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

[Glenna Kramer]

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

[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

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[Glenna Kramer]

Thank you for the thought!

So, to clarify do you use funannotate predict on the maker gff files, similar to the last example given here? https://github.com/nextgenusfs/funannotate/wiki. I'm completely willing to give it a shot...

Is brings up other questions for me, though. How do you do your functional annotation? Maker? I noticed that funannotate will do functional annotation, but currently was adding in my functional annotation using GAG when I was converting the maker gff to tbl.

Also, from what I understand, funannotate will output a gbk from the gff. Do you have a particular file conversion tool to get that onto the sqn format that you've had success with?

Thanks,
Glenna
________________________________________
From: Jason Stajich [jason....@gmail.com]
Sent: Wednesday, June 21, 2017 2:25 PM
To: Glenna Kramer; maker...@yandell-lab.org
Subject: Re: [maker-devel] How to address errors encountered in process of submitting genome

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...@utoronto.ca<mailto:glenna...@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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[Jason Stajich]

Quick answers for now. 

A) you can feed maker gff to

Funannotate  or run it alone

B) I run the annotate step in funannotate but generally transfer only swissprot annots as product desc. Have to manually edit to remove systematic orf names

In product desc that NCBI will flag - e.g. YAL001W, AN1234, ARB_xx. You have to edit the annotations.swissprot.txt file to use the product descriptor if you want to promote these to full product descriptions in the resulting  .tbl  file

May want to run iprscan locally or wait for it running remotely to get GO assignments included. 

C) you get .tbl and Fsa

Files from gag and these are processed by tbl2asn to get sqn file. All are produced in the result file. All automatic. 

Jason

--

Jason Stajich
jason....@gmail.com