[maker-devel] URGENT: Re: maker failure with example data

Thu Nov 6 22:39:51 MST 2014

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 <carson.holt at genetics.utah.edu>
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 <goutham.atla at gmail.com> 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 at motif jcf7180001838744]$ pwd
>
> /home/User/Maker_Annotation/Maker_test.maker.output/Maker_test_datastore/35/C1/jcf7180001838744
>  [User at 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 <goutham.atla at gmail.com>
> 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 <marc.hoeppner at imbim.uu.se>
>> 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
>>> marc.hoeppner at imbim.uu.se
>>>
>>>
>>>
>>>  On 30 Sep 2014, at 21:33, Carson Holt <carson.holt at genetics.utah.edu>
>>> 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 <goutham.atla at gmail.com>
>>> Date: Tuesday, September 30, 2014 at 10:49 AM
>>> To: Carson Holt <carson.holt at genetics.utah.edu>
>>> Cc: "maker-devel at yandell-lab.org" <maker-devel at yandell-lab.org>
>>> 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 <goutham.atla at gmail.com>
>>> 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 <
>>>> carson.holt at genetics.utah.edu> 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 <goutham.atla at gmail.com>
>>>>> Date: Monday, September 29, 2014 at 6:33 AM
>>>>> To: <maker-devel at yandell-lab.org>
>>>>> 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
>>> maker-devel at box290.bluehost.com
>>> http://box290.bluehost.com/mailman/listinfo/maker-devel_yandell-lab.org
>>>
>>>
>>>
>>
>>
>>  --
>>  Goutham Atla
>>
>
>
>
>  --
>  Goutham Atla
>
>
>

-- 
Goutham Atla
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