[maker-devel] Failed while polishig ESTs

[Carson Holt]

Just concatenating won't work.  Use the gff3_merge tool to safely merge
separate GFF3 files.

In the tutorial dataset their should only be one contig to train with, but
with real data you will have multiple contigs and will want to merge the
GFF3 files.

Augustus has a separate training procedure that is a little more
complicated than SNAP's.  You will need to read their documentation on
training which is a little cryptic.

I know Jason Stajich developed a tool for training augustus from snap
results called zff2augustus_gbk.pl (I've CC'd him).  Perhaps he would be
willing to share it with you ;-)

Thanks,
Carson



On 12-10-04 7:06 PM, "Parul Kudtarkar" <parulk at caltech.edu> wrote:

>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_pr
>>>ot
>>>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_e
>>>st
>>>%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_p
>>>ro
>>>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_pr
>>>ot
>>>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_e
>>>st
>>>%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_p
>>>ro
>>>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
>