aatpackage-users — Email list for help, comments, and discussion related to using the AAT software

Re: [Aatpackage-users] AAT parameters

[Brian H. <bh...@br...>]

The defaults should work well across diverse targets.

Each binary has separate help info if you want to explore them individually.

Best

-Brian
(by iPhone)


> On Aug 14, 2015, at 3:02 PM, Chandler Roe <cr...@tg...> wrote:
> 
> Hi guys, 
> 
> I am attempting to run the AAT pipeline on my data but I do not understand the parameters for the AAT.pl script. Is running the default parameters you provide the way to go? Or is there somewhere I can get an idea of how to optimize the parameters for my data? Thanks!
> 
> Chandler Roe
> This electronic message is intended to be for the use only of the named recipient, and may contain information that is confidential or privileged, including patient health information. If you are not the intended recipient, you are hereby notified that any disclosure, copying, distribution or use of the contents of this message is strictly prohibited. If you have received this message in error or are not the named recipient, please notify us immediately by contacting the sender at the electronic mail address noted above, and delete and destroy all copies of this message. Thank you.
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[Aatpackage-users] AAT parameters

[Chandler R. <cr...@tg...>]

Hi guys,

I am attempting to run the AAT pipeline on my data but I do not understand the parameters for the AAT.pl script. Is running the default parameters you provide the way to go? Or is there somewhere I can get an idea of how to optimize the parameters for my data? Thanks!

Chandler Roe
________________________________
________________________________

This electronic message is intended to be for the use only of the named recipient, and may contain information that is confidential or privileged, including patient health information. If you are not the intended recipient, you are hereby notified that any disclosure, copying, distribution or use of the contents of this message is strictly prohibited. If you have received this message in error or are not the named recipient, please notify us immediately by contacting the sender at the electronic mail address noted above, and delete and destroy all copies of this message. Thank you.

Re: [Aatpackage-users] AAT visualization

[Brian H. <bh...@br...>]

Hi Daniel,

There should be .btab files that contain the alignment data in
tab-delimited output format.

In a future release, we'll need to include a BTAB->GFF converter.

-brian



On Wed, Feb 29, 2012 at 5:25 PM, Daniel Fernandez <dan...@gm...>wrote:

> Hi,
>
> Can you tell me how I can visualize the result of "gap", "nap" and "show"
> files, please. I  tried with Artemis and Argo but it doesn't accept theses
> format.
>
> --
> Daniel Antonio Fernández Ugaz
> Molecular Biologist
> Lab. Virology and Molecular Genetics
> Faculty of Veterinary
> Universidad Nacional Mayor de San Marcos - UNMSM
> Av. Circunvalación 2800, San Borja
> Lima 41, Perú
>
>
>
>
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-- 
-- 
Brian J. Haas
Manager, Genome Annotation and Analysis Research and Development
The Broad Institute
http://broad.mit.edu/~bhaas

[Aatpackage-users] AAT visualization

[Daniel F. <dan...@gm...>]

Hi,

Can you tell me how I can visualize the result of "gap", "nap" and "show"
files, please. I  tried with Artemis and Argo but it doesn't accept theses
format.

-- 
Daniel Antonio Fernández Ugaz
Molecular Biologist
Lab. Virology and Molecular Genetics
Faculty of Veterinary
Universidad Nacional Mayor de San Marcos - UNMSM
Av. Circunvalación 2800, San Borja
Lima 41, Perú

Re: [Aatpackage-users] AAT doesn't work for proteins

[Brian H. <bh...@br...>]

Hi Daniel,

If you want to install this in /usr/local/bin, then you'll also have to
copy the matrices/ directory to /usr/local, because the AAT.pl script is
looking for it as /usr/local/matrices

best,

-b

On Tue, Feb 21, 2012 at 12:45 AM, Daniel Fernandez
<dan...@gm...>wrote:

> Dear Mr.
>
> I'm trying to run AAT program for genomic sequences against proteins but
> it doesn't work
>
> I run the "runMe.sh" script, this run ok
>
> But when I tried to run the command into the "runMe.sh" separately, the
> first command "AAT.pl -N ..." for nucleotide, this run ok but ..
> when I tried run the command
> $ AAT.pl -P -q arab.genomicSeq -s arab.pep --dps '-f 100 -i 30 -a 200'
> --filter '-c 10' --nap '-x 10'
> this doesn't work
>
> After I installed the AAT program, I copied the AAT.pl dds, dps, ext,
> filter, gap2, nap and show in /usr/local/bin
> Sorry but I don't know much about programming
> Could you tell me what is the problem, please?
>
> This is the result.
>
> ###################################################################
> $ AAT.pl -P -q arab.genomicSeq -s arab.pep --dps '-f 100 -i 30 -a 200'
> --filter '-c 10' --nap '-x 10'
> params: arab.pep, arab.genomicSeq, , arab.pep, -f 100 -i 30 -a 200, , -c
> 10, -x 10
>
> ## Processing (AAT-protein) bac_F8G22
> querySeq: bac_F8G22
> CMD: /usr/local/bin/dps bac_F8G22 arab.pep /usr/local/bin/../matrices/BS
> -f 100 -i 30 -a 200 2>&1 > bac_F8G22.arab.pep.dps
> ret(256)
> Error, command failed: /usr/local/bin/dps bac_F8G22 arab.pep
> /usr/local/bin/../matrices/BS -f 100 -i 30 -a 200 2>&1 >
> bac_F8G22.arab.pep.dps, returns(256), response: Cannot open
> /usr/local/bin/../matrices/BS.
>
> ----
> Error encountered while running pipeline:
> CMD: -P -q arab.genomicSeq -s arab.pep --dps -f 100 -i 30 -a 200 --filter
> -c 10 --nap -x 10
> protein (dps/nap) pipeline
> genomic acc: bac_F8G22
> searchDB: arab.pep
> queryDB: arab.genomicSeq
> dps_opts: -f 100 -i 30 -a 200
> ext_opts:
> filter_opts: -c 10
> nap_opts: -x 10
> ERROR running cmd: /usr/local/bin/dps bac_F8G22 arab.pep
> /usr/local/bin/../matrices/BS -f 100 -i 30 -a 200 2>&1 >
> bac_F8G22.arab.pep.dps, returns(256), reponse: Cannot open
> /usr/local/bin/../matrices/BS.
>
> Errors were encountered while running the AAT pipeline.
> Check the file (arab.pep.arab.genomicSeq.21988.AAT.errlog) for details.
> ###################################################################
>
> --
> Daniel Antonio Fernández Ugaz
> Lab. Virology and Molecular Genetics
> Faculty of Veterinary
> Universidad Nacional Mayor de San Marcos - UNMSM
> Av. Circunvalación 2800, San Borja
> Lima 41, Perú
>
>
>
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>


-- 
-- 
Brian J. Haas
Manager, Genome Annotation and Analysis Research and Development
The Broad Institute
http://broad.mit.edu/~bhaas

[Aatpackage-users] AAT doesn't work for proteins

[Daniel F. <dan...@gm...>]

Dear Mr.

I'm trying to run AAT program for genomic sequences against proteins but it
doesn't work

I run the "runMe.sh" script, this run ok

But when I tried to run the command into the "runMe.sh" separately, the
first command "AAT.pl -N ..." for nucleotide, this run ok but ..
when I tried run the command
$ AAT.pl -P -q arab.genomicSeq -s arab.pep --dps '-f 100 -i 30 -a 200'
--filter '-c 10' --nap '-x 10'
this doesn't work

After I installed the AAT program, I copied the AAT.pl dds, dps, ext,
filter, gap2, nap and show in /usr/local/bin
Sorry but I don't know much about programming
Could you tell me what is the problem, please?

This is the result.

###################################################################
$ AAT.pl -P -q arab.genomicSeq -s arab.pep --dps '-f 100 -i 30 -a 200'
--filter '-c 10' --nap '-x 10'
params: arab.pep, arab.genomicSeq, , arab.pep, -f 100 -i 30 -a 200, , -c
10, -x 10

## Processing (AAT-protein) bac_F8G22
querySeq: bac_F8G22
CMD: /usr/local/bin/dps bac_F8G22 arab.pep /usr/local/bin/../matrices/BS -f
100 -i 30 -a 200 2>&1 > bac_F8G22.arab.pep.dps
ret(256)
Error, command failed: /usr/local/bin/dps bac_F8G22 arab.pep
/usr/local/bin/../matrices/BS -f 100 -i 30 -a 200 2>&1 >
bac_F8G22.arab.pep.dps, returns(256), response: Cannot open
/usr/local/bin/../matrices/BS.

----
Error encountered while running pipeline:
CMD: -P -q arab.genomicSeq -s arab.pep --dps -f 100 -i 30 -a 200 --filter
-c 10 --nap -x 10
protein (dps/nap) pipeline
genomic acc: bac_F8G22
searchDB: arab.pep
queryDB: arab.genomicSeq
dps_opts: -f 100 -i 30 -a 200
ext_opts:
filter_opts: -c 10
nap_opts: -x 10
ERROR running cmd: /usr/local/bin/dps bac_F8G22 arab.pep
/usr/local/bin/../matrices/BS -f 100 -i 30 -a 200 2>&1 >
bac_F8G22.arab.pep.dps, returns(256), reponse: Cannot open
/usr/local/bin/../matrices/BS.

Errors were encountered while running the AAT pipeline.
Check the file (arab.pep.arab.genomicSeq.21988.AAT.errlog) for details.
###################################################################

-- 
Daniel Antonio Fernández Ugaz
Lab. Virology and Molecular Genetics
Faculty of Veterinary
Universidad Nacional Mayor de San Marcos - UNMSM
Av. Circunvalación 2800, San Borja
Lima 41, Perú

Re: [Aatpackage-users] About ATT package - error

[Brian H. <bh...@br...>]

Sounds great!

-b

2012/2/15 Daniel Fernández <dan...@gm...>:
> Ok that work, but I don't understand very well the --prefix= , but then I
> copied all executables to /usr/local/bin/ , so I think that's ok, it run, it
> work
>
> Thank you very much
>
> Daniel
>
>
> On 02/15/2012 06:39 AM, Brian Haas wrote:
>>
>> Let's try this:
>>
>> build like so:
>>
>>      configure --prefix=`pwd`
>>
>>      make
>>     make install
>>
>>
>> then, try running the demo by:
>>
>>    cd sample_data/
>>
>>    ./runMe.sh
>>
>> and let's see how that goes.
>>
>> best,
>>
>> -brian
>>
>>
>>
>



-- 
--
Brian J. Haas
Manager, Genome Annotation and Analysis Research and Development
The Broad Institute
http://broad.mit.edu/~bhaas

Re: [Aatpackage-users] About ATT package - error

[Brian H. <bh...@br...>]

Let's try this:

build like so:

      configure --prefix=`pwd`

      make

     make install


then, try running the demo by:

    cd sample_data/

    ./runMe.sh

and let's see how that goes.

best,

-brian

[Aatpackage-users] About ATT package - error

[Daniel F. <dan...@gm...>]

Dear sr.

I have some problems when I try to run the script runMe.sh in the AAT
package, it show me that:


> *************************************************
> running AAT nucleotide spliced alignment pipeline
> *************************************************
>
> ../bin/AAT.pl -N -q arab.genomicSeq -s arab.cdna --dds '-f 100 -i 20 -o 75
> -p 70 -a 2000' --filter '-c 10' --gap2 '-x 1'
> ## Processing (AAT-transcript) bac_F8G22
> CMD: /home/ubigem/PROGRAMAS/AAT/AAT/bin/dds bac_F8G22 arab.cdna -f 100 -i
> 20 -o 75 -p 70 -a 2000 2>&1 > bac_F8G22.arab.cdna.dds
> ret(512)
> Error, command failed: /home/ubigem/PROGRAMAS/AAT/AAT/bin/dds bac_F8G22
> arab.cdna -f 100 -i 20 -o 75 -p 70 -a 2000 2>&1 > bac_F8G22.arab.cdna.dds,
> returns(512), response: /home/ubigem/PROGRAMAS/AAT/AAT/bin/dds: 1: Syntax
> error: word unexpected (expecting ")")
> ----
> Error encountered while running pipeline:
> CMD: -N -q arab.genomicSeq -s arab.cdna --dds -f 100 -i 20 -o 75 -p 70 -a
> 2000 --filter -c 10 --gap2 -x 1
> transcript (dds/gap2) pipeline
> genomic acc: bac_F8G22
> searchDB: arab.cdna
> queryDB: arab.genomicSeq
> dds_opts: -f 100 -i 20 -o 75 -p 70 -a 2000
> ext_opts:
> filter_opts: -c 10
> gap2_opts: -x 1
> ERROR running cmd: /home/ubigem/PROGRAMAS/AAT/AAT/bin/dds bac_F8G22
> arab.cdna -f 100 -i 20 -o 75 -p 70 -a 2000 2>&1 > bac_F8G22.arab.cdna.dds,
> returns(512), reponse: /home/ubigem/PROGRAMAS/AAT/AAT/bin/dds: 1: Syntax
> error: word unexpected (expecting ")")
> Errors were encountered while running the AAT pipeline.
> Check the file (arab.cdna.arab.genomicSeq.1374.AAT.errlog) for details.
> **********************************************
> running AAT protein spliced alignment pipeline
> **********************************************
>
> ../bin/AAT.pl -P -q arab.genomicSeq -s arab.pep --dps '-f 100 -i 30 -a
> 200' --filter '-c 10' --nap '-x 10'
> params: arab.pep, arab.genomicSeq, , arab.pep, -f 100 -i 30 -a 200, , -c
> 10, -x 10
> ## Processing (AAT-protein) bac_F8G22
> querySeq: bac_F8G22
> CMD: /home/ubigem/PROGRAMAS/AAT/AAT/bin/dps bac_F8G22 arab.pep
> /home/ubigem/PROGRAMAS/AAT/AAT/bin/../matrices/BS -f 100 -i 30 -a 200 2>&1
> > bac_F8G22.arab.pep.dps
> ret(512)
> Error, command failed: /home/ubigem/PROGRAMAS/AAT/AAT/bin/dps bac_F8G22
> arab.pep /home/ubigem/PROGRAMAS/AAT/AAT/bin/../matrices/BS -f 100 -i 30 -a
> 200 2>&1 > bac_F8G22.arab.pep.dps, returns(512), response:
> /home/ubigem/PROGRAMAS/AAT/AAT/bin/dps: 2: Syntax error: word unexpected
> (expecting ")")
> ----
> Error encountered while running pipeline:
> CMD: -P -q arab.genomicSeq -s arab.pep --dps -f 100 -i 30 -a 200 --filter
> -c 10 --nap -x 10
> protein (dps/nap) pipeline
> genomic acc: bac_F8G22
> searchDB: arab.pep
> queryDB: arab.genomicSeq
> dps_opts: -f 100 -i 30 -a 200
> ext_opts:
> filter_opts: -c 10
> nap_opts: -x 10
> ERROR running cmd: /home/ubigem/PROGRAMAS/AAT/AAT/bin/dps bac_F8G22
> arab.pep /home/ubigem/PROGRAMAS/AAT/AAT/bin/../matrices/BS -f 100 -i 30 -a
> 200 2>&1 > bac_F8G22.arab.pep.dps, returns(512), reponse:
> /home/ubigem/PROGRAMAS/AAT/AAT/bin/dps: 2: Syntax error: word unexpected
> (expecting ")")
> Errors were encountered while running the AAT pipeline.
> Check the file (arab.pep.arab.genomicSeq.1379.AAT.errlog) for details.
> ************************************************
> combining results into a multiple alignment file
> ************************************************
>
> ../bin/show *gap2 *nap > multalignment.show.txt
> ./runMe.sh: línea 38: ../bin/show: no se puede ejecutar el fichero binario
>
> done.  See 'multalignment.show.txt' to examine all spliced alignments.
>


Can you tell me what is the solution, please?

Thanks for your time.

-- 
*Daniel Antonio Fernández Ugaz*
*Lab. Genetics of South American Camelids*
*Faculty of Veterinary*
*Universidad Nacional Mayor de San Marcos - UNMSM*
*Av. Circunvalación 2800, San Borja*
*Lima 41, Perú*