[maker-devel] Failed while polishig ESTs

[Carson Holt]

You probably need to reinstall Bio-perl.

Other things that can cause the same error are setting TMP in the
maker_opts.ctl file to a tmpfs type filesystem (i.e. in memory drive) or
sometimes setting it to an NFS mount.
A full drive can cause this as well or a broken Berkley DB.  Use df -h to
see if any of the drives used are full (either current working directory
or TMP location).  You can also swap Berkley DB for a different backend by
setting AnyDBM_ISA during setup.

Example:
cd ../maker/src/
perl Build.PL --AnyDBM_ISA SDBM_File
./Build install

--Carson



On 12-10-03 10:14 PM, "Parul Kudtarkar" <parulk at caltech.edu> wrote:

>I am running maker on example data that comes along with installation and
>is cited at http://gmod.org/wiki/MAKER_Tutorial_2012#Note
>
>Please advice on the aforementioned error.
>
>---------------------
>Maker is now finished!!!
>
>re reading blast report.
>/usr/local/maker/test/dpp_contig.maker.output/dpp_contig_datastore/05/1F/c
>ontig-dpp-500-500//theVoid.contig-dpp-500-500/contig-dpp-500-500.0.te_prot
>eins%2Efasta.repeatrunner
>deleted:0 hits
> in cluster:shadow cluster...
>    i_size:0 j_size:0
> sorting hits in shadow cluster...
>... finished.
>re reading blast report.
>/usr/local/maker/test/dpp_contig.maker.output/dpp_contig_datastore/05/1F/c
>ontig-dpp-500-500//theVoid.contig-dpp-500-500/contig-dpp-500-500.0.dpp_est
>%2Efasta.blastn
>deleted:-1 hits
>re reading blast report.
>/usr/local/maker/test/dpp_contig.maker.output/dpp_contig_datastore/05/1F/c
>ontig-dpp-500-500//theVoid.contig-dpp-500-500/contig-dpp-500-500.0.dpp_pro
>tein%2Efasta.blastx
>WARNING: Multiple MAKER processes have been started in the
>same directory.
>
>deleted:0 hits
>WARNING: Cannot find> dpp-mRNA-4, trying to re-index the fasta.
>stop here:dpp-mRNA-4
>ERROR: Fasta index error
>
>FATAL ERROR
>Maker is now finished!!!
>
>re reading blast report.
>/usr/local/maker/test/dpp_contig.maker.output/dpp_contig_datastore/05/1F/c
>ontig-dpp-500-500//theVoid.contig-dpp-500-500/contig-dpp-500-500.0.te_prot
>eins%2Efasta.repeatrunner
>deleted:0 hits
> in cluster:shadow cluster...
>    i_size:0 j_size:0
> sorting hits in shadow cluster...
>... finished.
>re reading blast report.
>/usr/local/maker/test/dpp_contig.maker.output/dpp_contig_datastore/05/1F/c
>ontig-dpp-500-500//theVoid.contig-dpp-500-500/contig-dpp-500-500.0.dpp_est
>%2Efasta.blastn
>deleted:-1 hits
>re reading blast report.
>/usr/local/maker/test/dpp_contig.maker.output/dpp_contig_datastore/05/1F/c
>ontig-dpp-500-500//theVoid.contig-dpp-500-500/contig-dpp-500-500.0.dpp_pro
>tein%2Efasta.blastx
>WARNING: Multiple MAKER processes have been started in the
>same directory.
>
>deleted:0 hits
>WARNING: Cannot find> dpp-mRNA-4, trying to re-index the fasta.
>stop here:dpp-mRNA-4
>ERROR: Fasta index error
>
>FATAL ERROR
>ERROR: Failed while polishig ESTs!!
>
>ERROR: Chunk failed at level 14
>!!
>FAILED CONTIG:contig-dpp-500-500
>
>
>
>ERROR: Chunk failed at level 14
>!!
>FAILED CONTIG:contig-dpp-500-500
>------------------------------------
>
>
>Many thanks,
>Parul Kudtarkar
>
>--
>Scientific Programmer
>Center for Computational Regulatory Genomics
>Beckman Institute,
>California Institute of Technology
>http://www.spbase.org
>
>
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