[maker-devel] tbl2asn errors

[Carson Holt]

The only one that may be a real error is the first one (I'm not sure what it
means).  You probably need to find them and open them in a viewer like
apollo.  The rest I would consider warnings (the NCBI tool doesn't like any
weirdness or uncertainty).  You often have to manually edit things to get
NCBI to accept all models without complaining (sometimes even going against
real biology).  I know some groups use the always_complete=1 option in MAKER
to force start and stop codons into every model for example (even though
those forced codons are probably false).


*Not sure about this one -->     4 ERROR:   SEQ_FEAT.BadTrailingCharacter
*These are partial genes with no stop (usually happen at the edge of contigs
or near strings of NNNN) -->    217 ERROR:   SEQ_FEAT.NoStop
*These are just short introns (intron size is under control of the ab initio
predictors) -->   438 ERROR:   SEQ_FEAT.ShortIntron
*These are partial genes with no start (usually happen at the edge of
contigs or near strings of NNNN) --> 171 ERROR:   SEQ_FEAT.StartCodon
*These are partial genes with no start (usually happen at the edge of
contigs or near strings of NNNN) -->    171 ERROR:
SEQ_INST.BadProteinStart
*Non-cononical splicing (can be produced by the ab initio predictor or
suggested by EST evidence) -->  291 WARNING:
SEQ_FEAT.NotSpliceConsensusAcceptor
*Non-cononical splicing (can be produced by the ab initio predictor or
suggested by EST evidence) -->  648 WARNING:
SEQ_FEAT.NotSpliceConsensusDonor
*These are just short exons (exon size is under control of the ab initio
predictors) -->   118 WARNING: SEQ_FEAT.ShortExon

You probably need to identify examples of models causing each issue, and
then look at the in Apollo.  Apollo lets you open tbl format and save back
to it.  I imagine the coordinate change is from NCBI using a 0 based
coordinate system as opposed to a 1 based system (I.e. first base is 0
rather than 1).  Unfortunately getting everything to go into NCBI is usually
a grueling task.

--Carson


From:  "Mack, Brian" <Brian.Mack at ARS.USDA.GOV>
Date:  Thursday, April 17, 2014 at 2:34 PM
To:  "maker-devel at yandell-lab.org" <maker-devel at yandell-lab.org>
Subject:  [maker-devel] tbl2asn errors

Hi, I thought I would try asking my question here as NCBI was not able to
give me much assistance.  In preparation for submitting to NCBI, I converted
my my MAKER gff3 to NCBI tbl format using the gff32tbl script that Carson
posted a link to in this thread
(http://gmod.827538.n3.nabble.com/NCBI-feature-table-tt4040473.html#a4040475
). It seemed to have converted fine, however when I use NCBIs tbl2asn
program I get numerous errors in my errorsummary.val file:
 
     4 ERROR:   SEQ_FEAT.BadTrailingCharacter
   217 ERROR:   SEQ_FEAT.NoStop
   438 ERROR:   SEQ_FEAT.ShortIntron
   171 ERROR:   SEQ_FEAT.StartCodon
   171 ERROR:   SEQ_INST.BadProteinStart
   291 WARNING: SEQ_FEAT.NotSpliceConsensusAcceptor
   648 WARNING: SEQ_FEAT.NotSpliceConsensusDonor
   118 WARNING: SEQ_FEAT.ShortExon
 
In addition, all of the genes, cds, and mRNA coordinates in the resulting
sqn files are decreased by one. For example my tbl file will have gene
coordinates of 440869 – 441931, but the sqn file will have 440868 – 441930.
Any ideas what might be causing this?
 
Thanks,
Brian




This electronic message contains information generated by the USDA solely
for the intended recipients. Any unauthorized interception of this message
or the use or disclosure of the information it contains may violate the law
and subject the violator to civil or criminal penalties. If you believe you
have received this message in error, please notify the sender and delete the
email immediately. 
_______________________________________________ maker-devel mailing list
maker-devel at box290.bluehost.com
http://box290.bluehost.com/mailman/listinfo/maker-devel_yandell-lab.org

-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://yandell-lab.org/pipermail/maker-devel_yandell-lab.org/attachments/20140417/bf738c42/attachment-0003.html>