[maker-devel] Failed while polishig ESTs

Thu Oct 4 23:34:37 MDT 2012

Carson, thanks for very quick response. Jason, could you please
elaborate/share document if any on using  zff2augustus_gbk.pl

Thanks,
Parul Kudtarkar

> 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
>>
>
>
>

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