[maker-devel] Failed while polishig ESTs

[Parul Kudtarkar]

Hi,

Thanks, reinstalling BioPerl fixed the issue. Now we are training our
genome to generate training dataset for SNAP and Augustus, as per the
instructions provided at
http://gmod.org/wiki/MAKER_Tutorial#Training_ab_initio_Gene_Predictors

However the training dataset would have multiple gff3 prediction files,
one for each contig. Is it recommended to cat(command) all the gff3 files
to generate a single file and finally generate hmm file with the steps
mentioned in the tutorial. Would the same hmm file work as training
dataset for AUGUSTUS?

Many thanks,
Parul Kudtarkar

> 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
>>
>>
>>_______________________________________________
>>maker-devel mailing list
>>maker-devel at box290.bluehost.com
>>http://box290.bluehost.com/mailman/listinfo/maker-devel_yandell-lab.org
>
>
>


--
Scientific Programmer
Center for Computational Regulatory Genomics
Beckman Institute,
California Institute of Technology
http://www.spbase.org