Re: MAKER error

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Re: MAKER error

Carson Hinton Holt
Re: MAKER error Hello,

MAKER should supply other output as well to STDERR.  If you were running with nohup this was likely captured in the file nohup.out.  The output there would be very informative for me in seeing what would have went wrong.

You could also upload your job to MWAS where I could then help you debug it.  You would just need to let me know the job_id after submission.

http://derringer.genetics.utah.edu/cgi-bin/MWAS/maker.cgi

Thanks,
Carson

On 11/8/10 2:50 PM, "Mark Yandell" <myandell@...> wrote:



Mark Yandell
Associate Professor of Human Genetics
Eccles Institute of Human Genetics
University of Utah
15 North 2030 East, Room 2100
Salt Lake City, UT 84112-5330
ph:801-587-7707
________________________________________
From: Praveen Kumar Raj Kumar [rpraveenkumardcb@...]
Sent: Monday, November 08, 2010 12:36 PM
To: Mark Yandell
Subject: Re: MAKER error

I did signup sir, but I didn't see any emails from mail list except the confirmation emial.

On Mon, Nov 8, 2010 at 1:19 PM, Mark Yandell <myandell@...<mailto:myandell@genetics.utah.edu>> wrote:
Praveen,

please sign up for the maker email list on the web site for further technical assistance.

thanks,

Mark Yandell
Associate Professor of Human Genetics
Eccles Institute of Human Genetics
University of Utah
15 North 2030 East, Room 2100
Salt Lake City, UT 84112-5330
ph:801-587-7707
________________________________________
From: Praveen Kumar Raj Kumar [rpraveenkumardcb@...<mailto:rpraveenkumardcb@gmail.com>]
Sent: Monday, November 08, 2010 8:14 AM
To: Mark Yandell
Subject: MAKER error

Hi Dr. Yandell,
      I am running MAKER for annotation of BAC sequences and it is running for over two weeks now. Shockingly I discovered in the master_datastore_index.log log file a single line is repeated several times,
gi|297747436|gb|AC241320.1|     pita.bacs.20100922_datastore/gi%7C297747436%7Cgb%7CAC241320.1%7C        STARTED
gi|297747436|gb|AC241320.1|     pita.bacs.20100922_datastore/gi%7C297747436%7Cgb%7CAC241320.1%7C        FAILED
is repeated over 15000 times.

Please let me know of this,

Thank you



--
Praveen K. Raj Kumar,
Ph.D Student,
Teaching Associate,
Miami University,
Oxford,OH,USA.
Lab: 513-529-4270
Office : 513-529-4210




--
Praveen K. Raj Kumar,
Ph.D Student,
Teaching Associate,
Miami University,
Oxford,OH,USA.
Lab: 513-529-4270
Office : 513-529-4210



_______________________________________________
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Re: MAKER error

Praveen Kumar Raj Kumar
Dear Carson,
       Thank you for the reply. I here attach the tail of nohup. Please have a look and let me know of the delay or how could I make MAKER to skip the erroneous sequences.
Thank you

On Mon, Nov 8, 2010 at 6:32 PM, Carson Holt <[hidden email]> wrote:
Hello,

MAKER should supply other output as well to STDERR.  If you were running with nohup this was likely captured in the file nohup.out.  The output there would be very informative for me in seeing what would have went wrong.

You could also upload your job to MWAS where I could then help you debug it.  You would just need to let me know the job_id after submission.

http://derringer.genetics.utah.edu/cgi-bin/MWAS/maker.cgi

Thanks,
Carson

On 11/8/10 2:50 PM, "Mark Yandell" <myandell@...> wrote:



Mark Yandell
Associate Professor of Human Genetics
Eccles Institute of Human Genetics
University of Utah
15 North 2030 East, Room 2100
Salt Lake City, UT 84112-5330
ph:801-587-7707
________________________________________
From: Praveen Kumar Raj Kumar [rpraveenkumardcb@...]
Sent: Monday, November 08, 2010 12:36 PM
To: Mark Yandell
Subject: Re: MAKER error

I did signup sir, but I didn't see any emails from mail list except the confirmation emial.

On Mon, Nov 8, 2010 at 1:19 PM, Mark Yandell <[hidden email]<mailto:myandell@genetics.utah.edu>> wrote:
Praveen,

please sign up for the maker email list on the web site for further technical assistance.

thanks,

Mark Yandell
Associate Professor of Human Genetics
Eccles Institute of Human Genetics
University of Utah
15 North 2030 East, Room 2100
Salt Lake City, UT 84112-5330
ph:801-587-7707
________________________________________
From: Praveen Kumar Raj Kumar [[hidden email]<mailto:rpraveenkumardcb@gmail.com>]
Sent: Monday, November 08, 2010 8:14 AM
To: Mark Yandell
Subject: MAKER error

Hi Dr. Yandell,
      I am running MAKER for annotation of BAC sequences and it is running for over two weeks now. Shockingly I discovered in the master_datastore_index.log log file a single line is repeated several times,
gi|297747436|gb|AC241320.1|     pita.bacs.20100922_datastore/gi%7C297747436%7Cgb%7CAC241320.1%7C        STARTED
gi|297747436|gb|AC241320.1|     pita.bacs.20100922_datastore/gi%7C297747436%7Cgb%7CAC241320.1%7C        FAILED
is repeated over 15000 times.

Please let me know of this,

Thank you



--
Praveen K. Raj Kumar,
Ph.D Student,
Teaching Associate,
Miami University,
Oxford,OH,USA.
Lab: 513-529-4270
Office : 513-529-4210




--
Praveen K. Raj Kumar,
Ph.D Student,
Teaching Associate,
Miami University,
Oxford,OH,USA.
Lab: 513-529-4270
Office : 513-529-4210





--
Praveen K. Raj Kumar,
Ph.D Student,
Teaching Associate,
Miami University,
Oxford,OH,USA.
Lab: 513-529-4270
Office : 513-529-4210


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

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Re: MAKER error

Carson Hinton Holt
Re: MAKER error The error may be further up toward the middle of the nohup.out.  The tail you gave me only contains the retry up to the point where the job was stopped (no error).

You may need to give me more of the output.

Thanks,
Carson


On 11/8/10 6:09 PM, "Praveen Kumar Raj Kumar" <rpraveenkumardcb@...> wrote:

Dear Carson,
       Thank you for the reply. I here attach the tail of nohup. Please have a look and let me know of the delay or how could I make MAKER to skip the erroneous sequences.
Thank you

On Mon, Nov 8, 2010 at 6:32 PM, Carson Holt <carson.holt@...> wrote:
Hello,

MAKER should supply other output as well to STDERR.  If you were running with nohup this was likely captured in the file nohup.out.  The output there would be very informative for me in seeing what would have went wrong.

You could also upload your job to MWAS where I could then help you debug it.  You would just need to let me know the job_id after submission.

http://derringer.genetics.utah.edu/cgi-bin/MWAS/maker.cgi

Thanks,
Carson

On 11/8/10 2:50 PM, "Mark Yandell" <myandell@... <http://myandell@...> > wrote:



Mark Yandell
Associate Professor of Human Genetics
Eccles Institute of Human Genetics
University of Utah
15 North 2030 East, Room 2100
Salt Lake City, UT 84112-5330
ph:801-587-7707
________________________________________
From: Praveen Kumar Raj Kumar [rpraveenkumardcb@... <http://rpraveenkumardcb@...> ]
Sent: Monday, November 08, 2010 12:36 PM
To: Mark Yandell
Subject: Re: MAKER error

I did signup sir, but I didn't see any emails from mail list except the confirmation emial.

On Mon, Nov 8, 2010 at 1:19 PM, Mark Yandell <myandell@...<mailto:myandell@genetics.utah.edu <http://genetics.utah.edu> >> wrote:
Praveen,

please sign up for the maker email list on the web site for further technical assistance.

thanks,

Mark Yandell
Associate Professor of Human Genetics
Eccles Institute of Human Genetics
University of Utah
15 North 2030 East, Room 2100
Salt Lake City, UT 84112-5330
ph:801-587-7707
________________________________________
From: Praveen Kumar Raj Kumar [rpraveenkumardcb@...<mailto:rpraveenkumardcb@gmail.com <http://gmail.com> >]
Sent: Monday, November 08, 2010 8:14 AM
To: Mark Yandell
Subject: MAKER error

Hi Dr. Yandell,
      I am running MAKER for annotation of BAC sequences and it is running for over two weeks now. Shockingly I discovered in the master_datastore_index.log log file a single line is repeated several times,
gi|297747436|gb|AC241320.1|     pita.bacs.20100922_datastore/gi%7C297747436%7Cgb%7CAC241320.1%7C        STARTED
gi|297747436|gb|AC241320.1|     pita.bacs.20100922_datastore/gi%7C297747436%7Cgb%7CAC241320.1%7C        FAILED
is repeated over 15000 times.

Please let me know of this,

Thank you



--
Praveen K. Raj Kumar,
Ph.D Student,
Teaching Associate,
Miami University,
Oxford,OH,USA.
Lab: 513-529-4270
Office : 513-529-4210




--
Praveen K. Raj Kumar,
Ph.D Student,
Teaching Associate,
Miami University,
Oxford,OH,USA.
Lab: 513-529-4270
Office : 513-529-4210





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

Praveen Kumar Raj Kumar
I extracted the lines corresponding to the erroneous sequence in the nohup.out. I attach this here.

On Mon, Nov 8, 2010 at 8:13 PM, Carson Holt <[hidden email]> wrote:
The error may be further up toward the middle of the nohup.out.  The tail you gave me only contains the retry up to the point where the job was stopped (no error).

You may need to give me more of the output.

Thanks,
Carson



On 11/8/10 6:09 PM, "Praveen Kumar Raj Kumar" <rpraveenkumardcb@...> wrote:

Dear Carson,
       Thank you for the reply. I here attach the tail of nohup. Please have a look and let me know of the delay or how could I make MAKER to skip the erroneous sequences.
Thank you

On Mon, Nov 8, 2010 at 6:32 PM, Carson Holt <carson.holt@...> wrote:
Hello,

MAKER should supply other output as well to STDERR.  If you were running with nohup this was likely captured in the file nohup.out.  The output there would be very informative for me in seeing what would have went wrong.

You could also upload your job to MWAS where I could then help you debug it.  You would just need to let me know the job_id after submission.

http://derringer.genetics.utah.edu/cgi-bin/MWAS/maker.cgi

Thanks,
Carson

On 11/8/10 2:50 PM, "Mark Yandell" <myandell@... <http://myandell@...> > wrote:



Mark Yandell
Associate Professor of Human Genetics
Eccles Institute of Human Genetics
University of Utah
15 North 2030 East, Room 2100
Salt Lake City, UT 84112-5330
ph:801-587-7707
________________________________________
From: Praveen Kumar Raj Kumar [rpraveenkumardcb@... <http://rpraveenkumardcb@...> ]

Sent: Monday, November 08, 2010 12:36 PM
To: Mark Yandell
Subject: Re: MAKER error

I did signup sir, but I didn't see any emails from mail list except the confirmation emial.

On Mon, Nov 8, 2010 at 1:19 PM, Mark Yandell <[hidden email]<mailto:myandell@genetics.utah.edu <http://genetics.utah.edu> >> wrote:
Praveen,

please sign up for the maker email list on the web site for further technical assistance.

thanks,

Mark Yandell
Associate Professor of Human Genetics
Eccles Institute of Human Genetics
University of Utah
15 North 2030 East, Room 2100
Salt Lake City, UT 84112-5330
ph:801-587-7707
________________________________________
From: Praveen Kumar Raj Kumar [[hidden email]<mailto:rpraveenkumardcb@gmail.com <http://gmail.com> >]

Sent: Monday, November 08, 2010 8:14 AM
To: Mark Yandell
Subject: MAKER error

Hi Dr. Yandell,
      I am running MAKER for annotation of BAC sequences and it is running for over two weeks now. Shockingly I discovered in the master_datastore_index.log log file a single line is repeated several times,
gi|297747436|gb|AC241320.1|     pita.bacs.20100922_datastore/gi%7C297747436%7Cgb%7CAC241320.1%7C        STARTED
gi|297747436|gb|AC241320.1|     pita.bacs.20100922_datastore/gi%7C297747436%7Cgb%7CAC241320.1%7C        FAILED
is repeated over 15000 times.

Please let me know of this,

Thank you



--
Praveen K. Raj Kumar,
Ph.D Student,
Teaching Associate,
Miami University,
Oxford,OH,USA.
Lab: 513-529-4270
Office : 513-529-4210




--
Praveen K. Raj Kumar,
Ph.D Student,
Teaching Associate,
Miami University,
Oxford,OH,USA.
Lab: 513-529-4270
Office : 513-529-4210







--
Praveen K. Raj Kumar,
Ph.D Student,
Teaching Associate,
Miami University,
Oxford,OH,USA.
Lab: 513-529-4270
Office : 513-529-4210


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

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FW: MAKER error

Carson Hinton Holt
In reply to this post by Carson Hinton Holt
FW: MAKER error I thing I’ve found the issue.  The EST file is contaminated with meta characters.  These appear as ‘^M’ if you look at the very end of the file using the program ‘less’ in a terminal.  This sometimes happen when data is prepared on a Mac, as apple supports the use of non-unicode characters to indicate an end line in addition to the standard character.



I’ve attached a handy perl script that will fix the file.

USAGE:    perl purify pita.cDNA-FLcDNA.fasta > pita.cDNA-FLcDNA_fixed.fasta

After cleaning the file, you must reconfigure the control option files to use the new file.  I would recommend clobbering all current control files using maker -CTL  and then re-entering all options.  This will make sure all options are updated to the current MAKER 2.04.  You will also want to do a completely new run to destroy old files contaminated by the bad data as it will affect many analyses.

Thanks,
Carson


On 11/10/10 11:54 AM, "Praveen Kumar Raj Kumar" <rpraveenkumardcb@...> wrote:

Dear carson,
         Please find the ESTs here,
http://134.53.9.96/MAKER_est.html
Thank you,

On Wed, Nov 10, 2010 at 12:11 PM, Carson Holt <carson.holt@...> wrote:
Thank you for sending the new nohup.out, it was very informative.

The error given is-->

Messed up acceptor:-T in Widget::exonerate::est2genome::get_acceptor!

FATAL ERROR
ERROR: Failed while polishig ESTs!!

ERROR: Chunk failed at level 14!!
FAILED CONTIG:gi|297747436|gb|AC241320.1|



So the error is related to the ESTs, and I will need the EST file.  You can upload it to MWAS, or you can use sites like https://www.dropbox.com to upload and share large files.

With respect to the MPI MAKER, mpiexec does not run correctly under nohup, but there is a work around.  You need to redirect STDIN from an empty file like /dev/null to nohup when running mpiexec.

Example:
mpdboot
nohup mpiexec -n 10 mpi_maker < /dev/null &

Also sometimes mpdboot will not run correctly but will not give informative errors.  If that is the case run mpd which does give informative errors.

Thanks,
Carson



On 11/10/10 8:22 AM, "Praveen Kumar Raj Kumar" <rpraveenkumardcb@... <http://rpraveenkumardcb@...> > wrote:

Dear Carson,
       Even though I failed to run mpi_maker, I did run serial version with that particular genome sequence using my EST dataset. I ended up in the similar error msg. I attach the nohup(appended to mpi_error) and master_log file. Please  have a look and let me know of this. 

Since my EST dataset is 1.4 Gb I am not attaching here, but if you need please lemme know.
Thank you,

---------- Forwarded message ----------
From: Praveen Kumar Raj Kumar <rpraveenkumardcb@... <http://rpraveenkumardcb@...> >
Date: Wed, Nov 10, 2010 at 10:01 AM
Subject: Re: MAKER error
To: Carson Holt <carson.holt@... <http://carson.holt@...> >


Dear Carson,
      I made success in installing both mpich2 with enabled sharedlibs and mpi_maker

[root@bioinfo3 Usingdev110910]# which mpi_maker
/usr/local/genome/maker-2.04/bin/mpi_maker

But I get the following error when I attempt to run mpi_maker

*****************************************
[root@bioinfo3 Usingdev110910]# less nohup.out 
[mpiexec@bioinfo3] HYDU_sock_read (./utils/sock/sock.c:213): read errno (Bad file descriptor)
[mpiexec@bioinfo3] HYDU_sock_forward_stdio (./utils/sock/sock.c:377): read error
[mpiexec@bioinfo3] HYDT_bscu_stdin_cb (./tools/bootstrap/utils/bscu_cb.c:63): stdin forwarding error
[mpiexec@bioinfo3] HYDT_dmxu_poll_wait_for_event (./tools/demux/demux_poll.c:76): callback returned error status
[mpiexec@bioinfo3] HYD_pmci_wait_for_completion (./pm/pmiserv/pmiserv_pmci.c:342): error waiting for event
[mpiexec@bioinfo3] main (./ui/mpich/mpiexec.c:294): process manager error waiting for completion
nohup.out (END) 
********************************************

Please let me know of this,

Thank you,





------ End of Forwarded Message

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