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

[Marc Höppner]

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<mailto:marc.hoeppner at imbim.uu.se>



On 30 Sep 2014, at 21:33, Carson Holt <carson.holt at genetics.utah.edu<mailto: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<mailto:goutham.atla at gmail.com>>
Date: Tuesday, September 30, 2014 at 10:49 AM
To: Carson Holt <carson.holt at genetics.utah.edu<mailto:carson.holt at genetics.utah.edu>>
Cc: "maker-devel at yandell-lab.org<mailto:maker-devel at yandell-lab.org>" <maker-devel at yandell-lab.org<mailto: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<mailto: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<mailto: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<mailto:goutham.atla at gmail.com>>
Date: Monday, September 29, 2014 at 6:33 AM
To: <maker-devel at yandell-lab.org<mailto: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
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