Re: URGENT: Re: maker failure with example data

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Re: URGENT: Re: maker failure with example data

Carson Hinton Holt
The message is warning that there are multiple instances of MAKER running, but no MPI communication. When you build MAKER (perl Build.PL step when installing MAKER), you need to specify the location of 'mpicc' and 'mpi.h' to build with MPI support.  Otherwise you won't be able to link against MPICH2 shared libraries.  You probably need to rerun that step.

--Carson


From: Goutham atla <[hidden email]>
Date: Tuesday, September 30, 2014 at 10:49 AM
To: Carson Holt <[hidden email]>
Cc: "[hidden email]" <[hidden email]>
Subject: URGENT: Re: maker failure with example data

Hi Carson,

I figured out the problem is with RepeatMasker installation and I fixed it.

I am running maker with MPICH2 and I get the following warning when I start it:

STATUS: Processing and indexing input FASTA files...
WARNING: Multiple MAKER processes have been started in the
same directory.


I would like to if this is common.

Regards,
Goutham


On Tue, Sep 30, 2014 at 12:02 PM, Goutham atla <[hidden email]> wrote:
Dear Carson,

Thank you for the reply. I reinstalled the BioPerl and now I am getting the following error on test data.

ERROR: RepeatMasker failed

--> rank=NA, hostname=motif

ERROR: Failed while doing repeat masking

ERROR: Chunk failed at level:0, tier_type:1

FAILED CONTIG:contig-dpp-500-500


On Mon, Sep 29, 2014 at 8:17 PM, Carson Holt <[hidden email]> wrote:
The error is caused by the BioPerl indexer returning an empty length for the indexed fasta sequence (possibly because of a corrupt index file or other reasons).  You may need to reinstall BioPerl (use the CPAN version not the BioPerl-live version), or reinstall Berkley DB (used by the BioPerl indexer), or reinstall the Perl module DB_File via CPAN (Perl's interface to Berkley DB). After reinstalling BioPerl, delete the mpi_blastdb directory for the MAKER run before retrying.

Also verify that the /tmp directory on your system or the directory pointed to by TMP= in the maker_opts,ctl file is not full and that TMP= is not set to an NFS mounted location.

Thanks,
Carson




From: Goutham atla <[hidden email]>
Date: Monday, September 29, 2014 at 6:33 AM
To: <[hidden email]>
Subject: maker failure with example data

Dear All, 


I am running maker with the demo file, i.e dip_contig.fasta by keeping all other parameters in .ctl files as default. But it do not progress and shows the following message that the length of the sequence is 0. Can anybody help me ?




--Next Contig--


MAKER WARNING: All old files will be erased before continuing

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

Skipping the contig because it is too short!!

SeqID: contig-dpp-500-500

Length: 0

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



Regards,
Goutham



--
Goutham Atla



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Re: URGENT: Re: maker failure with example data

Marc Höppner-2
Another possibility could be that MPICH2 wasn’t build properly, no? I remember something with enabling shared libraries during the compilation of mpich, without which the error below would appear. 

/Marc

Marc P. Hoeppner, PhD
Team Leader
BILS Genome Annotation Platform
Department for Medical Biochemistry and Microbiology
Uppsala University, Sweden



On 30 Sep 2014, at 21:33, Carson Holt <[hidden email]> wrote:

The message is warning that there are multiple instances of MAKER running, but no MPI communication. When you build MAKER (perl Build.PL step when installing MAKER), you need to specify the location of 'mpicc' and 'mpi.h' to build with MPI support.  Otherwise you won't be able to link against MPICH2 shared libraries.  You probably need to rerun that step.

--Carson


From: Goutham atla <[hidden email]>
Date: Tuesday, September 30, 2014 at 10:49 AM
To: Carson Holt <[hidden email]>
Cc: "[hidden email]" <[hidden email]>
Subject: URGENT: Re: maker failure with example data

Hi Carson,

I figured out the problem is with RepeatMasker installation and I fixed it.

I am running maker with MPICH2 and I get the following warning when I start it:

STATUS: Processing and indexing input FASTA files...
WARNING: Multiple MAKER processes have been started in the
same directory.


I would like to if this is common.

Regards,
Goutham


On Tue, Sep 30, 2014 at 12:02 PM, Goutham atla <[hidden email]> wrote:
Dear Carson,

Thank you for the reply. I reinstalled the BioPerl and now I am getting the following error on test data.

ERROR: RepeatMasker failed
--> rank=NA, hostname=motif
ERROR: Failed while doing repeat masking
ERROR: Chunk failed at level:0, tier_type:1
FAILED CONTIG:contig-dpp-500-500

On Mon, Sep 29, 2014 at 8:17 PM, Carson Holt <[hidden email]> wrote:
The error is caused by the BioPerl indexer returning an empty length for the indexed fasta sequence (possibly because of a corrupt index file or other reasons).  You may need to reinstall BioPerl (use the CPAN version not the BioPerl-live version), or reinstall Berkley DB (used by the BioPerl indexer), or reinstall the Perl module DB_File via CPAN (Perl's interface to Berkley DB). After reinstalling BioPerl, delete the mpi_blastdb directory for the MAKER run before retrying.

Also verify that the /tmp directory on your system or the directory pointed to by TMP= in the maker_opts,ctl file is not full and that TMP= is not set to an NFS mounted location.

Thanks,
Carson




From: Goutham atla <[hidden email]>
Date: Monday, September 29, 2014 at 6:33 AM
To: <[hidden email]>
Subject: maker failure with example data

Dear All, 

I am running maker with the demo file, i.e dip_contig.fasta by keeping all other parameters in .ctl files as default. But it do not progress and shows the following message that the length of the sequence is 0. Can anybody help me ?



--Next Contig--

MAKER WARNING: All old files will be erased before continuing
#---------------------------------------------------------------------
Skipping the contig because it is too short!!
SeqID: contig-dpp-500-500
Length: 0
#---------------------------------------------------------------------


Regards,
Goutham



--
Goutham Atla



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Re: URGENT: Re: maker failure with example data

Goutham atla
Dear All,

Thank you. I figured out th problem is with mpich2. I was behind mpich2 but was unsuccessful. I installed mpich v3 and its working fine now. Thank you all. The old GMDO tutorials are bit misleading as the new versions have come up.

On Wed, Oct 1, 2014 at 11:09 AM, Marc Höppner <[hidden email]> wrote:
Another possibility could be that MPICH2 wasn’t build properly, no? I remember something with enabling shared libraries during the compilation of mpich, without which the error below would appear. 

/Marc

Marc P. Hoeppner, PhD
Team Leader
BILS Genome Annotation Platform
Department for Medical Biochemistry and Microbiology
Uppsala University, Sweden



On 30 Sep 2014, at 21:33, Carson Holt <[hidden email]> wrote:

The message is warning that there are multiple instances of MAKER running, but no MPI communication. When you build MAKER (perl Build.PL step when installing MAKER), you need to specify the location of 'mpicc' and 'mpi.h' to build with MPI support.  Otherwise you won't be able to link against MPICH2 shared libraries.  You probably need to rerun that step.

--Carson


From: Goutham atla <[hidden email]>
Date: Tuesday, September 30, 2014 at 10:49 AM
To: Carson Holt <[hidden email]>
Cc: "[hidden email]" <[hidden email]>
Subject: URGENT: Re: maker failure with example data

Hi Carson,

I figured out the problem is with RepeatMasker installation and I fixed it.

I am running maker with MPICH2 and I get the following warning when I start it:

STATUS: Processing and indexing input FASTA files...
WARNING: Multiple MAKER processes have been started in the
same directory.


I would like to if this is common.

Regards,
Goutham


On Tue, Sep 30, 2014 at 12:02 PM, Goutham atla <[hidden email]> wrote:
Dear Carson,

Thank you for the reply. I reinstalled the BioPerl and now I am getting the following error on test data.

ERROR: RepeatMasker failed
--> rank=NA, hostname=motif
ERROR: Failed while doing repeat masking
ERROR: Chunk failed at level:0, tier_type:1
FAILED CONTIG:contig-dpp-500-500

On Mon, Sep 29, 2014 at 8:17 PM, Carson Holt <[hidden email]> wrote:
The error is caused by the BioPerl indexer returning an empty length for the indexed fasta sequence (possibly because of a corrupt index file or other reasons).  You may need to reinstall BioPerl (use the CPAN version not the BioPerl-live version), or reinstall Berkley DB (used by the BioPerl indexer), or reinstall the Perl module DB_File via CPAN (Perl's interface to Berkley DB). After reinstalling BioPerl, delete the mpi_blastdb directory for the MAKER run before retrying.

Also verify that the /tmp directory on your system or the directory pointed to by TMP= in the maker_opts,ctl file is not full and that TMP= is not set to an NFS mounted location.

Thanks,
Carson




From: Goutham atla <[hidden email]>
Date: Monday, September 29, 2014 at 6:33 AM
To: <[hidden email]>
Subject: maker failure with example data

Dear All, 

I am running maker with the demo file, i.e dip_contig.fasta by keeping all other parameters in .ctl files as default. But it do not progress and shows the following message that the length of the sequence is 0. Can anybody help me ?



--Next Contig--

MAKER WARNING: All old files will be erased before continuing
#---------------------------------------------------------------------
Skipping the contig because it is too short!!
SeqID: contig-dpp-500-500
Length: 0
#---------------------------------------------------------------------


Regards,
Goutham



--
Goutham Atla



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




--
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Re: URGENT: Re: maker failure with example data

Carson Hinton Holt
Here is the latest GMOD tutorial (May 2014).


--Carson


From: Goutham atla <[hidden email]>
Date: Tuesday, September 30, 2014 at 11:58 PM
To: Marc Höppner <[hidden email]>
Cc: Carson Holt <[hidden email]>, "[hidden email]" <[hidden email]>
Subject: Re: [maker-devel] URGENT: Re: maker failure with example data

Dear All,

Thank you. I figured out th problem is with mpich2. I was behind mpich2 but was unsuccessful. I installed mpich v3 and its working fine now. Thank you all. The old GMDO tutorials are bit misleading as the new versions have come up.

On Wed, Oct 1, 2014 at 11:09 AM, Marc Höppner <[hidden email]> wrote:
Another possibility could be that MPICH2 wasn’t build properly, no? I remember something with enabling shared libraries during the compilation of mpich, without which the error below would appear. 

/Marc

Marc P. Hoeppner, PhD
Team Leader
BILS Genome Annotation Platform
Department for Medical Biochemistry and Microbiology
Uppsala University, Sweden



On 30 Sep 2014, at 21:33, Carson Holt <[hidden email]> wrote:

The message is warning that there are multiple instances of MAKER running, but no MPI communication. When you build MAKER (perl Build.PL step when installing MAKER), you need to specify the location of 'mpicc' and 'mpi.h' to build with MPI support.  Otherwise you won't be able to link against MPICH2 shared libraries.  You probably need to rerun that step.

--Carson


From: Goutham atla <[hidden email]>
Date: Tuesday, September 30, 2014 at 10:49 AM
To: Carson Holt <[hidden email]>
Cc: "[hidden email]" <[hidden email]>
Subject: URGENT: Re: maker failure with example data

Hi Carson,

I figured out the problem is with RepeatMasker installation and I fixed it.

I am running maker with MPICH2 and I get the following warning when I start it:

STATUS: Processing and indexing input FASTA files...
WARNING: Multiple MAKER processes have been started in the
same directory.


I would like to if this is common.

Regards,
Goutham


On Tue, Sep 30, 2014 at 12:02 PM, Goutham atla <[hidden email]> wrote:
Dear Carson,

Thank you for the reply. I reinstalled the BioPerl and now I am getting the following error on test data.

ERROR: RepeatMasker failed
--> rank=NA, hostname=motif
ERROR: Failed while doing repeat masking
ERROR: Chunk failed at level:0, tier_type:1
FAILED CONTIG:contig-dpp-500-500

On Mon, Sep 29, 2014 at 8:17 PM, Carson Holt <[hidden email]> wrote:
The error is caused by the BioPerl indexer returning an empty length for the indexed fasta sequence (possibly because of a corrupt index file or other reasons).  You may need to reinstall BioPerl (use the CPAN version not the BioPerl-live version), or reinstall Berkley DB (used by the BioPerl indexer), or reinstall the Perl module DB_File via CPAN (Perl's interface to Berkley DB). After reinstalling BioPerl, delete the mpi_blastdb directory for the MAKER run before retrying.

Also verify that the /tmp directory on your system or the directory pointed to by TMP= in the maker_opts,ctl file is not full and that TMP= is not set to an NFS mounted location.

Thanks,
Carson




From: Goutham atla <[hidden email]>
Date: Monday, September 29, 2014 at 6:33 AM
To: <[hidden email]>
Subject: maker failure with example data

Dear All, 

I am running maker with the demo file, i.e dip_contig.fasta by keeping all other parameters in .ctl files as default. But it do not progress and shows the following message that the length of the sequence is 0. Can anybody help me ?



--Next Contig--

MAKER WARNING: All old files will be erased before continuing
#---------------------------------------------------------------------
Skipping the contig because it is too short!!
SeqID: contig-dpp-500-500
Length: 0
#---------------------------------------------------------------------


Regards,
Goutham



--
Goutham Atla



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




--
Goutham Atla

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Re: URGENT: Re: maker failure with example data

Carson Hinton Holt
In reply to this post by Goutham atla
The final transcript and proteins fasta files will only exists if there were gene models with evidence support.  If you did not provide an HMM  for one of the ab initio gene predictors (SNAP, Augustus, etc.) then there will be no gene models, and if you do not provide protein or est evidence fastas, then there will be no evidence support.  Also if your contigs are too short to contain gene models then there will be no models.

Thanks,
Carson



On Nov 5, 2014, at 11:49 PM, Goutham atla <[hidden email]> wrote:

Dear All,

I have finished running maker. But I realised that there are no *transcripts.fasta and *protein.fasta files in any of the directories that make has created. It has only gtf files.

Example output of a test run: I have similar results on original file also:

[User@motif jcf7180001838744]$ pwd
/home/User/Maker_Annotation/Maker_test.maker.output/Maker_test_datastore/35/C1/jcf7180001838744
[User@motif jcf7180001838744]$ ls
jcf7180001838744.gff  run.log  theVoid.jcf7180001838744

Any help from you in figuring out why there are no protein.fasta and transcripts.fast would be very helpful.

Regards,
Goutham

On Wed, Oct 1, 2014 at 11:28 AM, Goutham atla <[hidden email]> wrote:
Dear All,

Thank you. I figured out th problem is with mpich2. I was behind mpich2 but was unsuccessful. I installed mpich v3 and its working fine now. Thank you all. The old GMDO tutorials are bit misleading as the new versions have come up.

On Wed, Oct 1, 2014 at 11:09 AM, Marc Höppner <[hidden email]> wrote:
Another possibility could be that MPICH2 wasn’t build properly, no? I remember something with enabling shared libraries during the compilation of mpich, without which the error below would appear. 

/Marc

Marc P. Hoeppner, PhD
Team Leader
BILS Genome Annotation Platform
Department for Medical Biochemistry and Microbiology
Uppsala University, Sweden



On 30 Sep 2014, at 21:33, Carson Holt <[hidden email]> wrote:

The message is warning that there are multiple instances of MAKER running, but no MPI communication. When you build MAKER (perl Build.PL step when installing MAKER), you need to specify the location of 'mpicc' and 'mpi.h' to build with MPI support.  Otherwise you won't be able to link against MPICH2 shared libraries.  You probably need to rerun that step.

--Carson


From: Goutham atla <[hidden email]>
Date: Tuesday, September 30, 2014 at 10:49 AM
To: Carson Holt <[hidden email]>
Cc: "[hidden email]" <[hidden email]>
Subject: URGENT: Re: maker failure with example data

Hi Carson,

I figured out the problem is with RepeatMasker installation and I fixed it.

I am running maker with MPICH2 and I get the following warning when I start it:

STATUS: Processing and indexing input FASTA files...
WARNING: Multiple MAKER processes have been started in the
same directory.


I would like to if this is common.

Regards,
Goutham


On Tue, Sep 30, 2014 at 12:02 PM, Goutham atla <[hidden email]> wrote:
Dear Carson,

Thank you for the reply. I reinstalled the BioPerl and now I am getting the following error on test data.

ERROR: RepeatMasker failed
--> rank=NA, hostname=motif
ERROR: Failed while doing repeat masking
ERROR: Chunk failed at level:0, tier_type:1
FAILED CONTIG:contig-dpp-500-500

On Mon, Sep 29, 2014 at 8:17 PM, Carson Holt <[hidden email]> wrote:
The error is caused by the BioPerl indexer returning an empty length for the indexed fasta sequence (possibly because of a corrupt index file or other reasons).  You may need to reinstall BioPerl (use the CPAN version not the BioPerl-live version), or reinstall Berkley DB (used by the BioPerl indexer), or reinstall the Perl module DB_File via CPAN (Perl's interface to Berkley DB). After reinstalling BioPerl, delete the mpi_blastdb directory for the MAKER run before retrying.

Also verify that the /tmp directory on your system or the directory pointed to by TMP= in the maker_opts,ctl file is not full and that TMP= is not set to an NFS mounted location.

Thanks,
Carson




From: Goutham atla <[hidden email]>
Date: Monday, September 29, 2014 at 6:33 AM
To: <[hidden email]>
Subject: maker failure with example data

Dear All, 

I am running maker with the demo file, i.e dip_contig.fasta by keeping all other parameters in .ctl files as default. But it do not progress and shows the following message that the length of the sequence is 0. Can anybody help me ?



--Next Contig--

MAKER WARNING: All old files will be erased before continuing
#---------------------------------------------------------------------
Skipping the contig because it is too short!!
SeqID: contig-dpp-500-500
Length: 0
#---------------------------------------------------------------------


Regards,
Goutham



--
Goutham Atla



--
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maker-devel mailing list
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--
Goutham Atla



--
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Re: URGENT: Re: maker failure with example data

Goutham atla
Dear Carson,

Thanks for the quick reply. It worked after providing the assembled transcripts and protein fasta from closely related species.


Regards,
Goutham

On Thu, Nov 6, 2014 at 12:34 PM, Carson Holt <[hidden email]> wrote:
The final transcript and proteins fasta files will only exists if there were gene models with evidence support.  If you did not provide an HMM  for one of the ab initio gene predictors (SNAP, Augustus, etc.) then there will be no gene models, and if you do not provide protein or est evidence fastas, then there will be no evidence support.  Also if your contigs are too short to contain gene models then there will be no models.

Thanks,
Carson



On Nov 5, 2014, at 11:49 PM, Goutham atla <[hidden email]> wrote:

Dear All,

I have finished running maker. But I realised that there are no *transcripts.fasta and *protein.fasta files in any of the directories that make has created. It has only gtf files.

Example output of a test run: I have similar results on original file also:

[User@motif jcf7180001838744]$ pwd
/home/User/Maker_Annotation/Maker_test.maker.output/Maker_test_datastore/35/C1/jcf7180001838744
[User@motif jcf7180001838744]$ ls
jcf7180001838744.gff  run.log  theVoid.jcf7180001838744

Any help from you in figuring out why there are no protein.fasta and transcripts.fast would be very helpful.

Regards,
Goutham

On Wed, Oct 1, 2014 at 11:28 AM, Goutham atla <[hidden email]> wrote:
Dear All,

Thank you. I figured out th problem is with mpich2. I was behind mpich2 but was unsuccessful. I installed mpich v3 and its working fine now. Thank you all. The old GMDO tutorials are bit misleading as the new versions have come up.

On Wed, Oct 1, 2014 at 11:09 AM, Marc Höppner <[hidden email]> wrote:
Another possibility could be that MPICH2 wasn’t build properly, no? I remember something with enabling shared libraries during the compilation of mpich, without which the error below would appear. 

/Marc

Marc P. Hoeppner, PhD
Team Leader
BILS Genome Annotation Platform
Department for Medical Biochemistry and Microbiology
Uppsala University, Sweden



On 30 Sep 2014, at 21:33, Carson Holt <[hidden email]> wrote:

The message is warning that there are multiple instances of MAKER running, but no MPI communication. When you build MAKER (perl Build.PL step when installing MAKER), you need to specify the location of 'mpicc' and 'mpi.h' to build with MPI support.  Otherwise you won't be able to link against MPICH2 shared libraries.  You probably need to rerun that step.

--Carson


From: Goutham atla <[hidden email]>
Date: Tuesday, September 30, 2014 at 10:49 AM
To: Carson Holt <[hidden email]>
Cc: "[hidden email]" <[hidden email]>
Subject: URGENT: Re: maker failure with example data

Hi Carson,

I figured out the problem is with RepeatMasker installation and I fixed it.

I am running maker with MPICH2 and I get the following warning when I start it:

STATUS: Processing and indexing input FASTA files...
WARNING: Multiple MAKER processes have been started in the
same directory.


I would like to if this is common.

Regards,
Goutham


On Tue, Sep 30, 2014 at 12:02 PM, Goutham atla <[hidden email]> wrote:
Dear Carson,

Thank you for the reply. I reinstalled the BioPerl and now I am getting the following error on test data.

ERROR: RepeatMasker failed
--> rank=NA, hostname=motif
ERROR: Failed while doing repeat masking
ERROR: Chunk failed at level:0, tier_type:1
FAILED CONTIG:contig-dpp-500-500

On Mon, Sep 29, 2014 at 8:17 PM, Carson Holt <[hidden email]> wrote:
The error is caused by the BioPerl indexer returning an empty length for the indexed fasta sequence (possibly because of a corrupt index file or other reasons).  You may need to reinstall BioPerl (use the CPAN version not the BioPerl-live version), or reinstall Berkley DB (used by the BioPerl indexer), or reinstall the Perl module DB_File via CPAN (Perl's interface to Berkley DB). After reinstalling BioPerl, delete the mpi_blastdb directory for the MAKER run before retrying.

Also verify that the /tmp directory on your system or the directory pointed to by TMP= in the maker_opts,ctl file is not full and that TMP= is not set to an NFS mounted location.

Thanks,
Carson




From: Goutham atla <[hidden email]>
Date: Monday, September 29, 2014 at 6:33 AM
To: <[hidden email]>
Subject: maker failure with example data

Dear All, 

I am running maker with the demo file, i.e dip_contig.fasta by keeping all other parameters in .ctl files as default. But it do not progress and shows the following message that the length of the sequence is 0. Can anybody help me ?



--Next Contig--

MAKER WARNING: All old files will be erased before continuing
#---------------------------------------------------------------------
Skipping the contig because it is too short!!
SeqID: contig-dpp-500-500
Length: 0
#---------------------------------------------------------------------


Regards,
Goutham



--
Goutham Atla



--
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maker-devel mailing list
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--
Goutham Atla



--
Goutham Atla




--
Goutham Atla

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Re: URGENT: Re: maker failure with example data

Goutham atla
Dear Carson,

Maker is throwing error if I provide a rmlib file for repeat masking. It says

At this time the hmmer search engine can only be used with the Dfam

database.  Please rerun your search without the -lib option or switch to

a different search engine.


We have ran it without rmlib and it completed successfully. We got GFF, proteins and transcripts.fasta files.

We are working on Oryza sativa (subspecies indica) but we have fully annotated Oryza sative (subspecies japonica) which is fully annotated.
I would like to know what would be the best way to do a functional annotation of the GFF file given by maker. 

Regards,
Goutham

On Fri, Nov 7, 2014 at 11:09 AM, Goutham atla <[hidden email]> wrote:
Dear Carson,

Thanks for the quick reply. It worked after providing the assembled transcripts and protein fasta from closely related species.


Regards,
Goutham

On Thu, Nov 6, 2014 at 12:34 PM, Carson Holt <[hidden email]> wrote:
The final transcript and proteins fasta files will only exists if there were gene models with evidence support.  If you did not provide an HMM  for one of the ab initio gene predictors (SNAP, Augustus, etc.) then there will be no gene models, and if you do not provide protein or est evidence fastas, then there will be no evidence support.  Also if your contigs are too short to contain gene models then there will be no models.

Thanks,
Carson



On Nov 5, 2014, at 11:49 PM, Goutham atla <[hidden email]> wrote:

Dear All,

I have finished running maker. But I realised that there are no *transcripts.fasta and *protein.fasta files in any of the directories that make has created. It has only gtf files.

Example output of a test run: I have similar results on original file also:

[User@motif jcf7180001838744]$ pwd
/home/User/Maker_Annotation/Maker_test.maker.output/Maker_test_datastore/35/C1/jcf7180001838744
[User@motif jcf7180001838744]$ ls
jcf7180001838744.gff  run.log  theVoid.jcf7180001838744

Any help from you in figuring out why there are no protein.fasta and transcripts.fast would be very helpful.

Regards,
Goutham

On Wed, Oct 1, 2014 at 11:28 AM, Goutham atla <[hidden email]> wrote:
Dear All,

Thank you. I figured out th problem is with mpich2. I was behind mpich2 but was unsuccessful. I installed mpich v3 and its working fine now. Thank you all. The old GMDO tutorials are bit misleading as the new versions have come up.

On Wed, Oct 1, 2014 at 11:09 AM, Marc Höppner <[hidden email]> wrote:
Another possibility could be that MPICH2 wasn’t build properly, no? I remember something with enabling shared libraries during the compilation of mpich, without which the error below would appear. 

/Marc

Marc P. Hoeppner, PhD
Team Leader
BILS Genome Annotation Platform
Department for Medical Biochemistry and Microbiology
Uppsala University, Sweden



On 30 Sep 2014, at 21:33, Carson Holt <[hidden email]> wrote:

The message is warning that there are multiple instances of MAKER running, but no MPI communication. When you build MAKER (perl Build.PL step when installing MAKER), you need to specify the location of 'mpicc' and 'mpi.h' to build with MPI support.  Otherwise you won't be able to link against MPICH2 shared libraries.  You probably need to rerun that step.

--Carson


From: Goutham atla <[hidden email]>
Date: Tuesday, September 30, 2014 at 10:49 AM
To: Carson Holt <[hidden email]>
Cc: "[hidden email]" <[hidden email]>
Subject: URGENT: Re: maker failure with example data

Hi Carson,

I figured out the problem is with RepeatMasker installation and I fixed it.

I am running maker with MPICH2 and I get the following warning when I start it:

STATUS: Processing and indexing input FASTA files...
WARNING: Multiple MAKER processes have been started in the
same directory.


I would like to if this is common.

Regards,
Goutham


On Tue, Sep 30, 2014 at 12:02 PM, Goutham atla <[hidden email]> wrote:
Dear Carson,

Thank you for the reply. I reinstalled the BioPerl and now I am getting the following error on test data.

ERROR: RepeatMasker failed
--> rank=NA, hostname=motif
ERROR: Failed while doing repeat masking
ERROR: Chunk failed at level:0, tier_type:1
FAILED CONTIG:contig-dpp-500-500

On Mon, Sep 29, 2014 at 8:17 PM, Carson Holt <[hidden email]> wrote:
The error is caused by the BioPerl indexer returning an empty length for the indexed fasta sequence (possibly because of a corrupt index file or other reasons).  You may need to reinstall BioPerl (use the CPAN version not the BioPerl-live version), or reinstall Berkley DB (used by the BioPerl indexer), or reinstall the Perl module DB_File via CPAN (Perl's interface to Berkley DB). After reinstalling BioPerl, delete the mpi_blastdb directory for the MAKER run before retrying.

Also verify that the /tmp directory on your system or the directory pointed to by TMP= in the maker_opts,ctl file is not full and that TMP= is not set to an NFS mounted location.

Thanks,
Carson




From: Goutham atla <[hidden email]>
Date: Monday, September 29, 2014 at 6:33 AM
To: <[hidden email]>
Subject: maker failure with example data

Dear All, 

I am running maker with the demo file, i.e dip_contig.fasta by keeping all other parameters in .ctl files as default. But it do not progress and shows the following message that the length of the sequence is 0. Can anybody help me ?



--Next Contig--

MAKER WARNING: All old files will be erased before continuing
#---------------------------------------------------------------------
Skipping the contig because it is too short!!
SeqID: contig-dpp-500-500
Length: 0
#---------------------------------------------------------------------


Regards,
Goutham



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