI	/storage/tmp/software/perl-5.14.1/lib/site_perl/5.14.1/Bio/Factory/SequenceFactoryI.pm
	UNKNOWN	Bio::FeatureHolderI	/storage/tmp/software/perl-5.14.1/lib/site_perl/5.14.1/Bio/FeatureHolderI.pm
	UNKNOWN	Bio::IdentifiableI	/storage/tmp/software/perl-5.14.1/lib/site_perl/5.14.1/Bio/IdentifiableI.pm
	UNKNOWN	Bio::LocatableSeq	/storage/tmp/software/perl-5.14.1/lib/site_perl/5.14.1/Bio/LocatableSeq.pm
	UNKNOWN	Bio::Location::Atomic	/storage/tmp/software/perl-5.14.1/lib/site_perl/5.14.1/Bio/Location/Atomic.pm
	UNKNOWN	Bio::Location::CoordinatePolicyI	/storage/tmp/software/perl-5.14.1/lib/site_perl/5.14.1/Bio/Location/CoordinatePolicyI.pm
	UNKNOWN	Bio::Location::FuzzyLocationI	/storage/tmp/software/perl-5.14.1/lib/site_perl/5.14.1/Bio/Location/FuzzyLocationI.pm
	UNKNOWN	Bio::Location::Fuzzy	/storage/tmp/software/perl-5.14.1/lib/site_perl/5.14.1/Bio/Location/Fuzzy.pm
	UNKNOWN	Bio::LocationI	/storage/tmp/software/perl-5.14.1/lib/site_perl/5.14.1/Bio/LocationI.pm
	UNKNOWN	Bio::Location::Simple	/storage/tmp/software/perl-5.14.1/lib/site_perl/5.14.1/Bio/Location/Simple.pm
	UNKNOWN	Bio::Location::SplitLocationI	/storage/tmp/software/perl-5.14.1/lib/site_perl/5.14.1/Bio/Location/SplitLocationI.pm
	UNKNOWN	Bio::Location::Split	/storage/tmp/software/perl-5.14.1/lib/site_perl/5.14.1/Bio/Location/Split.pm
	UNKNOWN	Bio::Location::WidestCoordPolicy	/storage/tmp/software/perl-5.14.1/lib/site_perl/5.14.1/Bio/Location/WidestCoordPolicy.pm
	UNKNOWN	Bio::PrimarySeqI	/storage/tmp/software/perl-5.14.1/lib/site_perl/5.14.1/Bio/PrimarySeqI.pm
	UNKNOWN	Bio::PrimarySeq	/storage/tmp/software/perl-5.14.1/lib/site_perl/5.14.1/Bio/PrimarySeq.pm
	UNKNOWN	Bio::RangeI	/storage/tmp/software/perl-5.14.1/lib/site_perl/5.14.1/Bio/RangeI.pm
	UNKNOWN	Bio::Range	/storage/tmp/software/perl-5.14.1/lib/site_perl/5.14.1/Bio/Range.pm
	UNKNOWN	Bio::Root::HTTPget	/storage/tmp/software/perl-5.14.1/lib/site_perl/5.14.1/Bio/Root/HTTPget.pm
	UNKNOWN	Bio::Root::IO	/storage/tmp/software/perl-5.14.1/lib/site_perl/5.14.1/Bio/Root/IO.pm
	UNKNOWN	Bio::Root::Root	/storage/tmp/software/perl-5.14.1/lib/site_perl/5.14.1/Bio/Root/Root.pm
	UNKNOWN	Bio::Search::Hit::HitFactory	/storage/tmp/software/perl-5.14.1/lib/site_perl/5.14.1/Bio/Search/Hit/HitFactory.pm
	UNKNOWN	Bio::Search::Hit::HitI	/storage/tmp/software/perl-5.14.1/lib/site_perl/5.14.1/Bio/Search/Hit/HitI.pm
	UNKNOWN	Bio::Search::Hit::PhatHit::augustus	/storage/tmp/software/maker-2.24-debug/bin/../lib/Bio/Search/Hit/PhatHit/augustus.pm
	UNKNOWN	Bio::Search::Hit::PhatHit::est2genome	/storage/tmp/software/maker-2.24-debug/bin/../lib/Bio/Search/Hit/PhatHit/est2genome.pm
	UNKNOWN	Bio::Search::Hit::PhatHit::fgenesh	/storage/tmp/software/maker-2.24-debug/bin/../lib/Bio/Search/Hit/PhatHit/fgenesh.pm
	UNKNOWN	Bio::Search::Hit::PhatHit::genemark	/storage/tmp/software/maker-2.24-debug/bin/../lib/Bio/Search/Hit/PhatHit/genemark.pm
	UNKNOWN	Bio::Search::Hit::PhatHit::gff3	/storage/tmp/software/maker-2.24-debug/bin/../lib/Bio/Search/Hit/PhatHit/gff3.pm
	UNKNOWN	Bio::Search::Hit::PhatHit::protein2genome	/storage/tmp/software/maker-2.24-debug/bin/../lib/Bio/Search/Hit/PhatHit/protein2genome.pm
	UNKNOWN	Bio::Search::Hit::PhatHit::snap	/storage/tmp/software/maker-2.24-debug/bin/../lib/Bio/Search/Hit/PhatHit/snap.pm
	UNKNOWN	Bio::Search::HSP::GenericHSP	/storage/tmp/software/perl-5.14.1/lib/site_perl/5.14.1/Bio/Search/HSP/GenericHSP.pm
	UNKNOWN	Bio::Search::HSP::HSPFactory	/storage/tmp/software/perl-5.14.1/lib/site_perl/5.14.1/Bio/Search/HSP/HSPFactory.pm
	UNKNOWN	Bio::Search::HSP::HSPI	/storage/tmp/software/perl-5.14.1/lib/site_perl/5.14.1/Bio/Search/HSP/HSPI.pm
	UNKNOWN	Bio::Search::HSP::PhatHSP::augustus	/storage/tmp/software/maker-2.24-debug/bin/../lib/Bio/Search/HSP/PhatHSP/augustus.pm
	UNKNOWN	Bio::Search::HSP::PhatHSP::est2genome	/storage/tmp/software/maker-2.24-debug/bin/../lib/Bio/Search/HSP/PhatHSP/est2genome.pm
	UNKNOWN	Bio::Search::HSP::PhatHSP::fgenesh	/storage/tmp/software/maker-2.24-debug/bin/../lib/Bio/Search/HSP/PhatHSP/fgenesh.pm
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	UNKNOWN	Bio::SeqI	/storage/tmp/software/perl-5.14.1/lib/site_perl/5.14.1/Bio/SeqI.pm
	UNKNOWN	Bio::Seq::SeqFactory	/storage/tmp/software/perl-5.14.1/lib/site_perl/5.14.1/Bio/Seq/SeqFactory.pm
	UNKNOWN	Bio::Seq	/storage/tmp/software/perl-5.14.1/lib/site_perl/5.14.1/Bio/Seq.pm
	UNKNOWN	Bio::SeqUtils	/storage/tmp/software/perl-5.14.1/lib/site_perl/5.14.1/Bio/SeqUtils.pm
	UNKNOWN	Bio::Tools::CodonTable	/storage/tmp/software/perl-5.14.1/lib/site_perl/5.14.1/Bio/Tools/CodonTable.pm
	UNKNOWN	Bio::Tools::GFF	/storage/tmp/software/perl-5.14.1/lib/site_perl/5.14.1/Bio/Tools/GFF.pm
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	UNKNOWN	clean	/storage/tmp/software/maker-2.24-debug/bin/../lib/clean.pm
	UNKNOWN	cluster	/storage/tmp/software/maker-2.24-debug/bin/../lib/cluster.pm
	UNKNOWN	compare	/storage/tmp/software/maker-2.24-debug/bin/../lib/compare.pm
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	UNKNOWN	Dumper::GFF::GFFV3	/storage/tmp/software/maker-2.24-debug/bin/../lib/Dumper/GFF/GFFV3.pm
	UNKNOWN	Dumper::XML::Game	/storage/tmp/software/maker-2.24-debug/bin/../lib/Dumper/XML/Game.pm
	UNKNOWN	Dumper::XML::Game_Xml	/storage/tmp/software/maker-2.24-debug/bin/../lib/Dumper/XML/Game_Xml.pm
	UNKNOWN	Error::Simple	/storage/tmp/software/maker-2.24-debug/bin/../lib/Error/Simple.pm
	UNKNOWN	exonerate::splice_info	/storage/tmp/software/maker-2.24-debug/bin/../lib/exonerate/splice_info.pm
	UNKNOWN	FastaChunker	/storage/tmp/software/maker-2.24-debug/bin/../lib/FastaChunker.pm
	UNKNOWN	FastaChunk	/storage/tmp/software/maker-2.24-debug/bin/../lib/FastaChunk.pm
	UNKNOWN	FastaDB	/storage/tmp/software/maker-2.24-debug/bin/../lib/FastaDB.pm
	UNKNOWN	FastaFile	/storage/tmp/software/maker-2.24-debug/bin/../lib/FastaFile.pm
	UNKNOWN	FastaSeq	/storage/tmp/software/maker-2.24-debug/bin/../lib/FastaSeq.pm
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	UNKNOWN	Iterator::GFF3	/storage/tmp/software/maker-2.24-debug/bin/../lib/Iterator/GFF3.pm
	UNKNOWN	Iterator	/storage/tmp/software/maker-2.24-debug/bin/../lib/Iterator.pm
	UNKNOWN	LWP::MemberMixin	/storage/tmp/software/perl-5.14.1/lib/site_perl/5.14.1/LWP/MemberMixin.pm
	UNKNOWN	maker::auto_annotator	/storage/tmp/software/maker-2.24-debug/bin/../lib/maker/auto_annotator.pm
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	UNKNOWN	maker::join	/storage/tmp/software/maker-2.24-debug/bin/../lib/maker/join.pm
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	UNKNOWN	PhatHit_utils	/storage/tmp/software/maker-2.24-debug/bin/../lib/PhatHit_utils.pm
	UNKNOWN	polisher::exonerate::est	/storage/tmp/software/maker-2.24-debug/bin/../lib/polisher/exonerate/est.pm
	UNKNOWN	polisher::exonerate::protein	/storage/tmp/software/maker-2.24-debug/bin/../lib/polisher/exonerate/protein.pm
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	UNKNOWN	polisher	/storage/tmp/software/maker-2.24-debug/bin/../lib/polisher.pm
	UNKNOWN	PostData	/storage/tmp/software/maker-2.24-debug/bin/../lib/PostData.pm
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	UNKNOWN	repeat_mask_seq	/storage/tmp/software/maker-2.24-debug/bin/../lib/repeat_mask_seq.pm
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	UNKNOWN	Shadower	/storage/tmp/software/maker-2.24-debug/bin/../lib/Shadower.pm
	UNKNOWN	SimpleCluster	/storage/tmp/software/maker-2.24-debug/bin/../lib/SimpleCluster.pm
	UNKNOWN	SpaceBase	/storage/tmp/software/maker-2.24-debug/bin/../lib/SpaceBase.pm
	UNKNOWN	Widget::augustus	/storage/tmp/software/maker-2.24-debug/bin/../lib/Widget/augustus.pm
	UNKNOWN	Widget::blastn	/storage/tmp/software/maker-2.24-debug/bin/../lib/Widget/blastn.pm
	UNKNOWN	Widget::blastx	/storage/tmp/software/maker-2.24-debug/bin/../lib/Widget/blastx.pm
	UNKNOWN	Widget::exonerate::est2genome	/storage/tmp/software/maker-2.24-debug/bin/../lib/Widget/exonerate/est2genome.pm
	UNKNOWN	Widget::exonerate::protein2genome	/storage/tmp/software/maker-2.24-debug/bin/../lib/Widget/exonerate/protein2genome.pm
	UNKNOWN	Widget::exonerate	/storage/tmp/software/maker-2.24-debug/bin/../lib/Widget/exonerate.pm
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	UNKNOWN	Widget::genemark	/storage/tmp/software/maker-2.24-debug/bin/../lib/Widget/genemark.pm
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	UNKNOWN	Widget::snap	/storage/tmp/software/maker-2.24-debug/bin/../lib/Widget/snap.pm
	UNKNOWN	Widget	/storage/tmp/software/maker-2.24-debug/bin/../lib/Widget.pm
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Widget::augustus:
Widget::blastn:
Widget::blastx:
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Widget::exonerate::protein2genome:
Widget::formater:
Widget::RepeatMasker:

From scott at scottcain.net  Wed Mar 21 14:59:19 2012
From: scott at scottcain.net (Scott Cain)
Date: Wed, 21 Mar 2012 16:59:19 -0400
Subject: [maker-devel] loading scaffold features into chado
In-Reply-To: <4F6A290E.8000306@uwindsor.ca>
References: <4F68B686.6050800@uwindsor.ca> <CB8E2F50.97C7%carsonhh@gmail.com>
	<CA+JTaoy00sX+3Pdyrw=Apus09Lppg9YNQsr8k4uoYXHmK24Euw@mail.gmail.com>
	<4F68C66F.2010902@uwindsor.ca>
	<FFACED63-40D9-4810-9927-0E4984BA8465@scottcain.net>
	<web-60068456@uwindsor.ca>
	<CA+JTaoxshG4M+awmuw93=JkwqtisgFSw6igZE+_2tCFaN-ocrw@mail.gmail.com>
	<4F6A03D2.5010503@uwindsor.ca>
	<CA+JTaoyMT6_uxYG_b28j-PCJfiOeL6FUqgLRj1FNvwR7XZUOkA@mail.gmail.com>
	<4F6A290E.8000306@uwindsor.ca>
Message-ID: <CA+JTaowKA=wFW8A91wpOMZLAe+phkFdHdppO1ume+30sWN9T9g@mail.gmail.com>

Hi Claudia,

I wanted to bring this back to the mailing lists, so I cc'ed them here.

First, with the fasta loading issue: what command are you using to
load the fasta sequences?  It works for me whether the fasta is at the
bottom of the GFF file or if it is a separate fasta file (as long as I
supply the --fastafile flag to the loader).

About the searching problem: when I turn on full text searching (which
means both running gmod_chado_fts_prep.pl and adding "-fulltext 1" to
the db_args in the gbrowse config file), I can search for "cnot1" and
find both a gene and an mRNA (of course, they are really the same
feature, but GBrowse doesn't know that).  Also, searching for "maker"
works, but in a real database, this will not be an effective query,
since the number of results returned are limited, and presumably there
will be lots of features resulting from a query like that.  Please
remind me, is that what you wanted to do?

Scott




On Wed, Mar 21, 2012 at 3:16 PM, claudia <dinatal at uwindsor.ca> wrote:
> Hi Scott,
>
> ?Wanted to give you a quick heads up that the bulk loader seems to be
> loading my fasta files now after deleting the ' ##FASTA' header ( the first
> line of the file now looks like this >scaffold0001)...
> Never had this problem before, it seems the bulk loader wanted to see a '>'
> symbol in front of the first line...
>
> -- when I say seems, I will let you know if it finishes, as it currently
> ?states " Loading sequences ( if any)" ... and I never made it this far
> before :)
>
> Claudia
>
>
>
> On 21/03/2012 12:53 PM, Scott Cain wrote:
>>
>> Hi Claudia,
>>
>> I imagine one scaffold and gene models would be good--the problem is
>> finding genes, right?
>>
>> Also, with loading fasta: were the corresponding features from the GFF
>> file already loaded? ?If so, that should have worked, and if it didn't
>> it implies a bug. ?If not, that's why.
>>
>> Scott
>>
>>
>> On Wed, Mar 21, 2012 at 12:37 PM, claudia<dinatal at uwindsor.ca> ?wrote:
>>>
>>> Hi Scott,
>>> ?So would one scaffold with Maker gene models suffice? Do you want the
>>> analysis as well?
>>>
>>> --along those same lines, I did try and load the original sequence
>>> (fasta)
>>> file first that I ran the Pipeline on and chado seems to refuse the files
>>> saying they don't contain the appropriate feature '>' in the header which
>>> in
>>> fact they do i.e> ?scaffold00001 ... So not sure what is wrong with the
>>> fasta that chado doesn't want to load even if it is embedded in the GFF3,
>>> the bulk loader or maker2chado return errors stating 'feature not
>>> found'...
>>>
>>>
>>> Claudia
>>>
>>>
>>>
>>> On 21/03/2012 12:20 PM, Scott Cain wrote:
>>>>
>>>> Hi Claudia,
>>>>
>>>> I was hoping to get actual files that I could do testing on, not
>>>> pictures of files :-)
>>>>
>>>> Scott
>>>>
>>>>
>>>> On Tue, Mar 20, 2012 at 4:15 PM, Dinatale C<dinatal at uwindsor.ca>
>>>> ?wrote:
>>>>>
>>>>> Hi,
>>>>>
>>>>> Attached: ?I have samples of the contig file ( I extracted the contig
>>>>> features first to load prior to the gene models) the fasta of the
>>>>> sequences
>>>>> is in the footer of the gff3 file.
>>>>>
>>>>> --so basically, based on experience with contig annotations, I should
>>>>> be
>>>>> able to type in 'maker' in to the gbrowse search bar, and recieve all
>>>>> the
>>>>> maker gene annotations, but I don't. I must specifiy the exact ID i.e "
>>>>> maker-scaffold11323-augustus-gene...." or 'scaffold11323'
>>>>>
>>>>> --so I wonder if it has to do with the fasta files being named as
>>>>> 'scaffolds' and perhaps causing a problem with chado recognizing that
>>>>> they
>>>>> are linked to the gene annotations due to scaffold not being a SOFA
>>>>> type
>>>>> term, if in fact the sequences must be submitted to the database first?
>>>>>
>>>>>
>>>>> Thanks in advance,
>>>>>
>>>>> Claudia
>>>>>
>>>>> On Tue, 20 Mar 2012 15:50:55 -0400 Scott Cain wrote:
>>>>>>
>>>>>> Hi Claudia,
>>>>>>
>>>>>> Can you post a sample of the gff that shows what you are looking for
>>>>>> and
>>>>>> not finding?
>>>>>>
>>>>>> Scott
>>>>>>
>>>>>>
>>>>>> Sent from my iPad
>>>>>>
>>>>>> On Mar 20, 2012, at 2:03 PM, claudia wrote:
>>>>>>
>>>>>>> Hi,
>>>>>>>
>>>>>>> I have enabled full text searching and I still have this problem,
>>>>>>> another reason for
>>>>>>
>>>>>> concern... So I wondered if in fact I changed all the ID's in the GFF3
>>>>>> file to supercontigs,
>>>>>> then perhaps Chado would better link all the terms, annotations, and
>>>>>> fasta
>>>>>> files....
>>>>>> Although, i realize that the seq_id ( column 1) shouldn't need to be
>>>>>> specific since the
>>>>>> 'type' term would take care of designating the feature type, no?
>>>>>>>
>>>>>>> Claudia
>>>>>>>
>>>>>>>
>>>>>>>
>>>>>>> On 20/03/2012 1:25 PM, Scott Cain wrote:
>>>>>>>>
>>>>>>>> Hi Claudia,
>>>>>>>>
>>>>>>>> I agree with everything that Carson wrote, except about name
>>>>>>>> searching--it's a little trickier in Chado. What you probably want
>>>>>>>> to
>>>>>>>> do is implement full text searching. See:
>>>>>>>>
>>>>>>>> http://gmod.org/wiki/Chado_Full_Text_Search
>>>>>>>>
>>>>>>>> for more information on setting it up and maintaining it.
>>>>>>>>
>>>>>>>> Scott
>>>>>>>>
>>>>>>>>
>>>>>>>> On Tue, Mar 20, 2012 at 1:13 PM, Carson Holt wrote:
>>>>>>>>>>
>>>>>>>>>> I have 2 concerns, the first is: regarding representing scaffold
>>>>>>>>>> features in chado and gbrowse. I noticed that the Sequence
>>>>>>>>>> ontology
>>>>>>>>>> uses
>>>>>>>>>> the term supercontig and so if my assembly generated scaffolds
>>>>>>>>>> entitled
>>>>>>>>>> "scaffold" should I change the names to supercontigs so that chado
>>>>>>>>>> recognizes the terms?
>>>>>>>>>
>>>>>>>>> Yes. You must use valid SO terms. It is a requirement of GFF3, and
>>>>>>>>> Chado
>>>>>>>>> will enforce this requirement on loading a GFF3 file (note Chado
>>>>>>>>> will
>>>>>>>>> even
>>>>>>>>> go as far as to check the validity of the Ontology_term= attribute
>>>>>>>>> in
>>>>>>>>> GFF3
>>>>>>>>> if you use it). You can decide to use contig or supercontig as your
>>>>>>>>> sequence feature. It doesn?t really matter unless you are placing
>>>>>>>>>
>>>>>>>>> both
>>>>>>>>> into the database as separate features (i.e. You have a supercontig
>>>>>>>>> as
>>>>>>>>> the
>>>>>>>>> parent feature and then you enter contigs individually as children
>>>>>>>>> of
>>>>>>>>> the
>>>>>>>>> supercontig).
>>>>>>>>>
>>>>>>>>>
>>>>>>>>>> Corresponding to my first question, Maker does not know that the
>>>>>>>>>> contigs
>>>>>>>>>> are actually scaffold/supercontigs when annotating and so Maker
>>>>>>>>>> will
>>>>>>>>>> still call the "type" feature or column 3 in the GFF3, a 'contig',
>>>>>>>>>> how
>>>>>>>>>> can Maker be implemented to change this naming convention before
>>>>>>>>>> annotation, or after?
>>>>>>>>>
>>>>>>>>> Not really important unless you plan on making contigs children of
>>>>>>>>> the
>>>>>>>>> supercontig. But you can always do a search and replace. -->
>>>>>>>>> cat file.gff | perl -ane 's/\tcontig\t/\tsupercontig\t/s; print
>>>>>>>>> $_'>
>>>>>>>>> new_file.gff
>>>>>>>>>
>>>>>>>>>
>>>>>>>>>> Consequently, I am having problems pulling up gene features in
>>>>>>>>>> Gbrowse
>>>>>>>>>> when doing a generic gene search, and I must provide the maker
>>>>>>>>>> generated
>>>>>>>>>> unique-gene_id in the gbrowse search bar or the known sequence id
>>>>>>>>>> i.e
>>>>>>>>>> 'scaffold001', which is not useful for someone who does not have
>>>>>>>>>> this
>>>>>>>>>> information.
>>>>>>>>>> ---- I do not have this problem when my seq_id, and 'type' feature
>>>>>>>>>> id
>>>>>>>>>> match in the true case of 'contigs'. I can do a generic gene
>>>>>>>>>> search
>>>>>>>>>> in
>>>>>>>>>> gbrowse with the term 'maker' and gbrowse will provide me all the
>>>>>>>>>> associated maker generated gene calls.
>>>>>>>>>
>>>>>>>>> See "Adjusting GBrowse Name Searches" in the GBrowse tutorial -->
>>>>>>>>> http://gmod.org/gbrowse2/tutorial/tutorial.html#naming
>>>>>>>>>
>>>>>>>>>
>>>>>>>>> Thanks,
>>>>>>>>> Carson
>>>>>>>>>
>>>>>>>>>
>>>>>>>>>
>>>>>>>>>
>>>>>>>>>
>>>>>>>>>
>>>>>>>>>
>>>>>>>>>
>>>>>>>>>
>>>>>>>>>
>>>>>>>>>
>>>>>>>>>> Thank you for any guidance resolving these concerns,
>>>>>>>>>> Claudia
>>>>>>>>>>
>>>>>>>>>>
>>>>>>>>>>
>>>>>>>>>> --
>>>>>>>>>> Claudia DiNatale
>>>>>>>>>> Master's Candidate
>>>>>>>>>> The Crosby Lab
>>>>>>>>>> University of Windsor
>>>>>>>>>> 519-253-3000 ext: 4755
>>>>>>>>>>
>>>>>>>>>>
>>>>>>>>>> _______________________________________________
>>>>>>>>>> maker-devel mailing list
>>>>>>>>>> maker-devel at box290.bluehost.com
>>>>>>>>>>
>>>>>>>>>>
>>>>>>>>>>
>>>>>>>>>> http://box290.bluehost.com/mailman/listinfo/maker-devel_yandell-lab.org
>>>>>>>>>
>>>>>>>>>
>>>>>>>>> _______________________________________________
>>>>>>>>> maker-devel mailing list
>>>>>>>>> maker-devel at box290.bluehost.com
>>>>>>>>>
>>>>>>>>>
>>>>>>>>>
>>>>>>>>> http://box290.bluehost.com/mailman/listinfo/maker-devel_yandell-lab.org
>>>>>>>>
>>>>>>>>
>>>>>>> --
>>>>>>> Claudia DiNatale
>>>>>>> Master's Candidate
>>>>>>> The Crosby Lab
>>>>>>> University of Windsor
>>>>>>> 519-253-3000 ext: 4755
>>>>>>>
>>>>
>>>
>>> --
>>> Claudia DiNatale
>>> Master's Candidate
>>> The Crosby Lab
>>> University of Windsor
>>> 519-253-3000 ext: 4755
>>>
>>
>>
>
>
> --
> Claudia DiNatale
> Master's Candidate
> The Crosby Lab
> University of Windsor
> 519-253-3000 ext: 4755
>



-- 
------------------------------------------------------------------------
Scott Cain, Ph. D.? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ?? scott at scottcain dot net
GMOD Coordinator (http://gmod.org/)? ? ? ? ? ? ? ? ? ?? 216-392-3087
Ontario Institute for Cancer Research



From dinatal at uwindsor.ca  Wed Mar 21 15:14:54 2012
From: dinatal at uwindsor.ca (claudia)
Date: Wed, 21 Mar 2012 17:14:54 -0400
Subject: [maker-devel] loading scaffold features into chado
In-Reply-To: <CA+JTaowKA=wFW8A91wpOMZLAe+phkFdHdppO1ume+30sWN9T9g@mail.gmail.com>
References: <4F68B686.6050800@uwindsor.ca> <CB8E2F50.97C7%carsonhh@gmail.com>
	<CA+JTaoy00sX+3Pdyrw=Apus09Lppg9YNQsr8k4uoYXHmK24Euw@mail.gmail.com>
	<4F68C66F.2010902@uwindsor.ca>
	<FFACED63-40D9-4810-9927-0E4984BA8465@scottcain.net>
	<web-60068456@uwindsor.ca>
	<CA+JTaoxshG4M+awmuw93=JkwqtisgFSw6igZE+_2tCFaN-ocrw@mail.gmail.com>
	<4F6A03D2.5010503@uwindsor.ca>
	<CA+JTaoyMT6_uxYG_b28j-PCJfiOeL6FUqgLRj1FNvwR7XZUOkA@mail.gmail.com>
	<4F6A290E.8000306@uwindsor.ca>
	<CA+JTaowKA=wFW8A91wpOMZLAe+phkFdHdppO1ume+30sWN9T9g@mail.gmail.com>
Message-ID: <4F6A44CE.3010100@uwindsor.ca>

Hi Scott,
  I tried both maker2chado and gmod_bulk_load_gff.pl with fasta embedded 
or not... If the fastafile was seperate I used the command --fastafile 
and if it was embedded, it was simply --gfffile with the other 
appropriate commands for loading gene models not analysis ( i.e no 
exon).  It finally resulted that, as I mentioned, when I changed the 
header in the fasta file, the fasta loaded fine with the bulk-loader and 
using the --fastafile command..

Next, my gene models loaded fine with the bulk loader, so the db was 
populated. I turned on full-text searching by running the scripts, and 
stating -full text 1 in the conf file...
So it seems, I can do as you mentioned, query specific genes i.e cnot1, 
or with specific IDs or scaffold IDs, but what I really wanted is to be 
able to do generic gene searches using the 'maker' search, as done with 
my other databases, so that someone without knowledge of the contents of 
the database will recieve gene information. This I still can't do, but 
can be done with prior db's I set up that contained contig annotation 
vs. scaffolds, and I found was very useful returning all maker generated 
gene models.  With that, I thought the problem was with the nomenclature 
being used across annotations, scaffolds etc..

Claudia

On 21/03/2012 4:59 PM, Scott Cain wrote:
> Hi Claudia,
>
> I wanted to bring this back to the mailing lists, so I cc'ed them here.
>
> First, with the fasta loading issue: what command are you using to
> load the fasta sequences?  It works for me whether the fasta is at the
> bottom of the GFF file or if it is a separate fasta file (as long as I
> supply the --fastafile flag to the loader).
>
> About the searching problem: when I turn on full text searching (which
> means both running gmod_chado_fts_prep.pl and adding "-fulltext 1" to
> the db_args in the gbrowse config file), I can search for "cnot1" and
> find both a gene and an mRNA (of course, they are really the same
> feature, but GBrowse doesn't know that).  Also, searching for "maker"
> works, but in a real database, this will not be an effective query,
> since the number of results returned are limited, and presumably there
> will be lots of features resulting from a query like that.  Please
> remind me, is that what you wanted to do?
>
> Scott
>
>
>
>
> On Wed, Mar 21, 2012 at 3:16 PM, claudia<dinatal at uwindsor.ca>  wrote:
>> Hi Scott,
>>
>>   Wanted to give you a quick heads up that the bulk loader seems to be
>> loading my fasta files now after deleting the ' ##FASTA' header ( the first
>> line of the file now looks like this>scaffold0001)...
>> Never had this problem before, it seems the bulk loader wanted to see a '>'
>> symbol in front of the first line...
>>
>> -- when I say seems, I will let you know if it finishes, as it currently
>>   states " Loading sequences ( if any)" ... and I never made it this far
>> before :)
>>
>> Claudia
>>
>>
>>
>> On 21/03/2012 12:53 PM, Scott Cain wrote:
>>> Hi Claudia,
>>>
>>> I imagine one scaffold and gene models would be good--the problem is
>>> finding genes, right?
>>>
>>> Also, with loading fasta: were the corresponding features from the GFF
>>> file already loaded?  If so, that should have worked, and if it didn't
>>> it implies a bug.  If not, that's why.
>>>
>>> Scott
>>>
>>>
>>> On Wed, Mar 21, 2012 at 12:37 PM, claudia<dinatal at uwindsor.ca>    wrote:
>>>> Hi Scott,
>>>>   So would one scaffold with Maker gene models suffice? Do you want the
>>>> analysis as well?
>>>>
>>>> --along those same lines, I did try and load the original sequence
>>>> (fasta)
>>>> file first that I ran the Pipeline on and chado seems to refuse the files
>>>> saying they don't contain the appropriate feature '>' in the header which
>>>> in
>>>> fact they do i.e>    scaffold00001 ... So not sure what is wrong with the
>>>> fasta that chado doesn't want to load even if it is embedded in the GFF3,
>>>> the bulk loader or maker2chado return errors stating 'feature not
>>>> found'...
>>>>
>>>>
>>>> Claudia
>>>>
>>>>
>>>>
>>>> On 21/03/2012 12:20 PM, Scott Cain wrote:
>>>>> Hi Claudia,
>>>>>
>>>>> I was hoping to get actual files that I could do testing on, not
>>>>> pictures of files :-)
>>>>>
>>>>> Scott
>>>>>
>>>>>
>>>>> On Tue, Mar 20, 2012 at 4:15 PM, Dinatale C<dinatal at uwindsor.ca>
>>>>>   wrote:
>>>>>> Hi,
>>>>>>
>>>>>> Attached:  I have samples of the contig file ( I extracted the contig
>>>>>> features first to load prior to the gene models) the fasta of the
>>>>>> sequences
>>>>>> is in the footer of the gff3 file.
>>>>>>
>>>>>> --so basically, based on experience with contig annotations, I should
>>>>>> be
>>>>>> able to type in 'maker' in to the gbrowse search bar, and recieve all
>>>>>> the
>>>>>> maker gene annotations, but I don't. I must specifiy the exact ID i.e "
>>>>>> maker-scaffold11323-augustus-gene...." or 'scaffold11323'
>>>>>>
>>>>>> --so I wonder if it has to do with the fasta files being named as
>>>>>> 'scaffolds' and perhaps causing a problem with chado recognizing that
>>>>>> they
>>>>>> are linked to the gene annotations due to scaffold not being a SOFA
>>>>>> type
>>>>>> term, if in fact the sequences must be submitted to the database first?
>>>>>>
>>>>>>
>>>>>> Thanks in advance,
>>>>>>
>>>>>> Claudia
>>>>>>
>>>>>> On Tue, 20 Mar 2012 15:50:55 -0400 Scott Cain wrote:
>>>>>>> Hi Claudia,
>>>>>>>
>>>>>>> Can you post a sample of the gff that shows what you are looking for
>>>>>>> and
>>>>>>> not finding?
>>>>>>>
>>>>>>> Scott
>>>>>>>
>>>>>>>
>>>>>>> Sent from my iPad
>>>>>>>
>>>>>>> On Mar 20, 2012, at 2:03 PM, claudia wrote:
>>>>>>>
>>>>>>>> Hi,
>>>>>>>>
>>>>>>>> I have enabled full text searching and I still have this problem,
>>>>>>>> another reason for
>>>>>>> concern... So I wondered if in fact I changed all the ID's in the GFF3
>>>>>>> file to supercontigs,
>>>>>>> then perhaps Chado would better link all the terms, annotations, and
>>>>>>> fasta
>>>>>>> files....
>>>>>>> Although, i realize that the seq_id ( column 1) shouldn't need to be
>>>>>>> specific since the
>>>>>>> 'type' term would take care of designating the feature type, no?
>>>>>>>> Claudia
>>>>>>>>
>>>>>>>>
>>>>>>>>
>>>>>>>> On 20/03/2012 1:25 PM, Scott Cain wrote:
>>>>>>>>> Hi Claudia,
>>>>>>>>>
>>>>>>>>> I agree with everything that Carson wrote, except about name
>>>>>>>>> searching--it's a little trickier in Chado. What you probably want
>>>>>>>>> to
>>>>>>>>> do is implement full text searching. See:
>>>>>>>>>
>>>>>>>>> http://gmod.org/wiki/Chado_Full_Text_Search
>>>>>>>>>
>>>>>>>>> for more information on setting it up and maintaining it.
>>>>>>>>>
>>>>>>>>> Scott
>>>>>>>>>
>>>>>>>>>
>>>>>>>>> On Tue, Mar 20, 2012 at 1:13 PM, Carson Holt wrote:
>>>>>>>>>>> I have 2 concerns, the first is: regarding representing scaffold
>>>>>>>>>>> features in chado and gbrowse. I noticed that the Sequence
>>>>>>>>>>> ontology
>>>>>>>>>>> uses
>>>>>>>>>>> the term supercontig and so if my assembly generated scaffolds
>>>>>>>>>>> entitled
>>>>>>>>>>> "scaffold" should I change the names to supercontigs so that chado
>>>>>>>>>>> recognizes the terms?
>>>>>>>>>> Yes. You must use valid SO terms. It is a requirement of GFF3, and
>>>>>>>>>> Chado
>>>>>>>>>> will enforce this requirement on loading a GFF3 file (note Chado
>>>>>>>>>> will
>>>>>>>>>> even
>>>>>>>>>> go as far as to check the validity of the Ontology_term= attribute
>>>>>>>>>> in
>>>>>>>>>> GFF3
>>>>>>>>>> if you use it). You can decide to use contig or supercontig as your
>>>>>>>>>> sequence feature. It doesn?t really matter unless you are placing
>>>>>>>>>>
>>>>>>>>>> both
>>>>>>>>>> into the database as separate features (i.e. You have a supercontig
>>>>>>>>>> as
>>>>>>>>>> the
>>>>>>>>>> parent feature and then you enter contigs individually as children
>>>>>>>>>> of
>>>>>>>>>> the
>>>>>>>>>> supercontig).
>>>>>>>>>>
>>>>>>>>>>
>>>>>>>>>>> Corresponding to my first question, Maker does not know that the
>>>>>>>>>>> contigs
>>>>>>>>>>> are actually scaffold/supercontigs when annotating and so Maker
>>>>>>>>>>> will
>>>>>>>>>>> still call the "type" feature or column 3 in the GFF3, a 'contig',
>>>>>>>>>>> how
>>>>>>>>>>> can Maker be implemented to change this naming convention before
>>>>>>>>>>> annotation, or after?
>>>>>>>>>> Not really important unless you plan on making contigs children of
>>>>>>>>>> the
>>>>>>>>>> supercontig. But you can always do a search and replace. -->
>>>>>>>>>> cat file.gff | perl -ane 's/\tcontig\t/\tsupercontig\t/s; print
>>>>>>>>>> $_'>
>>>>>>>>>> new_file.gff
>>>>>>>>>>
>>>>>>>>>>
>>>>>>>>>>> Consequently, I am having problems pulling up gene features in
>>>>>>>>>>> Gbrowse
>>>>>>>>>>> when doing a generic gene search, and I must provide the maker
>>>>>>>>>>> generated
>>>>>>>>>>> unique-gene_id in the gbrowse search bar or the known sequence id
>>>>>>>>>>> i.e
>>>>>>>>>>> 'scaffold001', which is not useful for someone who does not have
>>>>>>>>>>> this
>>>>>>>>>>> information.
>>>>>>>>>>> ---- I do not have this problem when my seq_id, and 'type' feature
>>>>>>>>>>> id
>>>>>>>>>>> match in the true case of 'contigs'. I can do a generic gene
>>>>>>>>>>> search
>>>>>>>>>>> in
>>>>>>>>>>> gbrowse with the term 'maker' and gbrowse will provide me all the
>>>>>>>>>>> associated maker generated gene calls.
>>>>>>>>>> See "Adjusting GBrowse Name Searches" in the GBrowse tutorial -->
>>>>>>>>>> http://gmod.org/gbrowse2/tutorial/tutorial.html#naming
>>>>>>>>>>
>>>>>>>>>>
>>>>>>>>>> Thanks,
>>>>>>>>>> Carson
>>>>>>>>>>
>>>>>>>>>>
>>>>>>>>>>
>>>>>>>>>>
>>>>>>>>>>
>>>>>>>>>>
>>>>>>>>>>
>>>>>>>>>>
>>>>>>>>>>
>>>>>>>>>>
>>>>>>>>>>
>>>>>>>>>>> Thank you for any guidance resolving these concerns,
>>>>>>>>>>> Claudia
>>>>>>>>>>>
>>>>>>>>>>>
>>>>>>>>>>>
>>>>>>>>>>> --
>>>>>>>>>>> Claudia DiNatale
>>>>>>>>>>> Master's Candidate
>>>>>>>>>>> The Crosby Lab
>>>>>>>>>>> University of Windsor
>>>>>>>>>>> 519-253-3000 ext: 4755
>>>>>>>>>>>
>>>>>>>>>>>
>>>>>>>>>>> _______________________________________________
>>>>>>>>>>> maker-devel mailing list
>>>>>>>>>>> maker-devel at box290.bluehost.com
>>>>>>>>>>>
>>>>>>>>>>>
>>>>>>>>>>>
>>>>>>>>>>> http://box290.bluehost.com/mailman/listinfo/maker-devel_yandell-lab.org
>>>>>>>>>>
>>>>>>>>>> _______________________________________________
>>>>>>>>>> maker-devel mailing list
>>>>>>>>>> maker-devel at box290.bluehost.com
>>>>>>>>>>
>>>>>>>>>>
>>>>>>>>>>
>>>>>>>>>> http://box290.bluehost.com/mailman/listinfo/maker-devel_yandell-lab.org
>>>>>>>>>
>>>>>>>> --
>>>>>>>> Claudia DiNatale
>>>>>>>> Master's Candidate
>>>>>>>> The Crosby Lab
>>>>>>>> University of Windsor
>>>>>>>> 519-253-3000 ext: 4755
>>>>>>>>
>>>> --
>>>> Claudia DiNatale
>>>> Master's Candidate
>>>> The Crosby Lab
>>>> University of Windsor
>>>> 519-253-3000 ext: 4755
>>>>
>>>
>>
>> --
>> Claudia DiNatale
>> Master's Candidate
>> The Crosby Lab
>> University of Windsor
>> 519-253-3000 ext: 4755
>>
>
>


-- 
Claudia DiNatale
Master's Candidate
The Crosby Lab
University of Windsor
519-253-3000 ext: 4755




From carsonhh at gmail.com  Wed Mar 21 16:05:32 2012
From: carsonhh at gmail.com (Carson Holt)
Date: Wed, 21 Mar 2012 18:05:32 -0400
Subject: [maker-devel] maker 2.22/2.23: Segmentation fault while
 processing FASTA input
In-Reply-To: <4F68C963.3040108@uni-wuerzburg.de>
Message-ID: <CB8FC294.9902%carsonhh@gmail.com>

That is likely the strangest result I could imagine?  The --debug option
really only cause MAKER to print status messages everywhere and nothing
else, so there must be something else going on between the tests.


One things I did notice from the error log though -->
0.49	Inline	/home/s187512/perl/lib/perl5/site_perl/5.12.1/Inline.pm
	UNKNOWN	Inline::denter	/home/s187512/perl/lib/perl5/site_perl/5.12.1/Inlin
e/denter.pm


These are both being loaded from perl 5.12.1 (you are using 5.14.1).  That
can cause issues since I know the first one is executed at the C level and
I wouldn't be surprised if the same is true on the second one.



I also saw this -->
Can't locate package GDBM_File for @AnyDBM_File::ISA at
/storage/tmp/software/perl-5.14.1/lib/5.14.1/x86_64-linux-thread-multi/DB_F
ile.pm line 293.
Can't locate package NDBM_File for @AnyDBM_File::ISA at
/storage/tmp/software/perl-5.14.1/lib/5.14.1/x86_64-linux-thread-multi/DB_F
ile.pm line 293.
Can't locate package SDBM_File for @AnyDBM_File::ISA at
/storage/tmp/software/perl-5.14.1/lib/5.14.1/x86_64-linux-thread-multi/DB_F
ile.pm line 293.



This appears could be related to Bio::DB::Fasta (which would make sense
with the timing of the seg fault).  This is line 405 in the BEGIN
statement for Bio::DB::Fasta
-->  @AnyDBM_File::ISA = qw(DB_File GDBM_File NDBM_File SDBM_File)

I'm not sure what to do about those?  Are you able to install GDBM_File,
NDBM_File, or SDBM_File by themselves?  They really should just be
optional?  I know I don't have NDBM_File, and I don't get an error.
DB_File is part of the perl distribution, but can be updated via CPAN.
Perhaps that would be good to do.  It may just be that DB_file is broken
and falling back to the other modules doesn?t work because you don't have
them.  There is also the chance that the issue is really with Berkley_DB.
DB_File accesses Berkley_DB and it wants version 1.x, but will work with
2.x and 3.x.  You may need to even go as far as building a new Berkley_DB.

Well that's enough to try for now.

Thanks,
Carson


On 12-03-20 2:16 PM, "Thomas Hackl" <thomas.hackl at uni-wuerzburg.de> wrote:

>Hi,
>
>I installed and ran the debug version of maker. Without -debug it
>results in the expected segmentation fault. With -debug it paradoxically
>finishes without the error.
>
>I screened the debug log anyway but could not find anything that helped
>me to localize the problem. I attached a condensed version (sort | uniq)
>of the log.
>Any ideas are appreciated.
>
>Regards
>Thomas
>
>
>
>Am 19.03.2012 17:24, schrieb Carson Holt:
>> Ok.  I finished the special debug version over the weekend.  Run with
>> -debug set as a command line flag.  Capture and return the STDERR on
>> failure.  It will list all modules used, the versions, and when they are
>> called so we can see what happens right before failure.
>>
>> http://yandell-lab.org/research/maker_debug.tgz
>>
>>
>> Thanks,
>> Carson
>>
>>
>>
>> On 12-03-14 1:57 AM, "Felix Bemm"<felix.bemm at uni-wuerzburg.de>  wrote:
>>
>>> Hi,
>>>
>>> Thomas and I are colleagues and dealing with the same problem here. I
>>> wrote some test code that forced the indexing and it work fine. We are
>>> using most of the bioperl seqio and db modules in combination with
>>>other
>>> tools and don't experience the same problem there at the moment.
>>>
>>> Regards
>>> Felix
>>>
>>> Am 13.03.2012 22:37, schrieb Barry Moore:
>>>> You might also try a short perl script outside of MAKER to exercise
>>>> Bio::DB::Fasta (which I believe is the module MAKER uses for Fasta
>>>> indexing - correct Carson?).
>>>>
>>>> Something like this should work to force indexing:
>>>>
>>>> useBio::DB::Fasta;
>>>> my $db = Bio::DB::Fasta->new('/path/to/fasta/files');
>>>> my$seq=$db->seq($seqid, $start, $end);
>>>>
>>>> Point it at your fasta directory or file.
>>>>
>>>> B
>>>>
>>>> On Mar 13, 2012, at 3:41 AM, Thomas Hackl wrote:
>>>>
>>>>> Hello,
>>>>>
>>>>> We reinstalled the packages you suggested
>>>>>
>>>>> forks is up to date (0.34).
>>>>> forks::shared is up to date (0.34).
>>>>> Inline::C is up to date (0.50).
>>>>> Storable is up to date (2.30).
>>>>>
>>>>> as well as BioPerl.
>>>>>
>>>>> The problem is still the same.
>>>>>
>>>>> With MPI it terminates with this message:
>>>>>
>>>>> STATUS: Parsing control files...
>>>>> STATUS: Processing and indexing input FASTA files...
>>>>>
>>>>> 
>>>>>======================================================================
>>>>>==
>>>>> =============
>>>>>
>>>>>
>>>>> = BAD TERMINATION OF ONE OF YOUR APPLICATION PROCESSES
>>>>> = EXIT CODE: 11
>>>>> = CLEANING UP REMAINING PROCESSES
>>>>> = YOU CAN IGNORE THE BELOW CLEANUP MESSAGES
>>>>>
>>>>> 
>>>>>======================================================================
>>>>>==
>>>>> =============
>>>>>
>>>>> APPLICATION TERMINATED WITH THE EXIT STRING: Segmentation fault
>>>>> (signal 11)
>>>>>
>>>>> which I presume is also the same problem.
>>>>>
>>>>> I am with you that the error is caused somewhere on the C level. If
>>>>> the indexing step
>>>>> is handled by non-maker modules exclusively, than the fact that the
>>>>> 2.15 version works,
>>>>> suggests that you are using different modules/methods in the current
>>>>> releases?
>>>>>
>>>>> In any case, I think a version with verbose status messages might
>>>>>help
>>>>> to localize the
>>>>> source of the problem.
>>>>>
>>>>> Regards
>>>>> Thomas
>>>>>
>>>>> Am 07.03.2012 23:45, schrieb Carson Holt:
>>>>>> There should be no new hardware requirement. But there is always a
>>>>>> chance
>>>>>> that there is an issue with one of the perl modules being used. I
>>>>>> assume
>>>>>> the failure is happening when using maker serially and you are not
>>>>>> using
>>>>>> MPI.
>>>>>>
>>>>>> Could you reinstall the following perl modules, and try again. If
>>>>>>you
>>>>>> are
>>>>>> using CPAN, do a 'force install' to force it to reinstall.
>>>>>>
>>>>>> Modules:
>>>>>> *Storable
>>>>>> *Inline::C
>>>>>> *forks
>>>>>> *forks::shared
>>>>>>
>>>>>> Also try reinstalling the latest version of BioPerl.
>>>>>>
>>>>>> The fact that this is a seg fault suggests that something is
>>>>>> happemning at
>>>>>> the C level (just outside of Perl). Those area all the modules MAKER
>>>>>> uses
>>>>>> that will call back to the C level. BioPerl has a fasta indexing
>>>>>> module
>>>>>> that is also making calls outside of Perl, and the fact it fails at
>>>>>> that
>>>>>> point makes it a suspect.
>>>>>>
>>>>>> Let me know what happens. I can always generate an alternate MAKER
>>>>>> executable for you to run with additional status messages that may
>>>>>> help
>>>>>> identify exactly which module is being called right before the
>>>>>> failure.
>>>>>>
>>>>>> Thanks,
>>>>>> Carson
>>>>>>
>>>>>>
>>>>>>
>>>>>> On 12-03-07 3:31 AM, "Thomas Hackl"<thomas.hackl at uni-wuerzburg.de
>>>>>> <mailto:thomas.hackl at uni-wuerzburg.de>>  wrote:
>>>>>>
>>>>>>> Hello,
>>>>>>>
>>>>>>> we want to use a current release of maker (2.22, 2.23) but the
>>>>>>> program
>>>>>>> terminates with a seg fault while processing the input FASTA files.
>>>>>>> maker 2.15 , which we have been using for quite some time, runs
>>>>>>> perfectly with identical data and setup.
>>>>>>>
>>>>>>> Please contact me if you need specifics on hardware, OS or anything
>>>>>>> else.
>>>>>>>
>>>>>>> Best regards
>>>>>>> Thomas
>>>>>>>
>>>>>>> --
>>>>>>> Thomas Hackl
>>>>>>> Julius-Maximilians-Universit?t
>>>>>>> Department of Bioinformatics
>>>>>>> 97074 W?rzburg, Germany
>>>>>>> Fon: +49 931 - 31 86883
>>>>>>> Mail: thomas.hackl at uni-wuerzburg.de
>>>>>>> <mailto:thomas.hackl at uni-wuerzburg.de>
>>>>>>>
>>>>>>>
>>>>>>> _______________________________________________
>>>>>>> maker-devel mailing list
>>>>>>> maker-devel at box290.bluehost.com
>>>>>>> <mailto:maker-devel at box290.bluehost.com>
>>>>>>>
>>>>>>> 
>>>>>>>http://box290.bluehost.com/mailman/listinfo/maker-devel_yandell-lab.
>>>>>>>or
>>>>>>> g
>>>>>
>>>>> --
>>>>> Thomas Hackl
>>>>> Julius-Maximilians-Universit?t
>>>>> Department of Bioinformatics
>>>>> 97074 W?rzburg, Germany
>>>>> Fon: +49 931 - 31 86883
>>>>> Mail: thomas.hackl at uni-wuerzburg.de
>>>>> <mailto:thomas.hackl at uni-wuerzburg.de>
>>>>>
>>>>>
>>>>> _______________________________________________
>>>>> maker-devel mailing list
>>>>> maker-devel at box290.bluehost.com
>>>>> <mailto:maker-devel at box290.bluehost.com>
>>>>> 
>>>>>http://box290.bluehost.com/mailman/listinfo/maker-devel_yandell-lab.or
>>>>>g
>>>> Barry Moore
>>>> Research Scientist
>>>> Dept. of Human Genetics
>>>> University of Utah
>>>> Salt Lake City, UT 84112
>>>> --------------------------------------------
>>>> (801) 585-3543
>>>>
>>>>
>>>>
>>>>
>>>>
>>>>
>>>> _______________________________________________
>>>> maker-devel mailing list
>>>> maker-devel at box290.bluehost.com
>>>> 
>>>>http://box290.bluehost.com/mailman/listinfo/maker-devel_yandell-lab.org
>>> _______________________________________________
>>> maker-devel mailing list
>>> maker-devel at box290.bluehost.com
>>> http://box290.bluehost.com/mailman/listinfo/maker-devel_yandell-lab.org
>
>-- 
>Thomas Hackl
>Julius-Maximilians-Universit?t
>Department of Bioinformatics
>97074 W?rzburg, Germany
>Fon:  +49 931 - 31 86883
>Mail: thomas.hackl at uni-wuerzburg.de
>
>_______________________________________________
>maker-devel mailing list
>maker-devel at box290.bluehost.com
>http://box290.bluehost.com/mailman/listinfo/maker-devel_yandell-lab.org





From seoanezonjic at hotmail.com  Thu Mar 22 03:38:39 2012
From: seoanezonjic at hotmail.com (Seoane Zonjic)
Date: Thu, 22 Mar 2012 02:38:39 -0700 (PDT)
Subject: [maker-devel] Error: Can't call method "num_hsps" on unblessed
	reference
Message-ID: <16b63903-4205-4064-ab30-efe67b37f7fa@b18g2000vbz.googlegroups.com>

Hi!
First, sorry for my poor english. I updated Maker at last release and
I have triying it with a set of contigs. With one of contigs, Maker
give me this error:

Processing transcripts into genes
Calculating annotation quality statistics
Can't call method "num_hsps" on unblessed referenceERROR: Failed while
adding statistics to annotations
ERROR: Chunk failed at level:3, tier_type:3
FAILED CONTIG:contig_4_0

ERROR: Chunk failed at level:7, tier_type:0
FAILED CONTIG:contig_4_0

At first, I thought that problem were the length of contig (125Kb). I
cut the the sequence in parts of 10Kb but a part again give me the
same error. I have worked with the debugger version of maker (I took
it of post of segmentation fault).
The input fasta (the part that failed me) and all logs are in this
link:
http://dl.dropbox.com/u/54903225/log.tar.gz
Other contigs of same set,  bigger or equal, work fine without
problem. There are something in this sequence that broken the Maker
run.
Thanks in advance



From carsonhh at gmail.com  Thu Mar 22 08:36:37 2012
From: carsonhh at gmail.com (Carson Holt)
Date: Thu, 22 Mar 2012 10:36:37 -0400
Subject: [maker-devel] Error: Can't call method "num_hsps" on unblessed
 reference
In-Reply-To: <16b63903-4205-4064-ab30-efe67b37f7fa@b18g2000vbz.googlegroups.com>
Message-ID: <CB90B0FA.9946%carsonhh@gmail.com>

Could you make a tarball of this directory and send it to me exactly as is
 --> 
/export/home_users/home/cvi_114_uma/pedro/testmaker/Spliced2.maker.output/S
pliced2_datastore/72/86/contig_4_0/

Thanks,
Carson


On 12-03-22 5:38 AM, "Seoane Zonjic" <seoanezonjic at hotmail.com> wrote:

>Hi!
>First, sorry for my poor english. I updated Maker at last release and
>I have triying it with a set of contigs. With one of contigs, Maker
>give me this error:
>
>Processing transcripts into genes
>Calculating annotation quality statistics
>Can't call method "num_hsps" on unblessed referenceERROR: Failed while
>adding statistics to annotations
>ERROR: Chunk failed at level:3, tier_type:3
>FAILED CONTIG:contig_4_0
>
>ERROR: Chunk failed at level:7, tier_type:0
>FAILED CONTIG:contig_4_0
>
>At first, I thought that problem were the length of contig (125Kb). I
>cut the the sequence in parts of 10Kb but a part again give me the
>same error. I have worked with the debugger version of maker (I took
>it of post of segmentation fault).
>The input fasta (the part that failed me) and all logs are in this
>link:
>http://dl.dropbox.com/u/54903225/log.tar.gz
>Other contigs of same set,  bigger or equal, work fine without
>problem. There are something in this sequence that broken the Maker
>run.
>Thanks in advance
>
>_______________________________________________
>maker-devel mailing list
>maker-devel at box290.bluehost.com
>http://box290.bluehost.com/mailman/listinfo/maker-devel_yandell-lab.org





From thomas.hackl at uni-wuerzburg.de  Mon Mar 26 04:51:48 2012
From: thomas.hackl at uni-wuerzburg.de (Thomas Hackl)
Date: Mon, 26 Mar 2012 12:51:48 +0200
Subject: [maker-devel] maker 2.22/2.23: Segmentation fault while
 processing FASTA input
In-Reply-To: <CB8FC294.9902%carsonhh@gmail.com>
References: <CB8FC294.9902%carsonhh@gmail.com>
Message-ID: <4F704A44.2080707@uni-wuerzburg.de>

Hi,

I was finally able to "fix" the Problem. I tried everything you 
suggested, nice catch on my screwed up Perl lib path btw, but I could 
neither install GDBM_File or NDBM_File nor Berkley_DB separately. In the 
end I simply removed the  ISA relations to the modules in question from 
the source code and now it seems to works fine...

sed -i 's/qw(DB_File GDBM_File NDBM_File SDBM_File)/qw(DB_File)/'

So thanks a lot for your prompt and comprehensive response, the debug 
executables and the help with the messages.

Regards
Thomas



Am 21.03.2012 23:05, schrieb Carson Holt:
> That is likely the strangest result I could imagine?  The --debug option
> really only cause MAKER to print status messages everywhere and nothing
> else, so there must be something else going on between the tests.
>
>
> One things I did notice from the error log though -->
> 0.49	Inline	/home/s187512/perl/lib/perl5/site_perl/5.12.1/Inline.pm
> 	UNKNOWN	Inline::denter	/home/s187512/perl/lib/perl5/site_perl/5.12.1/Inlin
> e/denter.pm
>
>
> These are both being loaded from perl 5.12.1 (you are using 5.14.1).  That
> can cause issues since I know the first one is executed at the C level and
> I wouldn't be surprised if the same is true on the second one.
>
>
>
> I also saw this -->
> Can't locate package GDBM_File for @AnyDBM_File::ISA at
> /storage/tmp/software/perl-5.14.1/lib/5.14.1/x86_64-linux-thread-multi/DB_F
> ile.pm line 293.
> Can't locate package NDBM_File for @AnyDBM_File::ISA at
> /storage/tmp/software/perl-5.14.1/lib/5.14.1/x86_64-linux-thread-multi/DB_F
> ile.pm line 293.
> Can't locate package SDBM_File for @AnyDBM_File::ISA at
> /storage/tmp/software/perl-5.14.1/lib/5.14.1/x86_64-linux-thread-multi/DB_F
> ile.pm line 293.
>
>
>
> This appears could be related to Bio::DB::Fasta (which would make sense
> with the timing of the seg fault).  This is line 405 in the BEGIN
> statement for Bio::DB::Fasta
> -->   @AnyDBM_File::ISA = qw(DB_File GDBM_File NDBM_File SDBM_File)
>
> I'm not sure what to do about those?  Are you able to install GDBM_File,
> NDBM_File, or SDBM_File by themselves?  They really should just be
> optional?  I know I don't have NDBM_File, and I don't get an error.
> DB_File is part of the perl distribution, but can be updated via CPAN.
> Perhaps that would be good to do.  It may just be that DB_file is broken
> and falling back to the other modules doesn?t work because you don't have
> them.  There is also the chance that the issue is really with Berkley_DB.
> DB_File accesses Berkley_DB and it wants version 1.x, but will work with
> 2.x and 3.x.  You may need to even go as far as building a new Berkley_DB.
>
> Well that's enough to try for now.
>
> Thanks,
> Carson
>
>
> On 12-03-20 2:16 PM, "Thomas Hackl"<thomas.hackl at uni-wuerzburg.de>  wrote:
>
>> Hi,
>>
>> I installed and ran the debug version of maker. Without -debug it
>> results in the expected segmentation fault. With -debug it paradoxically
>> finishes without the error.
>>
>> I screened the debug log anyway but could not find anything that helped
>> me to localize the problem. I attached a condensed version (sort | uniq)
>> of the log.
>> Any ideas are appreciated.
>>
>> Regards
>> Thomas
>>
>>
>>
>> Am 19.03.2012 17:24, schrieb Carson Holt:
>>> Ok.  I finished the special debug version over the weekend.  Run with
>>> -debug set as a command line flag.  Capture and return the STDERR on
>>> failure.  It will list all modules used, the versions, and when they are
>>> called so we can see what happens right before failure.
>>>
>>> http://yandell-lab.org/research/maker_debug.tgz
>>>
>>>
>>> Thanks,
>>> Carson
>>>
>>>
>>>
>>> On 12-03-14 1:57 AM, "Felix Bemm"<felix.bemm at uni-wuerzburg.de>   wrote:
>>>
>>>> Hi,
>>>>
>>>> Thomas and I are colleagues and dealing with the same problem here. I
>>>> wrote some test code that forced the indexing and it work fine. We are
>>>> using most of the bioperl seqio and db modules in combination with
>>>> other
>>>> tools and don't experience the same problem there at the moment.
>>>>
>>>> Regards
>>>> Felix
>>>>
>>>> Am 13.03.2012 22:37, schrieb Barry Moore:
>>>>> You might also try a short perl script outside of MAKER to exercise
>>>>> Bio::DB::Fasta (which I believe is the module MAKER uses for Fasta
>>>>> indexing - correct Carson?).
>>>>>
>>>>> Something like this should work to force indexing:
>>>>>
>>>>> useBio::DB::Fasta;
>>>>> my $db = Bio::DB::Fasta->new('/path/to/fasta/files');
>>>>> my$seq=$db->seq($seqid, $start, $end);
>>>>>
>>>>> Point it at your fasta directory or file.
>>>>>
>>>>> B
>>>>>
>>>>> On Mar 13, 2012, at 3:41 AM, Thomas Hackl wrote:
>>>>>
>>>>>> Hello,
>>>>>>
>>>>>> We reinstalled the packages you suggested
>>>>>>
>>>>>> forks is up to date (0.34).
>>>>>> forks::shared is up to date (0.34).
>>>>>> Inline::C is up to date (0.50).
>>>>>> Storable is up to date (2.30).
>>>>>>
>>>>>> as well as BioPerl.
>>>>>>
>>>>>> The problem is still the same.
>>>>>>
>>>>>> With MPI it terminates with this message:
>>>>>>
>>>>>> STATUS: Parsing control files...
>>>>>> STATUS: Processing and indexing input FASTA files...
>>>>>>
>>>>>>
>>>>>> ======================================================================
>>>>>> ==
>>>>>> =============
>>>>>>
>>>>>>
>>>>>> = BAD TERMINATION OF ONE OF YOUR APPLICATION PROCESSES
>>>>>> = EXIT CODE: 11
>>>>>> = CLEANING UP REMAINING PROCESSES
>>>>>> = YOU CAN IGNORE THE BELOW CLEANUP MESSAGES
>>>>>>
>>>>>>
>>>>>> ======================================================================
>>>>>> ==
>>>>>> =============
>>>>>>
>>>>>> APPLICATION TERMINATED WITH THE EXIT STRING: Segmentation fault
>>>>>> (signal 11)
>>>>>>
>>>>>> which I presume is also the same problem.
>>>>>>
>>>>>> I am with you that the error is caused somewhere on the C level. If
>>>>>> the indexing step
>>>>>> is handled by non-maker modules exclusively, than the fact that the
>>>>>> 2.15 version works,
>>>>>> suggests that you are using different modules/methods in the current
>>>>>> releases?
>>>>>>
>>>>>> In any case, I think a version with verbose status messages might
>>>>>> help
>>>>>> to localize the
>>>>>> source of the problem.
>>>>>>
>>>>>> Regards
>>>>>> Thomas
>>>>>>
>>>>>> Am 07.03.2012 23:45, schrieb Carson Holt:
>>>>>>> There should be no new hardware requirement. But there is always a
>>>>>>> chance
>>>>>>> that there is an issue with one of the perl modules being used. I
>>>>>>> assume
>>>>>>> the failure is happening when using maker serially and you are not
>>>>>>> using
>>>>>>> MPI.
>>>>>>>
>>>>>>> Could you reinstall the following perl modules, and try again. If
>>>>>>> you
>>>>>>> are
>>>>>>> using CPAN, do a 'force install' to force it to reinstall.
>>>>>>>
>>>>>>> Modules:
>>>>>>> *Storable
>>>>>>> *Inline::C
>>>>>>> *forks
>>>>>>> *forks::shared
>>>>>>>
>>>>>>> Also try reinstalling the latest version of BioPerl.
>>>>>>>
>>>>>>> The fact that this is a seg fault suggests that something is
>>>>>>> happemning at
>>>>>>> the C level (just outside of Perl). Those area all the modules MAKER
>>>>>>> uses
>>>>>>> that will call back to the C level. BioPerl has a fasta indexing
>>>>>>> module
>>>>>>> that is also making calls outside of Perl, and the fact it fails at
>>>>>>> that
>>>>>>> point makes it a suspect.
>>>>>>>
>>>>>>> Let me know what happens. I can always generate an alternate MAKER
>>>>>>> executable for you to run with additional status messages that may
>>>>>>> help
>>>>>>> identify exactly which module is being called right before the
>>>>>>> failure.
>>>>>>>
>>>>>>> Thanks,
>>>>>>> Carson
>>>>>>>
>>>>>>>
>>>>>>>
>>>>>>> On 12-03-07 3:31 AM, "Thomas Hackl"<thomas.hackl at uni-wuerzburg.de
>>>>>>> <mailto:thomas.hackl at uni-wuerzburg.de>>   wrote:
>>>>>>>
>>>>>>>> Hello,
>>>>>>>>
>>>>>>>> we want to use a current release of maker (2.22, 2.23) but the
>>>>>>>> program
>>>>>>>> terminates with a seg fault while processing the input FASTA files.
>>>>>>>> maker 2.15 , which we have been using for quite some time, runs
>>>>>>>> perfectly with identical data and setup.
>>>>>>>>
>>>>>>>> Please contact me if you need specifics on hardware, OS or anything
>>>>>>>> else.
>>>>>>>>
>>>>>>>> Best regards
>>>>>>>> Thomas
>>>>>>>>
>>>>>>>> --
>>>>>>>> Thomas Hackl
>>>>>>>> Julius-Maximilians-Universit?t
>>>>>>>> Department of Bioinformatics
>>>>>>>> 97074 W?rzburg, Germany
>>>>>>>> Fon: +49 931 - 31 86883
>>>>>>>> Mail: thomas.hackl at uni-wuerzburg.de
>>>>>>>> <mailto:thomas.hackl at uni-wuerzburg.de>
>>>>>>>>
>>>>>>>>
>>>>>>>> _______________________________________________
>>>>>>>> maker-devel mailing list
>>>>>>>> maker-devel at box290.bluehost.com
>>>>>>>> <mailto:maker-devel at box290.bluehost.com>
>>>>>>>>
>>>>>>>>
>>>>>>>> http://box290.bluehost.com/mailman/listinfo/maker-devel_yandell-lab.
>>>>>>>> or
>>>>>>>> g
>>>>>> --
>>>>>> Thomas Hackl
>>>>>> Julius-Maximilians-Universit?t
>>>>>> Department of Bioinformatics
>>>>>> 97074 W?rzburg, Germany
>>>>>> Fon: +49 931 - 31 86883
>>>>>> Mail: thomas.hackl at uni-wuerzburg.de
>>>>>> <mailto:thomas.hackl at uni-wuerzburg.de>
>>>>>>
>>>>>>
>>>>>> _______________________________________________
>>>>>> maker-devel mailing list
>>>>>> maker-devel at box290.bluehost.com
>>>>>> <mailto:maker-devel at box290.bluehost.com>
>>>>>>
>>>>>> http://box290.bluehost.com/mailman/listinfo/maker-devel_yandell-lab.or
>>>>>> g
>>>>> Barry Moore
>>>>> Research Scientist
>>>>> Dept. of Human Genetics
>>>>> University of Utah
>>>>> Salt Lake City, UT 84112
>>>>> --------------------------------------------
>>>>> (801) 585-3543
>>>>>
>>>>>
>>>>>
>>>>>
>>>>>
>>>>>
>>>>> _______________________________________________
>>>>> maker-devel mailing list
>>>>> maker-devel at box290.bluehost.com
>>>>>
>>>>> http://box290.bluehost.com/mailman/listinfo/maker-devel_yandell-lab.org
>>>> _______________________________________________
>>>> maker-devel mailing list
>>>> maker-devel at box290.bluehost.com
>>>> http://box290.bluehost.com/mailman/listinfo/maker-devel_yandell-lab.org
>> --
>> Thomas Hackl
>> Julius-Maximilians-Universit?t
>> Department of Bioinformatics
>> 97074 W?rzburg, Germany
>> Fon:  +49 931 - 31 86883
>> Mail: thomas.hackl at uni-wuerzburg.de
>>
>> _______________________________________________
>> maker-devel mailing list
>> maker-devel at box290.bluehost.com
>> http://box290.bluehost.com/mailman/listinfo/maker-devel_yandell-lab.org


-- 
Thomas Hackl
Julius-Maximilians-Universit?t
Department of Bioinformatics
97074 W?rzburg, Germany
Fon:  +49 931 - 31 86883
Mail: thomas.hackl at uni-wuerzburg.de




From carsonhh at gmail.com  Mon Mar 26 07:01:52 2012
From: carsonhh at gmail.com (Carson Holt)
Date: Mon, 26 Mar 2012 09:01:52 -0400
Subject: [maker-devel] maker 2.22/2.23: Segmentation fault while
 processing FASTA input
In-Reply-To: <4F704A44.2080707@uni-wuerzburg.de>
Message-ID: <CB95E04E.9E8B%carsonhh@gmail.com>

Well, if that works, I'd call it a success.  Just be careful with any
future updates to BioPerl.  Since the root cause of the problem may still
be there.

Thanks,
Carson




On 12-03-26 6:51 AM, "Thomas Hackl" <thomas.hackl at uni-wuerzburg.de> wrote:

>Hi,
>
>I was finally able to "fix" the Problem. I tried everything you
>suggested, nice catch on my screwed up Perl lib path btw, but I could
>neither install GDBM_File or NDBM_File nor Berkley_DB separately. In the
>end I simply removed the  ISA relations to the modules in question from
>the source code and now it seems to works fine...
>
>sed -i 's/qw(DB_File GDBM_File NDBM_File SDBM_File)/qw(DB_File)/'
>
>So thanks a lot for your prompt and comprehensive response, the debug
>executables and the help with the messages.
>
>Regards
>Thomas
>
>
>
>Am 21.03.2012 23:05, schrieb Carson Holt:
>> That is likely the strangest result I could imagine?  The --debug option
>> really only cause MAKER to print status messages everywhere and nothing
>> else, so there must be something else going on between the tests.
>>
>>
>> One things I did notice from the error log though -->
>> 0.49	Inline	/home/s187512/perl/lib/perl5/site_perl/5.12.1/Inline.pm
>> 
>>	UNKNOWN	Inline::denter	/home/s187512/perl/lib/perl5/site_perl/5.12.1/Inl
>>in
>> e/denter.pm
>>
>>
>> These are both being loaded from perl 5.12.1 (you are using 5.14.1).
>>That
>> can cause issues since I know the first one is executed at the C level
>>and
>> I wouldn't be surprised if the same is true on the second one.
>>
>>
>>
>> I also saw this -->
>> Can't locate package GDBM_File for @AnyDBM_File::ISA at
>> 
>>/storage/tmp/software/perl-5.14.1/lib/5.14.1/x86_64-linux-thread-multi/DB
>>_F
>> ile.pm line 293.
>> Can't locate package NDBM_File for @AnyDBM_File::ISA at
>> 
>>/storage/tmp/software/perl-5.14.1/lib/5.14.1/x86_64-linux-thread-multi/DB
>>_F
>> ile.pm line 293.
>> Can't locate package SDBM_File for @AnyDBM_File::ISA at
>> 
>>/storage/tmp/software/perl-5.14.1/lib/5.14.1/x86_64-linux-thread-multi/DB
>>_F
>> ile.pm line 293.
>>
>>
>>
>> This appears could be related to Bio::DB::Fasta (which would make sense
>> with the timing of the seg fault).  This is line 405 in the BEGIN
>> statement for Bio::DB::Fasta
>> -->   @AnyDBM_File::ISA = qw(DB_File GDBM_File NDBM_File SDBM_File)
>>
>> I'm not sure what to do about those?  Are you able to install GDBM_File,
>> NDBM_File, or SDBM_File by themselves?  They really should just be
>> optional?  I know I don't have NDBM_File, and I don't get an error.
>> DB_File is part of the perl distribution, but can be updated via CPAN.
>> Perhaps that would be good to do.  It may just be that DB_file is broken
>> and falling back to the other modules doesn?t work because you don't
>>have
>> them.  There is also the chance that the issue is really with
>>Berkley_DB.
>> DB_File accesses Berkley_DB and it wants version 1.x, but will work with
>> 2.x and 3.x.  You may need to even go as far as building a new
>>Berkley_DB.
>>
>> Well that's enough to try for now.
>>
>> Thanks,
>> Carson
>>
>>
>> On 12-03-20 2:16 PM, "Thomas Hackl"<thomas.hackl at uni-wuerzburg.de>
>>wrote:
>>
>>> Hi,
>>>
>>> I installed and ran the debug version of maker. Without -debug it
>>> results in the expected segmentation fault. With -debug it
>>>paradoxically
>>> finishes without the error.
>>>
>>> I screened the debug log anyway but could not find anything that helped
>>> me to localize the problem. I attached a condensed version (sort |
>>>uniq)
>>> of the log.
>>> Any ideas are appreciated.
>>>
>>> Regards
>>> Thomas
>>>
>>>
>>>
>>> Am 19.03.2012 17:24, schrieb Carson Holt:
>>>> Ok.  I finished the special debug version over the weekend.  Run with
>>>> -debug set as a command line flag.  Capture and return the STDERR on
>>>> failure.  It will list all modules used, the versions, and when they
>>>>are
>>>> called so we can see what happens right before failure.
>>>>
>>>> http://yandell-lab.org/research/maker_debug.tgz
>>>>
>>>>
>>>> Thanks,
>>>> Carson
>>>>
>>>>
>>>>
>>>> On 12-03-14 1:57 AM, "Felix Bemm"<felix.bemm at uni-wuerzburg.de>
>>>>wrote:
>>>>
>>>>> Hi,
>>>>>
>>>>> Thomas and I are colleagues and dealing with the same problem here. I
>>>>> wrote some test code that forced the indexing and it work fine. We
>>>>>are
>>>>> using most of the bioperl seqio and db modules in combination with
>>>>> other
>>>>> tools and don't experience the same problem there at the moment.
>>>>>
>>>>> Regards
>>>>> Felix
>>>>>
>>>>> Am 13.03.2012 22:37, schrieb Barry Moore:
>>>>>> You might also try a short perl script outside of MAKER to exercise
>>>>>> Bio::DB::Fasta (which I believe is the module MAKER uses for Fasta
>>>>>> indexing - correct Carson?).
>>>>>>
>>>>>> Something like this should work to force indexing:
>>>>>>
>>>>>> useBio::DB::Fasta;
>>>>>> my $db = Bio::DB::Fasta->new('/path/to/fasta/files');
>>>>>> my$seq=$db->seq($seqid, $start, $end);
>>>>>>
>>>>>> Point it at your fasta directory or file.
>>>>>>
>>>>>> B
>>>>>>
>>>>>> On Mar 13, 2012, at 3:41 AM, Thomas Hackl wrote:
>>>>>>
>>>>>>> Hello,
>>>>>>>
>>>>>>> We reinstalled the packages you suggested
>>>>>>>
>>>>>>> forks is up to date (0.34).
>>>>>>> forks::shared is up to date (0.34).
>>>>>>> Inline::C is up to date (0.50).
>>>>>>> Storable is up to date (2.30).
>>>>>>>
>>>>>>> as well as BioPerl.
>>>>>>>
>>>>>>> The problem is still the same.
>>>>>>>
>>>>>>> With MPI it terminates with this message:
>>>>>>>
>>>>>>> STATUS: Parsing control files...
>>>>>>> STATUS: Processing and indexing input FASTA files...
>>>>>>>
>>>>>>>
>>>>>>> 
>>>>>>>====================================================================
>>>>>>>==
>>>>>>> ==
>>>>>>> =============
>>>>>>>
>>>>>>>
>>>>>>> = BAD TERMINATION OF ONE OF YOUR APPLICATION PROCESSES
>>>>>>> = EXIT CODE: 11
>>>>>>> = CLEANING UP REMAINING PROCESSES
>>>>>>> = YOU CAN IGNORE THE BELOW CLEANUP MESSAGES
>>>>>>>
>>>>>>>
>>>>>>> 
>>>>>>>====================================================================
>>>>>>>==
>>>>>>> ==
>>>>>>> =============
>>>>>>>
>>>>>>> APPLICATION TERMINATED WITH THE EXIT STRING: Segmentation fault
>>>>>>> (signal 11)
>>>>>>>
>>>>>>> which I presume is also the same problem.
>>>>>>>
>>>>>>> I am with you that the error is caused somewhere on the C level. If
>>>>>>> the indexing step
>>>>>>> is handled by non-maker modules exclusively, than the fact that the
>>>>>>> 2.15 version works,
>>>>>>> suggests that you are using different modules/methods in the
>>>>>>>current
>>>>>>> releases?
>>>>>>>
>>>>>>> In any case, I think a version with verbose status messages might
>>>>>>> help
>>>>>>> to localize the
>>>>>>> source of the problem.
>>>>>>>
>>>>>>> Regards
>>>>>>> Thomas
>>>>>>>
>>>>>>> Am 07.03.2012 23:45, schrieb Carson Holt:
>>>>>>>> There should be no new hardware requirement. But there is always a
>>>>>>>> chance
>>>>>>>> that there is an issue with one of the perl modules being used. I
>>>>>>>> assume
>>>>>>>> the failure is happening when using maker serially and you are not
>>>>>>>> using
>>>>>>>> MPI.
>>>>>>>>
>>>>>>>> Could you reinstall the following perl modules, and try again. If
>>>>>>>> you
>>>>>>>> are
>>>>>>>> using CPAN, do a 'force install' to force it to reinstall.
>>>>>>>>
>>>>>>>> Modules:
>>>>>>>> *Storable
>>>>>>>> *Inline::C
>>>>>>>> *forks
>>>>>>>> *forks::shared
>>>>>>>>
>>>>>>>> Also try reinstalling the latest version of BioPerl.
>>>>>>>>
>>>>>>>> The fact that this is a seg fault suggests that something is
>>>>>>>> happemning at
>>>>>>>> the C level (just outside of Perl). Those area all the modules
>>>>>>>>MAKER
>>>>>>>> uses
>>>>>>>> that will call back to the C level. BioPerl has a fasta indexing
>>>>>>>> module
>>>>>>>> that is also making calls outside of Perl, and the fact it fails
>>>>>>>>at
>>>>>>>> that
>>>>>>>> point makes it a suspect.
>>>>>>>>
>>>>>>>> Let me know what happens. I can always generate an alternate MAKER
>>>>>>>> executable for you to run with additional status messages that may
>>>>>>>> help
>>>>>>>> identify exactly which module is being called right before the
>>>>>>>> failure.
>>>>>>>>
>>>>>>>> Thanks,
>>>>>>>> Carson
>>>>>>>>
>>>>>>>>
>>>>>>>>
>>>>>>>> On 12-03-07 3:31 AM, "Thomas Hackl"<thomas.hackl at uni-wuerzburg.de
>>>>>>>> <mailto:thomas.hackl at uni-wuerzburg.de>>   wrote:
>>>>>>>>
>>>>>>>>> Hello,
>>>>>>>>>
>>>>>>>>> we want to use a current release of maker (2.22, 2.23) but the
>>>>>>>>> program
>>>>>>>>> terminates with a seg fault while processing the input FASTA
>>>>>>>>>files.
>>>>>>>>> maker 2.15 , which we have been using for quite some time, runs
>>>>>>>>> perfectly with identical data and setup.
>>>>>>>>>
>>>>>>>>> Please contact me if you need specifics on hardware, OS or
>>>>>>>>>anything
>>>>>>>>> else.
>>>>>>>>>
>>>>>>>>> Best regards
>>>>>>>>> Thomas
>>>>>>>>>
>>>>>>>>> --
>>>>>>>>> Thomas Hackl
>>>>>>>>> Julius-Maximilians-Universit?t
>>>>>>>>> Department of Bioinformatics
>>>>>>>>> 97074 W?rzburg, Germany
>>>>>>>>> Fon: +49 931 - 31 86883
>>>>>>>>> Mail: thomas.hackl at uni-wuerzburg.de
>>>>>>>>> <mailto:thomas.hackl at uni-wuerzburg.de>
>>>>>>>>>
>>>>>>>>>
>>>>>>>>> _______________________________________________
>>>>>>>>> maker-devel mailing list
>>>>>>>>> maker-devel at box290.bluehost.com
>>>>>>>>> <mailto:maker-devel at box290.bluehost.com>
>>>>>>>>>
>>>>>>>>>
>>>>>>>>> 
>>>>>>>>>http://box290.bluehost.com/mailman/listinfo/maker-devel_yandell-la
>>>>>>>>>b.
>>>>>>>>> or
>>>>>>>>> g
>>>>>>> --
>>>>>>> Thomas Hackl
>>>>>>> Julius-Maximilians-Universit?t
>>>>>>> Department of Bioinformatics
>>>>>>> 97074 W?rzburg, Germany
>>>>>>> Fon: +49 931 - 31 86883
>>>>>>> Mail: thomas.hackl at uni-wuerzburg.de
>>>>>>> <mailto:thomas.hackl at uni-wuerzburg.de>
>>>>>>>
>>>>>>>
>>>>>>> _______________________________________________
>>>>>>> maker-devel mailing list
>>>>>>> maker-devel at box290.bluehost.com
>>>>>>> <mailto:maker-devel at box290.bluehost.com>
>>>>>>>
>>>>>>> 
>>>>>>>http://box290.bluehost.com/mailman/listinfo/maker-devel_yandell-lab.
>>>>>>>or
>>>>>>> g
>>>>>> Barry Moore
>>>>>> Research Scientist
>>>>>> Dept. of Human Genetics
>>>>>> University of Utah
>>>>>> Salt Lake City, UT 84112
>>>>>> --------------------------------------------
>>>>>> (801) 585-3543
>>>>>>
>>>>>>
>>>>>>
>>>>>>
>>>>>>
>>>>>>
>>>>>> _______________________________________________
>>>>>> maker-devel mailing list
>>>>>> maker-devel at box290.bluehost.com
>>>>>>
>>>>>> 
>>>>>>http://box290.bluehost.com/mailman/listinfo/maker-devel_yandell-lab.o
>>>>>>rg
>>>>> _______________________________________________
>>>>> maker-devel mailing list
>>>>> maker-devel at box290.bluehost.com
>>>>> 
>>>>>http://box290.bluehost.com/mailman/listinfo/maker-devel_yandell-lab.or
>>>>>g
>>> --
>>> Thomas Hackl
>>> Julius-Maximilians-Universit?t
>>> Department of Bioinformatics
>>> 97074 W?rzburg, Germany
>>> Fon:  +49 931 - 31 86883
>>> Mail: thomas.hackl at uni-wuerzburg.de
>>>
>>> _______________________________________________
>>> maker-devel mailing list
>>> maker-devel at box290.bluehost.com
>>> http://box290.bluehost.com/mailman/listinfo/maker-devel_yandell-lab.org
>
>
>-- 
>Thomas Hackl
>Julius-Maximilians-Universit?t
>Department of Bioinformatics
>97074 W?rzburg, Germany
>Fon:  +49 931 - 31 86883
>Mail: thomas.hackl at uni-wuerzburg.de
>
>
>_______________________________________________
>maker-devel mailing list
>maker-devel at box290.bluehost.com
>http://box290.bluehost.com/mailman/listinfo/maker-devel_yandell-lab.org





From daniel.fer.u at gmail.com  Sun Mar 25 20:53:25 2012
From: daniel.fer.u at gmail.com (=?UTF-8?Q?Daniel_Fern=C3=A1ndez?=)
Date: Sun, 25 Mar 2012 19:53:25 -0700 (PDT)
Subject: [maker-devel] Problem with RMBlast installation
Message-ID: <8109224.101.1332730405163.JavaMail.geo-discussion-forums@ynlx41>

Hi,

I trying to install MAKER, I don't have WU-Blast, I have Blast+ so in the 
README file tell me that I need RMBlast, but I don't know what file I have 
to choose, rmblast-1.2-ncbi-blast-2.2.23+-src.tar.gz or rmblast-1.2-ncbi-blast-2.2.23+-x64-linux.tar.gz 
(I have Linux 64-bit) in each version the README file is the same, and 
there tell me how I can install it, but the instructions is only for rmblast-1.2-ncbi-blast-2.2.23+-src, 
well, when I try to install it, I type this 
$./configure --with-mt --prefix=/usr/local/bioinfo/repeatmasker/rmblast 
--without-debug
This show me error, and I type make and this show stop.

Can you help me please?

This show me when I type $./configure --with-mt 
--prefix=/usr/local/bioinfo/repeatmasker/rmblast --without-debug
-----------------------------------------------------------------------------------------------------------------------------------------------
configure: loading site script ./src/build-system/config.site
configure: loading cache config.cache
checking build system type... x86_64-unknown-linux-gnu
checking host system type... x86_64-unknown-linux-gnu
checking for a BSD-compatible install... /usr/bin/install -c
checking for gcc... gcc
checking for C compiler default output file name... a.out
checking whether the C compiler works... yes
checking whether we are cross compiling... no
checking for suffix of executables... 
checking for suffix of object files... o
checking whether we are using the GNU C compiler... yes
checking whether gcc accepts -g... yes
checking for gcc option to accept ANSI C... none needed
checking for g++... no
checking for c++... no
checking for gpp... no
checking for aCC... no
checking for CC... no
checking for cxx... no
checking for cc++... no
checking for cl... no
checking for FCC... no
checking for KCC... no
checking for RCC... no
checking for xlC_r... no
checking for xlC... no
checking whether we are using the GNU C++ compiler... no
checking whether g++ accepts -g... no
adjusted C   compiler: /usr/bin/gcc 
./src/build-system/configure: line 4404: type: g++: not found
dirname: missing operand
Try `dirname --help' for more information.
configure: error: Do not know how to build MT-safe with compiler g++ 
./src/build-system/configure: line 4187: g++: command not found
-----------------------------------------------------------------------------------------------------------------------------------
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From jason.stajich at gmail.com  Mon Mar 26 09:33:55 2012
From: jason.stajich at gmail.com (Jason Stajich)
Date: Mon, 26 Mar 2012 08:33:55 -0700
Subject: [maker-devel] Problem with RMBlast installation
In-Reply-To: <8109224.101.1332730405163.JavaMail.geo-discussion-forums@ynlx41>
References: <8109224.101.1332730405163.JavaMail.geo-discussion-forums@ynlx41>
Message-ID: <7A26C949-4ED3-4CEF-8455-2D3A85B35A2B@gmail.com>

Hi Daniel -

Just download, unpackage the precompiled ( rmblast-1.2-ncbi-blast-2.2.23+-x64-linux.tar.gz ) version and tell RepeatMasker where the exes are when you configure RepeatMasker.  RMBlast is for RepeatMasker.
 
For running BLAST in MAKAER would install NCBI-BLAST+ if you don't have wu-blast --- ftp://ftp.ncbi.nih.gov/blast/executables/blast+/LATEST - I believe current maker supports BLAST+, BLAST, and WU-BLAST so you have your pick.

Jason
On Mar 25, 2012, at 7:53 PM, Daniel Fern?ndez wrote:

> Hi,
> 
> I trying to install MAKER, I don't have WU-Blast, I have Blast+ so in the README file tell me that I need RMBlast, but I don't know what file I have to choose, rmblast-1.2-ncbi-blast-2.2.23+-src.tar.gz or rmblast-1.2-ncbi-blast-2.2.23+-x64-linux.tar.gz (I have Linux 64-bit) in each version the README file is the same, and there tell me how I can install it, but the instructions is only for rmblast-1.2-ncbi-blast-2.2.23+-src, well, when I try to install it, I type this 
> $./configure --with-mt --prefix=/usr/local/bioinfo/repeatmasker/rmblast --without-debug
> This show me error, and I type make and this show stop.
> 
> Can you help me please?
> 
> This show me when I type $./configure --with-mt --prefix=/usr/local/bioinfo/repeatmasker/rmblast --without-debug
> -----------------------------------------------------------------------------------------------------------------------------------------------
> configure: loading site script ./src/build-system/config.site
> configure: loading cache config.cache
> checking build system type... x86_64-unknown-linux-gnu
> checking host system type... x86_64-unknown-linux-gnu
> checking for a BSD-compatible install... /usr/bin/install -c
> checking for gcc... gcc
> checking for C compiler default output file name... a.out
> checking whether the C compiler works... yes
> checking whether we are cross compiling... no
> checking for suffix of executables... 
> checking for suffix of object files... o
> checking whether we are using the GNU C compiler... yes
> checking whether gcc accepts -g... yes
> checking for gcc option to accept ANSI C... none needed
> checking for g++... no
> checking for c++... no
> checking for gpp... no
> checking for aCC... no
> checking for CC... no
> checking for cxx... no
> checking for cc++... no
> checking for cl... no
> checking for FCC... no
> checking for KCC... no
> checking for RCC... no
> checking for xlC_r... no
> checking for xlC... no
> checking whether we are using the GNU C++ compiler... no
> checking whether g++ accepts -g... no
> adjusted C   compiler: /usr/bin/gcc 
> ./src/build-system/configure: line 4404: type: g++: not found
> dirname: missing operand
> Try `dirname --help' for more information.
> configure: error: Do not know how to build MT-safe with compiler g++ ./src/build-system/configure: line 4187: g++: command not found
> -----------------------------------------------------------------------------------------------------------------------------------
> _______________________________________________
> maker-devel mailing list
> maker-devel at box290.bluehost.com
> http://box290.bluehost.com/mailman/listinfo/maker-devel_yandell-lab.org

Jason Stajich
jason.stajich at gmail.com
jason at bioperl.org

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From eernst at cshl.edu  Mon Mar 26 10:29:45 2012
From: eernst at cshl.edu (Evan)
Date: Mon, 26 Mar 2012 09:29:45 -0700 (PDT)
Subject: [maker-devel] Can't call method "start" on an undefined value
Message-ID: <31251549.92.1332779385632.JavaMail.geo-discussion-forums@vbbfy7>

Hi,

I'm running maker 2.24-beta. At least 10-15% of scaffolds are failing with 
the following error:

Preparing evidence for hint based annotation
cleaning clusters....
total clusters:1 now processing 0
in cluster::shadow_cluster...
...finished clustering.
cleaning clusters....
total clusters:4 now processing 0
 ...processing 0 of 3
 ...processing 1 of 3
total clusters:4 now processing 0
 ...processing 0 of 2
total clusters:4 now processing 0
total clusters:4 now processing 0
Can't call method "start" on an undefined valueERROR: Failed while 
preparing evidence clusters for annotations
ERROR: Chunk failed at level:0, tier_type:3
FAILED CONTIG:scaffold93.1

ERROR: Chunk failed at level:7, tier_type:0
FAILED CONTIG:scaffold93.1

This occurs when running just a single maker instance. 

Thanks,
Evan
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From carsonhh at gmail.com  Mon Mar 26 11:22:15 2012
From: carsonhh at gmail.com (Carson Holt)
Date: Mon, 26 Mar 2012 13:22:15 -0400
Subject: [maker-devel] maker 2.22-beta: identical names and sequences
 repeated in maker.all.proteins fasta - attached FASTA, gff3
In-Reply-To: <407831381.989320.1332781349591.JavaMail.root@ksu-sfpop-mailstore03>
Message-ID: <CB961AC7.9EF5%carsonhh@gmail.com>

Thanks for the file.  I now see that the issue is caused by repeated model
entries in the maker_gff file (example from the following lines in the
input GFF3).


scaffold09875   maker   mRNA    255     1019    .       +       .
ID=maker-scaffold09875-est_gff_Cufflinks-gene-0.0-mRNA-1;Parent=maker-scaff
old09875-est_gff_Cufflinks-gene-0.0;
scaffold09875   model_gff:maker match   255     1019    .       +       .
     
ID=scaffold09875:hit:419759:0_0;Name=maker-scaffold09875-est_gff_Cufflinks-
gene-0.0-mRNA-1;


During recent MAKER updates, it was requested that MAKER add model_gff
features used from a previous run as a reference annotation, so you can
still see it even when it is not chosen on the second round.  However this
has an unexpected effect on multiple reruns using maker output as the new
input because both entries get interpreted as model_gff, they both then
end up in the results of a rerun (duplicated each round).

I've fixed this in the developers release (be a couple of days till it
hits the download page as a beta release), but in the mean time just
remove the model_gff:maker entries from the input fasta and it will work
as expected.

To do that use this command -->
   grep -v "model_gff:maker"
Msex05162011.genome.all.maker-2.22-15Feb2012.gff3 >
filtered_Msex05162011.genome.all.maker-2.22-15Feb2012.gff3


Then put filtered_Msex05162011.genome.all.maker-2.22-15Feb2012.gff3 as
your maker_gff file.

I also recommend that you delete and .db extension files from the maker
output directory (there will be only one there).  That will make extra
sure that the GFF3 file index gets rebuilt to the new file.

Note:  I also noticed that Msex05162011.genome.cegma.gff is not in GFF3
format (it is in ZFF format).  It would work for training SNAP but will
not work with MAKER.

Thanks,
Carson





On 12-03-26 1:02 PM, "Sanjay Chellapilla" wrote:

>
>
>----- Original Message -----
>> Since you are using it as input.  I'll need to see this file.
>> 
>> 
>>/home/sanjay/manduca_sexta/maker/maker-runs-2.22/Msex05162011.genome.all.
>>ma
>> ker-2.22-15Feb2012.gff3
>> 
>> Thanks,
>> Carson
>> 
>> 
>> 
>> On 12-03-26 12:42 PM, "Sanjay Chellapilla"
>> wrote:
>> 
>> >Attached
>> >"Msex-maker-2.22-identical-repeated-proteins-input-files.tar.bz2"
>> >containing 3 files
>> >
>> >maker-2.22_opts.ctl.28Feb2012
>> >est_gff = baylor_cufflinks_transcripts_gtf_no_G14G15.gff3
>> >model_gff = Msex05162011.genome.cegma.gff
>> >
>> >The maker_gff (Msex05162011.genome.all.maker-2.22-15Feb2012.gff3) is
>> >633MB so I didn't include it in this message. Please let me know if
>> >you'd want to see it - I'll send it separately.
>> >
>> >Thank you,
>> >Sanjay.
>> >
>> >----- Original Message -----
>> >> Could you send me the file you are passing to the est_gff,
>> >> model_gff,
>> >> or
>> >> maker_gff options.
>> >> 
>> >> Also could you send me your MAKER control files?
>> >> 
>> >> Thanks,
>> >> Carson
>> >> 
>> >> 
>> >> 
>> >> 
>> >> On 12-03-14 1:26 PM, "Sanjay Chellapilla"
>> >> wrote:
>> >> 
>> >> >Hi Carson,
>> >> >
>> >> >Sorry I forgot to attach files showing the issue. Attached zip
>> >> >containing one such maker proteins fasta file and corresponding
>> >> >maker gff3 for scaffold00126 having identical repeated sequence
>> >> >">maker-scaffold00126-est_gff_Cufflinks-gene-2.0-mRNA-1".
>> >> >
>> >> >Thank you.
>> >> >
>> >> >----- Forwarded Message -----
>> >> >> Hi Carson,
>> >> >> 
>> >> >> I ran maker-2.22-beta a total of 3 times with the same
>> >> >> evidence,
>> >> >> to annotate the Manduca.sexta genome, each time using
>> >> >> maker-gff3
>> >> >> for the re-annotation run and gene-predictors SNAP, Augustus
>> >> >> trained
>> >> >> on maker-gff3 from the previous run. At the end of the third
>> >> >> run,
>> >> >> I used fasta_merge script to obtain the various fasta files.
>> >> >> I notice that some sequences are repeated in the maker.all
>> >> >> transcripts/proteins fasta files. I found 34 repeated out of
>> >> >> 16128 transcripts/proteins, so there are actually only 16094
>> >> >> unique
>> >> >> sequences. Could this be related to the "repeated genes" issue
>> >> >> from the strange cufflinks cuffmerge gff3 that's used as input
>> >> >> to maker - we discussed this back in January when we first came
>> >> >> across and I had sent you a portion of the gff3 where we saw
>> >> >> this,
>> >> >> and then you recommended trying maker-2.22-beta where this was
>> >> >> fixed
>> >> >> ?
>> >> >> Naturally this also causes repeated short-IDs created using the
>> >> >> maker_map_ids, map_fasta_ids, map_gff_ids scripts.
>> >> >> 
>> >> >> Thanks,
>> >> >> Sanjay.





From carsonhh at gmail.com  Mon Mar 26 13:08:48 2012
From: carsonhh at gmail.com (Carson Holt)
Date: Mon, 26 Mar 2012 15:08:48 -0400
Subject: [maker-devel] FW: Can't call method "start" on an undefined value
In-Reply-To: <CB963617.9F28%carsonhh@gmail.com>
Message-ID: <CB9636EF.9F37%carsonhh@gmail.com>

Ok.  This is fixed (along with a few other things), and is available for
download as MAKER 2.25.

Thanks,
Carson



From:  Evan <eernst at cshl.edu>
Date:  Mon, 26 Mar 2012 09:29:45 -0700 (PDT)
To:  <maker-devel at googlegroups.com>
Subject:  [maker-devel] Can't call method "start" on an undefined value

Hi,

I'm running maker 2.24-beta. At least 10-15% of scaffolds are failing with
the following error:

Preparing evidence for hint based annotation
cleaning clusters....
total clusters:1 now processing 0
in cluster::shadow_cluster...
...finished clustering.
cleaning clusters....
total clusters:4 now processing 0
 ...processing 0 of 3
 ...processing 1 of 3
total clusters:4 now processing 0
 ...processing 0 of 2
total clusters:4 now processing 0
total clusters:4 now processing 0
Can't call method "start" on an undefined valueERROR: Failed while preparing
evidence clusters for annotations
ERROR: Chunk failed at level:0, tier_type:3
FAILED CONTIG:scaffold93.1

ERROR: Chunk failed at level:7, tier_type:0
FAILED CONTIG:scaffold93.1

This occurs when running just a single maker instance.

Thanks,
Evan
_______________________________________________ maker-devel mailing list
maker-devel at box290.bluehost.comhttp://box290.bluehost.com/mailman/listinfo/m
aker-devel_yandell-lab.org


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From carsonhh at gmail.com  Mon Mar 26 14:17:36 2012
From: carsonhh at gmail.com (Carson Holt)
Date: Mon, 26 Mar 2012 16:17:36 -0400
Subject: [maker-devel] Can't call method "start" on an undefined value
In-Reply-To: <CAOqGFX-wEA2weUPSZRrpXBd+gV8nHAEsR9ST-YA96u+q+RvgyA@mail.gmail.com>
Message-ID: <CB964686.9FBB%carsonhh@gmail.com>

 //= is a feature of perl versions 5.10 and above.

You must have an older version of perl.
Just change it to ||= and it will work for older versions.  I'll make that
change to the release as well to make it work with older perl.

Thanks,
Carson




From:  Evan Ernst <eernst at cshl.edu>
Date:  Mon, 26 Mar 2012 16:13:19 -0400
To:  Carson Holt <carsonhh at gmail.com>
Cc:  <maker-devel at googlegroups.com>
Subject:  Re: [maker-devel] Can't call method "start" on an undefined value

Hi Carson,

Line 242 of maker is causing a compilation failure in the version I
downloaded:

241 -> eval "\$ver = \$${name}::VERSION";
242 -> $ver //= 'UNKNOWN';
243 -> $ver = 'UNKNOWN' if($ver =~ /^\-1\,/);

Thanks,
Evan

On Mon, Mar 26, 2012 at 3:06 PM, Evan Ernst <eernst at cshl.edu> wrote:
> Fantastic. Thanks for your help.
> 
> Best,
> Evan
> 
> 
> On Mon, Mar 26, 2012 at 3:05 PM, Carson Holt <carsonhh at gmail.com> wrote:
>> Ok.  This is fixed (along with a few other things), and is available for
>> download as MAKER 2.25.
>> 
>> Thanks,
>> Carson
>> 
>> 
>> 
>> From:  Evan <eernst at cshl.edu>
>> Date:  Mon, 26 Mar 2012 09:29:45 -0700 (PDT)
>> To:  <maker-devel at googlegroups.com>
>> Subject:  [maker-devel] Can't call method "start" on an undefined value
>> 
>> Hi,
>> 
>> I'm running maker 2.24-beta. At least 10-15% of scaffolds are failing with
>> the following error:
>> 
>> Preparing evidence for hint based annotation
>> cleaning clusters....
>> total clusters:1 now processing 0
>> in cluster::shadow_cluster...
>> ...finished clustering.
>> cleaning clusters....
>> total clusters:4 now processing 0
>>  ...processing 0 of 3
>>  ...processing 1 of 3
>> total clusters:4 now processing 0
>>  ...processing 0 of 2
>> total clusters:4 now processing 0
>> total clusters:4 now processing 0
>> Can't call method "start" on an undefined valueERROR: Failed while preparing
>> evidence clusters for annotations
>> ERROR: Chunk failed at level:0, tier_type:3
>> FAILED CONTIG:scaffold93.1
>> 
>> ERROR: Chunk failed at level:7, tier_type:0
>> FAILED CONTIG:scaffold93.1
>> 
>> This occurs when running just a single maker instance.
>> 
>> Thanks,
>> Evan
>> _______________________________________________ maker-devel mailing list
>> maker-devel at box290.bluehost.comhttp://box290.bluehost.com/mailman/listinfo/ma
>> ker-devel_yandell-lab.org
> 
> 
> 
> -- 
> Evan Ernst
> Martienssen Lab
> 
> Delbruck #216
> Cold Spring Harbor Laboratory
> 1 Bungtown Rd.
> Cold Spring Harbor, NY 11724
> 



-- 
Evan Ernst
Martienssen Lab

Delbruck #216
Cold Spring Harbor Laboratory
1 Bungtown Rd.
Cold Spring Harbor, NY 11724



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From daniel.fer.u at gmail.com  Mon Mar 26 20:39:43 2012
From: daniel.fer.u at gmail.com (=?UTF-8?Q?Daniel_Fern=C3=A1ndez?=)
Date: Mon, 26 Mar 2012 19:39:43 -0700 (PDT)
Subject: [maker-devel] Problem with RMBlast installation
In-Reply-To: <7A26C949-4ED3-4CEF-8455-2D3A85B35A2B@gmail.com>
References: <8109224.101.1332730405163.JavaMail.geo-discussion-forums@ynlx41>
	<7A26C949-4ED3-4CEF-8455-2D3A85B35A2B@gmail.com>
Message-ID: <3452112.702.1332815983251.JavaMail.geo-discussion-forums@ynne2>

Ok, I unpack this file, I have 3 directories (bin include lib) and the 
readme file, you tell me add this to my $PATH, but I  add to my path all 
executables (bin), but the other 2 directories? I don't think that I have 
to add to my path, is different to Blast+, in blast+ I only copy the 
executables to my path, the other directories are only data

The bin directory have many executables like blast+, if I add all to my 
path, so I will have many duplicate executables, does this not cause a 
conflict?

On Monday, March 26, 2012 10:33:55 AM UTC-5, Jason Stajich wrote:
>
> Hi Daniel -
>
> Just download, unpackage the precompiled ( rmblast-1.2-ncbi-blast-2.2.23+-x64-linux.tar.gz 
> ) version and tell RepeatMasker where the exes are when you configure 
> RepeatMasker.  RMBlast is for RepeatMasker.
>  
> For running BLAST in MAKAER would install NCBI-BLAST+ if you don't have 
> wu-blast --- ftp://ftp.ncbi.nih.gov/blast/executables/blast+/LATEST - I 
> believe current maker supports BLAST+, BLAST, and WU-BLAST so you have your 
> pick.
>
> Jason
> On Mar 25, 2012, at 7:53 PM, Daniel Fern?ndez wrote:
>
> Hi,
>
> I trying to install MAKER, I don't have WU-Blast, I have Blast+ so in the 
> README file tell me that I need RMBlast, but I don't know what file I have 
> to choose, rmblast-1.2-ncbi-blast-2.2.23+-src.tar.gz or rmblast-1.2-ncbi-blast-2.2.23+-x64-linux.tar.gz 
> (I have Linux 64-bit) in each version the README file is the same, and 
> there tell me how I can install it, but the instructions is only for rmblast-1.2-ncbi-blast-2.2.23+-src, 
> well, when I try to install it, I type this 
> $./configure --with-mt --prefix=/usr/local/bioinfo/repeatmasker/rmblast 
> --without-debug
> This show me error, and I type make and this show stop.
>
> Can you help me please?
>
> This show me when I type $./configure --with-mt 
> --prefix=/usr/local/bioinfo/repeatmasker/rmblast --without-debug
>
> -----------------------------------------------------------------------------------------------------------------------------------------------
> configure: loading site script ./src/build-system/config.site
> configure: loading cache config.cache
> checking build system type... x86_64-unknown-linux-gnu
> checking host system type... x86_64-unknown-linux-gnu
> checking for a BSD-compatible install... /usr/bin/install -c
> checking for gcc... gcc
> checking for C compiler default output file name... a.out
> checking whether the C compiler works... yes
> checking whether we are cross compiling... no
> checking for suffix of executables... 
> checking for suffix of object files... o
> checking whether we are using the GNU C compiler... yes
> checking whether gcc accepts -g... yes
> checking for gcc option to accept ANSI C... none needed
> checking for g++... no
> checking for c++... no
> checking for gpp... no
> checking for aCC... no
> checking for CC... no
> checking for cxx... no
> checking for cc++... no
> checking for cl... no
> checking for FCC... no
> checking for KCC... no
> checking for RCC... no
> checking for xlC_r... no
> checking for xlC... no
> checking whether we are using the GNU C++ compiler... no
> checking whether g++ accepts -g... no
> adjusted C   compiler: /usr/bin/gcc 
> ./src/build-system/configure: line 4404: type: g++: not found
> dirname: missing operand
> Try `dirname --help' for more information.
> configure: error: Do not know how to build MT-safe with compiler g++ 
> ./src/build-system/configure: line 4187: g++: command not found
>
> -----------------------------------------------------------------------------------------------------------------------------------
> _______________________________________________
> maker-devel mailing list
> maker-devel at box290.bluehost.com
> http://box290.bluehost.com/mailman/listinfo/maker-devel_yandell-lab.org
>
>
> Jason Stajich
> jason.stajich at gmail.com
> jason at bioperl.org
>  
>
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From carsonhh at gmail.com  Mon Mar 26 20:47:37 2012
From: carsonhh at gmail.com (Carson Holt)
Date: Mon, 26 Mar 2012 22:47:37 -0400
Subject: [maker-devel] Problem with RMBlast installation
In-Reply-To: <3452112.702.1332815983251.JavaMail.geo-discussion-forums@ynne2>
Message-ID: <CB96A177.A1BD%carsonhh@gmail.com>

You only need to add the directory location for executables you plan on
calling yourself from the command line.  You don't need to add RMBlast to
the PATH for example because you should never use it directly.  RepeatMasker
knows where it is once configured, and you want to use NCBI's BLAST.

Thanks,
Carson

From:  Daniel Fern?ndez <daniel.fer.u at gmail.com>
Date:  Mon, 26 Mar 2012 19:39:43 -0700 (PDT)
To:  <maker-devel at googlegroups.com>
Cc:  "maker-devel at yandell-lab.org List" <maker-devel at yandell-lab.org>,
Daniel Fern?ndez <daniel.fer.u at gmail.com>
Subject:  Re: [maker-devel] Problem with RMBlast installation

Ok, I unpack this file, I have 3 directories (bin include lib) and the
readme file, you tell me add this to my $PATH, but I  add to my path all
executables (bin), but the other 2 directories? I don't think that I have to
add to my path, is different to Blast+, in blast+ I only copy the
executables to my path, the other directories are only data

The bin directory have many executables like blast+, if I add all to my
path, so I will have many duplicate executables, does this not cause a
conflict?

On Monday, March 26, 2012 10:33:55 AM UTC-5, Jason Stajich wrote:
> Hi Daniel -
> 
> Just download, unpackage the precompiled (
> rmblast-1.2-ncbi-blast-2.2.23+-x64-linux.tar.gz ) version and tell
> RepeatMasker where the exes are when you configure RepeatMasker.  RMBlast is
> for RepeatMasker.
>  
> For running BLAST in MAKAER would install NCBI-BLAST+ if you don't have
> wu-blast --- ftp://ftp.ncbi.nih.gov/blast/executables/blast+/LATEST - I
> believe current maker supports BLAST+, BLAST, and WU-BLAST so you have your
> pick.
> 
> Jason
> On Mar 25, 2012, at 7:53 PM, Daniel Fern?ndez wrote:
> 
>> Hi,
>> 
>> I trying to install MAKER, I don't have WU-Blast, I have Blast+ so in the
>> README file tell me that I need RMBlast, but I don't know what file I have to
>> choose, rmblast-1.2-ncbi-blast-2.2.23+-src.tar.gz or
>> rmblast-1.2-ncbi-blast-2.2.23+-x64-linux.tar.gz (I have Linux 64-bit) in each
>> version the README file is the same, and there tell me how I can install it,
>> but the instructions is only for rmblast-1.2-ncbi-blast-2.2.23+-src, well,
>> when I try to install it, I type this
>> $./configure --with-mt --prefix=/usr/local/bioinfo/repeatmasker/rmblast
>> --without-debug
>> This show me error, and I type make and this show stop.
>> 
>> Can you help me please?
>> 
>> This show me when I type $./configure --with-mt
>> --prefix=/usr/local/bioinfo/repeatmasker/rmblast --without-debug
>> -----------------------------------------------------------------------------
>> ------------------------------------------------------------------
>> configure: loading site script ./src/build-system/config.site
>> configure: loading cache config.cache
>> checking build system type... x86_64-unknown-linux-gnu
>> checking host system type... x86_64-unknown-linux-gnu
>> checking for a BSD-compatible install... /usr/bin/install -c
>> checking for gcc... gcc
>> checking for C compiler default output file name... a.out
>> checking whether the C compiler works... yes
>> checking whether we are cross compiling... no
>> checking for suffix of executables...
>> checking for suffix of object files... o
>> checking whether we are using the GNU C compiler... yes
>> checking whether gcc accepts -g... yes
>> checking for gcc option to accept ANSI C... none needed
>> checking for g++... no
>> checking for c++... no
>> checking for gpp... no
>> checking for aCC... no
>> checking for CC... no
>> checking for cxx... no
>> checking for cc++... no
>> checking for cl... no
>> checking for FCC... no
>> checking for KCC... no
>> checking for RCC... no
>> checking for xlC_r... no
>> checking for xlC... no
>> checking whether we are using the GNU C++ compiler... no
>> checking whether g++ accepts -g... no
>> adjusted C   compiler: /usr/bin/gcc
>> ./src/build-system/configure: line 4404: type: g++: not found
>> dirname: missing operand
>> Try `dirname --help' for more information.
>> configure: error: Do not know how to build MT-safe with compiler g++
>> ./src/build-system/configure: line 4187: g++: command not found
>> -----------------------------------------------------------------------------
>> ------------------------------------------------------
>> _______________________________________________
>> maker-devel mailing list
>> maker-devel at box290.bluehost.com
>> http://box290.bluehost.com/mailman/listinfo/maker-devel_yandell-lab.org
> 
> Jason Stajich
> jason.stajich at gmail.com
> jason at bioperl.org
> 
_______________________________________________ maker-devel mailing list
maker-devel at box290.bluehost.com
http://box290.bluehost.com/mailman/listinfo/maker-devel_yandell-lab.org

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From tr at ncgr.org  Wed Mar 28 12:34:39 2012
From: tr at ncgr.org (Thiru Ramaraj)
Date: Wed, 28 Mar 2012 12:34:39 -0600
Subject: [maker-devel] maker_functional_gff
Message-ID: <4F7359BF.5020900@ncgr.org>

Hi All,

I am in the process of using maker_functional_gff script th generate 
functional gff file. I was wondering if NCBI BLAST tab delimited output 
will work as it is or there any formatting needed to be  more like a 
WUBLAST output.

Any thoughts would be greatly appreciated.

Thanks,
-Thiru



From carsonhh at gmail.com  Thu Mar 29 08:58:18 2012
From: carsonhh at gmail.com (Carson Holt)
Date: Thu, 29 Mar 2012 10:58:18 -0400
Subject: [maker-devel] maker_functional_gff
In-Reply-To: <4F7359BF.5020900@ncgr.org>
Message-ID: <CB99EE84.A2F7%carsonhh@gmail.com>

It should work with NCBI BLAST as long as it is the optional tab delimited
format, and not the standard raw format report.

The report must be generated from UniProt/Swiss-prot formatted fasta files.

Here is an example of the header format for the fasta file -->
>sp|P18560|1101L_ASFB7 Protein MGF 110-1L OS=African swine fever virus
>(strain Badajoz 1971 Vero-adapted) GN=BA71V-008 PE=3 SV=1

This ia a description of what maker_functional_gff is looked for
>transcript_ID  Description  OS=species  GN=gene_name
>PE=any_text_from_this_point_on_is_ignored

Thanks,
Carson




On 12-03-28 2:34 PM, "Thiru Ramaraj" <tr at ncgr.org> wrote:

>Hi All,
>
>I am in the process of using maker_functional_gff script th generate
>functional gff file. I was wondering if NCBI BLAST tab delimited output
>will work as it is or there any formatting needed to be  more like a
>WUBLAST output.
>
>Any thoughts would be greatly appreciated.
>
>Thanks,
>-Thiru
>
>_______________________________________________
>maker-devel mailing list
>maker-devel at box290.bluehost.com
>http://box290.bluehost.com/mailman/listinfo/maker-devel_yandell-lab.org





From barry.utah at gmail.com  Thu Mar 29 13:29:48 2012
From: barry.utah at gmail.com (Barry Moore)
Date: Thu, 29 Mar 2012 13:29:48 -0600
Subject: [maker-devel] GFF3 Specification
Message-ID: <C8A5B771-CCB5-4629-9F02-CF2437493F39@genetics.utah.edu>

Hi All,

There has been active discussion on the song-devel mailing list over the past 12 months about various ambiguities and unresolved issues with the GFF3 specification.  The SO group is initiating a process to resolve these issues so that GFF3 can continue to serve it's role of unifying genome annotations in a format that promotes collaboration between genome projects and comparison of datasets across a wide variety of genomes.  With the rapid acceleration of genome sequencing, a simple, standard format for genome annotation and comparative genomics is more critical than ever.

Several issues have been raised, and they range from simple requests for clarification to more fundamental questions about the structure of the specification.  We can't address all of these issues in one update to the spec, so we've started the ball rolling with three steps:

Incorporate all the minor changes into a GFF3 1.21 candidate spec (http://www.sequenceontology.org/resources/gff3_1.21.html).
Organize remaining unresolved issues onto a wiki page and start working through those issues one by one (http://www.sequenceontology.org/wiki/index.php?title=GFF3_Developement).
Develop a set of wiki pages to describe 'GFF3 Best Practices' and existing community usage (http://www.sequenceontology.org/wiki/index.php?title=GFF3_best_practices).

We will work through the unresolved issues one at a time - soliciting feedback from the community, and clarify/update the GFF3 spec in a backwards compatible way with existing tools and datasets, adding documenting wiki pages as needed.

We welcome and encourage feedback from the genomics community and gratefully acknowledge those who have been active in the discussion thus far.  Please have a look at the pages described above and join the conversation.  The best place for discussion of all things GFF3 is the SO mailing list (song-devel at lists.sourceforge.net).  Please feel free to re-post this message to relevant mailing lists so that all interested parties can be involved.

On behalf of the SO developers - Thanks.

Barry Moore
Research Scientist
Dept. of Human Genetics
University of Utah
Salt Lake City, UT 84112
--------------------------------------------
(801) 585-3543




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From ianmisner at my.uri.edu  Thu Mar  1 15:25:06 2012
From: ianmisner at my.uri.edu (Ian Misner)
Date: Thu, 1 Mar 2012 17:25:06 -0500
Subject: [maker-devel] Rerunning Maker
Message-ID: <13A73C28-9CEF-4416-911E-2ACEE445533A@my.uri.edu>

Hello,

I have run maker 2.03 on a genome that we assembled a while back.  Now we have a new genome assembly.  Is there a way to rerun maker with the new assembly without losing all of the annotations I've done on the v2.03 predicted proteins?  I see the genome_gff option but all the contig numbers will have changed with the new assembly so that will not work.  The EST data will be the same as before.  From my original run I used a related species for protein homology, this time would I use the predicted set I have been working with?  Worst case scenario I need a way to link the old proteins with the new ones which I could do with BLAST post Maker but I'm hoping there is a better way.  Any help with this would be greatly appreciated.  


Cheers
Ian

*************************************
Mr. Ian Misner
PhD. Candidate
Department of Biological Sciences
University of Rhode Island
120 Flagg Road
Kingston, RI 02881
Office: CBLS 260
Ph: 1-401-874-9726
fax (401) 874-2065
ianmisner at my.uri.edu
http://cels.uri.edu/bio/lanelab/  










From joana.guimaraes at inrb.pt  Fri Mar  2 00:26:51 2012
From: joana.guimaraes at inrb.pt (=?iso-8859-1?Q?Maria_Joana_F=2E_B=2E_A=2E_Guimar=E3es?=)
Date: Fri, 2 Mar 2012 07:26:51 -0000
Subject: [maker-devel] maker-devel Digest, Vol 45, Issue 15
In-Reply-To: <mailman.3.1330455604.20855.maker-devel_yandell-lab.org@box290.bluehost.com>
References: <mailman.3.1330455604.20855.maker-devel_yandell-lab.org@box290.bluehost.com>
Message-ID: <F5B5DE3EA7B4FD48A549687F860198320100510E@INRBMSMXBE.INRB.PT>

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: ter?a-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
_______________________________________________ maker-devel mailing list
maker-devel at box290.bluehost.com
http://box290.bluehost.com/mailman/listinfo/maker-devel_yandell-lab.org

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End of maker-devel Digest, Vol 45, Issue 15
*******************************************



From carsonhh at gmail.com  Fri Mar  2 08:39:47 2012
From: carsonhh at gmail.com (Carson Holt)
Date: Fri, 02 Mar 2012 10:39:47 -0500
Subject: [maker-devel] Rerunning Maker
In-Reply-To: <13A73C28-9CEF-4416-911E-2ACEE445533A@my.uri.edu>
Message-ID: <CB764CB4.8AF8%carsonhh@gmail.com>

There is a way to do this and it sounds harder than it really is.

Previously there was a tool that came with MAKER called map2assembly that
is no longer included with the distribution (certain changes to the MAKER
libraries broke it beyond repair).  The replacement for this tool is still
somewhat under development, so is not documented but is included with the
distribution and works far better (and faster) than map2assembly.

The new tool is internal to MAKER and called by setting several flags in
the control files before running a regular MAKER job.

To map genes forward do this:
1. Supply your old transcript file to the est= option in MAKER.
2. Set est2genome=1
3. Set single_exon=1
4. Set single_length=1
5. Turn all repeat masking options off (either delete values in control
files or use -R flag on the command line)
6. Set est_forward=1 (this is not in the maker_opts.ctl file.  You will
have to add it manually.
7. Don't run any gene predictors and don't provide any other evidence
files (we only want MAKER to map things forward)
8. Now run MAKER (remember to supply the -R flag from the command line if
you didn't delete masking options from thew control files)

MAKER will now map the old gene models to the new assembly (with names)
generating a new GFF3 file that can be used as input to future MAKER runs.

Some things to know about the process.  You can set the minimum accepted
coverage and identity to use when mapping the genes forward using the
blastn filters in the maker_bopts.ctl file.  Some genes may not map
forward and will be lost.  Some will map to multiple locations, so review
your GFF3 results file.  Also the est_forward option accepts hints via a
tag (maker_coor=) in the fasta headers.  For example, if you add the
following flag to fasta headers for the input transcript file -->
	>gene1-RA  maker_coor=chr1;
Then MAKER will only try and map that transcript to the new genomes contig
labelled chr1.  Or you can do -->
	>gene1-RA  maker_coor=chr1:2000-200000;
Then MAKER will restrict the alignment to somewhere within a given region
(could be the first half of the chromosome for example).


In future releases of MAKER, everything will be simplified.  The
est_forward will always be in the control files and will accept a file
name.  MAKER will then do all the work upstream including setting flags
and sorting out multiple location alignments as part of it's normal run
(not as an independent run as is done in what I described).

Thanks,
Carson


On 12-03-01 5:25 PM, "Ian Misner" <ianmisner at my.uri.edu> wrote:

>Hello,
>
>I have run maker 2.03 on a genome that we assembled a while back.  Now we
>have a new genome assembly.  Is there a way to rerun maker with the new
>assembly without losing all of the annotations I've done on the v2.03
>predicted proteins?  I see the genome_gff option but all the contig
>numbers will have changed with the new assembly so that will not work.
>The EST data will be the same as before.  From my original run I used a
>related species for protein homology, this time would I use the predicted
>set I have been working with?  Worst case scenario I need a way to link
>the old proteins with the new ones which I could do with BLAST post Maker
>but I'm hoping there is a better way.  Any help with this would be
>greatly appreciated.
>
>
>Cheers
>Ian
>
>*************************************
>Mr. Ian Misner
>PhD. Candidate
>Department of Biological Sciences
>University of Rhode Island
>120 Flagg Road
>Kingston, RI 02881
>Office: CBLS 260
>Ph: 1-401-874-9726
>fax (401) 874-2065
>ianmisner at my.uri.edu
>http://cels.uri.edu/bio/lanelab/
>
>
>
>
>
>
>
>
>_______________________________________________
>maker-devel mailing list
>maker-devel at box290.bluehost.com
>http://box290.bluehost.com/mailman/listinfo/maker-devel_yandell-lab.org





From carsonhh at gmail.com  Fri Mar  2 09:05:49 2012
From: carsonhh at gmail.com (Carson Holt)
Date: Fri, 02 Mar 2012 11:05:49 -0500
Subject: [maker-devel] maker-devel Digest, Vol 45, Issue 15
In-Reply-To: <F5B5DE3EA7B4FD48A549687F860198320100510E@INRBMSMXBE.INRB.PT>
Message-ID: <CB76559D.8B38%carsonhh@gmail.com>

There is more than one way to train your predictors.  If you have protein
sequence, you can run MAKER with the protein2genome=1 option set which
will generate preliminary gene models based on protein homology alone, and
those results can be used to train SNAP and augustus.  You can also train
SNAP independently using CEGMA - a program from the same group as SNAP.
It finds a small set of core genes that should be in all eukaryotic
genomes.

For me this is more of a question of speed.  Using ESTs that are not from
the same organism has caveats.  If the organisms are very closely related
(example: chimp and human), you can do a direct alignment in nucleotide
space.  But if they are not (example: human and mouse), you can use
MAKER's alt_est option and MAKER will align in translated space using
TBLASTX.  TBLASTX is mind numbingly slow, taking about 20x longer than a
direct EST alignment, and should be avoided when possible.

So to summarize, if you have ESTs from your organism, use those first.  If
not, then use proteins. Finally use alternate organism ESTs if that's all
you have. Of course you can also supply all three, but I normally only do
that for the final run.  I limit the dataset for the training rounds.

After using MAKER's results for training SNAP/augustus etc., just supply
MAKER with the resulting training HMM and run again in the same directory.
 Why in the same directory?  So that you can keep the evidence files you
used on the first run.  MAKER will see that the only thing that changed
was the HMM (so it won't have to rerun any of the alignments).  It will
just add the predictions, interpret them in light of the evidence, and
produce new output.  So the first run is slow, and the second is fast
(because MAKER takes advantage of archived BLAST, RepeatMasker, and
Exonerate results).

Thanks,
Carson



On 12-03-02 2:26 AM, "Maria Joana F. B. A. Guimar?es"
<joana.guimaraes at inrb.pt> wrote:

>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-----
>From: maker-devel-bounces at yandell-lab.org
>[mailto:maker-devel-bounces at yandell-lab.org] On Behalf Of
>maker-devel-request at yandell-lab.org
>Sent: ter?a-feira, 28 de Fevereiro de 2012 19:00
>To: maker-devel at yandell-lab.org
>Subject: maker-devel Digest, Vol 45, Issue 15
>
>Send maker-devel mailing list submissions to
>	maker-devel at yandell-lab.org
>
>To subscribe or unsubscribe via the World Wide Web, visit
>	http://box290.bluehost.com/mailman/listinfo/maker-devel_yandell-lab.org
>
>or, via email, send a message with subject or body 'help' to
>	maker-devel-request at yandell-lab.org
>
>You can reach the person managing the list at
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>
>When replying, please edit your Subject line so it is more specific
>than "Re: Contents of maker-devel digest..."
>
>
>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_datast
>ore_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.repeat
>runner
>
>#-------------------------------#
>
>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//the
>Void.contig-dpp-500-500/contig-dpp-500-500.0.te_proteins%2Efasta.repeatrun
>ner
>
>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.repeat
>runner
>
>#-------------------------------#
>
>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//the
>Void.contig-dpp-500-500/contig-dpp-500-500.0.te_proteins%2Efasta.repeatrun
>ner
>
>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
>-------------- next part --------------
>An HTML attachment was scrubbed...
>URL: 
><http://box290.bluehost.com/pipermail/maker-devel_yandell-lab.org/attachme
>nts/20120228/8e6a3106/attachment-0001.html>
>
>------------------------------
>
>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_datast
>or
>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.r
>b
>-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_pr
>ot
>eins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunn
>er
>
>#-------------------------------#
>
>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//the
>Vo
>id.contig-dpp-500-500/contig-dpp-500-500.0.te_proteins%2Efasta.repeatrunne
>r
>
>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.r
>b.
>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_pr
>ot
>eins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunn
>er
>
>#-------------------------------#
>
>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//the
>Vo
>id.contig-dpp-500-500/contig-dpp-500-500.0.te_proteins%2Efasta.repeatrunne
>r
>
>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
>_______________________________________________ maker-devel mailing list
>maker-devel at box290.bluehost.com
>http://box290.bluehost.com/mailman/listinfo/maker-devel_yandell-lab.org
>
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>------------------------------
>
>_______________________________________________
>maker-devel mailing list
>maker-devel at box290.bluehost.com
>http://box290.bluehost.com/mailman/listinfo/maker-devel_yandell-lab.org
>
>
>End of maker-devel Digest, Vol 45, Issue 15
>*******************************************
>
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From njauxiongjie at gmail.com  Fri Mar  2 19:38:50 2012
From: njauxiongjie at gmail.com (Jie)
Date: Fri, 2 Mar 2012 18:38:50 -0800 (PST)
Subject: [maker-devel] question about augustus hints file
Message-ID: <078f6ced-b08d-4a1e-8fe4-c63a2ac68392@qr9g2000pbc.googlegroups.com>

Hi, all

I have aligned my EST to my genome and want to use the EST alignment
as hints of augustus. The command I run like your README file in
AUGUSTUS, and like bellow:

blat -minIdentity=92 genome.fa cdna.fa cdna.psl
blat2hints.pl --in=cdna.psl --out=hints.E.gff

but when I feed the hint file to augustus, it appeared some error like
bellow:
augustus: ERROR        FeatureCollection::esource: invalid source key:
E

How can I solve this problem?



From thomas.hackl at uni-wuerzburg.de  Wed Mar  7 01:31:39 2012
From: thomas.hackl at uni-wuerzburg.de (Thomas Hackl)
Date: Wed, 07 Mar 2012 09:31:39 +0100
Subject: [maker-devel] maker 2.22/2.23: Segmentation fault while processing
	FASTA input
Message-ID: <4F571CEB.7070707@uni-wuerzburg.de>

Hello,

we want to use a current release of maker (2.22, 2.23) but the program 
terminates with a seg fault while processing the input FASTA files. 
maker 2.15 , which we have been using for quite some time, runs 
perfectly with identical data and setup.

Please contact me if you need specifics on hardware, OS or anything else.

Best regards
Thomas

-- 
Thomas Hackl
Julius-Maximilians-Universit?t
Department of Bioinformatics
97074 W?rzburg, Germany
Fon:  +49 931 - 31 86883
Mail: thomas.hackl at uni-wuerzburg.de




From Carson.Holt at oicr.on.ca  Wed Mar  7 15:45:06 2012
From: Carson.Holt at oicr.on.ca (Carson Holt)
Date: Wed, 7 Mar 2012 22:45:06 +0000
Subject: [maker-devel] maker 2.22/2.23: Segmentation fault while
 processing FASTA input
In-Reply-To: <4F571CEB.7070707@uni-wuerzburg.de>
Message-ID: <CB7D4D49.8FCD%carson.holt@oicr.on.ca>

There should be no new hardware requirement.  But there is always a chance
that there is an issue with one of the perl modules being used.  I assume
the failure is happening when using maker serially and you are not using
MPI.

Could you reinstall the following perl modules, and try again.  If you are
using CPAN, do a 'force install' to force it to reinstall.

Modules:
*Storable
*Inline::C
*forks
*forks::shared

Also try reinstalling the latest version of BioPerl.

The fact that this is a seg fault suggests that something is happemning at
the C level (just outside of Perl).  Those area all the modules MAKER uses
that will call back to the C level.  BioPerl has a fasta indexing module
that is also making calls outside of Perl, and the fact it fails at that
point makes it a suspect.

Let me know what happens.  I can always generate an alternate MAKER
executable for you to run with additional status messages that may help
identify exactly which module is being called right before the failure.

Thanks,
Carson



On 12-03-07 3:31 AM, "Thomas Hackl" <thomas.hackl at uni-wuerzburg.de> wrote:

>Hello,
>
>we want to use a current release of maker (2.22, 2.23) but the program
>terminates with a seg fault while processing the input FASTA files.
>maker 2.15 , which we have been using for quite some time, runs
>perfectly with identical data and setup.
>
>Please contact me if you need specifics on hardware, OS or anything else.
>
>Best regards
>Thomas
>
>-- 
>Thomas Hackl
>Julius-Maximilians-Universit?t
>Department of Bioinformatics
>97074 W?rzburg, Germany
>Fon:  +49 931 - 31 86883
>Mail: thomas.hackl at uni-wuerzburg.de
>
>
>_______________________________________________
>maker-devel mailing list
>maker-devel at box290.bluehost.com
>http://box290.bluehost.com/mailman/listinfo/maker-devel_yandell-lab.org




From ianmisner at my.uri.edu  Thu Mar  8 07:15:05 2012
From: ianmisner at my.uri.edu (Ian Misner)
Date: Thu, 8 Mar 2012 09:15:05 -0500
Subject: [maker-devel] Error: Chunk failed at level
Message-ID: <6F68BCEE-BD5B-4059-BA87-188BA8585105@my.uri.edu>

Hello,

I've run maker with RM, SNAP, and gmhmm on my novel genome and I've some very large contigs that haven't annotated any proteins.  I have looked through the output from the run and of the 74 contigs that failed I only have three errors.

They are Chunk failed at level 3, 8, & 16

What are those errors?  How can I get the annotations for these failed runs to work?  I have the entire output if you would need to see that file.  In my opts ctl file I set it to retry failed contigs 2 times and do a fresh run each time.  All 74 contigs failed all 3 attempts to run.  Any help would be much appreciated.

Cheers
Ian


*************************************
Mr. Ian Misner
PhD. Candidate
Department of Biological Sciences
University of Rhode Island
120 Flagg Road
Kingston, RI 02881
Office: CBLS 260
Ph: 1-401-874-9726
fax (401) 874-2065
ianmisner at my.uri.edu
http://cels.uri.edu/bio/lanelab/  










From jason.stajich at gmail.com  Thu Mar  8 18:58:32 2012
From: jason.stajich at gmail.com (Jason Stajich)
Date: Thu, 8 Mar 2012 17:58:32 -0800
Subject: [maker-devel] Error: Chunk failed at level
In-Reply-To: <6F68BCEE-BD5B-4059-BA87-188BA8585105@my.uri.edu>
References: <6F68BCEE-BD5B-4059-BA87-188BA8585105@my.uri.edu>
Message-ID: <8CA12776-E69F-4868-B9CE-278062F83D32@gmail.com>

Hi Ian - 

Do you get any gene models if you run RM or SNAP on these directly?  I can't tell if this means there is no overlap between your different prediction sets or if you didn't get ab initio predictions?

Jason
On Mar 8, 2012, at 6:15 AM, Ian Misner wrote:

> Hello,
> 
> I've run maker with RM, SNAP, and gmhmm on my novel genome and I've some very large contigs that haven't annotated any proteins.  I have looked through the output from the run and of the 74 contigs that failed I only have three errors.
> 
> They are Chunk failed at level 3, 8, & 16
> 
> What are those errors?  How can I get the annotations for these failed runs to work?  I have the entire output if you would need to see that file.  In my opts ctl file I set it to retry failed contigs 2 times and do a fresh run each time.  All 74 contigs failed all 3 attempts to run.  Any help would be much appreciated.
> 
> Cheers
> Ian
> 
> 
> *************************************
> Mr. Ian Misner
> PhD. Candidate
> Department of Biological Sciences
> University of Rhode Island
> 120 Flagg Road
> Kingston, RI 02881
> Office: CBLS 260
> Ph: 1-401-874-9726
> fax (401) 874-2065
> ianmisner at my.uri.edu
> http://cels.uri.edu/bio/lanelab/  
> 
> 
> 
> 
> 
> 
> 
> 
> _______________________________________________
> maker-devel mailing list
> maker-devel at box290.bluehost.com
> http://box290.bluehost.com/mailman/listinfo/maker-devel_yandell-lab.org

Jason Stajich
jason.stajich at gmail.com
jason at bioperl.org

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From carsonhh at gmail.com  Fri Mar  9 12:02:58 2012
From: carsonhh at gmail.com (Carson Holt)
Date: Fri, 09 Mar 2012 14:02:58 -0500
Subject: [maker-devel] Error: Chunk failed at level
In-Reply-To: <6F68BCEE-BD5B-4059-BA87-188BA8585105@my.uri.edu>
Message-ID: <CB7FBDE5.90EB%carsonhh@gmail.com>

Those are the very last messages in a series of error handlers.  Look
further up the report, the errors triggering the handler should be further
back.  If your'e running parallel,  the other errors may be way back up
the report.  Also which version of MAKER are you using?

You can send my any failed contigs, the maker control files and any other
datasets/files you are using if you want me to take a look as well.

Thanks,
Carson



On 12-03-08 9:15 AM, "Ian Misner" <ianmisner at my.uri.edu> wrote:

>Hello,
>
>I've run maker with RM, SNAP, and gmhmm on my novel genome and I've some
>very large contigs that haven't annotated any proteins.  I have looked
>through the output from the run and of the 74 contigs that failed I only
>have three errors.
>
>They are Chunk failed at level 3, 8, & 16
>
>What are those errors?  How can I get the annotations for these failed
>runs to work?  I have the entire output if you would need to see that
>file.  In my opts ctl file I set it to retry failed contigs 2 times and
>do a fresh run each time.  All 74 contigs failed all 3 attempts to run.
>Any help would be much appreciated.
>
>Cheers
>Ian
>
>
>*************************************
>Mr. Ian Misner
>PhD. Candidate
>Department of Biological Sciences
>University of Rhode Island
>120 Flagg Road
>Kingston, RI 02881
>Office: CBLS 260
>Ph: 1-401-874-9726
>fax (401) 874-2065
>ianmisner at my.uri.edu
>http://cels.uri.edu/bio/lanelab/
>
>
>
>
>
>
>
>
>_______________________________________________
>maker-devel mailing list
>maker-devel at box290.bluehost.com
>http://box290.bluehost.com/mailman/listinfo/maker-devel_yandell-lab.org





From thomas.hackl at uni-wuerzburg.de  Tue Mar 13 03:41:40 2012
From: thomas.hackl at uni-wuerzburg.de (Thomas Hackl)
Date: Tue, 13 Mar 2012 10:41:40 +0100
Subject: [maker-devel] maker 2.22/2.23: Segmentation fault while
 processing FASTA input
In-Reply-To: <CB7D4D49.8FCD%carson.holt@oicr.on.ca>
References: <CB7D4D49.8FCD%carson.holt@oicr.on.ca>
Message-ID: <4F5F1654.1060100@uni-wuerzburg.de>

Hello,

We reinstalled the packages you suggested

forks is up to date (0.34).
forks::shared is up to date (0.34).
Inline::C is up to date (0.50).
Storable is up to date (2.30).

as well as BioPerl.

The problem is still the same.

With MPI it terminates with this message:

STATUS: Parsing control files...
STATUS: Processing and indexing input FASTA files...
===================================================================================== 


=   BAD TERMINATION OF ONE OF YOUR APPLICATION PROCESSES
=   EXIT CODE: 11
=   CLEANING UP REMAINING PROCESSES
=   YOU CAN IGNORE THE BELOW CLEANUP MESSAGES
===================================================================================== 

APPLICATION TERMINATED WITH THE EXIT STRING: Segmentation fault (signal 11)

which I presume is also the same problem.

I am with you that the error is caused somewhere on the C level. If the 
indexing step
is handled by non-maker modules exclusively, than the fact that the 2.15 
version works,
suggests that you are using different modules/methods in the current 
releases?

In any case, I think a version with verbose status messages might help 
to localize the
source of the problem.

Regards
Thomas

Am 07.03.2012 23:45, schrieb Carson Holt:
> There should be no new hardware requirement.  But there is always a chance
> that there is an issue with one of the perl modules being used.  I assume
> the failure is happening when using maker serially and you are not using
> MPI.
>
> Could you reinstall the following perl modules, and try again.  If you are
> using CPAN, do a 'force install' to force it to reinstall.
>
> Modules:
> *Storable
> *Inline::C
> *forks
> *forks::shared
>
> Also try reinstalling the latest version of BioPerl.
>
> The fact that this is a seg fault suggests that something is happemning at
> the C level (just outside of Perl).  Those area all the modules MAKER uses
> that will call back to the C level.  BioPerl has a fasta indexing module
> that is also making calls outside of Perl, and the fact it fails at that
> point makes it a suspect.
>
> Let me know what happens.  I can always generate an alternate MAKER
> executable for you to run with additional status messages that may help
> identify exactly which module is being called right before the failure.
>
> Thanks,
> Carson
>
>
>
> On 12-03-07 3:31 AM, "Thomas Hackl"<thomas.hackl at uni-wuerzburg.de>  wrote:
>
>> Hello,
>>
>> we want to use a current release of maker (2.22, 2.23) but the program
>> terminates with a seg fault while processing the input FASTA files.
>> maker 2.15 , which we have been using for quite some time, runs
>> perfectly with identical data and setup.
>>
>> Please contact me if you need specifics on hardware, OS or anything else.
>>
>> Best regards
>> Thomas
>>
>> -- 
>> Thomas Hackl
>> Julius-Maximilians-Universit?t
>> Department of Bioinformatics
>> 97074 W?rzburg, Germany
>> Fon:  +49 931 - 31 86883
>> Mail: thomas.hackl at uni-wuerzburg.de
>>
>>
>> _______________________________________________
>> maker-devel mailing list
>> maker-devel at box290.bluehost.com
>> http://box290.bluehost.com/mailman/listinfo/maker-devel_yandell-lab.org


-- 
Thomas Hackl
Julius-Maximilians-Universit?t
Department of Bioinformatics
97074 W?rzburg, Germany
Fon:  +49 931 - 31 86883
Mail: thomas.hackl at uni-wuerzburg.de




From carsonhh at gmail.com  Tue Mar 13 06:34:16 2012
From: carsonhh at gmail.com (Carson Holt)
Date: Tue, 13 Mar 2012 08:34:16 -0400
Subject: [maker-devel] maker 2.22/2.23: Segmentation fault while
 processing FASTA input
In-Reply-To: <4F5F1654.1060100@uni-wuerzburg.de>
Message-ID: <CB84B674.9207%carsonhh@gmail.com>

I've put together a new MAKER executable (mostly finished), and I will get
it to you soon.  This should help focus in on the exact module causing the
issue.

Thanks,
Carson



On 12-03-13 5:41 AM, "Thomas Hackl" <thomas.hackl at uni-wuerzburg.de> wrote:

>Hello,
>
>We reinstalled the packages you suggested
>
>forks is up to date (0.34).
>forks::shared is up to date (0.34).
>Inline::C is up to date (0.50).
>Storable is up to date (2.30).
>
>as well as BioPerl.
>
>The problem is still the same.
>
>With MPI it terminates with this message:
>
>STATUS: Parsing control files...
>STATUS: Processing and indexing input FASTA files...
>==========================================================================
>=========== 
>
>
>=   BAD TERMINATION OF ONE OF YOUR APPLICATION PROCESSES
>=   EXIT CODE: 11
>=   CLEANING UP REMAINING PROCESSES
>=   YOU CAN IGNORE THE BELOW CLEANUP MESSAGES
>==========================================================================
>=========== 
>
>APPLICATION TERMINATED WITH THE EXIT STRING: Segmentation fault (signal
>11)
>
>which I presume is also the same problem.
>
>I am with you that the error is caused somewhere on the C level. If the
>indexing step
>is handled by non-maker modules exclusively, than the fact that the 2.15
>version works,
>suggests that you are using different modules/methods in the current
>releases?
>
>In any case, I think a version with verbose status messages might help
>to localize the
>source of the problem.
>
>Regards
>Thomas
>
>Am 07.03.2012 23:45, schrieb Carson Holt:
>> There should be no new hardware requirement.  But there is always a
>>chance
>> that there is an issue with one of the perl modules being used.  I
>>assume
>> the failure is happening when using maker serially and you are not using
>> MPI.
>>
>> Could you reinstall the following perl modules, and try again.  If you
>>are
>> using CPAN, do a 'force install' to force it to reinstall.
>>
>> Modules:
>> *Storable
>> *Inline::C
>> *forks
>> *forks::shared
>>
>> Also try reinstalling the latest version of BioPerl.
>>
>> The fact that this is a seg fault suggests that something is happemning
>>at
>> the C level (just outside of Perl).  Those area all the modules MAKER
>>uses
>> that will call back to the C level.  BioPerl has a fasta indexing module
>> that is also making calls outside of Perl, and the fact it fails at that
>> point makes it a suspect.
>>
>> Let me know what happens.  I can always generate an alternate MAKER
>> executable for you to run with additional status messages that may help
>> identify exactly which module is being called right before the failure.
>>
>> Thanks,
>> Carson
>>
>>
>>
>> On 12-03-07 3:31 AM, "Thomas Hackl"<thomas.hackl at uni-wuerzburg.de>
>>wrote:
>>
>>> Hello,
>>>
>>> we want to use a current release of maker (2.22, 2.23) but the program
>>> terminates with a seg fault while processing the input FASTA files.
>>> maker 2.15 , which we have been using for quite some time, runs
>>> perfectly with identical data and setup.
>>>
>>> Please contact me if you need specifics on hardware, OS or anything
>>>else.
>>>
>>> Best regards
>>> Thomas
>>>
>>> -- 
>>> Thomas Hackl
>>> Julius-Maximilians-Universit?t
>>> Department of Bioinformatics
>>> 97074 W?rzburg, Germany
>>> Fon:  +49 931 - 31 86883
>>> Mail: thomas.hackl at uni-wuerzburg.de
>>>
>>>
>>> _______________________________________________
>>> maker-devel mailing list
>>> maker-devel at box290.bluehost.com
>>> http://box290.bluehost.com/mailman/listinfo/maker-devel_yandell-lab.org
>
>
>-- 
>Thomas Hackl
>Julius-Maximilians-Universit?t
>Department of Bioinformatics
>97074 W?rzburg, Germany
>Fon:  +49 931 - 31 86883
>Mail: thomas.hackl at uni-wuerzburg.de
>
>
>_______________________________________________
>maker-devel mailing list
>maker-devel at box290.bluehost.com
>http://box290.bluehost.com/mailman/listinfo/maker-devel_yandell-lab.org





From barry.moore at genetics.utah.edu  Tue Mar 13 15:37:13 2012
From: barry.moore at genetics.utah.edu (Barry Moore)
Date: Tue, 13 Mar 2012 15:37:13 -0600
Subject: [maker-devel] maker 2.22/2.23: Segmentation fault while
	processing FASTA input
In-Reply-To: <4F5F1654.1060100@uni-wuerzburg.de>
References: <CB7D4D49.8FCD%carson.holt@oicr.on.ca>
	<4F5F1654.1060100@uni-wuerzburg.de>
Message-ID: <33E794D7-81C6-4315-BE02-A92B8C82EB67@genetics.utah.edu>

You might also try a short perl script outside of MAKER to exercise Bio::DB::Fasta (which I believe is the module MAKER uses for Fasta indexing - correct Carson?).

Something like this should work to force indexing:

use Bio::DB::Fasta;
my $db      = Bio::DB::Fasta->new('/path/to/fasta/files');
my $seq      = $db->seq($seqid, $start, $end);

Point it at your fasta directory or file.

B

On Mar 13, 2012, at 3:41 AM, Thomas Hackl wrote:

> Hello,
> 
> We reinstalled the packages you suggested
> 
> forks is up to date (0.34).
> forks::shared is up to date (0.34).
> Inline::C is up to date (0.50).
> Storable is up to date (2.30).
> 
> as well as BioPerl.
> 
> The problem is still the same.
> 
> With MPI it terminates with this message:
> 
> STATUS: Parsing control files...
> STATUS: Processing and indexing input FASTA files...
> ===================================================================================== 
> 
> =   BAD TERMINATION OF ONE OF YOUR APPLICATION PROCESSES
> =   EXIT CODE: 11
> =   CLEANING UP REMAINING PROCESSES
> =   YOU CAN IGNORE THE BELOW CLEANUP MESSAGES
> ===================================================================================== 
> APPLICATION TERMINATED WITH THE EXIT STRING: Segmentation fault (signal 11)
> 
> which I presume is also the same problem.
> 
> I am with you that the error is caused somewhere on the C level. If the indexing step
> is handled by non-maker modules exclusively, than the fact that the 2.15 version works,
> suggests that you are using different modules/methods in the current releases?
> 
> In any case, I think a version with verbose status messages might help to localize the
> source of the problem.
> 
> Regards
> Thomas
> 
> Am 07.03.2012 23:45, schrieb Carson Holt:
>> There should be no new hardware requirement.  But there is always a chance
>> that there is an issue with one of the perl modules being used.  I assume
>> the failure is happening when using maker serially and you are not using
>> MPI.
>> 
>> Could you reinstall the following perl modules, and try again.  If you are
>> using CPAN, do a 'force install' to force it to reinstall.
>> 
>> Modules:
>> *Storable
>> *Inline::C
>> *forks
>> *forks::shared
>> 
>> Also try reinstalling the latest version of BioPerl.
>> 
>> The fact that this is a seg fault suggests that something is happemning at
>> the C level (just outside of Perl).  Those area all the modules MAKER uses
>> that will call back to the C level.  BioPerl has a fasta indexing module
>> that is also making calls outside of Perl, and the fact it fails at that
>> point makes it a suspect.
>> 
>> Let me know what happens.  I can always generate an alternate MAKER
>> executable for you to run with additional status messages that may help
>> identify exactly which module is being called right before the failure.
>> 
>> Thanks,
>> Carson
>> 
>> 
>> 
>> On 12-03-07 3:31 AM, "Thomas Hackl"<thomas.hackl at uni-wuerzburg.de>  wrote:
>> 
>>> Hello,
>>> 
>>> we want to use a current release of maker (2.22, 2.23) but the program
>>> terminates with a seg fault while processing the input FASTA files.
>>> maker 2.15 , which we have been using for quite some time, runs
>>> perfectly with identical data and setup.
>>> 
>>> Please contact me if you need specifics on hardware, OS or anything else.
>>> 
>>> Best regards
>>> Thomas
>>> 
>>> -- 
>>> Thomas Hackl
>>> Julius-Maximilians-Universit?t
>>> Department of Bioinformatics
>>> 97074 W?rzburg, Germany
>>> Fon:  +49 931 - 31 86883
>>> Mail: thomas.hackl at uni-wuerzburg.de
>>> 
>>> 
>>> _______________________________________________
>>> maker-devel mailing list
>>> maker-devel at box290.bluehost.com
>>> http://box290.bluehost.com/mailman/listinfo/maker-devel_yandell-lab.org
> 
> 
> -- 
> Thomas Hackl
> Julius-Maximilians-Universit?t
> Department of Bioinformatics
> 97074 W?rzburg, Germany
> Fon:  +49 931 - 31 86883
> Mail: thomas.hackl at uni-wuerzburg.de
> 
> 
> _______________________________________________
> maker-devel mailing list
> maker-devel at box290.bluehost.com
> http://box290.bluehost.com/mailman/listinfo/maker-devel_yandell-lab.org

Barry Moore
Research Scientist
Dept. of Human Genetics
University of Utah
Salt Lake City, UT 84112
--------------------------------------------
(801) 585-3543




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From felix.bemm at uni-wuerzburg.de  Tue Mar 13 23:57:58 2012
From: felix.bemm at uni-wuerzburg.de (Felix Bemm)
Date: Wed, 14 Mar 2012 06:57:58 +0100
Subject: [maker-devel] maker 2.22/2.23: Segmentation fault while
 processing FASTA input
In-Reply-To: <33E794D7-81C6-4315-BE02-A92B8C82EB67@genetics.utah.edu>
References: <CB7D4D49.8FCD%carson.holt@oicr.on.ca>
	<4F5F1654.1060100@uni-wuerzburg.de>
	<33E794D7-81C6-4315-BE02-A92B8C82EB67@genetics.utah.edu>
Message-ID: <4F603366.3090501@uni-wuerzburg.de>

Hi,

Thomas and I are colleagues and dealing with the same problem here. I 
wrote some test code that forced the indexing and it work fine. We are 
using most of the bioperl seqio and db modules in combination with other 
tools and don't experience the same problem there at the moment.

Regards
Felix

Am 13.03.2012 22:37, schrieb Barry Moore:
> You might also try a short perl script outside of MAKER to exercise
> Bio::DB::Fasta (which I believe is the module MAKER uses for Fasta
> indexing - correct Carson?).
>
> Something like this should work to force indexing:
>
> useBio::DB::Fasta;
> my $db = Bio::DB::Fasta->new('/path/to/fasta/files');
> my$seq=$db->seq($seqid, $start, $end);
>
> Point it at your fasta directory or file.
>
> B
>
> On Mar 13, 2012, at 3:41 AM, Thomas Hackl wrote:
>
>> Hello,
>>
>> We reinstalled the packages you suggested
>>
>> forks is up to date (0.34).
>> forks::shared is up to date (0.34).
>> Inline::C is up to date (0.50).
>> Storable is up to date (2.30).
>>
>> as well as BioPerl.
>>
>> The problem is still the same.
>>
>> With MPI it terminates with this message:
>>
>> STATUS: Parsing control files...
>> STATUS: Processing and indexing input FASTA files...
>> =====================================================================================
>>
>>
>> = BAD TERMINATION OF ONE OF YOUR APPLICATION PROCESSES
>> = EXIT CODE: 11
>> = CLEANING UP REMAINING PROCESSES
>> = YOU CAN IGNORE THE BELOW CLEANUP MESSAGES
>> =====================================================================================
>>
>> APPLICATION TERMINATED WITH THE EXIT STRING: Segmentation fault
>> (signal 11)
>>
>> which I presume is also the same problem.
>>
>> I am with you that the error is caused somewhere on the C level. If
>> the indexing step
>> is handled by non-maker modules exclusively, than the fact that the
>> 2.15 version works,
>> suggests that you are using different modules/methods in the current
>> releases?
>>
>> In any case, I think a version with verbose status messages might help
>> to localize the
>> source of the problem.
>>
>> Regards
>> Thomas
>>
>> Am 07.03.2012 23:45, schrieb Carson Holt:
>>> There should be no new hardware requirement. But there is always a chance
>>> that there is an issue with one of the perl modules being used. I assume
>>> the failure is happening when using maker serially and you are not using
>>> MPI.
>>>
>>> Could you reinstall the following perl modules, and try again. If you are
>>> using CPAN, do a 'force install' to force it to reinstall.
>>>
>>> Modules:
>>> *Storable
>>> *Inline::C
>>> *forks
>>> *forks::shared
>>>
>>> Also try reinstalling the latest version of BioPerl.
>>>
>>> The fact that this is a seg fault suggests that something is
>>> happemning at
>>> the C level (just outside of Perl). Those area all the modules MAKER uses
>>> that will call back to the C level. BioPerl has a fasta indexing module
>>> that is also making calls outside of Perl, and the fact it fails at that
>>> point makes it a suspect.
>>>
>>> Let me know what happens. I can always generate an alternate MAKER
>>> executable for you to run with additional status messages that may help
>>> identify exactly which module is being called right before the failure.
>>>
>>> Thanks,
>>> Carson
>>>
>>>
>>>
>>> On 12-03-07 3:31 AM, "Thomas Hackl"<thomas.hackl at uni-wuerzburg.de
>>> <mailto:thomas.hackl at uni-wuerzburg.de>> wrote:
>>>
>>>> Hello,
>>>>
>>>> we want to use a current release of maker (2.22, 2.23) but the program
>>>> terminates with a seg fault while processing the input FASTA files.
>>>> maker 2.15 , which we have been using for quite some time, runs
>>>> perfectly with identical data and setup.
>>>>
>>>> Please contact me if you need specifics on hardware, OS or anything
>>>> else.
>>>>
>>>> Best regards
>>>> Thomas
>>>>
>>>> --
>>>> Thomas Hackl
>>>> Julius-Maximilians-Universit?t
>>>> Department of Bioinformatics
>>>> 97074 W?rzburg, Germany
>>>> Fon: +49 931 - 31 86883
>>>> Mail: thomas.hackl at uni-wuerzburg.de
>>>> <mailto:thomas.hackl at uni-wuerzburg.de>
>>>>
>>>>
>>>> _______________________________________________
>>>> maker-devel mailing list
>>>> maker-devel at box290.bluehost.com <mailto:maker-devel at box290.bluehost.com>
>>>> http://box290.bluehost.com/mailman/listinfo/maker-devel_yandell-lab.org
>>
>>
>> --
>> Thomas Hackl
>> Julius-Maximilians-Universit?t
>> Department of Bioinformatics
>> 97074 W?rzburg, Germany
>> Fon: +49 931 - 31 86883
>> Mail: thomas.hackl at uni-wuerzburg.de <mailto:thomas.hackl at uni-wuerzburg.de>
>>
>>
>> _______________________________________________
>> maker-devel mailing list
>> maker-devel at box290.bluehost.com <mailto:maker-devel at box290.bluehost.com>
>> http://box290.bluehost.com/mailman/listinfo/maker-devel_yandell-lab.org
>
> Barry Moore
> Research Scientist
> Dept. of Human Genetics
> University of Utah
> Salt Lake City, UT 84112
> --------------------------------------------
> (801) 585-3543
>
>
>
>
>
>
> _______________________________________________
> maker-devel mailing list
> maker-devel at box290.bluehost.com
> http://box290.bluehost.com/mailman/listinfo/maker-devel_yandell-lab.org



From darkbring_05 at yahoo.com  Tue Mar 13 23:21:46 2012
From: darkbring_05 at yahoo.com (asdsa sdadsad)
Date: Tue, 13 Mar 2012 22:21:46 -0700 (PDT)
Subject: [maker-devel] maker gff3 to genbank tbl
Message-ID: <1331702506.55291.YahooMailNeo@web124906.mail.ne1.yahoo.com>

Dear MAKER experts,

i hope that you can share your expertise regarding, conversion of?maker gff3 to genbank tbl or gbk. im trying to produce a working genbank tbl, i tried converting to chado using maker2chado and ?gmodtools genbanksubmit writer. but so far it doesnt end well. most probably due to xml configuration(which im really loss, especially defining the "goldenpath") .is there any other way to produce the tbl from maker output??

thanks :)

Joe Wilders
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From joe.wilders at gmail.com  Tue Mar 13 23:31:48 2012
From: joe.wilders at gmail.com (Joe Wilders)
Date: Tue, 13 Mar 2012 22:31:48 -0700 (PDT)
Subject: [maker-devel] maker gff3 to genbank tbl/gbk
Message-ID: <214404c1-206e-474c-b01c-24b6cde2b91e@y17g2000yqg.googlegroups.com>

Dear MAKER experts,

i hope that you can share your expertise regarding, conversion of
maker gff3 to genbank tbl or gbk. im trying to produce a working
genbank tbl, i tried converting to chado using maker2chado and
gmodtools genbanksubmit writer. but so far it doesnt end well. most
probably due to xml configuration(which im really loss, especially
defining the "goldenpath") .is there any other way to produce the tbl
from maker output?

thanks :)

Joe Wilders



From carsonhh at gmail.com  Sun Mar 18 16:21:03 2012
From: carsonhh at gmail.com (Carson Holt)
Date: Sun, 18 Mar 2012 18:21:03 -0400
Subject: [maker-devel] maker gff3 to genbank tbl/gbk
In-Reply-To: <214404c1-206e-474c-b01c-24b6cde2b91e@y17g2000yqg.googlegroups.com>
Message-ID: <CB8BD6ED.935C%carsonhh@gmail.com>

Try using Apollo.  You can open up GFF3 files and them save them as
GenBank format.  That might be sufficient.

Alternatively.  I've attached a script that can convert SNAP's ZFF format
to GeneBank.  You could then use the maker2zff that comes with MAKER to
convert results to ZFF and then this script to get GenBank format.

Thanks,
Carson

On 12-03-14 1:31 AM, "Joe Wilders" <joe.wilders at gmail.com> wrote:

>Dear MAKER experts,
>
>i hope that you can share your expertise regarding, conversion of
>maker gff3 to genbank tbl or gbk. im trying to produce a working
>genbank tbl, i tried converting to chado using maker2chado and
>gmodtools genbanksubmit writer. but so far it doesnt end well. most
>probably due to xml configuration(which im really loss, especially
>defining the "goldenpath") .is there any other way to produce the tbl
>from maker output?
>
>thanks :)
>
>Joe Wilders
>
>_______________________________________________
>maker-devel mailing list
>maker-devel at box290.bluehost.com
>http://box290.bluehost.com/mailman/listinfo/maker-devel_yandell-lab.org

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From joe.wilders at gmail.com  Sun Mar 18 19:53:37 2012
From: joe.wilders at gmail.com (Joe Wilders)
Date: Mon, 19 Mar 2012 09:53:37 +0800
Subject: [maker-devel] maker gff3 to genbank tbl/gbk
In-Reply-To: <CB8BD6ED.935C%carsonhh@gmail.com>
References: <214404c1-206e-474c-b01c-24b6cde2b91e@y17g2000yqg.googlegroups.com>
	<CB8BD6ED.935C%carsonhh@gmail.com>
Message-ID: <CAGYDdgYv8=qMqsz_Vk0d8Y=iNLYW8siJrB0gEDz+m6Qr40qVpA@mail.gmail.com>

Hi Carson,
Thank you very much for your suggestion, will try that up and let you know.

by the way i did found this in one of the revisions at the svn
http://malachite.genetics.utah.edu/projects/maker/browser/bin/gff3_2_gbk?rev=217
,
i wonder why it gets pulled out on the later revision..


On Mon, Mar 19, 2012 at 6:21 AM, Carson Holt <carsonhh at gmail.com> wrote:

> Try using Apollo.  You can open up GFF3 files and them save them as
> GenBank format.  That might be sufficient.
>
> Alternatively.  I've attached a script that can convert SNAP's ZFF format
> to GeneBank.  You could then use the maker2zff that comes with MAKER to
> convert results to ZFF and then this script to get GenBank format.
>
> Thanks,
> Carson
>
> On 12-03-14 1:31 AM, "Joe Wilders" <joe.wilders at gmail.com> wrote:
>
> >Dear MAKER experts,
> >
> >i hope that you can share your expertise regarding, conversion of
> >maker gff3 to genbank tbl or gbk. im trying to produce a working
> >genbank tbl, i tried converting to chado using maker2chado and
> >gmodtools genbanksubmit writer. but so far it doesnt end well. most
> >probably due to xml configuration(which im really loss, especially
> >defining the "goldenpath") .is there any other way to produce the tbl
> >from maker output?
> >
> >thanks :)
> >
> >Joe Wilders
> >
> >_______________________________________________
> >maker-devel mailing list
> >maker-devel at box290.bluehost.com
> >http://box290.bluehost.com/mailman/listinfo/maker-devel_yandell-lab.org
>
>
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From carsonhh at gmail.com  Sun Mar 18 23:27:00 2012
From: carsonhh at gmail.com (Carson Holt)
Date: Mon, 19 Mar 2012 01:27:00 -0400
Subject: [maker-devel] maker gff3 to genbank tbl/gbk
In-Reply-To: <CAGYDdgYv8=qMqsz_Vk0d8Y=iNLYW8siJrB0gEDz+m6Qr40qVpA@mail.gmail.com>
Message-ID: <CB8C38D3.944D%carsonhh@gmail.com>

A lot of the early code in the SVN suppository, contains one-off scripts.
This one looks a lot like one of my old scripts.  If I remember, I was
trying to get GenBank format for Augustus training.  I started with just a
quick BioPerl based conversion, but the script didn't produce the right
types in GenBank format.  I found another way to do what I wanted (i.e.
someone gave me a different script that worked well enough), and I just
abandoned that script.

Thanks,
Carson


From:  Joe Wilders <joe.wilders at gmail.com>
Date:  Mon, 19 Mar 2012 09:53:37 +0800
To:  Carson Holt <carsonhh at gmail.com>
Cc:  <maker-devel at yandell-lab.org>
Subject:  Re: [maker-devel] maker gff3 to genbank tbl/gbk


Hi Carson,
Thank you very much for your suggestion, will try that up and let you know.

by the way i did found this in one of the revisions at the svn
http://malachite.genetics.utah.edu/projects/maker/browser/bin/gff3_2_gbk?rev
=217 , i wonder why it gets pulled out on the later revision..


On Mon, Mar 19, 2012 at 6:21 AM, Carson Holt <carsonhh at gmail.com> wrote:
> Try using Apollo.  You can open up GFF3 files and them save them as
> GenBank format.  That might be sufficient.
> 
> Alternatively.  I've attached a script that can convert SNAP's ZFF format
> to GeneBank.  You could then use the maker2zff that comes with MAKER to
> convert results to ZFF and then this script to get GenBank format.
> 
> Thanks,
> Carson
> 
> On 12-03-14 1:31 AM, "Joe Wilders" <joe.wilders at gmail.com> wrote:
> 
>> >Dear MAKER experts,
>> >
>> >i hope that you can share your expertise regarding, conversion of
>> >maker gff3 to genbank tbl or gbk. im trying to produce a working
>> >genbank tbl, i tried converting to chado using maker2chado and
>> >gmodtools genbanksubmit writer. but so far it doesnt end well. most
>> >probably due to xml configuration(which im really loss, especially
>> >defining the "goldenpath") .is there any other way to produce the tbl
>> >from maker output?
>> >
>> >thanks :)
>> >
>> >Joe Wilders
>> >
>> >_______________________________________________
>> >maker-devel mailing list
>> >maker-devel at box290.bluehost.com
>> >http://box290.bluehost.com/mailman/listinfo/maker-devel_yandell-lab.org
> 



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From dinatal at uwindsor.ca  Tue Mar 20 10:55:34 2012
From: dinatal at uwindsor.ca (claudia)
Date: Tue, 20 Mar 2012 12:55:34 -0400
Subject: [maker-devel] loading scaffold features into chado
Message-ID: <4F68B686.6050800@uwindsor.ca>

To whom it may concern,

I have 2 concerns, the first is:  regarding representing scaffold 
features in chado and gbrowse. I noticed that the Sequence ontology uses 
the term supercontig and so if my assembly generated scaffolds entitled 
"scaffold" should I change the names to supercontigs so that chado 
recognizes the terms?

Corresponding to my first question, Maker does not know that the contigs 
are actually scaffold/supercontigs when annotating and so Maker will 
still call the "type" feature or column 3 in the GFF3, a 'contig', how 
can Maker be implemented to change this naming convention before 
annotation, or after?

Consequently, I am having problems pulling up gene features in Gbrowse 
when doing a generic gene search, and I must provide the maker generated 
unique-gene_id in the gbrowse search bar or the known sequence id i.e 
'scaffold001', which is not useful for someone who does not have this 
information.
---- I do not have this problem when my seq_id, and 'type' feature id 
match in the true case of 'contigs'. I can do a generic gene search in 
gbrowse with the term 'maker' and gbrowse will provide me all the 
associated maker generated gene calls.

Thank you for any guidance resolving these concerns,
Claudia



-- 
Claudia DiNatale
Master's Candidate
The Crosby Lab
University of Windsor
519-253-3000 ext: 4755




From carsonhh at gmail.com  Tue Mar 20 11:13:35 2012
From: carsonhh at gmail.com (Carson Holt)
Date: Tue, 20 Mar 2012 13:13:35 -0400
Subject: [maker-devel] loading scaffold features into chado
In-Reply-To: <4F68B686.6050800@uwindsor.ca>
Message-ID: <CB8E2F50.97C7%carsonhh@gmail.com>


>I have 2 concerns, the first is:  regarding representing scaffold
>features in chado and gbrowse. I noticed that the Sequence ontology uses
>the term supercontig and so if my assembly generated scaffolds entitled
>"scaffold" should I change the names to supercontigs so that chado
>recognizes the terms?

Yes.  You must use valid SO terms.  It is a requirement of GFF3, and Chado
will enforce this requirement on loading a GFF3 file (note Chado will even
go as far as to check the validity of the Ontology_term= attribute in GFF3
if you use it).  You can decide to use contig or supercontig as your
sequence feature.  It doesn?t really matter unless you are placing both
into the database as separate features (i.e. You have a supercontig as the
parent feature and then you enter contigs individually as children of the
supercontig).


>
>Corresponding to my first question, Maker does not know that the contigs
>are actually scaffold/supercontigs when annotating and so Maker will
>still call the "type" feature or column 3 in the GFF3, a 'contig', how
>can Maker be implemented to change this naming convention before
>annotation, or after?

Not really important unless you plan on making contigs children of the
supercontig.  But you can always do a search and replace. -->
cat file.gff | perl -ane 's/\tcontig\t/\tsupercontig\t/s; print $_' >
new_file.gff


>
>Consequently, I am having problems pulling up gene features in Gbrowse
>when doing a generic gene search, and I must provide the maker generated
>unique-gene_id in the gbrowse search bar or the known sequence id i.e
>'scaffold001', which is not useful for someone who does not have this
>information.
>---- I do not have this problem when my seq_id, and 'type' feature id
>match in the true case of 'contigs'. I can do a generic gene search in
>gbrowse with the term 'maker' and gbrowse will provide me all the
>associated maker generated gene calls.

See "Adjusting GBrowse Name Searches" in the GBrowse tutorial -->
http://gmod.org/gbrowse2/tutorial/tutorial.html#naming


Thanks,
Carson











>
>Thank you for any guidance resolving these concerns,
>Claudia
>
>
>
>-- 
>Claudia DiNatale
>Master's Candidate
>The Crosby Lab
>University of Windsor
>519-253-3000 ext: 4755
>
>
>_______________________________________________
>maker-devel mailing list
>maker-devel at box290.bluehost.com
>http://box290.bluehost.com/mailman/listinfo/maker-devel_yandell-lab.org





From scott at scottcain.net  Tue Mar 20 11:25:04 2012
From: scott at scottcain.net (Scott Cain)
Date: Tue, 20 Mar 2012 13:25:04 -0400
Subject: [maker-devel] loading scaffold features into chado
In-Reply-To: <CB8E2F50.97C7%carsonhh@gmail.com>
References: <4F68B686.6050800@uwindsor.ca> <CB8E2F50.97C7%carsonhh@gmail.com>
Message-ID: <CA+JTaoy00sX+3Pdyrw=Apus09Lppg9YNQsr8k4uoYXHmK24Euw@mail.gmail.com>

Hi Claudia,

I agree with everything that Carson wrote, except about name
searching--it's a little trickier in Chado.  What you probably want to
do is implement full text searching.  See:

  http://gmod.org/wiki/Chado_Full_Text_Search

for more information on setting it up and maintaining it.

Scott


On Tue, Mar 20, 2012 at 1:13 PM, Carson Holt <carsonhh at gmail.com> wrote:
>
>>I have 2 concerns, the first is: ?regarding representing scaffold
>>features in chado and gbrowse. I noticed that the Sequence ontology uses
>>the term supercontig and so if my assembly generated scaffolds entitled
>>"scaffold" should I change the names to supercontigs so that chado
>>recognizes the terms?
>
> Yes. ?You must use valid SO terms. ?It is a requirement of GFF3, and Chado
> will enforce this requirement on loading a GFF3 file (note Chado will even
> go as far as to check the validity of the Ontology_term= attribute in GFF3
> if you use it). ?You can decide to use contig or supercontig as your
> sequence feature. ?It doesn?t really matter unless you are placing both
> into the database as separate features (i.e. You have a supercontig as the
> parent feature and then you enter contigs individually as children of the
> supercontig).
>
>
>>
>>Corresponding to my first question, Maker does not know that the contigs
>>are actually scaffold/supercontigs when annotating and so Maker will
>>still call the "type" feature or column 3 in the GFF3, a 'contig', how
>>can Maker be implemented to change this naming convention before
>>annotation, or after?
>
> Not really important unless you plan on making contigs children of the
> supercontig. ?But you can always do a search and replace. -->
> cat file.gff | perl -ane 's/\tcontig\t/\tsupercontig\t/s; print $_' >
> new_file.gff
>
>
>>
>>Consequently, I am having problems pulling up gene features in Gbrowse
>>when doing a generic gene search, and I must provide the maker generated
>>unique-gene_id in the gbrowse search bar or the known sequence id i.e
>>'scaffold001', which is not useful for someone who does not have this
>>information.
>>---- I do not have this problem when my seq_id, and 'type' feature id
>>match in the true case of 'contigs'. I can do a generic gene search in
>>gbrowse with the term 'maker' and gbrowse will provide me all the
>>associated maker generated gene calls.
>
> See "Adjusting GBrowse Name Searches" in the GBrowse tutorial -->
> http://gmod.org/gbrowse2/tutorial/tutorial.html#naming
>
>
> Thanks,
> Carson
>
>
>
>
>
>
>
>
>
>
>
>>
>>Thank you for any guidance resolving these concerns,
>>Claudia
>>
>>
>>
>>--
>>Claudia DiNatale
>>Master's Candidate
>>The Crosby Lab
>>University of Windsor
>>519-253-3000 ext: 4755
>>
>>
>>_______________________________________________
>>maker-devel mailing list
>>maker-devel at box290.bluehost.com
>>http://box290.bluehost.com/mailman/listinfo/maker-devel_yandell-lab.org
>
>
>
> _______________________________________________
> maker-devel mailing list
> maker-devel at box290.bluehost.com
> http://box290.bluehost.com/mailman/listinfo/maker-devel_yandell-lab.org



-- 
------------------------------------------------------------------------
Scott Cain, Ph. D.? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ?? scott at scottcain dot net
GMOD Coordinator (http://gmod.org/)? ? ? ? ? ? ? ? ? ?? 216-392-3087
Ontario Institute for Cancer Research



From carsonhh at gmail.com  Tue Mar 20 11:27:10 2012
From: carsonhh at gmail.com (Carson Holt)
Date: Tue, 20 Mar 2012 13:27:10 -0400
Subject: [maker-devel] loading scaffold features into chado
In-Reply-To: <CA+JTaoy00sX+3Pdyrw=Apus09Lppg9YNQsr8k4uoYXHmK24Euw@mail.gmail.com>
Message-ID: <CB8E3600.97EA%carsonhh@gmail.com>

Yes. thank you Scott.  My answer would work for GBrowse NOT Chado :-)

--Carson



On 12-03-20 1:25 PM, "Scott Cain" <scott at scottcain.net> wrote:

>Hi Claudia,
>
>I agree with everything that Carson wrote, except about name
>searching--it's a little trickier in Chado.  What you probably want to
>do is implement full text searching.  See:
>
>  http://gmod.org/wiki/Chado_Full_Text_Search
>
>for more information on setting it up and maintaining it.
>
>Scott
>
>
>On Tue, Mar 20, 2012 at 1:13 PM, Carson Holt <carsonhh at gmail.com> wrote:
>>
>>>I have 2 concerns, the first is:  regarding representing scaffold
>>>features in chado and gbrowse. I noticed that the Sequence ontology uses
>>>the term supercontig and so if my assembly generated scaffolds entitled
>>>"scaffold" should I change the names to supercontigs so that chado
>>>recognizes the terms?
>>
>> Yes.  You must use valid SO terms.  It is a requirement of GFF3, and
>>Chado
>> will enforce this requirement on loading a GFF3 file (note Chado will
>>even
>> go as far as to check the validity of the Ontology_term= attribute in
>>GFF3
>> if you use it).  You can decide to use contig or supercontig as your
>> sequence feature.  It doesn?t really matter unless you are placing both
>> into the database as separate features (i.e. You have a supercontig as
>>the
>> parent feature and then you enter contigs individually as children of
>>the
>> supercontig).
>>
>>
>>>
>>>Corresponding to my first question, Maker does not know that the contigs
>>>are actually scaffold/supercontigs when annotating and so Maker will
>>>still call the "type" feature or column 3 in the GFF3, a 'contig', how
>>>can Maker be implemented to change this naming convention before
>>>annotation, or after?
>>
>> Not really important unless you plan on making contigs children of the
>> supercontig.  But you can always do a search and replace. -->
>> cat file.gff | perl -ane 's/\tcontig\t/\tsupercontig\t/s; print $_' >
>> new_file.gff
>>
>>
>>>
>>>Consequently, I am having problems pulling up gene features in Gbrowse
>>>when doing a generic gene search, and I must provide the maker generated
>>>unique-gene_id in the gbrowse search bar or the known sequence id i.e
>>>'scaffold001', which is not useful for someone who does not have this
>>>information.
>>>---- I do not have this problem when my seq_id, and 'type' feature id
>>>match in the true case of 'contigs'. I can do a generic gene search in
>>>gbrowse with the term 'maker' and gbrowse will provide me all the
>>>associated maker generated gene calls.
>>
>> See "Adjusting GBrowse Name Searches" in the GBrowse tutorial -->
>> http://gmod.org/gbrowse2/tutorial/tutorial.html#naming
>>
>>
>> Thanks,
>> Carson
>>
>>
>>
>>
>>
>>
>>
>>
>>
>>
>>
>>>
>>>Thank you for any guidance resolving these concerns,
>>>Claudia
>>>
>>>
>>>
>>>--
>>>Claudia DiNatale
>>>Master's Candidate
>>>The Crosby Lab
>>>University of Windsor
>>>519-253-3000 ext: 4755
>>>
>>>
>>>_______________________________________________
>>>maker-devel mailing list
>>>maker-devel at box290.bluehost.com
>>>http://box290.bluehost.com/mailman/listinfo/maker-devel_yandell-lab.org
>>
>>
>>
>> _______________________________________________
>> maker-devel mailing list
>> maker-devel at box290.bluehost.com
>> http://box290.bluehost.com/mailman/listinfo/maker-devel_yandell-lab.org
>
>
>
>-- 
>------------------------------------------------------------------------
>Scott Cain, Ph. D.                                   scott at scottcain
>dot net
>GMOD Coordinator (http://gmod.org/)                     216-392-3087
>Ontario Institute for Cancer Research





From dinatal at uwindsor.ca  Tue Mar 20 12:03:27 2012
From: dinatal at uwindsor.ca (claudia)
Date: Tue, 20 Mar 2012 14:03:27 -0400
Subject: [maker-devel] loading scaffold features into chado
In-Reply-To: <CA+JTaoy00sX+3Pdyrw=Apus09Lppg9YNQsr8k4uoYXHmK24Euw@mail.gmail.com>
References: <4F68B686.6050800@uwindsor.ca> <CB8E2F50.97C7%carsonhh@gmail.com>
	<CA+JTaoy00sX+3Pdyrw=Apus09Lppg9YNQsr8k4uoYXHmK24Euw@mail.gmail.com>
Message-ID: <4F68C66F.2010902@uwindsor.ca>

Hi,

  I have enabled full text searching and I still have this problem, 
another reason for concern... So I wondered if in fact I changed all the 
ID's in the GFF3 file to supercontigs, then perhaps Chado would better 
link all the terms, annotations, and fasta files.... Although, i realize 
that the seq_id ( column 1) shouldn't need to be specific since the 
'type' term would take care of designating the feature type, no?

Claudia



On 20/03/2012 1:25 PM, Scott Cain wrote:
> Hi Claudia,
>
> I agree with everything that Carson wrote, except about name
> searching--it's a little trickier in Chado.  What you probably want to
> do is implement full text searching.  See:
>
>    http://gmod.org/wiki/Chado_Full_Text_Search
>
> for more information on setting it up and maintaining it.
>
> Scott
>
>
> On Tue, Mar 20, 2012 at 1:13 PM, Carson Holt<carsonhh at gmail.com>  wrote:
>>> I have 2 concerns, the first is:  regarding representing scaffold
>>> features in chado and gbrowse. I noticed that the Sequence ontology uses
>>> the term supercontig and so if my assembly generated scaffolds entitled
>>> "scaffold" should I change the names to supercontigs so that chado
>>> recognizes the terms?
>> Yes.  You must use valid SO terms.  It is a requirement of GFF3, and Chado
>> will enforce this requirement on loading a GFF3 file (note Chado will even
>> go as far as to check the validity of the Ontology_term= attribute in GFF3
>> if you use it).  You can decide to use contig or supercontig as your
>> sequence feature.  It doesn?t really matter unless you are placing both
>> into the database as separate features (i.e. You have a supercontig as the
>> parent feature and then you enter contigs individually as children of the
>> supercontig).
>>
>>
>>> Corresponding to my first question, Maker does not know that the contigs
>>> are actually scaffold/supercontigs when annotating and so Maker will
>>> still call the "type" feature or column 3 in the GFF3, a 'contig', how
>>> can Maker be implemented to change this naming convention before
>>> annotation, or after?
>> Not really important unless you plan on making contigs children of the
>> supercontig.  But you can always do a search and replace. -->
>> cat file.gff | perl -ane 's/\tcontig\t/\tsupercontig\t/s; print $_'>
>> new_file.gff
>>
>>
>>> Consequently, I am having problems pulling up gene features in Gbrowse
>>> when doing a generic gene search, and I must provide the maker generated
>>> unique-gene_id in the gbrowse search bar or the known sequence id i.e
>>> 'scaffold001', which is not useful for someone who does not have this
>>> information.
>>> ---- I do not have this problem when my seq_id, and 'type' feature id
>>> match in the true case of 'contigs'. I can do a generic gene search in
>>> gbrowse with the term 'maker' and gbrowse will provide me all the
>>> associated maker generated gene calls.
>> See "Adjusting GBrowse Name Searches" in the GBrowse tutorial -->
>> http://gmod.org/gbrowse2/tutorial/tutorial.html#naming
>>
>>
>> Thanks,
>> Carson
>>
>>
>>
>>
>>
>>
>>
>>
>>
>>
>>
>>> Thank you for any guidance resolving these concerns,
>>> Claudia
>>>
>>>
>>>
>>> --
>>> Claudia DiNatale
>>> Master's Candidate
>>> The Crosby Lab
>>> University of Windsor
>>> 519-253-3000 ext: 4755
>>>
>>>
>>> _______________________________________________
>>> maker-devel mailing list
>>> maker-devel at box290.bluehost.com
>>> http://box290.bluehost.com/mailman/listinfo/maker-devel_yandell-lab.org
>>
>>
>> _______________________________________________
>> maker-devel mailing list
>> maker-devel at box290.bluehost.com
>> http://box290.bluehost.com/mailman/listinfo/maker-devel_yandell-lab.org
>
>


-- 
Claudia DiNatale
Master's Candidate
The Crosby Lab
University of Windsor
519-253-3000 ext: 4755




From scott at scottcain.net  Tue Mar 20 13:50:55 2012
From: scott at scottcain.net (Scott Cain)
Date: Tue, 20 Mar 2012 15:50:55 -0400
Subject: [maker-devel] loading scaffold features into chado
In-Reply-To: <4F68C66F.2010902@uwindsor.ca>
References: <4F68B686.6050800@uwindsor.ca> <CB8E2F50.97C7%carsonhh@gmail.com>
	<CA+JTaoy00sX+3Pdyrw=Apus09Lppg9YNQsr8k4uoYXHmK24Euw@mail.gmail.com>
	<4F68C66F.2010902@uwindsor.ca>
Message-ID: <FFACED63-40D9-4810-9927-0E4984BA8465@scottcain.net>

Hi Claudia,

Can you post a sample of the gff that shows what you are looking for and not finding?

Scott


Sent from my iPad

On Mar 20, 2012, at 2:03 PM, claudia <dinatal at uwindsor.ca> wrote:

> Hi,
> 
> I have enabled full text searching and I still have this problem, another reason for concern... So I wondered if in fact I changed all the ID's in the GFF3 file to supercontigs, then perhaps Chado would better link all the terms, annotations, and fasta files.... Although, i realize that the seq_id ( column 1) shouldn't need to be specific since the 'type' term would take care of designating the feature type, no?
> 
> Claudia
> 
> 
> 
> On 20/03/2012 1:25 PM, Scott Cain wrote:
>> Hi Claudia,
>> 
>> I agree with everything that Carson wrote, except about name
>> searching--it's a little trickier in Chado.  What you probably want to
>> do is implement full text searching.  See:
>> 
>>   http://gmod.org/wiki/Chado_Full_Text_Search
>> 
>> for more information on setting it up and maintaining it.
>> 
>> Scott
>> 
>> 
>> On Tue, Mar 20, 2012 at 1:13 PM, Carson Holt<carsonhh at gmail.com>  wrote:
>>>> I have 2 concerns, the first is:  regarding representing scaffold
>>>> features in chado and gbrowse. I noticed that the Sequence ontology uses
>>>> the term supercontig and so if my assembly generated scaffolds entitled
>>>> "scaffold" should I change the names to supercontigs so that chado
>>>> recognizes the terms?
>>> Yes.  You must use valid SO terms.  It is a requirement of GFF3, and Chado
>>> will enforce this requirement on loading a GFF3 file (note Chado will even
>>> go as far as to check the validity of the Ontology_term= attribute in GFF3
>>> if you use it).  You can decide to use contig or supercontig as your
>>> sequence feature.  It doesn?t really matter unless you are placing both
>>> into the database as separate features (i.e. You have a supercontig as the
>>> parent feature and then you enter contigs individually as children of the
>>> supercontig).
>>> 
>>> 
>>>> Corresponding to my first question, Maker does not know that the contigs
>>>> are actually scaffold/supercontigs when annotating and so Maker will
>>>> still call the "type" feature or column 3 in the GFF3, a 'contig', how
>>>> can Maker be implemented to change this naming convention before
>>>> annotation, or after?
>>> Not really important unless you plan on making contigs children of the
>>> supercontig.  But you can always do a search and replace. -->
>>> cat file.gff | perl -ane 's/\tcontig\t/\tsupercontig\t/s; print $_'>
>>> new_file.gff
>>> 
>>> 
>>>> Consequently, I am having problems pulling up gene features in Gbrowse
>>>> when doing a generic gene search, and I must provide the maker generated
>>>> unique-gene_id in the gbrowse search bar or the known sequence id i.e
>>>> 'scaffold001', which is not useful for someone who does not have this
>>>> information.
>>>> ---- I do not have this problem when my seq_id, and 'type' feature id
>>>> match in the true case of 'contigs'. I can do a generic gene search in
>>>> gbrowse with the term 'maker' and gbrowse will provide me all the
>>>> associated maker generated gene calls.
>>> See "Adjusting GBrowse Name Searches" in the GBrowse tutorial -->
>>> http://gmod.org/gbrowse2/tutorial/tutorial.html#naming
>>> 
>>> 
>>> Thanks,
>>> Carson
>>> 
>>> 
>>> 
>>> 
>>> 
>>> 
>>> 
>>> 
>>> 
>>> 
>>> 
>>>> Thank you for any guidance resolving these concerns,
>>>> Claudia
>>>> 
>>>> 
>>>> 
>>>> --
>>>> Claudia DiNatale
>>>> Master's Candidate
>>>> The Crosby Lab
>>>> University of Windsor
>>>> 519-253-3000 ext: 4755
>>>> 
>>>> 
>>>> _______________________________________________
>>>> maker-devel mailing list
>>>> maker-devel at box290.bluehost.com
>>>> http://box290.bluehost.com/mailman/listinfo/maker-devel_yandell-lab.org
>>> 
>>> 
>>> _______________________________________________
>>> maker-devel mailing list
>>> maker-devel at box290.bluehost.com
>>> http://box290.bluehost.com/mailman/listinfo/maker-devel_yandell-lab.org
>> 
>> 
> 
> 
> -- 
> Claudia DiNatale
> Master's Candidate
> The Crosby Lab
> University of Windsor
> 519-253-3000 ext: 4755
> 



From thomas.hackl at uni-wuerzburg.de  Tue Mar 20 12:16:03 2012
From: thomas.hackl at uni-wuerzburg.de (Thomas Hackl)
Date: Tue, 20 Mar 2012 19:16:03 +0100
Subject: [maker-devel] maker 2.22/2.23: Segmentation fault while
 processing FASTA input
In-Reply-To: <CB8CD562.94D0%carsonhh@gmail.com>
References: <CB8CD562.94D0%carsonhh@gmail.com>
Message-ID: <4F68C963.3040108@uni-wuerzburg.de>

Hi,

I installed and ran the debug version of maker. Without -debug it 
results in the expected segmentation fault. With -debug it paradoxically 
finishes without the error.

I screened the debug log anyway but could not find anything that helped 
me to localize the problem. I attached a condensed version (sort | uniq) 
of the log.
Any ideas are appreciated.

Regards
Thomas



Am 19.03.2012 17:24, schrieb Carson Holt:
> Ok.  I finished the special debug version over the weekend.  Run with
> -debug set as a command line flag.  Capture and return the STDERR on
> failure.  It will list all modules used, the versions, and when they are
> called so we can see what happens right before failure.
>
> http://yandell-lab.org/research/maker_debug.tgz
>
>
> Thanks,
> Carson
>
>
>
> On 12-03-14 1:57 AM, "Felix Bemm"<felix.bemm at uni-wuerzburg.de>  wrote:
>
>> Hi,
>>
>> Thomas and I are colleagues and dealing with the same problem here. I
>> wrote some test code that forced the indexing and it work fine. We are
>> using most of the bioperl seqio and db modules in combination with other
>> tools and don't experience the same problem there at the moment.
>>
>> Regards
>> Felix
>>
>> Am 13.03.2012 22:37, schrieb Barry Moore:
>>> You might also try a short perl script outside of MAKER to exercise
>>> Bio::DB::Fasta (which I believe is the module MAKER uses for Fasta
>>> indexing - correct Carson?).
>>>
>>> Something like this should work to force indexing:
>>>
>>> useBio::DB::Fasta;
>>> my $db = Bio::DB::Fasta->new('/path/to/fasta/files');
>>> my$seq=$db->seq($seqid, $start, $end);
>>>
>>> Point it at your fasta directory or file.
>>>
>>> B
>>>
>>> On Mar 13, 2012, at 3:41 AM, Thomas Hackl wrote:
>>>
>>>> Hello,
>>>>
>>>> We reinstalled the packages you suggested
>>>>
>>>> forks is up to date (0.34).
>>>> forks::shared is up to date (0.34).
>>>> Inline::C is up to date (0.50).
>>>> Storable is up to date (2.30).
>>>>
>>>> as well as BioPerl.
>>>>
>>>> The problem is still the same.
>>>>
>>>> With MPI it terminates with this message:
>>>>
>>>> STATUS: Parsing control files...
>>>> STATUS: Processing and indexing input FASTA files...
>>>>
>>>> ========================================================================
>>>> =============
>>>>
>>>>
>>>> = BAD TERMINATION OF ONE OF YOUR APPLICATION PROCESSES
>>>> = EXIT CODE: 11
>>>> = CLEANING UP REMAINING PROCESSES
>>>> = YOU CAN IGNORE THE BELOW CLEANUP MESSAGES
>>>>
>>>> ========================================================================
>>>> =============
>>>>
>>>> APPLICATION TERMINATED WITH THE EXIT STRING: Segmentation fault
>>>> (signal 11)
>>>>
>>>> which I presume is also the same problem.
>>>>
>>>> I am with you that the error is caused somewhere on the C level. If
>>>> the indexing step
>>>> is handled by non-maker modules exclusively, than the fact that the
>>>> 2.15 version works,
>>>> suggests that you are using different modules/methods in the current
>>>> releases?
>>>>
>>>> In any case, I think a version with verbose status messages might help
>>>> to localize the
>>>> source of the problem.
>>>>
>>>> Regards
>>>> Thomas
>>>>
>>>> Am 07.03.2012 23:45, schrieb Carson Holt:
>>>>> There should be no new hardware requirement. But there is always a
>>>>> chance
>>>>> that there is an issue with one of the perl modules being used. I
>>>>> assume
>>>>> the failure is happening when using maker serially and you are not
>>>>> using
>>>>> MPI.
>>>>>
>>>>> Could you reinstall the following perl modules, and try again. If you
>>>>> are
>>>>> using CPAN, do a 'force install' to force it to reinstall.
>>>>>
>>>>> Modules:
>>>>> *Storable
>>>>> *Inline::C
>>>>> *forks
>>>>> *forks::shared
>>>>>
>>>>> Also try reinstalling the latest version of BioPerl.
>>>>>
>>>>> The fact that this is a seg fault suggests that something is
>>>>> happemning at
>>>>> the C level (just outside of Perl). Those area all the modules MAKER
>>>>> uses
>>>>> that will call back to the C level. BioPerl has a fasta indexing
>>>>> module
>>>>> that is also making calls outside of Perl, and the fact it fails at
>>>>> that
>>>>> point makes it a suspect.
>>>>>
>>>>> Let me know what happens. I can always generate an alternate MAKER
>>>>> executable for you to run with additional status messages that may
>>>>> help
>>>>> identify exactly which module is being called right before the
>>>>> failure.
>>>>>
>>>>> Thanks,
>>>>> Carson
>>>>>
>>>>>
>>>>>
>>>>> On 12-03-07 3:31 AM, "Thomas Hackl"<thomas.hackl at uni-wuerzburg.de
>>>>> <mailto:thomas.hackl at uni-wuerzburg.de>>  wrote:
>>>>>
>>>>>> Hello,
>>>>>>
>>>>>> we want to use a current release of maker (2.22, 2.23) but the
>>>>>> program
>>>>>> terminates with a seg fault while processing the input FASTA files.
>>>>>> maker 2.15 , which we have been using for quite some time, runs
>>>>>> perfectly with identical data and setup.
>>>>>>
>>>>>> Please contact me if you need specifics on hardware, OS or anything
>>>>>> else.
>>>>>>
>>>>>> Best regards
>>>>>> Thomas
>>>>>>
>>>>>> --
>>>>>> Thomas Hackl
>>>>>> Julius-Maximilians-Universit?t
>>>>>> Department of Bioinformatics
>>>>>> 97074 W?rzburg, Germany
>>>>>> Fon: +49 931 - 31 86883
>>>>>> Mail: thomas.hackl at uni-wuerzburg.de
>>>>>> <mailto:thomas.hackl at uni-wuerzburg.de>
>>>>>>
>>>>>>
>>>>>> _______________________________________________
>>>>>> maker-devel mailing list
>>>>>> maker-devel at box290.bluehost.com
>>>>>> <mailto:maker-devel at box290.bluehost.com>
>>>>>>
>>>>>> http://box290.bluehost.com/mailman/listinfo/maker-devel_yandell-lab.or
>>>>>> g
>>>>
>>>> --
>>>> Thomas Hackl
>>>> Julius-Maximilians-Universit?t
>>>> Department of Bioinformatics
>>>> 97074 W?rzburg, Germany
>>>> Fon: +49 931 - 31 86883
>>>> Mail: thomas.hackl at uni-wuerzburg.de
>>>> <mailto:thomas.hackl at uni-wuerzburg.de>
>>>>
>>>>
>>>> _______________________________________________
>>>> maker-devel mailing list
>>>> maker-devel at box290.bluehost.com
>>>> <mailto:maker-devel at box290.bluehost.com>
>>>> http://box290.bluehost.com/mailman/listinfo/maker-devel_yandell-lab.org
>>> Barry Moore
>>> Research Scientist
>>> Dept. of Human Genetics
>>> University of Utah
>>> Salt Lake City, UT 84112
>>> --------------------------------------------
>>> (801) 585-3543
>>>
>>>
>>>
>>>
>>>
>>>
>>> _______________________________________________
>>> maker-devel mailing list
>>> maker-devel at box290.bluehost.com
>>> http://box290.bluehost.com/mailman/listinfo/maker-devel_yandell-lab.org
>> _______________________________________________
>> maker-devel mailing list
>> maker-devel at box290.bluehost.com
>> http://box290.bluehost.com/mailman/listinfo/maker-devel_yandell-lab.org

-- 
Thomas Hackl
Julius-Maximilians-Universit?t
Department of Bioinformatics
97074 W?rzburg, Germany
Fon:  +49 931 - 31 86883
Mail: thomas.hackl at uni-wuerzburg.de

-------------- next part --------------

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	0.01	Bio::Search::Hit::PhatHit::Base	/storage/tmp/software/maker-2.24-debug/bin/../lib/Bio/Search/Hit/PhatHit/Base.pm
	0.01	Bio::Search::Hit::PhatHit::blastn	/storage/tmp/software/maker-2.24-debug/bin/../lib/Bio/Search/Hit/PhatHit/blastn.pm
	0.01	Bio::Search::Hit::PhatHit::blastx	/storage/tmp/software/maker-2.24-debug/bin/../lib/Bio/Search/Hit/PhatHit/blastx.pm
	0.01	Bio::Search::Hit::PhatHit::tblastx	/storage/tmp/software/maker-2.24-debug/bin/../lib/Bio/Search/Hit/PhatHit/tblastx.pm
	0.01	Bio::Search::HSP::PhatHSP::Base	/storage/tmp/software/maker-2.24-debug/bin/../lib/Bio/Search/HSP/PhatHSP/Base.pm
	0.01	Bio::Search::HSP::PhatHSP::blastn	/storage/tmp/software/maker-2.24-debug/bin/../lib/Bio/Search/HSP/PhatHSP/blastn.pm
	0.01	Bio::Search::HSP::PhatHSP::blastx	/storage/tmp/software/maker-2.24-debug/bin/../lib/Bio/Search/HSP/PhatHSP/blastx.pm
	0.01	Bio::Search::HSP::PhatHSP::tblastx	/storage/tmp/software/maker-2.24-debug/bin/../lib/Bio/Search/HSP/PhatHSP/tblastx.pm
	0.01	CGL::Annotation::Feature::Contig	/storage/tmp/software/maker-2.24-debug/bin/../lib/CGL/Annotation/Feature/Contig.pm
	0.01	CGL::Annotation::Feature::Exon	/storage/tmp/software/maker-2.24-debug/bin/../lib/CGL/Annotation/Feature/Exon.pm
	0.01	CGL::Annotation::Feature::Gene	/storage/tmp/software/maker-2.24-debug/bin/../lib/CGL/Annotation/Feature/Gene.pm
	0.01	CGL::Annotation::Feature::Intron	/storage/tmp/software/maker-2.24-debug/bin/../lib/CGL/Annotation/Feature/Intron.pm
	0.01	CGL::Annotation::FeatureLocation	/storage/tmp/software/maker-2.24-debug/bin/../lib/CGL/Annotation/FeatureLocation.pm
	0.01	CGL::Annotation::Feature::Protein	/storage/tmp/software/maker-2.24-debug/bin/../lib/CGL/Annotation/Feature/Protein.pm
	0.01	CGL::Annotation::FeatureRelationship	/storage/tmp/software/maker-2.24-debug/bin/../lib/CGL/Annotation/FeatureRelationship.pm
	0.01	CGL::Annotation::Feature::Sequence_variant	/storage/tmp/software/maker-2.24-debug/bin/../lib/CGL/Annotation/Feature/Sequence_variant.pm
	0.01	CGL::Annotation::Feature	/storage/tmp/software/maker-2.24-debug/bin/../lib/CGL/Annotation/Feature.pm
	0.01	CGL::Annotation::Feature::Transcript	/storage/tmp/software/maker-2.24-debug/bin/../lib/CGL/Annotation/Feature/Transcript.pm
	0.01	CGL::Annotation::Iterator	/storage/tmp/software/maker-2.24-debug/bin/../lib/CGL/Annotation/Iterator.pm
	0.01	CGL::Annotation	/storage/tmp/software/maker-2.24-debug/bin/../lib/CGL/Annotation.pm
	0.01	CGL::Annotation::Trace	/storage/tmp/software/maker-2.24-debug/bin/../lib/CGL/Annotation/Trace.pm
	0.01	CGL::Clone	/storage/tmp/software/maker-2.24-debug/bin/../lib/CGL/Clone.pm
	0.01	CGL::Ontology::NodeRelationship	/storage/tmp/software/maker-2.24-debug/bin/../lib/CGL/Ontology/NodeRelationship.pm
	0.01	CGL::Ontology::Node	/storage/tmp/software/maker-2.24-debug/bin/../lib/CGL/Ontology/Node.pm
	0.01	CGL::Ontology::Ontology	/storage/tmp/software/maker-2.24-debug/bin/../lib/CGL/Ontology/Ontology.pm
	0.01	CGL::Ontology::Parser::OBO	/storage/tmp/software/maker-2.24-debug/bin/../lib/CGL/Ontology/Parser/OBO.pm
	0.01	CGL::Ontology::SO	/storage/tmp/software/maker-2.24-debug/bin/../lib/CGL/Ontology/SO.pm
	0.01	CGL::Ontology::Trace	/storage/tmp/software/maker-2.24-debug/bin/../lib/CGL/Ontology/Trace.pm
	0.01	CGL::Revcomp	/storage/tmp/software/maker-2.24-debug/bin/../lib/CGL/Revcomp.pm
	0.01	CGL::TranslationMachine	/storage/tmp/software/maker-2.24-debug/bin/../lib/CGL/TranslationMachine.pm
	0.01	Datastore::MD5	/storage/tmp/software/maker-2.24-debug/bin/../lib/Datastore/MD5.pm
	0.01	Parallel::Application::MPI	/storage/tmp/software/maker-2.24-debug/bin/../perl/lib/Parallel/Application/MPI.pm
	0.02	Perl::Unsafe::Signals	/storage/tmp/software/perl-5.14.1/lib/site_perl/5.14.1/x86_64-linux-thread-multi/Perl/Unsafe/Signals.pm
	0.02	Proc::ProcessTable::Process	/storage/tmp/software/perl-5.14.1/lib/site_perl/5.14.1/x86_64-linux-thread-multi/Proc/ProcessTable/Process.pm
	0.04	Acme::Damn	/storage/tmp/software/perl-5.14.1/lib/site_perl/5.14.1/x86_64-linux-thread-multi/Acme/Damn.pm
	0.11	Datastore::Base	/storage/tmp/software/maker-2.24-debug/bin/../lib/Datastore/Base.pm
	0.13	XSLoader	/storage/tmp/software/perl-5.14.1/lib/5.14.1/XSLoader.pm
	0.14	attributes	/storage/tmp/software/perl-5.14.1/lib/5.14.1/x86_64-linux-thread-multi/attributes.pm
	0.15	Sys::SigAction	/storage/tmp/software/perl-5.14.1/lib/site_perl/5.14.1/Sys/SigAction.pm
	0.17015	Error	/storage/tmp/software/maker-2.24-debug/bin/../lib/Error.pm
	0.1	runlog	/storage/tmp/software/maker-2.24-debug/bin/../lib/runlog.pm
	0.22	File::Temp	/storage/tmp/software/perl-5.14.1/lib/5.14.1/File/Temp.pm
	0.32	List::MoreUtils	/storage/tmp/software/perl-5.14.1/lib/site_perl/5.14.1/x86_64-linux-thread-multi/List/MoreUtils.pm
	0.34	forks::shared	/storage/tmp/software/perl-5.14.1/lib/site_perl/5.14.1/x86_64-linux-thread-multi/forks/shared.pm
	0.34	forks::signals	/storage/tmp/software/perl-5.14.1/lib/site_perl/5.14.1/x86_64-linux-thread-multi/forks/signals.pm
	0.34	forks	/storage/tmp/software/perl-5.14.1/lib/site_perl/5.14.1/x86_64-linux-thread-multi/forks.pm
	0.45	Proc::ProcessTable	/storage/tmp/software/perl-5.14.1/lib/site_perl/5.14.1/x86_64-linux-thread-multi/Proc/ProcessTable.pm
	0.49	Inline	/home/s187512/perl/lib/perl5/site_perl/5.12.1/Inline.pm
	0.63	Class::Struct	/storage/tmp/software/perl-5.14.1/lib/5.14.1/Class/Struct.pm
	0.63	lib	/storage/tmp/software/perl-5.14.1/lib/5.14.1/x86_64-linux-thread-multi/lib.pm
	1.006001	Bio::DB::Fasta	/storage/tmp/software/perl-5.14.1/lib/site_perl/5.14.1/Bio/DB/Fasta.pm
	1.006001	Bio::DB::RandomAccessI	/storage/tmp/software/perl-5.14.1/lib/site_perl/5.14.1/Bio/DB/RandomAccessI.pm
	1.006001	Bio::DB::SeqI	/storage/tmp/software/perl-5.14.1/lib/site_perl/5.14.1/Bio/DB/SeqI.pm
	1.006001	Bio::Root::Exception	/storage/tmp/software/perl-5.14.1/lib/site_perl/5.14.1/Bio/Root/Exception.pm
	1.006001	Bio::Root::RootI	/storage/tmp/software/perl-5.14.1/lib/site_perl/5.14.1/Bio/Root/RootI.pm
	1.006001	Bio::Root::Version	/storage/tmp/software/perl-5.14.1/lib/site_perl/5.14.1/Bio/Root/Version.pm
	1.006001	Bio::Search::Hit::GenericHit	/storage/tmp/software/perl-5.14.1/lib/site_perl/5.14.1/Bio/Search/Hit/GenericHit.pm
	1.006001	Bio::Search::Hit::PhatHit::repeatmasker	/storage/tmp/software/maker-2.24-debug/bin/../lib/Bio/Search/Hit/PhatHit/repeatmasker.pm
	1.006001	Bio::Search::SearchUtils	/storage/tmp/software/perl-5.14.1/lib/site_perl/5.14.1/Bio/Search/SearchUtils.pm
	1.00	AnyDBM_File	/storage/tmp/software/perl-5.14.1/lib/5.14.1/AnyDBM_File.pm
	1.00	integer	/storage/tmp/software/perl-5.14.1/lib/5.14.1/integer.pm
	1.00	locale	/storage/tmp/software/perl-5.14.1/lib/5.14.1/locale.pm
	1.02	SelectSaver	/storage/tmp/software/perl-5.14.1/lib/5.14.1/SelectSaver.pm
	1.02	vars	/storage/tmp/software/perl-5.14.1/lib/5.14.1/vars.pm
	1.02	warnings::register	/storage/tmp/software/perl-5.14.1/lib/5.14.1/warnings/register.pm
	1.04	bytes	/storage/tmp/software/perl-5.14.1/lib/5.14.1/bytes.pm
	1.04	strict	/storage/tmp/software/perl-5.14.1/lib/5.14.1/strict.pm
	1.04	Tie::Hash	/storage/tmp/software/perl-5.14.1/lib/5.14.1/Tie/Hash.pm
	1.05	sigtrap	/storage/tmp/software/perl-5.14.1/lib/5.14.1/sigtrap.pm
	1.07	Symbol	/storage/tmp/software/perl-5.14.1/lib/5.14.1/Symbol.pm
	1.09	File::Which	/storage/tmp/software/maker-2.24-debug/bin/../lib/File/Which.pm
	1.09	IPC::Open3	/storage/tmp/software/perl-5.14.1/lib/5.14.1/IPC/Open3.pm
	1.0	Proc::Signal	/storage/tmp/software/maker-2.24-debug/bin/../lib/Proc/Signal.pm
	1.11	Fcntl	/storage/tmp/software/perl-5.14.1/lib/5.14.1/x86_64-linux-thread-multi/Fcntl.pm
	1.12	File::Glob	/storage/tmp/software/perl-5.14.1/lib/5.14.1/x86_64-linux-thread-multi/File/Glob.pm
	1.12	warnings	/storage/tmp/software/perl-5.14.1/lib/5.14.1/warnings.pm
	1.13	DynaLoader	/storage/tmp/software/perl-5.14.1/lib/5.14.1/x86_64-linux-thread-multi/DynaLoader.pm
	1.13	Errno	/storage/tmp/software/perl-5.14.1/lib/5.14.1/x86_64-linux-thread-multi/Errno.pm
	1.13	overload	/storage/tmp/software/perl-5.14.1/lib/5.14.1/overload.pm
	1.15	IO::File	/storage/tmp/software/perl-5.14.1/lib/5.14.1/x86_64-linux-thread-multi/IO/File.pm
	1.16	Digest::base	/storage/tmp/software/perl-5.14.1/lib/5.14.1/Digest/base.pm
	1.16	Sys::Hostname	/storage/tmp/software/perl-5.14.1/lib/5.14.1/x86_64-linux-thread-multi/Sys/Hostname.pm
	1.19	File::Find	/storage/tmp/software/perl-5.14.1/lib/5.14.1/File/Find.pm
	1.1	IO::Seekable	/storage/tmp/software/perl-5.14.1/lib/5.14.1/x86_64-linux-thread-multi/IO/Seekable.pm
	1.2000	Time::Local	/storage/tmp/software/perl-5.14.1/lib/5.14.1/Time/Local.pm
	1.20	Carp	/storage/tmp/software/perl-5.14.1/lib/5.14.1/Carp.pm
	1.20	feature	/storage/tmp/software/perl-5.14.1/lib/5.14.1/feature.pm
	1.20	File::NFSLock	/storage/tmp/software/maker-2.24-debug/bin/../lib/File/NFSLock.pm
	1.20	IO::Select	/storage/tmp/software/perl-5.14.1/lib/5.14.1/x86_64-linux-thread-multi/IO/Select.pm
	1.21	constant	/storage/tmp/software/perl-5.14.1/lib/5.14.1/constant.pm
	1.23	IO::Socket::UNIX	/storage/tmp/software/perl-5.14.1/lib/5.14.1/x86_64-linux-thread-multi/IO/Socket/UNIX.pm
	1.23	List::Util	/storage/tmp/software/perl-5.14.1/lib/5.14.1/x86_64-linux-thread-multi/List/Util.pm
	1.23	Scalar::Util	/storage/tmp/software/perl-5.14.1/lib/5.14.1/x86_64-linux-thread-multi/Scalar/Util.pm
	1.24	POSIX	/storage/tmp/software/perl-5.14.1/lib/5.14.1/x86_64-linux-thread-multi/POSIX.pm
	1.25_04	IO	/storage/tmp/software/perl-5.14.1/lib/5.14.1/x86_64-linux-thread-multi/IO.pm
	1.31	IO::Handle	/storage/tmp/software/perl-5.14.1/lib/5.14.1/x86_64-linux-thread-multi/IO/Handle.pm
	1.31	IO::Socket::INET	/storage/tmp/software/perl-5.14.1/lib/5.14.1/x86_64-linux-thread-multi/IO/Socket/INET.pm
	1.32	IO::Socket	/storage/tmp/software/perl-5.14.1/lib/5.14.1/x86_64-linux-thread-multi/IO/Socket.pm
	1.33	DBD::SQLite	/storage/tmp/software/perl-5.14.1/lib/site_perl/5.14.1/x86_64-linux-thread-multi/DBD/SQLite.pm
	1.33	threads::shared	/storage/tmp/software/perl-5.14.1/lib/site_perl/5.14.1/x86_64-linux-thread-multi/forks/shared.pm
	1.50	FindBin	/storage/tmp/software/perl-5.14.1/lib/5.14.1/FindBin.pm
	1.58	URI	/storage/tmp/software/perl-5.14.1/lib/site_perl/5.14.1/URI.pm
	1.616	DBI	/storage/tmp/software/perl-5.14.1/lib/site_perl/5.14.1/x86_64-linux-thread-multi/DBI.pm
	1.77	threads	/storage/tmp/software/perl-5.14.1/lib/site_perl/5.14.1/x86_64-linux-thread-multi/forks.pm
	1.822	DB_File	/storage/tmp/software/perl-5.14.1/lib/5.14.1/x86_64-linux-thread-multi/DB_File.pm
	1.94	Socket	/storage/tmp/software/perl-5.14.1/lib/5.14.1/x86_64-linux-thread-multi/Socket.pm
	1.972101	Time::HiRes	/storage/tmp/software/perl-5.14.1/lib/5.14.1/x86_64-linux-thread-multi/Time/HiRes.pm
	2.02	FileHandle	/storage/tmp/software/perl-5.14.1/lib/5.14.1/FileHandle.pm
	2.08001	forks::Devel::Symdump	/storage/tmp/software/perl-5.14.1/lib/site_perl/5.14.1/x86_64-linux-thread-multi/forks/Devel/Symdump.pm
	2.08_01	File::Path	/storage/tmp/software/perl-5.14.1/lib/5.14.1/File/Path.pm
	2.131	Data::Dumper	/storage/tmp/software/perl-5.14.1/lib/5.14.1/x86_64-linux-thread-multi/Data/Dumper.pm
	2.16	base	/storage/tmp/software/perl-5.14.1/lib/5.14.1/base.pm
	2.21	File::Copy	/storage/tmp/software/perl-5.14.1/lib/5.14.1/File/Copy.pm
	2.30	Storable	/storage/tmp/software/perl-5.14.1/lib/5.14.1/x86_64-linux-thread-multi/Storable.pm
	2.38	Getopt::Long	/storage/tmp/software/perl-5.14.1/lib/5.14.1/Getopt/Long.pm
	2.51	Digest::MD5	/storage/tmp/software/perl-5.14.1/lib/5.14.1/x86_64-linux-thread-multi/Digest/MD5.pm
	2.82	File::Basename	/storage/tmp/software/perl-5.14.1/lib/5.14.1/File/Basename.pm
	3.00	Term::ANSIColor	/storage/tmp/software/perl-5.14.1/lib/5.14.1/Term/ANSIColor.pm
	3.30	URI::Escape	/storage/tmp/software/perl-5.14.1/lib/site_perl/5.14.1/URI/Escape.pm
	3.33	File::Spec	/storage/tmp/software/perl-5.14.1/lib/5.14.1/x86_64-linux-thread-multi/File/Spec.pm
	3.33	File::Spec::Unix	/storage/tmp/software/perl-5.14.1/lib/5.14.1/x86_64-linux-thread-multi/File/Spec/Unix.pm
	3.36	Cwd	/storage/tmp/software/perl-5.14.1/lib/5.14.1/x86_64-linux-thread-multi/Cwd.pm
	4.2	Tie::Handle	/storage/tmp/software/perl-5.14.1/lib/5.14.1/Tie/Handle.pm
	4.2	Tie::StdHandle	/storage/tmp/software/perl-5.14.1/lib/5.14.1/Tie/StdHandle.pm
	5.64_03	Exporter::Heavy	/storage/tmp/software/perl-5.14.1/lib/5.14.1/Exporter/Heavy.pm
	5.64_03	Exporter	/storage/tmp/software/perl-5.14.1/lib/5.14.1/Exporter.pm
	5.71	AutoLoader	/storage/tmp/software/perl-5.14.1/lib/5.14.1/AutoLoader.pm
	6.00	HTTP::Date	/storage/tmp/software/perl-5.14.1/lib/site_perl/5.14.1/HTTP/Date.pm
	6.00	HTTP::Headers	/storage/tmp/software/perl-5.14.1/lib/site_perl/5.14.1/HTTP/Headers.pm
	6.00	HTTP::Request	/storage/tmp/software/perl-5.14.1/lib/site_perl/5.14.1/HTTP/Request.pm
	6.00	HTTP::Status	/storage/tmp/software/perl-5.14.1/lib/site_perl/5.14.1/HTTP/Status.pm
	6.00	LWP::Protocol	/storage/tmp/software/perl-5.14.1/lib/site_perl/5.14.1/LWP/Protocol.pm
	6.01	HTTP::Response	/storage/tmp/software/perl-5.14.1/lib/site_perl/5.14.1/HTTP/Response.pm
	6.02	HTTP::Message	/storage/tmp/software/perl-5.14.1/lib/site_perl/5.14.1/HTTP/Message.pm
	6.02	LWP	/storage/tmp/software/perl-5.14.1/lib/site_perl/5.14.1/LWP.pm
	6.02	LWP::UserAgent	/storage/tmp/software/perl-5.14.1/lib/site_perl/5.14.1/LWP/UserAgent.pm
	7.1	Bit::Vector	/storage/tmp/software/perl-5.14.1/lib/site_perl/5.14.1/x86_64-linux-thread-multi/Bit/Vector.pm
A data structure will be created for you at:
Calculating annotation quality statistics
Calling Datastore::MD5::id_to_dir at /storage/tmp/software/maker-2.24-debug/bin/../lib/Process/MpiChunk.pm line 428
Calling Datastore::MD5::mkdir at /storage/tmp/software/maker-2.24-debug/bin/../lib/Process/MpiChunk.pm line 428
Calling Datastore::MD5::new at /storage/tmp/software/maker-2.24-debug/bin/maker line 536
Calling ds_utility::new at /storage/tmp/software/maker-2.24-debug/bin/maker line 535
Calling FastaDB::add_to_global_index at /storage/tmp/software/maker-2.24-debug/bin/maker line 523
Calling FastaDB::makeid from BioPerl Bio::DB::Fasta hook at /storage/tmp/software/perl-5.14.1/lib/site_perl/5.14.1/Bio/DB/Fasta.pm line 760
Calling FastaDB::new at /storage/tmp/software/maker-2.24-debug/bin/../lib/Process/MpiChunk.pm line 1066
Calling FastaDB::new at /storage/tmp/software/maker-2.24-debug/bin/../lib/Process/MpiChunk.pm line 1067
Calling FastaDB::new at /storage/tmp/software/maker-2.24-debug/bin/../lib/Process/MpiChunk.pm line 1515
Calling FastaDB::new at /storage/tmp/software/maker-2.24-debug/bin/../lib/Process/MpiChunk.pm line 1636
Calling FastaDB::new at /storage/tmp/software/maker-2.24-debug/bin/../lib/Process/MpiChunk.pm line 2460
Calling FastaDB::new at /storage/tmp/software/maker-2.24-debug/bin/../lib/Process/MpiChunk.pm line 2573
Calling FastaDB::new at /storage/tmp/software/maker-2.24-debug/bin/../lib/Process/MpiChunk.pm line 449
Calling FastaDB::new at /storage/tmp/software/maker-2.24-debug/bin/../lib/Widget/augustus.pm line 417
Calling FastaDB::new at /storage/tmp/software/maker-2.24-debug/bin/maker line 432
Calling FastaDB::new at /storage/tmp/software/maker-2.24-debug/bin/maker line 522
Calling Fasta::def2SeqID at /storage/tmp/software/maker-2.24-debug/bin/maker line 430
Calling Fasta::fasta2seqRef at /storage/tmp/software/maker-2.24-debug/bin/maker line 430
Calling Fasta::getDef at /storage/tmp/software/maker-2.24-debug/bin/maker line 430
Calling Fasta::seq2fastaRef at /storage/tmp/software/maker-2.24-debug/bin/maker line 430
Calling File::NFSLock::maintain at /storage/tmp/software/maker-2.24-debug/bin/../lib/GI.pm line 1670
Calling File::NFSLock::new at /storage/tmp/software/maker-2.24-debug/bin/../lib/GI.pm line 1670
Calling File::NFSLock::new at /storage/tmp/software/maker-2.24-debug/bin/maker line 430
Calling File::NFSLock::new at /storage/tmp/software/maker-2.24-debug/bin/maker line 468
Calling File::NFSLock::unlock at /storage/tmp/software/maker-2.24-debug/bin/maker line 430
Calling File::NFSLock::unlock at /storage/tmp/software/maker-2.24-debug/bin/maker line 468
Calling File::Path::mkpath at /storage/tmp/software/maker-2.24-debug/bin/../lib/Process/MpiChunk.pm line 428
Calling File::Path::rmtree at /storage/tmp/software/maker-2.24-debug/bin/maker line 430
Calling GFFDB::new at /storage/tmp/software/maker-2.24-debug/bin/maker line 529
Calling GFFDB::next_build at /storage/tmp/software/maker-2.24-debug/bin/maker line 531
Calling GI::build_fasta_index at /storage/tmp/software/maker-2.24-debug/bin/maker line 431
Calling GI::build_fasta_index at /storage/tmp/software/maker-2.24-debug/bin/maker line 521
Calling GI::create_blastdb at /storage/tmp/software/maker-2.24-debug/bin/maker line 467
Calling GI::load_control_files at /storage/tmp/software/maker-2.24-debug/bin/maker line 346
Calling GI::mount_check at /storage/tmp/software/maker-2.24-debug/bin/maker line 359
Calling GI::new_instance_temp at /storage/tmp/software/maker-2.24-debug/bin/maker line 357
Calling GI::s_abs_path at /storage/tmp/software/maker-2.24-debug/bin/maker line 412
Calling GI::set_global_temp at /storage/tmp/software/maker-2.24-debug/bin/maker line 377
Calling GI::split_db at /storage/tmp/software/maker-2.24-debug/bin/maker line 429
Calling Iterator::Any::new at /storage/tmp/software/maker-2.24-debug/bin/maker line 430
Calling Iterator::Any::nextDef at /storage/tmp/software/maker-2.24-debug/bin/maker line 430
Calling Iterator::Any::nextFastaRef at /storage/tmp/software/maker-2.24-debug/bin/maker line 430
Calling Iterator::Fasta::new at /storage/tmp/software/maker-2.24-debug/bin/maker line 539
Calling Iterator::Fasta::skip_file at /storage/tmp/software/maker-2.24-debug/bin/maker line 541
Calling Iterator::Fasta::step at /storage/tmp/software/maker-2.24-debug/bin/maker line 543
Calling List::Util::shuffle at /storage/tmp/software/maker-2.24-debug/bin/maker line 422
Calling mkdir at /storage/tmp/software/maker-2.24-debug/bin/maker line 430
Calling out to BioPerl Bio::DB::Fasta::_close_index at /storage/tmp/software/maker-2.24-debug/bin/../lib/Process/MpiChunk.pm line 1066
Calling out to BioPerl Bio::DB::Fasta::new at /storage/tmp/software/maker-2.24-debug/bin/../lib/Error.pm line 339
Calling out to BioPerl get_PrimarySeq_stream at /storage/tmp/software/maker-2.24-debug/bin/../lib/GI.pm line 1670
Calling out to FastaSeq::convert at /storage/tmp/software/maker-2.24-debug/bin/../lib/GI.pm line 1413
Calling system at /storage/tmp/software/maker-2.24-debug/bin/maker line 430
Calling uri_escape at /storage/tmp/software/maker-2.24-debug/bin/../lib/Process/MpiChunk.pm line 428
Can't locate package GDBM_File for @AnyDBM_File::ISA at /storage/tmp/software/perl-5.14.1/lib/5.14.1/x86_64-linux-thread-multi/DB_File.pm line 293.
Can't locate package NDBM_File for @AnyDBM_File::ISA at /storage/tmp/software/perl-5.14.1/lib/5.14.1/x86_64-linux-thread-multi/DB_File.pm line 293.
Can't locate package SDBM_File for @AnyDBM_File::ISA at /storage/tmp/software/perl-5.14.1/lib/5.14.1/x86_64-linux-thread-multi/DB_File.pm line 293.
cd /tmp/maker_mOO8LA; /storage/tmp/software/repeatmasker-3.3.0/RepeatMasker /storage/tmp/jobs/dmuscipula/experiments/SLAx/maker/SLAx_merged_02_03.maker.output/SLAx_merged_02_03_datastore/AB/FC/MblContig1//theVoid.MblContig1/MblContig1.0.all.rb -species all -dir /storage/tmp/jobs/dmuscipula/experiments/SLAx/maker/SLAx_merged_02_03.maker.output/SLAx_merged_02_03_datastore/AB/FC/MblContig1//theVoid.MblContig1 -pa 1
Choosing best annotations
cleaning blastn...
cleaning blastx...
cleaning clusters....
#--------- command -------------#
cycle 1 
cycle 10 
cycle 2 
cycle 3 
cycle 4 
cycle 5 
cycle 6 
cycle 7 
cycle 8 
cycle 9 
deleted:0 genes
deleted:0 hits
done
...finished clustering.
formating database...
Generating output... 
in cluster::shadow_cluster...
Length: 3612
Maker is now finished!!!
Making transcripts
masking
****MODULE VERSION INFO
--Next Contig--
Now starting the contig!!
Preparing evidence for hint based annotation
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processing output: 
Processing transcripts into genes
running  augustus.
running  blast search.
running  est2genome search.
running  exonerate search.
running  repeat masker.
SeqID: MblContig1
STATUS: Now running MAKER...
STATUS: Parsing control files...
STATUS: Processing and indexing input FASTA files...
STATUS: Setting up database for any GFF3 input...
/storage/tmp/jobs/dmuscipula/experiments/SLAx/maker/SLAx_merged_02_03.maker.output/SLAx_merged_02_03_datastore
/storage/tmp/jobs/dmuscipula/experiments/SLAx/maker/SLAx_merged_02_03.maker.output/SLAx_merged_02_03_master_datastore_index.log
/storage/tmp/software/augustus-2.5.5/bin/augustus --species=arabidopsis --strand=backward --UTR=off --hintsfile=/storage/tmp/jobs/dmuscipula/experiments/SLAx/maker/SLAx_merged_02_03.maker.output/SLAx_merged_02_03_datastore/AB/FC/MblContig1//theVoid.MblContig1/2_0.1976-3065.arabidopsis.auto_annotator.xdef.augustus --extrinsicCfgFile=/storage/tmp/software/augustus/config//extrinsic/extrinsic.MPE.cfg /storage/tmp/jobs/dmuscipula/experiments/SLAx/maker/SLAx_merged_02_03.maker.output/SLAx_merged_02_03_datastore/AB/FC/MblContig1//theVoid.MblContig1/2_0.1976-3065.arabidopsis.auto_annotator.augustus.fasta > /storage/tmp/jobs/dmuscipula/experiments/SLAx/maker/SLAx_merged_02_03.maker.output/SLAx_merged_02_03_datastore/AB/FC/MblContig1//theVoid.MblContig1/2_0.1976-3065.arabidopsis.auto_annotator.augustus
/storage/tmp/software/augustus-2.5.5/bin/augustus --species=arabidopsis --strand=forward --UTR=off --hintsfile=/storage/tmp/jobs/dmuscipula/experiments/SLAx/maker/SLAx_merged_02_03.maker.output/SLAx_merged_02_03_datastore/AB/FC/MblContig1//theVoid.MblContig1/1_0.0-3612.arabidopsis.auto_annotator.xdef.augustus --extrinsicCfgFile=/storage/tmp/software/augustus/config//extrinsic/extrinsic.MPE.cfg /storage/tmp/jobs/dmuscipula/experiments/SLAx/maker/SLAx_merged_02_03.maker.output/SLAx_merged_02_03_datastore/AB/FC/MblContig1//theVoid.MblContig1/1_0.0-3612.arabidopsis.auto_annotator.augustus.fasta > /storage/tmp/jobs/dmuscipula/experiments/SLAx/maker/SLAx_merged_02_03.maker.output/SLAx_merged_02_03_datastore/AB/FC/MblContig1//theVoid.MblContig1/1_0.0-3612.arabidopsis.auto_annotator.augustus
/storage/tmp/software/augustus-2.5.5/bin/augustus --species=arabidopsis --UTR=off /storage/tmp/jobs/dmuscipula/experiments/SLAx/maker/SLAx_merged_02_03.maker.output/SLAx_merged_02_03_datastore/AB/FC/MblContig1//theVoid.MblContig1/query.masked.fasta > /storage/tmp/jobs/dmuscipula/experiments/SLAx/maker/SLAx_merged_02_03.maker.output/SLAx_merged_02_03_datastore/AB/FC/MblContig1//theVoid.MblContig1/MblContig1.masked.all.arabidopsis.augustus
/storage/tmp/software/blast/bin/blastn -db /tmp/maker_mOO8LA/DM_Tra02%2Emerged%2Efasta.mpi.10.0 -query /tmp/maker_mOO8LA/rank0/MblContig1.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-10 -word_size 28 -reward 1 -penalty -5 -gapopen 5 -gapextend 5 -dbsize 1000 -searchsp 500000000 -num_threads 1 -lcase_masking -dust yes -soft_masking true -show_gis -out /storage/tmp/jobs/dmuscipula/experiments/SLAx/maker/SLAx_merged_02_03.maker.output/SLAx_merged_02_03_datastore/AB/FC/MblContig1//theVoid.MblContig1/MblContig1.0.DM_Tra02%2Emerged%2Efasta.blastn.temp_dir/DM_Tra02%2Emerged%2Efasta.mpi.10.0.blastn
/storage/tmp/software/blast/bin/blastn -db /tmp/maker_mOO8LA/DM_Tra02%2Emerged%2Efasta.mpi.10.1 -query /tmp/maker_mOO8LA/rank0/MblContig1.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-10 -word_size 28 -reward 1 -penalty -5 -gapopen 5 -gapextend 5 -dbsize 1000 -searchsp 500000000 -num_threads 1 -lcase_masking -dust yes -soft_masking true -show_gis -out /storage/tmp/jobs/dmuscipula/experiments/SLAx/maker/SLAx_merged_02_03.maker.output/SLAx_merged_02_03_datastore/AB/FC/MblContig1//theVoid.MblContig1/MblContig1.0.DM_Tra02%2Emerged%2Efasta.blastn.temp_dir/DM_Tra02%2Emerged%2Efasta.mpi.10.1.blastn
/storage/tmp/software/blast/bin/blastn -db /tmp/maker_mOO8LA/DM_Tra02%2Emerged%2Efasta.mpi.10.2 -query /tmp/maker_mOO8LA/rank0/MblContig1.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-10 -word_size 28 -reward 1 -penalty -5 -gapopen 5 -gapextend 5 -dbsize 1000 -searchsp 500000000 -num_threads 1 -lcase_masking -dust yes -soft_masking true -show_gis -out /storage/tmp/jobs/dmuscipula/experiments/SLAx/maker/SLAx_merged_02_03.maker.output/SLAx_merged_02_03_datastore/AB/FC/MblContig1//theVoid.MblContig1/MblContig1.0.DM_Tra02%2Emerged%2Efasta.blastn.temp_dir/DM_Tra02%2Emerged%2Efasta.mpi.10.2.blastn
/storage/tmp/software/blast/bin/blastn -db /tmp/maker_mOO8LA/DM_Tra02%2Emerged%2Efasta.mpi.10.3 -query /tmp/maker_mOO8LA/rank0/MblContig1.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-10 -word_size 28 -reward 1 -penalty -5 -gapopen 5 -gapextend 5 -dbsize 1000 -searchsp 500000000 -num_threads 1 -lcase_masking -dust yes -soft_masking true -show_gis -out /storage/tmp/jobs/dmuscipula/experiments/SLAx/maker/SLAx_merged_02_03.maker.output/SLAx_merged_02_03_datastore/AB/FC/MblContig1//theVoid.MblContig1/MblContig1.0.DM_Tra02%2Emerged%2Efasta.blastn.temp_dir/DM_Tra02%2Emerged%2Efasta.mpi.10.3.blastn
/storage/tmp/software/blast/bin/blastn -db /tmp/maker_mOO8LA/DM_Tra02%2Emerged%2Efasta.mpi.10.4 -query /tmp/maker_mOO8LA/rank0/MblContig1.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-10 -word_size 28 -reward 1 -penalty -5 -gapopen 5 -gapextend 5 -dbsize 1000 -searchsp 500000000 -num_threads 1 -lcase_masking -dust yes -soft_masking true -show_gis -out /storage/tmp/jobs/dmuscipula/experiments/SLAx/maker/SLAx_merged_02_03.maker.output/SLAx_merged_02_03_datastore/AB/FC/MblContig1//theVoid.MblContig1/MblContig1.0.DM_Tra02%2Emerged%2Efasta.blastn.temp_dir/DM_Tra02%2Emerged%2Efasta.mpi.10.4.blastn
/storage/tmp/software/blast/bin/blastn -db /tmp/maker_mOO8LA/DM_Tra02%2Emerged%2Efasta.mpi.10.5 -query /tmp/maker_mOO8LA/rank0/MblContig1.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-10 -word_size 28 -reward 1 -penalty -5 -gapopen 5 -gapextend 5 -dbsize 1000 -searchsp 500000000 -num_threads 1 -lcase_masking -dust yes -soft_masking true -show_gis -out /storage/tmp/jobs/dmuscipula/experiments/SLAx/maker/SLAx_merged_02_03.maker.output/SLAx_merged_02_03_datastore/AB/FC/MblContig1//theVoid.MblContig1/MblContig1.0.DM_Tra02%2Emerged%2Efasta.blastn.temp_dir/DM_Tra02%2Emerged%2Efasta.mpi.10.5.blastn
/storage/tmp/software/blast/bin/blastn -db /tmp/maker_mOO8LA/DM_Tra02%2Emerged%2Efasta.mpi.10.6 -query /tmp/maker_mOO8LA/rank0/MblContig1.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-10 -word_size 28 -reward 1 -penalty -5 -gapopen 5 -gapextend 5 -dbsize 1000 -searchsp 500000000 -num_threads 1 -lcase_masking -dust yes -soft_masking true -show_gis -out /storage/tmp/jobs/dmuscipula/experiments/SLAx/maker/SLAx_merged_02_03.maker.output/SLAx_merged_02_03_datastore/AB/FC/MblContig1//theVoid.MblContig1/MblContig1.0.DM_Tra02%2Emerged%2Efasta.blastn.temp_dir/DM_Tra02%2Emerged%2Efasta.mpi.10.6.blastn
/storage/tmp/software/blast/bin/blastn -db /tmp/maker_mOO8LA/DM_Tra02%2Emerged%2Efasta.mpi.10.7 -query /tmp/maker_mOO8LA/rank0/MblContig1.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-10 -word_size 28 -reward 1 -penalty -5 -gapopen 5 -gapextend 5 -dbsize 1000 -searchsp 500000000 -num_threads 1 -lcase_masking -dust yes -soft_masking true -show_gis -out /storage/tmp/jobs/dmuscipula/experiments/SLAx/maker/SLAx_merged_02_03.maker.output/SLAx_merged_02_03_datastore/AB/FC/MblContig1//theVoid.MblContig1/MblContig1.0.DM_Tra02%2Emerged%2Efasta.blastn.temp_dir/DM_Tra02%2Emerged%2Efasta.mpi.10.7.blastn
/storage/tmp/software/blast/bin/blastn -db /tmp/maker_mOO8LA/DM_Tra02%2Emerged%2Efasta.mpi.10.8 -query /tmp/maker_mOO8LA/rank0/MblContig1.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-10 -word_size 28 -reward 1 -penalty -5 -gapopen 5 -gapextend 5 -dbsize 1000 -searchsp 500000000 -num_threads 1 -lcase_masking -dust yes -soft_masking true -show_gis -out /storage/tmp/jobs/dmuscipula/experiments/SLAx/maker/SLAx_merged_02_03.maker.output/SLAx_merged_02_03_datastore/AB/FC/MblContig1//theVoid.MblContig1/MblContig1.0.DM_Tra02%2Emerged%2Efasta.blastn.temp_dir/DM_Tra02%2Emerged%2Efasta.mpi.10.8.blastn
/storage/tmp/software/blast/bin/blastn -db /tmp/maker_mOO8LA/DM_Tra02%2Emerged%2Efasta.mpi.10.9 -query /tmp/maker_mOO8LA/rank0/MblContig1.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-10 -word_size 28 -reward 1 -penalty -5 -gapopen 5 -gapextend 5 -dbsize 1000 -searchsp 500000000 -num_threads 1 -lcase_masking -dust yes -soft_masking true -show_gis -out /storage/tmp/jobs/dmuscipula/experiments/SLAx/maker/SLAx_merged_02_03.maker.output/SLAx_merged_02_03_datastore/AB/FC/MblContig1//theVoid.MblContig1/MblContig1.0.DM_Tra02%2Emerged%2Efasta.blastn.temp_dir/DM_Tra02%2Emerged%2Efasta.mpi.10.9.blastn
/storage/tmp/software/blast/bin/blastx -db /tmp/maker_mOO8LA/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_mOO8LA/rank0/MblContig1.0 -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 /storage/tmp/jobs/dmuscipula/experiments/SLAx/maker/SLAx_merged_02_03.maker.output/SLAx_merged_02_03_datastore/AB/FC/MblContig1//theVoid.MblContig1/MblContig1.0.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
/storage/tmp/software/blast/bin/blastx -db /tmp/maker_mOO8LA/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_mOO8LA/rank0/MblContig1.0 -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 /storage/tmp/jobs/dmuscipula/experiments/SLAx/maker/SLAx_merged_02_03.maker.output/SLAx_merged_02_03_datastore/AB/FC/MblContig1//theVoid.MblContig1/MblContig1.0.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
/storage/tmp/software/blast/bin/blastx -db /tmp/maker_mOO8LA/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_mOO8LA/rank0/MblContig1.0 -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 /storage/tmp/jobs/dmuscipula/experiments/SLAx/maker/SLAx_merged_02_03.maker.output/SLAx_merged_02_03_datastore/AB/FC/MblContig1//theVoid.MblContig1/MblContig1.0.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
/storage/tmp/software/blast/bin/blastx -db /tmp/maker_mOO8LA/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_mOO8LA/rank0/MblContig1.0 -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 /storage/tmp/jobs/dmuscipula/experiments/SLAx/maker/SLAx_merged_02_03.maker.output/SLAx_merged_02_03_datastore/AB/FC/MblContig1//theVoid.MblContig1/MblContig1.0.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
/storage/tmp/software/blast/bin/blastx -db /tmp/maker_mOO8LA/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_mOO8LA/rank0/MblContig1.0 -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 /storage/tmp/jobs/dmuscipula/experiments/SLAx/maker/SLAx_merged_02_03.maker.output/SLAx_merged_02_03_datastore/AB/FC/MblContig1//theVoid.MblContig1/MblContig1.0.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
/storage/tmp/software/blast/bin/blastx -db /tmp/maker_mOO8LA/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_mOO8LA/rank0/MblContig1.0 -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 /storage/tmp/jobs/dmuscipula/experiments/SLAx/maker/SLAx_merged_02_03.maker.output/SLAx_merged_02_03_datastore/AB/FC/MblContig1//theVoid.MblContig1/MblContig1.0.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
/storage/tmp/software/blast/bin/blastx -db /tmp/maker_mOO8LA/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_mOO8LA/rank0/MblContig1.0 -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 /storage/tmp/jobs/dmuscipula/experiments/SLAx/maker/SLAx_merged_02_03.maker.output/SLAx_merged_02_03_datastore/AB/FC/MblContig1//theVoid.MblContig1/MblContig1.0.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
/storage/tmp/software/blast/bin/blastx -db /tmp/maker_mOO8LA/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_mOO8LA/rank0/MblContig1.0 -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 /storage/tmp/jobs/dmuscipula/experiments/SLAx/maker/SLAx_merged_02_03.maker.output/SLAx_merged_02_03_datastore/AB/FC/MblContig1//theVoid.MblContig1/MblContig1.0.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
/storage/tmp/software/blast/bin/blastx -db /tmp/maker_mOO8LA/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_mOO8LA/rank0/MblContig1.0 -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 /storage/tmp/jobs/dmuscipula/experiments/SLAx/maker/SLAx_merged_02_03.maker.output/SLAx_merged_02_03_datastore/AB/FC/MblContig1//theVoid.MblContig1/MblContig1.0.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
/storage/tmp/software/blast/bin/blastx -db /tmp/maker_mOO8LA/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_mOO8LA/rank0/MblContig1.0 -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 /storage/tmp/jobs/dmuscipula/experiments/SLAx/maker/SLAx_merged_02_03.maker.output/SLAx_merged_02_03_datastore/AB/FC/MblContig1//theVoid.MblContig1/MblContig1.0.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
/storage/tmp/software/blast/bin/blastx -db /tmp/maker_mOO8LA/uniprotkb_viridiplantae%2Efasta.mpi.10.0 -query /tmp/maker_mOO8LA/rank0/MblContig1.0 -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 /storage/tmp/jobs/dmuscipula/experiments/SLAx/maker/SLAx_merged_02_03.maker.output/SLAx_merged_02_03_datastore/AB/FC/MblContig1//theVoid.MblContig1/MblContig1.0.uniprotkb_viridiplantae%2Efasta.blastx.temp_dir/uniprotkb_viridiplantae%2Efasta.mpi.10.0.blastx
/storage/tmp/software/blast/bin/blastx -db /tmp/maker_mOO8LA/uniprotkb_viridiplantae%2Efasta.mpi.10.1 -query /tmp/maker_mOO8LA/rank0/MblContig1.0 -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 /storage/tmp/jobs/dmuscipula/experiments/SLAx/maker/SLAx_merged_02_03.maker.output/SLAx_merged_02_03_datastore/AB/FC/MblContig1//theVoid.MblContig1/MblContig1.0.uniprotkb_viridiplantae%2Efasta.blastx.temp_dir/uniprotkb_viridiplantae%2Efasta.mpi.10.1.blastx
/storage/tmp/software/blast/bin/blastx -db /tmp/maker_mOO8LA/uniprotkb_viridiplantae%2Efasta.mpi.10.2 -query /tmp/maker_mOO8LA/rank0/MblContig1.0 -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 /storage/tmp/jobs/dmuscipula/experiments/SLAx/maker/SLAx_merged_02_03.maker.output/SLAx_merged_02_03_datastore/AB/FC/MblContig1//theVoid.MblContig1/MblContig1.0.uniprotkb_viridiplantae%2Efasta.blastx.temp_dir/uniprotkb_viridiplantae%2Efasta.mpi.10.2.blastx
/storage/tmp/software/blast/bin/blastx -db /tmp/maker_mOO8LA/uniprotkb_viridiplantae%2Efasta.mpi.10.3 -query /tmp/maker_mOO8LA/rank0/MblContig1.0 -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 /storage/tmp/jobs/dmuscipula/experiments/SLAx/maker/SLAx_merged_02_03.maker.output/SLAx_merged_02_03_datastore/AB/FC/MblContig1//theVoid.MblContig1/MblContig1.0.uniprotkb_viridiplantae%2Efasta.blastx.temp_dir/uniprotkb_viridiplantae%2Efasta.mpi.10.3.blastx
/storage/tmp/software/blast/bin/blastx -db /tmp/maker_mOO8LA/uniprotkb_viridiplantae%2Efasta.mpi.10.4 -query /tmp/maker_mOO8LA/rank0/MblContig1.0 -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 /storage/tmp/jobs/dmuscipula/experiments/SLAx/maker/SLAx_merged_02_03.maker.output/SLAx_merged_02_03_datastore/AB/FC/MblContig1//theVoid.MblContig1/MblContig1.0.uniprotkb_viridiplantae%2Efasta.blastx.temp_dir/uniprotkb_viridiplantae%2Efasta.mpi.10.4.blastx
/storage/tmp/software/blast/bin/blastx -db /tmp/maker_mOO8LA/uniprotkb_viridiplantae%2Efasta.mpi.10.5 -query /tmp/maker_mOO8LA/rank0/MblContig1.0 -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 /storage/tmp/jobs/dmuscipula/experiments/SLAx/maker/SLAx_merged_02_03.maker.output/SLAx_merged_02_03_datastore/AB/FC/MblContig1//theVoid.MblContig1/MblContig1.0.uniprotkb_viridiplantae%2Efasta.blastx.temp_dir/uniprotkb_viridiplantae%2Efasta.mpi.10.5.blastx
/storage/tmp/software/blast/bin/blastx -db /tmp/maker_mOO8LA/uniprotkb_viridiplantae%2Efasta.mpi.10.6 -query /tmp/maker_mOO8LA/rank0/MblContig1.0 -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 /storage/tmp/jobs/dmuscipula/experiments/SLAx/maker/SLAx_merged_02_03.maker.output/SLAx_merged_02_03_datastore/AB/FC/MblContig1//theVoid.MblContig1/MblContig1.0.uniprotkb_viridiplantae%2Efasta.blastx.temp_dir/uniprotkb_viridiplantae%2Efasta.mpi.10.6.blastx
/storage/tmp/software/blast/bin/blastx -db /tmp/maker_mOO8LA/uniprotkb_viridiplantae%2Efasta.mpi.10.7 -query /tmp/maker_mOO8LA/rank0/MblContig1.0 -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 /storage/tmp/jobs/dmuscipula/experiments/SLAx/maker/SLAx_merged_02_03.maker.output/SLAx_merged_02_03_datastore/AB/FC/MblContig1//theVoid.MblContig1/MblContig1.0.uniprotkb_viridiplantae%2Efasta.blastx.temp_dir/uniprotkb_viridiplantae%2Efasta.mpi.10.7.blastx
/storage/tmp/software/blast/bin/blastx -db /tmp/maker_mOO8LA/uniprotkb_viridiplantae%2Efasta.mpi.10.8 -query /tmp/maker_mOO8LA/rank0/MblContig1.0 -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 /storage/tmp/jobs/dmuscipula/experiments/SLAx/maker/SLAx_merged_02_03.maker.output/SLAx_merged_02_03_datastore/AB/FC/MblContig1//theVoid.MblContig1/MblContig1.0.uniprotkb_viridiplantae%2Efasta.blastx.temp_dir/uniprotkb_viridiplantae%2Efasta.mpi.10.8.blastx
/storage/tmp/software/blast/bin/blastx -db /tmp/maker_mOO8LA/uniprotkb_viridiplantae%2Efasta.mpi.10.9 -query /tmp/maker_mOO8LA/rank0/MblContig1.0 -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 /storage/tmp/jobs/dmuscipula/experiments/SLAx/maker/SLAx_merged_02_03.maker.output/SLAx_merged_02_03_datastore/AB/FC/MblContig1//theVoid.MblContig1/MblContig1.0.uniprotkb_viridiplantae%2Efasta.blastx.temp_dir/uniprotkb_viridiplantae%2Efasta.mpi.10.9.blastx
/storage/tmp/software/blast/bin/makeblastdb -dbtype nucl -in /tmp/maker_mOO8LA/DM_Tra02%2Emerged%2Efasta.mpi.10.0
/storage/tmp/software/blast/bin/makeblastdb -dbtype nucl -in /tmp/maker_mOO8LA/DM_Tra02%2Emerged%2Efasta.mpi.10.1
/storage/tmp/software/blast/bin/makeblastdb -dbtype nucl -in /tmp/maker_mOO8LA/DM_Tra02%2Emerged%2Efasta.mpi.10.2
/storage/tmp/software/blast/bin/makeblastdb -dbtype nucl -in /tmp/maker_mOO8LA/DM_Tra02%2Emerged%2Efasta.mpi.10.3
/storage/tmp/software/blast/bin/makeblastdb -dbtype nucl -in /tmp/maker_mOO8LA/DM_Tra02%2Emerged%2Efasta.mpi.10.4
/storage/tmp/software/blast/bin/makeblastdb -dbtype nucl -in /tmp/maker_mOO8LA/DM_Tra02%2Emerged%2Efasta.mpi.10.5
/storage/tmp/software/blast/bin/makeblastdb -dbtype nucl -in /tmp/maker_mOO8LA/DM_Tra02%2Emerged%2Efasta.mpi.10.6
/storage/tmp/software/blast/bin/makeblastdb -dbtype nucl -in /tmp/maker_mOO8LA/DM_Tra02%2Emerged%2Efasta.mpi.10.7
/storage/tmp/software/blast/bin/makeblastdb -dbtype nucl -in /tmp/maker_mOO8LA/DM_Tra02%2Emerged%2Efasta.mpi.10.8
/storage/tmp/software/blast/bin/makeblastdb -dbtype nucl -in /tmp/maker_mOO8LA/DM_Tra02%2Emerged%2Efasta.mpi.10.9
/storage/tmp/software/blast/bin/makeblastdb -dbtype prot -in /tmp/maker_mOO8LA/te_proteins%2Efasta.mpi.10.0
/storage/tmp/software/blast/bin/makeblastdb -dbtype prot -in /tmp/maker_mOO8LA/te_proteins%2Efasta.mpi.10.1
/storage/tmp/software/blast/bin/makeblastdb -dbtype prot -in /tmp/maker_mOO8LA/te_proteins%2Efasta.mpi.10.2
/storage/tmp/software/blast/bin/makeblastdb -dbtype prot -in /tmp/maker_mOO8LA/te_proteins%2Efasta.mpi.10.3
/storage/tmp/software/blast/bin/makeblastdb -dbtype prot -in /tmp/maker_mOO8LA/te_proteins%2Efasta.mpi.10.4
/storage/tmp/software/blast/bin/makeblastdb -dbtype prot -in /tmp/maker_mOO8LA/te_proteins%2Efasta.mpi.10.5
/storage/tmp/software/blast/bin/makeblastdb -dbtype prot -in /tmp/maker_mOO8LA/te_proteins%2Efasta.mpi.10.6
/storage/tmp/software/blast/bin/makeblastdb -dbtype prot -in /tmp/maker_mOO8LA/te_proteins%2Efasta.mpi.10.7
/storage/tmp/software/blast/bin/makeblastdb -dbtype prot -in /tmp/maker_mOO8LA/te_proteins%2Efasta.mpi.10.8
/storage/tmp/software/blast/bin/makeblastdb -dbtype prot -in /tmp/maker_mOO8LA/te_proteins%2Efasta.mpi.10.9
/storage/tmp/software/blast/bin/makeblastdb -dbtype prot -in /tmp/maker_mOO8LA/uniprotkb_viridiplantae%2Efasta.mpi.10.0
/storage/tmp/software/blast/bin/makeblastdb -dbtype prot -in /tmp/maker_mOO8LA/uniprotkb_viridiplantae%2Efasta.mpi.10.1
/storage/tmp/software/blast/bin/makeblastdb -dbtype prot -in /tmp/maker_mOO8LA/uniprotkb_viridiplantae%2Efasta.mpi.10.2
/storage/tmp/software/blast/bin/makeblastdb -dbtype prot -in /tmp/maker_mOO8LA/uniprotkb_viridiplantae%2Efasta.mpi.10.3
/storage/tmp/software/blast/bin/makeblastdb -dbtype prot -in /tmp/maker_mOO8LA/uniprotkb_viridiplantae%2Efasta.mpi.10.4
/storage/tmp/software/blast/bin/makeblastdb -dbtype prot -in /tmp/maker_mOO8LA/uniprotkb_viridiplantae%2Efasta.mpi.10.5
/storage/tmp/software/blast/bin/makeblastdb -dbtype prot -in /tmp/maker_mOO8LA/uniprotkb_viridiplantae%2Efasta.mpi.10.6
/storage/tmp/software/blast/bin/makeblastdb -dbtype prot -in /tmp/maker_mOO8LA/uniprotkb_viridiplantae%2Efasta.mpi.10.7
/storage/tmp/software/blast/bin/makeblastdb -dbtype prot -in /tmp/maker_mOO8LA/uniprotkb_viridiplantae%2Efasta.mpi.10.8
/storage/tmp/software/blast/bin/makeblastdb -dbtype prot -in /tmp/maker_mOO8LA/uniprotkb_viridiplantae%2Efasta.mpi.10.9
/storage/tmp/software/exonerate-2.2.0-x86_64/bin/exonerate  -q /storage/tmp/jobs/dmuscipula/experiments/SLAx/maker/SLAx_merged_02_03.maker.output/SLAx_merged_02_03_datastore/AB/FC/MblContig1//theVoid.MblContig1/DM_Tra02_c148766.for.2237-2794.0.fasta -t /storage/tmp/jobs/dmuscipula/experiments/SLAx/maker/SLAx_merged_02_03.maker.output/SLAx_merged_02_03_datastore/AB/FC/MblContig1//theVoid.MblContig1/MblContig1.2237-2794.0.fasta -Q dna -T dna --model est2genome  --minintron 20 --maxintron 10000 --showcigar --percent 20 > /storage/tmp/jobs/dmuscipula/experiments/SLAx/maker/SLAx_merged_02_03.maker.output/SLAx_merged_02_03_datastore/AB/FC/MblContig1//theVoid.MblContig1/MblContig1.2237-2794.DM_Tra02_c148766.est_exonerate.0
/storage/tmp/software/exonerate-2.2.0-x86_64/bin/exonerate  -q /storage/tmp/jobs/dmuscipula/experiments/SLAx/maker/SLAx_merged_02_03.maker.output/SLAx_merged_02_03_datastore/AB/FC/MblContig1//theVoid.MblContig1/DM_Tra02_c22210.for.2531-3447.0.fasta -t /storage/tmp/jobs/dmuscipula/experiments/SLAx/maker/SLAx_merged_02_03.maker.output/SLAx_merged_02_03_datastore/AB/FC/MblContig1//theVoid.MblContig1/MblContig1.2531-3447.0.fasta -Q dna -T dna --model est2genome  --minintron 20 --maxintron 10000 --showcigar --percent 20 > /storage/tmp/jobs/dmuscipula/experiments/SLAx/maker/SLAx_merged_02_03.maker.output/SLAx_merged_02_03_datastore/AB/FC/MblContig1//theVoid.MblContig1/MblContig1.2531-3447.DM_Tra02_c22210.est_exonerate.0
/storage/tmp/software/exonerate-2.2.0-x86_64/bin/exonerate  -q /storage/tmp/jobs/dmuscipula/experiments/SLAx/maker/SLAx_merged_02_03.maker.output/SLAx_merged_02_03_datastore/AB/FC/MblContig1//theVoid.MblContig1/DM_Tra02_c28558.for.1766-3612.0.fasta -t /storage/tmp/jobs/dmuscipula/experiments/SLAx/maker/SLAx_merged_02_03.maker.output/SLAx_merged_02_03_datastore/AB/FC/MblContig1//theVoid.MblContig1/MblContig1.1766-3612.0.fasta -Q dna -T dna --model est2genome  --minintron 20 --maxintron 10000 --showcigar --percent 20 > /storage/tmp/jobs/dmuscipula/experiments/SLAx/maker/SLAx_merged_02_03.maker.output/SLAx_merged_02_03_datastore/AB/FC/MblContig1//theVoid.MblContig1/MblContig1.1766-3612.DM_Tra02_c28558.est_exonerate.0
/storage/tmp/software/exonerate-2.2.0-x86_64/bin/exonerate  -q /storage/tmp/jobs/dmuscipula/experiments/SLAx/maker/SLAx_merged_02_03.maker.output/SLAx_merged_02_03_datastore/AB/FC/MblContig1//theVoid.MblContig1/DM_Tra02_c46480.for.1375-1980.0.fasta -t /storage/tmp/jobs/dmuscipula/experiments/SLAx/maker/SLAx_merged_02_03.maker.output/SLAx_merged_02_03_datastore/AB/FC/MblContig1//theVoid.MblContig1/MblContig1.1375-1980.0.fasta -Q dna -T dna --model est2genome  --minintron 20 --maxintron 10000 --showcigar --percent 20 > /storage/tmp/jobs/dmuscipula/experiments/SLAx/maker/SLAx_merged_02_03.maker.output/SLAx_merged_02_03_datastore/AB/FC/MblContig1//theVoid.MblContig1/MblContig1.1375-1980.DM_Tra02_c46480.est_exonerate.0
/storage/tmp/software/exonerate-2.2.0-x86_64/bin/exonerate  -q /storage/tmp/jobs/dmuscipula/experiments/SLAx/maker/SLAx_merged_02_03.maker.output/SLAx_merged_02_03_datastore/AB/FC/MblContig1//theVoid.MblContig1/DM_Tra02_rep_c103390.for.2176-2881.0.fasta -t /storage/tmp/jobs/dmuscipula/experiments/SLAx/maker/SLAx_merged_02_03.maker.output/SLAx_merged_02_03_datastore/AB/FC/MblContig1//theVoid.MblContig1/MblContig1.2176-2881.0.fasta -Q dna -T dna --model est2genome  --minintron 20 --maxintron 10000 --showcigar --percent 20 > /storage/tmp/jobs/dmuscipula/experiments/SLAx/maker/SLAx_merged_02_03.maker.output/SLAx_merged_02_03_datastore/AB/FC/MblContig1//theVoid.MblContig1/MblContig1.2176-2881.DM_Tra02_rep_c103390.est_exonerate.0
/storage/tmp/software/exonerate-2.2.0-x86_64/bin/exonerate  -q /storage/tmp/jobs/dmuscipula/experiments/SLAx/maker/SLAx_merged_02_03.maker.output/SLAx_merged_02_03_datastore/AB/FC/MblContig1//theVoid.MblContig1/DM_Tra02_rep_c150200.for.2198-2924.0.fasta -t /storage/tmp/jobs/dmuscipula/experiments/SLAx/maker/SLAx_merged_02_03.maker.output/SLAx_merged_02_03_datastore/AB/FC/MblContig1//theVoid.MblContig1/MblContig1.2198-2924.0.fasta -Q dna -T dna --model est2genome  --minintron 20 --maxintron 10000 --showcigar --percent 20 > /storage/tmp/jobs/dmuscipula/experiments/SLAx/maker/SLAx_merged_02_03.maker.output/SLAx_merged_02_03_datastore/AB/FC/MblContig1//theVoid.MblContig1/MblContig1.2198-2924.DM_Tra02_rep_c150200.est_exonerate.0
/storage/tmp/software/exonerate-2.2.0-x86_64/bin/exonerate  -q /storage/tmp/jobs/dmuscipula/experiments/SLAx/maker/SLAx_merged_02_03.maker.output/SLAx_merged_02_03_datastore/AB/FC/MblContig1//theVoid.MblContig1/DM_Tra02_rep_c152823.for.2191-2815.0.fasta -t /storage/tmp/jobs/dmuscipula/experiments/SLAx/maker/SLAx_merged_02_03.maker.output/SLAx_merged_02_03_datastore/AB/FC/MblContig1//theVoid.MblContig1/MblContig1.2191-2815.0.fasta -Q dna -T dna --model est2genome  --minintron 20 --maxintron 10000 --showcigar --percent 20 > /storage/tmp/jobs/dmuscipula/experiments/SLAx/maker/SLAx_merged_02_03.maker.output/SLAx_merged_02_03_datastore/AB/FC/MblContig1//theVoid.MblContig1/MblContig1.2191-2815.DM_Tra02_rep_c152823.est_exonerate.0
/storage/tmp/software/exonerate-2.2.0-x86_64/bin/exonerate  -q /storage/tmp/jobs/dmuscipula/experiments/SLAx/maker/SLAx_merged_02_03.maker.output/SLAx_merged_02_03_datastore/AB/FC/MblContig1//theVoid.MblContig1/DM_Tra02_rep_c152902.for.2182-2808.0.fasta -t /storage/tmp/jobs/dmuscipula/experiments/SLAx/maker/SLAx_merged_02_03.maker.output/SLAx_merged_02_03_datastore/AB/FC/MblContig1//theVoid.MblContig1/MblContig1.2182-2808.0.fasta -Q dna -T dna --model est2genome  --minintron 20 --maxintron 10000 --showcigar --percent 20 > /storage/tmp/jobs/dmuscipula/experiments/SLAx/maker/SLAx_merged_02_03.maker.output/SLAx_merged_02_03_datastore/AB/FC/MblContig1//theVoid.MblContig1/MblContig1.2182-2808.DM_Tra02_rep_c152902.est_exonerate.0
/storage/tmp/software/exonerate-2.2.0-x86_64/bin/exonerate  -q /storage/tmp/jobs/dmuscipula/experiments/SLAx/maker/SLAx_merged_02_03.maker.output/SLAx_merged_02_03_datastore/AB/FC/MblContig1//theVoid.MblContig1/DM_Tra02_rep_c59058.for.2219-2853.0.fasta -t /storage/tmp/jobs/dmuscipula/experiments/SLAx/maker/SLAx_merged_02_03.maker.output/SLAx_merged_02_03_datastore/AB/FC/MblContig1//theVoid.MblContig1/MblContig1.2219-2853.0.fasta -Q dna -T dna --model est2genome  --minintron 20 --maxintron 10000 --showcigar --percent 20 > /storage/tmp/jobs/dmuscipula/experiments/SLAx/maker/SLAx_merged_02_03.maker.output/SLAx_merged_02_03_datastore/AB/FC/MblContig1//theVoid.MblContig1/MblContig1.2219-2853.DM_Tra02_rep_c59058.est_exonerate.0
/storage/tmp/software/exonerate-2.2.0-x86_64/bin/exonerate  -q /storage/tmp/jobs/dmuscipula/experiments/SLAx/maker/SLAx_merged_02_03.maker.output/SLAx_merged_02_03_datastore/AB/FC/MblContig1//theVoid.MblContig1/DM_Tra02_rep_c62416.for.2337-2853.0.fasta -t /storage/tmp/jobs/dmuscipula/experiments/SLAx/maker/SLAx_merged_02_03.maker.output/SLAx_merged_02_03_datastore/AB/FC/MblContig1//theVoid.MblContig1/MblContig1.2337-2853.0.fasta -Q dna -T dna --model est2genome  --minintron 20 --maxintron 10000 --showcigar --percent 20 > /storage/tmp/jobs/dmuscipula/experiments/SLAx/maker/SLAx_merged_02_03.maker.output/SLAx_merged_02_03_datastore/AB/FC/MblContig1//theVoid.MblContig1/MblContig1.2337-2853.DM_Tra02_rep_c62416.est_exonerate.0
/storage/tmp/software/exonerate-2.2.0-x86_64/bin/exonerate  -q /storage/tmp/jobs/dmuscipula/experiments/SLAx/maker/SLAx_merged_02_03.maker.output/SLAx_merged_02_03_datastore/AB/FC/MblContig1//theVoid.MblContig1/DM_Tra02_rep_c64040.for.2253-2808.0.fasta -t /storage/tmp/jobs/dmuscipula/experiments/SLAx/maker/SLAx_merged_02_03.maker.output/SLAx_merged_02_03_datastore/AB/FC/MblContig1//theVoid.MblContig1/MblContig1.2253-2808.0.fasta -Q dna -T dna --model est2genome  --minintron 20 --maxintron 10000 --showcigar --percent 20 > /storage/tmp/jobs/dmuscipula/experiments/SLAx/maker/SLAx_merged_02_03.maker.output/SLAx_merged_02_03_datastore/AB/FC/MblContig1//theVoid.MblContig1/MblContig1.2253-2808.DM_Tra02_rep_c64040.est_exonerate.0
/storage/tmp/software/exonerate-2.2.0-x86_64/bin/exonerate  -q /storage/tmp/jobs/dmuscipula/experiments/SLAx/maker/SLAx_merged_02_03.maker.output/SLAx_merged_02_03_datastore/AB/FC/MblContig1//theVoid.MblContig1/DM_Tra02_rep_c85280.for.2222-2887.0.fasta -t /storage/tmp/jobs/dmuscipula/experiments/SLAx/maker/SLAx_merged_02_03.maker.output/SLAx_merged_02_03_datastore/AB/FC/MblContig1//theVoid.MblContig1/MblContig1.2222-2887.0.fasta -Q dna -T dna --model est2genome  --minintron 20 --maxintron 10000 --showcigar --percent 20 > /storage/tmp/jobs/dmuscipula/experiments/SLAx/maker/SLAx_merged_02_03.maker.output/SLAx_merged_02_03_datastore/AB/FC/MblContig1//theVoid.MblContig1/MblContig1.2222-2887.DM_Tra02_rep_c85280.est_exonerate.0
/storage/tmp/software/exonerate-2.2.0-x86_64/bin/exonerate  -q /storage/tmp/jobs/dmuscipula/experiments/SLAx/maker/SLAx_merged_02_03.maker.output/SLAx_merged_02_03_datastore/AB/FC/MblContig1//theVoid.MblContig1/DM_Tra02_rep_c85677.for.2174-2811.0.fasta -t /storage/tmp/jobs/dmuscipula/experiments/SLAx/maker/SLAx_merged_02_03.maker.output/SLAx_merged_02_03_datastore/AB/FC/MblContig1//theVoid.MblContig1/MblContig1.2174-2811.0.fasta -Q dna -T dna --model est2genome  --minintron 20 --maxintron 10000 --showcigar --percent 20 > /storage/tmp/jobs/dmuscipula/experiments/SLAx/maker/SLAx_merged_02_03.maker.output/SLAx_merged_02_03_datastore/AB/FC/MblContig1//theVoid.MblContig1/MblContig1.2174-2811.DM_Tra02_rep_c85677.est_exonerate.0
/storage/tmp/software/exonerate-2.2.0-x86_64/bin/exonerate  -q /storage/tmp/jobs/dmuscipula/experiments/SLAx/maker/SLAx_merged_02_03.maker.output/SLAx_merged_02_03_datastore/AB/FC/MblContig1//theVoid.MblContig1/DM_Tra02_rep_c86203.for.2191-2894.0.fasta -t /storage/tmp/jobs/dmuscipula/experiments/SLAx/maker/SLAx_merged_02_03.maker.output/SLAx_merged_02_03_datastore/AB/FC/MblContig1//theVoid.MblContig1/MblContig1.2191-2894.0.fasta -Q dna -T dna --model est2genome  --minintron 20 --maxintron 10000 --showcigar --percent 20 > /storage/tmp/jobs/dmuscipula/experiments/SLAx/maker/SLAx_merged_02_03.maker.output/SLAx_merged_02_03_datastore/AB/FC/MblContig1//theVoid.MblContig1/MblContig1.2191-2894.DM_Tra02_rep_c86203.est_exonerate.0
/storage/tmp/software/exonerate-2.2.0-x86_64/bin/exonerate  -q /storage/tmp/jobs/dmuscipula/experiments/SLAx/maker/SLAx_merged_02_03.maker.output/SLAx_merged_02_03_datastore/AB/FC/MblContig1//theVoid.MblContig1/DM_Tra02_rep_c88538.for.2176-2837.0.fasta -t /storage/tmp/jobs/dmuscipula/experiments/SLAx/maker/SLAx_merged_02_03.maker.output/SLAx_merged_02_03_datastore/AB/FC/MblContig1//theVoid.MblContig1/MblContig1.2176-2837.0.fasta -Q dna -T dna --model est2genome  --minintron 20 --maxintron 10000 --showcigar --percent 20 > /storage/tmp/jobs/dmuscipula/experiments/SLAx/maker/SLAx_merged_02_03.maker.output/SLAx_merged_02_03_datastore/AB/FC/MblContig1//theVoid.MblContig1/MblContig1.2176-2837.DM_Tra02_rep_c88538.est_exonerate.0
/storage/tmp/software/exonerate-2.2.0-x86_64/bin/exonerate  -q /storage/tmp/jobs/dmuscipula/experiments/SLAx/maker/SLAx_merged_02_03.maker.output/SLAx_merged_02_03_datastore/AB/FC/MblContig1//theVoid.MblContig1/DM_Tra02_rep_c94992.for.2269-2918.0.fasta -t /storage/tmp/jobs/dmuscipula/experiments/SLAx/maker/SLAx_merged_02_03.maker.output/SLAx_merged_02_03_datastore/AB/FC/MblContig1//theVoid.MblContig1/MblContig1.2269-2918.0.fasta -Q dna -T dna --model est2genome  --minintron 20 --maxintron 10000 --showcigar --percent 20 > /storage/tmp/jobs/dmuscipula/experiments/SLAx/maker/SLAx_merged_02_03.maker.output/SLAx_merged_02_03_datastore/AB/FC/MblContig1//theVoid.MblContig1/MblContig1.2269-2918.DM_Tra02_rep_c94992.est_exonerate.0
/storage/tmp/software/exonerate-2.2.0-x86_64/bin/exonerate  -q /storage/tmp/jobs/dmuscipula/experiments/SLAx/maker/SLAx_merged_02_03.maker.output/SLAx_merged_02_03_datastore/AB/FC/MblContig1//theVoid.MblContig1/NODE_1236506_length_398_cov_6%2E628141.for.1385-2206.0.fasta -t /storage/tmp/jobs/dmuscipula/experiments/SLAx/maker/SLAx_merged_02_03.maker.output/SLAx_merged_02_03_datastore/AB/FC/MblContig1//theVoid.MblContig1/MblContig1.1385-2206.0.fasta -Q dna -T dna --model est2genome  --minintron 20 --maxintron 10000 --showcigar --percent 20 > /storage/tmp/jobs/dmuscipula/experiments/SLAx/maker/SLAx_merged_02_03.maker.output/SLAx_merged_02_03_datastore/AB/FC/MblContig1//theVoid.MblContig1/MblContig1.1385-2206.NODE_1236506_length_398_cov_6%2E628141.est_exonerate.0
/storage/tmp/software/exonerate-2.2.0-x86_64/bin/exonerate  -q /storage/tmp/jobs/dmuscipula/experiments/SLAx/maker/SLAx_merged_02_03.maker.output/SLAx_merged_02_03_datastore/AB/FC/MblContig1//theVoid.MblContig1/NODE_139529_length_544_cov_11%2E053308.for.841-1808.0.fasta -t /storage/tmp/jobs/dmuscipula/experiments/SLAx/maker/SLAx_merged_02_03.maker.output/SLAx_merged_02_03_datastore/AB/FC/MblContig1//theVoid.MblContig1/MblContig1.841-1808.0.fasta -Q dna -T dna --model est2genome  --minintron 20 --maxintron 10000 --showcigar --percent 20 > /storage/tmp/jobs/dmuscipula/experiments/SLAx/maker/SLAx_merged_02_03.maker.output/SLAx_merged_02_03_datastore/AB/FC/MblContig1//theVoid.MblContig1/MblContig1.841-1808.NODE_139529_length_544_cov_11%2E053308.est_exonerate.0
/storage/tmp/software/exonerate-2.2.0-x86_64/bin/exonerate -q /storage/tmp/jobs/dmuscipula/experiments/SLAx/maker/SLAx_merged_02_03.maker.output/SLAx_merged_02_03_datastore/AB/FC/MblContig1//theVoid.MblContig1/SP%3ASLAC1_ARATH.for.1120-3518.0.fasta -t /storage/tmp/jobs/dmuscipula/experiments/SLAx/maker/SLAx_merged_02_03.maker.output/SLAx_merged_02_03_datastore/AB/FC/MblContig1//theVoid.MblContig1/MblContig1.1120-3518.0.fasta -Q protein -T dna -m protein2genome --softmasktarget  --percent 20 --showcigar  > /storage/tmp/jobs/dmuscipula/experiments/SLAx/maker/SLAx_merged_02_03.maker.output/SLAx_merged_02_03_datastore/AB/FC/MblContig1//theVoid.MblContig1/MblContig1.1120-3518.SP%3ASLAC1_ARATH.p_exonerate.0
/storage/tmp/software/exonerate-2.2.0-x86_64/bin/exonerate -q /storage/tmp/jobs/dmuscipula/experiments/SLAx/maker/SLAx_merged_02_03.maker.output/SLAx_merged_02_03_datastore/AB/FC/MblContig1//theVoid.MblContig1/SP%3ASLAH2_ARATH.for.248-3548.0.fasta -t /storage/tmp/jobs/dmuscipula/experiments/SLAx/maker/SLAx_merged_02_03.maker.output/SLAx_merged_02_03_datastore/AB/FC/MblContig1//theVoid.MblContig1/MblContig1.248-3548.0.fasta -Q protein -T dna -m protein2genome --softmasktarget  --percent 20 --showcigar  > /storage/tmp/jobs/dmuscipula/experiments/SLAx/maker/SLAx_merged_02_03.maker.output/SLAx_merged_02_03_datastore/AB/FC/MblContig1//theVoid.MblContig1/MblContig1.248-3548.SP%3ASLAH2_ARATH.p_exonerate.0
/storage/tmp/software/exonerate-2.2.0-x86_64/bin/exonerate -q /storage/tmp/jobs/dmuscipula/experiments/SLAx/maker/SLAx_merged_02_03.maker.output/SLAx_merged_02_03_datastore/AB/FC/MblContig1//theVoid.MblContig1/SP%3ASLAH3_ARATH.for.86-3612.0.fasta -t /storage/tmp/jobs/dmuscipula/experiments/SLAx/maker/SLAx_merged_02_03.maker.output/SLAx_merged_02_03_datastore/AB/FC/MblContig1//theVoid.MblContig1/MblContig1.86-3612.0.fasta -Q protein -T dna -m protein2genome --softmasktarget  --percent 20 --showcigar  > /storage/tmp/jobs/dmuscipula/experiments/SLAx/maker/SLAx_merged_02_03.maker.output/SLAx_merged_02_03_datastore/AB/FC/MblContig1//theVoid.MblContig1/MblContig1.86-3612.SP%3ASLAH3_ARATH.p_exonerate.0
/storage/tmp/software/exonerate-2.2.0-x86_64/bin/exonerate -q /storage/tmp/jobs/dmuscipula/experiments/SLAx/maker/SLAx_merged_02_03.maker.output/SLAx_merged_02_03_datastore/AB/FC/MblContig1//theVoid.MblContig1/TR%3AA2WMT8_ORYSI.for.1180-3500.0.fasta -t /storage/tmp/jobs/dmuscipula/experiments/SLAx/maker/SLAx_merged_02_03.maker.output/SLAx_merged_02_03_datastore/AB/FC/MblContig1//theVoid.MblContig1/MblContig1.1180-3500.0.fasta -Q protein -T dna -m protein2genome --softmasktarget  --percent 20 --showcigar  > /storage/tmp/jobs/dmuscipula/experiments/SLAx/maker/SLAx_merged_02_03.maker.output/SLAx_merged_02_03_datastore/AB/FC/MblContig1//theVoid.MblContig1/MblContig1.1180-3500.TR%3AA2WMT8_ORYSI.p_exonerate.0
/storage/tmp/software/exonerate-2.2.0-x86_64/bin/exonerate -q /storage/tmp/jobs/dmuscipula/experiments/SLAx/maker/SLAx_merged_02_03.maker.output/SLAx_merged_02_03_datastore/AB/FC/MblContig1//theVoid.MblContig1/TR%3AA2WQC0_ORYSI.for.1120-3536.0.fasta -t /storage/tmp/jobs/dmuscipula/experiments/SLAx/maker/SLAx_merged_02_03.maker.output/SLAx_merged_02_03_datastore/AB/FC/MblContig1//theVoid.MblContig1/MblContig1.1120-3536.0.fasta -Q protein -T dna -m protein2genome --softmasktarget  --percent 20 --showcigar  > /storage/tmp/jobs/dmuscipula/experiments/SLAx/maker/SLAx_merged_02_03.maker.output/SLAx_merged_02_03_datastore/AB/FC/MblContig1//theVoid.MblContig1/MblContig1.1120-3536.TR%3AA2WQC0_ORYSI.p_exonerate.0
/storage/tmp/software/exonerate-2.2.0-x86_64/bin/exonerate -q /storage/tmp/jobs/dmuscipula/experiments/SLAx/maker/SLAx_merged_02_03.maker.output/SLAx_merged_02_03_datastore/AB/FC/MblContig1//theVoid.MblContig1/TR%3AA2WSR8_ORYSI.for.110-3584.0.fasta -t /storage/tmp/jobs/dmuscipula/experiments/SLAx/maker/SLAx_merged_02_03.maker.output/SLAx_merged_02_03_datastore/AB/FC/MblContig1//theVoid.MblContig1/MblContig1.110-3584.0.fasta -Q protein -T dna -m protein2genome --softmasktarget  --percent 20 --showcigar  > /storage/tmp/jobs/dmuscipula/experiments/SLAx/maker/SLAx_merged_02_03.maker.output/SLAx_merged_02_03_datastore/AB/FC/MblContig1//theVoid.MblContig1/MblContig1.110-3584.TR%3AA2WSR8_ORYSI.p_exonerate.0
/storage/tmp/software/exonerate-2.2.0-x86_64/bin/exonerate -q /storage/tmp/jobs/dmuscipula/experiments/SLAx/maker/SLAx_merged_02_03.maker.output/SLAx_merged_02_03_datastore/AB/FC/MblContig1//theVoid.MblContig1/TR%3AA2XWN1_ORYSI.for.1120-3518.0.fasta -t /storage/tmp/jobs/dmuscipula/experiments/SLAx/maker/SLAx_merged_02_03.maker.output/SLAx_merged_02_03_datastore/AB/FC/MblContig1//theVoid.MblContig1/MblContig1.1120-3518.0.fasta -Q protein -T dna -m protein2genome --softmasktarget  --percent 20 --showcigar  > /storage/tmp/jobs/dmuscipula/experiments/SLAx/maker/SLAx_merged_02_03.maker.output/SLAx_merged_02_03_datastore/AB/FC/MblContig1//theVoid.MblContig1/MblContig1.1120-3518.TR%3AA2XWN1_ORYSI.p_exonerate.0
/storage/tmp/software/exonerate-2.2.0-x86_64/bin/exonerate -q /storage/tmp/jobs/dmuscipula/experiments/SLAx/maker/SLAx_merged_02_03.maker.output/SLAx_merged_02_03_datastore/AB/FC/MblContig1//theVoid.MblContig1/TR%3AA2Y1P3_ORYSI.for.1141-3521.0.fasta -t /storage/tmp/jobs/dmuscipula/experiments/SLAx/maker/SLAx_merged_02_03.maker.output/SLAx_merged_02_03_datastore/AB/FC/MblContig1//theVoid.MblContig1/MblContig1.1141-3521.0.fasta -Q protein -T dna -m protein2genome --softmasktarget  --percent 20 --showcigar  > /storage/tmp/jobs/dmuscipula/experiments/SLAx/maker/SLAx_merged_02_03.maker.output/SLAx_merged_02_03_datastore/AB/FC/MblContig1//theVoid.MblContig1/MblContig1.1141-3521.TR%3AA2Y1P3_ORYSI.p_exonerate.0
/storage/tmp/software/exonerate-2.2.0-x86_64/bin/exonerate -q /storage/tmp/jobs/dmuscipula/experiments/SLAx/maker/SLAx_merged_02_03.maker.output/SLAx_merged_02_03_datastore/AB/FC/MblContig1//theVoid.MblContig1/TR%3AA2Y7Z7_ORYSI.for.110-3569.0.fasta -t /storage/tmp/jobs/dmuscipula/experiments/SLAx/maker/SLAx_merged_02_03.maker.output/SLAx_merged_02_03_datastore/AB/FC/MblContig1//theVoid.MblContig1/MblContig1.110-3569.0.fasta -Q protein -T dna -m protein2genome --softmasktarget  --percent 20 --showcigar  > /storage/tmp/jobs/dmuscipula/experiments/SLAx/maker/SLAx_merged_02_03.maker.output/SLAx_merged_02_03_datastore/AB/FC/MblContig1//theVoid.MblContig1/MblContig1.110-3569.TR%3AA2Y7Z7_ORYSI.p_exonerate.0
/storage/tmp/software/exonerate-2.2.0-x86_64/bin/exonerate -q /storage/tmp/jobs/dmuscipula/experiments/SLAx/maker/SLAx_merged_02_03.maker.output/SLAx_merged_02_03_datastore/AB/FC/MblContig1//theVoid.MblContig1/TR%3AA2YIS4_ORYSI.for.1141-3539.0.fasta -t /storage/tmp/jobs/dmuscipula/experiments/SLAx/maker/SLAx_merged_02_03.maker.output/SLAx_merged_02_03_datastore/AB/FC/MblContig1//theVoid.MblContig1/MblContig1.1141-3539.0.fasta -Q protein -T dna -m protein2genome --softmasktarget  --percent 20 --showcigar  > /storage/tmp/jobs/dmuscipula/experiments/SLAx/maker/SLAx_merged_02_03.maker.output/SLAx_merged_02_03_datastore/AB/FC/MblContig1//theVoid.MblContig1/MblContig1.1141-3539.TR%3AA2YIS4_ORYSI.p_exonerate.0
/storage/tmp/software/exonerate-2.2.0-x86_64/bin/exonerate -q /storage/tmp/jobs/dmuscipula/experiments/SLAx/maker/SLAx_merged_02_03.maker.output/SLAx_merged_02_03_datastore/AB/FC/MblContig1//theVoid.MblContig1/TR%3AA2ZR94_ORYSJ.for.1180-3500.0.fasta -t /storage/tmp/jobs/dmuscipula/experiments/SLAx/maker/SLAx_merged_02_03.maker.output/SLAx_merged_02_03_datastore/AB/FC/MblContig1//theVoid.MblContig1/MblContig1.1180-3500.0.fasta -Q protein -T dna -m protein2genome --softmasktarget  --percent 20 --showcigar  > /storage/tmp/jobs/dmuscipula/experiments/SLAx/maker/SLAx_merged_02_03.maker.output/SLAx_merged_02_03_datastore/AB/FC/MblContig1//theVoid.MblContig1/MblContig1.1180-3500.TR%3AA2ZR94_ORYSJ.p_exonerate.0
/storage/tmp/software/exonerate-2.2.0-x86_64/bin/exonerate -q /storage/tmp/jobs/dmuscipula/experiments/SLAx/maker/SLAx_merged_02_03.maker.output/SLAx_merged_02_03_datastore/AB/FC/MblContig1//theVoid.MblContig1/TR%3AA3AWM0_ORYSJ.for.1120-2182.0.fasta -t /storage/tmp/jobs/dmuscipula/experiments/SLAx/maker/SLAx_merged_02_03.maker.output/SLAx_merged_02_03_datastore/AB/FC/MblContig1//theVoid.MblContig1/MblContig1.1120-2182.0.fasta -Q protein -T dna -m protein2genome --softmasktarget  --percent 20 --showcigar  > /storage/tmp/jobs/dmuscipula/experiments/SLAx/maker/SLAx_merged_02_03.maker.output/SLAx_merged_02_03_datastore/AB/FC/MblContig1//theVoid.MblContig1/MblContig1.1120-2182.TR%3AA3AWM0_ORYSJ.p_exonerate.0
/storage/tmp/software/exonerate-2.2.0-x86_64/bin/exonerate -q /storage/tmp/jobs/dmuscipula/experiments/SLAx/maker/SLAx_merged_02_03.maker.output/SLAx_merged_02_03_datastore/AB/FC/MblContig1//theVoid.MblContig1/TR%3AA5B4F4_VITVI.for.1174-3479.0.fasta -t /storage/tmp/jobs/dmuscipula/experiments/SLAx/maker/SLAx_merged_02_03.maker.output/SLAx_merged_02_03_datastore/AB/FC/MblContig1//theVoid.MblContig1/MblContig1.1174-3479.0.fasta -Q protein -T dna -m protein2genome --softmasktarget  --percent 20 --showcigar  > /storage/tmp/jobs/dmuscipula/experiments/SLAx/maker/SLAx_merged_02_03.maker.output/SLAx_merged_02_03_datastore/AB/FC/MblContig1//theVoid.MblContig1/MblContig1.1174-3479.TR%3AA5B4F4_VITVI.p_exonerate.0
/storage/tmp/software/exonerate-2.2.0-x86_64/bin/exonerate -q /storage/tmp/jobs/dmuscipula/experiments/SLAx/maker/SLAx_merged_02_03.maker.output/SLAx_merged_02_03_datastore/AB/FC/MblContig1//theVoid.MblContig1/TR%3AA9RQS2_PHYPA.for.1141-3515.0.fasta -t /storage/tmp/jobs/dmuscipula/experiments/SLAx/maker/SLAx_merged_02_03.maker.output/SLAx_merged_02_03_datastore/AB/FC/MblContig1//theVoid.MblContig1/MblContig1.1141-3515.0.fasta -Q protein -T dna -m protein2genome --softmasktarget  --percent 20 --showcigar  > /storage/tmp/jobs/dmuscipula/experiments/SLAx/maker/SLAx_merged_02_03.maker.output/SLAx_merged_02_03_datastore/AB/FC/MblContig1//theVoid.MblContig1/MblContig1.1141-3515.TR%3AA9RQS2_PHYPA.p_exonerate.0
/storage/tmp/software/exonerate-2.2.0-x86_64/bin/exonerate -q /storage/tmp/jobs/dmuscipula/experiments/SLAx/maker/SLAx_merged_02_03.maker.output/SLAx_merged_02_03_datastore/AB/FC/MblContig1//theVoid.MblContig1/TR%3AA9RU49_PHYPA.for.1120-3518.0.fasta -t /storage/tmp/jobs/dmuscipula/experiments/SLAx/maker/SLAx_merged_02_03.maker.output/SLAx_merged_02_03_datastore/AB/FC/MblContig1//theVoid.MblContig1/MblContig1.1120-3518.0.fasta -Q protein -T dna -m protein2genome --softmasktarget  --percent 20 --showcigar  > /storage/tmp/jobs/dmuscipula/experiments/SLAx/maker/SLAx_merged_02_03.maker.output/SLAx_merged_02_03_datastore/AB/FC/MblContig1//theVoid.MblContig1/MblContig1.1120-3518.TR%3AA9RU49_PHYPA.p_exonerate.0
/storage/tmp/software/exonerate-2.2.0-x86_64/bin/exonerate -q /storage/tmp/jobs/dmuscipula/experiments/SLAx/maker/SLAx_merged_02_03.maker.output/SLAx_merged_02_03_datastore/AB/FC/MblContig1//theVoid.MblContig1/TR%3AA9SH15_PHYPA.for.1141-3518.0.fasta -t /storage/tmp/jobs/dmuscipula/experiments/SLAx/maker/SLAx_merged_02_03.maker.output/SLAx_merged_02_03_datastore/AB/FC/MblContig1//theVoid.MblContig1/MblContig1.1141-3518.0.fasta -Q protein -T dna -m protein2genome --softmasktarget  --percent 20 --showcigar  > /storage/tmp/jobs/dmuscipula/experiments/SLAx/maker/SLAx_merged_02_03.maker.output/SLAx_merged_02_03_datastore/AB/FC/MblContig1//theVoid.MblContig1/MblContig1.1141-3518.TR%3AA9SH15_PHYPA.p_exonerate.0
/storage/tmp/software/exonerate-2.2.0-x86_64/bin/exonerate -q /storage/tmp/jobs/dmuscipula/experiments/SLAx/maker/SLAx_merged_02_03.maker.output/SLAx_merged_02_03_datastore/AB/FC/MblContig1//theVoid.MblContig1/TR%3AA9TDH3_PHYPA.for.1150-3590.0.fasta -t /storage/tmp/jobs/dmuscipula/experiments/SLAx/maker/SLAx_merged_02_03.maker.output/SLAx_merged_02_03_datastore/AB/FC/MblContig1//theVoid.MblContig1/MblContig1.1150-3590.0.fasta -Q protein -T dna -m protein2genome --softmasktarget  --percent 20 --showcigar  > /storage/tmp/jobs/dmuscipula/experiments/SLAx/maker/SLAx_merged_02_03.maker.output/SLAx_merged_02_03_datastore/AB/FC/MblContig1//theVoid.MblContig1/MblContig1.1150-3590.TR%3AA9TDH3_PHYPA.p_exonerate.0
/storage/tmp/software/exonerate-2.2.0-x86_64/bin/exonerate -q /storage/tmp/jobs/dmuscipula/experiments/SLAx/maker/SLAx_merged_02_03.maker.output/SLAx_merged_02_03_datastore/AB/FC/MblContig1//theVoid.MblContig1/TR%3AB6SQ55_MAIZE.for.1162-3500.0.fasta -t /storage/tmp/jobs/dmuscipula/experiments/SLAx/maker/SLAx_merged_02_03.maker.output/SLAx_merged_02_03_datastore/AB/FC/MblContig1//theVoid.MblContig1/MblContig1.1162-3500.0.fasta -Q protein -T dna -m protein2genome --softmasktarget  --percent 20 --showcigar  > /storage/tmp/jobs/dmuscipula/experiments/SLAx/maker/SLAx_merged_02_03.maker.output/SLAx_merged_02_03_datastore/AB/FC/MblContig1//theVoid.MblContig1/MblContig1.1162-3500.TR%3AB6SQ55_MAIZE.p_exonerate.0
/storage/tmp/software/exonerate-2.2.0-x86_64/bin/exonerate -q /storage/tmp/jobs/dmuscipula/experiments/SLAx/maker/SLAx_merged_02_03.maker.output/SLAx_merged_02_03_datastore/AB/FC/MblContig1//theVoid.MblContig1/TR%3AB6SWN8_MAIZE.for.1120-3551.0.fasta -t /storage/tmp/jobs/dmuscipula/experiments/SLAx/maker/SLAx_merged_02_03.maker.output/SLAx_merged_02_03_datastore/AB/FC/MblContig1//theVoid.MblContig1/MblContig1.1120-3551.0.fasta -Q protein -T dna -m protein2genome --softmasktarget  --percent 20 --showcigar  > /storage/tmp/jobs/dmuscipula/experiments/SLAx/maker/SLAx_merged_02_03.maker.output/SLAx_merged_02_03_datastore/AB/FC/MblContig1//theVoid.MblContig1/MblContig1.1120-3551.TR%3AB6SWN8_MAIZE.p_exonerate.0
/storage/tmp/software/exonerate-2.2.0-x86_64/bin/exonerate -q /storage/tmp/jobs/dmuscipula/experiments/SLAx/maker/SLAx_merged_02_03.maker.output/SLAx_merged_02_03_datastore/AB/FC/MblContig1//theVoid.MblContig1/TR%3AB8AAY8_ORYSI.for.1132-3551.0.fasta -t /storage/tmp/jobs/dmuscipula/experiments/SLAx/maker/SLAx_merged_02_03.maker.output/SLAx_merged_02_03_datastore/AB/FC/MblContig1//theVoid.MblContig1/MblContig1.1132-3551.0.fasta -Q protein -T dna -m protein2genome --softmasktarget  --percent 20 --showcigar  > /storage/tmp/jobs/dmuscipula/experiments/SLAx/maker/SLAx_merged_02_03.maker.output/SLAx_merged_02_03_datastore/AB/FC/MblContig1//theVoid.MblContig1/MblContig1.1132-3551.TR%3AB8AAY8_ORYSI.p_exonerate.0
/storage/tmp/software/exonerate-2.2.0-x86_64/bin/exonerate -q /storage/tmp/jobs/dmuscipula/experiments/SLAx/maker/SLAx_merged_02_03.maker.output/SLAx_merged_02_03_datastore/AB/FC/MblContig1//theVoid.MblContig1/TR%3AB8B7U9_ORYSI.for.2933-3539.0.fasta -t /storage/tmp/jobs/dmuscipula/experiments/SLAx/maker/SLAx_merged_02_03.maker.output/SLAx_merged_02_03_datastore/AB/FC/MblContig1//theVoid.MblContig1/MblContig1.2933-3539.0.fasta -Q protein -T dna -m protein2genome --softmasktarget  --percent 20 --showcigar  > /storage/tmp/jobs/dmuscipula/experiments/SLAx/maker/SLAx_merged_02_03.maker.output/SLAx_merged_02_03_datastore/AB/FC/MblContig1//theVoid.MblContig1/MblContig1.2933-3539.TR%3AB8B7U9_ORYSI.p_exonerate.0
/storage/tmp/software/exonerate-2.2.0-x86_64/bin/exonerate -q /storage/tmp/jobs/dmuscipula/experiments/SLAx/maker/SLAx_merged_02_03.maker.output/SLAx_merged_02_03_datastore/AB/FC/MblContig1//theVoid.MblContig1/TR%3AB9EU69_ORYSJ.for.1132-3575.0.fasta -t /storage/tmp/jobs/dmuscipula/experiments/SLAx/maker/SLAx_merged_02_03.maker.output/SLAx_merged_02_03_datastore/AB/FC/MblContig1//theVoid.MblContig1/MblContig1.1132-3575.0.fasta -Q protein -T dna -m protein2genome --softmasktarget  --percent 20 --showcigar  > /storage/tmp/jobs/dmuscipula/experiments/SLAx/maker/SLAx_merged_02_03.maker.output/SLAx_merged_02_03_datastore/AB/FC/MblContig1//theVoid.MblContig1/MblContig1.1132-3575.TR%3AB9EU69_ORYSJ.p_exonerate.0
/storage/tmp/software/exonerate-2.2.0-x86_64/bin/exonerate -q /storage/tmp/jobs/dmuscipula/experiments/SLAx/maker/SLAx_merged_02_03.maker.output/SLAx_merged_02_03_datastore/AB/FC/MblContig1//theVoid.MblContig1/TR%3AB9EY47_ORYSJ.for.110-3584.0.fasta -t /storage/tmp/jobs/dmuscipula/experiments/SLAx/maker/SLAx_merged_02_03.maker.output/SLAx_merged_02_03_datastore/AB/FC/MblContig1//theVoid.MblContig1/MblContig1.110-3584.0.fasta -Q protein -T dna -m protein2genome --softmasktarget  --percent 20 --showcigar  > /storage/tmp/jobs/dmuscipula/experiments/SLAx/maker/SLAx_merged_02_03.maker.output/SLAx_merged_02_03_datastore/AB/FC/MblContig1//theVoid.MblContig1/MblContig1.110-3584.TR%3AB9EY47_ORYSJ.p_exonerate.0
/storage/tmp/software/exonerate-2.2.0-x86_64/bin/exonerate -q /storage/tmp/jobs/dmuscipula/experiments/SLAx/maker/SLAx_merged_02_03.maker.output/SLAx_merged_02_03_datastore/AB/FC/MblContig1//theVoid.MblContig1/TR%3AB9F0C5_ORYSJ.for.1120-1777.0.fasta -t /storage/tmp/jobs/dmuscipula/experiments/SLAx/maker/SLAx_merged_02_03.maker.output/SLAx_merged_02_03_datastore/AB/FC/MblContig1//theVoid.MblContig1/MblContig1.1120-1777.0.fasta -Q protein -T dna -m protein2genome --softmasktarget  --percent 20 --showcigar  > /storage/tmp/jobs/dmuscipula/experiments/SLAx/maker/SLAx_merged_02_03.maker.output/SLAx_merged_02_03_datastore/AB/FC/MblContig1//theVoid.MblContig1/MblContig1.1120-1777.TR%3AB9F0C5_ORYSJ.p_exonerate.0
/storage/tmp/software/exonerate-2.2.0-x86_64/bin/exonerate -q /storage/tmp/jobs/dmuscipula/experiments/SLAx/maker/SLAx_merged_02_03.maker.output/SLAx_merged_02_03_datastore/AB/FC/MblContig1//theVoid.MblContig1/TR%3AB9FIR4_ORYSJ.for.110-3612.0.fasta -t /storage/tmp/jobs/dmuscipula/experiments/SLAx/maker/SLAx_merged_02_03.maker.output/SLAx_merged_02_03_datastore/AB/FC/MblContig1//theVoid.MblContig1/MblContig1.110-3612.0.fasta -Q protein -T dna -m protein2genome --softmasktarget  --percent 20 --showcigar  > /storage/tmp/jobs/dmuscipula/experiments/SLAx/maker/SLAx_merged_02_03.maker.output/SLAx_merged_02_03_datastore/AB/FC/MblContig1//theVoid.MblContig1/MblContig1.110-3612.TR%3AB9FIR4_ORYSJ.p_exonerate.0
/storage/tmp/software/exonerate-2.2.0-x86_64/bin/exonerate -q /storage/tmp/jobs/dmuscipula/experiments/SLAx/maker/SLAx_merged_02_03.maker.output/SLAx_merged_02_03_datastore/AB/FC/MblContig1//theVoid.MblContig1/TR%3AB9FVU2_ORYSJ.for.1141-2117.0.fasta -t /storage/tmp/jobs/dmuscipula/experiments/SLAx/maker/SLAx_merged_02_03.maker.output/SLAx_merged_02_03_datastore/AB/FC/MblContig1//theVoid.MblContig1/MblContig1.1141-2117.0.fasta -Q protein -T dna -m protein2genome --softmasktarget  --percent 20 --showcigar  > /storage/tmp/jobs/dmuscipula/experiments/SLAx/maker/SLAx_merged_02_03.maker.output/SLAx_merged_02_03_datastore/AB/FC/MblContig1//theVoid.MblContig1/MblContig1.1141-2117.TR%3AB9FVU2_ORYSJ.p_exonerate.0
/storage/tmp/software/exonerate-2.2.0-x86_64/bin/exonerate -q /storage/tmp/jobs/dmuscipula/experiments/SLAx/maker/SLAx_merged_02_03.maker.output/SLAx_merged_02_03_datastore/AB/FC/MblContig1//theVoid.MblContig1/TR%3AB9FVU3_ORYSJ.for.2894-3539.0.fasta -t /storage/tmp/jobs/dmuscipula/experiments/SLAx/maker/SLAx_merged_02_03.maker.output/SLAx_merged_02_03_datastore/AB/FC/MblContig1//theVoid.MblContig1/MblContig1.2894-3539.0.fasta -Q protein -T dna -m protein2genome --softmasktarget  --percent 20 --showcigar  > /storage/tmp/jobs/dmuscipula/experiments/SLAx/maker/SLAx_merged_02_03.maker.output/SLAx_merged_02_03_datastore/AB/FC/MblContig1//theVoid.MblContig1/MblContig1.2894-3539.TR%3AB9FVU3_ORYSJ.p_exonerate.0
/storage/tmp/software/exonerate-2.2.0-x86_64/bin/exonerate -q /storage/tmp/jobs/dmuscipula/experiments/SLAx/maker/SLAx_merged_02_03.maker.output/SLAx_merged_02_03_datastore/AB/FC/MblContig1//theVoid.MblContig1/TR%3AB9I506_POPTR.for.1822-3612.0.fasta -t /storage/tmp/jobs/dmuscipula/experiments/SLAx/maker/SLAx_merged_02_03.maker.output/SLAx_merged_02_03_datastore/AB/FC/MblContig1//theVoid.MblContig1/MblContig1.1822-3612.0.fasta -Q protein -T dna -m protein2genome --softmasktarget  --percent 20 --showcigar  > /storage/tmp/jobs/dmuscipula/experiments/SLAx/maker/SLAx_merged_02_03.maker.output/SLAx_merged_02_03_datastore/AB/FC/MblContig1//theVoid.MblContig1/MblContig1.1822-3612.TR%3AB9I506_POPTR.p_exonerate.0
/storage/tmp/software/exonerate-2.2.0-x86_64/bin/exonerate -q /storage/tmp/jobs/dmuscipula/experiments/SLAx/maker/SLAx_merged_02_03.maker.output/SLAx_merged_02_03_datastore/AB/FC/MblContig1//theVoid.MblContig1/TR%3AB9N343_POPTR.for.1564-3612.0.fasta -t /storage/tmp/jobs/dmuscipula/experiments/SLAx/maker/SLAx_merged_02_03.maker.output/SLAx_merged_02_03_datastore/AB/FC/MblContig1//theVoid.MblContig1/MblContig1.1564-3612.0.fasta -Q protein -T dna -m protein2genome --softmasktarget  --percent 20 --showcigar  > /storage/tmp/jobs/dmuscipula/experiments/SLAx/maker/SLAx_merged_02_03.maker.output/SLAx_merged_02_03_datastore/AB/FC/MblContig1//theVoid.MblContig1/MblContig1.1564-3612.TR%3AB9N343_POPTR.p_exonerate.0
/storage/tmp/software/exonerate-2.2.0-x86_64/bin/exonerate -q /storage/tmp/jobs/dmuscipula/experiments/SLAx/maker/SLAx_merged_02_03.maker.output/SLAx_merged_02_03_datastore/AB/FC/MblContig1//theVoid.MblContig1/TR%3AB9N344_POPTR.for.335-1648.0.fasta -t /storage/tmp/jobs/dmuscipula/experiments/SLAx/maker/SLAx_merged_02_03.maker.output/SLAx_merged_02_03_datastore/AB/FC/MblContig1//theVoid.MblContig1/MblContig1.335-1648.0.fasta -Q protein -T dna -m protein2genome --softmasktarget  --percent 20 --showcigar  > /storage/tmp/jobs/dmuscipula/experiments/SLAx/maker/SLAx_merged_02_03.maker.output/SLAx_merged_02_03_datastore/AB/FC/MblContig1//theVoid.MblContig1/MblContig1.335-1648.TR%3AB9N344_POPTR.p_exonerate.0
/storage/tmp/software/exonerate-2.2.0-x86_64/bin/exonerate -q /storage/tmp/jobs/dmuscipula/experiments/SLAx/maker/SLAx_merged_02_03.maker.output/SLAx_merged_02_03_datastore/AB/FC/MblContig1//theVoid.MblContig1/TR%3AB9RBW3_RICCO.for.1120-3612.0.fasta -t /storage/tmp/jobs/dmuscipula/experiments/SLAx/maker/SLAx_merged_02_03.maker.output/SLAx_merged_02_03_datastore/AB/FC/MblContig1//theVoid.MblContig1/MblContig1.1120-3612.0.fasta -Q protein -T dna -m protein2genome --softmasktarget  --percent 20 --showcigar  > /storage/tmp/jobs/dmuscipula/experiments/SLAx/maker/SLAx_merged_02_03.maker.output/SLAx_merged_02_03_datastore/AB/FC/MblContig1//theVoid.MblContig1/MblContig1.1120-3612.TR%3AB9RBW3_RICCO.p_exonerate.0
/storage/tmp/software/exonerate-2.2.0-x86_64/bin/exonerate -q /storage/tmp/jobs/dmuscipula/experiments/SLAx/maker/SLAx_merged_02_03.maker.output/SLAx_merged_02_03_datastore/AB/FC/MblContig1//theVoid.MblContig1/TR%3AB9RIQ3_RICCO.for.80-3612.0.fasta -t /storage/tmp/jobs/dmuscipula/experiments/SLAx/maker/SLAx_merged_02_03.maker.output/SLAx_merged_02_03_datastore/AB/FC/MblContig1//theVoid.MblContig1/MblContig1.80-3612.0.fasta -Q protein -T dna -m protein2genome --softmasktarget  --percent 20 --showcigar  > /storage/tmp/jobs/dmuscipula/experiments/SLAx/maker/SLAx_merged_02_03.maker.output/SLAx_merged_02_03_datastore/AB/FC/MblContig1//theVoid.MblContig1/MblContig1.80-3612.TR%3AB9RIQ3_RICCO.p_exonerate.0
/storage/tmp/software/exonerate-2.2.0-x86_64/bin/exonerate -q /storage/tmp/jobs/dmuscipula/experiments/SLAx/maker/SLAx_merged_02_03.maker.output/SLAx_merged_02_03_datastore/AB/FC/MblContig1//theVoid.MblContig1/TR%3AB9SFR4_RICCO.for.1720-3518.0.fasta -t /storage/tmp/jobs/dmuscipula/experiments/SLAx/maker/SLAx_merged_02_03.maker.output/SLAx_merged_02_03_datastore/AB/FC/MblContig1//theVoid.MblContig1/MblContig1.1720-3518.0.fasta -Q protein -T dna -m protein2genome --softmasktarget  --percent 20 --showcigar  > /storage/tmp/jobs/dmuscipula/experiments/SLAx/maker/SLAx_merged_02_03.maker.output/SLAx_merged_02_03_datastore/AB/FC/MblContig1//theVoid.MblContig1/MblContig1.1720-3518.TR%3AB9SFR4_RICCO.p_exonerate.0
/storage/tmp/software/exonerate-2.2.0-x86_64/bin/exonerate -q /storage/tmp/jobs/dmuscipula/experiments/SLAx/maker/SLAx_merged_02_03.maker.output/SLAx_merged_02_03_datastore/AB/FC/MblContig1//theVoid.MblContig1/TR%3AC5XJG5_SORBI.for.1180-3542.0.fasta -t /storage/tmp/jobs/dmuscipula/experiments/SLAx/maker/SLAx_merged_02_03.maker.output/SLAx_merged_02_03_datastore/AB/FC/MblContig1//theVoid.MblContig1/MblContig1.1180-3542.0.fasta -Q protein -T dna -m protein2genome --softmasktarget  --percent 20 --showcigar  > /storage/tmp/jobs/dmuscipula/experiments/SLAx/maker/SLAx_merged_02_03.maker.output/SLAx_merged_02_03_datastore/AB/FC/MblContig1//theVoid.MblContig1/MblContig1.1180-3542.TR%3AC5XJG5_SORBI.p_exonerate.0
/storage/tmp/software/exonerate-2.2.0-x86_64/bin/exonerate -q /storage/tmp/jobs/dmuscipula/experiments/SLAx/maker/SLAx_merged_02_03.maker.output/SLAx_merged_02_03_datastore/AB/FC/MblContig1//theVoid.MblContig1/TR%3AC5XK99_SORBI.for.1342-3518.0.fasta -t /storage/tmp/jobs/dmuscipula/experiments/SLAx/maker/SLAx_merged_02_03.maker.output/SLAx_merged_02_03_datastore/AB/FC/MblContig1//theVoid.MblContig1/MblContig1.1342-3518.0.fasta -Q protein -T dna -m protein2genome --softmasktarget  --percent 20 --showcigar  > /storage/tmp/jobs/dmuscipula/experiments/SLAx/maker/SLAx_merged_02_03.maker.output/SLAx_merged_02_03_datastore/AB/FC/MblContig1//theVoid.MblContig1/MblContig1.1342-3518.TR%3AC5XK99_SORBI.p_exonerate.0
/storage/tmp/software/exonerate-2.2.0-x86_64/bin/exonerate -q /storage/tmp/jobs/dmuscipula/experiments/SLAx/maker/SLAx_merged_02_03.maker.output/SLAx_merged_02_03_datastore/AB/FC/MblContig1//theVoid.MblContig1/TR%3AC5XR65_SORBI.for.110-3578.0.fasta -t /storage/tmp/jobs/dmuscipula/experiments/SLAx/maker/SLAx_merged_02_03.maker.output/SLAx_merged_02_03_datastore/AB/FC/MblContig1//theVoid.MblContig1/MblContig1.110-3578.0.fasta -Q protein -T dna -m protein2genome --softmasktarget  --percent 20 --showcigar  > /storage/tmp/jobs/dmuscipula/experiments/SLAx/maker/SLAx_merged_02_03.maker.output/SLAx_merged_02_03_datastore/AB/FC/MblContig1//theVoid.MblContig1/MblContig1.110-3578.TR%3AC5XR65_SORBI.p_exonerate.0
/storage/tmp/software/exonerate-2.2.0-x86_64/bin/exonerate -q /storage/tmp/jobs/dmuscipula/experiments/SLAx/maker/SLAx_merged_02_03.maker.output/SLAx_merged_02_03_datastore/AB/FC/MblContig1//theVoid.MblContig1/TR%3AC5Y2R5_SORBI.for.1159-3536.0.fasta -t /storage/tmp/jobs/dmuscipula/experiments/SLAx/maker/SLAx_merged_02_03.maker.output/SLAx_merged_02_03_datastore/AB/FC/MblContig1//theVoid.MblContig1/MblContig1.1159-3536.0.fasta -Q protein -T dna -m protein2genome --softmasktarget  --percent 20 --showcigar  > /storage/tmp/jobs/dmuscipula/experiments/SLAx/maker/SLAx_merged_02_03.maker.output/SLAx_merged_02_03_datastore/AB/FC/MblContig1//theVoid.MblContig1/MblContig1.1159-3536.TR%3AC5Y2R5_SORBI.p_exonerate.0
/storage/tmp/software/exonerate-2.2.0-x86_64/bin/exonerate -q /storage/tmp/jobs/dmuscipula/experiments/SLAx/maker/SLAx_merged_02_03.maker.output/SLAx_merged_02_03_datastore/AB/FC/MblContig1//theVoid.MblContig1/TR%3AC5YEF3_SORBI.for.1120-3518.0.fasta -t /storage/tmp/jobs/dmuscipula/experiments/SLAx/maker/SLAx_merged_02_03.maker.output/SLAx_merged_02_03_datastore/AB/FC/MblContig1//theVoid.MblContig1/MblContig1.1120-3518.0.fasta -Q protein -T dna -m protein2genome --softmasktarget  --percent 20 --showcigar  > /storage/tmp/jobs/dmuscipula/experiments/SLAx/maker/SLAx_merged_02_03.maker.output/SLAx_merged_02_03_datastore/AB/FC/MblContig1//theVoid.MblContig1/MblContig1.1120-3518.TR%3AC5YEF3_SORBI.p_exonerate.0
/storage/tmp/software/exonerate-2.2.0-x86_64/bin/exonerate -q /storage/tmp/jobs/dmuscipula/experiments/SLAx/maker/SLAx_merged_02_03.maker.output/SLAx_merged_02_03_datastore/AB/FC/MblContig1//theVoid.MblContig1/TR%3AC5YN44_SORBI.for.1120-3551.0.fasta -t /storage/tmp/jobs/dmuscipula/experiments/SLAx/maker/SLAx_merged_02_03.maker.output/SLAx_merged_02_03_datastore/AB/FC/MblContig1//theVoid.MblContig1/MblContig1.1120-3551.0.fasta -Q protein -T dna -m protein2genome --softmasktarget  --percent 20 --showcigar  > /storage/tmp/jobs/dmuscipula/experiments/SLAx/maker/SLAx_merged_02_03.maker.output/SLAx_merged_02_03_datastore/AB/FC/MblContig1//theVoid.MblContig1/MblContig1.1120-3551.TR%3AC5YN44_SORBI.p_exonerate.0
/storage/tmp/software/exonerate-2.2.0-x86_64/bin/exonerate -q /storage/tmp/jobs/dmuscipula/experiments/SLAx/maker/SLAx_merged_02_03.maker.output/SLAx_merged_02_03_datastore/AB/FC/MblContig1//theVoid.MblContig1/TR%3AC5YUS9_SORBI.for.1120-3536.0.fasta -t /storage/tmp/jobs/dmuscipula/experiments/SLAx/maker/SLAx_merged_02_03.maker.output/SLAx_merged_02_03_datastore/AB/FC/MblContig1//theVoid.MblContig1/MblContig1.1120-3536.0.fasta -Q protein -T dna -m protein2genome --softmasktarget  --percent 20 --showcigar  > /storage/tmp/jobs/dmuscipula/experiments/SLAx/maker/SLAx_merged_02_03.maker.output/SLAx_merged_02_03_datastore/AB/FC/MblContig1//theVoid.MblContig1/MblContig1.1120-3536.TR%3AC5YUS9_SORBI.p_exonerate.0
/storage/tmp/software/exonerate-2.2.0-x86_64/bin/exonerate -q /storage/tmp/jobs/dmuscipula/experiments/SLAx/maker/SLAx_merged_02_03.maker.output/SLAx_merged_02_03_datastore/AB/FC/MblContig1//theVoid.MblContig1/TR%3AC5YWJ1_SORBI.for.32-3527.0.fasta -t /storage/tmp/jobs/dmuscipula/experiments/SLAx/maker/SLAx_merged_02_03.maker.output/SLAx_merged_02_03_datastore/AB/FC/MblContig1//theVoid.MblContig1/MblContig1.32-3527.0.fasta -Q protein -T dna -m protein2genome --softmasktarget  --percent 20 --showcigar  > /storage/tmp/jobs/dmuscipula/experiments/SLAx/maker/SLAx_merged_02_03.maker.output/SLAx_merged_02_03_datastore/AB/FC/MblContig1//theVoid.MblContig1/MblContig1.32-3527.TR%3AC5YWJ1_SORBI.p_exonerate.0
/storage/tmp/software/exonerate-2.2.0-x86_64/bin/exonerate -q /storage/tmp/jobs/dmuscipula/experiments/SLAx/maker/SLAx_merged_02_03.maker.output/SLAx_merged_02_03_datastore/AB/FC/MblContig1//theVoid.MblContig1/TR%3AC5YWJ2_SORBI.for.41-3527.0.fasta -t /storage/tmp/jobs/dmuscipula/experiments/SLAx/maker/SLAx_merged_02_03.maker.output/SLAx_merged_02_03_datastore/AB/FC/MblContig1//theVoid.MblContig1/MblContig1.41-3527.0.fasta -Q protein -T dna -m protein2genome --softmasktarget  --percent 20 --showcigar  > /storage/tmp/jobs/dmuscipula/experiments/SLAx/maker/SLAx_merged_02_03.maker.output/SLAx_merged_02_03_datastore/AB/FC/MblContig1//theVoid.MblContig1/MblContig1.41-3527.TR%3AC5YWJ2_SORBI.p_exonerate.0
/storage/tmp/software/exonerate-2.2.0-x86_64/bin/exonerate -q /storage/tmp/jobs/dmuscipula/experiments/SLAx/maker/SLAx_merged_02_03.maker.output/SLAx_merged_02_03_datastore/AB/FC/MblContig1//theVoid.MblContig1/TR%3AC5YWJ3_SORBI.for.1120-3527.0.fasta -t /storage/tmp/jobs/dmuscipula/experiments/SLAx/maker/SLAx_merged_02_03.maker.output/SLAx_merged_02_03_datastore/AB/FC/MblContig1//theVoid.MblContig1/MblContig1.1120-3527.0.fasta -Q protein -T dna -m protein2genome --softmasktarget  --percent 20 --showcigar  > /storage/tmp/jobs/dmuscipula/experiments/SLAx/maker/SLAx_merged_02_03.maker.output/SLAx_merged_02_03_datastore/AB/FC/MblContig1//theVoid.MblContig1/MblContig1.1120-3527.TR%3AC5YWJ3_SORBI.p_exonerate.0
/storage/tmp/software/exonerate-2.2.0-x86_64/bin/exonerate -q /storage/tmp/jobs/dmuscipula/experiments/SLAx/maker/SLAx_merged_02_03.maker.output/SLAx_merged_02_03_datastore/AB/FC/MblContig1//theVoid.MblContig1/TR%3AC5YZG0_SORBI.for.365-3530.0.fasta -t /storage/tmp/jobs/dmuscipula/experiments/SLAx/maker/SLAx_merged_02_03.maker.output/SLAx_merged_02_03_datastore/AB/FC/MblContig1//theVoid.MblContig1/MblContig1.365-3530.0.fasta -Q protein -T dna -m protein2genome --softmasktarget  --percent 20 --showcigar  > /storage/tmp/jobs/dmuscipula/experiments/SLAx/maker/SLAx_merged_02_03.maker.output/SLAx_merged_02_03_datastore/AB/FC/MblContig1//theVoid.MblContig1/MblContig1.365-3530.TR%3AC5YZG0_SORBI.p_exonerate.0
/storage/tmp/software/exonerate-2.2.0-x86_64/bin/exonerate -q /storage/tmp/jobs/dmuscipula/experiments/SLAx/maker/SLAx_merged_02_03.maker.output/SLAx_merged_02_03_datastore/AB/FC/MblContig1//theVoid.MblContig1/TR%3AC7IXE7_ORYSJ.for.2897-3500.0.fasta -t /storage/tmp/jobs/dmuscipula/experiments/SLAx/maker/SLAx_merged_02_03.maker.output/SLAx_merged_02_03_datastore/AB/FC/MblContig1//theVoid.MblContig1/MblContig1.2897-3500.0.fasta -Q protein -T dna -m protein2genome --softmasktarget  --percent 20 --showcigar  > /storage/tmp/jobs/dmuscipula/experiments/SLAx/maker/SLAx_merged_02_03.maker.output/SLAx_merged_02_03_datastore/AB/FC/MblContig1//theVoid.MblContig1/MblContig1.2897-3500.TR%3AC7IXE7_ORYSJ.p_exonerate.0
/storage/tmp/software/exonerate-2.2.0-x86_64/bin/exonerate -q /storage/tmp/jobs/dmuscipula/experiments/SLAx/maker/SLAx_merged_02_03.maker.output/SLAx_merged_02_03_datastore/AB/FC/MblContig1//theVoid.MblContig1/TR%3AD2U834_9ROSI.for.1168-3536.0.fasta -t /storage/tmp/jobs/dmuscipula/experiments/SLAx/maker/SLAx_merged_02_03.maker.output/SLAx_merged_02_03_datastore/AB/FC/MblContig1//theVoid.MblContig1/MblContig1.1168-3536.0.fasta -Q protein -T dna -m protein2genome --softmasktarget  --percent 20 --showcigar  > /storage/tmp/jobs/dmuscipula/experiments/SLAx/maker/SLAx_merged_02_03.maker.output/SLAx_merged_02_03_datastore/AB/FC/MblContig1//theVoid.MblContig1/MblContig1.1168-3536.TR%3AD2U834_9ROSI.p_exonerate.0
/storage/tmp/software/exonerate-2.2.0-x86_64/bin/exonerate -q /storage/tmp/jobs/dmuscipula/experiments/SLAx/maker/SLAx_merged_02_03.maker.output/SLAx_merged_02_03_datastore/AB/FC/MblContig1//theVoid.MblContig1/TR%3AD7KND2_ARALL.for.1120-3518.0.fasta -t /storage/tmp/jobs/dmuscipula/experiments/SLAx/maker/SLAx_merged_02_03.maker.output/SLAx_merged_02_03_datastore/AB/FC/MblContig1//theVoid.MblContig1/MblContig1.1120-3518.0.fasta -Q protein -T dna -m protein2genome --softmasktarget  --percent 20 --showcigar  > /storage/tmp/jobs/dmuscipula/experiments/SLAx/maker/SLAx_merged_02_03.maker.output/SLAx_merged_02_03_datastore/AB/FC/MblContig1//theVoid.MblContig1/MblContig1.1120-3518.TR%3AD7KND2_ARALL.p_exonerate.0
/storage/tmp/software/exonerate-2.2.0-x86_64/bin/exonerate -q /storage/tmp/jobs/dmuscipula/experiments/SLAx/maker/SLAx_merged_02_03.maker.output/SLAx_merged_02_03_datastore/AB/FC/MblContig1//theVoid.MblContig1/TR%3AD7M2F7_ARALL.for.344-3612.0.fasta -t /storage/tmp/jobs/dmuscipula/experiments/SLAx/maker/SLAx_merged_02_03.maker.output/SLAx_merged_02_03_datastore/AB/FC/MblContig1//theVoid.MblContig1/MblContig1.344-3612.0.fasta -Q protein -T dna -m protein2genome --softmasktarget  --percent 20 --showcigar  > /storage/tmp/jobs/dmuscipula/experiments/SLAx/maker/SLAx_merged_02_03.maker.output/SLAx_merged_02_03_datastore/AB/FC/MblContig1//theVoid.MblContig1/MblContig1.344-3612.TR%3AD7M2F7_ARALL.p_exonerate.0
/storage/tmp/software/exonerate-2.2.0-x86_64/bin/exonerate -q /storage/tmp/jobs/dmuscipula/experiments/SLAx/maker/SLAx_merged_02_03.maker.output/SLAx_merged_02_03_datastore/AB/FC/MblContig1//theVoid.MblContig1/TR%3AD7MDP9_ARALL.for.236-3612.0.fasta -t /storage/tmp/jobs/dmuscipula/experiments/SLAx/maker/SLAx_merged_02_03.maker.output/SLAx_merged_02_03_datastore/AB/FC/MblContig1//theVoid.MblContig1/MblContig1.236-3612.0.fasta -Q protein -T dna -m protein2genome --softmasktarget  --percent 20 --showcigar  > /storage/tmp/jobs/dmuscipula/experiments/SLAx/maker/SLAx_merged_02_03.maker.output/SLAx_merged_02_03_datastore/AB/FC/MblContig1//theVoid.MblContig1/MblContig1.236-3612.TR%3AD7MDP9_ARALL.p_exonerate.0
/storage/tmp/software/exonerate-2.2.0-x86_64/bin/exonerate -q /storage/tmp/jobs/dmuscipula/experiments/SLAx/maker/SLAx_merged_02_03.maker.output/SLAx_merged_02_03_datastore/AB/FC/MblContig1//theVoid.MblContig1/TR%3AD7TWC1_VITVI.for.1120-3518.0.fasta -t /storage/tmp/jobs/dmuscipula/experiments/SLAx/maker/SLAx_merged_02_03.maker.output/SLAx_merged_02_03_datastore/AB/FC/MblContig1//theVoid.MblContig1/MblContig1.1120-3518.0.fasta -Q protein -T dna -m protein2genome --softmasktarget  --percent 20 --showcigar  > /storage/tmp/jobs/dmuscipula/experiments/SLAx/maker/SLAx_merged_02_03.maker.output/SLAx_merged_02_03_datastore/AB/FC/MblContig1//theVoid.MblContig1/MblContig1.1120-3518.TR%3AD7TWC1_VITVI.p_exonerate.0
/storage/tmp/software/exonerate-2.2.0-x86_64/bin/exonerate -q /storage/tmp/jobs/dmuscipula/experiments/SLAx/maker/SLAx_merged_02_03.maker.output/SLAx_merged_02_03_datastore/AB/FC/MblContig1//theVoid.MblContig1/TR%3AD8R497_SELML.for.1120-3518.0.fasta -t /storage/tmp/jobs/dmuscipula/experiments/SLAx/maker/SLAx_merged_02_03.maker.output/SLAx_merged_02_03_datastore/AB/FC/MblContig1//theVoid.MblContig1/MblContig1.1120-3518.0.fasta -Q protein -T dna -m protein2genome --softmasktarget  --percent 20 --showcigar  > /storage/tmp/jobs/dmuscipula/experiments/SLAx/maker/SLAx_merged_02_03.maker.output/SLAx_merged_02_03_datastore/AB/FC/MblContig1//theVoid.MblContig1/MblContig1.1120-3518.TR%3AD8R497_SELML.p_exonerate.0
/storage/tmp/software/exonerate-2.2.0-x86_64/bin/exonerate -q /storage/tmp/jobs/dmuscipula/experiments/SLAx/maker/SLAx_merged_02_03.maker.output/SLAx_merged_02_03_datastore/AB/FC/MblContig1//theVoid.MblContig1/TR%3AD8RQR2_SELML.for.1120-3518.0.fasta -t /storage/tmp/jobs/dmuscipula/experiments/SLAx/maker/SLAx_merged_02_03.maker.output/SLAx_merged_02_03_datastore/AB/FC/MblContig1//theVoid.MblContig1/MblContig1.1120-3518.0.fasta -Q protein -T dna -m protein2genome --softmasktarget  --percent 20 --showcigar  > /storage/tmp/jobs/dmuscipula/experiments/SLAx/maker/SLAx_merged_02_03.maker.output/SLAx_merged_02_03_datastore/AB/FC/MblContig1//theVoid.MblContig1/MblContig1.1120-3518.TR%3AD8RQR2_SELML.p_exonerate.0
/storage/tmp/software/exonerate-2.2.0-x86_64/bin/exonerate -q /storage/tmp/jobs/dmuscipula/experiments/SLAx/maker/SLAx_merged_02_03.maker.output/SLAx_merged_02_03_datastore/AB/FC/MblContig1//theVoid.MblContig1/TR%3AD8S028_SELML.for.1120-3518.0.fasta -t /storage/tmp/jobs/dmuscipula/experiments/SLAx/maker/SLAx_merged_02_03.maker.output/SLAx_merged_02_03_datastore/AB/FC/MblContig1//theVoid.MblContig1/MblContig1.1120-3518.0.fasta -Q protein -T dna -m protein2genome --softmasktarget  --percent 20 --showcigar  > /storage/tmp/jobs/dmuscipula/experiments/SLAx/maker/SLAx_merged_02_03.maker.output/SLAx_merged_02_03_datastore/AB/FC/MblContig1//theVoid.MblContig1/MblContig1.1120-3518.TR%3AD8S028_SELML.p_exonerate.0
/storage/tmp/software/exonerate-2.2.0-x86_64/bin/exonerate -q /storage/tmp/jobs/dmuscipula/experiments/SLAx/maker/SLAx_merged_02_03.maker.output/SLAx_merged_02_03_datastore/AB/FC/MblContig1//theVoid.MblContig1/TR%3AD8S5U7_SELML.for.1141-3521.0.fasta -t /storage/tmp/jobs/dmuscipula/experiments/SLAx/maker/SLAx_merged_02_03.maker.output/SLAx_merged_02_03_datastore/AB/FC/MblContig1//theVoid.MblContig1/MblContig1.1141-3521.0.fasta -Q protein -T dna -m protein2genome --softmasktarget  --percent 20 --showcigar  > /storage/tmp/jobs/dmuscipula/experiments/SLAx/maker/SLAx_merged_02_03.maker.output/SLAx_merged_02_03_datastore/AB/FC/MblContig1//theVoid.MblContig1/MblContig1.1141-3521.TR%3AD8S5U7_SELML.p_exonerate.0
/storage/tmp/software/exonerate-2.2.0-x86_64/bin/exonerate -q /storage/tmp/jobs/dmuscipula/experiments/SLAx/maker/SLAx_merged_02_03.maker.output/SLAx_merged_02_03_datastore/AB/FC/MblContig1//theVoid.MblContig1/TR%3AD8SMW1_SELML.for.1141-3521.0.fasta -t /storage/tmp/jobs/dmuscipula/experiments/SLAx/maker/SLAx_merged_02_03.maker.output/SLAx_merged_02_03_datastore/AB/FC/MblContig1//theVoid.MblContig1/MblContig1.1141-3521.0.fasta -Q protein -T dna -m protein2genome --softmasktarget  --percent 20 --showcigar  > /storage/tmp/jobs/dmuscipula/experiments/SLAx/maker/SLAx_merged_02_03.maker.output/SLAx_merged_02_03_datastore/AB/FC/MblContig1//theVoid.MblContig1/MblContig1.1141-3521.TR%3AD8SMW1_SELML.p_exonerate.0
/storage/tmp/software/exonerate-2.2.0-x86_64/bin/exonerate -q /storage/tmp/jobs/dmuscipula/experiments/SLAx/maker/SLAx_merged_02_03.maker.output/SLAx_merged_02_03_datastore/AB/FC/MblContig1//theVoid.MblContig1/TR%3AD8SQB3_SELML.for.1150-3521.0.fasta -t /storage/tmp/jobs/dmuscipula/experiments/SLAx/maker/SLAx_merged_02_03.maker.output/SLAx_merged_02_03_datastore/AB/FC/MblContig1//theVoid.MblContig1/MblContig1.1150-3521.0.fasta -Q protein -T dna -m protein2genome --softmasktarget  --percent 20 --showcigar  > /storage/tmp/jobs/dmuscipula/experiments/SLAx/maker/SLAx_merged_02_03.maker.output/SLAx_merged_02_03_datastore/AB/FC/MblContig1//theVoid.MblContig1/MblContig1.1150-3521.TR%3AD8SQB3_SELML.p_exonerate.0
/storage/tmp/software/exonerate-2.2.0-x86_64/bin/exonerate -q /storage/tmp/jobs/dmuscipula/experiments/SLAx/maker/SLAx_merged_02_03.maker.output/SLAx_merged_02_03_datastore/AB/FC/MblContig1//theVoid.MblContig1/TR%3AD8SUM0_SELML.for.1150-3542.0.fasta -t /storage/tmp/jobs/dmuscipula/experiments/SLAx/maker/SLAx_merged_02_03.maker.output/SLAx_merged_02_03_datastore/AB/FC/MblContig1//theVoid.MblContig1/MblContig1.1150-3542.0.fasta -Q protein -T dna -m protein2genome --softmasktarget  --percent 20 --showcigar  > /storage/tmp/jobs/dmuscipula/experiments/SLAx/maker/SLAx_merged_02_03.maker.output/SLAx_merged_02_03_datastore/AB/FC/MblContig1//theVoid.MblContig1/MblContig1.1150-3542.TR%3AD8SUM0_SELML.p_exonerate.0
/storage/tmp/software/exonerate-2.2.0-x86_64/bin/exonerate -q /storage/tmp/jobs/dmuscipula/experiments/SLAx/maker/SLAx_merged_02_03.maker.output/SLAx_merged_02_03_datastore/AB/FC/MblContig1//theVoid.MblContig1/TR%3AE0CUQ2_VITVI.for.1-3612.0.fasta -t /storage/tmp/jobs/dmuscipula/experiments/SLAx/maker/SLAx_merged_02_03.maker.output/SLAx_merged_02_03_datastore/AB/FC/MblContig1//theVoid.MblContig1/MblContig1.1-3612.0.fasta -Q protein -T dna -m protein2genome --softmasktarget  --percent 20 --showcigar  > /storage/tmp/jobs/dmuscipula/experiments/SLAx/maker/SLAx_merged_02_03.maker.output/SLAx_merged_02_03_datastore/AB/FC/MblContig1//theVoid.MblContig1/MblContig1.1-3612.TR%3AE0CUQ2_VITVI.p_exonerate.0
/storage/tmp/software/exonerate-2.2.0-x86_64/bin/exonerate -q /storage/tmp/jobs/dmuscipula/experiments/SLAx/maker/SLAx_merged_02_03.maker.output/SLAx_merged_02_03_datastore/AB/FC/MblContig1//theVoid.MblContig1/TR%3AE5FYR7_BRARC.for.1120-3521.0.fasta -t /storage/tmp/jobs/dmuscipula/experiments/SLAx/maker/SLAx_merged_02_03.maker.output/SLAx_merged_02_03_datastore/AB/FC/MblContig1//theVoid.MblContig1/MblContig1.1120-3521.0.fasta -Q protein -T dna -m protein2genome --softmasktarget  --percent 20 --showcigar  > /storage/tmp/jobs/dmuscipula/experiments/SLAx/maker/SLAx_merged_02_03.maker.output/SLAx_merged_02_03_datastore/AB/FC/MblContig1//theVoid.MblContig1/MblContig1.1120-3521.TR%3AE5FYR7_BRARC.p_exonerate.0
/storage/tmp/software/exonerate-2.2.0-x86_64/bin/exonerate -q /storage/tmp/jobs/dmuscipula/experiments/SLAx/maker/SLAx_merged_02_03.maker.output/SLAx_merged_02_03_datastore/AB/FC/MblContig1//theVoid.MblContig1/TR%3AE5GBD8_CUCME.for.119-3612.0.fasta -t /storage/tmp/jobs/dmuscipula/experiments/SLAx/maker/SLAx_merged_02_03.maker.output/SLAx_merged_02_03_datastore/AB/FC/MblContig1//theVoid.MblContig1/MblContig1.119-3612.0.fasta -Q protein -T dna -m protein2genome --softmasktarget  --percent 20 --showcigar  > /storage/tmp/jobs/dmuscipula/experiments/SLAx/maker/SLAx_merged_02_03.maker.output/SLAx_merged_02_03_datastore/AB/FC/MblContig1//theVoid.MblContig1/MblContig1.119-3612.TR%3AE5GBD8_CUCME.p_exonerate.0
/storage/tmp/software/exonerate-2.2.0-x86_64/bin/exonerate -q /storage/tmp/jobs/dmuscipula/experiments/SLAx/maker/SLAx_merged_02_03.maker.output/SLAx_merged_02_03_datastore/AB/FC/MblContig1//theVoid.MblContig1/TR%3AE6NU71_9ROSI.for.1180-3530.0.fasta -t /storage/tmp/jobs/dmuscipula/experiments/SLAx/maker/SLAx_merged_02_03.maker.output/SLAx_merged_02_03_datastore/AB/FC/MblContig1//theVoid.MblContig1/MblContig1.1180-3530.0.fasta -Q protein -T dna -m protein2genome --softmasktarget  --percent 20 --showcigar  > /storage/tmp/jobs/dmuscipula/experiments/SLAx/maker/SLAx_merged_02_03.maker.output/SLAx_merged_02_03_datastore/AB/FC/MblContig1//theVoid.MblContig1/MblContig1.1180-3530.TR%3AE6NU71_9ROSI.p_exonerate.0
/storage/tmp/software/exonerate-2.2.0-x86_64/bin/exonerate -q /storage/tmp/jobs/dmuscipula/experiments/SLAx/maker/SLAx_merged_02_03.maker.output/SLAx_merged_02_03_datastore/AB/FC/MblContig1//theVoid.MblContig1/TR%3AF2DB49_HORVD.for.110-3578.0.fasta -t /storage/tmp/jobs/dmuscipula/experiments/SLAx/maker/SLAx_merged_02_03.maker.output/SLAx_merged_02_03_datastore/AB/FC/MblContig1//theVoid.MblContig1/MblContig1.110-3578.0.fasta -Q protein -T dna -m protein2genome --softmasktarget  --percent 20 --showcigar  > /storage/tmp/jobs/dmuscipula/experiments/SLAx/maker/SLAx_merged_02_03.maker.output/SLAx_merged_02_03_datastore/AB/FC/MblContig1//theVoid.MblContig1/MblContig1.110-3578.TR%3AF2DB49_HORVD.p_exonerate.0
/storage/tmp/software/exonerate-2.2.0-x86_64/bin/exonerate -q /storage/tmp/jobs/dmuscipula/experiments/SLAx/maker/SLAx_merged_02_03.maker.output/SLAx_merged_02_03_datastore/AB/FC/MblContig1//theVoid.MblContig1/TR%3AF2DVZ2_HORVD.for.1120-3536.0.fasta -t /storage/tmp/jobs/dmuscipula/experiments/SLAx/maker/SLAx_merged_02_03.maker.output/SLAx_merged_02_03_datastore/AB/FC/MblContig1//theVoid.MblContig1/MblContig1.1120-3536.0.fasta -Q protein -T dna -m protein2genome --softmasktarget  --percent 20 --showcigar  > /storage/tmp/jobs/dmuscipula/experiments/SLAx/maker/SLAx_merged_02_03.maker.output/SLAx_merged_02_03_datastore/AB/FC/MblContig1//theVoid.MblContig1/MblContig1.1120-3536.TR%3AF2DVZ2_HORVD.p_exonerate.0
/storage/tmp/software/exonerate-2.2.0-x86_64/bin/exonerate -q /storage/tmp/jobs/dmuscipula/experiments/SLAx/maker/SLAx_merged_02_03.maker.output/SLAx_merged_02_03_datastore/AB/FC/MblContig1//theVoid.MblContig1/TR%3AF2EEJ5_HORVD.for.1120-3533.0.fasta -t /storage/tmp/jobs/dmuscipula/experiments/SLAx/maker/SLAx_merged_02_03.maker.output/SLAx_merged_02_03_datastore/AB/FC/MblContig1//theVoid.MblContig1/MblContig1.1120-3533.0.fasta -Q protein -T dna -m protein2genome --softmasktarget  --percent 20 --showcigar  > /storage/tmp/jobs/dmuscipula/experiments/SLAx/maker/SLAx_merged_02_03.maker.output/SLAx_merged_02_03_datastore/AB/FC/MblContig1//theVoid.MblContig1/MblContig1.1120-3533.TR%3AF2EEJ5_HORVD.p_exonerate.0
/storage/tmp/software/exonerate-2.2.0-x86_64/bin/exonerate -q /storage/tmp/jobs/dmuscipula/experiments/SLAx/maker/SLAx_merged_02_03.maker.output/SLAx_merged_02_03_datastore/AB/FC/MblContig1//theVoid.MblContig1/TR%3AF6GZQ2_VITVI.for.1180-2308.0.fasta -t /storage/tmp/jobs/dmuscipula/experiments/SLAx/maker/SLAx_merged_02_03.maker.output/SLAx_merged_02_03_datastore/AB/FC/MblContig1//theVoid.MblContig1/MblContig1.1180-2308.0.fasta -Q protein -T dna -m protein2genome --softmasktarget  --percent 20 --showcigar  > /storage/tmp/jobs/dmuscipula/experiments/SLAx/maker/SLAx_merged_02_03.maker.output/SLAx_merged_02_03_datastore/AB/FC/MblContig1//theVoid.MblContig1/MblContig1.1180-2308.TR%3AF6GZQ2_VITVI.p_exonerate.0
/storage/tmp/software/exonerate-2.2.0-x86_64/bin/exonerate -q /storage/tmp/jobs/dmuscipula/experiments/SLAx/maker/SLAx_merged_02_03.maker.output/SLAx_merged_02_03_datastore/AB/FC/MblContig1//theVoid.MblContig1/TR%3AF6GZQ3_VITVI.for.2897-3500.0.fasta -t /storage/tmp/jobs/dmuscipula/experiments/SLAx/maker/SLAx_merged_02_03.maker.output/SLAx_merged_02_03_datastore/AB/FC/MblContig1//theVoid.MblContig1/MblContig1.2897-3500.0.fasta -Q protein -T dna -m protein2genome --softmasktarget  --percent 20 --showcigar  > /storage/tmp/jobs/dmuscipula/experiments/SLAx/maker/SLAx_merged_02_03.maker.output/SLAx_merged_02_03_datastore/AB/FC/MblContig1//theVoid.MblContig1/MblContig1.2897-3500.TR%3AF6GZQ3_VITVI.p_exonerate.0
/storage/tmp/software/exonerate-2.2.0-x86_64/bin/exonerate -q /storage/tmp/jobs/dmuscipula/experiments/SLAx/maker/SLAx_merged_02_03.maker.output/SLAx_merged_02_03_datastore/AB/FC/MblContig1//theVoid.MblContig1/TR%3AF6H7H3_VITVI.for.1144-3500.0.fasta -t /storage/tmp/jobs/dmuscipula/experiments/SLAx/maker/SLAx_merged_02_03.maker.output/SLAx_merged_02_03_datastore/AB/FC/MblContig1//theVoid.MblContig1/MblContig1.1144-3500.0.fasta -Q protein -T dna -m protein2genome --softmasktarget  --percent 20 --showcigar  > /storage/tmp/jobs/dmuscipula/experiments/SLAx/maker/SLAx_merged_02_03.maker.output/SLAx_merged_02_03_datastore/AB/FC/MblContig1//theVoid.MblContig1/MblContig1.1144-3500.TR%3AF6H7H3_VITVI.p_exonerate.0
/storage/tmp/software/exonerate-2.2.0-x86_64/bin/exonerate -q /storage/tmp/jobs/dmuscipula/experiments/SLAx/maker/SLAx_merged_02_03.maker.output/SLAx_merged_02_03_datastore/AB/FC/MblContig1//theVoid.MblContig1/TR%3AF6HIC6_VITVI.for.1174-3479.0.fasta -t /storage/tmp/jobs/dmuscipula/experiments/SLAx/maker/SLAx_merged_02_03.maker.output/SLAx_merged_02_03_datastore/AB/FC/MblContig1//theVoid.MblContig1/MblContig1.1174-3479.0.fasta -Q protein -T dna -m protein2genome --softmasktarget  --percent 20 --showcigar  > /storage/tmp/jobs/dmuscipula/experiments/SLAx/maker/SLAx_merged_02_03.maker.output/SLAx_merged_02_03_datastore/AB/FC/MblContig1//theVoid.MblContig1/MblContig1.1174-3479.TR%3AF6HIC6_VITVI.p_exonerate.0
/storage/tmp/software/exonerate-2.2.0-x86_64/bin/exonerate -q /storage/tmp/jobs/dmuscipula/experiments/SLAx/maker/SLAx_merged_02_03.maker.output/SLAx_merged_02_03_datastore/AB/FC/MblContig1//theVoid.MblContig1/TR%3AG7JEQ3_MEDTR.for.1204-3467.0.fasta -t /storage/tmp/jobs/dmuscipula/experiments/SLAx/maker/SLAx_merged_02_03.maker.output/SLAx_merged_02_03_datastore/AB/FC/MblContig1//theVoid.MblContig1/MblContig1.1204-3467.0.fasta -Q protein -T dna -m protein2genome --softmasktarget  --percent 20 --showcigar  > /storage/tmp/jobs/dmuscipula/experiments/SLAx/maker/SLAx_merged_02_03.maker.output/SLAx_merged_02_03_datastore/AB/FC/MblContig1//theVoid.MblContig1/MblContig1.1204-3467.TR%3AG7JEQ3_MEDTR.p_exonerate.0
/storage/tmp/software/exonerate-2.2.0-x86_64/bin/exonerate -q /storage/tmp/jobs/dmuscipula/experiments/SLAx/maker/SLAx_merged_02_03.maker.output/SLAx_merged_02_03_datastore/AB/FC/MblContig1//theVoid.MblContig1/TR%3AG7JK66_MEDTR.for.1120-3518.0.fasta -t /storage/tmp/jobs/dmuscipula/experiments/SLAx/maker/SLAx_merged_02_03.maker.output/SLAx_merged_02_03_datastore/AB/FC/MblContig1//theVoid.MblContig1/MblContig1.1120-3518.0.fasta -Q protein -T dna -m protein2genome --softmasktarget  --percent 20 --showcigar  > /storage/tmp/jobs/dmuscipula/experiments/SLAx/maker/SLAx_merged_02_03.maker.output/SLAx_merged_02_03_datastore/AB/FC/MblContig1//theVoid.MblContig1/MblContig1.1120-3518.TR%3AG7JK66_MEDTR.p_exonerate.0
/storage/tmp/software/exonerate-2.2.0-x86_64/bin/exonerate -q /storage/tmp/jobs/dmuscipula/experiments/SLAx/maker/SLAx_merged_02_03.maker.output/SLAx_merged_02_03_datastore/AB/FC/MblContig1//theVoid.MblContig1/TR%3AG7KJM6_MEDTR.for.110-3612.0.fasta -t /storage/tmp/jobs/dmuscipula/experiments/SLAx/maker/SLAx_merged_02_03.maker.output/SLAx_merged_02_03_datastore/AB/FC/MblContig1//theVoid.MblContig1/MblContig1.110-3612.0.fasta -Q protein -T dna -m protein2genome --softmasktarget  --percent 20 --showcigar  > /storage/tmp/jobs/dmuscipula/experiments/SLAx/maker/SLAx_merged_02_03.maker.output/SLAx_merged_02_03_datastore/AB/FC/MblContig1//theVoid.MblContig1/MblContig1.110-3612.TR%3AG7KJM6_MEDTR.p_exonerate.0
/storage/tmp/software/exonerate-2.2.0-x86_64/bin/exonerate -q /storage/tmp/jobs/dmuscipula/experiments/SLAx/maker/SLAx_merged_02_03.maker.output/SLAx_merged_02_03_datastore/AB/FC/MblContig1//theVoid.MblContig1/TR%3AG7KK21_MEDTR.for.110-3612.0.fasta -t /storage/tmp/jobs/dmuscipula/experiments/SLAx/maker/SLAx_merged_02_03.maker.output/SLAx_merged_02_03_datastore/AB/FC/MblContig1//theVoid.MblContig1/MblContig1.110-3612.0.fasta -Q protein -T dna -m protein2genome --softmasktarget  --percent 20 --showcigar  > /storage/tmp/jobs/dmuscipula/experiments/SLAx/maker/SLAx_merged_02_03.maker.output/SLAx_merged_02_03_datastore/AB/FC/MblContig1//theVoid.MblContig1/MblContig1.110-3612.TR%3AG7KK21_MEDTR.p_exonerate.0
/storage/tmp/software/exonerate-2.2.0-x86_64/bin/exonerate -q /storage/tmp/jobs/dmuscipula/experiments/SLAx/maker/SLAx_merged_02_03.maker.output/SLAx_merged_02_03_datastore/AB/FC/MblContig1//theVoid.MblContig1/TR%3AG7KK46_MEDTR.for.1249-3612.0.fasta -t /storage/tmp/jobs/dmuscipula/experiments/SLAx/maker/SLAx_merged_02_03.maker.output/SLAx_merged_02_03_datastore/AB/FC/MblContig1//theVoid.MblContig1/MblContig1.1249-3612.0.fasta -Q protein -T dna -m protein2genome --softmasktarget  --percent 20 --showcigar  > /storage/tmp/jobs/dmuscipula/experiments/SLAx/maker/SLAx_merged_02_03.maker.output/SLAx_merged_02_03_datastore/AB/FC/MblContig1//theVoid.MblContig1/MblContig1.1249-3612.TR%3AG7KK46_MEDTR.p_exonerate.0
/storage/tmp/software/exonerate-2.2.0-x86_64/bin/exonerate -q /storage/tmp/jobs/dmuscipula/experiments/SLAx/maker/SLAx_merged_02_03.maker.output/SLAx_merged_02_03_datastore/AB/FC/MblContig1//theVoid.MblContig1/TR%3AQ0DFK6_ORYSJ.for.1129-3612.0.fasta -t /storage/tmp/jobs/dmuscipula/experiments/SLAx/maker/SLAx_merged_02_03.maker.output/SLAx_merged_02_03_datastore/AB/FC/MblContig1//theVoid.MblContig1/MblContig1.1129-3612.0.fasta -Q protein -T dna -m protein2genome --softmasktarget  --percent 20 --showcigar  > /storage/tmp/jobs/dmuscipula/experiments/SLAx/maker/SLAx_merged_02_03.maker.output/SLAx_merged_02_03_datastore/AB/FC/MblContig1//theVoid.MblContig1/MblContig1.1129-3612.TR%3AQ0DFK6_ORYSJ.p_exonerate.0
/storage/tmp/software/exonerate-2.2.0-x86_64/bin/exonerate -q /storage/tmp/jobs/dmuscipula/experiments/SLAx/maker/SLAx_merged_02_03.maker.output/SLAx_merged_02_03_datastore/AB/FC/MblContig1//theVoid.MblContig1/TR%3AQ0JL49_ORYSJ.for.110-2308.0.fasta -t /storage/tmp/jobs/dmuscipula/experiments/SLAx/maker/SLAx_merged_02_03.maker.output/SLAx_merged_02_03_datastore/AB/FC/MblContig1//theVoid.MblContig1/MblContig1.110-2308.0.fasta -Q protein -T dna -m protein2genome --softmasktarget  --percent 20 --showcigar  > /storage/tmp/jobs/dmuscipula/experiments/SLAx/maker/SLAx_merged_02_03.maker.output/SLAx_merged_02_03_datastore/AB/FC/MblContig1//theVoid.MblContig1/MblContig1.110-2308.TR%3AQ0JL49_ORYSJ.p_exonerate.0
/storage/tmp/software/exonerate-2.2.0-x86_64/bin/exonerate -q /storage/tmp/jobs/dmuscipula/experiments/SLAx/maker/SLAx_merged_02_03.maker.output/SLAx_merged_02_03_datastore/AB/FC/MblContig1//theVoid.MblContig1/TR%3AQ0JPE8_ORYSJ.for.1120-3551.0.fasta -t /storage/tmp/jobs/dmuscipula/experiments/SLAx/maker/SLAx_merged_02_03.maker.output/SLAx_merged_02_03_datastore/AB/FC/MblContig1//theVoid.MblContig1/MblContig1.1120-3551.0.fasta -Q protein -T dna -m protein2genome --softmasktarget  --percent 20 --showcigar  > /storage/tmp/jobs/dmuscipula/experiments/SLAx/maker/SLAx_merged_02_03.maker.output/SLAx_merged_02_03_datastore/AB/FC/MblContig1//theVoid.MblContig1/MblContig1.1120-3551.TR%3AQ0JPE8_ORYSJ.p_exonerate.0
/storage/tmp/software/exonerate-2.2.0-x86_64/bin/exonerate -q /storage/tmp/jobs/dmuscipula/experiments/SLAx/maker/SLAx_merged_02_03.maker.output/SLAx_merged_02_03_datastore/AB/FC/MblContig1//theVoid.MblContig1/TR%3AQ5NAK3_ORYSJ.for.1120-3551.0.fasta -t /storage/tmp/jobs/dmuscipula/experiments/SLAx/maker/SLAx_merged_02_03.maker.output/SLAx_merged_02_03_datastore/AB/FC/MblContig1//theVoid.MblContig1/MblContig1.1120-3551.0.fasta -Q protein -T dna -m protein2genome --softmasktarget  --percent 20 --showcigar  > /storage/tmp/jobs/dmuscipula/experiments/SLAx/maker/SLAx_merged_02_03.maker.output/SLAx_merged_02_03_datastore/AB/FC/MblContig1//theVoid.MblContig1/MblContig1.1120-3551.TR%3AQ5NAK3_ORYSJ.p_exonerate.0
/storage/tmp/software/exonerate-2.2.0-x86_64/bin/exonerate -q /storage/tmp/jobs/dmuscipula/experiments/SLAx/maker/SLAx_merged_02_03.maker.output/SLAx_merged_02_03_datastore/AB/FC/MblContig1//theVoid.MblContig1/TR%3AQ5NAK4_ORYSJ.for.1132-3551.0.fasta -t /storage/tmp/jobs/dmuscipula/experiments/SLAx/maker/SLAx_merged_02_03.maker.output/SLAx_merged_02_03_datastore/AB/FC/MblContig1//theVoid.MblContig1/MblContig1.1132-3551.0.fasta -Q protein -T dna -m protein2genome --softmasktarget  --percent 20 --showcigar  > /storage/tmp/jobs/dmuscipula/experiments/SLAx/maker/SLAx_merged_02_03.maker.output/SLAx_merged_02_03_datastore/AB/FC/MblContig1//theVoid.MblContig1/MblContig1.1132-3551.TR%3AQ5NAK4_ORYSJ.p_exonerate.0
/storage/tmp/software/exonerate-2.2.0-x86_64/bin/exonerate -q /storage/tmp/jobs/dmuscipula/experiments/SLAx/maker/SLAx_merged_02_03.maker.output/SLAx_merged_02_03_datastore/AB/FC/MblContig1//theVoid.MblContig1/TR%3AQ5ZE68_ORYSJ.for.110-3584.0.fasta -t /storage/tmp/jobs/dmuscipula/experiments/SLAx/maker/SLAx_merged_02_03.maker.output/SLAx_merged_02_03_datastore/AB/FC/MblContig1//theVoid.MblContig1/MblContig1.110-3584.0.fasta -Q protein -T dna -m protein2genome --softmasktarget  --percent 20 --showcigar  > /storage/tmp/jobs/dmuscipula/experiments/SLAx/maker/SLAx_merged_02_03.maker.output/SLAx_merged_02_03_datastore/AB/FC/MblContig1//theVoid.MblContig1/MblContig1.110-3584.TR%3AQ5ZE68_ORYSJ.p_exonerate.0
/storage/tmp/software/exonerate-2.2.0-x86_64/bin/exonerate -q /storage/tmp/jobs/dmuscipula/experiments/SLAx/maker/SLAx_merged_02_03.maker.output/SLAx_merged_02_03_datastore/AB/FC/MblContig1//theVoid.MblContig1/TR%3AQ6I589_ORYSJ.for.1210-3612.0.fasta -t /storage/tmp/jobs/dmuscipula/experiments/SLAx/maker/SLAx_merged_02_03.maker.output/SLAx_merged_02_03_datastore/AB/FC/MblContig1//theVoid.MblContig1/MblContig1.1210-3612.0.fasta -Q protein -T dna -m protein2genome --softmasktarget  --percent 20 --showcigar  > /storage/tmp/jobs/dmuscipula/experiments/SLAx/maker/SLAx_merged_02_03.maker.output/SLAx_merged_02_03_datastore/AB/FC/MblContig1//theVoid.MblContig1/MblContig1.1210-3612.TR%3AQ6I589_ORYSJ.p_exonerate.0
/storage/tmp/software/exonerate-2.2.0-x86_64/bin/exonerate -q /storage/tmp/jobs/dmuscipula/experiments/SLAx/maker/SLAx_merged_02_03.maker.output/SLAx_merged_02_03_datastore/AB/FC/MblContig1//theVoid.MblContig1/TR%3AQ6ZLB6_ORYSJ.for.1141-3539.0.fasta -t /storage/tmp/jobs/dmuscipula/experiments/SLAx/maker/SLAx_merged_02_03.maker.output/SLAx_merged_02_03_datastore/AB/FC/MblContig1//theVoid.MblContig1/MblContig1.1141-3539.0.fasta -Q protein -T dna -m protein2genome --softmasktarget  --percent 20 --showcigar  > /storage/tmp/jobs/dmuscipula/experiments/SLAx/maker/SLAx_merged_02_03.maker.output/SLAx_merged_02_03_datastore/AB/FC/MblContig1//theVoid.MblContig1/MblContig1.1141-3539.TR%3AQ6ZLB6_ORYSJ.p_exonerate.0
/storage/tmp/software/exonerate-2.2.0-x86_64/bin/exonerate -q /storage/tmp/jobs/dmuscipula/experiments/SLAx/maker/SLAx_merged_02_03.maker.output/SLAx_merged_02_03_datastore/AB/FC/MblContig1//theVoid.MblContig1/TR%3AQ75G55_ORYSJ.for.1141-3521.0.fasta -t /storage/tmp/jobs/dmuscipula/experiments/SLAx/maker/SLAx_merged_02_03.maker.output/SLAx_merged_02_03_datastore/AB/FC/MblContig1//theVoid.MblContig1/MblContig1.1141-3521.0.fasta -Q protein -T dna -m protein2genome --softmasktarget  --percent 20 --showcigar  > /storage/tmp/jobs/dmuscipula/experiments/SLAx/maker/SLAx_merged_02_03.maker.output/SLAx_merged_02_03_datastore/AB/FC/MblContig1//theVoid.MblContig1/MblContig1.1141-3521.TR%3AQ75G55_ORYSJ.p_exonerate.0
/storage/tmp/software/exonerate-2.2.0-x86_64/bin/exonerate -q /storage/tmp/jobs/dmuscipula/experiments/SLAx/maker/SLAx_merged_02_03.maker.output/SLAx_merged_02_03_datastore/AB/FC/MblContig1//theVoid.MblContig1/TR%3AQ7XTX7_ORYSJ.for.1120-3518.0.fasta -t /storage/tmp/jobs/dmuscipula/experiments/SLAx/maker/SLAx_merged_02_03.maker.output/SLAx_merged_02_03_datastore/AB/FC/MblContig1//theVoid.MblContig1/MblContig1.1120-3518.0.fasta -Q protein -T dna -m protein2genome --softmasktarget  --percent 20 --showcigar  > /storage/tmp/jobs/dmuscipula/experiments/SLAx/maker/SLAx_merged_02_03.maker.output/SLAx_merged_02_03_datastore/AB/FC/MblContig1//theVoid.MblContig1/MblContig1.1120-3518.TR%3AQ7XTX7_ORYSJ.p_exonerate.0
/storage/tmp/software/exonerate-2.2.0-x86_64/bin/exonerate -q /storage/tmp/jobs/dmuscipula/experiments/SLAx/maker/SLAx_merged_02_03.maker.output/SLAx_merged_02_03_datastore/AB/FC/MblContig1//theVoid.MblContig1/TR%3AQ8L4G8_ORYSJ.for.1120-3536.0.fasta -t /storage/tmp/jobs/dmuscipula/experiments/SLAx/maker/SLAx_merged_02_03.maker.output/SLAx_merged_02_03_datastore/AB/FC/MblContig1//theVoid.MblContig1/MblContig1.1120-3536.0.fasta -Q protein -T dna -m protein2genome --softmasktarget  --percent 20 --showcigar  > /storage/tmp/jobs/dmuscipula/experiments/SLAx/maker/SLAx_merged_02_03.maker.output/SLAx_merged_02_03_datastore/AB/FC/MblContig1//theVoid.MblContig1/MblContig1.1120-3536.TR%3AQ8L4G8_ORYSJ.p_exonerate.0
/storage/tmp/software/exonerate-2.2.0-x86_64/bin/exonerate -q /storage/tmp/jobs/dmuscipula/experiments/SLAx/maker/SLAx_merged_02_03.maker.output/SLAx_merged_02_03_datastore/AB/FC/MblContig1//theVoid.MblContig1/TR%3AQ9FTK9_ORYSJ.for.1180-3500.0.fasta -t /storage/tmp/jobs/dmuscipula/experiments/SLAx/maker/SLAx_merged_02_03.maker.output/SLAx_merged_02_03_datastore/AB/FC/MblContig1//theVoid.MblContig1/MblContig1.1180-3500.0.fasta -Q protein -T dna -m protein2genome --softmasktarget  --percent 20 --showcigar  > /storage/tmp/jobs/dmuscipula/experiments/SLAx/maker/SLAx_merged_02_03.maker.output/SLAx_merged_02_03_datastore/AB/FC/MblContig1//theVoid.MblContig1/MblContig1.1180-3500.TR%3AQ9FTK9_ORYSJ.p_exonerate.0
/storage/tmp/software/exonerate-2.2.0-x86_64/bin/exonerate -q /storage/tmp/jobs/dmuscipula/experiments/SLAx/maker/SLAx_merged_02_03.maker.output/SLAx_merged_02_03_datastore/AB/FC/MblContig1//theVoid.MblContig1/TR%3AQ9XHX8_ORYSJ.for.1180-2344.0.fasta -t /storage/tmp/jobs/dmuscipula/experiments/SLAx/maker/SLAx_merged_02_03.maker.output/SLAx_merged_02_03_datastore/AB/FC/MblContig1//theVoid.MblContig1/MblContig1.1180-2344.0.fasta -Q protein -T dna -m protein2genome --softmasktarget  --percent 20 --showcigar  > /storage/tmp/jobs/dmuscipula/experiments/SLAx/maker/SLAx_merged_02_03.maker.output/SLAx_merged_02_03_datastore/AB/FC/MblContig1//theVoid.MblContig1/MblContig1.1180-2344.TR%3AQ9XHX8_ORYSJ.p_exonerate.0
To access files for individual sequences use the datastore index:
total clusters:1 now processing 0
total clusters:2 now processing 0
	UNKNOWN	Bio::AnalysisParserI	/storage/tmp/software/perl-5.14.1/lib/site_perl/5.14.1/Bio/AnalysisParserI.pm
	UNKNOWN	Bio::AnnotatableI	/storage/tmp/software/perl-5.14.1/lib/site_perl/5.14.1/Bio/AnnotatableI.pm
	UNKNOWN	Bio::AnnotationCollectionI	/storage/tmp/software/perl-5.14.1/lib/site_perl/5.14.1/Bio/AnnotationCollectionI.pm
	UNKNOWN	Bio::Annotation::Collection	/storage/tmp/software/perl-5.14.1/lib/site_perl/5.14.1/Bio/Annotation/Collection.pm
	UNKNOWN	Bio::AnnotationI	/storage/tmp/software/perl-5.14.1/lib/site_perl/5.14.1/Bio/AnnotationI.pm
	UNKNOWN	Bio::Annotation::SimpleValue	/storage/tmp/software/perl-5.14.1/lib/site_perl/5.14.1/Bio/Annotation/SimpleValue.pm
	UNKNOWN	Bio::Annotation::TypeManager	/storage/tmp/software/perl-5.14.1/lib/site_perl/5.14.1/Bio/Annotation/TypeManager.pm
	UNKNOWN	Bio::DB::InMemoryCache	/storage/tmp/software/perl-5.14.1/lib/site_perl/5.14.1/Bio/DB/InMemoryCache.pm
	UNKNOWN	Bio::DescribableI	/storage/tmp/software/perl-5.14.1/lib/site_perl/5.14.1/Bio/DescribableI.pm
	UNKNOWN	Bio::Event::EventGeneratorI	/storage/tmp/software/perl-5.14.1/lib/site_perl/5.14.1/Bio/Event/EventGeneratorI.pm
	UNKNOWN	Bio::Event::EventHandlerI	/storage/tmp/software/perl-5.14.1/lib/site_perl/5.14.1/Bio/Event/EventHandlerI.pm
	UNKNOWN	Bio::Factory::ObjectFactoryI	/storage/tmp/software/perl-5.14.1/lib/site_perl/5.14.1/Bio/Factory/ObjectFactoryI.pm
	UNKNOWN	Bio::Factory::ObjectFactory	/storage/tmp/software/perl-5.14.1/lib/site_perl/5.14.1/Bio/Factory/ObjectFactory.pm
	UNKNOWN	Bio::Factory::SequenceFactoryI	/storage/tmp/software/perl-5.14.1/lib/site_perl/5.14.1/Bio/Factory/SequenceFactoryI.pm
	UNKNOWN	Bio::FeatureHolderI	/storage/tmp/software/perl-5.14.1/lib/site_perl/5.14.1/Bio/FeatureHolderI.pm
	UNKNOWN	Bio::IdentifiableI	/storage/tmp/software/perl-5.14.1/lib/site_perl/5.14.1/Bio/IdentifiableI.pm
	UNKNOWN	Bio::LocatableSeq	/storage/tmp/software/perl-5.14.1/lib/site_perl/5.14.1/Bio/LocatableSeq.pm
	UNKNOWN	Bio::Location::Atomic	/storage/tmp/software/perl-5.14.1/lib/site_perl/5.14.1/Bio/Location/Atomic.pm
	UNKNOWN	Bio::Location::CoordinatePolicyI	/storage/tmp/software/perl-5.14.1/lib/site_perl/5.14.1/Bio/Location/CoordinatePolicyI.pm
	UNKNOWN	Bio::Location::FuzzyLocationI	/storage/tmp/software/perl-5.14.1/lib/site_perl/5.14.1/Bio/Location/FuzzyLocationI.pm
	UNKNOWN	Bio::Location::Fuzzy	/storage/tmp/software/perl-5.14.1/lib/site_perl/5.14.1/Bio/Location/Fuzzy.pm
	UNKNOWN	Bio::LocationI	/storage/tmp/software/perl-5.14.1/lib/site_perl/5.14.1/Bio/LocationI.pm
	UNKNOWN	Bio::Location::Simple	/storage/tmp/software/perl-5.14.1/lib/site_perl/5.14.1/Bio/Location/Simple.pm
	UNKNOWN	Bio::Location::SplitLocationI	/storage/tmp/software/perl-5.14.1/lib/site_perl/5.14.1/Bio/Location/SplitLocationI.pm
	UNKNOWN	Bio::Location::Split	/storage/tmp/software/perl-5.14.1/lib/site_perl/5.14.1/Bio/Location/Split.pm
	UNKNOWN	Bio::Location::WidestCoordPolicy	/storage/tmp/software/perl-5.14.1/lib/site_perl/5.14.1/Bio/Location/WidestCoordPolicy.pm
	UNKNOWN	Bio::PrimarySeqI	/storage/tmp/software/perl-5.14.1/lib/site_perl/5.14.1/Bio/PrimarySeqI.pm
	UNKNOWN	Bio::PrimarySeq	/storage/tmp/software/perl-5.14.1/lib/site_perl/5.14.1/Bio/PrimarySeq.pm
	UNKNOWN	Bio::RangeI	/storage/tmp/software/perl-5.14.1/lib/site_perl/5.14.1/Bio/RangeI.pm
	UNKNOWN	Bio::Range	/storage/tmp/software/perl-5.14.1/lib/site_perl/5.14.1/Bio/Range.pm
	UNKNOWN	Bio::Root::HTTPget	/storage/tmp/software/perl-5.14.1/lib/site_perl/5.14.1/Bio/Root/HTTPget.pm
	UNKNOWN	Bio::Root::IO	/storage/tmp/software/perl-5.14.1/lib/site_perl/5.14.1/Bio/Root/IO.pm
	UNKNOWN	Bio::Root::Root	/storage/tmp/software/perl-5.14.1/lib/site_perl/5.14.1/Bio/Root/Root.pm
	UNKNOWN	Bio::Search::Hit::HitFactory	/storage/tmp/software/perl-5.14.1/lib/site_perl/5.14.1/Bio/Search/Hit/HitFactory.pm
	UNKNOWN	Bio::Search::Hit::HitI	/storage/tmp/software/perl-5.14.1/lib/site_perl/5.14.1/Bio/Search/Hit/HitI.pm
	UNKNOWN	Bio::Search::Hit::PhatHit::augustus	/storage/tmp/software/maker-2.24-debug/bin/../lib/Bio/Search/Hit/PhatHit/augustus.pm
	UNKNOWN	Bio::Search::Hit::PhatHit::est2genome	/storage/tmp/software/maker-2.24-debug/bin/../lib/Bio/Search/Hit/PhatHit/est2genome.pm
	UNKNOWN	Bio::Search::Hit::PhatHit::fgenesh	/storage/tmp/software/maker-2.24-debug/bin/../lib/Bio/Search/Hit/PhatHit/fgenesh.pm
	UNKNOWN	Bio::Search::Hit::PhatHit::genemark	/storage/tmp/software/maker-2.24-debug/bin/../lib/Bio/Search/Hit/PhatHit/genemark.pm
	UNKNOWN	Bio::Search::Hit::PhatHit::gff3	/storage/tmp/software/maker-2.24-debug/bin/../lib/Bio/Search/Hit/PhatHit/gff3.pm
	UNKNOWN	Bio::Search::Hit::PhatHit::protein2genome	/storage/tmp/software/maker-2.24-debug/bin/../lib/Bio/Search/Hit/PhatHit/protein2genome.pm
	UNKNOWN	Bio::Search::Hit::PhatHit::snap	/storage/tmp/software/maker-2.24-debug/bin/../lib/Bio/Search/Hit/PhatHit/snap.pm
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	UNKNOWN	Bio::SearchIO	/storage/tmp/software/perl-5.14.1/lib/site_perl/5.14.1/Bio/SearchIO.pm
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	UNKNOWN	Bio::SeqFeature::FeaturePair	/storage/tmp/software/perl-5.14.1/lib/site_perl/5.14.1/Bio/SeqFeature/FeaturePair.pm
	UNKNOWN	Bio::SeqFeature::Generic	/storage/tmp/software/perl-5.14.1/lib/site_perl/5.14.1/Bio/SeqFeature/Generic.pm
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	UNKNOWN	Bio::SeqFeature::SimilarityPair	/storage/tmp/software/perl-5.14.1/lib/site_perl/5.14.1/Bio/SeqFeature/SimilarityPair.pm
	UNKNOWN	Bio::SeqFeature::Similarity	/storage/tmp/software/perl-5.14.1/lib/site_perl/5.14.1/Bio/SeqFeature/Similarity.pm
	UNKNOWN	Bio::SeqI	/storage/tmp/software/perl-5.14.1/lib/site_perl/5.14.1/Bio/SeqI.pm
	UNKNOWN	Bio::Seq::SeqFactory	/storage/tmp/software/perl-5.14.1/lib/site_perl/5.14.1/Bio/Seq/SeqFactory.pm
	UNKNOWN	Bio::Seq	/storage/tmp/software/perl-5.14.1/lib/site_perl/5.14.1/Bio/Seq.pm
	UNKNOWN	Bio::SeqUtils	/storage/tmp/software/perl-5.14.1/lib/site_perl/5.14.1/Bio/SeqUtils.pm
	UNKNOWN	Bio::Tools::CodonTable	/storage/tmp/software/perl-5.14.1/lib/site_perl/5.14.1/Bio/Tools/CodonTable.pm
	UNKNOWN	Bio::Tools::GFF	/storage/tmp/software/perl-5.14.1/lib/site_perl/5.14.1/Bio/Tools/GFF.pm
	UNKNOWN	Bio::Tools::IUPAC	/storage/tmp/software/perl-5.14.1/lib/site_perl/5.14.1/Bio/Tools/IUPAC.pm
	UNKNOWN	Carp::Heavy	/storage/tmp/software/perl-5.14.1/lib/5.14.1/Carp/Heavy.pm
	UNKNOWN	clean	/storage/tmp/software/maker-2.24-debug/bin/../lib/clean.pm
	UNKNOWN	cluster	/storage/tmp/software/maker-2.24-debug/bin/../lib/cluster.pm
	UNKNOWN	compare	/storage/tmp/software/maker-2.24-debug/bin/../lib/compare.pm
	UNKNOWN	Config	/storage/tmp/software/perl-5.14.1/lib/5.14.1/x86_64-linux-thread-multi/Config.pm
	UNKNOWN	ds_utility	/storage/tmp/software/maker-2.24-debug/bin/../lib/ds_utility.pm
	UNKNOWN	Dumper::GFF::GFFV3	/storage/tmp/software/maker-2.24-debug/bin/../lib/Dumper/GFF/GFFV3.pm
	UNKNOWN	Dumper::XML::Game	/storage/tmp/software/maker-2.24-debug/bin/../lib/Dumper/XML/Game.pm
	UNKNOWN	Dumper::XML::Game_Xml	/storage/tmp/software/maker-2.24-debug/bin/../lib/Dumper/XML/Game_Xml.pm
	UNKNOWN	Error::Simple	/storage/tmp/software/maker-2.24-debug/bin/../lib/Error/Simple.pm
	UNKNOWN	exonerate::splice_info	/storage/tmp/software/maker-2.24-debug/bin/../lib/exonerate/splice_info.pm
	UNKNOWN	FastaChunker	/storage/tmp/software/maker-2.24-debug/bin/../lib/FastaChunker.pm
	UNKNOWN	FastaChunk	/storage/tmp/software/maker-2.24-debug/bin/../lib/FastaChunk.pm
	UNKNOWN	FastaDB	/storage/tmp/software/maker-2.24-debug/bin/../lib/FastaDB.pm
	UNKNOWN	FastaFile	/storage/tmp/software/maker-2.24-debug/bin/../lib/FastaFile.pm
	UNKNOWN	FastaSeq	/storage/tmp/software/maker-2.24-debug/bin/../lib/FastaSeq.pm
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	UNKNOWN	Iterator::GFF3	/storage/tmp/software/maker-2.24-debug/bin/../lib/Iterator/GFF3.pm
	UNKNOWN	Iterator	/storage/tmp/software/maker-2.24-debug/bin/../lib/Iterator.pm
	UNKNOWN	LWP::MemberMixin	/storage/tmp/software/perl-5.14.1/lib/site_perl/5.14.1/LWP/MemberMixin.pm
	UNKNOWN	maker::auto_annotator	/storage/tmp/software/maker-2.24-debug/bin/../lib/maker/auto_annotator.pm
	UNKNOWN	MAKER::ConfigData	/storage/tmp/software/maker-2.24-debug/bin/../perl/lib/MAKER/ConfigData.pm
	UNKNOWN	maker::join	/storage/tmp/software/maker-2.24-debug/bin/../lib/maker/join.pm
	UNKNOWN	maker::quality_index	/storage/tmp/software/maker-2.24-debug/bin/../lib/maker/quality_index.pm
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	UNKNOWN	PhatHit_utils	/storage/tmp/software/maker-2.24-debug/bin/../lib/PhatHit_utils.pm
	UNKNOWN	polisher::exonerate::est	/storage/tmp/software/maker-2.24-debug/bin/../lib/polisher/exonerate/est.pm
	UNKNOWN	polisher::exonerate::protein	/storage/tmp/software/maker-2.24-debug/bin/../lib/polisher/exonerate/protein.pm
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	UNKNOWN	polisher	/storage/tmp/software/maker-2.24-debug/bin/../lib/polisher.pm
	UNKNOWN	PostData	/storage/tmp/software/maker-2.24-debug/bin/../lib/PostData.pm
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	UNKNOWN	repeat_mask_seq	/storage/tmp/software/maker-2.24-debug/bin/../lib/repeat_mask_seq.pm
	UNKNOWN	shadow_AED	/storage/tmp/software/maker-2.24-debug/bin/../lib/shadow_AED.pm
	UNKNOWN	Shadower	/storage/tmp/software/maker-2.24-debug/bin/../lib/Shadower.pm
	UNKNOWN	SimpleCluster	/storage/tmp/software/maker-2.24-debug/bin/../lib/SimpleCluster.pm
	UNKNOWN	SpaceBase	/storage/tmp/software/maker-2.24-debug/bin/../lib/SpaceBase.pm
	UNKNOWN	Widget::augustus	/storage/tmp/software/maker-2.24-debug/bin/../lib/Widget/augustus.pm
	UNKNOWN	Widget::blastn	/storage/tmp/software/maker-2.24-debug/bin/../lib/Widget/blastn.pm
	UNKNOWN	Widget::blastx	/storage/tmp/software/maker-2.24-debug/bin/../lib/Widget/blastx.pm
	UNKNOWN	Widget::exonerate::est2genome	/storage/tmp/software/maker-2.24-debug/bin/../lib/Widget/exonerate/est2genome.pm
	UNKNOWN	Widget::exonerate::protein2genome	/storage/tmp/software/maker-2.24-debug/bin/../lib/Widget/exonerate/protein2genome.pm
	UNKNOWN	Widget::exonerate	/storage/tmp/software/maker-2.24-debug/bin/../lib/Widget/exonerate.pm
	UNKNOWN	Widget::fgenesh	/storage/tmp/software/maker-2.24-debug/bin/../lib/Widget/fgenesh.pm
	UNKNOWN	Widget::formater	/storage/tmp/software/maker-2.24-debug/bin/../lib/Widget/formater.pm
	UNKNOWN	Widget::genemark	/storage/tmp/software/maker-2.24-debug/bin/../lib/Widget/genemark.pm
	UNKNOWN	Widget::RepeatMasker	/storage/tmp/software/maker-2.24-debug/bin/../lib/Widget/RepeatMasker.pm
	UNKNOWN	Widget::snap	/storage/tmp/software/maker-2.24-debug/bin/../lib/Widget/snap.pm
	UNKNOWN	Widget	/storage/tmp/software/maker-2.24-debug/bin/../lib/Widget.pm
	UNKNOWN	Widget::tblastx	/storage/tmp/software/maker-2.24-debug/bin/../lib/Widget/tblastx.pm
Widget::augustus:
Widget::blastn:
Widget::blastx:
Widget::exonerate::est2genome:
Widget::exonerate::protein2genome:
Widget::formater:
Widget::RepeatMasker:

From scott at scottcain.net  Wed Mar 21 14:59:19 2012
From: scott at scottcain.net (Scott Cain)
Date: Wed, 21 Mar 2012 16:59:19 -0400
Subject: [maker-devel] loading scaffold features into chado
In-Reply-To: <4F6A290E.8000306@uwindsor.ca>
References: <4F68B686.6050800@uwindsor.ca> <CB8E2F50.97C7%carsonhh@gmail.com>
	<CA+JTaoy00sX+3Pdyrw=Apus09Lppg9YNQsr8k4uoYXHmK24Euw@mail.gmail.com>
	<4F68C66F.2010902@uwindsor.ca>
	<FFACED63-40D9-4810-9927-0E4984BA8465@scottcain.net>
	<web-60068456@uwindsor.ca>
	<CA+JTaoxshG4M+awmuw93=JkwqtisgFSw6igZE+_2tCFaN-ocrw@mail.gmail.com>
	<4F6A03D2.5010503@uwindsor.ca>
	<CA+JTaoyMT6_uxYG_b28j-PCJfiOeL6FUqgLRj1FNvwR7XZUOkA@mail.gmail.com>
	<4F6A290E.8000306@uwindsor.ca>
Message-ID: <CA+JTaowKA=wFW8A91wpOMZLAe+phkFdHdppO1ume+30sWN9T9g@mail.gmail.com>

Hi Claudia,

I wanted to bring this back to the mailing lists, so I cc'ed them here.

First, with the fasta loading issue: what command are you using to
load the fasta sequences?  It works for me whether the fasta is at the
bottom of the GFF file or if it is a separate fasta file (as long as I
supply the --fastafile flag to the loader).

About the searching problem: when I turn on full text searching (which
means both running gmod_chado_fts_prep.pl and adding "-fulltext 1" to
the db_args in the gbrowse config file), I can search for "cnot1" and
find both a gene and an mRNA (of course, they are really the same
feature, but GBrowse doesn't know that).  Also, searching for "maker"
works, but in a real database, this will not be an effective query,
since the number of results returned are limited, and presumably there
will be lots of features resulting from a query like that.  Please
remind me, is that what you wanted to do?

Scott




On Wed, Mar 21, 2012 at 3:16 PM, claudia <dinatal at uwindsor.ca> wrote:
> Hi Scott,
>
> ?Wanted to give you a quick heads up that the bulk loader seems to be
> loading my fasta files now after deleting the ' ##FASTA' header ( the first
> line of the file now looks like this >scaffold0001)...
> Never had this problem before, it seems the bulk loader wanted to see a '>'
> symbol in front of the first line...
>
> -- when I say seems, I will let you know if it finishes, as it currently
> ?states " Loading sequences ( if any)" ... and I never made it this far
> before :)
>
> Claudia
>
>
>
> On 21/03/2012 12:53 PM, Scott Cain wrote:
>>
>> Hi Claudia,
>>
>> I imagine one scaffold and gene models would be good--the problem is
>> finding genes, right?
>>
>> Also, with loading fasta: were the corresponding features from the GFF
>> file already loaded? ?If so, that should have worked, and if it didn't
>> it implies a bug. ?If not, that's why.
>>
>> Scott
>>
>>
>> On Wed, Mar 21, 2012 at 12:37 PM, claudia<dinatal at uwindsor.ca> ?wrote:
>>>
>>> Hi Scott,
>>> ?So would one scaffold with Maker gene models suffice? Do you want the
>>> analysis as well?
>>>
>>> --along those same lines, I did try and load the original sequence
>>> (fasta)
>>> file first that I ran the Pipeline on and chado seems to refuse the files
>>> saying they don't contain the appropriate feature '>' in the header which
>>> in
>>> fact they do i.e> ?scaffold00001 ... So not sure what is wrong with the
>>> fasta that chado doesn't want to load even if it is embedded in the GFF3,
>>> the bulk loader or maker2chado return errors stating 'feature not
>>> found'...
>>>
>>>
>>> Claudia
>>>
>>>
>>>
>>> On 21/03/2012 12:20 PM, Scott Cain wrote:
>>>>
>>>> Hi Claudia,
>>>>
>>>> I was hoping to get actual files that I could do testing on, not
>>>> pictures of files :-)
>>>>
>>>> Scott
>>>>
>>>>
>>>> On Tue, Mar 20, 2012 at 4:15 PM, Dinatale C<dinatal at uwindsor.ca>
>>>> ?wrote:
>>>>>
>>>>> Hi,
>>>>>
>>>>> Attached: ?I have samples of the contig file ( I extracted the contig
>>>>> features first to load prior to the gene models) the fasta of the
>>>>> sequences
>>>>> is in the footer of the gff3 file.
>>>>>
>>>>> --so basically, based on experience with contig annotations, I should
>>>>> be
>>>>> able to type in 'maker' in to the gbrowse search bar, and recieve all
>>>>> the
>>>>> maker gene annotations, but I don't. I must specifiy the exact ID i.e "
>>>>> maker-scaffold11323-augustus-gene...." or 'scaffold11323'
>>>>>
>>>>> --so I wonder if it has to do with the fasta files being named as
>>>>> 'scaffolds' and perhaps causing a problem with chado recognizing that
>>>>> they
>>>>> are linked to the gene annotations due to scaffold not being a SOFA
>>>>> type
>>>>> term, if in fact the sequences must be submitted to the database first?
>>>>>
>>>>>
>>>>> Thanks in advance,
>>>>>
>>>>> Claudia
>>>>>
>>>>> On Tue, 20 Mar 2012 15:50:55 -0400 Scott Cain wrote:
>>>>>>
>>>>>> Hi Claudia,
>>>>>>
>>>>>> Can you post a sample of the gff that shows what you are looking for
>>>>>> and
>>>>>> not finding?
>>>>>>
>>>>>> Scott
>>>>>>
>>>>>>
>>>>>> Sent from my iPad
>>>>>>
>>>>>> On Mar 20, 2012, at 2:03 PM, claudia wrote:
>>>>>>
>>>>>>> Hi,
>>>>>>>
>>>>>>> I have enabled full text searching and I still have this problem,
>>>>>>> another reason for
>>>>>>
>>>>>> concern... So I wondered if in fact I changed all the ID's in the GFF3
>>>>>> file to supercontigs,
>>>>>> then perhaps Chado would better link all the terms, annotations, and
>>>>>> fasta
>>>>>> files....
>>>>>> Although, i realize that the seq_id ( column 1) shouldn't need to be
>>>>>> specific since the
>>>>>> 'type' term would take care of designating the feature type, no?
>>>>>>>
>>>>>>> Claudia
>>>>>>>
>>>>>>>
>>>>>>>
>>>>>>> On 20/03/2012 1:25 PM, Scott Cain wrote:
>>>>>>>>
>>>>>>>> Hi Claudia,
>>>>>>>>
>>>>>>>> I agree with everything that Carson wrote, except about name
>>>>>>>> searching--it's a little trickier in Chado. What you probably want
>>>>>>>> to
>>>>>>>> do is implement full text searching. See:
>>>>>>>>
>>>>>>>> http://gmod.org/wiki/Chado_Full_Text_Search
>>>>>>>>
>>>>>>>> for more information on setting it up and maintaining it.
>>>>>>>>
>>>>>>>> Scott
>>>>>>>>
>>>>>>>>
>>>>>>>> On Tue, Mar 20, 2012 at 1:13 PM, Carson Holt wrote:
>>>>>>>>>>
>>>>>>>>>> I have 2 concerns, the first is: regarding representing scaffold
>>>>>>>>>> features in chado and gbrowse. I noticed that the Sequence
>>>>>>>>>> ontology
>>>>>>>>>> uses
>>>>>>>>>> the term supercontig and so if my assembly generated scaffolds
>>>>>>>>>> entitled
>>>>>>>>>> "scaffold" should I change the names to supercontigs so that chado
>>>>>>>>>> recognizes the terms?
>>>>>>>>>
>>>>>>>>> Yes. You must use valid SO terms. It is a requirement of GFF3, and
>>>>>>>>> Chado
>>>>>>>>> will enforce this requirement on loading a GFF3 file (note Chado
>>>>>>>>> will
>>>>>>>>> even
>>>>>>>>> go as far as to check the validity of the Ontology_term= attribute
>>>>>>>>> in
>>>>>>>>> GFF3
>>>>>>>>> if you use it). You can decide to use contig or supercontig as your
>>>>>>>>> sequence feature. It doesn?t really matter unless you are placing
>>>>>>>>>
>>>>>>>>> both
>>>>>>>>> into the database as separate features (i.e. You have a supercontig
>>>>>>>>> as
>>>>>>>>> the
>>>>>>>>> parent feature and then you enter contigs individually as children
>>>>>>>>> of
>>>>>>>>> the
>>>>>>>>> supercontig).
>>>>>>>>>
>>>>>>>>>
>>>>>>>>>> Corresponding to my first question, Maker does not know that the
>>>>>>>>>> contigs
>>>>>>>>>> are actually scaffold/supercontigs when annotating and so Maker
>>>>>>>>>> will
>>>>>>>>>> still call the "type" feature or column 3 in the GFF3, a 'contig',
>>>>>>>>>> how
>>>>>>>>>> can Maker be implemented to change this naming convention before
>>>>>>>>>> annotation, or after?
>>>>>>>>>
>>>>>>>>> Not really important unless you plan on making contigs children of
>>>>>>>>> the
>>>>>>>>> supercontig. But you can always do a search and replace. -->
>>>>>>>>> cat file.gff | perl -ane 's/\tcontig\t/\tsupercontig\t/s; print
>>>>>>>>> $_'>
>>>>>>>>> new_file.gff
>>>>>>>>>
>>>>>>>>>
>>>>>>>>>> Consequently, I am having problems pulling up gene features in
>>>>>>>>>> Gbrowse
>>>>>>>>>> when doing a generic gene search, and I must provide the maker
>>>>>>>>>> generated
>>>>>>>>>> unique-gene_id in the gbrowse search bar or the known sequence id
>>>>>>>>>> i.e
>>>>>>>>>> 'scaffold001', which is not useful for someone who does not have
>>>>>>>>>> this
>>>>>>>>>> information.
>>>>>>>>>> ---- I do not have this problem when my seq_id, and 'type' feature
>>>>>>>>>> id
>>>>>>>>>> match in the true case of 'contigs'. I can do a generic gene
>>>>>>>>>> search
>>>>>>>>>> in
>>>>>>>>>> gbrowse with the term 'maker' and gbrowse will provide me all the
>>>>>>>>>> associated maker generated gene calls.
>>>>>>>>>
>>>>>>>>> See "Adjusting GBrowse Name Searches" in the GBrowse tutorial -->
>>>>>>>>> http://gmod.org/gbrowse2/tutorial/tutorial.html#naming
>>>>>>>>>
>>>>>>>>>
>>>>>>>>> Thanks,
>>>>>>>>> Carson
>>>>>>>>>
>>>>>>>>>
>>>>>>>>>
>>>>>>>>>
>>>>>>>>>
>>>>>>>>>
>>>>>>>>>
>>>>>>>>>
>>>>>>>>>
>>>>>>>>>
>>>>>>>>>
>>>>>>>>>> Thank you for any guidance resolving these concerns,
>>>>>>>>>> Claudia
>>>>>>>>>>
>>>>>>>>>>
>>>>>>>>>>
>>>>>>>>>> --
>>>>>>>>>> Claudia DiNatale
>>>>>>>>>> Master's Candidate
>>>>>>>>>> The Crosby Lab
>>>>>>>>>> University of Windsor
>>>>>>>>>> 519-253-3000 ext: 4755
>>>>>>>>>>
>>>>>>>>>>
>>>>>>>>>> _______________________________________________
>>>>>>>>>> maker-devel mailing list
>>>>>>>>>> maker-devel at box290.bluehost.com
>>>>>>>>>>
>>>>>>>>>>
>>>>>>>>>>
>>>>>>>>>> http://box290.bluehost.com/mailman/listinfo/maker-devel_yandell-lab.org
>>>>>>>>>
>>>>>>>>>
>>>>>>>>> _______________________________________________
>>>>>>>>> maker-devel mailing list
>>>>>>>>> maker-devel at box290.bluehost.com
>>>>>>>>>
>>>>>>>>>
>>>>>>>>>
>>>>>>>>> http://box290.bluehost.com/mailman/listinfo/maker-devel_yandell-lab.org
>>>>>>>>
>>>>>>>>
>>>>>>> --
>>>>>>> Claudia DiNatale
>>>>>>> Master's Candidate
>>>>>>> The Crosby Lab
>>>>>>> University of Windsor
>>>>>>> 519-253-3000 ext: 4755
>>>>>>>
>>>>
>>>
>>> --
>>> Claudia DiNatale
>>> Master's Candidate
>>> The Crosby Lab
>>> University of Windsor
>>> 519-253-3000 ext: 4755
>>>
>>
>>
>
>
> --
> Claudia DiNatale
> Master's Candidate
> The Crosby Lab
> University of Windsor
> 519-253-3000 ext: 4755
>



-- 
------------------------------------------------------------------------
Scott Cain, Ph. D.? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ?? scott at scottcain dot net
GMOD Coordinator (http://gmod.org/)? ? ? ? ? ? ? ? ? ?? 216-392-3087
Ontario Institute for Cancer Research



From dinatal at uwindsor.ca  Wed Mar 21 15:14:54 2012
From: dinatal at uwindsor.ca (claudia)
Date: Wed, 21 Mar 2012 17:14:54 -0400
Subject: [maker-devel] loading scaffold features into chado
In-Reply-To: <CA+JTaowKA=wFW8A91wpOMZLAe+phkFdHdppO1ume+30sWN9T9g@mail.gmail.com>
References: <4F68B686.6050800@uwindsor.ca> <CB8E2F50.97C7%carsonhh@gmail.com>
	<CA+JTaoy00sX+3Pdyrw=Apus09Lppg9YNQsr8k4uoYXHmK24Euw@mail.gmail.com>
	<4F68C66F.2010902@uwindsor.ca>
	<FFACED63-40D9-4810-9927-0E4984BA8465@scottcain.net>
	<web-60068456@uwindsor.ca>
	<CA+JTaoxshG4M+awmuw93=JkwqtisgFSw6igZE+_2tCFaN-ocrw@mail.gmail.com>
	<4F6A03D2.5010503@uwindsor.ca>
	<CA+JTaoyMT6_uxYG_b28j-PCJfiOeL6FUqgLRj1FNvwR7XZUOkA@mail.gmail.com>
	<4F6A290E.8000306@uwindsor.ca>
	<CA+JTaowKA=wFW8A91wpOMZLAe+phkFdHdppO1ume+30sWN9T9g@mail.gmail.com>
Message-ID: <4F6A44CE.3010100@uwindsor.ca>

Hi Scott,
  I tried both maker2chado and gmod_bulk_load_gff.pl with fasta embedded 
or not... If the fastafile was seperate I used the command --fastafile 
and if it was embedded, it was simply --gfffile with the other 
appropriate commands for loading gene models not analysis ( i.e no 
exon).  It finally resulted that, as I mentioned, when I changed the 
header in the fasta file, the fasta loaded fine with the bulk-loader and 
using the --fastafile command..

Next, my gene models loaded fine with the bulk loader, so the db was 
populated. I turned on full-text searching by running the scripts, and 
stating -full text 1 in the conf file...
So it seems, I can do as you mentioned, query specific genes i.e cnot1, 
or with specific IDs or scaffold IDs, but what I really wanted is to be 
able to do generic gene searches using the 'maker' search, as done with 
my other databases, so that someone without knowledge of the contents of 
the database will recieve gene information. This I still can't do, but 
can be done with prior db's I set up that contained contig annotation 
vs. scaffolds, and I found was very useful returning all maker generated 
gene models.  With that, I thought the problem was with the nomenclature 
being used across annotations, scaffolds etc..

Claudia

On 21/03/2012 4:59 PM, Scott Cain wrote:
> Hi Claudia,
>
> I wanted to bring this back to the mailing lists, so I cc'ed them here.
>
> First, with the fasta loading issue: what command are you using to
> load the fasta sequences?  It works for me whether the fasta is at the
> bottom of the GFF file or if it is a separate fasta file (as long as I
> supply the --fastafile flag to the loader).
>
> About the searching problem: when I turn on full text searching (which
> means both running gmod_chado_fts_prep.pl and adding "-fulltext 1" to
> the db_args in the gbrowse config file), I can search for "cnot1" and
> find both a gene and an mRNA (of course, they are really the same
> feature, but GBrowse doesn't know that).  Also, searching for "maker"
> works, but in a real database, this will not be an effective query,
> since the number of results returned are limited, and presumably there
> will be lots of features resulting from a query like that.  Please
> remind me, is that what you wanted to do?
>
> Scott
>
>
>
>
> On Wed, Mar 21, 2012 at 3:16 PM, claudia<dinatal at uwindsor.ca>  wrote:
>> Hi Scott,
>>
>>   Wanted to give you a quick heads up that the bulk loader seems to be
>> loading my fasta files now after deleting the ' ##FASTA' header ( the first
>> line of the file now looks like this>scaffold0001)...
>> Never had this problem before, it seems the bulk loader wanted to see a '>'
>> symbol in front of the first line...
>>
>> -- when I say seems, I will let you know if it finishes, as it currently
>>   states " Loading sequences ( if any)" ... and I never made it this far
>> before :)
>>
>> Claudia
>>
>>
>>
>> On 21/03/2012 12:53 PM, Scott Cain wrote:
>>> Hi Claudia,
>>>
>>> I imagine one scaffold and gene models would be good--the problem is
>>> finding genes, right?
>>>
>>> Also, with loading fasta: were the corresponding features from the GFF
>>> file already loaded?  If so, that should have worked, and if it didn't
>>> it implies a bug.  If not, that's why.
>>>
>>> Scott
>>>
>>>
>>> On Wed, Mar 21, 2012 at 12:37 PM, claudia<dinatal at uwindsor.ca>    wrote:
>>>> Hi Scott,
>>>>   So would one scaffold with Maker gene models suffice? Do you want the
>>>> analysis as well?
>>>>
>>>> --along those same lines, I did try and load the original sequence
>>>> (fasta)
>>>> file first that I ran the Pipeline on and chado seems to refuse the files
>>>> saying they don't contain the appropriate feature '>' in the header which
>>>> in
>>>> fact they do i.e>    scaffold00001 ... So not sure what is wrong with the
>>>> fasta that chado doesn't want to load even if it is embedded in the GFF3,
>>>> the bulk loader or maker2chado return errors stating 'feature not
>>>> found'...
>>>>
>>>>
>>>> Claudia
>>>>
>>>>
>>>>
>>>> On 21/03/2012 12:20 PM, Scott Cain wrote:
>>>>> Hi Claudia,
>>>>>
>>>>> I was hoping to get actual files that I could do testing on, not
>>>>> pictures of files :-)
>>>>>
>>>>> Scott
>>>>>
>>>>>
>>>>> On Tue, Mar 20, 2012 at 4:15 PM, Dinatale C<dinatal at uwindsor.ca>
>>>>>   wrote:
>>>>>> Hi,
>>>>>>
>>>>>> Attached:  I have samples of the contig file ( I extracted the contig
>>>>>> features first to load prior to the gene models) the fasta of the
>>>>>> sequences
>>>>>> is in the footer of the gff3 file.
>>>>>>
>>>>>> --so basically, based on experience with contig annotations, I should
>>>>>> be
>>>>>> able to type in 'maker' in to the gbrowse search bar, and recieve all
>>>>>> the
>>>>>> maker gene annotations, but I don't. I must specifiy the exact ID i.e "
>>>>>> maker-scaffold11323-augustus-gene...." or 'scaffold11323'
>>>>>>
>>>>>> --so I wonder if it has to do with the fasta files being named as
>>>>>> 'scaffolds' and perhaps causing a problem with chado recognizing that
>>>>>> they
>>>>>> are linked to the gene annotations due to scaffold not being a SOFA
>>>>>> type
>>>>>> term, if in fact the sequences must be submitted to the database first?
>>>>>>
>>>>>>
>>>>>> Thanks in advance,
>>>>>>
>>>>>> Claudia
>>>>>>
>>>>>> On Tue, 20 Mar 2012 15:50:55 -0400 Scott Cain wrote:
>>>>>>> Hi Claudia,
>>>>>>>
>>>>>>> Can you post a sample of the gff that shows what you are looking for
>>>>>>> and
>>>>>>> not finding?
>>>>>>>
>>>>>>> Scott
>>>>>>>
>>>>>>>
>>>>>>> Sent from my iPad
>>>>>>>
>>>>>>> On Mar 20, 2012, at 2:03 PM, claudia wrote:
>>>>>>>
>>>>>>>> Hi,
>>>>>>>>
>>>>>>>> I have enabled full text searching and I still have this problem,
>>>>>>>> another reason for
>>>>>>> concern... So I wondered if in fact I changed all the ID's in the GFF3
>>>>>>> file to supercontigs,
>>>>>>> then perhaps Chado would better link all the terms, annotations, and
>>>>>>> fasta
>>>>>>> files....
>>>>>>> Although, i realize that the seq_id ( column 1) shouldn't need to be
>>>>>>> specific since the
>>>>>>> 'type' term would take care of designating the feature type, no?
>>>>>>>> Claudia
>>>>>>>>
>>>>>>>>
>>>>>>>>
>>>>>>>> On 20/03/2012 1:25 PM, Scott Cain wrote:
>>>>>>>>> Hi Claudia,
>>>>>>>>>
>>>>>>>>> I agree with everything that Carson wrote, except about name
>>>>>>>>> searching--it's a little trickier in Chado. What you probably want
>>>>>>>>> to
>>>>>>>>> do is implement full text searching. See:
>>>>>>>>>
>>>>>>>>> http://gmod.org/wiki/Chado_Full_Text_Search
>>>>>>>>>
>>>>>>>>> for more information on setting it up and maintaining it.
>>>>>>>>>
>>>>>>>>> Scott
>>>>>>>>>
>>>>>>>>>
>>>>>>>>> On Tue, Mar 20, 2012 at 1:13 PM, Carson Holt wrote:
>>>>>>>>>>> I have 2 concerns, the first is: regarding representing scaffold
>>>>>>>>>>> features in chado and gbrowse. I noticed that the Sequence
>>>>>>>>>>> ontology
>>>>>>>>>>> uses
>>>>>>>>>>> the term supercontig and so if my assembly generated scaffolds
>>>>>>>>>>> entitled
>>>>>>>>>>> "scaffold" should I change the names to supercontigs so that chado
>>>>>>>>>>> recognizes the terms?
>>>>>>>>>> Yes. You must use valid SO terms. It is a requirement of GFF3, and
>>>>>>>>>> Chado
>>>>>>>>>> will enforce this requirement on loading a GFF3 file (note Chado
>>>>>>>>>> will
>>>>>>>>>> even
>>>>>>>>>> go as far as to check the validity of the Ontology_term= attribute
>>>>>>>>>> in
>>>>>>>>>> GFF3
>>>>>>>>>> if you use it). You can decide to use contig or supercontig as your
>>>>>>>>>> sequence feature. It doesn?t really matter unless you are placing
>>>>>>>>>>
>>>>>>>>>> both
>>>>>>>>>> into the database as separate features (i.e. You have a supercontig
>>>>>>>>>> as
>>>>>>>>>> the
>>>>>>>>>> parent feature and then you enter contigs individually as children
>>>>>>>>>> of
>>>>>>>>>> the
>>>>>>>>>> supercontig).
>>>>>>>>>>
>>>>>>>>>>
>>>>>>>>>>> Corresponding to my first question, Maker does not know that the
>>>>>>>>>>> contigs
>>>>>>>>>>> are actually scaffold/supercontigs when annotating and so Maker
>>>>>>>>>>> will
>>>>>>>>>>> still call the "type" feature or column 3 in the GFF3, a 'contig',
>>>>>>>>>>> how
>>>>>>>>>>> can Maker be implemented to change this naming convention before
>>>>>>>>>>> annotation, or after?
>>>>>>>>>> Not really important unless you plan on making contigs children of
>>>>>>>>>> the
>>>>>>>>>> supercontig. But you can always do a search and replace. -->
>>>>>>>>>> cat file.gff | perl -ane 's/\tcontig\t/\tsupercontig\t/s; print
>>>>>>>>>> $_'>
>>>>>>>>>> new_file.gff
>>>>>>>>>>
>>>>>>>>>>
>>>>>>>>>>> Consequently, I am having problems pulling up gene features in
>>>>>>>>>>> Gbrowse
>>>>>>>>>>> when doing a generic gene search, and I must provide the maker
>>>>>>>>>>> generated
>>>>>>>>>>> unique-gene_id in the gbrowse search bar or the known sequence id
>>>>>>>>>>> i.e
>>>>>>>>>>> 'scaffold001', which is not useful for someone who does not have
>>>>>>>>>>> this
>>>>>>>>>>> information.
>>>>>>>>>>> ---- I do not have this problem when my seq_id, and 'type' feature
>>>>>>>>>>> id
>>>>>>>>>>> match in the true case of 'contigs'. I can do a generic gene
>>>>>>>>>>> search
>>>>>>>>>>> in
>>>>>>>>>>> gbrowse with the term 'maker' and gbrowse will provide me all the
>>>>>>>>>>> associated maker generated gene calls.
>>>>>>>>>> See "Adjusting GBrowse Name Searches" in the GBrowse tutorial -->
>>>>>>>>>> http://gmod.org/gbrowse2/tutorial/tutorial.html#naming
>>>>>>>>>>
>>>>>>>>>>
>>>>>>>>>> Thanks,
>>>>>>>>>> Carson
>>>>>>>>>>
>>>>>>>>>>
>>>>>>>>>>
>>>>>>>>>>
>>>>>>>>>>
>>>>>>>>>>
>>>>>>>>>>
>>>>>>>>>>
>>>>>>>>>>
>>>>>>>>>>
>>>>>>>>>>
>>>>>>>>>>> Thank you for any guidance resolving these concerns,
>>>>>>>>>>> Claudia
>>>>>>>>>>>
>>>>>>>>>>>
>>>>>>>>>>>
>>>>>>>>>>> --
>>>>>>>>>>> Claudia DiNatale
>>>>>>>>>>> Master's Candidate
>>>>>>>>>>> The Crosby Lab
>>>>>>>>>>> University of Windsor
>>>>>>>>>>> 519-253-3000 ext: 4755
>>>>>>>>>>>
>>>>>>>>>>>
>>>>>>>>>>> _______________________________________________
>>>>>>>>>>> maker-devel mailing list
>>>>>>>>>>> maker-devel at box290.bluehost.com
>>>>>>>>>>>
>>>>>>>>>>>
>>>>>>>>>>>
>>>>>>>>>>> http://box290.bluehost.com/mailman/listinfo/maker-devel_yandell-lab.org
>>>>>>>>>>
>>>>>>>>>> _______________________________________________
>>>>>>>>>> maker-devel mailing list
>>>>>>>>>> maker-devel at box290.bluehost.com
>>>>>>>>>>
>>>>>>>>>>
>>>>>>>>>>
>>>>>>>>>> http://box290.bluehost.com/mailman/listinfo/maker-devel_yandell-lab.org
>>>>>>>>>
>>>>>>>> --
>>>>>>>> Claudia DiNatale
>>>>>>>> Master's Candidate
>>>>>>>> The Crosby Lab
>>>>>>>> University of Windsor
>>>>>>>> 519-253-3000 ext: 4755
>>>>>>>>
>>>> --
>>>> Claudia DiNatale
>>>> Master's Candidate
>>>> The Crosby Lab
>>>> University of Windsor
>>>> 519-253-3000 ext: 4755
>>>>
>>>
>>
>> --
>> Claudia DiNatale
>> Master's Candidate
>> The Crosby Lab
>> University of Windsor
>> 519-253-3000 ext: 4755
>>
>
>


-- 
Claudia DiNatale
Master's Candidate
The Crosby Lab
University of Windsor
519-253-3000 ext: 4755




From carsonhh at gmail.com  Wed Mar 21 16:05:32 2012
From: carsonhh at gmail.com (Carson Holt)
Date: Wed, 21 Mar 2012 18:05:32 -0400
Subject: [maker-devel] maker 2.22/2.23: Segmentation fault while
 processing FASTA input
In-Reply-To: <4F68C963.3040108@uni-wuerzburg.de>
Message-ID: <CB8FC294.9902%carsonhh@gmail.com>

That is likely the strangest result I could imagine?  The --debug option
really only cause MAKER to print status messages everywhere and nothing
else, so there must be something else going on between the tests.


One things I did notice from the error log though -->
0.49	Inline	/home/s187512/perl/lib/perl5/site_perl/5.12.1/Inline.pm
	UNKNOWN	Inline::denter	/home/s187512/perl/lib/perl5/site_perl/5.12.1/Inlin
e/denter.pm


These are both being loaded from perl 5.12.1 (you are using 5.14.1).  That
can cause issues since I know the first one is executed at the C level and
I wouldn't be surprised if the same is true on the second one.



I also saw this -->
Can't locate package GDBM_File for @AnyDBM_File::ISA at
/storage/tmp/software/perl-5.14.1/lib/5.14.1/x86_64-linux-thread-multi/DB_F
ile.pm line 293.
Can't locate package NDBM_File for @AnyDBM_File::ISA at
/storage/tmp/software/perl-5.14.1/lib/5.14.1/x86_64-linux-thread-multi/DB_F
ile.pm line 293.
Can't locate package SDBM_File for @AnyDBM_File::ISA at
/storage/tmp/software/perl-5.14.1/lib/5.14.1/x86_64-linux-thread-multi/DB_F
ile.pm line 293.



This appears could be related to Bio::DB::Fasta (which would make sense
with the timing of the seg fault).  This is line 405 in the BEGIN
statement for Bio::DB::Fasta
-->  @AnyDBM_File::ISA = qw(DB_File GDBM_File NDBM_File SDBM_File)

I'm not sure what to do about those?  Are you able to install GDBM_File,
NDBM_File, or SDBM_File by themselves?  They really should just be
optional?  I know I don't have NDBM_File, and I don't get an error.
DB_File is part of the perl distribution, but can be updated via CPAN.
Perhaps that would be good to do.  It may just be that DB_file is broken
and falling back to the other modules doesn?t work because you don't have
them.  There is also the chance that the issue is really with Berkley_DB.
DB_File accesses Berkley_DB and it wants version 1.x, but will work with
2.x and 3.x.  You may need to even go as far as building a new Berkley_DB.

Well that's enough to try for now.

Thanks,
Carson


On 12-03-20 2:16 PM, "Thomas Hackl" <thomas.hackl at uni-wuerzburg.de> wrote:

>Hi,
>
>I installed and ran the debug version of maker. Without -debug it
>results in the expected segmentation fault. With -debug it paradoxically
>finishes without the error.
>
>I screened the debug log anyway but could not find anything that helped
>me to localize the problem. I attached a condensed version (sort | uniq)
>of the log.
>Any ideas are appreciated.
>
>Regards
>Thomas
>
>
>
>Am 19.03.2012 17:24, schrieb Carson Holt:
>> Ok.  I finished the special debug version over the weekend.  Run with
>> -debug set as a command line flag.  Capture and return the STDERR on
>> failure.  It will list all modules used, the versions, and when they are
>> called so we can see what happens right before failure.
>>
>> http://yandell-lab.org/research/maker_debug.tgz
>>
>>
>> Thanks,
>> Carson
>>
>>
>>
>> On 12-03-14 1:57 AM, "Felix Bemm"<felix.bemm at uni-wuerzburg.de>  wrote:
>>
>>> Hi,
>>>
>>> Thomas and I are colleagues and dealing with the same problem here. I
>>> wrote some test code that forced the indexing and it work fine. We are
>>> using most of the bioperl seqio and db modules in combination with
>>>other
>>> tools and don't experience the same problem there at the moment.
>>>
>>> Regards
>>> Felix
>>>
>>> Am 13.03.2012 22:37, schrieb Barry Moore:
>>>> You might also try a short perl script outside of MAKER to exercise
>>>> Bio::DB::Fasta (which I believe is the module MAKER uses for Fasta
>>>> indexing - correct Carson?).
>>>>
>>>> Something like this should work to force indexing:
>>>>
>>>> useBio::DB::Fasta;
>>>> my $db = Bio::DB::Fasta->new('/path/to/fasta/files');
>>>> my$seq=$db->seq($seqid, $start, $end);
>>>>
>>>> Point it at your fasta directory or file.
>>>>
>>>> B
>>>>
>>>> On Mar 13, 2012, at 3:41 AM, Thomas Hackl wrote:
>>>>
>>>>> Hello,
>>>>>
>>>>> We reinstalled the packages you suggested
>>>>>
>>>>> forks is up to date (0.34).
>>>>> forks::shared is up to date (0.34).
>>>>> Inline::C is up to date (0.50).
>>>>> Storable is up to date (2.30).
>>>>>
>>>>> as well as BioPerl.
>>>>>
>>>>> The problem is still the same.
>>>>>
>>>>> With MPI it terminates with this message:
>>>>>
>>>>> STATUS: Parsing control files...
>>>>> STATUS: Processing and indexing input FASTA files...
>>>>>
>>>>> 
>>>>>======================================================================
>>>>>==
>>>>> =============
>>>>>
>>>>>
>>>>> = BAD TERMINATION OF ONE OF YOUR APPLICATION PROCESSES
>>>>> = EXIT CODE: 11
>>>>> = CLEANING UP REMAINING PROCESSES
>>>>> = YOU CAN IGNORE THE BELOW CLEANUP MESSAGES
>>>>>
>>>>> 
>>>>>======================================================================
>>>>>==
>>>>> =============
>>>>>
>>>>> APPLICATION TERMINATED WITH THE EXIT STRING: Segmentation fault
>>>>> (signal 11)
>>>>>
>>>>> which I presume is also the same problem.
>>>>>
>>>>> I am with you that the error is caused somewhere on the C level. If
>>>>> the indexing step
>>>>> is handled by non-maker modules exclusively, than the fact that the
>>>>> 2.15 version works,
>>>>> suggests that you are using different modules/methods in the current
>>>>> releases?
>>>>>
>>>>> In any case, I think a version with verbose status messages might
>>>>>help
>>>>> to localize the
>>>>> source of the problem.
>>>>>
>>>>> Regards
>>>>> Thomas
>>>>>
>>>>> Am 07.03.2012 23:45, schrieb Carson Holt:
>>>>>> There should be no new hardware requirement. But there is always a
>>>>>> chance
>>>>>> that there is an issue with one of the perl modules being used. I
>>>>>> assume
>>>>>> the failure is happening when using maker serially and you are not
>>>>>> using
>>>>>> MPI.
>>>>>>
>>>>>> Could you reinstall the following perl modules, and try again. If
>>>>>>you
>>>>>> are
>>>>>> using CPAN, do a 'force install' to force it to reinstall.
>>>>>>
>>>>>> Modules:
>>>>>> *Storable
>>>>>> *Inline::C
>>>>>> *forks
>>>>>> *forks::shared
>>>>>>
>>>>>> Also try reinstalling the latest version of BioPerl.
>>>>>>
>>>>>> The fact that this is a seg fault suggests that something is
>>>>>> happemning at
>>>>>> the C level (just outside of Perl). Those area all the modules MAKER
>>>>>> uses
>>>>>> that will call back to the C level. BioPerl has a fasta indexing
>>>>>> module
>>>>>> that is also making calls outside of Perl, and the fact it fails at
>>>>>> that
>>>>>> point makes it a suspect.
>>>>>>
>>>>>> Let me know what happens. I can always generate an alternate MAKER
>>>>>> executable for you to run with additional status messages that may
>>>>>> help
>>>>>> identify exactly which module is being called right before the
>>>>>> failure.
>>>>>>
>>>>>> Thanks,
>>>>>> Carson
>>>>>>
>>>>>>
>>>>>>
>>>>>> On 12-03-07 3:31 AM, "Thomas Hackl"<thomas.hackl at uni-wuerzburg.de
>>>>>> <mailto:thomas.hackl at uni-wuerzburg.de>>  wrote:
>>>>>>
>>>>>>> Hello,
>>>>>>>
>>>>>>> we want to use a current release of maker (2.22, 2.23) but the
>>>>>>> program
>>>>>>> terminates with a seg fault while processing the input FASTA files.
>>>>>>> maker 2.15 , which we have been using for quite some time, runs
>>>>>>> perfectly with identical data and setup.
>>>>>>>
>>>>>>> Please contact me if you need specifics on hardware, OS or anything
>>>>>>> else.
>>>>>>>
>>>>>>> Best regards
>>>>>>> Thomas
>>>>>>>
>>>>>>> --
>>>>>>> Thomas Hackl
>>>>>>> Julius-Maximilians-Universit?t
>>>>>>> Department of Bioinformatics
>>>>>>> 97074 W?rzburg, Germany
>>>>>>> Fon: +49 931 - 31 86883
>>>>>>> Mail: thomas.hackl at uni-wuerzburg.de
>>>>>>> <mailto:thomas.hackl at uni-wuerzburg.de>
>>>>>>>
>>>>>>>
>>>>>>> _______________________________________________
>>>>>>> maker-devel mailing list
>>>>>>> maker-devel at box290.bluehost.com
>>>>>>> <mailto:maker-devel at box290.bluehost.com>
>>>>>>>
>>>>>>> 
>>>>>>>http://box290.bluehost.com/mailman/listinfo/maker-devel_yandell-lab.
>>>>>>>or
>>>>>>> g
>>>>>
>>>>> --
>>>>> Thomas Hackl
>>>>> Julius-Maximilians-Universit?t
>>>>> Department of Bioinformatics
>>>>> 97074 W?rzburg, Germany
>>>>> Fon: +49 931 - 31 86883
>>>>> Mail: thomas.hackl at uni-wuerzburg.de
>>>>> <mailto:thomas.hackl at uni-wuerzburg.de>
>>>>>
>>>>>
>>>>> _______________________________________________
>>>>> maker-devel mailing list
>>>>> maker-devel at box290.bluehost.com
>>>>> <mailto:maker-devel at box290.bluehost.com>
>>>>> 
>>>>>http://box290.bluehost.com/mailman/listinfo/maker-devel_yandell-lab.or
>>>>>g
>>>> Barry Moore
>>>> Research Scientist
>>>> Dept. of Human Genetics
>>>> University of Utah
>>>> Salt Lake City, UT 84112
>>>> --------------------------------------------
>>>> (801) 585-3543
>>>>
>>>>
>>>>
>>>>
>>>>
>>>>
>>>> _______________________________________________
>>>> maker-devel mailing list
>>>> maker-devel at box290.bluehost.com
>>>> 
>>>>http://box290.bluehost.com/mailman/listinfo/maker-devel_yandell-lab.org
>>> _______________________________________________
>>> maker-devel mailing list
>>> maker-devel at box290.bluehost.com
>>> http://box290.bluehost.com/mailman/listinfo/maker-devel_yandell-lab.org
>
>-- 
>Thomas Hackl
>Julius-Maximilians-Universit?t
>Department of Bioinformatics
>97074 W?rzburg, Germany
>Fon:  +49 931 - 31 86883
>Mail: thomas.hackl at uni-wuerzburg.de
>
>_______________________________________________
>maker-devel mailing list
>maker-devel at box290.bluehost.com
>http://box290.bluehost.com/mailman/listinfo/maker-devel_yandell-lab.org





From seoanezonjic at hotmail.com  Thu Mar 22 03:38:39 2012
From: seoanezonjic at hotmail.com (Seoane Zonjic)
Date: Thu, 22 Mar 2012 02:38:39 -0700 (PDT)
Subject: [maker-devel] Error: Can't call method "num_hsps" on unblessed
	reference
Message-ID: <16b63903-4205-4064-ab30-efe67b37f7fa@b18g2000vbz.googlegroups.com>

Hi!
First, sorry for my poor english. I updated Maker at last release and
I have triying it with a set of contigs. With one of contigs, Maker
give me this error:

Processing transcripts into genes
Calculating annotation quality statistics
Can't call method "num_hsps" on unblessed referenceERROR: Failed while
adding statistics to annotations
ERROR: Chunk failed at level:3, tier_type:3
FAILED CONTIG:contig_4_0

ERROR: Chunk failed at level:7, tier_type:0
FAILED CONTIG:contig_4_0

At first, I thought that problem were the length of contig (125Kb). I
cut the the sequence in parts of 10Kb but a part again give me the
same error. I have worked with the debugger version of maker (I took
it of post of segmentation fault).
The input fasta (the part that failed me) and all logs are in this
link:
http://dl.dropbox.com/u/54903225/log.tar.gz
Other contigs of same set,  bigger or equal, work fine without
problem. There are something in this sequence that broken the Maker
run.
Thanks in advance



From carsonhh at gmail.com  Thu Mar 22 08:36:37 2012
From: carsonhh at gmail.com (Carson Holt)
Date: Thu, 22 Mar 2012 10:36:37 -0400
Subject: [maker-devel] Error: Can't call method "num_hsps" on unblessed
 reference
In-Reply-To: <16b63903-4205-4064-ab30-efe67b37f7fa@b18g2000vbz.googlegroups.com>
Message-ID: <CB90B0FA.9946%carsonhh@gmail.com>

Could you make a tarball of this directory and send it to me exactly as is
 --> 
/export/home_users/home/cvi_114_uma/pedro/testmaker/Spliced2.maker.output/S
pliced2_datastore/72/86/contig_4_0/

Thanks,
Carson


On 12-03-22 5:38 AM, "Seoane Zonjic" <seoanezonjic at hotmail.com> wrote:

>Hi!
>First, sorry for my poor english. I updated Maker at last release and
>I have triying it with a set of contigs. With one of contigs, Maker
>give me this error:
>
>Processing transcripts into genes
>Calculating annotation quality statistics
>Can't call method "num_hsps" on unblessed referenceERROR: Failed while
>adding statistics to annotations
>ERROR: Chunk failed at level:3, tier_type:3
>FAILED CONTIG:contig_4_0
>
>ERROR: Chunk failed at level:7, tier_type:0
>FAILED CONTIG:contig_4_0
>
>At first, I thought that problem were the length of contig (125Kb). I
>cut the the sequence in parts of 10Kb but a part again give me the
>same error. I have worked with the debugger version of maker (I took
>it of post of segmentation fault).
>The input fasta (the part that failed me) and all logs are in this
>link:
>http://dl.dropbox.com/u/54903225/log.tar.gz
>Other contigs of same set,  bigger or equal, work fine without
>problem. There are something in this sequence that broken the Maker
>run.
>Thanks in advance
>
>_______________________________________________
>maker-devel mailing list
>maker-devel at box290.bluehost.com
>http://box290.bluehost.com/mailman/listinfo/maker-devel_yandell-lab.org





From thomas.hackl at uni-wuerzburg.de  Mon Mar 26 04:51:48 2012
From: thomas.hackl at uni-wuerzburg.de (Thomas Hackl)
Date: Mon, 26 Mar 2012 12:51:48 +0200
Subject: [maker-devel] maker 2.22/2.23: Segmentation fault while
 processing FASTA input
In-Reply-To: <CB8FC294.9902%carsonhh@gmail.com>
References: <CB8FC294.9902%carsonhh@gmail.com>
Message-ID: <4F704A44.2080707@uni-wuerzburg.de>

Hi,

I was finally able to "fix" the Problem. I tried everything you 
suggested, nice catch on my screwed up Perl lib path btw, but I could 
neither install GDBM_File or NDBM_File nor Berkley_DB separately. In the 
end I simply removed the  ISA relations to the modules in question from 
the source code and now it seems to works fine...

sed -i 's/qw(DB_File GDBM_File NDBM_File SDBM_File)/qw(DB_File)/'

So thanks a lot for your prompt and comprehensive response, the debug 
executables and the help with the messages.

Regards
Thomas



Am 21.03.2012 23:05, schrieb Carson Holt:
> That is likely the strangest result I could imagine?  The --debug option
> really only cause MAKER to print status messages everywhere and nothing
> else, so there must be something else going on between the tests.
>
>
> One things I did notice from the error log though -->
> 0.49	Inline	/home/s187512/perl/lib/perl5/site_perl/5.12.1/Inline.pm
> 	UNKNOWN	Inline::denter	/home/s187512/perl/lib/perl5/site_perl/5.12.1/Inlin
> e/denter.pm
>
>
> These are both being loaded from perl 5.12.1 (you are using 5.14.1).  That
> can cause issues since I know the first one is executed at the C level and
> I wouldn't be surprised if the same is true on the second one.
>
>
>
> I also saw this -->
> Can't locate package GDBM_File for @AnyDBM_File::ISA at
> /storage/tmp/software/perl-5.14.1/lib/5.14.1/x86_64-linux-thread-multi/DB_F
> ile.pm line 293.
> Can't locate package NDBM_File for @AnyDBM_File::ISA at
> /storage/tmp/software/perl-5.14.1/lib/5.14.1/x86_64-linux-thread-multi/DB_F
> ile.pm line 293.
> Can't locate package SDBM_File for @AnyDBM_File::ISA at
> /storage/tmp/software/perl-5.14.1/lib/5.14.1/x86_64-linux-thread-multi/DB_F
> ile.pm line 293.
>
>
>
> This appears could be related to Bio::DB::Fasta (which would make sense
> with the timing of the seg fault).  This is line 405 in the BEGIN
> statement for Bio::DB::Fasta
> -->   @AnyDBM_File::ISA = qw(DB_File GDBM_File NDBM_File SDBM_File)
>
> I'm not sure what to do about those?  Are you able to install GDBM_File,
> NDBM_File, or SDBM_File by themselves?  They really should just be
> optional?  I know I don't have NDBM_File, and I don't get an error.
> DB_File is part of the perl distribution, but can be updated via CPAN.
> Perhaps that would be good to do.  It may just be that DB_file is broken
> and falling back to the other modules doesn?t work because you don't have
> them.  There is also the chance that the issue is really with Berkley_DB.
> DB_File accesses Berkley_DB and it wants version 1.x, but will work with
> 2.x and 3.x.  You may need to even go as far as building a new Berkley_DB.
>
> Well that's enough to try for now.
>
> Thanks,
> Carson
>
>
> On 12-03-20 2:16 PM, "Thomas Hackl"<thomas.hackl at uni-wuerzburg.de>  wrote:
>
>> Hi,
>>
>> I installed and ran the debug version of maker. Without -debug it
>> results in the expected segmentation fault. With -debug it paradoxically
>> finishes without the error.
>>
>> I screened the debug log anyway but could not find anything that helped
>> me to localize the problem. I attached a condensed version (sort | uniq)
>> of the log.
>> Any ideas are appreciated.
>>
>> Regards
>> Thomas
>>
>>
>>
>> Am 19.03.2012 17:24, schrieb Carson Holt:
>>> Ok.  I finished the special debug version over the weekend.  Run with
>>> -debug set as a command line flag.  Capture and return the STDERR on
>>> failure.  It will list all modules used, the versions, and when they are
>>> called so we can see what happens right before failure.
>>>
>>> http://yandell-lab.org/research/maker_debug.tgz
>>>
>>>
>>> Thanks,
>>> Carson
>>>
>>>
>>>
>>> On 12-03-14 1:57 AM, "Felix Bemm"<felix.bemm at uni-wuerzburg.de>   wrote:
>>>
>>>> Hi,
>>>>
>>>> Thomas and I are colleagues and dealing with the same problem here. I
>>>> wrote some test code that forced the indexing and it work fine. We are
>>>> using most of the bioperl seqio and db modules in combination with
>>>> other
>>>> tools and don't experience the same problem there at the moment.
>>>>
>>>> Regards
>>>> Felix
>>>>
>>>> Am 13.03.2012 22:37, schrieb Barry Moore:
>>>>> You might also try a short perl script outside of MAKER to exercise
>>>>> Bio::DB::Fasta (which I believe is the module MAKER uses for Fasta
>>>>> indexing - correct Carson?).
>>>>>
>>>>> Something like this should work to force indexing:
>>>>>
>>>>> useBio::DB::Fasta;
>>>>> my $db = Bio::DB::Fasta->new('/path/to/fasta/files');
>>>>> my$seq=$db->seq($seqid, $start, $end);
>>>>>
>>>>> Point it at your fasta directory or file.
>>>>>
>>>>> B
>>>>>
>>>>> On Mar 13, 2012, at 3:41 AM, Thomas Hackl wrote:
>>>>>
>>>>>> Hello,
>>>>>>
>>>>>> We reinstalled the packages you suggested
>>>>>>
>>>>>> forks is up to date (0.34).
>>>>>> forks::shared is up to date (0.34).
>>>>>> Inline::C is up to date (0.50).
>>>>>> Storable is up to date (2.30).
>>>>>>
>>>>>> as well as BioPerl.
>>>>>>
>>>>>> The problem is still the same.
>>>>>>
>>>>>> With MPI it terminates with this message:
>>>>>>
>>>>>> STATUS: Parsing control files...
>>>>>> STATUS: Processing and indexing input FASTA files...
>>>>>>
>>>>>>
>>>>>> ======================================================================
>>>>>> ==
>>>>>> =============
>>>>>>
>>>>>>
>>>>>> = BAD TERMINATION OF ONE OF YOUR APPLICATION PROCESSES
>>>>>> = EXIT CODE: 11
>>>>>> = CLEANING UP REMAINING PROCESSES
>>>>>> = YOU CAN IGNORE THE BELOW CLEANUP MESSAGES
>>>>>>
>>>>>>
>>>>>> ======================================================================
>>>>>> ==
>>>>>> =============
>>>>>>
>>>>>> APPLICATION TERMINATED WITH THE EXIT STRING: Segmentation fault
>>>>>> (signal 11)
>>>>>>
>>>>>> which I presume is also the same problem.
>>>>>>
>>>>>> I am with you that the error is caused somewhere on the C level. If
>>>>>> the indexing step
>>>>>> is handled by non-maker modules exclusively, than the fact that the
>>>>>> 2.15 version works,
>>>>>> suggests that you are using different modules/methods in the current
>>>>>> releases?
>>>>>>
>>>>>> In any case, I think a version with verbose status messages might
>>>>>> help
>>>>>> to localize the
>>>>>> source of the problem.
>>>>>>
>>>>>> Regards
>>>>>> Thomas
>>>>>>
>>>>>> Am 07.03.2012 23:45, schrieb Carson Holt:
>>>>>>> There should be no new hardware requirement. But there is always a
>>>>>>> chance
>>>>>>> that there is an issue with one of the perl modules being used. I
>>>>>>> assume
>>>>>>> the failure is happening when using maker serially and you are not
>>>>>>> using
>>>>>>> MPI.
>>>>>>>
>>>>>>> Could you reinstall the following perl modules, and try again. If
>>>>>>> you
>>>>>>> are
>>>>>>> using CPAN, do a 'force install' to force it to reinstall.
>>>>>>>
>>>>>>> Modules:
>>>>>>> *Storable
>>>>>>> *Inline::C
>>>>>>> *forks
>>>>>>> *forks::shared
>>>>>>>
>>>>>>> Also try reinstalling the latest version of BioPerl.
>>>>>>>
>>>>>>> The fact that this is a seg fault suggests that something is
>>>>>>> happemning at
>>>>>>> the C level (just outside of Perl). Those area all the modules MAKER
>>>>>>> uses
>>>>>>> that will call back to the C level. BioPerl has a fasta indexing
>>>>>>> module
>>>>>>> that is also making calls outside of Perl, and the fact it fails at
>>>>>>> that
>>>>>>> point makes it a suspect.
>>>>>>>
>>>>>>> Let me know what happens. I can always generate an alternate MAKER
>>>>>>> executable for you to run with additional status messages that may
>>>>>>> help
>>>>>>> identify exactly which module is being called right before the
>>>>>>> failure.
>>>>>>>
>>>>>>> Thanks,
>>>>>>> Carson
>>>>>>>
>>>>>>>
>>>>>>>
>>>>>>> On 12-03-07 3:31 AM, "Thomas Hackl"<thomas.hackl at uni-wuerzburg.de
>>>>>>> <mailto:thomas.hackl at uni-wuerzburg.de>>   wrote:
>>>>>>>
>>>>>>>> Hello,
>>>>>>>>
>>>>>>>> we want to use a current release of maker (2.22, 2.23) but the
>>>>>>>> program
>>>>>>>> terminates with a seg fault while processing the input FASTA files.
>>>>>>>> maker 2.15 , which we have been using for quite some time, runs
>>>>>>>> perfectly with identical data and setup.
>>>>>>>>
>>>>>>>> Please contact me if you need specifics on hardware, OS or anything
>>>>>>>> else.
>>>>>>>>
>>>>>>>> Best regards
>>>>>>>> Thomas
>>>>>>>>
>>>>>>>> --
>>>>>>>> Thomas Hackl
>>>>>>>> Julius-Maximilians-Universit?t
>>>>>>>> Department of Bioinformatics
>>>>>>>> 97074 W?rzburg, Germany
>>>>>>>> Fon: +49 931 - 31 86883
>>>>>>>> Mail: thomas.hackl at uni-wuerzburg.de
>>>>>>>> <mailto:thomas.hackl at uni-wuerzburg.de>
>>>>>>>>
>>>>>>>>
>>>>>>>> _______________________________________________
>>>>>>>> maker-devel mailing list
>>>>>>>> maker-devel at box290.bluehost.com
>>>>>>>> <mailto:maker-devel at box290.bluehost.com>
>>>>>>>>
>>>>>>>>
>>>>>>>> http://box290.bluehost.com/mailman/listinfo/maker-devel_yandell-lab.
>>>>>>>> or
>>>>>>>> g
>>>>>> --
>>>>>> Thomas Hackl
>>>>>> Julius-Maximilians-Universit?t
>>>>>> Department of Bioinformatics
>>>>>> 97074 W?rzburg, Germany
>>>>>> Fon: +49 931 - 31 86883
>>>>>> Mail: thomas.hackl at uni-wuerzburg.de
>>>>>> <mailto:thomas.hackl at uni-wuerzburg.de>
>>>>>>
>>>>>>
>>>>>> _______________________________________________
>>>>>> maker-devel mailing list
>>>>>> maker-devel at box290.bluehost.com
>>>>>> <mailto:maker-devel at box290.bluehost.com>
>>>>>>
>>>>>> http://box290.bluehost.com/mailman/listinfo/maker-devel_yandell-lab.or
>>>>>> g
>>>>> Barry Moore
>>>>> Research Scientist
>>>>> Dept. of Human Genetics
>>>>> University of Utah
>>>>> Salt Lake City, UT 84112
>>>>> --------------------------------------------
>>>>> (801) 585-3543
>>>>>
>>>>>
>>>>>
>>>>>
>>>>>
>>>>>
>>>>> _______________________________________________
>>>>> maker-devel mailing list
>>>>> maker-devel at box290.bluehost.com
>>>>>
>>>>> http://box290.bluehost.com/mailman/listinfo/maker-devel_yandell-lab.org
>>>> _______________________________________________
>>>> maker-devel mailing list
>>>> maker-devel at box290.bluehost.com
>>>> http://box290.bluehost.com/mailman/listinfo/maker-devel_yandell-lab.org
>> --
>> Thomas Hackl
>> Julius-Maximilians-Universit?t
>> Department of Bioinformatics
>> 97074 W?rzburg, Germany
>> Fon:  +49 931 - 31 86883
>> Mail: thomas.hackl at uni-wuerzburg.de
>>
>> _______________________________________________
>> maker-devel mailing list
>> maker-devel at box290.bluehost.com
>> http://box290.bluehost.com/mailman/listinfo/maker-devel_yandell-lab.org


-- 
Thomas Hackl
Julius-Maximilians-Universit?t
Department of Bioinformatics
97074 W?rzburg, Germany
Fon:  +49 931 - 31 86883
Mail: thomas.hackl at uni-wuerzburg.de




From carsonhh at gmail.com  Mon Mar 26 07:01:52 2012
From: carsonhh at gmail.com (Carson Holt)
Date: Mon, 26 Mar 2012 09:01:52 -0400
Subject: [maker-devel] maker 2.22/2.23: Segmentation fault while
 processing FASTA input
In-Reply-To: <4F704A44.2080707@uni-wuerzburg.de>
Message-ID: <CB95E04E.9E8B%carsonhh@gmail.com>

Well, if that works, I'd call it a success.  Just be careful with any
future updates to BioPerl.  Since the root cause of the problem may still
be there.

Thanks,
Carson




On 12-03-26 6:51 AM, "Thomas Hackl" <thomas.hackl at uni-wuerzburg.de> wrote:

>Hi,
>
>I was finally able to "fix" the Problem. I tried everything you
>suggested, nice catch on my screwed up Perl lib path btw, but I could
>neither install GDBM_File or NDBM_File nor Berkley_DB separately. In the
>end I simply removed the  ISA relations to the modules in question from
>the source code and now it seems to works fine...
>
>sed -i 's/qw(DB_File GDBM_File NDBM_File SDBM_File)/qw(DB_File)/'
>
>So thanks a lot for your prompt and comprehensive response, the debug
>executables and the help with the messages.
>
>Regards
>Thomas
>
>
>
>Am 21.03.2012 23:05, schrieb Carson Holt:
>> That is likely the strangest result I could imagine?  The --debug option
>> really only cause MAKER to print status messages everywhere and nothing
>> else, so there must be something else going on between the tests.
>>
>>
>> One things I did notice from the error log though -->
>> 0.49	Inline	/home/s187512/perl/lib/perl5/site_perl/5.12.1/Inline.pm
>> 
>>	UNKNOWN	Inline::denter	/home/s187512/perl/lib/perl5/site_perl/5.12.1/Inl
>>in
>> e/denter.pm
>>
>>
>> These are both being loaded from perl 5.12.1 (you are using 5.14.1).
>>That
>> can cause issues since I know the first one is executed at the C level
>>and
>> I wouldn't be surprised if the same is true on the second one.
>>
>>
>>
>> I also saw this -->
>> Can't locate package GDBM_File for @AnyDBM_File::ISA at
>> 
>>/storage/tmp/software/perl-5.14.1/lib/5.14.1/x86_64-linux-thread-multi/DB
>>_F
>> ile.pm line 293.
>> Can't locate package NDBM_File for @AnyDBM_File::ISA at
>> 
>>/storage/tmp/software/perl-5.14.1/lib/5.14.1/x86_64-linux-thread-multi/DB
>>_F
>> ile.pm line 293.
>> Can't locate package SDBM_File for @AnyDBM_File::ISA at
>> 
>>/storage/tmp/software/perl-5.14.1/lib/5.14.1/x86_64-linux-thread-multi/DB
>>_F
>> ile.pm line 293.
>>
>>
>>
>> This appears could be related to Bio::DB::Fasta (which would make sense
>> with the timing of the seg fault).  This is line 405 in the BEGIN
>> statement for Bio::DB::Fasta
>> -->   @AnyDBM_File::ISA = qw(DB_File GDBM_File NDBM_File SDBM_File)
>>
>> I'm not sure what to do about those?  Are you able to install GDBM_File,
>> NDBM_File, or SDBM_File by themselves?  They really should just be
>> optional?  I know I don't have NDBM_File, and I don't get an error.
>> DB_File is part of the perl distribution, but can be updated via CPAN.
>> Perhaps that would be good to do.  It may just be that DB_file is broken
>> and falling back to the other modules doesn?t work because you don't
>>have
>> them.  There is also the chance that the issue is really with
>>Berkley_DB.
>> DB_File accesses Berkley_DB and it wants version 1.x, but will work with
>> 2.x and 3.x.  You may need to even go as far as building a new
>>Berkley_DB.
>>
>> Well that's enough to try for now.
>>
>> Thanks,
>> Carson
>>
>>
>> On 12-03-20 2:16 PM, "Thomas Hackl"<thomas.hackl at uni-wuerzburg.de>
>>wrote:
>>
>>> Hi,
>>>
>>> I installed and ran the debug version of maker. Without -debug it
>>> results in the expected segmentation fault. With -debug it
>>>paradoxically
>>> finishes without the error.
>>>
>>> I screened the debug log anyway but could not find anything that helped
>>> me to localize the problem. I attached a condensed version (sort |
>>>uniq)
>>> of the log.
>>> Any ideas are appreciated.
>>>
>>> Regards
>>> Thomas
>>>
>>>
>>>
>>> Am 19.03.2012 17:24, schrieb Carson Holt:
>>>> Ok.  I finished the special debug version over the weekend.  Run with
>>>> -debug set as a command line flag.  Capture and return the STDERR on
>>>> failure.  It will list all modules used, the versions, and when they
>>>>are
>>>> called so we can see what happens right before failure.
>>>>
>>>> http://yandell-lab.org/research/maker_debug.tgz
>>>>
>>>>
>>>> Thanks,
>>>> Carson
>>>>
>>>>
>>>>
>>>> On 12-03-14 1:57 AM, "Felix Bemm"<felix.bemm at uni-wuerzburg.de>
>>>>wrote:
>>>>
>>>>> Hi,
>>>>>
>>>>> Thomas and I are colleagues and dealing with the same problem here. I
>>>>> wrote some test code that forced the indexing and it work fine. We
>>>>>are
>>>>> using most of the bioperl seqio and db modules in combination with
>>>>> other
>>>>> tools and don't experience the same problem there at the moment.
>>>>>
>>>>> Regards
>>>>> Felix
>>>>>
>>>>> Am 13.03.2012 22:37, schrieb Barry Moore:
>>>>>> You might also try a short perl script outside of MAKER to exercise
>>>>>> Bio::DB::Fasta (which I believe is the module MAKER uses for Fasta
>>>>>> indexing - correct Carson?).
>>>>>>
>>>>>> Something like this should work to force indexing:
>>>>>>
>>>>>> useBio::DB::Fasta;
>>>>>> my $db = Bio::DB::Fasta->new('/path/to/fasta/files');
>>>>>> my$seq=$db->seq($seqid, $start, $end);
>>>>>>
>>>>>> Point it at your fasta directory or file.
>>>>>>
>>>>>> B
>>>>>>
>>>>>> On Mar 13, 2012, at 3:41 AM, Thomas Hackl wrote:
>>>>>>
>>>>>>> Hello,
>>>>>>>
>>>>>>> We reinstalled the packages you suggested
>>>>>>>
>>>>>>> forks is up to date (0.34).
>>>>>>> forks::shared is up to date (0.34).
>>>>>>> Inline::C is up to date (0.50).
>>>>>>> Storable is up to date (2.30).
>>>>>>>
>>>>>>> as well as BioPerl.
>>>>>>>
>>>>>>> The problem is still the same.
>>>>>>>
>>>>>>> With MPI it terminates with this message:
>>>>>>>
>>>>>>> STATUS: Parsing control files...
>>>>>>> STATUS: Processing and indexing input FASTA files...
>>>>>>>
>>>>>>>
>>>>>>> 
>>>>>>>====================================================================
>>>>>>>==
>>>>>>> ==
>>>>>>> =============
>>>>>>>
>>>>>>>
>>>>>>> = BAD TERMINATION OF ONE OF YOUR APPLICATION PROCESSES
>>>>>>> = EXIT CODE: 11
>>>>>>> = CLEANING UP REMAINING PROCESSES
>>>>>>> = YOU CAN IGNORE THE BELOW CLEANUP MESSAGES
>>>>>>>
>>>>>>>
>>>>>>> 
>>>>>>>====================================================================
>>>>>>>==
>>>>>>> ==
>>>>>>> =============
>>>>>>>
>>>>>>> APPLICATION TERMINATED WITH THE EXIT STRING: Segmentation fault
>>>>>>> (signal 11)
>>>>>>>
>>>>>>> which I presume is also the same problem.
>>>>>>>
>>>>>>> I am with you that the error is caused somewhere on the C level. If
>>>>>>> the indexing step
>>>>>>> is handled by non-maker modules exclusively, than the fact that the
>>>>>>> 2.15 version works,
>>>>>>> suggests that you are using different modules/methods in the
>>>>>>>current
>>>>>>> releases?
>>>>>>>
>>>>>>> In any case, I think a version with verbose status messages might
>>>>>>> help
>>>>>>> to localize the
>>>>>>> source of the problem.
>>>>>>>
>>>>>>> Regards
>>>>>>> Thomas
>>>>>>>
>>>>>>> Am 07.03.2012 23:45, schrieb Carson Holt:
>>>>>>>> There should be no new hardware requirement. But there is always a
>>>>>>>> chance
>>>>>>>> that there is an issue with one of the perl modules being used. I
>>>>>>>> assume
>>>>>>>> the failure is happening when using maker serially and you are not
>>>>>>>> using
>>>>>>>> MPI.
>>>>>>>>
>>>>>>>> Could you reinstall the following perl modules, and try again. If
>>>>>>>> you
>>>>>>>> are
>>>>>>>> using CPAN, do a 'force install' to force it to reinstall.
>>>>>>>>
>>>>>>>> Modules:
>>>>>>>> *Storable
>>>>>>>> *Inline::C
>>>>>>>> *forks
>>>>>>>> *forks::shared
>>>>>>>>
>>>>>>>> Also try reinstalling the latest version of BioPerl.
>>>>>>>>
>>>>>>>> The fact that this is a seg fault suggests that something is
>>>>>>>> happemning at
>>>>>>>> the C level (just outside of Perl). Those area all the modules
>>>>>>>>MAKER
>>>>>>>> uses
>>>>>>>> that will call back to the C level. BioPerl has a fasta indexing
>>>>>>>> module
>>>>>>>> that is also making calls outside of Perl, and the fact it fails
>>>>>>>>at
>>>>>>>> that
>>>>>>>> point makes it a suspect.
>>>>>>>>
>>>>>>>> Let me know what happens. I can always generate an alternate MAKER
>>>>>>>> executable for you to run with additional status messages that may
>>>>>>>> help
>>>>>>>> identify exactly which module is being called right before the
>>>>>>>> failure.
>>>>>>>>
>>>>>>>> Thanks,
>>>>>>>> Carson
>>>>>>>>
>>>>>>>>
>>>>>>>>
>>>>>>>> On 12-03-07 3:31 AM, "Thomas Hackl"<thomas.hackl at uni-wuerzburg.de
>>>>>>>> <mailto:thomas.hackl at uni-wuerzburg.de>>   wrote:
>>>>>>>>
>>>>>>>>> Hello,
>>>>>>>>>
>>>>>>>>> we want to use a current release of maker (2.22, 2.23) but the
>>>>>>>>> program
>>>>>>>>> terminates with a seg fault while processing the input FASTA
>>>>>>>>>files.
>>>>>>>>> maker 2.15 , which we have been using for quite some time, runs
>>>>>>>>> perfectly with identical data and setup.
>>>>>>>>>
>>>>>>>>> Please contact me if you need specifics on hardware, OS or
>>>>>>>>>anything
>>>>>>>>> else.
>>>>>>>>>
>>>>>>>>> Best regards
>>>>>>>>> Thomas
>>>>>>>>>
>>>>>>>>> --
>>>>>>>>> Thomas Hackl
>>>>>>>>> Julius-Maximilians-Universit?t
>>>>>>>>> Department of Bioinformatics
>>>>>>>>> 97074 W?rzburg, Germany
>>>>>>>>> Fon: +49 931 - 31 86883
>>>>>>>>> Mail: thomas.hackl at uni-wuerzburg.de
>>>>>>>>> <mailto:thomas.hackl at uni-wuerzburg.de>
>>>>>>>>>
>>>>>>>>>
>>>>>>>>> _______________________________________________
>>>>>>>>> maker-devel mailing list
>>>>>>>>> maker-devel at box290.bluehost.com
>>>>>>>>> <mailto:maker-devel at box290.bluehost.com>
>>>>>>>>>
>>>>>>>>>
>>>>>>>>> 
>>>>>>>>>http://box290.bluehost.com/mailman/listinfo/maker-devel_yandell-la
>>>>>>>>>b.
>>>>>>>>> or
>>>>>>>>> g
>>>>>>> --
>>>>>>> Thomas Hackl
>>>>>>> Julius-Maximilians-Universit?t
>>>>>>> Department of Bioinformatics
>>>>>>> 97074 W?rzburg, Germany
>>>>>>> Fon: +49 931 - 31 86883
>>>>>>> Mail: thomas.hackl at uni-wuerzburg.de
>>>>>>> <mailto:thomas.hackl at uni-wuerzburg.de>
>>>>>>>
>>>>>>>
>>>>>>> _______________________________________________
>>>>>>> maker-devel mailing list
>>>>>>> maker-devel at box290.bluehost.com
>>>>>>> <mailto:maker-devel at box290.bluehost.com>
>>>>>>>
>>>>>>> 
>>>>>>>http://box290.bluehost.com/mailman/listinfo/maker-devel_yandell-lab.
>>>>>>>or
>>>>>>> g
>>>>>> Barry Moore
>>>>>> Research Scientist
>>>>>> Dept. of Human Genetics
>>>>>> University of Utah
>>>>>> Salt Lake City, UT 84112
>>>>>> --------------------------------------------
>>>>>> (801) 585-3543
>>>>>>
>>>>>>
>>>>>>
>>>>>>
>>>>>>
>>>>>>
>>>>>> _______________________________________________
>>>>>> maker-devel mailing list
>>>>>> maker-devel at box290.bluehost.com
>>>>>>
>>>>>> 
>>>>>>http://box290.bluehost.com/mailman/listinfo/maker-devel_yandell-lab.o
>>>>>>rg
>>>>> _______________________________________________
>>>>> maker-devel mailing list
>>>>> maker-devel at box290.bluehost.com
>>>>> 
>>>>>http://box290.bluehost.com/mailman/listinfo/maker-devel_yandell-lab.or
>>>>>g
>>> --
>>> Thomas Hackl
>>> Julius-Maximilians-Universit?t
>>> Department of Bioinformatics
>>> 97074 W?rzburg, Germany
>>> Fon:  +49 931 - 31 86883
>>> Mail: thomas.hackl at uni-wuerzburg.de
>>>
>>> _______________________________________________
>>> maker-devel mailing list
>>> maker-devel at box290.bluehost.com
>>> http://box290.bluehost.com/mailman/listinfo/maker-devel_yandell-lab.org
>
>
>-- 
>Thomas Hackl
>Julius-Maximilians-Universit?t
>Department of Bioinformatics
>97074 W?rzburg, Germany
>Fon:  +49 931 - 31 86883
>Mail: thomas.hackl at uni-wuerzburg.de
>
>
>_______________________________________________
>maker-devel mailing list
>maker-devel at box290.bluehost.com
>http://box290.bluehost.com/mailman/listinfo/maker-devel_yandell-lab.org





From daniel.fer.u at gmail.com  Sun Mar 25 20:53:25 2012
From: daniel.fer.u at gmail.com (=?UTF-8?Q?Daniel_Fern=C3=A1ndez?=)
Date: Sun, 25 Mar 2012 19:53:25 -0700 (PDT)
Subject: [maker-devel] Problem with RMBlast installation
Message-ID: <8109224.101.1332730405163.JavaMail.geo-discussion-forums@ynlx41>

Hi,

I trying to install MAKER, I don't have WU-Blast, I have Blast+ so in the 
README file tell me that I need RMBlast, but I don't know what file I have 
to choose, rmblast-1.2-ncbi-blast-2.2.23+-src.tar.gz or rmblast-1.2-ncbi-blast-2.2.23+-x64-linux.tar.gz 
(I have Linux 64-bit) in each version the README file is the same, and 
there tell me how I can install it, but the instructions is only for rmblast-1.2-ncbi-blast-2.2.23+-src, 
well, when I try to install it, I type this 
$./configure --with-mt --prefix=/usr/local/bioinfo/repeatmasker/rmblast 
--without-debug
This show me error, and I type make and this show stop.

Can you help me please?

This show me when I type $./configure --with-mt 
--prefix=/usr/local/bioinfo/repeatmasker/rmblast --without-debug
-----------------------------------------------------------------------------------------------------------------------------------------------
configure: loading site script ./src/build-system/config.site
configure: loading cache config.cache
checking build system type... x86_64-unknown-linux-gnu
checking host system type... x86_64-unknown-linux-gnu
checking for a BSD-compatible install... /usr/bin/install -c
checking for gcc... gcc
checking for C compiler default output file name... a.out
checking whether the C compiler works... yes
checking whether we are cross compiling... no
checking for suffix of executables... 
checking for suffix of object files... o
checking whether we are using the GNU C compiler... yes
checking whether gcc accepts -g... yes
checking for gcc option to accept ANSI C... none needed
checking for g++... no
checking for c++... no
checking for gpp... no
checking for aCC... no
checking for CC... no
checking for cxx... no
checking for cc++... no
checking for cl... no
checking for FCC... no
checking for KCC... no
checking for RCC... no
checking for xlC_r... no
checking for xlC... no
checking whether we are using the GNU C++ compiler... no
checking whether g++ accepts -g... no
adjusted C   compiler: /usr/bin/gcc 
./src/build-system/configure: line 4404: type: g++: not found
dirname: missing operand
Try `dirname --help' for more information.
configure: error: Do not know how to build MT-safe with compiler g++ 
./src/build-system/configure: line 4187: g++: command not found
-----------------------------------------------------------------------------------------------------------------------------------
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From jason.stajich at gmail.com  Mon Mar 26 09:33:55 2012
From: jason.stajich at gmail.com (Jason Stajich)
Date: Mon, 26 Mar 2012 08:33:55 -0700
Subject: [maker-devel] Problem with RMBlast installation
In-Reply-To: <8109224.101.1332730405163.JavaMail.geo-discussion-forums@ynlx41>
References: <8109224.101.1332730405163.JavaMail.geo-discussion-forums@ynlx41>
Message-ID: <7A26C949-4ED3-4CEF-8455-2D3A85B35A2B@gmail.com>

Hi Daniel -

Just download, unpackage the precompiled ( rmblast-1.2-ncbi-blast-2.2.23+-x64-linux.tar.gz ) version and tell RepeatMasker where the exes are when you configure RepeatMasker.  RMBlast is for RepeatMasker.
 
For running BLAST in MAKAER would install NCBI-BLAST+ if you don't have wu-blast --- ftp://ftp.ncbi.nih.gov/blast/executables/blast+/LATEST - I believe current maker supports BLAST+, BLAST, and WU-BLAST so you have your pick.

Jason
On Mar 25, 2012, at 7:53 PM, Daniel Fern?ndez wrote:

> Hi,
> 
> I trying to install MAKER, I don't have WU-Blast, I have Blast+ so in the README file tell me that I need RMBlast, but I don't know what file I have to choose, rmblast-1.2-ncbi-blast-2.2.23+-src.tar.gz or rmblast-1.2-ncbi-blast-2.2.23+-x64-linux.tar.gz (I have Linux 64-bit) in each version the README file is the same, and there tell me how I can install it, but the instructions is only for rmblast-1.2-ncbi-blast-2.2.23+-src, well, when I try to install it, I type this 
> $./configure --with-mt --prefix=/usr/local/bioinfo/repeatmasker/rmblast --without-debug
> This show me error, and I type make and this show stop.
> 
> Can you help me please?
> 
> This show me when I type $./configure --with-mt --prefix=/usr/local/bioinfo/repeatmasker/rmblast --without-debug
> -----------------------------------------------------------------------------------------------------------------------------------------------
> configure: loading site script ./src/build-system/config.site
> configure: loading cache config.cache
> checking build system type... x86_64-unknown-linux-gnu
> checking host system type... x86_64-unknown-linux-gnu
> checking for a BSD-compatible install... /usr/bin/install -c
> checking for gcc... gcc
> checking for C compiler default output file name... a.out
> checking whether the C compiler works... yes
> checking whether we are cross compiling... no
> checking for suffix of executables... 
> checking for suffix of object files... o
> checking whether we are using the GNU C compiler... yes
> checking whether gcc accepts -g... yes
> checking for gcc option to accept ANSI C... none needed
> checking for g++... no
> checking for c++... no
> checking for gpp... no
> checking for aCC... no
> checking for CC... no
> checking for cxx... no
> checking for cc++... no
> checking for cl... no
> checking for FCC... no
> checking for KCC... no
> checking for RCC... no
> checking for xlC_r... no
> checking for xlC... no
> checking whether we are using the GNU C++ compiler... no
> checking whether g++ accepts -g... no
> adjusted C   compiler: /usr/bin/gcc 
> ./src/build-system/configure: line 4404: type: g++: not found
> dirname: missing operand
> Try `dirname --help' for more information.
> configure: error: Do not know how to build MT-safe with compiler g++ ./src/build-system/configure: line 4187: g++: command not found
> -----------------------------------------------------------------------------------------------------------------------------------
> _______________________________________________
> maker-devel mailing list
> maker-devel at box290.bluehost.com
> http://box290.bluehost.com/mailman/listinfo/maker-devel_yandell-lab.org

Jason Stajich
jason.stajich at gmail.com
jason at bioperl.org

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From eernst at cshl.edu  Mon Mar 26 10:29:45 2012
From: eernst at cshl.edu (Evan)
Date: Mon, 26 Mar 2012 09:29:45 -0700 (PDT)
Subject: [maker-devel] Can't call method "start" on an undefined value
Message-ID: <31251549.92.1332779385632.JavaMail.geo-discussion-forums@vbbfy7>

Hi,

I'm running maker 2.24-beta. At least 10-15% of scaffolds are failing with 
the following error:

Preparing evidence for hint based annotation
cleaning clusters....
total clusters:1 now processing 0
in cluster::shadow_cluster...
...finished clustering.
cleaning clusters....
total clusters:4 now processing 0
 ...processing 0 of 3
 ...processing 1 of 3
total clusters:4 now processing 0
 ...processing 0 of 2
total clusters:4 now processing 0
total clusters:4 now processing 0
Can't call method "start" on an undefined valueERROR: Failed while 
preparing evidence clusters for annotations
ERROR: Chunk failed at level:0, tier_type:3
FAILED CONTIG:scaffold93.1

ERROR: Chunk failed at level:7, tier_type:0
FAILED CONTIG:scaffold93.1

This occurs when running just a single maker instance. 

Thanks,
Evan
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From carsonhh at gmail.com  Mon Mar 26 11:22:15 2012
From: carsonhh at gmail.com (Carson Holt)
Date: Mon, 26 Mar 2012 13:22:15 -0400
Subject: [maker-devel] maker 2.22-beta: identical names and sequences
 repeated in maker.all.proteins fasta - attached FASTA, gff3
In-Reply-To: <407831381.989320.1332781349591.JavaMail.root@ksu-sfpop-mailstore03>
Message-ID: <CB961AC7.9EF5%carsonhh@gmail.com>

Thanks for the file.  I now see that the issue is caused by repeated model
entries in the maker_gff file (example from the following lines in the
input GFF3).


scaffold09875   maker   mRNA    255     1019    .       +       .
ID=maker-scaffold09875-est_gff_Cufflinks-gene-0.0-mRNA-1;Parent=maker-scaff
old09875-est_gff_Cufflinks-gene-0.0;
scaffold09875   model_gff:maker match   255     1019    .       +       .
     
ID=scaffold09875:hit:419759:0_0;Name=maker-scaffold09875-est_gff_Cufflinks-
gene-0.0-mRNA-1;


During recent MAKER updates, it was requested that MAKER add model_gff
features used from a previous run as a reference annotation, so you can
still see it even when it is not chosen on the second round.  However this
has an unexpected effect on multiple reruns using maker output as the new
input because both entries get interpreted as model_gff, they both then
end up in the results of a rerun (duplicated each round).

I've fixed this in the developers release (be a couple of days till it
hits the download page as a beta release), but in the mean time just
remove the model_gff:maker entries from the input fasta and it will work
as expected.

To do that use this command -->
   grep -v "model_gff:maker"
Msex05162011.genome.all.maker-2.22-15Feb2012.gff3 >
filtered_Msex05162011.genome.all.maker-2.22-15Feb2012.gff3


Then put filtered_Msex05162011.genome.all.maker-2.22-15Feb2012.gff3 as
your maker_gff file.

I also recommend that you delete and .db extension files from the maker
output directory (there will be only one there).  That will make extra
sure that the GFF3 file index gets rebuilt to the new file.

Note:  I also noticed that Msex05162011.genome.cegma.gff is not in GFF3
format (it is in ZFF format).  It would work for training SNAP but will
not work with MAKER.

Thanks,
Carson





On 12-03-26 1:02 PM, "Sanjay Chellapilla" wrote:

>
>
>----- Original Message -----
>> Since you are using it as input.  I'll need to see this file.
>> 
>> 
>>/home/sanjay/manduca_sexta/maker/maker-runs-2.22/Msex05162011.genome.all.
>>ma
>> ker-2.22-15Feb2012.gff3
>> 
>> Thanks,
>> Carson
>> 
>> 
>> 
>> On 12-03-26 12:42 PM, "Sanjay Chellapilla"
>> wrote:
>> 
>> >Attached
>> >"Msex-maker-2.22-identical-repeated-proteins-input-files.tar.bz2"
>> >containing 3 files
>> >
>> >maker-2.22_opts.ctl.28Feb2012
>> >est_gff = baylor_cufflinks_transcripts_gtf_no_G14G15.gff3
>> >model_gff = Msex05162011.genome.cegma.gff
>> >
>> >The maker_gff (Msex05162011.genome.all.maker-2.22-15Feb2012.gff3) is
>> >633MB so I didn't include it in this message. Please let me know if
>> >you'd want to see it - I'll send it separately.
>> >
>> >Thank you,
>> >Sanjay.
>> >
>> >----- Original Message -----
>> >> Could you send me the file you are passing to the est_gff,
>> >> model_gff,
>> >> or
>> >> maker_gff options.
>> >> 
>> >> Also could you send me your MAKER control files?
>> >> 
>> >> Thanks,
>> >> Carson
>> >> 
>> >> 
>> >> 
>> >> 
>> >> On 12-03-14 1:26 PM, "Sanjay Chellapilla"
>> >> wrote:
>> >> 
>> >> >Hi Carson,
>> >> >
>> >> >Sorry I forgot to attach files showing the issue. Attached zip
>> >> >containing one such maker proteins fasta file and corresponding
>> >> >maker gff3 for scaffold00126 having identical repeated sequence
>> >> >">maker-scaffold00126-est_gff_Cufflinks-gene-2.0-mRNA-1".
>> >> >
>> >> >Thank you.
>> >> >
>> >> >----- Forwarded Message -----
>> >> >> Hi Carson,
>> >> >> 
>> >> >> I ran maker-2.22-beta a total of 3 times with the same
>> >> >> evidence,
>> >> >> to annotate the Manduca.sexta genome, each time using
>> >> >> maker-gff3
>> >> >> for the re-annotation run and gene-predictors SNAP, Augustus
>> >> >> trained
>> >> >> on maker-gff3 from the previous run. At the end of the third
>> >> >> run,
>> >> >> I used fasta_merge script to obtain the various fasta files.
>> >> >> I notice that some sequences are repeated in the maker.all
>> >> >> transcripts/proteins fasta files. I found 34 repeated out of
>> >> >> 16128 transcripts/proteins, so there are actually only 16094
>> >> >> unique
>> >> >> sequences. Could this be related to the "repeated genes" issue
>> >> >> from the strange cufflinks cuffmerge gff3 that's used as input
>> >> >> to maker - we discussed this back in January when we first came
>> >> >> across and I had sent you a portion of the gff3 where we saw
>> >> >> this,
>> >> >> and then you recommended trying maker-2.22-beta where this was
>> >> >> fixed
>> >> >> ?
>> >> >> Naturally this also causes repeated short-IDs created using the
>> >> >> maker_map_ids, map_fasta_ids, map_gff_ids scripts.
>> >> >> 
>> >> >> Thanks,
>> >> >> Sanjay.





From carsonhh at gmail.com  Mon Mar 26 13:08:48 2012
From: carsonhh at gmail.com (Carson Holt)
Date: Mon, 26 Mar 2012 15:08:48 -0400
Subject: [maker-devel] FW: Can't call method "start" on an undefined value
In-Reply-To: <CB963617.9F28%carsonhh@gmail.com>
Message-ID: <CB9636EF.9F37%carsonhh@gmail.com>

Ok.  This is fixed (along with a few other things), and is available for
download as MAKER 2.25.

Thanks,
Carson



From:  Evan <eernst at cshl.edu>
Date:  Mon, 26 Mar 2012 09:29:45 -0700 (PDT)
To:  <maker-devel at googlegroups.com>
Subject:  [maker-devel] Can't call method "start" on an undefined value

Hi,

I'm running maker 2.24-beta. At least 10-15% of scaffolds are failing with
the following error:

Preparing evidence for hint based annotation
cleaning clusters....
total clusters:1 now processing 0
in cluster::shadow_cluster...
...finished clustering.
cleaning clusters....
total clusters:4 now processing 0
 ...processing 0 of 3
 ...processing 1 of 3
total clusters:4 now processing 0
 ...processing 0 of 2
total clusters:4 now processing 0
total clusters:4 now processing 0
Can't call method "start" on an undefined valueERROR: Failed while preparing
evidence clusters for annotations
ERROR: Chunk failed at level:0, tier_type:3
FAILED CONTIG:scaffold93.1

ERROR: Chunk failed at level:7, tier_type:0
FAILED CONTIG:scaffold93.1

This occurs when running just a single maker instance.

Thanks,
Evan
_______________________________________________ maker-devel mailing list
maker-devel at box290.bluehost.comhttp://box290.bluehost.com/mailman/listinfo/m
aker-devel_yandell-lab.org


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From carsonhh at gmail.com  Mon Mar 26 14:17:36 2012
From: carsonhh at gmail.com (Carson Holt)
Date: Mon, 26 Mar 2012 16:17:36 -0400
Subject: [maker-devel] Can't call method "start" on an undefined value
In-Reply-To: <CAOqGFX-wEA2weUPSZRrpXBd+gV8nHAEsR9ST-YA96u+q+RvgyA@mail.gmail.com>
Message-ID: <CB964686.9FBB%carsonhh@gmail.com>

 //= is a feature of perl versions 5.10 and above.

You must have an older version of perl.
Just change it to ||= and it will work for older versions.  I'll make that
change to the release as well to make it work with older perl.

Thanks,
Carson




From:  Evan Ernst <eernst at cshl.edu>
Date:  Mon, 26 Mar 2012 16:13:19 -0400
To:  Carson Holt <carsonhh at gmail.com>
Cc:  <maker-devel at googlegroups.com>
Subject:  Re: [maker-devel] Can't call method "start" on an undefined value

Hi Carson,

Line 242 of maker is causing a compilation failure in the version I
downloaded:

241 -> eval "\$ver = \$${name}::VERSION";
242 -> $ver //= 'UNKNOWN';
243 -> $ver = 'UNKNOWN' if($ver =~ /^\-1\,/);

Thanks,
Evan

On Mon, Mar 26, 2012 at 3:06 PM, Evan Ernst <eernst at cshl.edu> wrote:
> Fantastic. Thanks for your help.
> 
> Best,
> Evan
> 
> 
> On Mon, Mar 26, 2012 at 3:05 PM, Carson Holt <carsonhh at gmail.com> wrote:
>> Ok.  This is fixed (along with a few other things), and is available for
>> download as MAKER 2.25.
>> 
>> Thanks,
>> Carson
>> 
>> 
>> 
>> From:  Evan <eernst at cshl.edu>
>> Date:  Mon, 26 Mar 2012 09:29:45 -0700 (PDT)
>> To:  <maker-devel at googlegroups.com>
>> Subject:  [maker-devel] Can't call method "start" on an undefined value
>> 
>> Hi,
>> 
>> I'm running maker 2.24-beta. At least 10-15% of scaffolds are failing with
>> the following error:
>> 
>> Preparing evidence for hint based annotation
>> cleaning clusters....
>> total clusters:1 now processing 0
>> in cluster::shadow_cluster...
>> ...finished clustering.
>> cleaning clusters....
>> total clusters:4 now processing 0
>>  ...processing 0 of 3
>>  ...processing 1 of 3
>> total clusters:4 now processing 0
>>  ...processing 0 of 2
>> total clusters:4 now processing 0
>> total clusters:4 now processing 0
>> Can't call method "start" on an undefined valueERROR: Failed while preparing
>> evidence clusters for annotations
>> ERROR: Chunk failed at level:0, tier_type:3
>> FAILED CONTIG:scaffold93.1
>> 
>> ERROR: Chunk failed at level:7, tier_type:0
>> FAILED CONTIG:scaffold93.1
>> 
>> This occurs when running just a single maker instance.
>> 
>> Thanks,
>> Evan
>> _______________________________________________ maker-devel mailing list
>> maker-devel at box290.bluehost.comhttp://box290.bluehost.com/mailman/listinfo/ma
>> ker-devel_yandell-lab.org
> 
> 
> 
> -- 
> Evan Ernst
> Martienssen Lab
> 
> Delbruck #216
> Cold Spring Harbor Laboratory
> 1 Bungtown Rd.
> Cold Spring Harbor, NY 11724
> 



-- 
Evan Ernst
Martienssen Lab

Delbruck #216
Cold Spring Harbor Laboratory
1 Bungtown Rd.
Cold Spring Harbor, NY 11724



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From daniel.fer.u at gmail.com  Mon Mar 26 20:39:43 2012
From: daniel.fer.u at gmail.com (=?UTF-8?Q?Daniel_Fern=C3=A1ndez?=)
Date: Mon, 26 Mar 2012 19:39:43 -0700 (PDT)
Subject: [maker-devel] Problem with RMBlast installation
In-Reply-To: <7A26C949-4ED3-4CEF-8455-2D3A85B35A2B@gmail.com>
References: <8109224.101.1332730405163.JavaMail.geo-discussion-forums@ynlx41>
	<7A26C949-4ED3-4CEF-8455-2D3A85B35A2B@gmail.com>
Message-ID: <3452112.702.1332815983251.JavaMail.geo-discussion-forums@ynne2>

Ok, I unpack this file, I have 3 directories (bin include lib) and the 
readme file, you tell me add this to my $PATH, but I  add to my path all 
executables (bin), but the other 2 directories? I don't think that I have 
to add to my path, is different to Blast+, in blast+ I only copy the 
executables to my path, the other directories are only data

The bin directory have many executables like blast+, if I add all to my 
path, so I will have many duplicate executables, does this not cause a 
conflict?

On Monday, March 26, 2012 10:33:55 AM UTC-5, Jason Stajich wrote:
>
> Hi Daniel -
>
> Just download, unpackage the precompiled ( rmblast-1.2-ncbi-blast-2.2.23+-x64-linux.tar.gz 
> ) version and tell RepeatMasker where the exes are when you configure 
> RepeatMasker.  RMBlast is for RepeatMasker.
>  
> For running BLAST in MAKAER would install NCBI-BLAST+ if you don't have 
> wu-blast --- ftp://ftp.ncbi.nih.gov/blast/executables/blast+/LATEST - I 
> believe current maker supports BLAST+, BLAST, and WU-BLAST so you have your 
> pick.
>
> Jason
> On Mar 25, 2012, at 7:53 PM, Daniel Fern?ndez wrote:
>
> Hi,
>
> I trying to install MAKER, I don't have WU-Blast, I have Blast+ so in the 
> README file tell me that I need RMBlast, but I don't know what file I have 
> to choose, rmblast-1.2-ncbi-blast-2.2.23+-src.tar.gz or rmblast-1.2-ncbi-blast-2.2.23+-x64-linux.tar.gz 
> (I have Linux 64-bit) in each version the README file is the same, and 
> there tell me how I can install it, but the instructions is only for rmblast-1.2-ncbi-blast-2.2.23+-src, 
> well, when I try to install it, I type this 
> $./configure --with-mt --prefix=/usr/local/bioinfo/repeatmasker/rmblast 
> --without-debug
> This show me error, and I type make and this show stop.
>
> Can you help me please?
>
> This show me when I type $./configure --with-mt 
> --prefix=/usr/local/bioinfo/repeatmasker/rmblast --without-debug
>
> -----------------------------------------------------------------------------------------------------------------------------------------------
> configure: loading site script ./src/build-system/config.site
> configure: loading cache config.cache
> checking build system type... x86_64-unknown-linux-gnu
> checking host system type... x86_64-unknown-linux-gnu
> checking for a BSD-compatible install... /usr/bin/install -c
> checking for gcc... gcc
> checking for C compiler default output file name... a.out
> checking whether the C compiler works... yes
> checking whether we are cross compiling... no
> checking for suffix of executables... 
> checking for suffix of object files... o
> checking whether we are using the GNU C compiler... yes
> checking whether gcc accepts -g... yes
> checking for gcc option to accept ANSI C... none needed
> checking for g++... no
> checking for c++... no
> checking for gpp... no
> checking for aCC... no
> checking for CC... no
> checking for cxx... no
> checking for cc++... no
> checking for cl... no
> checking for FCC... no
> checking for KCC... no
> checking for RCC... no
> checking for xlC_r... no
> checking for xlC... no
> checking whether we are using the GNU C++ compiler... no
> checking whether g++ accepts -g... no
> adjusted C   compiler: /usr/bin/gcc 
> ./src/build-system/configure: line 4404: type: g++: not found
> dirname: missing operand
> Try `dirname --help' for more information.
> configure: error: Do not know how to build MT-safe with compiler g++ 
> ./src/build-system/configure: line 4187: g++: command not found
>
> -----------------------------------------------------------------------------------------------------------------------------------
> _______________________________________________
> maker-devel mailing list
> maker-devel at box290.bluehost.com
> http://box290.bluehost.com/mailman/listinfo/maker-devel_yandell-lab.org
>
>
> Jason Stajich
> jason.stajich at gmail.com
> jason at bioperl.org
>  
>
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From carsonhh at gmail.com  Mon Mar 26 20:47:37 2012
From: carsonhh at gmail.com (Carson Holt)
Date: Mon, 26 Mar 2012 22:47:37 -0400
Subject: [maker-devel] Problem with RMBlast installation
In-Reply-To: <3452112.702.1332815983251.JavaMail.geo-discussion-forums@ynne2>
Message-ID: <CB96A177.A1BD%carsonhh@gmail.com>

You only need to add the directory location for executables you plan on
calling yourself from the command line.  You don't need to add RMBlast to
the PATH for example because you should never use it directly.  RepeatMasker
knows where it is once configured, and you want to use NCBI's BLAST.

Thanks,
Carson

From:  Daniel Fern?ndez <daniel.fer.u at gmail.com>
Date:  Mon, 26 Mar 2012 19:39:43 -0700 (PDT)
To:  <maker-devel at googlegroups.com>
Cc:  "maker-devel at yandell-lab.org List" <maker-devel at yandell-lab.org>,
Daniel Fern?ndez <daniel.fer.u at gmail.com>
Subject:  Re: [maker-devel] Problem with RMBlast installation

Ok, I unpack this file, I have 3 directories (bin include lib) and the
readme file, you tell me add this to my $PATH, but I  add to my path all
executables (bin), but the other 2 directories? I don't think that I have to
add to my path, is different to Blast+, in blast+ I only copy the
executables to my path, the other directories are only data

The bin directory have many executables like blast+, if I add all to my
path, so I will have many duplicate executables, does this not cause a
conflict?

On Monday, March 26, 2012 10:33:55 AM UTC-5, Jason Stajich wrote:
> Hi Daniel -
> 
> Just download, unpackage the precompiled (
> rmblast-1.2-ncbi-blast-2.2.23+-x64-linux.tar.gz ) version and tell
> RepeatMasker where the exes are when you configure RepeatMasker.  RMBlast is
> for RepeatMasker.
>  
> For running BLAST in MAKAER would install NCBI-BLAST+ if you don't have
> wu-blast --- ftp://ftp.ncbi.nih.gov/blast/executables/blast+/LATEST - I
> believe current maker supports BLAST+, BLAST, and WU-BLAST so you have your
> pick.
> 
> Jason
> On Mar 25, 2012, at 7:53 PM, Daniel Fern?ndez wrote:
> 
>> Hi,
>> 
>> I trying to install MAKER, I don't have WU-Blast, I have Blast+ so in the
>> README file tell me that I need RMBlast, but I don't know what file I have to
>> choose, rmblast-1.2-ncbi-blast-2.2.23+-src.tar.gz or
>> rmblast-1.2-ncbi-blast-2.2.23+-x64-linux.tar.gz (I have Linux 64-bit) in each
>> version the README file is the same, and there tell me how I can install it,
>> but the instructions is only for rmblast-1.2-ncbi-blast-2.2.23+-src, well,
>> when I try to install it, I type this
>> $./configure --with-mt --prefix=/usr/local/bioinfo/repeatmasker/rmblast
>> --without-debug
>> This show me error, and I type make and this show stop.
>> 
>> Can you help me please?
>> 
>> This show me when I type $./configure --with-mt
>> --prefix=/usr/local/bioinfo/repeatmasker/rmblast --without-debug
>> -----------------------------------------------------------------------------
>> ------------------------------------------------------------------
>> configure: loading site script ./src/build-system/config.site
>> configure: loading cache config.cache
>> checking build system type... x86_64-unknown-linux-gnu
>> checking host system type... x86_64-unknown-linux-gnu
>> checking for a BSD-compatible install... /usr/bin/install -c
>> checking for gcc... gcc
>> checking for C compiler default output file name... a.out
>> checking whether the C compiler works... yes
>> checking whether we are cross compiling... no
>> checking for suffix of executables...
>> checking for suffix of object files... o
>> checking whether we are using the GNU C compiler... yes
>> checking whether gcc accepts -g... yes
>> checking for gcc option to accept ANSI C... none needed
>> checking for g++... no
>> checking for c++... no
>> checking for gpp... no
>> checking for aCC... no
>> checking for CC... no
>> checking for cxx... no
>> checking for cc++... no
>> checking for cl... no
>> checking for FCC... no
>> checking for KCC... no
>> checking for RCC... no
>> checking for xlC_r... no
>> checking for xlC... no
>> checking whether we are using the GNU C++ compiler... no
>> checking whether g++ accepts -g... no
>> adjusted C   compiler: /usr/bin/gcc
>> ./src/build-system/configure: line 4404: type: g++: not found
>> dirname: missing operand
>> Try `dirname --help' for more information.
>> configure: error: Do not know how to build MT-safe with compiler g++
>> ./src/build-system/configure: line 4187: g++: command not found
>> -----------------------------------------------------------------------------
>> ------------------------------------------------------
>> _______________________________________________
>> maker-devel mailing list
>> maker-devel at box290.bluehost.com
>> http://box290.bluehost.com/mailman/listinfo/maker-devel_yandell-lab.org
> 
> Jason Stajich
> jason.stajich at gmail.com
> jason at bioperl.org
> 
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From tr at ncgr.org  Wed Mar 28 12:34:39 2012
From: tr at ncgr.org (Thiru Ramaraj)
Date: Wed, 28 Mar 2012 12:34:39 -0600
Subject: [maker-devel] maker_functional_gff
Message-ID: <4F7359BF.5020900@ncgr.org>

Hi All,

I am in the process of using maker_functional_gff script th generate 
functional gff file. I was wondering if NCBI BLAST tab delimited output 
will work as it is or there any formatting needed to be  more like a 
WUBLAST output.

Any thoughts would be greatly appreciated.

Thanks,
-Thiru



From carsonhh at gmail.com  Thu Mar 29 08:58:18 2012
From: carsonhh at gmail.com (Carson Holt)
Date: Thu, 29 Mar 2012 10:58:18 -0400
Subject: [maker-devel] maker_functional_gff
In-Reply-To: <4F7359BF.5020900@ncgr.org>
Message-ID: <CB99EE84.A2F7%carsonhh@gmail.com>

It should work with NCBI BLAST as long as it is the optional tab delimited
format, and not the standard raw format report.

The report must be generated from UniProt/Swiss-prot formatted fasta files.

Here is an example of the header format for the fasta file -->
>sp|P18560|1101L_ASFB7 Protein MGF 110-1L OS=African swine fever virus
>(strain Badajoz 1971 Vero-adapted) GN=BA71V-008 PE=3 SV=1

This ia a description of what maker_functional_gff is looked for
>transcript_ID  Description  OS=species  GN=gene_name
>PE=any_text_from_this_point_on_is_ignored

Thanks,
Carson




On 12-03-28 2:34 PM, "Thiru Ramaraj" <tr at ncgr.org> wrote:

>Hi All,
>
>I am in the process of using maker_functional_gff script th generate
>functional gff file. I was wondering if NCBI BLAST tab delimited output
>will work as it is or there any formatting needed to be  more like a
>WUBLAST output.
>
>Any thoughts would be greatly appreciated.
>
>Thanks,
>-Thiru
>
>_______________________________________________
>maker-devel mailing list
>maker-devel at box290.bluehost.com
>http://box290.bluehost.com/mailman/listinfo/maker-devel_yandell-lab.org





From barry.utah at gmail.com  Thu Mar 29 13:29:48 2012
From: barry.utah at gmail.com (Barry Moore)
Date: Thu, 29 Mar 2012 13:29:48 -0600
Subject: [maker-devel] GFF3 Specification
Message-ID: <C8A5B771-CCB5-4629-9F02-CF2437493F39@genetics.utah.edu>

Hi All,

There has been active discussion on the song-devel mailing list over the past 12 months about various ambiguities and unresolved issues with the GFF3 specification.  The SO group is initiating a process to resolve these issues so that GFF3 can continue to serve it's role of unifying genome annotations in a format that promotes collaboration between genome projects and comparison of datasets across a wide variety of genomes.  With the rapid acceleration of genome sequencing, a simple, standard format for genome annotation and comparative genomics is more critical than ever.

Several issues have been raised, and they range from simple requests for clarification to more fundamental questions about the structure of the specification.  We can't address all of these issues in one update to the spec, so we've started the ball rolling with three steps:

Incorporate all the minor changes into a GFF3 1.21 candidate spec (http://www.sequenceontology.org/resources/gff3_1.21.html).
Organize remaining unresolved issues onto a wiki page and start working through those issues one by one (http://www.sequenceontology.org/wiki/index.php?title=GFF3_Developement).
Develop a set of wiki pages to describe 'GFF3 Best Practices' and existing community usage (http://www.sequenceontology.org/wiki/index.php?title=GFF3_best_practices).

We will work through the unresolved issues one at a time - soliciting feedback from the community, and clarify/update the GFF3 spec in a backwards compatible way with existing tools and datasets, adding documenting wiki pages as needed.

We welcome and encourage feedback from the genomics community and gratefully acknowledge those who have been active in the discussion thus far.  Please have a look at the pages described above and join the conversation.  The best place for discussion of all things GFF3 is the SO mailing list (song-devel at lists.sourceforge.net).  Please feel free to re-post this message to relevant mailing lists so that all interested parties can be involved.

On behalf of the SO developers - Thanks.

Barry Moore
Research Scientist
Dept. of Human Genetics
University of Utah
Salt Lake City, UT 84112
--------------------------------------------
(801) 585-3543




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