[maker-devel] maker failure with example data

[Carson Holt]

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
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