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<div>I wrote up how to use it on this list msg - <a href="http://brie4.cshl.edu/pipermail/gmod-help/2012-June/001724.html">http://brie4.cshl.edu/pipermail/gmod-help/2012-June/001724.html</a></div>
<div>Script is in this github repo -</div>
<a href="https://github.com/hyphaltip/genome-scripts/blob/master/gene_prediction/zff2augustus_gbk.pl">https://github.com/hyphaltip/genome-scripts/blob/master/gene_prediction/zff2augustus_gbk.pl</a>
<div><br>
</div>
<div>Patches and documentation updates are always welcomed, I'll get around to that eventually.</div>
<div><br>
</div>
<div>Jason<br>
<div>
<div>On Oct 4, 2012, at 10:34 PM, Parul Kudtarkar <<a href="mailto:parulk@caltech.edu">parulk@caltech.edu</a>></div>
<div> wrote:</div>
<br class="Apple-interchange-newline">
<blockquote type="cite">Carson, thanks for very quick response. Jason, could you please<br>
elaborate/share document if any on using zff2augustus_gbk.pl<br>
<br>
Thanks,<br>
Parul Kudtarkar<br>
<br>
<blockquote type="cite">Just concatenating won't work. Use the gff3_merge tool to safely merge<br>
separate GFF3 files.<br>
<br>
In the tutorial dataset their should only be one contig to train with, but<br>
with real data you will have multiple contigs and will want to merge the<br>
GFF3 files.<br>
<br>
Augustus has a separate training procedure that is a little more<br>
complicated than SNAP's. You will need to read their documentation on<br>
training which is a little cryptic.<br>
<br>
I know Jason Stajich developed a tool for training augustus from snap<br>
results called zff2augustus_gbk.pl (I've CC'd him). Perhaps he would be<br>
willing to share it with you ;-)<br>
<br>
Thanks,<br>
Carson<br>
<br>
<br>
<br>
On 12-10-04 7:06 PM, "Parul Kudtarkar" <<a href="mailto:parulk@caltech.edu">parulk@caltech.edu</a>> wrote:<br>
<br>
<blockquote type="cite">Hi,<br>
<br>
Thanks, reinstalling BioPerl fixed the issue. Now we are training our<br>
genome to generate training dataset for SNAP and Augustus, as per the<br>
instructions provided at<br>
<a href="http://gmod.org/wiki/MAKER_Tutorial#Training_ab_initio_Gene_Predictors">http://gmod.org/wiki/MAKER_Tutorial#Training_ab_initio_Gene_Predictors</a><br>
<br>
However the training dataset would have multiple gff3 prediction files,<br>
one for each contig. Is it recommended to cat(command) all the gff3 files<br>
to generate a single file and finally generate hmm file with the steps<br>
mentioned in the tutorial. Would the same hmm file work as training<br>
dataset for AUGUSTUS?<br>
<br>
Many thanks,<br>
Parul Kudtarkar<br>
<br>
<blockquote type="cite">You probably need to reinstall Bio-perl.<br>
<br>
Other things that can cause the same error are setting TMP in the<br>
maker_opts.ctl file to a tmpfs type filesystem (i.e. in memory drive)<br>
or<br>
sometimes setting it to an NFS mount.<br>
A full drive can cause this as well or a broken Berkley DB. Use df -h<br>
to<br>
see if any of the drives used are full (either current working<br>
directory<br>
or TMP location). You can also swap Berkley DB for a different backend<br>
by<br>
setting AnyDBM_ISA during setup.<br>
<br>
Example:<br>
cd ../maker/src/<br>
perl Build.PL --AnyDBM_ISA SDBM_File<br>
./Build install<br>
<br>
--Carson<br>
<br>
<br>
<br>
On 12-10-03 10:14 PM, "Parul Kudtarkar" <parulk@caltech.edu> wrote:<br>
<br>
<blockquote type="cite">I am running maker on example data that comes along with installation<br>
and<br>
is cited at http://gmod.org/wiki/MAKER_Tutorial_2012#Note<br>
<br>
Please advice on the aforementioned error.<br>
<br>
---------------------<br>
Maker is now finished!!!<br>
<br>
re reading blast report.<br>
/usr/local/maker/test/dpp_contig.maker.output/dpp_contig_datastore/05/1F<br>
/c<br>
ontig-dpp-500-500//theVoid.contig-dpp-500-500/contig-dpp-500-500.0.te_pr<br>
ot<br>
eins%2Efasta.repeatrunner<br>
deleted:0 hits<br>
in cluster:shadow cluster...<br>
i_size:0 j_size:0<br>
sorting hits in shadow cluster...<br>
... finished.<br>
re reading blast report.<br>
/usr/local/maker/test/dpp_contig.maker.output/dpp_contig_datastore/05/1F<br>
/c<br>
ontig-dpp-500-500//theVoid.contig-dpp-500-500/contig-dpp-500-500.0.dpp_e<br>
st<br>
%2Efasta.blastn<br>
deleted:-1 hits<br>
re reading blast report.<br>
/usr/local/maker/test/dpp_contig.maker.output/dpp_contig_datastore/05/1F<br>
/c<br>
ontig-dpp-500-500//theVoid.contig-dpp-500-500/contig-dpp-500-500.0.dpp_p<br>
ro<br>
tein%2Efasta.blastx<br>
WARNING: Multiple MAKER processes have been started in the<br>
same directory.<br>
<br>
deleted:0 hits<br>
WARNING: Cannot find> dpp-mRNA-4, trying to re-index the fasta.<br>
stop here:dpp-mRNA-4<br>
ERROR: Fasta index error<br>
<br>
FATAL ERROR<br>
Maker is now finished!!!<br>
<br>
re reading blast report.<br>
/usr/local/maker/test/dpp_contig.maker.output/dpp_contig_datastore/05/1F<br>
/c<br>
ontig-dpp-500-500//theVoid.contig-dpp-500-500/contig-dpp-500-500.0.te_pr<br>
ot<br>
eins%2Efasta.repeatrunner<br>
deleted:0 hits<br>
in cluster:shadow cluster...<br>
i_size:0 j_size:0<br>
sorting hits in shadow cluster...<br>
... finished.<br>
re reading blast report.<br>
/usr/local/maker/test/dpp_contig.maker.output/dpp_contig_datastore/05/1F<br>
/c<br>
ontig-dpp-500-500//theVoid.contig-dpp-500-500/contig-dpp-500-500.0.dpp_e<br>
st<br>
%2Efasta.blastn<br>
deleted:-1 hits<br>
re reading blast report.<br>
/usr/local/maker/test/dpp_contig.maker.output/dpp_contig_datastore/05/1F<br>
/c<br>
ontig-dpp-500-500//theVoid.contig-dpp-500-500/contig-dpp-500-500.0.dpp_p<br>
ro<br>
tein%2Efasta.blastx<br>
WARNING: Multiple MAKER processes have been started in the<br>
same directory.<br>
<br>
deleted:0 hits<br>
WARNING: Cannot find> dpp-mRNA-4, trying to re-index the fasta.<br>
stop here:dpp-mRNA-4<br>
ERROR: Fasta index error<br>
<br>
FATAL ERROR<br>
ERROR: Failed while polishig ESTs!!<br>
<br>
ERROR: Chunk failed at level 14<br>
!!<br>
FAILED CONTIG:contig-dpp-500-500<br>
<br>
<br>
<br>
ERROR: Chunk failed at level 14<br>
!!<br>
FAILED CONTIG:contig-dpp-500-500<br>
------------------------------------<br>
<br>
<br>
Many thanks,<br>
Parul Kudtarkar<br>
<br>
--<br>
Scientific Programmer<br>
Center for Computational Regulatory Genomics<br>
Beckman Institute,<br>
California Institute of Technology<br>
http://www.spbase.org<br>
<br>
<br>
_______________________________________________<br>
maker-devel mailing list<br>
maker-devel@box290.bluehost.com<br>
http://box290.bluehost.com/mailman/listinfo/maker-devel_yandell-lab.org<br>
</blockquote>
<br>
<br>
<br>
</blockquote>
<br>
<br>
--<br>
Scientific Programmer<br>
Center for Computational Regulatory Genomics<br>
Beckman Institute,<br>
California Institute of Technology<br>
http://www.spbase.org<br>
<br>
</blockquote>
<br>
<br>
<br>
</blockquote>
<br>
<br>
--<br>
Scientific Programmer<br>
Center for Computational Regulatory Genomics<br>
Beckman Institute,<br>
California Institute of Technology<br>
<a href="http://www.spbase.org">http://www.spbase.org</a><br>
<br>
</blockquote>
</div>
<br>
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<div>-- <br>
Jason E Stajich, PhD<br>
Assistant Professor<br>
Plant Pathology & Microbiology<br>
University of California, Riverside<br>
951.827.2363</div>
<div><a href="http://lab.stajich.org/">http://lab.stajich.org</a> <a href="http://fungalgenomes.org/">http://fungalgenomes.org</a> <a href="http://fungidb.org/">http://fungidb.org</a> <a href="http://1000.fungalgenomes.org/">http://1000.fungalgenomes.org/</a></div>
<div>twitter @stajichlab @hyphaltip @fungalgenomes @fungidb<br>
<a href="http://plantpathology.ucr.edu/">http://plantpathology.ucr.edu</a> <a href="http://genomics.ucr.edu/">http://genomics.ucr.edu</a> </div>
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