[maker-devel] How to address errors encountered in process of submitting genome

[Jason Stajich]

Glenna -

FWIW - I've switched to doing an EVM cleanup with funannotate after MAKER
due to these issues with MAKER and fungal genomes I submit.

Jason

On Wed, Jun 21, 2017 at 8:51 AM Glenna Kramer <glenna.kramer at utoronto.ca>
wrote:

> Hi there,
>
> I am attempting to submit a fungal genome to NCBI and have run into quite
> a few errors running tbl2asn.  I know this isn't directly related to MAKER,
> but I'm hoping that someone here has been through this process and would be
> able to give some insight (or at least point me in the direction of another
> knowledgeable source)!
>
> Here is a general overview of the process that have used so far:
> 1. Converted MAKER GFF3 files to tbl files using GAG (ran options
> remove_introns_shorter_than 10 and fix_start_stop and added functional
> annotation as well).  This seems to work well to convert the GFF3 to tbl.
> 2. Use tbl2asn to convert the tbl to sqn file.  This also seems to work,
> but I am getting lots of errors in the .val output file, which I am unsure
> how to address.  There are...
>
>     56 ERROR:   SEQ_FEAT.BadTrailingHyphen
>   1525 ERROR:   SEQ_FEAT.InternalStop
>   1142 ERROR:   SEQ_FEAT.NoStop
>     10 ERROR:   SEQ_FEAT.PartialProblem
>   2368 ERROR:   SEQ_FEAT.StartCodon
>   2368 ERROR:   SEQ_INST.BadProteinStart
>   1525 ERROR:   SEQ_INST.StopInProtein
>   8821 WARNING: SEQ_FEAT.NotSpliceConsensusAcceptor
>   8543 WARNING: SEQ_FEAT.NotSpliceConsensusDonor
>     83 WARNING: SEQ_FEAT.PartialProblem
>      1 WARNING: SEQ_FEAT.ProteinNameEndsInBracket
>     19 WARNING: SEQ_FEAT.ShortExon
>    270 INFO:    SEQ_FEAT.RareSpliceConsensusDonor
>
> Also, just as a side note, has anyone tried the new table2asn_GFF
> converter that is up to convert GFF3 directly to sqn?  I was thinking that
> I would give that a shot hoping that it would help with some of these
> errors.  However, I was instantly met with an error as well.  "Too many
> positional arguments (1), the offending value: ends."
>
> Thank you so much in advance for any help you are able to give!
>
> Glenna
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